ESMO Glossary Molecular Biology Cancer Molecular Techniques 2015

Prepared by the
ESMO Translational
Research and Personalised
Medicine Working Group
ESMO Glossary in
Molecular Biology of Cancer
and Molecular Techniques
Scientific Resources
CM36 ESMO A5 Glossary Cover 2015 v01.indd 1 16/08/2015 14:31

ESMO Glossary in
ESMO Glossary in
The Translational Research
and Personalised Medicine Working Group
ESMO Press
First edition published in 1999. Second edition published in 2012 by ESMO Press. Reprinted 2014. Third edition published in 2015.
© 2015 European Society for Medical Oncology
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Contents
Learning objectives 1
Target audience 1
Introduction 2
How to use the ESMO Glossary in Molecular Biology of Cancer and Molecular Techniques 2
Contributing members of the ESMO Translational Research and Personalised Medicine Working Group 3
Declarations of interest 16
Glossary in Molecular Biology of Cancer 18
Glossary in Molecular Techniques 216
Acknowledgments 264
Learning objectives
The aim of the ESMO Glossary in Molecular Biology of Cancer and Molecular Techniques is to serve as an aid to practising
oncologists while they are acquiring knowledge and developing an awareness and appreciation of the molecular processes
underlying the development of cancer.
The second goal is to help them to understand the basic requirements for the common laboratory techniques used to
demonstrate molecular features of malignancy when critically evaluating and interpreting research findings.
The ultimate goal of this Glossary is to develop a common terminology and to enable oncology practitioners to speak the
same language with basic scientists and translational researchers when analysing research findings and translating cancer
biology to cancer medicine.
Target audience
The Glossary is dedicated to all oncologists keen to keep abreast of the latest advances in knowledge of the molecular
biology of cancer and molecular techniques that enable selection of specific molecular alterations and underlying
molecular processes.
1
Introduction
In developing this Glossary, the ESMO Translational Research and Personalised Medicine Working Group (TR and PM)
considered a review of a previous ESMO document, the Glossary in Molecular Biology of Cancer, as a priority. The first
edition was produced more than a decade ago on the occasion of an ESMO educational course. The aim was to enhance
the understanding of attendees in a difficult area for most clinicians. In the meantime, the field of cancer biology has become
increasingly important and new complex terms and knowledge have emerged, as well as molecular techniques in oncology.
Therefore, the members of the ESMO TR and PM have revised the textual content of the previous Glossary, basically the
definitions of terms ordered from A to Z. During the revision process, the question of having more incentives from such
a publication was raised, and the idea of adding images illustrative of the terms was born. Images for certain terms have
been selected with permission from the respective journals where they were initially published. In addition, TR and PM
members wished to see incentives beyond classical reading and suggested accompanying each selected term by an image
consisting of two panes, one of the structure of the gene, and the second of its network. The same logic was used for
description of molecular techniques in cancer research.
How to use the ESMO Glossary

This Glossary explains scientific terms in a narrative way in alphabetical order. The explanations concern common
terminologies that can be associated with different types of cancer. For selected numbers of terms, images with exact gene
structures and/or signalling pathways accompany the text. The Glossary is foreseen as an aid tool, especially during reading
of the ESMO Handbook in Translational Research.
The booklet will be printed in a limited number of copies and available to download at the ESMO Website and at the
ESMO unique educational and scientific portal for oncologists: OncologyPRO. All images from the Glossary will be
available in slide resources.
2
Contributing members of the ESMO Translational Research and
Personalised Medicine Working Group
Chair
Prof. Giampaolo Tortora, MD, PhD
Institute: Medical Oncology Unit and Medical School, University Hospital Verona, Verona, Italy
Giampaolo Tortora is currently Professor of Medical Oncology and Director of the Medical Oncology Unit at the Medical
School and the University Hospital of the University of Verona, Italy. He is also Director of the Specialty School and
Residency Program in Medical Oncology.
Prof. Tortora obtained an MD degree (Summa cum Laude), the Specialty in Oncology (Summa cum Laude), and a PhD
in Molecular Biology and Pathology at the University of Napoli “Federico II”. He received research training for almost
five years at the National Cancer Institute, Bethesda, MD, USA and visited for short sabbaticals several academic and
research institutions in Europe and the USA.
Prof. Tortora’s main research areas are: the study of tyrosine kinase receptors, angiogenic factors, and the
microenvironment as targets for cancer therapy; development of novel targeted agents and therapeutic strategies
integrating targeted agents and chemoradiotherapy from the preclinical to clinical setting; and analysis of biomarkers.
3
Prof. Tortora is the author of over 140 publications in international journals with impact factors, the great majority as senior
author, including the New England Journal of Medicine, Journal of the National Cancer Institute, PNAS, Journal of Clinical
Oncology, and Clinical Cancer Research (total impact factor over 900 and h-index 49).
He has received several awards and grants for his studies on novel anti-cancer targeted agents.
He is a member of scientific boards and committees of several national and international research societies and
organisations and is Associate Editor/board member of several scientific journals in the field of oncology. He is an Associate
Editor of Annals of Oncology and Chair of the Translational Research Working Group of ESMO.
Prof. Tortora teaches Medical Oncology at residential courses for MD students, Residents in Oncology, and PhD students.
He routinely lectures at national and international academic and research institutions.
Co-chair
Prof. Cristiana Sessa, MD, PhD
Institute: Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
Professor Cristiana Sessa graduated in Medicine and Surgery at the University of Milan in 1978, followed by a Degree in
Pharmacology at the Mario Negri Institute of Milan in 1981, Specialisation in Obstetrics and Gynaecology at the University of
Verona in 1983, Diploma in Palliative Medicine at the College of Medicine of the University of Wales in 1991 and a Masters
degree in Economics and Health Management at the University of Lugano in 2002. Since 2009, Cristiana Sessa has been
Professor at the University of Bern (Switzerland).
4
Prof. Cristiana Sessa has been working at the Oncology Institute of Southern Switzerland, Ospedale San Giovanni,
Bellinzona since 1981, she has been appointed as Head of Phase I-II Unit and Pharmacology and she is currently Vice
Head of Medical Oncology and Head of Clinical Research. She has been the Bellinzona Site Director of the Clinical Trial Unit
of the Ente Ospedaliero Cantonale (CTU-EOC) since 2012.
Cristiana Sessa is a Member of the European Society for Medical Oncology (ESMO), where she is a committee member of
the ESMO Guidelines Working Group and of the Translational Research Working Group.
She is also President of the Swiss Group for Clinical Cancer Research (SAKK) New Anticancer Drugs project group and of
the working group on Gynaecological Tumours.
Prof. Cristiana Sessa was appointed to the Executive Board of the European Society of Gynaecological Oncology (ESGO) in
2013.
Members
Prof. Lothar Bergmann, MD, PhD
Institute: Department of Internal Medicine II, J.W. Goethe University Frankfurt, Frankfurt, Germany
Prof. Lothar Bergmann graduated in medicine at the J.W. Goethe University Frankfurt in 1976. He was trained in internal
medicine and in 1988 admitted as a specialist in haematology and medical oncology. From 1987 he acted as Assistant
Medical Director of the Department of Internal Medicine III at the University in Frankfurt. From 1997 to 1999 he served as a
Provisional Professor and Medical Director at the Department of Internal Medicine at the University in Ulm, and until 2007
5
as a Provisional Professor and Medical Director at the Department of Internal Medicine II at the J.W. Goethe University in
Frankfurt. Since August 2007, he has served at the same department as Deputy Medical Director.
Prof. Bergmann is a Chair of the Cancer Center Rhein-Main e.V. and chairs the Haematology/Oncology section of
the University Cancer Centre (UCT) Frankfurt. In addition, he is a permanent member of the Scientific Advisory Group
Oncology (SAG - Oncology) of the European Medicines Agency. Prof. Bergmann chairs the Interdisciplinary Study Group
for Renal Cell Cancer of the German Cancer Society (DKG). He serves as a reviewer for various national and international
medical journals.
Prof. Bergmann is a member of many international societies such as the American Society of Clinical Oncology (ASCO),
the American Association for Cancer Research (AACR), the European Society for Medical Oncology (ESMO), the European
Hematology Association (EHA), the International Society for Experimental Hematology (ISEH), and the American Society of
Hematology (ASH). Additionally, he is a member of various German societies including the German Society of Haematology and
Oncology (DGHO), the German Cancer Society (DKG), the Study Group for Medical Oncology (AIO), and the German Society of
Internal Medicine.
Clinically he focuses on the therapies of lymphomas and chronic lymphatic leukaemias and various solid tumours as well.
Scientifically he deals with tumour-suppressor genes and oncogene regulation, apoptosis in cancer cells, and immune
regulation, in which the blocking of signal transduction via gene silencing and targeted agents plays a major role.
6
Maja Bradic Lindh, MD, PhD
Institute: Cancer Centre Karolinska, Stockholm, Sweden
Dr Maja Bradic Lindh obtained a Medical Doctor degree at the Medical School, University of Novi Sad, Serbia. She worked
for five years as a general practitioner and had five years’ working experience as a clinician at the Medical Oncology
Department of the Oncology Institute of Vojvodina. She mostly worked with breast cancer patients.
She has been an active member of the Young Oncologists Committee and active member of the Translational Research
Working Group of the European Society for Medical Oncology for four years.
She undertook her PhD studies in cancer research at the Cancer Centre Karolinska, Stockholm, Sweden and defended her
thesis in April 2011 with the title: “Mechanisms determining efficacy of tyrosine kinase-targeting anti-cancer drugs”.
Dr Bradic Lindh’s most significant publications are in the area of identification of a SOX2-dependent subset of tumour- and
sphere-forming glioblastoma cells with a distinct tyrosine kinase inhibitor sensitivity profile.
Prof. Andrés Cervantes-Ruiperez, MD, PhD

Institute: Department of Hematology and Medical Oncology, University Hospital, Valencia, Spain
Prof. Cervantes trained as a medical oncologist at the University Hospital in Valencia. After this period, he worked as
a research fellow at the Free University Hospital in Amsterdam under the direction of Prof. H.M. Pinedo in a project on
multidrug resistance. He gained his PhD degree on this topic.
Prof. Cervantes was appointed as a full-time cancer specialist at the University Hospital, Valencia in 1998 and was
primarily involved in gastrointestinal and ovarian cancer management. He became Associate Professor of Medicine and
7
Medical Oncology at the University of Valencia in 1992. Prof. Cervantes was appointed head of section and responsible for
the early drug development programme (phase I) at the same institution in 2004. He has led the Cancer Research Group at
the Institute of Health Research INCLIVA since 2009. His main area of research is early clinical trials with pharmacodynamic
end points and molecular determinants of sensitivity to targeted anti-cancer agents.
Prof. Cervantes has been a member of the ESMO executive board since 2011, chairs the Guidelines Working Group at
ESMO, and served as an Educational Committee member since 2002. In 2010 he served as the Educational Chair of the
ESMO Congress in Milan. He is editor in chief of Clinical and Translational Oncology and editorial board member of Cancer
Treatment Reviews. He has contributed to over 170 peer-reviewed publications, including publications in the New England
Journal of Medicine, Journal of the National Cancer Institute, Journal of Clinical Oncology, Annals of Oncology, European
Journal of Cancer, Cancer, Cancer Research, and Clinical Cancer Research.
Rafal Dziadziuszko, MD
Institute: Department of Oncology and Radiotherapy, Medical University of Gdansk, Gdansk, Poland
Dr Rafal Dziadziuszko completed his training in Radiotherapy (2001) and Medical Oncology (2004) at the Department of
Oncology and Radiotherapy of the Medical University of Gdansk, Poland.
He subsequently completed a translational cancer research fellowship at the University of Colorado Cancer Center.
Between 2005 and 2007 he worked on predictive assays for EGFR targeted therapies in lung cancer, including
immunohistochemistry, gene copy number, and activating mutations. He then returned to his home institution to serve
as a deputy chair of the department.
Dr Dziadziuszko’s main interests include lung cancer translational and clinical research methodology, and he is a coauthor
of several peer-reviewed articles and book chapters on this topic. He is a member of the European Organisation for
8
Research and Treatment of Cancer – Lung Cancer and Radiotherapy Groups, European Society for Medical Oncology,
American Society of Clinical Oncology, and American Association for Cancer Research. He has also participated in the
organisation of several academic clinical research studies in Poland and Central Europe through the Polish Lung Cancer
Group and serves as the Vice-Chairman of the Central and East European Oncology Group.
His current work includes the identification of novel targets for lung cancer trials and early lung cancer detection. He has
been involved in IGF-1R, ALK, and MET translational and clinical research.
Prof. S. Gail Eckhardt, MD, PhD

Institute: School of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus,
Aurora, CO, USA
S. Gail Eckhardt, MD is a tenured Professor and Head of the Division of Medical Oncology at the University of Colorado
at Denver and Health Sciences Center, where she also holds the Stapp/Harlow Endowed Chair for Cancer Research and
is the Senior Associate Director for Translational and Collaborative Research at the University of Colorado Comprehensive
Cancer Center.
Dr Eckhardt is a member of ESMO and has served on the Translational Research Working Group since 2009. Dr Eckhardt
has also served on numerous committees/study sections, including the ASCO Molecular Oncology Task Force, the ASCO
Board of Directors, the FDA Oncology Drugs Advisory Committee, the NCI Developmental Therapeutics Study Section, and
the NCI Cancer Centers Study Section. She is also a member of the NCI Colon Cancer Task Force. In addition, Dr Eckhardt
has been an Associate Editor of Clinical Cancer Research, Journal of Clinical Oncology, and Investigational New Drugs.
Dr Eckhardt is the Principal Investigator on grants involving early clinical trials and colorectal cancer research and has
conducted numerous phase I and II clinical trials. She has published over 135 manuscripts and serves on numerous
9
advisory boards. Her area of interest is in the preclinical and clinical development of combinations of molecularly targeted
compounds, with a laboratory focus on colorectal cancer and melanoma.
Prof. Heinz-Josef Lenz, MD, FACP

Institute: Division of Medical Oncology, University of Southern California, Norris Comprehensive Cancer Center,
Los Angeles, CA, USA
Heinz-Josef Lenz is Professor of Medicine and Professor of Preventive Medicine, holds the Kathryn Balakrishnan Chair
for Cancer Research, is Associate Director, Clinical Research, Co-Chair of GI Oncology, Co-Director USC Center for
Molecular Pathways and Drug Discover at the University of Southern California Keck School of Medicine and USC/Norris
Comprehensive Cancer Center in Los Angeles, California.
Dr Lenz received his medical degree from Johannes-Gutenberg Universität in Mainz, Germany, and went on to complete a
residency in haematology and oncology at the Eberhard-Karls Universität Tübingen, Germany before completing clerkships
in oncology and haematology at George Washington University and the Beth Israel Hospital of Harvard Medical School,
respectively. He completed a postdoctoral fellowship in the Department of Biochemistry and Molecular Biology at the USC
Keck School of Medicine.
Dr Lenz’s research focus is in the identification of biomarkers in GI cancers, early drug development, and novel clinical
trials. He is Co-Chair of the SWOG GI Committee, Co-Chair of SWOG GI Translational Medicine, and member of the NCI
GI Steering Committee and NCI Gastroesophageal Task Force and NCI Correlative Science Committee. He is the USC
Principal Investigator for NIH U01, N01, and U10.
10
Nicola Normanno, MD
Institute: Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori di Napoli–Fondazione Pascale, Naples, Italy
Dr Normanno is a medical oncologist but he is mainly involved in preclinical research and in molecular diagnostics. His
research interest is focused on the study of the mechanism of action of target-based agents with particular regard to anti-
EGFR drugs, and on the identification of biomarkers that are associated with sensitivity or resistance to these agents. He
is actively involved in several clinical trials in which his laboratory is assessing the correlation between expression of tissue
and serum biomarkers and the activity of treatments with novel drugs or novel drug combinations. He is also involved in the
organisation of national and European external quality assessment (EQA) schemes in molecular diagnostics. In particular, he
is collaborating with the European EQA programme for EGFR testing.
Desamparados Roda Perez, MD

Institute: Department of Medical Oncology, University Hospital, Valencia, Spain
Desamparados Roda Perez’s career in translational oncology has been associated mainly with her work in the Phase I
Trials Unit and in collaboration in the development of new drugs, especially during the last year, during the beginning of her
formative period in basic research.
Her training in clinical research is aimed at conducting phase I clinical trials in the Phase I Cancer Unit within the Department
of Haematology and Medical Oncology directed by Prof. Andrés Cervantes. In January 2009, she joined the First in Human
11
Unit and since then she has participated actively in all phases of the biologically most relevant questions in phase I studies:
individualised therapy for each patient according to molecular selection; biomarkers identification and study of each
pathway; and pharmacodynamic and pharmacokinetic analysis for each new drug.
She has contributed to the development of phase I and II trials with novel therapeutic inhibitors of key signalling pathways
deregulated in cancer, including the IGFR/PI3K/AKT pathway and the MAP kinase pathway. In addition the group is working
to develop treatments to overcome resistance to anti-EGFR therapies.
In January 2011, she received a Río-Hortega grant awarded by the Carlos III Health Institute. This is a three-year grant for
training in basic and clinical research. Her training in cellular and molecular biology is carried out in the laboratory of Prof.
Juan R. Viña at the Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Valencia, where
she is involved in a project on colorectal cancer cell lines concerning resistance to anti-EGFR therapies mediated by K-Ras
oncogene mutation.
Prof. Aldo Scarpa, MD, PhD

Institute: ARC-NET Research Centre for Applied Research on Cancer, Department of Pathology and
Diagnostics, University and Hospital Trust of Verona, Verona, Italy
Aldo Scarpa is the Director of the ARC-NET Research Centre for Applied Research on Cancer and Chair of the Department
of Pathology and Diagnostics at the University and Hospital Trust of Verona.
Prof. Scarpa received his MD from the University of Padua and his PhD in Human Oncology and Molecular Pathology
from the University of Verona. He trained in Japan at the National Cancer Center of Tokyo, at the New York University
and La Jolla Cancer Research Center, USA, and at the Nürnberg Universität, Germany. His main research interests are:
12
molecular genetics of tumours; validation, quality control and automation in molecular diagnostics; and molecular and
cellular biology of pancreatic tumours.
His work has been published in over 250 peer-reviewed publications. Prof. Scarpa has also participated in the creation of
facilities addressing cancer research needs such as biobanks (creation/standardisation of processes for cancer/normal
biological materials and data sets), cancer models (creation of primary human cancer xenografting facility), and molecular
diagnostics (development, standardisation, and automation).
Prof. Scarpa was instrumental in the foundation in the early 2000s of the Laboratory of Molecular Diagnostics at the Cancer
Center in Cuenca, Ecuador, fully implemented through the participation of local staff including the ability to write projects to
raise funds. He received the honorary citizenship of Cuenca, Ecuador.
Prof. Scarpa’s recent achievements include the design, financing, and development of a research centre for the identification
and clinical validation of diagnostic/prognostic markers and therapeutic targets in oncology (ARC-NET). He is also
responsible for the Italian initiative within the International Cancer Genome Consortium (ICGC) sequencing rare pancreatic
tumours and collaborates with Australia on pancreatic ductal carcinoma.
Prof. Konstantinos Syrigos, MD, PhD

Institute: Oncology Unit, 3rd Department of Medicine, Athens University School of Medicine, Athens, Greece
Professor Kostas Syrigos graduated from Athens School of Medicine in 1988. He was trained in Internal Medicine at the
Laikon University Hospital (Athens University) and in Medical Oncology at the Hammersmith Hospital (London University).
He completed his MD thesis with distinction from the Athens School of Medicine in 1995 and his PhD thesis from the Imperial
College of Science, Technology and Medicine, London University in 2000. He worked as Senior Registrar in Medical Oncology
13
at the Hammersmith and St Bartholomew’s Hospitals in London and as Consultant at the Sotiria General Hospital in Athens.
In 2002 he was appointed Associate Professor of Oncology in Medicine and Head of the Sotiria Oncology Unit. From 2006
he has also been Visiting Professor of Thoracic Oncology at Yale University, CT, USA. His main fields of interest are targeted
therapies, drug development, as well as thoracic and head & neck oncology.
Professor Syrigos has participated in several international phase I–IV clinical trials in lung, colon, head & neck, and
pancreatic cancer. His research interests include neoangiogenesis and the role of adhesion molecules in the neovasculature.
He has published several papers on the role of the E-cadherin–catenin pathway in the pathogenesis, prognosis, and
prediction of neoplastic diseases. He has also conducted early phase (I–II) clinical trials with agents targeting this pathway.
He is a member of numerous scientific societies. He is a manuscript reviewer for 18 scientific journals and currently serves
on the editorial board of 5 scientific journals. He is the editor of 6 International Scientific Volumes, including Tumors of The
Chest (2006, Springer). He has contributed 80 chapters in international books and he is the author of 230 peer-reviewed,
international articles.
Josep Tabernero, MD
Institute: Medical Oncology Department, Vall d’Hebron University Hospital, Barcelona, Spain
Josep Tabernero is currently the Head of the Medical Oncology Department at the Vall d’Hebron University Hospital in
Barcelona, Spain and Head of the Gastrointestinal Tumours and Phase I Unit. He is actively involved in translational research
and pharmacodynamic phase I studies with molecular-targeted therapies and related translational research, with a special
focus on EGFR-family inhibitors and IGFR-PI3K-Akt-mTOR pathway inhibitors, and phase II and III studies with new
chemotherapy agents in gastrointestinal tumours.
14
Dr Tabernero received his medical degree from the Universitat Autònoma de Barcelona and completed his specialist training
in medical oncology. He is a member of the European Society for Medical Oncology (ESMO) and the American Society of
Clinical Oncology (ASCO), and different editorial boards including the Journal of Clinical Oncology, Clinical Cancer
Research, Cancer Discovery, Clinical Colorectal Cancer, and Annals of Oncology. He has (co)authored approximately
180 peer-reviewed papers. He has also been a member of the Educational and Scientific Committees of ESMO, ECCO,
ASCO Gastrointestinal, and WCGIC meetings.
Teresa Troiani, MD
Institute: Università degli Studi di Napoli Federico II, Naples, Italy
Dr Troiani is a young oncologist, highly motivated, and clearly committed to clinical and translational research and an
academic career. In fact, after completing her medical school studies, she was awarded a Fellowship in Oncology at
the “Università degli Studi di Napoli Federico II”. She decided to join the laboratory of Prof. Ciardiello and Prof. Tortora.
Dr Troiani has worked in their laboratory since 1998, studying the role of growth factors and their receptors in neoplastic
transformation and the novel therapeutic strategies targeting growth factor receptor signalling.
Her long-term interest is translational oncology, developing new therapeutic strategies and initiating clinical trials. Therefore,
Dr Troiani decided to join Dr Gail Eckhardt’s group and train in this area. She worked with Dr Eckhardt for two years and
together they published several papers in international journals. After that experience, Dr Troiani moved back to Naples,
where she has continued to work with Prof. Ciardiello at the Second University of Naples.
She has run a series of translational research projects, with both clinical and basic science investigational arms, at an
academic medical centre. During her career, she has learnt that to fight cancer is a big challenge and only by connecting the
preclinical with the clinical work is it possible to make one piece of the wider puzzle.
15
Declarations of interest
Lothar Bergmann: Nothing to declare.
Maja Bradic Lindh: Nothing to declare.
Andrés Cervantes-Ruiperez: A member of the speakers’ bureau for Merck Serono and Roche. Conducting research
sponsored by Roche.
Rafal Dziadziuszko: Honoraria for presentations from Roche, Pfizer, and Boehringer Ingelheim.
S. Gail Eckhardt: Research funding from Pfizer, Genentech, Millennium/Takeda, and AstraZeneca. Consultant to
Genentech, Sanofi-Aventis, and Millennium/Takeda.
Heinz-Josef Lenz: Grant support from NCI/NIH, CTEP, and SWOG. Consultant to Response Genetics, Genentech,
Merck KG, Novartis, and BMS. Stock ownership in Response Genetics. Contracted research for BMS, Novartis, Roche,
Sanofi-Aventis, Pfizer, NCI, CTEP, Merck, and Eli Lilly. Clinical trial support from Roche, Bristol-Myers Squibb, Eli Lilly,
Sanofi-Aventis, Novartis, Genetech, Pfizer, and GSK. Honoraria from Response Genetics, Genentech, Merck KG, and
BMS.
Nicola Normanno: Nothing to declare.
Desamparados Roda Perez: Nothing to declare.
Aldo Scarpa: Conducting research for Novartis and GSK.
Cristiana Sessa: Nothing to declare.
16
Konstantinos Syrigos: Conducting research for Eli Lilly, Merck Serono, Amgen, and Roche.
Josep Tabernero: Advisory role for Amgen, Genentech, Sanofi, Roche, and Celgene.
Giampaolo Tortora: Consultant for GSK, Novartis, Roche, and Pfizer.
Teresa Troiani: Nothing to declare.
17
ESMO Glossary
in Molecular Biology of Cancer
Molecular Biology
18
A ABCC5 gene: Gene encoding one of the proteins in the family of ATP-binding cassette (ABC) transporters, subfamily C.
Also called MOAT C or multidrug resistance-associated protein (MRP1) homologue MRP5, ABCC5 confers resistance to
fluorouracil and platinum drugs.
ABL (Abelson tyrosine kinase): The gene coding for the Abelson tyrosine kinase. Abelson kinase is a nonreceptor tyrosine
kinase. Nuclear and cytoplasmic forms of ABL are implicated in apoptosis and cell adhesion, respectively. Nuclear ABL is
typically activated by DNA strand breaks.
ACTB gene: The ACTB gene provides instructions for making a protein called beta (β)-actin, which is part of the actin protein family.
Proteins in this family are organised into a network of fibres called the actin cytoskeleton, which makes up the structural framework
inside cells. There are six types of actin; four are present only in muscle cells, where they are involved in the tensing of muscle fibres
(muscle contraction). The other two actin proteins, β-actin and gamma (γ)-actin (produced from the ACTG1 gene), are found in cells
throughout the body. These proteins play important roles in determining cell shape and controlling cell movement (motility). Studies
suggest that β-actin may also be involved in relaying chemical signals within cells.
Activator domains: Transcriptional activation domains (TADs) are regions of a transcription factor which, in conjunction with a
DNA binding domain, can activate transcription from a promoter by contacting transcriptional machinery (general transcription
factors + RNA polymerase), either directly or through other proteins known as co-activators. Similarly, transcriptional repressor
domains (TRDs) are regions of a transcription factor which, in conjunction with a DNA binding domain, can repress transcription
from a promoter by contacting transcriptional machinery (general transcription factors + RNA polymerase), either directly or
through other proteins known as corepressors. A transcriptional activator is a protein (transcription factor) that increases
gene transcription of a gene or set of genes. Most activators are DNA-binding proteins that bind to enhancers or promoter-
proximal elements. Most activators function by binding sequence-specifically to a DNA site located in or near a promoter and
making protein–protein interactions with the general transcription machinery (RNA polymerase + general transcription factors),
thereby facilitating the binding of the general transcription machinery to the promoter. The DNA site bound by the activator is
referred to as an “activator site.” The part of the activator that makes protein–protein interactions with the general transcription
Molecular Biology
19
machinery is referred to as an “activating region”. The part of the general transcription machinery that makes protein–protein
interactions with the activator is referred to as an “activation target”.
Activator protein-1 (AP-1): In the field of molecular biology, the activator protein 1 (AP-1) is a transcription factor which is a
heterodimeric protein composed of proteins belonging to the c-Fos, c-Jun, ATF, and JDP families. It regulates gene expression
in response to a variety of stimuli, including cytokines, growth factors, stress, and bacterial and viral infections. AP-1 in turn
controls a number of cellular processes including differentiation, proliferation, and apoptosis. AP-1 upregulates transcription
of genes containing the TPA DNA response element (TRE; 5’-TGAG/CTCA-3’). AP-1 binds to this DNA sequence via a basic
amino acid region, while the dimeric structure is formed by a leucine zipper.
ADCC (antibody-dependent cell-mediated cytotoxicity): A mechanism of cell-mediated immune defence whereby an
effector cell of the immune system actively lyses a target cell that has been bound by specific antibodies. Classical ADCC
is mediated by natural killer (NK) cells; neutrophils and eosinophils can also mediate ADCC. ADCC is part of the adaptive
immune response due to its dependence on a prior antibody response.
Adenine: One of the two purine nucleobases (the other being guanine) used in forming nucleotides of the nucleic acids. In
DNA, adenine binds to thymine via two hydrogen bonds to assist in stabilising the nucleic acid structures. In RNA, which is
used for protein synthesis, adenine binds to uracil. Adenine forms adenosine, a nucleoside, when attached to ribose, and
deoxyadenosine when attached to deoxyribose. It forms adenosine triphosphate (ATP), a nucleotide, when three phosphate
groups are added to adenosine.
Adenomatous polyposis coli: Adenomatous polyposis coli (APC), also known as Deleted in polyposis 2.5 (DP2.5), is a
protein that in humans is encoded by the APC gene. The APC protein is a negative regulator that controls beta-catenin
concentrations and interacts with E-cadherin, which are involved in cell adhesion. Mutations in the APC gene may result in
colorectal cancer.
Molecular Biology
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Adenomatous polyposis coli gene: Adenomatous polyposis coli (APC), also known as Deleted in polyposis 2.5 (DP2.5),
is a protein that in humans is encoded by the APC gene. The APC protein is a negative regulator that controls beta-catenin
concentrations and interacts with E-cadherin, which are involved in cell adhesion. APC is classified as a tumour-suppressor gene.
The protein made by the APC gene plays a critical role in several cellular processes that determine whether a cell may develop
into a tumour. The APC protein helps control how often a cell divides, how it attaches to other cells within a tissue, or whether a
cell moves within or away from a tissue. This protein also helps ensure that the chromosome number in cells produced through
cell division is correct. The APC protein accomplishes these tasks mainly through association with other proteins, especially
those that are involved in cell attachment and signalling. The activity of one protein in particular, beta-catenin, is controlled by the
APC protein. Regulation of beta-catenin prevents genes that stimulate cell division from being turned on too often and prevents
cell overgrowth. Mutations in the APC gene may result in colorectal cancer.
ADP ribosylation factor (ARF): Belongs to the GTP-binding family of proteins and is chiefly responsible for regulating vesicle
biogenesis in intracellular transport. The family of these regulators is growing and contains Arl (Arf-like), Arp (Arf-related proteins),
and Sar (secretion-associated and Ras-related). Arf proteins oscillate between an inactive form (that binds GDP) and an active
form (that binds GTP) which selectively bind to effector molecules.
AIB1 (SRC-3): An abbreviation for Amplified In Breast Cancer, AIB1 is a coactivator of nuclear receptors and interacts
with nuclear receptors (e.g. estrogen receptor). The multiprotein complex acts as a transcriptional activator. AIB1 is also
overexpressed and/or amplified in several other cancers (e.g. ovarian, prostate).
Akt: Also known as protein kinase B (PKB), is a serine/threonine-specific protein kinase that plays a key role in multiple cellular
processes such as glucose metabolism, apoptosis, cell proliferation, transcription, and cell migration. Akt regulates cellular
survival and metabolism by binding and regulating many downstream effectors. It is associated with tumour cell survival,
proliferation, and invasiveness. The activation of Akt is also one of the most frequent alterations observed in human cancer
and tumour cells. Tumour cells that have constantly active Akt may depend on Akt for survival. AKT family members are:
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• Akt1 is involved in cellular survival pathways, by inhibiting apoptotic processes. Akt1 manifests growth retardation and
increased spontaneous apoptosis in tissues such as testes and thymus. Since it can block apoptosis, and thereby promote
cell survival, Akt1 has been implicated as a major factor in many types of cancer. Akt (now also called Akt1) was originally
identified as the oncogene in the transforming retrovirus, AKT8.
• Akt2 is an important signalling molecule in the insulin signalling pathway. It is required to induce glucose transport.
• The role of Akt3 is less clear, though it appears to be predominantly expressed in the brain (Figure 1).
ALDH1A1 gene: This protein belongs to the aldehyde dehydrogenases family of proteins. Aldehyde dehydrogenase is the
second enzyme of the major oxidative pathway of alcohol metabolism. Two major liver isoforms of this enzyme, cytosolic and
mitochondrial, can be distinguished by their electrophoretic mobilities, kinetic properties, and subcellular localisations. Most
Caucasians have two major isozymes, while approximately 50% of East Asians have only the cytosolic isozyme, missing
the mitochondrial isozyme. This gene encodes the main cytosolic isoform, which has a lower affinity for aldehydes than the
mitochondrial enzyme.
ALK1: The ALK gene provides instructions for making a protein called anaplastic lymphoma kinase, part of a family of proteins
called receptor tyrosine kinases (RTKs). The ALK gene belongs to a family of genes called CD (CD molecules). The ALK gene
has been found to be rearranged, mutated, or amplified in a series of tumours including anaplastic large cell lymphomas,
neuroblastoma, and non-small cell lung cancer. The chromosomal rearrangements are the most common genetic alterations
in this gene, which result in creation of multiple fusion genes in tumourigenesis (Figure 2).
Allele: A copy of a gene or a DNA sequence located on corresponding loci of homologous chromosomes. The “normal”
form (sequence) of an allele is known as the wild-type allele or wild-type sequence. In a population several variants of normal
alleles may exist.
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Figure 1. Regulation of Akt activity.
Reprinted by permission from

Macmillan Publishers Ltd: Nature Reviews
Cancer 2002; 2 (7): 489-501.
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Figure 2. ALK in cancer.
Reprinted by permission from Macmillan Publishers Ltd: Nat Rev Cancer 2013; 13: 685-700.
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Alu: An Alu element is a short stretch of DNA originally characterised by the action of the Alu (Arthrobacter luteus) restriction
endonuclease. Alu elements are the most abundant transposable elements in the human genome. They are derived from
the small cytoplasmic 7SL RNA, a component of the signal recognition particle. The event, when a copy of the 7SL RNA
became a precursor of the Alu elements, took place in the genome of an ancestor of supraprimates. Alu insertions have been
implicated in several inherited human diseases and in various forms of cancer.
AML-ETO: The t(8;21)(q22;q22) translocation replaces the C-terminus of AML, including its transactivation domain, with
ETO, a nuclear protein of unknown function. The fusion protein acts as a transcriptional repressor.
Amplification: The increase of the copy number of a relatively narrow region of the genome, with the magnitude of the
increase being large enough so that its generation requires more than a single aberrant event (e.g. typically more than the gain
of a single copy of the region).
Angiogenesis: The process of angiogenesis is controlled by chemical signals in the body. These signals can stimulate both
the repair of damaged blood vessels and the formation of new blood vessels. Other chemical signals, called angiogenesis
inhibitors, interfere with blood vessel formation. Normally, the stimulating and inhibiting effects of these chemical signals are
balanced so that blood vessels form only when and where they are needed. Angiogenesis plays a critical role in the growth
and spread of cancer. A blood supply is necessary for tumours to grow beyond a few millimetres in size. Tumours can cause
this blood supply to form by giving off chemical signals that stimulate angiogenesis. Tumours can also stimulate nearby normal
cells to produce angiogenesis signalling molecules. The resulting new blood vessels “feed” growing tumours with oxygen and
nutrients, allowing the cancer cells to invade nearby tissue, to move throughout the body, and to form new colonies of cancer
cells, called metastases (Figure 3).
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Figure 3. Angiogenesis signalling pathways. Angiopoietins (Ang): A family of
proteins, Ang1–4 are ligands for the
tyrosine kinase receptor Tie2. Ang1 and
Ang2 are survival factors that prevent
apoptosis and are important for blood
vessel sprouting and remodelling. Ang1
promotes sprouting in the presence of
VEGF and stabilises the endothelial
cell–pericyte interactions. Ang2
exerts a vessel-destabilising effect
that allows VEGF-mediated vascular
reorganisation. Although Ang3 and
Ang4 were identified as an antagonist
and agonist of Tie2, respectively, the
biological roles of Ang3 and Ang4 have
not been defined.
Reprinted by permission from Macmillan Publishers Ltd: Nature Med 2011; 17: 1359–1370.
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Angiostatin: Angiostatin is a 38-kDa fragment of a larger protein, plasmin (itself a fragment of plasminogen), enclosing three
to five contiguous kringle modules. Each module contains two small beta sheets and three disulphide bonds. Angiostatin
is produced, for example, by autoproteolytic cleavage of plasminogen, involving extracellular disulphide bond reduction
by phosphoglycerate kinase. Furthermore, angiostatin can be cleaved from plasminogen by different metalloproteinases
(MMPs), elastase, prostate-specific antigen (PSA), 13 KD serine protease, or 24KD endopeptidase. Angiostatin is known
to bind many proteins, especially to angiomotin and endothelial cell surface ATP synthase, but also integrins, annexin II,
C-met receptor, NG2 proteoglycan, tissue-type plasminogen activator, chondroitin sulphate proteoglycans, and CD26.
Additionally, smaller fragments of angiostatin may bind several other proteins. It is involved in inhibition of endothelial cell
migration, proliferation, and induction of apoptosis. It has been proposed that angiostatin activity is related, among other
things, to the coupling of its mechanical and redox properties.
Antiangiogenic: A process involved blocking the generation of new blood vessels in a tumour, which disrupts the blood
supply, thereby preventing tumour growth.
Antibody: A type of protein made by plasma cells in response to an antigen. Antibodies are glycoproteins belonging to
the immunoglobulin superfamily; the terms “antibody” and “immunoglobulin” are often used interchangeably. Though the
general structure of all antibodies is very similar, a small region at the tip of the protein is extremely variable, allowing millions
of antibodies with slightly different tip structures, or antigen-binding sites, to exist. This region is known as the hypervariable
region. Each of these variants can bind to a different target, known as an antigen. This enormous diversity of antibodies allows
the immune system to recognise an equally wide variety of antigens. The purpose of this binding is to help destroy the antigen.
Antibodies can work in several ways, depending on the nature of the antigen. Some antibodies destroy antigens directly.
Others make it easier for white blood cells to destroy the antigen (Figure 4).
Antigen: In immunology, an antigen (Ag) is any structural substance that serves as a target for the receptors of an adaptive
immune response, T-cell receptor or B-cell receptor, respectively. Each antibody is specifically selected after binding to a
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Figure 4. Mechanisms of tumour cell killing by antibodies.

Macmillan Publishers Ltd:
Nat Rev Cancer 2012; 12: 278-287.
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certain antigen because of random somatic diversification in the antibody complementarity determining regions. A common
analogy used to describe this is the fit between a lock and a key. In summary an antigen is a molecule that binds to Ag-
specific receptors, but cannot induce an immune response in the body by itself. The term originally described a structural
molecule that binds specifically to an antibody. It expanded to refer to any molecule or a linear molecular fragment that can be
recognised by highly variable antigen receptors (B-cell receptor or T-cell receptor) of the adaptive immune system.
Antigen-presenting cells (APCs): Cells of the immune system that play a major role in adaptive immunity, APCs are
responsible for binding and processing antigens for presentation to T lymphocytes and producing signals that lead to
lymphocyte proliferation and differentiation. Dendritic cells and macrophages are examples of APCs.
Antisense: A noncoding strand of DNA within the RNA-coding region of a gene; it is complementary to the “sense” strand in
DNA and it is used as a template for RNA synthesis.
Apidophilin: Also called adipose differentiation related protein (ADRP). It is highly expressed in adipose tissues and is found
associated with the surface of lipid droplets in a wide range of cells and tissues that store or synthesise lipids.
Apo-2L: Another name for TRAIL.
Apoptosis: An orderly process of programmed cell death governed by a concerted action of diverse genes and thus quite
distinct from cell death due to necrosis (a total collapse of cellular metabolism) and other forms of tissue damage. The typical
morphological features of apoptotic cells include chromatin condensation and fragmentation of the nucleus into apoptotic
bodies; distinct nuclear fragments (visualised as a DNA ladder on gel electrophoresis) are produced by an endonuclease
cleaving the cell’s chromatin at internucleosomal linker sites; the end result of apoptosis often is that a cell dies without
necessarily inflicting damage to viable neighbouring cells. Apoptosis may occur spontaneously in many tumours, and may be
induced by chemotherapy or radiotherapy; p53 protein is thought to be one of the mediators inducing apoptosis in irradiated
cells; another gene involved in apoptosis is Bcl-2, conferring resistance to various inducers of programmed cell death (Figure 5).
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Figure 5. Major pathways of apoptosis.
Bcl-2 and Bax.
Reprinted by permission from Macmillan Publishers Ltd: Nature Reviews Cancer 2009; 9 (7): 501-507.
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Apoptotic protease activating factor 1 (Apaf1): A cytoplasmic protein that contains a WD-40 domain, a caspase
recruitment domain (CARD), and an ATPase domain and is involved in the initiation of apoptosis.
Ataxia telangiectasia mutated (ATM): Ataxia telangiectasia mutated (ATM) is a serine/threonine protein kinase that is
recruited and activated by DNA double-strand breaks. It phosphorylates several key proteins that initiate activation of the DNA
damage checkpoint, leading to cell cycle arrest, DNA repair, or apoptosis. Several of these targets, including p53, CHK2, and
H2AX, are tumour suppressors.
Ataxia telangiectasia and Rad3-related (ATR): ATR is a member of the phosphoinositol-3 kinases like the protein kinase
(PIKK) family of proteins that play key roles in signal-transduction pathways following DNA damage. Unlike ATM (ataxia
telangiectasia mutated protein), which is activated following DNA double-strand breakage, ATR responds to single-strand
regions of DNA exposed during stalling of DNA replication forks and during the repair of certain DNA adducts. Homozygous
mutation of the ATR allele can result in the rare, autosomal recessive condition Seckel syndrome, which is characterised by
developmental abnormalities, chromosomal instability, and a predisposition to cancer.
ATM gene: Ataxia telangiectasia mutated (ATM) belongs to the PI3K family and is mutated in the human autosomal recessive
disease, ataxia telangiectasia. ATM is activated during DNA damage (e.g. exposure to ionising irradiation or chemical agents).
The activation of ATM kinase leads to a cascade of kinase reactions that regulate the cell cycle, apoptosis, and DNA damage
repair. ATM can bind p53 directly and is responsible for its phosphorylation, thereby contributing to the activation and
stabilisation of p53 during the IR-induced DNA damage response.
ATP-binding cassette: ATP-binding cassette transporters (ABC transporters) are members of a protein superfamily that is
one of the largest and oldest families with representatives in all extant phyla from prokaryotes to humans. ABC transporters
are transmembrane proteins that utilise the energy of adenosine triphosphate (ATP) binding and hydrolysis to carry out certain
biological processes including translocation of various substrates across membranes and non-transport-related processes
such as translation of RNA and DNA repair. They transport a wide variety of substrates across extra- and intracellular
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membranes, including metabolic products, lipids and sterols, and drugs. ABC transporters are classified as proteins based
on the sequence and organisation of their ATP-binding cassette (ABC) domain(s). ABC transporters are involved in tumour
resistance, cystic fibrosis, and a range of other inherited human diseases.
ATP-binding cassette protein B1 (ABCB1): A member of the ATP-binding cassette (ABC) transporters, which are divided
into seven subfamilies. ABCB1 is a member of the MDR/TAP subfamily and is involved in multidrug resistance. The protein
behaves as a pump and is responsible for the efflux of xenobiotic compounds from the cell, thereby decreasing drug levels
in multidrug-resistant cells. Resistance to chemotherapeutic agents in cancer is often due to the presence of this transporter
(Figure 6).
ATP-binding cassette protein C2 (ABCC2): Member 2 of the subfamily C in the family of ATP-binding cassette (ABC)
transporters. Most often expressed in canalicular membranes of hepatocytes.
ATP-binding cassette protein G2 (ABCG2): Member 2 of the subfamily G in the family of ATP-binding cassette (ABC)
transporters. ABCG2 is expressed in the placenta and involved in transport of specific molecules into or out of the placenta.
ATP5D gene: Gene coding for the delta (δ) subunit of the F1 complex of ATP synthase. The F1 complex is made of several
proteins in stoichiometric proportions: α3β3γδε (alpha-3-beta-3-gamma-delta-epsilon). Mitochondrial ATP synthase catalyses
ATP synthesis, utilising an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation.
ATP synthase is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-
spanning component, Fo, comprising the proton channel. The catalytic portion of mitochondrial ATP synthase consists of
5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled with a stoichiometry of 3 alpha, 3 beta, and a single
representative of the other 3. The proton channel consists of three main subunits (a, b, c).
Autocrine: Secretion of a substance, for example, a growth factor, which stimulates the secretory cell itself.
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Autosome: An autosome is a chromosome that is not an allosome (i.e. not a sex chromosome). Autosomes appear in pairs
whose members have the same form but differ from other pairs in a diploid cell, whereas members of an allosome pair may
differ from one another and thereby determine sex.
Figure 6. ABC transporters and multidrug resistance.
Reprinted by permission from Macmillan Publishers Ltd:

Nat Rev Cancer 2010; 10: 147-156.
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B B7: B7 is a type of peripheral membrane protein found on activated antigen-presenting cells (APC) that, when paired with
either a CD28 or CD152 (CTLA-4) surface protein on a T cell, can produce a costimulatory signal or a co-inhibitory signal to
enhance or decrease the activity of a MHC-TCR signal between the APC and the T cell, respectively. Besides being present
on activated APCs, B7 is also found on T-cells themselves. Binding of the B7 on T-cells to CTLA-4 causes inhibition of the
activity of T-cells.
B7.1 (CD80): Ligand for CD28 and CTLA4, it belongs to the immunoglobulin superfamily and is present on antigen-presenting
cells. In its interaction with CD28, it is a costimulator for T-cell activation. Its interaction with CTLA4 occurs with a higher affinity
than its interaction with CD28, leading to inhibition of CD28 signalling.
B7.2 (CD86): A ligand for CD28 and CTLA4, it belongs to the immunoglobulin superfamily and is present on antigen-
presenting cells. In its interaction with CD28, it is a costimulator for T-cell activation. Its interaction with CTLA4 occurs with a
higher affinity than its interaction with CD28, leading to inhibition of CD28 signalling.
BAALC gene: The BAALC gene, located on chromosome 8q22.3, encodes a protein with no homology to any known proteins
or functional domains. Expression of this gene was found mainly in neuroectoderm-derived tissues and haematopoietic
precursors.
BAD: A pro-apoptotic member of the Bcl-2 family of proteins, BAD’s phosphorylation leads to its inability to interact with, and
inhibit, proteins that are involved in cell-survival pathways.
BAG1: BAG1 (BCL2-associated athanogene) is a membrane protein that blocks a step in a pathway leading to apoptosis or
programmed cell death. The protein encoded by the gene binds to BCL2 and is referred to as BCL2-associated athanogene.
It enhances the anti-apoptotic effects of BCL2 and represents a link between growth factor receptors and anti-apoptotic
mechanisms. At least three protein isoforms are encoded by this mRNA through the use of alternative translation initiation
sites, including a non-AUG site.
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BAGE: Also called B melanoma antigen 1 precursor, the gene family codes for tumour-associated antigens that are presented
by human leukocyte antigen class I molecules and recognised by CD8 cytolytic T lymphocytes.
Bak: Bcl-2 homologous antagonist/killer is a protein that in humans is encoded by the BAK1 gene on chromosome 6. The
protein encoded by this gene belongs to the BCL2 protein family. BCL2 family members form oligomers or heterodimers
and act as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities. This protein localises to
mitochondria, and functions to induce apoptosis. It interacts with and accelerates the opening of the mitochondrial voltage-
dependent anion channel, which leads to a loss in membrane potential and the release of cytochrome c. This protein also
interacts with the tumour suppressor p53 after exposure to cell stress.
Base excision repair (BER): BER is one of the major DNA-repair pathways that repairs simple DNA base lesions, such as
the products of deamination, oxidation, and alkylation. In BER, a damaged base is removed by a DNA glycosylase, followed
by excision of the resulting sugar phosphate. The small gap left in the DNA helix is then filled in by the sequential action of DNA
polymerase and DNA ligase (Figure 7).
Basic fibroblast growth factor 2 (bFGF): bFGF is the prototype of the fibroblast growth factor family, which currently has up to
18 members of structurally related proteins. It acts as a mitogen or proliferative signal for several cell types, including fibroblasts,
smooth muscle cells, and endothelial cells and is also involved in the angiogenic process and in the formation of mesenchyme.
Basic helix–loop–helix (bHLH) proteins: Transcription factors that play critical roles in biological pathways such as cell
lineage determination, proliferation, and differentiation. They are involved in various differentiation processes such as skeletal
myogenesis, neurogenesis, and haematopoiesis. Possessing highly basic regions and helix–loop–helix motifs (as determined
by x-ray crystallography), bHLH proteins form homo- or heterodimers (with other bHLH proteins) through their helix–loop–
helix domains, which enable their basic regions to form DNA-binding motifs that recognise specific sequences called E-box
sequences. They can act as transcription activators as well as repressors.
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Figure 7. DNA repair.
a Base excision repair b Mismatch repair

A A
3´ 5´ 3´ 5´
5´ 3´ 5´ 3´
U X
DNA glycosylase MSH2

MLH1
MUTSα MUTLα
PMS2
5´ AP endonuclease MSH6
MSH2 MSH2
dRPase + DNA polymerase MLH1 MLH1
MUTSβ
PMS2 MLH3
MSH6 MSH3
DNA ligase
A A Reprinted by permission from Macmillan Publishers Ltd:

3´ 5´ 3´ 5´
5´ 3´ 5´ 3´ Nat Rev Cancer 2001; 1: 22-33.
T T
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Bax: Apoptosis regulator BAX, also known as bcl-2-like protein 4, is a protein that in humans is encoded by the BAX gene. BAX is
a member of the Bcl-2 gene family. BCL2 family members form hetero- or homodimers and act as anti- or pro-apoptotic regulators
that are involved in a wide variety of cellular activities. This protein forms a heterodimer with BCL2, and functions as an apoptotic
activator. This protein is reported to interact with, and increase the opening of, the mitochondrial voltage-dependent anion channel
(VDAC), which leads to the loss in membrane potential and the release of cytochrome c. The expression of this gene is regulated
by the tumour suppressor p53 and has been shown to be involved in p53-mediated apoptosis (Figure 5).
BBC3 gene: The p53 upregulated modulator of apoptosis (PUMA), also known as Bcl-2-binding component 3 (BBC3), is a
pro-apoptotic protein, member of the Bcl-2 protein family. In humans, the Bcl-2-binding component 3 protein is encoded by
the BBC3 gene. The expression of PUMA is regulated by the tumour suppressor p53. PUMA is involved in p53-dependent
and -independent apoptosis induced by a variety of signals, and is regulated by transcription factors, not by post-translational
modifications. After activation, PUMA interacts with anti-apoptotic Bcl-2 family members, thus freeing Bax and/or Bak, which
are then able to signal apoptosis to the mitochondria. Following mitochondrial dysfunction, the caspase cascade is activated,
ultimately leading to cell death.
B-cell CLL/lymphoma 7A (BCL7A): Identified from a three-way translocation t(8;14;12)(q24.1;q32.3;q24.1), which also
involved myc and IgH, in a Burkitt’s lymphoma cell line, the protein coded by this gene (BCL7A), exhibits no recognisable
protein motifs, but shows homology with the actin-binding protein caldesmon.
Bcl-2: Bcl-2 (B-cell lymphoma 2), encoded in humans by the BCL2 gene, is the founding member of the Bcl-2 family of
regulator proteins that regulate cell death (apoptosis), by either inducing (pro-apoptotic) or inhibiting (anti-apoptotic) apoptosis.
Bcl-2 is specifically considered as an important anti-apoptotic protein and is thus classified as an oncogene. Bcl-2 derives
its name from B-cell lymphoma 2, as it is the second member of a range of proteins initially described in chromosomal
translocations involving chromosomes 14 and 18 in follicular lymphomas. There are two isoforms of Bcl-2, isoform 1, also
known as 1G5M, and isoform 2, also known as 1G5O/1GJH. However, results in the ability of these isoforms to bind to
the BAD and BAK proteins, as well as in the structural topology and electrostatic potential of the binding groove, suggest
differences in anti-apoptotic activity for the two isoforms (Figure 5).
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Bcl-2 homology 3 (BH3) domain: The BH3 interacting-domain death agonist, or BID, gene is a pro-apoptotic member of
the Bcl-2 protein family. Bcl-2 family members share one or more of the four characteristic domains of homology entitled the
Bcl-2 homology (BH) domains (named BH1, BH2, BH3, and BH4), and can form hetero- or homodimers. Bcl-2 proteins act
as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities.
Bcl-2-associated death promoter (BAD): The Bcl-2-associated death promoter (BAD) protein is a pro-apoptotic member
of the Bcl-2 gene family which is involved in initiating apoptosis. BAD is a member of the BH3-only family, a subfamily of the
Bcl-2 family. It does not contain a C-terminal transmembrane domain for outer mitochondrial membrane and nuclear envelope
targeting, unlike most other members of the Bcl-2 family. After activation, it is able to form a heterodimer with anti-apoptotic
proteins and prevent them from stopping apoptosis.
Bcl-6: The protein encoded by this gene is an evolutionarily conserved zinc finger transcription factor and contains an
N-terminal POZ/BTB domain. This protein acts as a sequence-specific repressor of transcription, and has been shown to
modulate the STAT-dependent interleukin-4 (IL-4) responses of B cells. This protein can interact with several corepressor
complexes to inhibit transcription. This gene is found to be frequently translocated and hypermutated in diffuse large B-cell
lymphoma (DLBCL), and contributes to the pathogenesis of DLBCL. Physiologically, BCL6 is a master transcription factor
which leads the differentiation of naive helper T cells in follicular helper T cells (TFH cells). Its action is negatively regulated by
the gene PRDM1 encoding the transcription factor Blimp-1.
Bcl-XL: B-cell lymphoma-extra large (Bcl-xl, or BCL2-like 1 isoform 1) is a transmembrane molecule in the mitochondria. It is
a member of the Bcl-2 family of proteins, and acts as a pro-survival protein by preventing the release of mitochondrial contents
such as cytochrome c, which would lead to caspase activation. It is a well-established concept in the field of apoptosis that
relative amounts of pro- and anti-survival Bcl-2 family of proteins define whether the cell will undergo cell death: if more Bcl-xL
is present, then pores are nonpermeable to pro-apoptotic molecules and the cell survives. However, if Bax and Bak become
activated, and Bcl-xL is sequestered away by gatekeeper BH3-only factors (e.g. Bim), causing a pore to form, cytochrome c is
released, leading to initiation of caspase cascade and to apoptotic events.
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BCoR: A corepressor that interacts with Bcl-6.
BCR-ABL: A hallmark feature of patients with chronic myelogenous leukaemia, the fusion of BCR-ABL results from a genetic
translocation, t(9;22), between chromosome 9 (the locus for abl) and 22 (the locus for bcr), resulting in the Philadelphia
chromosome. The BCR-ABL gene product has constitutive tyrosine kinase activity that is responsible for unfettered proliferation
(Figure 8).
Beta-actin: Beta-actin (human gene symbol ACTB/ACTB) is one of six different actin isoforms that have been identified in
humans. This is one of the two nonmuscle cytoskeletal actins. Actins are highly conserved proteins that are involved in cell
motility, structure, and integrity. Alpha-actins are a major constituent of the contractile apparatus.
Beta-catenin: Beta (β)-catenin is a dual function protein, regulating the co-ordination of cell–cell adhesion and gene
transcription. In humans, the CTNNB1 protein is encoded by the CTNNB1 gene. β-catenin is a subunit of the cadherin protein
complex and acts as an intracellular signal transducer in the Wnt signalling pathway. It is a member of the catenin protein
family and homologous to γ-catenin. Mutations and overexpression of β-catenin are associated with many cancers, including
hepatocellular carcinoma, colorectal carcinoma, lung cancer, malignant breast tumours, ovarian, and endometrial cancer.
β-catenin is regulated and destroyed by the β-catenin destruction complex, and in particular by the adenomatous polyposis
coli (APC) protein, encoded by the tumour-suppressing APC gene. Therefore genetic mutation of the APC gene is also
strongly linked to cancers, and in particular colorectal cancer resulting from familial adenomatous polyposis (FAP) (Figure 9).
Bid: The BH3 interacting-domain death agonist, or Bid, gene is a pro-apoptotic member of the Bcl-2 protein family. Bcl-2
family members share one or more of the four characteristic domains of homology entitled the Bcl-2 homology (BH) domains
(named BH1, BH2, BH3, and BH4), and can form hetero- or homodimers. Bcl-2 proteins act as anti- or pro-apoptotic
regulators that are involved in a wide variety of cellular activities.
Bioreductive drugs: Drugs that become activated under hypoxic conditions to produce toxic metabolites.
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Figure 8. Diagram of the translocation that creates the Philadelphia chromosome.
Reprinted by permission from Macmillan

Publishers Ltd: Nature Medicine 2009;
15 (10): 1153-1157.
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Figure 9. The β‑catenin‑dependent or canonical Wnt signalling pathway.

Nature Reviews Molecular Cell Biology 2009; 10 (4): 276-286.
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Biotin: Formally known as vitamin H of the B2 complex, biotin can be isolated from raw egg whites, and is a growth factor for
most yeasts and an essential cofactor in humans.
Bivalent hapten: Two incomplete, covalently linked antigens that are incapable of causing the production of antibodies but
capable of combining with a specific antibody.
Bmi-1 protein: A product of the bmi-1 (B-cell-specific Moloney murine leukaemia virus insertion site 1) gene, bmi-1 protein is
homologous to the polycomb group proteins, which regulate gene expression by altering chromatin structure.
Bp: Base pair; commonly used unit to indicate the size of nucleic acid fragments; partnerships between A and T, or C with
G, in DNA double helix.
BRAF: BRAF is an isoform of RAF. Raf proteins (Raf-1, A-Raf, B-Raf) are intermediate to Ras and MAPK in the cellular
proliferative pathway. Raf proteins are typically activated by Ras via phosphorylation, and activated Raf proteins in turn activate
MAPK via phosphorylation. However, Raf proteins may also be independently activated by other kinases (Figure 10).
BRCA1: BRCA1 (breast cancer 1, early onset) is a gene encoding for a nuclear phosphoprotein (E3 ubiquitin-protein ligase)
that plays a role in maintaining genomic stability, and it also acts as a tumour suppressor. The encoded protein combines
with other tumour suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex
known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase
II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role
in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for
approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers (Figure 11).
BRCA2: Known as Breast cancer 2 early onset gene, BRCA2 is a tumour-suppressor gene whose protein product is involved
in repairing chromosomal damage. Although structurally different from BRCA1, BRCA2 has cellular functions similar to
BRCA1. BRCA2 binds to RAD51 to fix DNA breaks caused by irradiation and other environmental agents (Figure 11).
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Figure 10. The BRAF and KIT.

Nature Reviews Cancer 2004; 4 (9): 718-727.
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Figure 11. The structure of BRCA1 and BRCA2 genes.
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Brg: BRG1 is the catalytic ATPase subunit of the human SWI/SNF complex, which couples the energy of ATP hydrolysis to
remodel nucleosome-organised DNA, facilitate transcription factor binding, and stimulate transcription. It has been shown to
function as a coactivator for numerous members of the nuclear receptor superfamily of transcription factors. BRG-1, like many
nuclear receptor coregulators, has a broad expression profile, with peaks in the central nervous system, the reproductive
system, and the thymus. Overexpression of BRG-1 has been demonstrated in gastric cancer and prostate cancer, while
polymorphisms and loss of heterozygosity have been reported in lung cancer and breast cancer respectively. Allelic deletion
and mutation experiments have demonstrated essential roles for BRG-1 in erythroid and thymocyte development, and limb
morphogenesis.
Brm: Brahma is a member of the Swi/Snf family of chromatin-remodelling complex. Because of its helicase and ATPase
activities, Brm increases gene accessibility by overcoming the repressive effects of nucleosomal histones.
BTBD3 gene: Gene coding for the BTB (POZ) domain containing 3 protein, whose function is yet unknown.
BTB/POZ (bric á brac, tramtrack, broad complex/pox virus zinc-finger) domain: The BTB/POZ domain defines a
conserved region of about 120 residues. It is located predominantly at the N terminus of Zn-finger DNA-binding proteins,
where it may function as a repression domain, and less frequently in actin-binding and poxvirus-encoded proteins, where it
may function as a protein–protein interaction interface. A prototypic human BTB/POZ protein, PLZF (promyelocytic leukaemia
zinc finger), is fused to RARalpha (retinoic acid receptor alpha) in a subset of acute promyelocytic leukaemias (APLs), where
it acts as a potent oncogene.
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C CA-125: CA-125 (cancer antigen 125, carcinoma antigen 125, or carbohydrate antigen 125), also known as mucin 16 or
MUC16, is a protein that in humans is encoded by the MUC16 gene. MUC16 is a member of the mucin family glycoproteins
that possesses a single transmembrane domain and contains about 22 000 amino acids. MUC16 is a component of the
ocular surface, the respiratory tract, and the female reproductive tract epithelia. The expression of mucin 16 has been
shown to be altered in various medical conditions, including several types of cancers including ovarian cancer. CA-125 has
found application as a tumour marker or biomarker that may be elevated in the blood of some patients with specific types
of cancers or other, benign conditions. MUC16 has been shown to play a role in advancing tumourigenesis and tumour
proliferation by several different mechanisms: immune system evasion, metastatic invasion, induced motility, chemotherapy
resistance (Figure 12).
Cadherins: A family of adhesion molecules that bind homophilically and heterophically in a cation-dependent manner.
Cadherins are important in cell–cell adhesion, which properly maintains cell–cell contacts vital for communicating intracellular
signals. Interactions of cadherins with cytoskeletal components result in changes in cell motility, migration, and proliferation.
Cadherins exist in several subclasses such as E-cadherins, P-cadherins, N-cadherins, and VE-cadherins (vascular endothelial
cadherins). VE-cadherins are specifically found at interendothelial cells’ junctions. Their expression on endothelial cells declines
during angiogenesis because cell–cell contacts are lost due to endothelial cell proliferation and chemotaxis.
Cancer stem cells: Cancer cells that possess characteristics associated with normal stem cells, specifically the ability to
give rise to all cell types found in a particular cancer sample. They are therefore tumourigenic and may generate tumours
through the stem cell processes of self-renewal and differentiation into multiple cell types. Such cells are proposed to persist
in tumours as a distinct population and cause relapse and metastasis by giving rise to new tumours.
Caspases: Caspases, or cysteine-aspartic proteases, or cysteine-dependent aspartate-directed proteases are a family of
cysteine proteases that play essential roles in apoptosis (programmed cell death), necrosis, and inflammation. Caspases are
essential in cells for apoptosis, or programmed cell death, in development, and most other stages of adult life, and have
been termed “executioner” proteins for their roles in the cell. Some caspases are also required in the immune system for the
maturation of lymphocytes. Failure of apoptosis is one of the main contributions to tumour development and autoimmune
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Figure 12. Structure of CA-125. diseases.There are two types of apoptotic caspases: initiator (apical)
caspases and effector (executioner) caspases. Initiator caspases
(e.g. CASP2, CASP8, CASP9, and CASP10) cleave inactive pro-
forms of effector caspases, thereby activating them. Effector caspases
(e.g. CASP3, CASP6, CASP7) in turn cleave other protein substrates
within the cell, to trigger the apoptotic process. The initiation of this
cascade reaction is regulated by caspase inhibitors. Caspases are
regulated at a post-translational level, ensuring that they can be rapidly
activated. They are first synthesised as inactive pro-caspases, which
consist of a prodomain, a small subunit, and a large subunit. Initiator
caspases possess a longer prodomain than the effector caspases,
whose prodomain is very small. The prodomain of the initiator
caspases contains domains such as a CARD domain (e.g. caspase-2
and caspase-9) or a death effector domain (DED) (caspase-8 and
caspase-10) that enables the caspases to interact with other molecules
that regulate their activation. These molecules respond to stimuli that
cause the clustering of the initiator caspases. Such clustering allows
them to activate automatically, so that they can proceed to activate the
effector caspases (Figure 13).
Cathepsins: Proteins belonging to the papain family. Two members,
cathepsin L1 and cathepsin L2, are cysteine proteinase enzymes,
which may function in protein turnover, antigen presentation, and
Reprinted by permission from www.intechopen.com/books bone remodelling (Figure 14).
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Figure 13. Role of caspases in the initiation and execution of apoptosis.
Reprinted by permission from Trends Immunol 2014; 35: 631–640.
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Figure 14. Cathepsins function in proteolytic pathways.

Publishers Ltd: Nature Reviews Cancer
2006; 6 (10): 764–775.
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CBFβ-MYH11: A chromosomal rearrangement seen in acute myeloid leukaemia that results in the expression of a chimeric
protein, a transcriptional repressor. The inv(16) rearrangement produces a fusion gene, CBFβ/MYH11, which causes a
juxtaposition of bands 16q22 (containing the CBFβ [core-binding factor β] gene) and 16p13 (containing MYH11 [myosin heavy
chain] gene).
CD1a: A spliced variant of the CD1 gene that is present on epidermal Langerhans cells in skin and some B-cell malignancies.
CD2: Cell-surface marker on thymocytes, T cells, and natural killer cells that is involved in T-cell activation.
CD3: A component of the T-cell receptor complex, CD3 is a surface marker specific to T cells and, hence, used to characterise
T cells (Figure 15).
CD3+/CD8+/CD56+ lymphocytes: This phenotype defines T lymphocytes that exert major histocompatibility complex-
unrestricted cytotoxicity, such as lymphokine-activated killer (LAK) cells.
CD3+/HLA-DR+ lymphocytes: Activated T cells in which there is upregulation of human leukocyte antigen (HLA) class II
antigens, such as HLA-DR, and which are associated with cellular activation.
CD4/CD8: Ratio of helper and cytotoxic T cells.
CD4+ CD25+ T cells: A subset of T regulatory cells that have anergic and suppressive properties and play an important role
in the maintenance of self-tolerance. CD4 and CD25 are markers present on regulatory T cells. CD4 is a coreceptor for major
histocompatibility complex class II molecules, whereas CD25 is the chain of the interleukin-2 receptor (IL-2R), which associates
with CD122 (IL-2Rb chain) and with CD132 (IL-2Rg chain).
CD4+ T cells: T-helper cells, which are characterised by the presence of the CD4 cell-surface marker. Their primary role is to
help in the activation of CD8+ T cells specific for a certain antigen.
CD5: A membrane-associated glycoprotein found on all T cells and at low levels on some B cells, CD5 is associated with the
T-cell receptor (TCR)/CD3 complex in T cells and with the B-cell receptor (BCR) in B cells.
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Figure 15. Basic mechanisms of T-cell stimulation and inhibition.

Nat Rev Cancer 2011; 11: 805-812.
CD7: Belonging to the immunoglobulin gene superfamily, CD7 is the earliest surface marker expressed on T- and natural killer
(NK)-cell lineages. It is also expressed on bone marrow-derived T, B, NK, and myeloid lineage precursors.
CD8: The surface antigen that characterises CD8+ T lymphocytes, CD8 is associated with the T-cell receptor and major
histocompatibility complex, necessary for antigen recognition.
CD8+ T cells: Cytotoxic T cells that are the primary effector cells of the immune system. They are characterised by the
presence of the CD8 cell-surface marker.
CD10: Initially identified as a common acute lymphoblastic leukaemia antigen (and called CALLA), CD10 is cell-surface
protein with zinc-binding metalloproteinase activity. It is expressed on the surface of neoplastic (e.g. lymphoblastic, Burkitt’s,
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and follicular germinal centre leukaemias) and normal (e.g. early lymphoid progenitors, immature B and germinal B cells, T-cell
precursors, and neutrophils) cells.
CD11b/CD18: Forms part of the integrin family of adhesion proteins and is present on the surface of neutrophils, macrophages,
and lymphocytes. The CD11/CD18 complexes are transmembrane complexes formed from three different CD11 alpha chains
and a common CD18 beta chain (e.g. CD11a/CD18, CD11b/CD18, CD11c/CD18).
CD11c: CD11c is an integrin alpha X chain protein. Integrins are heterodimeric integral membrane proteins composed of an
alpha chain and a beta chain. This protein combines with the beta 2 chain (ITGB2) to form a leukocyte-specific integrin referred
to as inactivated-C3b (iC3b) receptor 4 (CR4). The alpha X beta 2 complex seems to overlap the properties of the alpha M
beta 2 integrin in the adherence of neutrophils and monocytes to stimulated endothelium cells, and in the phagocytosis of
complement-coated particles. CD11c is a type I transmembrane protein found at high levels on most human dendritic cells,
but also on monocytes, macrophages, neutrophils, and some B cells, which induces cellular activation and helps trigger the
neutrophil respiratory burst; expressed in hairy cell leukaemias, acute nonlymphocytic leukaemias, and some B-cell chronic
lymphocytic leukaemias.
CD14: Receptor for a lipopolysaccharide and lipopolysaccharide-binding protein that is present on myelomonocytic cells.
CD14+ cells: CD14 (cluster of differentiation 14), also known as CD14, is a human gene. The protein encoded by CD14 gene is a
component of the innate immune system. CD14 exists in two forms, one anchored to the membrane by a glycosylphosphatidylinositol
tail (mCD14), the other a soluble form (sCD14). CD14 is expressed mainly by macrophages and (at 10-times lesser extent) by
neutrophils. It is also expressed by dendritic cells. CD14+ nonproliferating monocytic precursors could be used to generate
dendritic cells. CD14+ monocytes can differentiate into a host of different cells, including dendritic cells, a differentiation pathway
encouraged by cytokines, including GM-CSF and IL-4.
CD16: A component of the low-affinity Fc receptor involved in phagocytosis and antibody-dependent cellular cytotoxicity, it is
found on neutrophils, natural killer cells, and macrophages.
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CD19: Found on B cells, CD19 complexes with CD21 and CD81, and acts as a coreceptor for the B-cell receptor leading to
B-cell activation and differentiation.
CD20: Cell-surface antigen present on lymphoid B cells, it is a widely used phenotypic marker for typing malignant lymphomas.
It is involved in B-cell activation.
CD23: Cell-surface receptor present on follicular mantle B cells, activated macrophages, eosinophils, and platelets, CD23
functions as a low-affinity receptor for IgE.
CD25: A transmembrane protein present on activated T and B cells, CD25 is normally associated with human alloactivated
T lymphocytes. CD25 is the alpha chain of the interleukin-2 (IL-2) receptor, which associates with the receptor b and g chain
to form the high-affinity IL-2R complex.
CD27: Binds a tumour necrosis factor-like ligand (CD70) and is present on medullary thymocytes and T cells.
CD27-CD45RA+ cells: Describes a population of activated T cells that are effector cells.
CD28: Activating receptor for B7 molecules (B7.1 and B7.2) present on naive T cells. Interaction of CD28 with B7 molecules
provides the costimulatory or second signal for T-cell activation.
CD31: Expressed on haematopoietic stem cells, CD31 is also expressed on endothelial cells and belongs to the immunoglobulin
superfamily. It mediates adhesion between cells (platelets, monocytes, polymorphonuclear cells, endothelial cells, and discrete
populations of circulating lymphocytes) that express CD31. It is an adhesion receptor molecule, responsible for transmitting
signals through the adhesion cascade, which involves the integrin family of proteins.
CD34: An antigen selectively expressed on human lymphoid and myeloid haematopoietic progenitor cells, CD34 is also
expressed on vascular endothelium.
CD36: A major glycoprotein found on monocytes, macrophages, and some endothelial cells, it plays a major role in cell
adhesion and phagocytosis. Also called CD36 antigen, its names include fatty acid translocase, collagen type 1 receptor, and
thrombospondin receptor.
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CD38: Present on macrophages, dendritic cells, and activated B and NK cells, CD38 may mediate the adhesion between
lymphocytes and endothelial cells.
CD40: Receptor for costimulatory signals for B cells through its binding to the CD40 ligand (CD40L). It is present on B cells,
monocytes, and dendritic cells.
CD45: Also called leukocyte common antigen, multiple CD45 isoforms are found on haematopoietic cells. It shows tyrosine
phosphatase activity and augments signalling through the B- and T-cell receptor.
CD56: Also called neural cell adhesion molecule (N-CAM), it is present on natural killer cells, a subset of T cells, myeloid
leukaemia cells, and some large granular lymphocyte leukaemias, and is involved in cell adhesion.
CD56+/CD3- lymphocytes: The phenotype that defines regulatory natural killer cells that secrete cytokines.
CD68: A marker that is used to determine cells of monocyte/macrophage or dendritic lineage.
CD80/CD86: Members of the immunoglobulin superfamily and present on mature antigen-presenting cells. CD80 and CD86
molecules share their ligands (CD28 and CTLA-4) on T cells and play a major role as costimulatory molecules in major
histocompatibility complex class II-mediated peptide antigen presentation.
CD95+: Another name for the death receptor Fas. Hence, these are cells that express the Fas receptor.
CD105: Also known as endoglin, CD105 is selectively expressed on endothelial cells, a subset of bone marrow cells, and
activated macrophages.
CD138 microbeads: Magnetic particles coupled to CD138 monoclonal antibody and used for the positive selection of
plasma cells from peripheral blood, bone marrow, and leukapheresis collections from patients with malignant plasma cell
diseases. CD138 (also called syndecan 1) is expressed on normal and malignant plasma cells but not on virgin/naive B cells,
memory B cells, T cells, or monocytes. CD138 microbeads are also used for the depletion of CD138+ cells.
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CDC20: Gene coding for the cell division cycle 20 homologue, CDC20 is a WD-repeat protein that may regulate APC-
dependent proteolysis of mitotic cyclins. It is required for two microtubule-dependent events in cell division (nuclear movement
prior to anaphase and chromosome separation).
CDC25: The CDC25 gene family includes three homologues: CDC25A, CDC25B, and CDC25C. The encoded proteins are
all phosphatases. CDC25A activates cyclin E–CDK2 complexes, is expressed in late G1, and is essential for G1–S phase
transition. CDC25B and CDC25C are present in the G2 phase and are necessary for cells to enter mitosis. Of these, CDC25A
and CDC25B are frequently overexpressed in human cancers and experimentally exhibit oncogenic potential.
CDR: Complementarity determining regions (CDRs) are part of the variable chains in immunoglobulins (antibodies) and T-cell
receptors, generated by B cells and T cells respectively, where these molecules bind to their specific antigen. As the most
variable parts of the molecules, CDRs are crucial to the diversity of antigen specificities generated by lymphocytes.
Cell adhesion molecules: Integral transmembrane proteins with a cytoplasmic tail acting as an anchor, interacting with
cytoskeletal proteins within the cell. The extracellular domains interact with extracellular matrix proteins or with cell adhesion
molecules from other cells in a homophilic (interacting with the same molecule) or heterophilic (interacting with a different
molecule) manner. They have important roles in tissue remodelling and organogenesis.
Cell cycle: A cell cycle is the period from one division of the cell to the next one in line; classically the cell cycle is divided into
G1 (gap 1, so called because in the early days of research into cell biology no events were visible during this phase) followed
by S phase (DNA synthesis); during G2 (gap 2) there is another break in the visible action, the replication machinery of the
cell having signalled that DNA replication is complete; the cell is ready for M (mitosis) and eventually two progeny cells are
produced in G1; resting/non-dividing cells reside in G0.
Cell division: Cell division is the process by which a parent cell divides into two or more daughter cells. Cell division usually
occurs as part of a larger cell cycle. In eukaryotes, there are two distinct types of cell division: a vegetative division, whereby
each daughter cell is genetically identical to the parent cell (mitosis), and a reductive cell division, whereby the number
of chromosomes in the daughter cells is reduced by half, to produce haploid gametes (meiosis). Meiosis results in four
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haploid daughter cells by undergoing one round of DNA replication followed by two divisions: homologous chromosomes are
separated in the first division, and sister chromatids are separated in the second division. Both of these cell division cycles are
in sexually reproducing organisms at some point in their life cycle, and both are believed to be present in the last eukaryotic
common ancestor. All cell divisions, regardless of organism, are preceded by a single round of DNA replication.
Cell growth: The term cell growth is used in the contexts of cell development and cell division (reproduction). When used in
the context of cell division, it refers to growth of cell populations, where a cell, known as the “mother cell”, grows and divides to
produce two “daughter cells” (M phase). When used in the context of cell development, the term refers to increase in cytoplasmic
and organelle volume (G1 phase), as well as increase in genetic material (G2 phase) following the replication during S phase.
Cell growth arrest: Inhibiting the cell cycle at one of several stages.
Centroid: Mean expression profile of a group of samples for a given set of genes.
Centromere: DNA sequences that are responsible for the segregation of each chromosome into daughter cells during
cell division, centromeres are contained in the heterochromatin in cells. As is the case with heterochromatin, the DNA of
centromeres does not code for proteins.
Chaperones: Produced in response to stress stimuli, including heat, oxidising conditions, and exposure to toxic compounds,
molecular chaperones (also called heat shock proteins) protect cells from stress-induced damage by blocking protein
aggregation. They can do this by binding and stabilising proteins at intermediate stages of folding, assembly, translocation,
and degradation. Chaperones discriminate against folded proteins by recognising the hydrophobic features of unfolded
proteins. Chaperones also fulfil physiological functions at normal temperatures, although their expression is low (Figure 16).
Chemokines: Cytokines that are responsible for chemotactic responses, chemokines are heparin-binding proteins, which
play a role in a variety of biological processes, the most important one being leukocyte chemotaxis. Their classification as
C, CC, CXC, and CX3C is based on the position of cysteine residues that form two disulphide bonds. Typically, chemokines
mediate their effects through G protein-coupled seven-transmembrane domain receptors, which belong to four families based
on their affinity for a given chemokine: CXCR1 to CXCR5, CCR1 to CCR9, XCR1, and CX3CR1.
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Figure 16. Participation of molecular chaperones in regulating
many aspects of post-translational protein homeostasis.
Newly synthesised,
but inactive, client Client ER
protein Client
a b
Antiaggregation
Membrane translocation,
intracellular disposition
Client
Ubiquitylation
c
d
Dynamic multiprotein Ligand binding, Client
chaperone–client phosphorylation,
complex dimerisation, etc
Proteasome-mediated Active state
degradation (protein turnover Reprinted by permission from Macmillan Publishers Ltd:
and antigen processing) Nat Rev Cancer 2005; 5: 761-772.
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CHFR: One of several checkpoint systems that regulate mitosis. The CHFR protein possesses an N-terminal forkhead-
associated (FHA) domain, a central ring finger (RF) domain, and a C-terminal cysteine-rich (CR) region. CHFR regulates a
prophase delay when cells are exposed to agents that disrupt microtubules, such as nocodazole and taxol. Loss of CHFR
function may be indicative of cancers that are sensitive to chemotherapy.
Chromatin: Chromatin is a complex of macromolecules found in cells, consisting of DNA, protein, and RNA. The primary
functions of chromatin are: (1) to package DNA into a smaller volume to fit in the cell, (2) to reinforce the DNA macromolecule
to allow mitosis, (3) to prevent DNA damage, and (4) to control gene expression and DNA replication. The primary protein
components of chromatin are histones that compact the DNA. Chromatin is found only in eukaryotic cells (cells with defined
nuclei). Prokaryotic cells have a different organisation of their DNA (the prokaryotic chromosome equivalent is called a
genophore and is localised within the nucleoid region).
Chromodomain: A motif present in chromatin-remodelling and histone-modifying complexes, chromodomains are involved
in reading the histone code by binding methylated histone tails.
Chromosomal translocations: A translocation of genetic material from one chromosome to another, chromosomal
translocations occur during meiosis when chromosomal breaks occur. However, in translocations, fragments of one
chromosome rejoin to other chromosomes.
Chromosomes: Band: a chromosomal area that is distinguishable from adjacent segments by appearing darker or lighter
on light microscopy by banding/staining techniques; centromere separates the long and the short arm of a chromosome;
p short chromosomal arm; q long chromosomal arm; region consists of one or more bands and is defined as the area on a
chromosome that lies between two adjacent landmarks. Regions are numbered consecutively from the centromere outward
to the telomere along each chromosomal arm; telomere is the end of a chromosome arm.
Circulating DNA: Cell-free DNA that is present in blood. Can be detected in free form in sera or plasma. Circulating tumour
DNA in the blood of cancer patients can be identical to that of the patients’ tumours. Therefore, circulating DNA has the
potential of being a useful surrogate assay for cancer detection.
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Circulating endothelial cells: First detected in the 1970s, although convenient techniques to isolate them have only recently
become available. With regard to their phenotype, they may differ considerably depending on the type of underlying disorder.
Circulating tumour cell (CTC): Cells that have detached from a primary tumour and circulate in the bloodstream. CTCs may
constitute seeds for subsequent growth of metastasis in different tissues.
c-Jun: c-Jun is a protein that in humans is encoded by the JUN gene. c-Jun in combination with c-Fos forms the AP-1 early
response transcription factor. It is activated through double phosphorylation by the JNK pathway but has also a phosphorylation-
independent function. This gene is intron-less and is mapped to 1p32-p31, a chromosomal region involved in both translocations
and deletions in human malignancies. c-Jun is a proto-oncogene (its protein is Jun) and is the cellular homologue of the viral
oncoprotein v-jun. Jun is the first discovered oncogenic transcription factor (Figure 17).
c-Kit: Mast/stem cell growth factor receptor (SCFR), also known as proto-oncogene c-Kit or tyrosine-protein kinase
Kit or CD117, is a receptor tyrosine kinase protein of the PDGFR family that dimerises following ligand binding and is
autophosphorylated on intracellular tyrosine residues. In humans it is encoded by the KIT gene. Multiple transcript variants
encoding different isoforms have been found for this gene. It binds to a substance called stem cell factor (SCF), which causes
certain types of blood cells to grow. c-Kit may also be found in higher than normal amounts, or in a changed form, on some
types of cancer cells, including gastrointestinal stromal tumours and melanoma. Measuring the amount of c-Kit in tumour
tissue may help diagnose cancer and plan treatment (Figure 10).
Clathrin: Clathrin is a protein that plays a major role in the formation of coated vesicles. It forms a triskelion shape composed
of three clathrin heavy chains and three light chains. When the triskelia interact they form a polyhedral lattice that surrounds
the vesicle. The endocytosis and exocytosis of vesicles allows cells to communicate, to transfer nutrients, to import signalling
receptors, to mediate an immune response after sampling the extracellular world, and to clean up the cell debris left by tissue
inflammation.
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Figure 17. Schematic of c-Jun signalling.
Clonal evolution of tumour: Accumulation of mutations in cancer cells guided by selective forces. The genomic content of
cells within a single tumour can be heterogeneous due to differences in the mutation history of the “lineage” of individual cells.
A growth (dis)advantage as a result of the mostly random mutations creates selective pressure. Cells with the relatively “best”
genotype eventually dominate in the tumour.
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Clone: Population of cells derived from a single somatic cell of origin (= ancestral cell or founder cell) through mitotic division.
C-Myc: Myc protein is a transcription factor that activates expression of many genes through binding on consensus
sequences (Enhancer Box sequences [E-boxes]) and recruiting histone acetyltransferases (HATs). Myc family of transcription
factors contain bHLH/LZ (basic Helix-Loop-Helix Leucine Zipper) domain. It can also act as a transcriptional repressor.
Myc is activated upon various mitogenic signals such as Wnt, Shh, and EGF (via the MAPK/ERK pathway). By modifying
the expression of its target genes, Myc activation results in numerous biological effects. The first to be discovered was its
capability to drive cell proliferation (upregulates cyclins, downregulates p21), but it also plays a very important role in regulating
cell growth (upregulates ribosomal RNA and proteins), apoptosis (downregulates Bcl-2), differentiation, and stem cell
self-renewal. Myc is a very strong proto-oncogene and it is very often found to be upregulated in many types of cancers.
Myc overexpression stimulates gene amplification, presumably through DNA over-replication (Figure 18).
Coactivators: Proteins that bind to transcription activators and assist in transcription.
Coding DNA strand: A strand of DNA which contains the genetic code and which is identical to the mRNA sequence; the
DNA template for synthesising mRNA is known as the anti-coding strand.
Coding polymorphism: Genetic polymorphism that occurs in the coding sequence of a gene.
Codon: A sequence of three nucleotides (triplet) in a messenger RNA molecule coding for a particular amino acid in a protein
chain. 64 codons encompass the genetic code, the molecular alphabet.
Collapsin: Collapsin response mediator protein family, or CRMP family, consists of five intracellular phosphoproteins (CRMP-
1, CRMP-2, CRMP-3, CRMP-4, CRMP-5) of similar molecular size (60–66 kDa) and high (50–70%) amino acid sequence
identity. CRMPs are predominantly expressed in the nervous system during development and play important roles in axon
formation from neurites and in growth cone guidance and collapse through their interactions with microtubules. Cleaved forms
of CRMPs have also been linked to neuron degeneration after trauma-induced injury.
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Figure 18. Gene regulation by the MYC network.
MYC regulates diverse biological processes.

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Colony stimulating factor 1 receptor (CSF1R): The receptor for colony stimulating factor 1, a cytokine that controls the
production, differentiation, and function of macrophages. CSF1R is a transmembrane tyrosine kinase and member of the
CSF1/PDGF receptor family. Mutations in the CSF1R gene have been associated with a predisposition to myeloid malignancy.
Complementary sequences of nucleic acids: Sequences in single DNA and/or RNA strands which are able to form
specific stable hybrid double strands, a thymine (T; pyrimidine) in one strand pairs with the corresponding adenine (A; purine)
in the other strand, and each cytosine (C) teams up with guanine (G) via hydrogen bonds.
Connective-tissue growth factor (CTGF): A secreted protein belonging to the family of CCN proteins (CTGF, cysteine-
rich 61, nephroblastoma overexpressed) with functional domains that mediate interactions with growth factors, integrins,
proteoglycans, and extracellular matrix. It is implicated in several cellular events, including angiogenesis, chondrogenesis, and
formation of connective tissues. Induced by TGF-β/SMAD-dependent pathway, CTGF activates cell signalling, attachment,
migration, cytoskeletal reorganisation, and extracellular matrix production.
Consensus sequence or conserved domain: In molecular biology and bioinformatics, the consensus sequence is the
calculated order of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment.
It represents the result of multiple sequence alignments in which related sequences are compared to each other and similar
sequence motifs are calculated.
Constitutive gene expression: Continuous expression of genes when it is not needed without any overt external stimuli and
at the same level for most of the cell cycle; physiological feature of housekeeping genes.
Copy number aberration: Defines the net increase or net decrease in gene copy number (i.e. “gene dosage”). It includes
extensive low-amplitude and focal high-amplitude changes in gene copy number. Large regional copy number changes—involving
chromosomal fragments, chromosomal arms, or whole chromosomes—are typically of low amplitude and commonly referred to
as gains and losses. Focal reduction or increment in copy number of a specific gene in the genome without a proportional increase
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in other—or only few neighbouring—genes are commonly denoted as amplification and deletion, respectively. Amplifications can
include hundreds of repeat copies of a gene, which may sometimes occur via the excision of a copy of the repeating sequence
from the chromosome and its extrachromosomal replication (so-called “double minute chromosomes”). In a deletion, one or both
copies—so-called “alleles”— of a gene (which are present at an autosomal locus of the normal human genome) can be lost,
commonly designated as hemizygous and homozygous deletion, respectively.
Copy number gain/loss: Chromosomal amplifications or deletions that result in gains or losses, respectively, of genes in the
affected regions of the chromosome. Chromosomal amplification may result in chromosomes acquiring multiple copies of genes.
Chromosomal deletions may result in bi-allelic gene loss when deletions occur in corresponding regions of both chromosomes.
Core-binding factor subunit beta (CBFB): Core-binding factor subunit beta (CBFB) is a protein that in humans is encoded
by the CBFB gene. The protein encoded by this gene is the beta subunit of a heterodimeric core-binding transcription factor
belonging to the PEBP2/CBF transcription factor family, which master-regulates a host of genes specific to haematopoiesis
(e.g. RUNX1) and osteogenesis (e.g. RUNX2). The beta subunit is a non-DNA binding regulatory subunit; it allosterically
enhances DNA binding by alpha subunit as the complex binds to the core site of various enhancers and promoters, including
murine leukaemia virus, polyomavirus enhancer, T-cell receptor enhancers, and GM-CSF promoters. In some cases, a
pericentric inversion of chromosome 16 [inv(16)(p13q22)] produces a chimeric transcript consisting of the N terminus of core-
binding factor beta in a fusion with the C-terminal portion of the smooth muscle myosin heavy chain 11. This chromosomal
rearrangement is associated with acute myeloid leukaemia of the M4Eo subtype. Two transcript variants encoding different
isoforms have been found for this gene. Mutations in CBFB are implicated in cases of breast cancer. The presence of CBFB
helps the complex bind to DNA and protects the RUNX protein from being broken down. The function of CBF depends
on which RUNX protein it includes. Once bound to DNA, the RUNX1 protein controls the activity of genes involved in the
development of blood cells (haematopoiesis). The RUNX2 protein regulates genes important for bone cell development and
formation of the skeleton. The RUNX3 protein primarily affects genes involved in the development of nerve cells.
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Corepressors: Accessory proteins that bind to transcriptional factor repressor domains and recruit other components to the
transcriptional machinery.
Costimulatory molecules: Molecules that transmit additional signals through B-cell and T-cell receptors. During the
activation of lymphocytes, costimulation is often crucial to the development of an effective immune response. Costimulation
is required in addition to the antigen-specific signal from their antigen receptors. Molecules that transmit additional signals
through B-cell and T-cell receptors are called costimulatory molecules. T cells require two signals to become fully activated.
A first signal, which is antigen-specific, is provided through the T-cell receptor which interacts with peptide-MHC molecules
on the membrane of antigen-presenting cells (APC). A second signal, the costimulatory signal, is antigen nonspecific and
is provided by the interaction between costimulatory molecules expressed on the membrane of APC and the T cell. The B
cell binds antigens with its BCR (a membrane-bound antibody), which transfers intracellular signals to the B cell as well as
inducing the B cell to engulf the antigen, process it, and present it on the MHC II molecules. The latter case induces recognition
by antigen-specific Th2 cells, leading to activation of the B cell through binding of TCR to the MHC–antigen complex. It is
followed by synthesis and presentation of CD40L (CD154) on the Th2 cell, which binds to CD40 on the B cell, thus the Th2
cell can costimulate the B cell. Without this costimulation the B cell cannot proliferate further.
CpG island: DNA sequences with a high density of CpGs are termed CpG islands. CpG islands are typically unmethylated
in normal tissues but often become methylated in tumours. The patterns of hypermethylated CpG islands vary according to
the histological origin of the tumour.
CREB-binding protein (CBP): CREB-binding protein, also known as CREBBP or CBP, is a protein that in humans is
encoded by the CREBBP gene. The CREB protein carries out its function by activating transcription, where interaction with
transcription factors is managed by one or more CREB domains: the nuclear receptor interaction domain (RID), the CREB
and MYB interaction domain (KIX), the cysteine/histidine regions (TAZ1/CH1 and TAZ2/CH3), and the interferon response
binding domain (IBiD). The CREB protein domains, KIX, TAZ1 and TAZ2, each bind tightly to a sequence spanning both
transactivation domains (9aaTADs) of transcription factor p53.
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CREM: A cAMP response-element modulator protein, which binds to promoter elements of genes that are transcribed in a
cAMP-dependent manner. CREM belongs to the CREB (cAMP response-element binding protein) family of transcriptional
factors and to the bZIP (basic region-leucine zipper) superfamily of proteins characterised by a C-terminal basic domain
(mediating DNA binding) and a leucine-zipper motif (mediating dimerisation).
Cross-talk: Biological cross-talk refers to instances in which one or more components of one signal transduction pathway
affect another. This can be achieved through a number of ways, with the most common form being cross-talk between
proteins of signalling cascades. In these signal transduction pathways, there are often shared components that can interact
with either pathway. A more complex instance of cross-talk can be observed with transmembrane cross-talk between the
extracellular matrix (ECM) and the cytoskeleton.
CTLA4 (CD152): Receptor on activated T cells that binds B7 molecules with a higher affinity than CD28, downregulating
T-cell responses by inhibiting CD28 signalling.
CTSB gene: Cathepsin B (CatB) is an enzymatic protein belonging to the peptidase (or protease) families. In humans, it
is coded by the CTSB gene. The protein encoded by this gene is a lysosomal cysteine protease composed of a dimer of
disulphide-linked heavy and light chains, both produced from a single protein precursor. It is a member of the peptidase C1
family. At least five transcript variants encoding the same protein have been found for this gene. A wide array of diseases
result in elevated levels of cathepsin B, which causes numerous pathological processes including cell death, inflammation,
and production of toxic peptides.
CX3CR1: CX3C chemokine receptor 1 (CX3CR1), also known as the fractalkine receptor or G-protein coupled receptor
13 (GPR13), is a protein that in humans is encoded by the CX3CR1 gene. This receptor binds the chemokine CX3CL1
(also called neurotactin or fractalkine). Fractalkine is a transmembrane protein and chemokine involved in the adhesion and
migration of leukocytes. The protein encoded by this gene is a receptor for fractalkine. Expression of this receptor appears to
be associated with lymphocytes. CX3CR1 is also expressed by monocytes and plays a major role in the survival of monocytes.
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CXCR4: Gene encoding chemokine (CXC motif) receptor 4, which is a G protein-coupled receptor for the chemokine stromal
cell-derived factor-1. CXCR4 signalling activates Ras and PI3 kinase pathways and induces the transcription factors AP-1 and
chemokine-regulated genes.
CYBA gene: Cytochrome b-245 light chain is a protein that in humans is encoded by the CYBA gene involved in superoxide
production and phagocytosis. Cytochrome b is composed of a light chain (alpha) and a heavy chain (beta). This gene encodes
the light, alpha subunit, which has been proposed as a primary component of the microbicidal oxidase system of phagocytes.
Mutations in this gene are associated with autosomal recessive chronic granulomatous disease (CGD), which is characterised
by the failure of activated phagocytes to generate superoxide, which is important for the microbicidal activity of these cells.
Cyclic AMP response-element binding protein (CREB): A transcription factor whose expression is induced in the
presence of cyclic AMP.
Cyclin A: Each phase of the cell cycle is characterised by different cyclin-dependent kinases and cyclin complexes. Cyclin A
is the positive regulatory subunit of the CDK2–cyclin A complex, active during the S phase of the cell cycle.
Cyclin B1: Gene coding for cyclin B1, which is required for the activation of mitosis (or maturation) promoting factor (MPF).
Cyclin B1 expression varies in the cell cycle, is minimally expressed in G1, begins to rise in S phase, and peaks at the G2/M
transition.
Cyclin D: A protein that is present at high levels when resting cells enter a state of active division, cyclin D acts in the G1 phase
of the cell cycle. Cyclins are typically paired with cyclin-dependent kinases (CDK) that need to be activated for the cell cycle to
proceed. Cyclin D pairs with CDK4 and CDK6 and acts in the G1 phase of the cell cycle.
Cyclin D2: Belongs to the family of cyclin D.
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Cyclin E: A positive regulator of cyclin-dependent kinase 2 (CDK2), cyclin E is a G1 cyclin expressed in the G1 phase of the cell
cycle with its peak activity seen at the G1/S boundary of the cell cycle. Its expression is downregulated in the S phase of growth;
however, it is a critical molecule that dictates cell entry into the S phase and is considered the master regulator for S-phase entry.
Cyclins: Proteins that operate in the cell cycle at particular points in time (in fact their cyclic appearance in the cell cycle is
responsible for their name); cyclin A operates in S phase, cyclin B chiefly in G2 and mitosis; cyclins D and E are essential
in G1 control of the cell cycle. Cyclins form complexes with kinases (so-called cyclin-dependent kinases, CDK) to produce
phosphorylation of critical components on the mitotic machinery and thus to drive the cell from one stage of the cell cycle to
another; negative control of CDK is important to keep the cell cycle and thus cell proliferation under control: inhibitors of CDK
complexes (cyclin-dependent kinase inhibitors, CKI) block CDK either in G1 or throughout the cell cycle; altered expression of
some of the cyclins is associated with malignancy, for example mantle cell lymphoma is characterised by overexpression of
cyclin D1 (a G1-phase cyclin) due to a specific chromosomal translocation t(11;14).
Cyclin-dependent kinase inhibitors (CKI or CDKI): Small proteins which play an important role in the cell cycle; they
inhibit the action of cyclin–kinase complexes important in the cell cycle; the nomenclature of CKI is usually based on the
molecular weight of their proteins (i.e. p16 refers to a CKI with a molecular mass of 16 kDa), but unfortunately other names
abound in the literature: for example, p21 is also known as WAF1 (wild-type p53 activated fragment, since it is induced in cells
harbouring wild-type but not mutant p53), CIP1 (cyclin-dependent kinase-interacting protein 1), and SDI1 (senescent cell-
derived inhibitor); some CKI genes, for example p16, are often mutated (deleted) in cancer cell lines and also in some human
cancers, and are thought to represent a new class of tumour-suppressor genes.
Cyclooxygenase (COX): A prostaglandin endoperoxide synthase, COX enzymes are responsible for the production of
prostaglandins, intracellular messengers found at high levels at inflammation sites. Of COX-1 and COX-2, the latter has
received much attention due to drug development that has targeted COX-2 for selectively downregulating inflammatory
processes (Figure 19).
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Figure 19. The COX mechanistic network. CYP3A4: Gene encoding cytochrome P450,
subfamily IIIA (nifedipine oxidase), polypeptide 4.
Notably present in the liver, the mixed-function
oxidase is the most important enzyme involved
Inflammatory cell
in the metabolism of xenobiotics and oxidises a
events inhibited by NSAIDs
(Mf) wide range of substrates, including taxanes.
Stromal Cytochrome C: A protein present in

Cancer cell
COX-2 fibroblast mitochondrial membranes, it is important in
the energy generation machinery of the cell.
COX-2
COX-2 In addition, when cells are damaged as a result
of apoptosis, the release of cytochrome C is
a part of the cascade of reactions leading to
VEGF PG / TX VEGF programmed cell death.
Cytochrome P450: A family of mixed-function
VEGF
oxidase enzymes that are involved in the oxidative
VEGF-R2 metabolism of endogenous substances and
cAMP Integrin
COX-2 aVb3 xenobiotics. Several isoforms of cytochrome P450
exist with specificity for a given class of drugs,
MAPK
Rac
which are metabolised via the system. In addition,
several classes of drugs have been shown to
induce and/or inhibit cytochrome 450. This
Permeability Proliferation Migration
interaction may have important consequences for
the pharmacokinetics of numerous drugs and may
serve as a mechanism for drug–drug interactions.
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Cytokeratin-19 (CK-19): CK-19 belongs to the intermediate filaments, which create a cytoskeleton in almost all cells. CK-
19 is normally not expressed in haematopoietic cells, although it is commonly expressed in epithelial cells such as mammary
cells, either normal or neoplastic.
Cytokeratins: Members of a large family of intermediate filament (IF) cytoskeletal proteins. IF proteins are expressed in
a tissue-specific manner and are assembled as filamentous arrays. IF proteins have diverse biological functions and their
association with a wide array of human diseases is due to aberrant post-translational modifications, limited proteolysis, and
cross-linking.
Cytokines: Cell communication molecules that are secreted in response to external stimuli.
Cytopathic effect (CPE): Viruses can infect target cells and cause cell death, referred to as the CPE. A CPE assay can be
used to determine the titre of viral stocks.
Cytosine: Pyrimidine base.
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D Death-associated protein kinase (DAPK): A tumour-suppressor gene whose gene product is a positive mediator of
interferon gamma-induced programmed cell death. It shows serine/threonine kinase activity.
Death-inducing signalling complex (DISC): A death complex containing Fas-associated death domain-containing protein
(FADD), caspase-8, caspase-10, and, most importantly, cellular FADD-like interleukin 1β-converting enzyme-inhibitory protein
(c-FLIP).
Deletion (del): A loss of a chromosomal segment; for example del(1)(q21q31) means an interstitial deletion with breakage
and reunion at bands 1q21 and 1q31.
Dendritic cells: The most efficient antigen-presenting cells of the immune system, which play a critical role in the regulation of
the adaptive immune response. Immature dendritic cells internalise and process antigens. Their maturation leads to dendritic
cells migrating to draining lymph nodes where they prime and activate T lymphocytes.
Deoxycytidine kinase: An important enzyme in the salvage reaction of nucleotide synthesis, deoxycytidine kinase has broad
substrate specificity and can catalyse the phosphorylation of deoxycytidine, deoxyguanosine, and deoxyadenosine, using
ATP or UTP as phosphate donors.
Desmin: A member of the type III family of intermediate filaments, a class of cytoskeletal elements. Desmin expression is
muscle specific and found in skeletal, cardiac, and heart muscles, but also in rhabdomyosarcoma, for which it serves as a
general marker.
Diplotype: A specific combination of two haplotypes.
Disseminated tumour cell (DTC): Demonstration of isolated tumour cells disseminated in the bone marrow.
DNA-binding domains: A DNA-binding domain (DBD) is an independently folded protein domain that contains at least
one motif that recognises double- or single-stranded DNA. A DBD can recognise a specific DNA sequence (a recognition
sequence) or have a general affinity to DNA. Many proteins involved in the regulation of gene expression contain DNA-binding
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domains. For example, proteins that regulate transcription by binding DNA are called transcription factors. The final output of
most cellular signalling cascades is gene regulation. Many DNA-binding domains must recognise specific DNA sequences,
such as DBDs of transcription factors that activate specific genes, or those of enzymes that modify DNA at specific sites, like
restriction enzymes and telomerase.
DNA methylation: DNA methylation is a biochemical process where a methyl group is added to the cytosine or adenine DNA
nucleotides. DNA methylation may stably alter the expression of genes in cells as cells divide and differentiate from embryonic stem
cells into specific tissues. The resulting change is normally permanent and unidirectional, preventing a cell from reverting to a stem
cell or converting into a different cell type. DNA methylation is typically removed during zygote formation and re-established through
successive cell divisions during development. Some methylation modifications that regulate gene expression are heritable and cause
genomic imprinting. Aberrant DNA methylation patterns – hypermethylation and hypomethylation compared to normal tissue – have
been associated with a large number of human malignancies. Hypermethylation typically occurs at CpG islands in the promoter
region and is associated with gene inactivation. A lower level of leukocyte DNA methylation is associated with many types of cancer.
Global hypomethylation has also been implicated in the development and progression of cancer through different mechanisms.
Typically, there is hypermethylation of tumour-suppressor genes and hypomethylation of oncogenes (Figure 20).
DNA methyltransferase inhibitors: Inhibitors of the DNA methyltransferase enzyme, resulting in a loss of DNA methylation
and a loss of gene silencing.
DNA mutation: A mutation is a permanent change of the nucleotide sequence of the genome of an organism, virus, or
extrachromosomal DNA or other genetic elements. Mutations result from damage to DNA which is not repaired or to RNA
genomes (typically caused by radiation or chemical mutagens), errors in the process of replication, or from the insertion
or deletion of segments of DNA by mobile genetic elements. Mutations may or may not produce discernible changes in
the observable characteristics (phenotype) of an organism. Mutations play a part in both normal and abnormal biological
processes including: evolution, cancer, and the development of the immune system, including junctional diversity.
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Figure 20. DNA methylation patterns in normal and cancer cells.
a Gene
Incorrect
TSS
Normal ON OFF
Incorrect
Gene TSS
Cancer OFF ON
CpG island shore CpG island Gene body
b Incorrect Genomic
TSS instability Transposition
Normal OFF OFF OFF
Incorrect Genomic
TSS instability Transposition
Cancer ON ON ON

Repetitive sequence Transposon Nat Med 2011; 17: 330-339.
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DNA replication: DNA replication is the process of producing two identical replicas from one original DNA molecule. This
biological process occurs in all living organisms and is the basis for biological inheritance. DNA is made up of two strands and
each strand of the original DNA molecule serves as a template for the production of the complementary strand, a process
referred to as semiconservative replication. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity
for DNA replication. In a cell, DNA replication begins at specific locations, or origins of replication, in the genome. Unwinding
of DNA at the origin and synthesis of new strands results in replication forks growing bidirectionally from the origin. A number
of proteins are associated with the replication fork which helps in terms of the initiation and continuation of DNA synthesis.
Most prominently, DNA polymerase synthesises the new DNA by adding complementary nucleotides to the template strand.
DNA repair: DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that
encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can
cause DNA damage. Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell’s ability
to transcribe the gene that the affected DNA encodes. Other lesions induce potentially harmful mutations in the cell’s genome, which
affect the survival of its daughter cells after it undergoes mitosis. As a consequence, the DNA repair process is constantly active
as it responds to damage in the DNA structure. When normal repair processes fail, and when cellular apoptosis does not occur,
irreparable DNA damage may occur, including double-strand breaks and DNA cross-linkages (interstrand crosslinks or ICLs).The
rate of DNA repair is dependent on many factors, including the cell type, the age of the cell, and the extracellular environment. A
cell that has accumulated a large amount of DNA damage, or one that no longer effectively repairs damage incurred to its DNA,
can enter one of three possible states: 1. an irreversible state of dormancy, known as senescence; 2. cell suicide, also known as
apoptosis or programmed cell death; 3. unregulated cell division, which can lead to the formation of a tumour that is cancerous.
Domains in a protein: Regions which exert specific functions, for example binding to DNA.
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Dual specificity phosphatase 1 (DUSP1): DUSP1 specifies a protein with structural features similar to members of the
nonreceptor-type protein-tyrosine phosphatase family. DUSP1 protein has intrinsic phosphatase activity and specifically
inactivates mitogen-activated protein (MAP) kinase in vitro by the concomitant dephosphorylation of both its phosphothreonine
and phosphotyrosine residues. Furthermore, it suppresses the activation of MAP kinase by oncogenic ras in extracts of
Xenopus oocytes. Thus, DUSP1 may play an important role in the human cellular response to environmental stress as well as
in the negative regulation of cellular proliferation.
Dual specificity protein phosphatase 4 (DUSP4): Also known as MKP2, a tumour-suppressor gene coding for a protein
phosphatase that inactivates MAP kinase in vitro and MAP kinase-dependent gene transcription in vivo.
Dynamin: A family of proteins with GTPase activity that plays an essential role in endocytosis by catalysing the fission of clathrin-
coated vesicles from the plasma membrane. When bound to another protein, amphiphysin, dynamin exists in a non-oligomeric
state in clathrin-coated pits. When recruited to sites of endocytosis, dynamin redistributes and polymerises around the vesicle
necks forming dynamin rings. Lengthwise conformational changes in the dynamin rings are responsible for spring-like changes in
the dynamin helix, a process important in vesicle fission.
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E
5＇and 3＇ends: Of a gene or a nucleic acid sequence: the nucleotides in a DNA or RNA sequence are attached to each
other via phosphate bonds bridging the C5 atom of one sugar molecule (e.g. ribose) in one nucleotide and the C3 atom of the
sugar of its neighbour; the 5’ end of a gene is where transcription begins, and the 3’ end is where transcription usually ends.
E1A: An adenovirus protein, E1A is an oncoprotein that affects cellular functions indirectly when it binds to and sequesters
cellular proteins, thereby preventing them from taking part in cellular processes. Some key cellular proteins that E1A has been
documented to interact with include Rb, cyclins, and cyclin-dependent kinases.
E2F1: Regulator of S-phase-specific genes required for cell cycle progression; the acetylation of E2F has a positive effect on
its DNA-binding functions, thereby stimulating transcription. When complexed with Rb, it acts as a transcriptional repressor.
4E-binding protein1 (4E-BP1): A cellular protein, which, in its unphosphorylated state, inhibits translation due to its
association with eIF-4E. This prevents the binding of the scaffold protein eIF-4G and prevents the formation of the translational
initiation complex.
Early response genes: Are rapidly induced following growth factor stimulation without the necessity for previous protein
synthesis; the ability of early response genes to express specific mRNA in the presence of protein synthesis inhibitors indicates
that their transcription is regulated by preexisting modulators activated following growth factor stimulation; the polypeptide
products of many such genes such as c-fos and c-Jun encode transcription factors with DNA-binding properties that in
turn promote or suppress gene activity elsewhere, leading to specific biological responses; early response genes are often
expressed during the earliest phase (G1) of the cell cycle.
E-cadherin: A calcium-dependent cell adhesion molecule that belongs to a family of developmental proteins responsible for
maintaining structural integrity in tissues.
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eEF2: A eukaryotic elongation factor that regulates the elongation phase of the translational process by translocating the
growing mRNA from the ribosomal A site to the ribosomal P site. In mechanisms yet to be elucidated, mTOR signalling
regulates eEF2 activity. Phosphorylation of eEF2 (which occurs during nutrient starvation) is accompanied by a decrease in
elongation rates, whereas dephosphorylation of eEF2 (which occurs in the presence of nutrients) is accompanied by increases
in elongation rates.
EEF2: Gene coding for the eukaryotic translation elongation factor 2, which is responsible for translational elongation by
translocation of the peptidyl-tRNA from the A site to the P site on the ribosome.
EGFR signalling pathway: Signalling pathways and inhibitors of EGFR. Activation of EGFR leads to homodimerisation/
heterodimerisation, phosphorylation of specific tyrosine residues, and recruitment of several proteins at the intracellular portion
of the receptors. Phospholipase Cγ (pink – see Figure 21) and STAT transcription factors (blue) bind directly to the receptor,
whereas Ras/Raf/MAPK pathway (orange) and PI3K pathway (green) need several specific adaptor molecules (yellow). PI3K
can also bind directly to any of the erbB partners of EGFR heterodimers. Concomitantly, the activated receptors undergo
endocytosis and follow two possible routes: lysosomal degradation or importin-mediated nuclear translocation. Once in the
nucleus, EGFR can either behave as a proper transcription factor (for cyclin D1 upregulation) or as coregulator of other
gene transactivators. Both pathways result in nuclear activation of genes related with cell proliferation, survival, invasion, and
metastasis. Two main strategies are available for EGFR kinase inhibition: mAb and small-molecule TKIs. mAbs act extracellularly,
avoiding EGFR ligands binding, whereas TKIs compete with the ATP binding to the kinase domain of the receptor (Figure 21).
eIF-2: A eukaryotic translation initiation factor that forms a heterotrimeric complex with Met-tRNAiMet and GTP that is delivered
to the 40S ribosome primed by eIF-3, resulting in a 43S pre-initiation complex ready to interact with capped mRNA.
eIF-3: A eukaryotic translation initiation factor that binds to the 40S subunit of the ribosome, impeding its association with the
60S subunit. This primes the complex for the delivery of Met-tRNAiMet to the ribosome, setting the stage for initiation of translation.
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Figure 21. The epidermal growth factor receptor pathway.
DAG, 1,2-diacylglycerol; IP3, inositol 1,3,5-triphosphate;

PLCγ, phospholipase Cγ; Erk-1, extracellular signal-regulated
kinase-1; Erk-2, extracellular signal-regulated kinase-2;
FAK, focal adhesion kinase; PKC, protein kinase C
Clin Cancer Res 2006; 12: 5268-5272.
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eIF-3κ: Eukaryotic initiation factors (eIFs) are proteins involved in the initiation phase of eukaryotic translation. eIF-3 binds
to the ribosome subunit–mRNA complex and is implicated in preventing the large ribosomal subunit from binding the small
subunit before it is ready to commence elongation. In mammals, eIF-3 is the largest scaffolding initiation factor, made up of 13
subunits (a-m). In many cancers, eIF-3 is overexpressed. Under serum-deprived conditions (inactive state), eIF-3 is bound to
S6K1. On stimulation by either mitogens, growth factors, or drugs, mTOR/Raptor complex gets activated and, in turn, binds
and phosphorylates S6K1 on T389 (linker region), causing a conformational change that causes the kinase S6K1 to dissociate
from eIF-3. The T389 phosphorylated S6k1 is then further phosphorylated by PDK1 on T229. This second phosphorylation
fully activates the S6K1 kinase, which can then phosphorylate eIF-4B, S6, and other protein targets.
eIF-4: Also called eIF-4F, it is a complex of eIF-4A, eIF-4E, and eIF-4-γ. These eukaryotic translation initiation factors collectively
recruit capped mRNA to the ribosome for translation. The eIF-4F complex is involved in unwinding the secondary structure
of mRNA during the process of translation initiation. eIF-4E is a cap-binding protein. eIF-4A possesses ATP-dependent RNA
helicase activity and RNA-dependent ATPase activity. eIF-4B is an RNA-binding protein that greatly enhances the activity of
eIF-4A. eIF-4-γ is a protein of unknown function.
eIF-4A: Eukaryotic initiation factors (eIFs) are proteins involved in the initiation phase of eukaryotic translation. The eIF-4
initiation factors include eIF-4A, eIF-4B, eIF-4E, and eIF-4G. eIF-4F is often used to refer to the complex of eIF-4A, eIF-4E,
and eIF-4G. eIF-4G is a 175.5-kDa scaffolding protein that interacts with eIF-3, as well as the other members of the eIF-
4F complex. eIF-4E recognises and binds to the 5′ cap structure of mRNA, while eIF-4G binds to poly(A)-binding protein,
which binds the poly(A) tail, circularising and activating the bound mRNA. eIF-4A – a DEAD box RNA helicase – is important
for resolving mRNA secondary structures. eIF-4B contains two RNA-binding domains – one nonspecifically interacts with
mRNA, whereas the second specifically binds the 18S portion of the small ribosomal subunit. It acts as an anchor, as well as
a critical cofactor for eIF-4A. It is a substrate of S6K, and, when phosphorylated, it promotes the formation of the pre-initiation
complex. In vertebrates, eIF-4H is an additional initiation factor with similar function to eIF-4B.
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eIF-4B: Along with eIF-4F, eIF-4B shows an RNA helicase activity.
eIF-4G: A scaffold protein that interacts with eIF-4E, and allows the binding of eIF-4A, eIF-3 and the poly(A)-binding protein
to form the translation complex.
Elongation factor: Elongation factors are a set of proteins that are used in protein synthesis in the process of cell cycle and
elongation in some cells. In the ribosome, they facilitate translational elongation, from the formation of the first peptide bond
to the formation of the last one.
Enhancer: A DNA sequence motif upstream, within, or downstream of a gene which increases/enhances the activity of
promoters regulating transcription of that gene. Enhancers may act in either direction of a DNA strand over distances of up
to several kb.
Enzyme-linked immunosorbent assay (ELISA): ELISA is used to detect the presence of an antibody or an antigen in a sample.
Epidermal growth factor (EGF): Epidermal growth factor or EGF is a growth factor that stimulates cell growth, proliferation,
and differentiation by binding to its receptor EGFR. Human EGF is a 6045-Da protein with 53 amino acid residues and three
intramolecular disulphide bonds. EGF acts by binding with high affinity to epidermal growth factor receptor (EGFR) on the cell
surface. This stimulates ligand-induced dimerisation, activating the intrinsic protein-tyrosine kinase activity of the receptor. The
tyrosine kinase activity, in turn, initiates a signal transduction cascade that results in a variety of biochemical changes within the
cell – a rise in intracellular calcium levels, increased glycolysis and protein synthesis, and increases in the expression of certain
genes including the gene for EGFR – that ultimately lead to DNA synthesis and cell proliferation.
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Epidermal growth factor receptor (EGFR): Also known as HER-1, EGFR belongs to a family of receptors (HER-2, HER-3,
HER-4 are other members of the family) and binds to the EGF, TGF-α, and other related proteins, leading to the generation of
proliferative and survival signals within the cell. It also belongs to the larger family of tyrosine kinase receptors and is generally
overexpressed in several solid tumours of epithelial origin.
Epigenetic: Epigenetic modification is defined as heritable changes in gene activity and expression that occur without
alteration in DNA sequence. The methylation of the promoter to inactivate a gene is an example of an epigenetic change.
Episome: A genetic particle of certain cells (i.e. bacteria) that can exist on its own in the cytoplasm or as part of a chromosome.
A plasmid is an example of an episome.
Epitope: Region within an antigen that has the potential to give rise to an antibody response. With respect to protein antigens,
epitopes may be defined on the basis of the primary, secondary, or tertiary structure of the molecule and, consequently, may
be exposed or hidden within the molecule.
ErbB: The ErbB family of proteins contains four receptor tyrosine kinases, structurally related to the epidermal growth factor
receptor (EGFR), its first discovered member. In humans, the family includes HER-1 (EGFR, ErbB1), HER-2 (Neu, ErbB2), HER-
3 (ErbB3), and HER-4 (ErbB4). The gene symbol, ErbB, is derived from the name of a viral oncogene to which these receptors
are homologous: erythroblastic leukaemia viral oncogene. Excessive ErbB signalling is associated with the development of
a wide variety of types of solid tumour. ErbB-1 and ErbB-2 are found in many human cancers, and their excessive signalling
may be critical factors in the development and malignancy of these tumours.
ERCC1: Excision repair cross-complementing gene. Encodes a nucleotide excision repair protein that repairs a range of lesions,
including ultraviolet-induced thymine dimers and other photoproducts, and also lesions caused by a variety of chemical agents.
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ERK1: ERK1 is a serine/threonine kinase of the GMGC group that plays a critical role in the regulation of cell growth and
differentiation. ERK1 (MAPK3) and ERK2 (MAPK1) play central roles in MAPK cascades and are activated by a wide variety
of extracellular signals including growth and neurotrophic factors, cytokines, hormones, and neurotransmitters. Depending
on the cellular context, MAPK cascades mediate diverse biological functions such as cell growth, adhesion, survival, and
differentiation through the regulation of transcription, translation, and cytoskeletal rearrangements.
ERK-MAP kinase pathway: The MAP kinases can be grouped into three main families. In mammals, these are ERKs
(extracellular-signal-regulated kinases), JNKs (Jun amino-terminal kinases), and p38/SAPKs (stress-activated protein
kinases). ERK family members possess a TEY motif in the activation segment and can be subdivided into two groups: the
classic ERKs that consist mainly of a kinase domain (ERK1 and ERK2) and the larger ERKs (such as ERK5) that contain a
much more extended sequence carboxy-terminal to their kinase domain. The classic ERK1/2 module responds primarily to
growth factors and mitogens to induce cell growth and differentiation. Important upstream regulators of this module include
cell surface receptors, such as receptor tyrosine kinases (RTKs), G-protein-coupled receptors (GPCRs), and integrins, as
well as the small GTPases Ras and Rap. MAPKKs for the classic ERK1/2 module are MEK1 and MEK2, and the MAPKKKs
include members of the Raf family, Mos, and Tpl2 (Figure 22).
Erythropoietin receptor (EpoR): A receptor found on the surface of erythroid progenitor cells in the bone marrow that,
when bound with erythropoietin, stimulates erythroid progenitor cells to transform into erythrocytes.
Estrogen receptor (ER): Belonging to the class of nuclear receptors, estrogen receptors are ligand-activated nuclear
proteins present in many breast cancer cells that are important in the progression of hormone-dependent cancers. After
binding, the receptor–ligand complex activates gene transcription. There are two types of estrogen receptor (α and β). ERα
is one of the most important proteins controlling breast cancer function. ERβ is present in much lower levels in breast cancer
and its function is uncertain. Estrogen-receptor status guides therapeutic decisions in breast cancer (Figure 23).
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Figure 22. The ERK MAPK pathway.
Growth factors Integrins

RTKs
Ion channels GPCRs
SOS Ras SOS Pax Tal
GRB2
RTKs
FRS2
Shc
IRS
CAS FAK
GRB2
PLCγ Gβγ AC
Spry Src Gαs
Pl3K
cAMP
Ca2+ ATP C3G
Crk
Src
PYK2 PAK Rac EPAC
Spred
PKA B-Raf rpS6
Raf1 Rap1
PKC
14-3-3 Raf1 B-Raf 14-3-3 elF4B
IMP
MEK1
p14 Tpl2 Filamin A
KSR
MP1 Ion channels,
IκBα
receptors PP1 MEK1/2
cPLA2 Cytoskeletal
Erk1 PP2A
proteins
eEF2K GSK3
Translation
Late endosome control MNK1/2 Bim
DAPK METTL1
MKP3 ERK1/2 p90RSK
PEA15 BAD nNos
Cell adhesion TSC2
Cytoplasm
PPARγ
Cdc25
Progression
Nucleus of cell cycle
BUB1 p90RSK p27 KIP1
MKP1/2 ERK1/2 MSK1/2
ER Ets Elk-1 TIF1A Fox03 CREB ATF1 ETV1 SRF Fos ERα Nur77 MITF C/EBPβ
Myc/ Histone HMGN1
Stat1/3 N-Myc Pax6 Fos ETV1 TIF1A ATF4 Myt1 Mad1 Ran BP3
H3
UBF
Source of information: Cold Spring Harb Perspect Biol 2012; 4(11): pii: a011254.
Transcription
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Figure 23. Structural composition of estrogen receptor (ER)α and ERβ.
Intracellular signalling pathways used to regulate the activity of estrogens,
estrogen receptors, and selective estrogen receptor modulators.
Roman-Blas et al. Arthritis Research & Therapy 2009; 11: 241.

BioMed Central - original publisher.
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ETS-related gene (ERG): ERG, located on chromosome 21q22, encodes a transforming proto-oncogene that is expressed
in haematopoietic progenitor and endothelial cells. Furthermore, ERG is expressed in early thymocytes and becomes
downregulated as cells develop toward the T-cell lineage. ERG and other members of the ETS family are downstream
effectors of mitogenic signal-transduction pathways and are involved in key steps regulating cell proliferation, differentiation,
and apoptosis.
ETS transcription factors: The ETS family of transcription factors, characterised by an evolutionarily conserved DNA-binding
domain, regulates expression of more than 300 target genes by binding to a purine-rich GGAA/T core sequence. At present, nearly
30 mammalian family members have been isolated. ETS signal transduction is implicated in haematopoiesis and angiogenesis
at the earliest stages of embryogenesis, and is later involved in tissue development. Deregulated expression and/or formation of
chimeric fusion proteins of the ETS family due to proviral insertion or chromosomal translocation is associated with leukaemias
and with specific types of solid tumours.
Eukaryotic initiation factors: Eukaryotic initiation factors (eIFs) are proteins involved in the initiation phase of eukaryotic
translation. Competent translation requires at least nine eukaryotic initiation factors, described below. They function in forming
a complex with the 40S ribosomal subunit and Met-tRNAMeti called the 43S preinitiation complex (PIC), which then recognises
the five-prime cap structure of messenger RNA and recruiting the 43S PIC to mRNA, promoting ribosomal scanning of mRNA
and regulating recognition of the AUG initiation codon, to form the 48S complex, which then joins to the 60S ribosomal
subunit to create the 80S ribosome. There exist many more eukaryotic initiation factors than prokaryotic initiation factors due
to the greater biological complexity of eukaryotic cells (Figure 24).
Exon: Sequence in a gene which is represented in mature messenger RNA. In a gene, exons are typically interrupted by
introns which, in the process of transcription, are being eliminated through splicing; genes may harbour a few or a great
number of exons.
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Figure 24. Translation initiation.

Nat Rev Drug Disc 2015; 14: 261-278.
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Exon deletion: A deletion of a segment of a gene that consists of a sequence of nucleotides that encodes amino acids in
the protein.
Extracellular domain: A part of the receptor that sticks out of the membrane on the outside of the cell. By definition,
a receptor’s main function is to recognise and respond to a specific ligand, and in many receptors these ligands bind to the
extracellular domain.
Extracellular matrix (ECM): Components that are extracellular and composed of secreted fibrous proteins (e.g. collagen)
and gel-like polysaccharides (e.g. glycosaminoglycans) binding cells and tissues together. In addition, the ECM contains
adhesion proteins (e.g. fibronectin and laminin) that link components of the matrix both to one another and to attached cells.
Depending on the tissue, the composition of the ECM differs. For example, collagen is the major component of ECM; elastin
fibres contain cross-linked elastin; and integrins are cell-surface receptors responsible for the attachment of cells to the ECM
(Figure 25).
Extracellular receptor kinase (ERK): A second messenger kinase (an enzyme adding phosphate groups from ATP), ERK
belongs to the MAPK family and is responsible for transmitting signals from the cellular surface to the nucleus by the activation
of transcription factors, including NF-κB. It belongs to the proliferative/mitogenic signal-transduction pathway activated by
tyrosine kinase receptors.
EZH2: Enhancer of zeste homologue 2 (EZH2) is a histone-lysine N-methyltransferase enzyme encoded by EZH2 gene,
which participates in DNA methylation and, ultimately, transcriptional repression. EZH2 catalyses the addition of methyl groups
to histone H3 at lysine 27, by using the cofactor S-adenosyl-L-methionine. EZH2 inhibits genes responsible for suppressing
tumour development, and blocking EZH2 activity may slow tumour growth. EZH2 has been targeted for inhibition because it
is upregulated in multiple cancers including, but not limited to, breast, prostate, melanoma, and bladder cancer.
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Figure 25. Types and variants of collective cell migration.
a 2D sheet b Branching morphogenesis (mammary gland)
c Vascular sprouting
d Multicellular 3D invasion strands
e Border cells
f Detached cluster
Basement membrane Adherens junction Proteolytically Integrins (b1 and b3) Proteases (MMPs, Reprinted by permission from Macmillan Publishers Ltd:
Cortical F-actin Tight junction remodelled ECM in focal contacts MT1MMP and UPA) Nat Rev Mol Cell Biol 2009; 10: 445-457.
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F Factor VIII-related antigen (FVIII-RA): Also called von Willebrand factor, it has been used to identify early megakaryoblasts
in myeloproliferative disorders and differentiate megakaryocytes from other multinucleated cells. A highly specific endothelial
cell marker, FVIII-RA may also be used to demonstrate an abnormal vascular network, which is often seen in myeloproliferative
and myelodysplastic diseases. In conjunction with CD34, FVIII-RA is used to mark endothelial cells that originate in tumours.
Because its expression is sufficiently restricted to endothelial cells, it is a specific marker of these cells (with the exception of
megakaryocytes).
Farnesyltransferase (FT): Enzymatic activity that allows for the covalent addition of a farnesyl group (a 15-carbon moiety) to
a cysteine residue in a protein. Farnesylation is known to occur in proteins with a variety of cellular functions.
Fas: The Fas receptor (FasR), also known as apoptosis antigen 1 (APO-1 or APT), cluster of differentiation 95 (CD95), or
tumour necrosis factor receptor superfamily member 6 (TNFRSF6), is a protein that in humans is encoded by the TNFRSF6
gene. The Fas receptor is a death receptor on the surface of cells that leads to programmed cell death (apoptosis). It is one
of two apoptosis pathways, the other being the mitochondrial pathway.
Fas ligand: Fas ligand (FasL or CD95L) is a type-II transmembrane protein that belongs to the tumour necrosis factor (TNF)
family. Its binding with its receptor induces apoptosis. Fas ligand/receptor interactions play an important role in the regulation
of the immune system and the progression of cancer.
FBL: Gene coding for fibrillarin, which is a component of a nucleolar small nuclear ribonucleoprotein (snRNP) particle thought
to participate in the first step in processing preribosomal RNA. In humans, fibrillarin is associated with the U3, U8, and U13
small nuclear RNAs.
FBXO5: This gene encodes a member of the F-box protein family, which is characterised by an approximately 40 amino acid
motif, the F-box. The F-box proteins constitute one of the four subunits of the ubiquitin protein ligase complex called SCFs (SKP1-
cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws
containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein–protein interaction
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modules or no recognisable motifs. The protein encoded by this gene belongs to the Fbxs class. This protein is similar to Xenopus
early mitotic inhibitor-1 (Emi1), which is a mitotic regulator that interacts with Cdc20 and inhibits the anaphase promoting complex.
Fibroblast growth factor (FGF): Belongs to the FGF family of proteins that are involved in proliferation and differentiation of
several cell types. It binds to receptors belonging to the tyrosine kinase family (Figure 26).
Fibroblast growth factor receptor (FGFR): A family of tyrosine kinase receptors that has four members, FGFR1–4. Like
other tyrosine kinase receptors, intracellular signalling follows receptor dimerisation in response to ligand binding. This leads
to autophosphorylation of the tyrosine molecules in the intracellular tyrosine kinase region of the receptor (Figure 26).
FIP1L1–PDGFRA: A constitutively activated tyrosine kinase that transforms haematopoietic cells, the FIP1L1–PDGFRA fusion
protein is expressed as a result of a chromosomal abnormality identified in patients with the hypereosinophilic syndrome. The
abnormality occurs as a consequence of the fusion of FIP1L1 (coding for Fip1-like 1 protein) gene to the PDGFRA (coding for
PDGFRA) gene and is generated by an interstitial deletion on chromosome 4q12.
FK506: Also called tacrolimus, it is a hydrophobic macrolide lactone and functions as a potent immunosuppressant. FK506
forms a complex with rapamycin binding protein and inhibits mTOR activity.
FLT3: A FLT3 gene, located at chromosome band 13q12, encodes a membrane-bound protein member of the class III
tyrosine kinase receptor family. Receptors belonging to the tyrosine kinase receptor family (e.g. EGFR, PDGFR) are activated
through the auto- or transphosphorylation of tyrosine residues in the cytoplasmic region of the receptors in an ATP-dependent
manner. An internal tandem duplication of FLT3 is one of the most common mutations in normal-karyotype acute myeloid
leukaemia, occurring in approximately 28% to 38% of these patients.
Focal adhesion kinase (FAK): FAK is a protein tyrosine kinase recruited at focal adhesions, which are sites at cell membranes
where cytoskeletal elements interact with extracellular matrix proteins. Cell migration and differentiation are initiated at these
sites. Typically, FAKs are activated by Src.
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Figure 26. FGF and FGFR structure.
FGF signalling pathway.
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Forkhead group of transcriptional factors: FOX (forkhead box) proteins are a family of transcription factors that play
important roles in regulating the expression of genes involved in cell growth, proliferation, differentiation, and longevity. Many
genes encoding FOX proteins have been identified. Some FOX genes are downstream targets of the hedgehog signalling
pathway.
Fos: The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper
proteins that can dimerise with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such,
the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. In some cases,
expression of the Fos gene has also been associated with apoptotic cell death.
Fragile sites: Fragile chromosomal sites demonstrate the following features: 1) they appear as chromosome gaps;
2) they are inherited as codominant traits; 3) the fragility is expressed by the production of acentric fragments or by deleted
chromosomes.
FRAP1: The mammalian target of rapamycin (mTOR), also known as mechanistic target of rapamycin or FK506 binding
protein 12-rapamycin associated protein 1 (FRAP1), is a protein which in humans is encoded by the FRAP1 gene. mTOR is
a serine/threonine protein kinase that regulates cell growth, cell proliferation, cell motility, cell survival, protein synthesis, and
transcription. mTOR belongs to the phosphatidylinositol-3-kinase-related kinase protein family.
FRs (framework regions): Four regions (FR1–4) in the rearranged IgH gene that connect the complementarity determining
regions (CDR1–3). The CDR1–3 regions are the main determinants of antigen binding of the antibody.
FRZB1: Gene coding for the frizzled-related protein 1, which functions as negative modulator of Wnt signalling through
direct interaction with Wnts. Soluble frizzled-related proteins (SFRPs) have a role in regulating cell growth and differentiation
in specific cell types. Methylation silencing of SFRPs may be one of the important mechanisms of aberrant Wnt signalling
activation in multiple myeloma; FRZB1 is thought to play a role in the transition from MGUS (monoclonal gammopathy of
undetermined significance) to multiple myeloma.
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Fyn kinase: A member of the src family of nonreceptor tyrosine kinases, fyn is localised at growth cones and postsynaptic
membranes of neurons. Fyn expression is seen in several regions of the brain, including the olfactory bulb, cerebellum,
hippocampus, and limbic system. Fyn phosphorylates several receptors (e.g. the NMDA receptor) and modulates their
functions. Fyn is also implicated in the regulation of protein expression in activated T cells, galectin being among one of the
proteins regulated.
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G G1 arrest: Arresting cells in the G1 phase of the cell cycle, which is an ordered cycle of complex events, resulting in cell
division. The GAP-1 and GAP-2 stages are separated by the S (DNA synthesis) and M (mitosis) phases, respectively.
GADD45: A gene whose expression is upregulated during DNA damage and/or growth arrest. GADD45 is supposed to be
involved in DNA-repair mechanisms.
GADPH: Gene coding for glyceraldehyde-3-phosphate dehydrogenase, an enzyme belonging to the glycolytic pathway.
GADPH is a ubiquitously expressed cellular enzyme. This gene is often used as a reference (“housekeeping”) gene for
normalisation of RT-PCR data.
GAGE: A family of genes expressed in various tumours which code tumour-associated antigens that are presented by human
leukocyte antigen class I molecules and recognised by T cells.
Galectin-1: A member of the family of galectins—animal lectins characterised by conserved carbohydrate recognition domains
and binding affinity for β-galactosidases. Galectins are involved in intracellular signalling following binding to glycoproteins/
glycolipids on cell surfaces and in the extracellular matrix. Found in invasive tumour environments, galectins play a role in
pathological processes, including proliferation, cell aggregation, adhesion, migration, apoptosis, and immunoregulation.
GATA3: A member of the GATA family of transcription factors. GATA3 is abundantly expressed in the T-cell lineage and
possibly participates in T-cell receptor gene activation via enhancer binding.
GBP1: Interferon-induced guanylate-binding protein 1 (GBP1) is a protein that in humans is encoded by the GBP1 gene.
It belongs to the dynamin superfamily of large GTPases. Guanylate binding protein expression is induced by interferon.
Guanylate binding proteins are characterised by their ability to specifically bind guanine nucleotides (GMP, GDP, and GTP) and
are distinguished from the GTP-binding proteins by the presence of 2 binding motifs rather than 3.
GD3 ganglioside: A carbohydrate-rich sphingolipid that contains sialic acid, GD3 ganglioside is synthesised during the
onset of apoptotic signalling. GD3 ganglioside is an attractive target for immunotherapy of melanoma because it is expressed
abundantly on all melanomas, but not expressed on most healthy tissues.
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Gelsolin: A calcium-regulated, actin-modulating protein, gelsolin caps actin filaments by virtue of binding to their plus end.
It also promotes the assembly of actin monomers to actin filaments. Thus gelsolin controls the organisation of the actin
cytoskeleton in cells and controls cell morphology, motility, signalling, and apoptosis.
Gene: A DNA sequence (a segment of DNA) coding for a specific function or structure, i.e. the polypeptide chain of a protein.
Genes are typically composed of exons separated by introns, in addition to promoter regions and other sequences; about
100 000 different genes are thought to reside in the human genome.
Gene amplification: The presence of multiple copies of a gene or genes that leads to overexpression of that gene or genes.
Gene encoding growth factor receptor-bound protein 7 (GRB7): Gene encoding growth factor receptor-bound protein
7, which belongs to the GRB family of proteins (e.g. GRB2, GRB10, and GRB14). Functions in mitogenic signalling and is an
important component of insulin and IGF and EGFR signal-transduction pathways.
Genetic polymorphisms: A genetic variant seen in at least 1% of the population. Because proteins are gene products,
their polymorphisms reflect allelic differences in the gene. The advent of restriction enzymes, which digest DNA to fragments
based on sequence specificity, has ushered in an era of restriction fragment length polymorphisms (RFLPs) in which changes
in DNA sequence(s) are manifest as restriction fragments of different size(s) when cleaved with a specific restriction enzyme.
Polymorphisms are used in tissue typing, in determining disease, in pharmacogenetics, and in assessing genetic diversity.
Genomic signature: Genomic signature refers to the characteristic frequency of oligonucleotides in a genome or sequence.
Oligonucleotide composition is similar for phylogenetically related organisms.
Genotype: The specific genetic makeup of a given individual. Although genotypes give rise to the phenotype of an individual,
genotypes and phenotypes are not always correlative. For example, some genotypes are expressed only under specific
environmental conditions.
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Geranylgeranyltransferase: An enzyme that covalently adds a geranylgeranyl group (a 20-carbon moiety) to a protein. Rab
geranylgeranyltransferase (RabGGTase) is classified as a transferase enzyme; specifically, it is in the protein prenyltransferase
family along with two other enzymes (protein farnesyltransferase and protein geranylgeranyltransferase type-I). The reaction
catalysed by RabGGTase is summarised as follows: geranylgeranyl diphosphate + protein-cysteine = S-geranylgeranyl-
protein + diphosphate. This reaction is essential in the control of membrane docking and fusion.
Germline mutation: An inherited variation in the lineage of germ cells. Germline mutations can be passed on to offspring.
Germline polymorphism: Germline polymorphism is a difference in DNA sequence among individuals in the germ cells. Unlike
somatic cell genetic mutations, these polymorphisms can be transmitted to an organism’s offspring. Genetic polymorphisms
may be the result of a chance process or may have been induced by external agents (such as viruses or radiation). Changes
in DNA sequence that have been confirmed to be caused by external agents are generally called “mutations” rather than
“polymorphisms.”
Glial fibrillary acidic protein (GFAP): GFAP is a member of the intermediate filament family that provides support and strength
to cells. Several molecules of GFAP protein bind together to form the main intermediate filament found in astrocytes.
GNAT: Histone acetyltransferases belonging to the GNAT (Gcn5-related N-acetyltransferase) superfamily are grouped on the
basis of their similarity in several homology regions and acetylation-related motifs.
GNB2L1: Guanine nucleotide-binding protein subunit beta-2-like 1, also known as Receptor for activated C kinase 1 (RACK1),
is a 32-kDa protein that in humans is encoded by the GNB2L1 gene.
gp100: A melanocyte differentiation antigen that is shared between melanomas and melanocytes, which is the origin of
melanomas. It is a matrix protein involved in melanin synthesis. gp100 protein expression is detected by the gp100-specific
antibodies HMB-45 and NKI-beteb.
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G protein–coupled receptors (GPCR): G protein-coupled receptors (GPCRs), also known as seven-transmembrane
domain receptors, 7TM receptors, heptahelical receptors, serpentine receptor, and G protein-linked receptors (GPLR),
constitute a large protein family of receptors that sense molecules outside the cell and activate inside signal transduction
pathways and, ultimately, cellular responses. They are called seven-transmembrane receptors because they pass through the
cell membrane seven times. The ligands that bind and activate these receptors include light-sensitive compounds, odours,
pheromones, hormones, and neurotransmitters, and vary in size from small molecules to peptides to large proteins. There
are two principal signal transduction pathways involving the G protein-coupled receptors: • the cAMP signal pathway and
• the phosphatidylinositol signal pathwayWhen a ligand binds to the GPCR it causes a conformational change in the GPCR,
which allows it to act as a guanine nucleotide exchange factor (GEF). The GPCR can then activate an associated G protein
by exchanging its bound GDP for a GTP. The G protein’s α subunit, together with the bound GTP, can then dissociate from
the β and γ subunits to further affect intracellular signalling proteins or target functional proteins directly, depending on the α
subunit type (Gαs, Gαi/o, Gαq/11, Gα12/13).
Granulocyte–macrophage colony-stimulating factor (GM-CSF): A growth factor that stimulates the production of
white blood cells. Normally used in cancer therapy and bone marrow transplantation, GM-CSF augments white blood cell
production, decreasing the risk of infection. In vaccine therapy, it is an effective vaccine adjuvant administered to activate
endogenous dendritic cells, the most effective antigen-presenting cells of the immune system (Figure 27).
Growth factor receptor-bound protein 2 (Grb2): An adapter protein involved in signal-transduction pathways governed by
protein tyrosine kinases. The single SH2 (src-homology 2) domain in Grb2 recognises phosphotyrosine-containing domains
in receptor tyrosine kinases such as the EGFR and PDGFR, on docking proteins such as Sch, and on nonreceptor tyrosine
kinases such as FAK. SH3 (src-homology 3) domains that flank the single SH2 domain bind to proline-rich regions of SOS, a
GDP releasing factor (Figure 28).
Guanine: Purine base.
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Figure 27. Role of GM-CSF in prostate cancer immunotherapy.

Nat Rev Immunol 2010; 10: 580-593.
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Figure 28. Role of Grb2 in mammary tumour growth.
Reprinted by permission from Carcinogenesis 2008; 29: 244-251.
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H Hamartin: The protein product of the tuberous sclerosis 1 (TSC1) gene, hamartin binds directly to tuberin, the GTPase that
inactivates Rheb. Mutations in TSC1 or TSC2 lead to the same disease phenotype, suggesting that hamartin and tuberin
are both required for the proper functioning of the tuberin–hamartin heterodimers. Phosphorylation may regulate both the
formation of the heterodimer and the activity of the tuberin–hamartin complex.
Haplotype: A combination of alleles (DNA sequences) at adjacent locations (loci) on the chromosome that are transmitted
together. A haplotype may be one locus, several loci, or an entire chromosome, depending on the number of recombination
events that have occurred between a given set of loci.
Haplotype-tagging single nucleotide polymorphisms (SNPs): Markers that are statistically associated with and are
therefore considered to be representative of a set of SNPs within a particular region. Using this technique, the identification of a
few alleles of a haplotype block allows for the identification of all other polymorphic sites in this region of linkage disequilibrium.
Hapten: An incomplete antigen, typically a small molecular weight substance, being incapable of causing the production of
antibodies, but capable of combining with a specific antibody.
Heat shock protein: General class of proteins important for cell viability that are typically expressed in response to stress, heat
shock proteins act as “molecular chaperones” for other proteins that have important regulatory roles in refolding denatured
proteins, intracellular transportation of proteins, and preventing protein unfolding and aggregation.
Helicase: Helicases are a class of enzymes vital to all living organisms. Their main function is to unpackage an organism’s
genes. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two
annealed nucleic acid strands (i.e. DNA, RNA, or RNA–DNA hybrid) using energy derived from ATP hydrolysis. There are
many helicases resulting from the great variety of processes in which strand separation must be catalysed. Approximately 1%
of eukaryotic genes code for helicases. The human genome codes for 95 non-redundant helicases: 64 RNA helicases and 31
DNA helicases. Many cellular processes, such as DNA replication, transcription, translation, recombination, DNA repair, and
ribosome biogenesis, involve the separation of nucleic acid strands that necessitates the use of helicases.
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Hepatocyte growth factor (HGF): A growth factor with strong mitogenic activity on hepatocytes and primary epithelial cells
through its interaction with its receptor (c-met); HGF has multifunctional activities that regulate cell growth and motility.
HER-1: Also known as the epidermal growth factor receptor (EGFR - see definition), HER-1 drives the development of
multiple solid tumour types.
HER-2/CEP17: The CEP17 DNA probe is a fluorescent DNA probe specific for the alpha satellite DNA sequence at the
centromeric region of chromosome 17 (17p11.1-q11.1). The assay is rapid, non-radioactive, requires little tumour material,
and is capable of detecting few copies of the oncogene.
HER-2/neu (human epithelial growth factor receptor-2): Also called ErbB2, HER-2/neu belongs to the EGFR family and
is overexpressed in several solid tumours. Like EGFR, it is a tyrosine kinase receptor whose activation leads to proliferative
signals within the cells. On activation, the HER family of receptors is known to form homodimers and heterodimers, each with
a distinct signalling activity. Because HER-2 is the preferred dimerisation partner when heterodimers are formed, it is important
for signalling through ligands specific for any members of the family. It is typically overexpressed in several epithelial tumours
(Figure 29).
HER-3: It plays a distinct role in the HER family signalling network. Although it is kinase inactive and therefore incapable of
initiating downstream signalling pathways on its own, HER-3 can dimerise with other receptors, particularly HER-2, for potent
cellular signalling.
HER-4: A receptor tyrosine kinase. Ligand binding induces a variety of cellular responses including mitogenesis and
differentiation. Alternatively spliced variants that encode different protein isoforms have been described; however, not all
variants have been fully characterised.
Heregulin: Belongs to a family of proteins known to activate ErbB2 in association with ErbB3 and ErbB4.
Heterochromatin: A chromatin structure consisting of nucleosomes tightly wound in a solenoid fashion along with accessory
proteins. In this configuration, the DNA in nucleosomes is inaccessible to the transcription machinery.
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Figure 29. Signal transduction by the HER family. As shown in Panel A, the four members of the HER
family are HER-1, HER-2, HER-3, and HER-4.
The New England Journal of Medicine 2007; 357 (1): 39-51.
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Heterochromatin protein 1 (HP1): A protein that helps fold and condense chromatin. The chromodomain of HP1 binds to
methylated tails of histone 3, an interaction important for proper localisation of HP1 to heterochromatin.
HGS-ETR2: Currently in developmental stages, HGS-ETR2 is a monoclonal antibody designed to function as an agonist for
TRAIL-R2. By binding to TRAIL-R2, HGS-ETR2 induces apoptosis in preclinical studies in xenograft tumour models.
Histone acetyltransferases (HATs): Histone acetyltransferases (HATs) are enzymes that acetylate conserved lysine amino
acids on histone proteins by transferring an acetyl group from acetyl CoA to form ε-N-acetyllysine. DNA is wrapped around
histones, and, by transferring an acetyl group to the histones, genes can be turned on and off. In general, histone acetylation
increases gene expression. In general, histone acetylation is linked to transcriptional activation and associated with euchromatin.
When it was first discovered, it was thought that acetylation of lysine neutralises the positive charge normally present, thus
reducing affinity between histone and (negatively charged) DNA, which renders DNA more accessible to transcription factors.
Histone code: The histone code is a concept that the transcription of genetic information encoded in DNA is in part regulated
by chemical modifications to histone proteins, primarily on their unstructured ends. Together with similar modifications such
as DNA methylation, it is part of the epigenetic code. Histones associate with DNA to form nucleosomes, which themselves
bundle to form chromatin fibres, which in turn make up the more familiar chromosome. Histones are globular proteins with a
flexible N-terminus (taken to be the tail) that protrudes from the nucleosome. Many of the histone tail modifications correlate
very well to chromatin structure and both histone modification state and chromatin structure correlate well to gene expression
levels. The critical concept of the histone code hypothesis is that the histone modifications serve to recruit other proteins by
specific recognition of the modified histone via protein domains specialised for such purposes, rather than through simply
stabilising or destabilising the interaction between histone and the underlying DNA. These recruited proteins then act to alter
chromatin structure actively or to promote transcription.
Histone deacetylases (HDACs): Enzymes that catalyse the removal of acetyl groups from the post-translationally modified
acetylated amino functions of lysine residues in histones and non-histone proteins. HDACs act as remodelling factors and may
act as transcriptional repressors. Classification of HDACs is based on sequence homology to yeast HDAC.
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Histone demethylases: Enzymes that remove the methyl group from methylated histones, facilitating repression of gene
expression.
Histone methyltransferases: Enzymes that catalyse the transfer of methyl groups from S-adenosylmethionine to lysine and
arginine residues of histone proteins. The activity is sometimes associated with EZH2 proteins.
Histone-modifying enzymes: Enzymes that modify chromatin, a complex of DNA and proteins located in the nucleus
of each cell. Chromatin is made up of DNA molecules wound tightly around proteins called histones. These proteins help
organise the DNA and package it into larger thread-like structures called chromosomes. Chromatin-modifying enzymes alter
histones by adding or removing certain small molecules. These changes regulate chromatin structure and influence gene
transcription, which is the first step in the production of proteins from genes. Histone modification also influences the repair of
damaged DNA and the copying (replication) of DNA molecules.
HLA-DPB1: Gene encoding the major histocompatibility complex, class II, DP beta 1. It functions in antigen presentation.
HLA-DR: Human class II histocompatibility antigen. Present on several cell types, including antigen-presenting cells, B cells,
monocytes, macrophages, and activated T cells.
HLA/peptide tetramers: Multimerised human leukocyte antigen (HLA)/peptide molecules consisting of four soluble and
biotinylated HLA molecules with bound peptides that are linked to fluorochrome-labelled streptavidin. On the basis that HLA/
peptide tetramers bind specifically to T-cell receptors on human T lymphocytes, they are used to detect and isolate antigen-
specific T cells independent of their cytokine secretion profile.
HLH and HTH motifs: Helix–loop–helix and helix–turn–helix motifs, respectively; structural motifs of DNA-binding proteins
which, through a particular three-dimensional structure, are able to bind to particular segments of the DNA double helix;
represent transcription factors.
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hMLH1: A human gene located on chromosome 3. It is a gene commonly associated with hereditary nonpolyposis colorectal
cancer.
hMSH2: An integral component of the DNA mismatch-repair pathway, the protein coded by the gene binds to mispairs and
insertion/deletion loops in DNA and is responsible for fidelity of DNA replication.
Homeobox: A sequence that codes for a conserved domain of amino acids present in some proteins which function as
regulatory proteins or transcription factors (Figure 30).
Homozygosity: The presence of the same alleles at a particular gene locus on homologous chromosomes.
Housekeeping gene: Housekeeping genes are typically constitutive genes that are required for the maintenance of basic
cellular function, and are expressed in all cells of an organism under normal and pathophysiological conditions. Although
some housekeeping genes (such as LDHA, NONO, PGK1, PPIH) are expressed at relatively constant levels in most non-
pathological situations, other housekeeping genes may vary depending on experimental conditions.
H-Ras: An isoform of Ras. The Ras gene family consists of H-Ras, N-Ras, and K-Ras. The Ras proteins are typically small
triphosphate-binding proteins, and are the common upstream molecule of several signalling pathways that play a key role in
signal transduction, which results in cellular proliferation and transformation.
HRR (homologous recombination repair): A DNA-repair pathway that repairs the broken ends of DNA by using information
on the intact sister chromatid or homologous chromosome.
HSP90: Belonging to the family of heat shock proteins (HSPs), HSP90 is important for cellular viability and acts as a “molecular
chaperone” for other proteins by forming multimolecular complexes. These complexes are important regulatory elements in
the fate of proteins, which include refolding of denatured proteins, intracellular transport of proteins, and preventing protein
unfolding and aggregation. Although HSPs are usually produced in response to stress (e.g. heat, nutrient deprivation), HSP90
is normally expressed at high levels even under nonstress conditions.
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Figure 30. HOM-C/HOX gene clusters: conservation through evolution.
Drosophila Mouse embryo
BX-C ANT-C HoxB

Abd-B Abd-A Ubx Antp Scr Dfd Pb Lab B1 B2 B3 B4 B5 B6 B7 B8 B9
Human leukocyte antigen (HLA): The human major histocompatibility complex, which is expressed as two sets of highly
polymorphic cell-surface molecules, termed HLA class I and HLA class II. HLA class I molecules are expressed on all nucleated
cells and are encoded by diverse alleles of the HLA-A, HLA-B, or HLA-C genes (e.g. HLA-A1 [HLA molecule encoded by the
A1 allele of the HLA-A gene] and HLA-B7 [HLA molecule encoded by the B7 allele of the HLA-B gene]). HLA class I molecules
bind peptides derived from cellular proteins upon processing. Cytotoxic T lymphocytes, expressing the CD8 coreceptor,
recognise cell-bound peptides in association with HLA class I molecules on target cells.
Hypomorph: Less-than-normal levels of expression of wild-type gene.
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Hypoxia-inducible factors (HIFs): Hypoxia-inducible factors (HIFs) are transcription factors that respond to changes
in available oxygen in the cellular environment – to be specific, to decreases in oxygen, or hypoxia. The HIF signalling
cascade mediates the effects of hypoxia, the state of low oxygen concentration, on the cell. Hypoxia often keeps cells from
differentiating. However, hypoxia promotes the formation of blood vessels, and is important for the formation of a vascular
system in embryos, and cancer tumours. The hypoxia in wounds also promotes the migration of keratinocytes and the
restoration of the epithelium. In general, HIFs are vital to development. In mammals, deletion of the HIF-1 genes results in
perinatal death. HIF-1 has been shown to be vital to chondrocyte survival, allowing the cells to adapt to low-oxygen conditions
within the growth plates of bones. HIF plays a central role in the regulation of human metabolism (Figure 31).
Hypoxia-inducible factor 1α: The hypoxia-inducible factor-1α protein (HIF-1α) is a subunit of the HIF-1 transcription
factor, which induces transcription of several genes involved in the cellular response to hypoxia. The Von Hippel-Lindau
tumour suppressor protein (pVHL) ubiquitinates HIF-1α when cell oxygen levels are normal. This leads to the degradation of
HIF-1α and prevents the transcription of hypoxic response genes such as vascular endothelial growth factor, platelet-derived
growth factor B, and erythropoietin. USP20 deubiquitinates HIF-1α, preventing its proteasomal degradation, and allowing it
to transcribe the hypoxic response genes.
Hypoxia-inducible factor 2α: Endothelial PAS domain-containing protein 1 (EPAS1, also known as hypoxia-inducible
factor-2 α [HIF-2 α]) is a protein that in humans is encoded by the EPAS1 gene. It is a type of hypoxia-inducible factor, a group
of transcription factors involved in body response to oxygen level. The gene is active under low oxygen conditions called
hypoxia. It is also important in the development of heart, and maintaining catecholamine balance required for protection of the
heart. Mutation often leads to neuroendocrine tumours.
Hypoxia-response element (5HRE): An inducible promoter in the 5＇-untranslated region of human vascular endothelial
growth factor (VEGF) that shows excellent transcriptional activation at low oxygen tension. This region has been isolated and
several copies have been cloned in vectors upstream of genes whose expression is desired under conditions of hypoxia.
When these vectors are introduced in tumours, for example, the cloned genes are expressed due to hypoxic conditions that
are characteristic of tumours. Thus, the technology allows for expression of therapeutic genes in tumour cells.
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Figure 31. Hypoxia promotes ECM remodelling to facilitate metastasis.
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I IGF-2R: Also called the IGF-2R/M6P, IGF-2R is functionally different from IGF-1R. The receptor has an extracellular domain
that binds M6P and IGF-2. The receptor also binds lysosomal enzymes. IGF-2R/M6P may be involved in clearing IGF-2
from circulation by endocytosis. The receptor has also been shown to bind to retinoic acid and urokinase-type plasminogen
activator receptor at different sites. Intracellular IGF-2R/M6P functions to direct lysosomal enzymes to lysosomes. In addition,
IGF-2R/M6P has been shown to be a death receptor for granzyme B during cytotoxic T-cell-induced apoptosis.
IGF-binding proteins (IGFBPs): The IGFBPs represent a family of six conserved proteins that share the ability to bind the
insulin-like growth factors IGF-1 and IGF-2. They are secreted proteins and are found in serum, all biological fluids, and tissue
extracts. The amino and carboxyl termini of the members belonging to this family show sequence similarity, with variability
present in the central region of the molecules. IGFBPs function by binding to IGFs and inhibit interactions of IGFs with their
receptors, IGF-1R and IGF-2R. The roles of different IGFBPs may differ depending on their tissue expression, regulation by
hormones and growth factors, proteolytic degradation, and association with cell membranes or cell membrane receptors.
Some IGFBPs have nuclear localisation signals and may be found within the nucleus.
IgH VDJ region: A unique region in the immunoglobulin heavy (IgH) chain that connects the variable (V) region of the molecule
with the constant region. Briefly, the genetic locus that comprises IgH is made up of heavy chain V genes, heavy chain diversity
(D) segments, heavy chain joining (J) segments, and heavy chain constant (C) regions. B-cell development results in changes
at the IgH locus that involve DNA rearrangements. VDJ joining occurs at the pro-B-cell stage, prior to activation of V genes.
Class switching occurs later in B-cell development. Ultimately, unique combinations of V, D, J, and C segments result in the
expression of unique heavy chains.
IκB kinase (IKK): A complex of two subunits, IKKα and IKKβ, IκB kinase directly phosphorylates IκB in complex with
NF-κB. The phosphorylation leads to the dissociation of IκB from NF-κB, an event responsible for the activation of NF-κB.
Phosphorylated IκB is targeted for degradation.
ILT: A family of genes encoding Ig-like transcripts. A subset of ILTs (ILT2, ILT3, ILT4, ILT5, and leukocyte Ig-like receptor 8) displays
long cytoplasmic tails, which have immunoreceptor tyrosine-based inhibitory motifs. A second subset (ILT1, ILT7, ILT8, and
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leukocyte Ig-like receptor 6) contains short cytoplasmic domains lacking signal transduction motifs, but having basic arginine
residues within the transmembrane domain, which associates with the FcR γ-chain and transduces stimulatory signals.
Immunogenic: Capable of inducing an immune response.
Immunoglobulin: Immunoglobulins, also known as antibodies, are glycoprotein molecules produced by plasma cells (white
blood cells). They act as a critical part of the immune response by specifically recognising and binding to particular antigens,
such as bacteria or viruses, and aiding in their destruction.
Immunoglobulin heavy (IgH) chain genes: The genetic locus that comprises the IgH chain genes is made up of heavy
chain variable (V) genes, heavy chain diversity (D) segments, heavy chain joining (J) segments, and heavy chain constant
(C) regions. B-cell development results in changes at the IgH locus that involve DNA rearrangements. VDJ joining occurs
at the pro-B-cell stage, prior to activation of V genes. Class switching occurs later in B-cell development. Ultimately, unique
combinations of V, D, J, and C segments result in the expression of unique heavy chains.
Importin-α7: Responsible for importing substrates across the nuclear membrane.
Initiation codon: A ribonucleotide triplet AUG that translates into the amino acid methionine; this is always the first amino
acid codon in every RNA.
Insert: DNA fragment inserted into a vector. Vectors (mostly phages, plasmids, and cosmids) represent DNA molecules which
can take up foreign DNA and replicate in microorganisms. DNA inserts replicate alongside the vector, an essential feature of
cloning procedures.
Insulin-like growth factor (IGF): Proteins with sequences similar to insulin, insulin-like growth factors trigger similar cellular
responses as insulin, including mitogenesis. IGF-1 (secreted by the liver) and IGF-2 (secreted by brain, kidney, pancreas, and
muscle) function through cell-surface receptors.
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Insulin-like growth factor (IGF) axis: The insulin-like growth factors are part of a complex system that cells use to
communicate with their physiological environment. This complex system (often referred to as the IGF axis) consists of two
cell-surface receptors (IGF-1R and IGF-2R), two ligands (IGF-1 and IGF-2), a family of six high-affinity IGF-binding proteins
(IGFBP-1 to IGFBP-6), as well as associated IGFBP-degrading enzymes, referred to collectively as proteases.
Insulin-like growth factor-1 receptor (IGF-1R): A tyrosine kinase receptor that protects several cell types from apoptotic
injuries via the activation of PI3K, Akt/PKB, and phosphorylation of BAD (leading to its inactivation). IGF-1R also mediates
regulation of angiogenic factors in tumour cells (Figure 32).
Insulin-like growth factor-binding protein-3 (IGFBP-3): A member of the family of high-affinity proteins, IGFBP-3 influences
cell proliferation by modulating access of IGFs to the IGF receptors. IGFBP-3 is known to inhibit cell growth by sequestering
IGFs and induces apoptosis in an IGF-independent manner. In some circumstances, IGFBP-3 can have an opposite effect
because it acts as a carrier of IGFs toward its receptor, thus supporting the proliferative effect of this growth factor.
Integrin-linked kinase (ILK): A serine/threonine kinase with ankyrin-like repeats, ILK regulates transduction of extracellular
matrix signalling through integrins by interacting with the cytoplasmic domain of beta-1 and beta-3 integrins. ILK links integrins
and growth factor receptors to the actin cytoskeleton, where it facilitates interaction with several proteins. It phosphorylates a
variety of substrates, including Akt (important in survival pathways), beta-1 integrin, and glycogen synthase kinase.
Integrins: Integrins are transmembrane receptors that are the bridges for cell–cell and cell–extracellular matrix (ECM)
interactions. When triggered, integrins in turn trigger chemical pathways to the interior (signal transduction), such as the
chemical composition and mechanical status of the ECM, which results in a response (activation of transcription), such as
regulation of the cell cycle, cell shape, and/or motility, or new receptors being added to the cell membrane. This allows rapid
and flexible responses to events at the cell surface, for example to signal platelets to initiate an interaction with coagulation
factors (Figure 33).
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Figure 32. Key components of the IGF-1R pathway.
Clin Cancer Res 2010; 16 (9): 2512-2517.
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Figure 33. Integrins in the host response to cancer.

Nat Rev Cancer 2010; 10: 9-22.
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Intercellular cell adhesion molecule (I-CAM): A member of the superfamily of immunoglobulin-like molecules, I-CAM
may be expressed on activated endothelial cells and leukocytes. These are target ligands for the integrins expressed by white
blood cells (heterophilic binding).
Interferon gamma (IFN-γ): Interferon gamma (IFN-γ) or type II interferon is a dimerised soluble cytokine that is the only
member of the type II class of interferons. It is critical for innate and adaptive immunity against viral, some bacterial, and
protozoal infections. IFN-γ is an important activator of macrophages and inducer of Class I major histocompatibility complex
(MHC) molecule expression. Aberrant IFN-γ expression is associated with a number of autoinflammatory and autoimmune
diseases. IFN-γ is produced predominantly by natural killer (NK) and natural killer T (NKT) cells as part of the innate immune
response, and by CD4 Th1 and CD8 cytotoxic T-lymphocyte (CTL) effector T cells once antigen-specific immunity develops.
Interleukin 1 (IL-1): Produced by activated macrophages, endothelial cells, and B cells, IL-1 is a cytokine that induces
inflammatory responses. As a proinflammatory cytokine, IL-1 has a role in immune, degradative, and growth-promoting
processes. Belonging to this class of cytokines, IL-1β and IL-1α are agonists while IL-1Ra is an antagonist of the IL-1
receptor.
Interleukin 2 (IL-2): A cytokine that stimulates proliferation of activated T cells and, at high doses, is used as antitumour
therapy in metastatic renal cell carcinoma (Figure 34).
Interleukin 4 (IL-4): Cytokine that is responsible for B-cell differentiation, activation, proliferation, and immunoglobulin E
switch, it is produced by T cells, mast cells, and basophils. It functions through the CD124 receptor.
Interleukin 6 (IL-6): IL-6 is produced predominantly by activated immune cells such as microglia and is involved in the
amplification of inflammatory reactions.
Interleukin 8 (IL-8): A proinflammatory cytokine structurally related to platelet factor 4, IL-8 is released by several cell types
(e.g. monocytes, macrophages, T cells, endothelial cells, tumour cells) in response to an inflammatory stimulus. It activates
neutrophils and is a chemokine for neutrophils and T lymphocytes. It is also an angiogenic factor.
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Figure 34. Working mechanism of immunocytokines exemplified for tumour-targeted IL-2.
Cytokine T cell
(for example, IL-2)
CD3
TCR
Natural killer cell Expansion
Cytokine
receptor
Fc
receptor Surface antigen
(for example, Tumour cell
CEA, GD2)

Nat Drug Discov 2006; 5: 147-159.
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Interleukin 11 (IL-11): A pleiotropic cytokine with diverse biological activities on several cell types. In general IL-11 modulates
inflammatory processes. It also stimulates T-cell-dependent development of immunoglobulin, proliferation of haematopoietic
stem cells, osteoclastic activity in bone, and decidualisation of endometrium.
Intron: An intervening DNA sequence usually placed between two exons in a gene. In a first round of transcription, introns
are read and incorporated into RNA; however, such sequences will in a later step be eliminated from mRNA through splicing.
The precise function of introns is largely unknown.
IRS1: Gene encoding insulin receptor substrate 1. It mediates the biological response to insulin stimulation by binding and
activating various enzymes or adaptor molecules.
ISG20: Gene coding for the exonuclease protein Isg20, which is stimulated by interferon and is directly induced by synthetic
dsRNA via NF-κB and IRK-1 activation.
Isoforms: Arising from a differential exon-splicing process, isoforms are proteins derived from the same gene but have
distinct physical, and sometimes biological, properties.
ISWI: An ATPase that has sequence similarity to the Swi/Snf homologue in Drosophila, the name implies Imitation SWItch.
ITGβ7: Integrin beta-7 is an integrin protein that in humans is encoded by the ITGB7 gene. It can pair with ITGA4 (CD49d) to
form the heterodimeric integrin receptor α4β7, or with ITGAE (CD103) to form αEβ7. Like all integrin subunits, β7 is a highly
flexible, membrane-bound, extracellular protein that must pair with an α subunit for stability. The molecule’s flexibility allows it
to dynamically regulate its affinity for ligand through conformational changes.
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J Jak/STAT pathway: The pathway usually (not always) activated by cytokine receptors, where binding of a ligand to the
cytokine receptor leads to recruitment and subsequent autophosphorylation of Jak proteins (activated state) at the cellular
membrane level. Activated Jaks phosphorylate the receptor, creating docking sites for specific signalling proteins, including
STAT proteins. When coupled to the activated receptor, STAT proteins are phosphorylated (activated) by Jak proteins. In
contrast to cytokine receptor signalling, receptors with intrinsic tyrosine kinase activity (e.g. EGFR, PDGFR) may bypass JAK
activation and directly phosphorylate STAT proteins (Figure 35).
Janus kinase: Janus kinase (JAK) is a family of intracellular, nonreceptor tyrosine kinases that transduce cytokine-mediated
signals via the Jak/STAT pathway. The four JAK family members are:
• Janus kinase 1 (JAK1)
• Tyrosine kinase 2 (TYK2)
Since members of the type I and type II cytokine receptor families possess no catalytic kinase activity, they rely on the JAK
family of tyrosine kinases to phosphorylate and activate downstream proteins involved in their signal transduction pathways.
The receptors exist as paired polypeptides, thus exhibiting two intracellular signal-transducing domains. JAKs associate with
a proline-rich region in each intracellular domain, which is adjacent to the cell membrane and called a box1/box2 region.
After the receptor associates with its respective cytokine/ligand, it goes through a conformational change, bringing the two
JAKs close enough to phosphorylate each other. The JAK autophosphorylation induces a conformational change within itself,
enabling it to transduce the intracellular signal by further phosphorylating and activating transcription factors called STATs
(Signal Transducer and Activator of Transcription, or Signal Transduction And Transcription). The activated STATs dissociate
from the receptor and form dimers before translocating to the cell nucleus, where they regulate transcription of selected genes
(Figure 35).
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Figure 35. The domain structure of JAK and STAT.
Regulation of JAK-STAT signalling, the cross-talk between signalling pathways.
a a c
c
Publishers Ltd: Nature Reviews Immunology
2003; 3 (11): 900-911.
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JNK signalling pathway: C-Jun N-terminal kinases (JNKs) regulate cell survival and apoptosis by distinct mechanisms.
JNKs play a key role in regulating the transcription and translation of cellular genes involved in the stress response. Activated
JNKs interact with activator protein-1 (AP-1) and other transcription factors to modulate transcription of a number of genes.
JNKs can also modulate the half-life of a set of genes that contain AU-rich elements (AURE) in their 3′ untranslated regions
(UTR), an element associated with rapid turnover and short half-life. Activation of JNKs results in a repression of turnover via
these elements, thereby enhancing translation of these messenger RNAs. Activated JNKs can also promote cellular apoptosis
by activating an intrinsic pathway whereby Bcl2 (B-cell lymphomas 2) and BCL-xL promote release of pro-apoptotic molecules
including cytochrome c from mitochondria. This leads to the activation of caspases and cell death (Figure 36).
JNK/SAPK: Jun-activated kinase/stress-activated protein kinases belong to pathways that are parallel to the mitogenic Raf/
MEK/ERK kinase cascade. These kinases are induced in the event of extracellular stresses, including inflammatory cytokines,
interleukin 1, TNF-α, heat, ultraviolet and ionising irradiation, and osmotic shock.
Jun kinase (JNK): This gene encodes a dual specificity protein kinase that belongs to the Ser/Thr protein kinase family.
This kinase is a direct activator of mitogen-activated protein (MAP) kinases in response to various environmental stresses or
mitogenic stimuli. It has been shown to activate MAPK8/JNK1, MAPK9/JNK2, and MAPK14/p38, but not MAPK1/ERK2 or
MAPK3/ERK3.
JUNB: Transcription factor jun-B is a protein that in humans is encoded by the JUNB gene. Transcription factor jun-B is
a transcription factor involved in regulating gene activity following the primary growth factor response. It binds to the DNA
sequence 5′-TGA[CG]TCA-3′.
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Figure 36. Biological functions of JNK.
JIP, JNK-interacting protein;

MKK, mitogen-activated protein (MAP) kinase kinase;
MKKK, MAP kinase kinase; TNF, tumour-necrosis factor

Nat Rev Drug Disc 2003; 2: 554-565
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K KAP1: Tripartite motif-containing 28 (TRIM28), also known as transcriptional intermediary factor 1β (TIF1β) and KAP1 (KRAB-
associated protein-1), is a protein that in humans is encoded by the TRIM28 gene. The protein encoded by this gene mediates
transcriptional control by interaction with the Krüppel-associated box repression domain found in many transcription factors.
The protein localises to the nucleus and is thought to associate with specific chromatin regions. The protein is a member of
the tripartite motif family. This tripartite motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2,
and a coiled-coil region. KAP1 is a ubiquitously expressed protein involved in many critical functions including: transcriptional
regulation, cellular differentiation and proliferation, DNA damage repair, viral suppression, and apoptosis. Its functionality is
dependent upon post-translational modifications. Phosphorylation of KAP1 acts as a deactivator of the protein in many of its
mechanisms while sumoylation acts as an activator.
Karyotype: An organised chromosomal profile defining chromosomal arrangement and number. In a karyotype, chromosomes
are photographically arranged and displayed in pairs, ordered by size. Chromosomal size, banding pattern, and centromere
position are typically used as guides to determine chromosomal abnormalities, but improved resolution may be obtained by
combining traditional banding techniques with genome-wide molecular cytogenetics such as multicolour fluorescence in situ
hybridisation (FISH) and locus-specific FISH.
Kb: Kilobase = 1000 base pairs in nucleic acids; a commonly used unit to indicate the size of nucleic acid fragments.
KCNS3: Gene coding for the potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3.
kDa: Kilodalton; unit indicating the atomic mass, commonly used for proteins.
Ki67: A marker of proliferation, Ki67 is a protein that is expressed in the nucleus of proliferating cells. Absent only in resting
cells, cells in the G1, S, G2, and M phase of the cell cycle express this marker.
Kinases: Enzymes transferring phosphate groups from ATP to the 5＇OH group of a nucleic acid chain; or enzymes transferring
phosphate groups from ATP to either tyrosine, threonine, or serine residues of proteins (protein kinases); protein kinases are
among the most important signalling molecules in mammalian cell biology.
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Kip1/p27: Belongs to the family of cell cycle regulators, typically known as cyclin-dependent kinase inhibitors (CDKIs).
Kip1/p27, like other CDKIs, binds cyclin–CDK complexes, leading to cell cycle arrest in the G1 phase of growth.
KIT: A member of the PDGFR family, c-Kit is a tyrosine kinase receptor that dimerises following ligand binding and is
autophosphorylated on intracellular tyrosine residues.
KRAB domain: The Krüppel-associated box (KRAB) domain is a category of transcriptional repression domains present
in approximately 400 human zinc finger protein-based transcription factors (KRAB zinc finger proteins). The KRAB domain
typically consists of about 75 amino acid residues, while the minimal repression module is approximately 45 amino acid
residues. It is predicted to function through protein–protein interactions via two amphipathic helices. The most prominent
interacting protein is called TRIM28 initially identified as SMP1, cloned as KAP1 and TIF1-beta. Substitutions for the conserved
residues abolish repression.
K-Ras: Isoform of Ras. The gene that encodes K-Ras, a protein that is a member of the small GTPase superfamily, in which a
single amino acid substitution results in an activating mutation. Alternative splicing gives rise to variants encoding two isoforms
that differ in the C-terminal region (Figure 37).
Krüppel-like factor 6 (KLF6): This gene encodes a nuclear protein that has three zinc fingers at the end of its C-terminal
domain, a serine/threonine-rich central region, and an acidic domain lying within the N-terminal region. The zinc fingers of this
protein are responsible for the specific DNA binding with the guanine-rich core promoter elements. The central region might
be involved in activation or post-translational regulatory pathways, and the acidic N-terminal domain might play an important
role in the process of transcriptional activation.
Ku70: DNA-repair enzyme that is involved in repairing DNA double-strand breaks by nonhomologous end joining with
assistance from Ku80, XRCC4, and DNA ligase IV.
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Figure 37. Context-specific K-RAS dependency in colon cancers.
BMP-7
BMPRII
BMPRI
P
WNT P Smad1/5 P
ACTIVATORS TRAF6
K-RAS ? TAB1/2 TAK1 5Z-7-Oxo
GSK-3 β-catenin K-RAS MUTANT β-catenin

MUTANT TAK1
APC APC
β-catenin β-catenin
TCF/LEF NF-кB
ANTI-APOPTOTIC GENES TCF/LEF
ANTI-APOPTOTIC GENES
K-RAS INDEPENDENT CELL K-RAS DEPENDENT CELL

BMP-7/TAK1 INDEPENDENT BMP-7/TAK1 DEPENDENT Reprinted by permission from Cell 2012; 148: 639-650.
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L LAGE-1: Member of the NY-ESO-1 gene family. LAGE-1 is also called CTAG2. This gene encodes an autoimmunogenic
tumour antigen that belongs to the ESO/LAGE family of cancer-testis antigens. This protein is expressed in a wide array of
cancers including melanoma, breast cancer, bladder cancer, and prostate cancer. This protein is also expressed in normal
testis tissue.
Lamins: Members of the intermediate filament family of proteins, lamins are helical filament-shaped proteins that provide
structural support for the nuclear envelope through a meshwork of filaments attached to the inner layer of the nuclear
membrane. Lamins are categorised into A-type (expressed in differentiated somatic cells) and B-type (expressed in all cells)
subfamilies.
Latent membrane protein 1 (LMP 1): Epstein–Barr virus (EBV)-expressed protein expressed in latent phases II and III of
EBV infection. LMP 1 is an activation protein that is responsible for the activation of several cellular pathways (e.g. JAK-STAT,
NF-κB, JNK, SAPK) that are normally not activated in quiescent cells.
LCK: A lymphocyte-specific protein tyrosine kinase belonging to the Src family of nonreceptor protein tyrosine kinases, LCK
is mostly expressed on T cells and some B cells and is involved in the development of immature thymocytes.
Leucine-zipper motif: Refers to a structural motif in DNA-binding proteins characterised through a typical array of one
particular amino acid, leucine; two proteins can interact via such amino acid sequences similar to a zipper.
Leukotriene B4 (LTB4): Secreted by myeloid and nonmyeloid cells from arachidonic acid through the action of several
enzymes, including 5-lipoxygenase, leukotriene B4 modulates immune responses and mediates inflammatory reactions,
including those involved in chemotaxis, chemokinesis, and vasoactive responses. It is also important in neutrophil and
endothelial cell adhesion.
Ligase: DNA ligases are enzymes creating phosphodiester bonds between the 5＇end of a nucleotide and the 3＇OH end of
the neighbouring nucleotide in a nucleic acid chain.
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Lipoxygenases: Arachidonate 5-lipoxygenase, also known as 5-lipoxygenase, 5-LOX, or 5-LO, is an enzyme that in humans
is encoded by the ALOX5 gene. Arachidonate 5-lipoxygenase is a member of the lipoxygenase family of enzymes. It transforms
EFAs into leukotrienes that are key mediators of inflammation.
LIV-1: Gene encoding LIV-1, a protein belonging to the subfamily of zinc transporters. An estrogen-regulated gene, LIV-1 has
been implicated in the metastatic spread of estrogen-positive breast cancer to the lymph nodes.
Linkers: Chemically synthesised DNA strands bearing the recognition sequences of restriction enzymes; such sites are
specifically designed to insert DNA fragments of interest into a vector in gene cloning.
LMP 2: Epstein–Barr virus (EBV)-expressed protein expressed in latent phases II and III of EBV infection. The protein interacts with
B-cell receptor tyrosine kinase and regulates its activity negatively. It prevents the activation of the lytic cycle after EBV infection.
Loss of heterozygosity (LOH): A situation where one chromosome has a normal allele of a gene and one chromosome has
a mutant or deleted allele.
LTB4 receptor: Belonging to the G protein-coupled receptors, which are members of the rhodopsin-like receptor superfamily
and present on human leukocytes. The LTB4 receptor on the surface of neutrophils has high- and low-affinity binding sites for
LTB4. Binding of LTB4 to the receptor induces neutrophil chemotaxis.
Lymphangiogenesis: Formation of the lymphatic network of capillaries. Unlike capillaries of the blood vascular system,
lymphatic capillaries are characterised by a lining of a single layer of endothelial cells, devoid of fenestrations, with poorly
developed junctions and the presence of frequent, large interendothelial gaps. Additionally, lymphatic capillaries lack a
continuous basement membrane and are devoid of pericytes. Although lymphangiogenesis has an important physiological
role in homeostasis, metabolism, and immunity, it has also been implicated in diseases such as neoplasm metastasis,
oedema, rheumatoid arthritis, psoriasis, and impaired wound healing. Podoplanin, LYVE (lymphatic vessel endothelial
hyaluronan receptor)-1, PROX-1, desmoplakin, and the VEGF-C/VEGF-D receptor VEGFR-3 are important markers specific
to lymphangiogenesis (Figure 38).
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Figure 38. Function of lymphoangiogenic factors in tumour biology.
a Tumour angiogenesis – increased tumour growth

Vascular
Tumour-cell
endothelial cells
proliferation
Macrophage
Chemotaxis
VEGFR2
Stromal cell
Tumour cell Unprocessed

VEGF-C/D
b Tumour lymphangiogenesis – increased lymphatic metastasis

Lymphatic
endothelial cells Tumour-cell
Macrophage invasion
Chemotaxis
VEGFR2
Stromal cell VEGFR3

Tumour cell Nat Rev Cancer 2002; 2: 573-583.
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M Macrophage colony-stimulating factor (M-CSF): A secreted cytokine which influences haematopoietic stem cells to
differentiate into macrophages or other related cell types. It is involved in the proliferation, differentiation, and survival of
monocytes, macrophages, and bone marrow progenitor cells.
Macrophages: Macrophages are a type of white blood cell that engulfs and digests cellular debris, foreign substances,
microbes, cancer cells, and anything else that does not have the types of proteins specific to the surface of healthy body cells
on its surface, in a process called phagocytosis. They play a critical role in nonspecific defence (innate immunity), and also help
initiate specific defence mechanisms (adaptive immunity) by recruiting other immune cells such as lymphocytes. In humans,
dysfunctional macrophages cause severe diseases such as chronic granulomatous disease that result in frequent infections.
Beyond increasing inflammation and stimulating the immune system, macrophages also play an important anti-inflammatory
role and can decrease immune reactions through the release of cytokines. Macrophages that encourage inflammation are
called M1 macrophages, whereas those that decrease inflammation and encourage tissue repair are called M2 macrophages.
This difference is reflected in their metabolism, where macrophages have the unique ability to metabolise one amino acid,
arginine, to either a “killer” molecule (nitric oxide) or a “repair” molecule (ornithine).
Mad/Max: Mad is a family of proteins with basic helix–loop–helix motifs and shows transcriptional repressor activity. Max
is a transcriptional modulator that can heterodimerise with Mad or myc proteins, enhancing transcriptional repression or
activation, respectively.
MAF: Gene coding for MAF, which belongs to the basic region-leucine zipper (bZIP) family of transcriptional factors. Members
of the family are c-Maf, MafA, MafB, and NRL. Differing from the canonical bZIP proteins, Maf proteins differ in the length of
the DNA-recognition sequence and a requirement of a region outside the bZIP region for specific DNA binding. The gene is
involved in t(14;16)(q32;q23) chromosomal translocation found in a limited fraction (less than 5%) of multiple myelomas.
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MAGE genes: The first member of the human MAGE family was identified as a gene encoding a tumour-specific antigen.
This gene was later found to belong to a cluster of 12 hMAGE-A genes located in the q28 region of the X chromosome. The
genes belonging to the hMAGE-A, -B, and -C subfamilies are characterised by a large terminal exon encoding the entire
protein. They are completely silent in normal tissues, with the exception of male germ cells, and, for some of them, placenta.
Some are expressed in tumour cells of various histological types, where they code for antigens recognised by cytolytic T
lymphocytes. For example, MAGE-1 directs the expression of a tumour antigen recognised on a melanoma by autologous
cytolytic T-lymphocytes.
Major histocompatibility complex I (MHC class I): MHC class I molecules are found on almost every nucleated cell of
the body. In humans, these are often referred to as HLA (human leukocyte antigen) molecules. These molecules act as “sign
posts” by displaying fragments of protein antigens on the cell surface. The presented fragments (epitopes) can be derived
from self or nonself (viral) antigens. MHC class I molecules presenting epitopes are recognised by cytotoxic T cells. When a
nucleated cell is aberrant (malignant or virally infected), intracellularly derived epitopes that are foreign to circulating T cells
will be presented, leading to immune activation. In humans, there are three major loci that encode MHC class I molecules—
HLA-A, HLA-B, and HLA-C (Figure 39).
Major histocompatibility complex II (MHC class II): MHC class II molecules are found only on a few types of cells in the
body, most notably antigen-presenting cells such as macrophages and dendritic cells. Like MHC class I, these molecules
present fragments of protein antigens. Unlike MHC class I, MHC class II peptides are usually derived from extracellular
antigens that may be released by bacteria or tumours. MHC class II molecules presenting epitopes are recognised by helper
T cells. In humans, there are three major loci that encode MHC class II molecules—HLA-DR, HLA-DP, and HLA-DQ.
Mammaglobin: Mammaglobin is a gene that encodes a 10-kDa glycoprotein. In humans, expression of the gene is limited
to the adult mammary gland; a correlation between increased expression of the gene and breast cancer has been reported.
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Figure 39. Antigen-related mechanisms of immune evasion.
T cell
Apoptosis CXCL12
e RCAS1
TCR TGF-β Tumour

T-cell signalling
IL-10 cell
Peptide–MHC
FASL complex
Endoplasmic
reticulum
FAS
MHC complex
d
MHC c
TAP Peptides
f
β2-Microglobulin
Granzyme B Proteasome
b
FLIP
IAP family (survivin) a

Tumour protein
P19
Apoptosis Reprinted by permission from Macmillan Publishers Ltd:
mRNA Nat Rev Cancer 2002; 2: 409-419.
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MAP kinase pathways: Mitogen-activated protein kinases (MAPKs) are a highly conserved family of serine/threonine protein
kinases involved in a variety of fundamental cellular processes such as proliferation, differentiation, motility, stress response,
apoptosis, and survival and contain three sequentially activated protein kinases. Each cascade is initiated by a broad range
of extracellular stimuli including mitogens, cytokines, growth factors, and environmental stressors stimulating the activation of
one or more MAPKK kinases (MAPKKKs) via receptor-dependent and -independent mechanisms. The MAPKKK is typically
activated by interactions with a small GTPase and/or phosphorylation by protein kinases downstream from cell surface
receptors. The MAPKKK directly phosphorylates and activates the MAPKK, which, in turn, activates the MAPK by dual
phosphorylation of a conserved tripeptide TxY motif in the activation segment. Once activated, the MAPK phosphorylates
diverse substrates in the cytosol and nucleus to bring about changes in protein function and gene expression that execute
the appropriate biological response (Figure 40).
MAPKs: Family of enzymes that form an integrated network influencing cellular functions such as differentiation, proliferation,
and cell death. These cytoplasmic proteins modulate the activities of other intracellular proteins by adding phosphate groups
to their serine/threonine amino acids. The phosphorylated form of MAPK is being used as a surrogate to the activated form
of the receptor (Figure 41).
MART-1: A melanoma-related antigen. MART-1 is absent in all normal cells except for melanocytes and the retina. In addition,
apart from melanomas, MART-1 has not been observed in any other cancers. Consequently, the MART-1 antigen is considered
to have a melanocyte lineage.
Masscode: The Masscode (BioServe, Laurel, MD) system is a high-throughput genotyping process, which uses a polymerase
chain reaction-based, allele-specific discrimination assay measured by means of cleavable mass spectrometry tags.
Matrix-assisted laser desorption and ionisation (MALDI): A soft ionisation technique used in mass spectrometry,
allowing the analysis of biomolecules and large organic molecules, which tend to be fragile and fragment when ionised by
more conventional ionisation methods.
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Figure 40. MAPK pathways.
Stress Stress
Stimulus Growth factors GPCR agonists Growth factors
Mitogens Inflammatory cytokines Mitogens
GPCR agonists Growth factors GPCR agonists
A-Raf, MEKK1-4, MEKK1-4, TpI2,

MAPKKK B-Raf, Raf1, MLK2/3, DLK, TpI2, MLK2/3, ASK1/2, DLK, MEK2/3, TpI2
Mos, TpI1 ASK1, TAK1, TAK1, TAO1/2
MAPKK MEK1/2 MKK4/7 MKK3/6 MEK5
JNK1/2/3 p38 MAPK ERK5

MAPK ERK1/2
α/β/γ/δ
Growth Inflammation Growth Source of information: Cold Spring Harb

Biological response
Survival Apoptosis Differentiation Perspect Biol 2012; 4(11): pii: a011254.
Differentiation Growth Development
Development Differentiation
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Figure 41. The MAPK signalling role in cancer.

Macmillan Publishers Ltd: Nature Reviews
Cancer 2002; 2 (7): 489-501.
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Matrix-degrading factors: Proteases involved in the degradation of extracellular matrix (ECM) components, a process regulated
by proteases and protease inhibitors. Several growth factors stimulate protease production, leading to ECM degradation. Thus,
epidermal growth factor (EGF), platelet-derived growth factor (PDGF), basic fibroblast growth factor (bFGF), and interleukin 1 (IL-2)
induce the expression of ECM-degrading proteinases and their activators (e.g. metalloproteinases and plasminogen activators).
Matrix metalloproteinases (MMPs): MMPs belong to a family of enzymes (zinc-dependent endoproteinases) that are involved
in the degradation of the extracellular matrix. MMPs are involved in both normal and pathological tissue remodelling, where their
selective proteolysis is now appreciated to help regulate cell growth, angiogenesis, and invasiveness (Figure 42).
Matrix-producing factors: Involved in the formation of the extracellular matrix (ECM), a complex structure that surrounds
and supports cells within mammalian tissues. The biological molecules that constitute this structure can be classified as
structural proteins (e.g. collagen and elastin), specialised proteins (e.g. fibrillin, fibronectin, and laminin), and proteoglycans
(proteins with complex carbohydrates).
MBD2: Belongs to the class of nuclear proteins related by the presence of a methyl CpG-binding domain and is capable of
binding methylated DNA, thereby preventing transcription from methylated gene promoters.
MC1R: Melanocortin-1 receptor, a Gs protein-coupled receptor, is primarily expressed in cutaneous and hair follicle
melanocytes. MC1R is activated by α-melanocyte stimulating hormone (α-MSH) or adrenocorticotropin (ACTH). Many MC1R
allelic variants exist in nature; these mutants correlate with phenotypes, such as red hair, associated with greater ultraviolet
radiation sensitivity and melanoma risk.
Mcl-1: An anti-apoptotic protein belonging to the Bcl-2 family, Mcl-1 was first identified in a human myeloblastic leukaemia
cell line that was induced to differentiate along the monocyte lineage.
MDM2: An E3 ubiquitin ligase that recognises the N-terminal activation domain (TAD) of proteins belonging to the p53
family. By blocking the ability of p53 to associate with factors involved in protein transcription, the MDM2 interaction with p53
prevents transcriptional activation. Further, interaction with p53 leads to ubiquitinylation and subsequent degradation of p53.
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Figure 42. The role of matrix metalloproteinases in cancer.
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MDR-1: P-glycoprotein 1 (permeability glycoprotein, abbreviated as P-gp or Pgp), also known as multidrug resistance protein
1, ATP-binding cassette subfamily B member 1 (ABCB1), or cluster of differentiation 243 (CD243), is an important protein of
the cell membrane that pumps many foreign substances out of cells.
MEK/MAP/ERK kinase: A family of kinases that activates the MAPK family of proteins through phosphorylation of both a
threonine (Thr) and tyrosine (Tyr) residue. These kinases belong to the signal-transduction pathway governing proliferation. Growth
factors involved in proliferative pathways such as EGF, FGF, and PDGF are the extracellular stimuli that activate these kinases.
Messenger RNA: Messenger RNA (mRNA) is a large family of RNA molecules that convey genetic information from DNA to
the ribosome, where they specify the amino acid sequence of the protein products of gene expression. Following transcription
of primary transcript mRNA (known as pre-mRNA) by RNA polymerase, processed, mature mRNA is translated into a polymer
of amino acids: a protein, as summarised in the central dogma of molecular biology. As in DNA, mRNA genetic information
is in the sequence of nucleotides, which are arranged into codons consisting of three bases each. Each codon encodes for
a specific amino acid, except the stop codons, which terminate protein synthesis. This process of translation of codons into
amino acids requires two other types of RNA: transfer RNA (tRNA), which mediates recognition of the codon and provides
the corresponding amino acid, and ribosomal RNA (rRNA), which is the central component of the ribosome’s protein-
manufacturing machinery.
MET: c-Met, also called MET and hepatocyte growth factor receptor (HGFR), is a protein that in humans is encoded by
the MET gene (MET proto-oncogene, receptor tyrosine kinase). The protein possesses tyrosine kinase activity. MET is a
membrane receptor that is essential for embryonic development and wound healing. Hepatocyte growth factor (HGF) is the
only known ligand of the MET receptor. MET is normally expressed by cells of epithelial origin, while expression of HGF is
restricted to cells of mesenchymal origin. Upon HGF stimulation, MET induces several biological responses that collectively
give rise to a programme known as invasive growth. Abnormal MET activation in cancer correlates with poor prognosis,
where aberrantly active MET triggers tumour growth, formation of new blood vessels (angiogenesis) that supply the tumour
with nutrients, and cancer spread to other organs (metastasis). MET is deregulated in many types of human malignancies,
including cancers of kidney, liver, stomach, breast, and brain (Figure 43).
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Figure 43. Domain structures of HGF and MET.
Downstream signalling and specific inhibition of c-MET/HGF pathway.
Reprinted by permission from Macmillan Publishers Ltd: Reprinted by permission from Macmillan Publishers Ltd on behalf of Cancer Research UK:
Nature Reviews Molecular Cell Biology 2010; 11 (12): 834-848. British Journal of Cancer 2007; 97 (3): 368-377.
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Metabolic response: Tumour glucose utilisation is quantitatively assessed by FDG-PET prior to chemotherapy and 14 days
after initiation of therapy. Patients are classified as metabolic responders when the metabolic activity of the primary tumour
has decreased by more than 35% at the time of the second PET.
Methylation: A gene methylation refers to enzymatic modification of DNA or RNA through the incorporation of methyl groups,
mostly in cytosine residues at the C5 position in the nucleotide; methylation of C residues in a gene may have profound effects
on its expression, either activating it or silencing it.
Methyl-binding domains: Domains in transcription factors that bind to methyl-CpGs and attract transcriptional repressors.
Methyl-CpG binding proteins (MBPs): Inhibit transcription by binding methylated DNA and other proteins that regulate
transcription.
Mi2: A member of the Swi/Snf family of proteins with helicase and ATPase activities, Mi2 is part of the NuRD complex and is
responsible for its chromatin-remodelling activity.
Microphthalmia-associated transcription factor (MITF): Microphthalmia-associated transcription factor is an early
marker for melanocyte lineage and essential for normal melanocyte development. It induces transcription of genes important
for melanin production, including tyrosinase. Currently, there is contradictory data regarding MITF, both supporting and
negating a role in melanomagenesis.
MicroRNA profiles: The study of the global expression of microRNAs in tissues.
Microsatellite DNA: A short tandemly repeated sequence in the DNA of a genome. The short sequences repeat many times
and are frequent in all genomes. Larger than 10 to 25 repeats tend to harbour polymorphisms. Microsatellite sequences are
often used for genetic fingerprinting and are not useful in evolutionary studies due to their propensity for mutations.
Microsatellite instability (MSI): A condition manifested by damaged DNA due to defects in the normal DNA-repair process.
Sections of DNA called microsatellites, which consist of a sequence of repeating units of 1–6 base pairs in length, become
unstable and can shorten or lengthen. MSI is a key factor in several cancers including colorectal, endometrial, ovarian, and
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gastric cancers. Colorectal cancer studies have demonstrated two mechanisms for MSI occurrence. The first is in hereditary
nonpolyposis colorectal cancer (HNPCC) or Lynch syndrome, where an inherited mutation in a mismatch-repair gene causes
a microsatellite repeat replication error to go unfixed. Most cases result in changes in the lengths of dinucleotide repeats of
the nucleobases cytosine and adenine. The replication error results in a frameshift mutation that inactivates or alters major
tumour-suppressor genes – key genes in the regulation of the cell cycle and, ultimately, the prevention of cancer. The second
mechanism whereby MSI causes colorectal cancer is an epigenetic change that silences an essential mismatch-repair gene.
In both cases, microsatellite insertions and deletions within tumour-suppressor gene coding regions result in uncontrolled cell
division and tumour growth (Figure 44).
Microsatellite markers: Microsatellites are short, tandemly repeated DNA sequences scattered throughout the genome.
The length of a repeat unit is different in the two (paternal and maternal) alleles and is highly specific for every individual.
Microsatellite sequences are therefore often used as markers for genetic fingerprinting and to detect the loss of one of the
two alleles of one or more genes.
Microsatellites: Abundant DNA polymorphisms dispersed throughout the human genome. Microsatellites are composed
of dinucleotide, trinucleotide, or tetranucleotide repeat sequences present outside genes or within intronic gene sequences.
Examples are CACACACAC repeats or CAGCAGCAGCAG repeats, and others. Allelic variation in a given population is
determined by the number of repeat motifs reiterated in the fragments. Microsatellites are easily detectable by PCR amplification
of DNA fragments containing the repeat sequences. Important markers for mapping of the human genome, for linkage studies
to look for somatic loss of heterozygosity (LOH) in tumours (pointing at the localisation of putative tumour-suppressor genes),
and to trace RER+ tumours showing microsatellite instability, for example tumours in the hereditary nonpolyposis colorectal
cancer syndrome (HNPCC).
Minichromosome maintenance (MCM) proteins: Essential for eukaryotic genome replication. MCM proteins form
a hexameric complex and are important components involved in the formation of replication forks and in recruiting DNA
replication-related proteins. The MCM2, 4, 6, and 7 complex possesses DNA helicase activity, which has a role in regulating
DNA replication.
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Figure 44. Model of the proposed mechanism of mismatch repair proteins.
Colorectal cancer progression models and therapeutic targets in microsatellite instability and
microsatellite stable tumours.

Nature Reviews Clinical Oncology, 2010; 7 (3): 153-162.
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Mismatch repair: One of four major pathways of DNA repair in mammalian cells. Mismatch repair recognises and corrects
errors in DNA replication leading to single base-pair mismatches or insertions/deletions in small repetitive tracts of DNA known
as microsatellites.
Mismatch-repair genes (MMR): Mismatch-repair genes recognise and correct errors in DNA replication leading to single
base-pair mismatches or insertions/deletions in small repetitive tracts of DNA known as microsatellites.
Missense mutation: A change (mutation) in one nucleotide that results in the coding of a different amino acid.
Mitogen-activated protein kinase (MAPK): MAPKs are a family of enzymes that form an integrated network influencing
cellular functions such as differentiation, proliferation, and cell death. These cytoplasmic proteins modulate the activities of
other intracellular proteins by adding phosphate groups to their serine/threonine amino acids.
mLST8: Originally identified as a G protein-β-like subunit, mLST8 independently and specifically interacts with the kinase
domain of mTOR and stabilises the mTOR–raptor association.
MMSET: First identified in multiple myeloma, MMSET belongs to the class of nuclear-receptor binding, SET domain-containing
proteins.
MMSET-FGFR3: A translocation t(4;14)(p16;q32) seen in multiple myeloma that results in the fusion of MMSET with FGFR3
(fibroblast growth factor receptor 3). The fusion protein lacks the SET domain.
MMSET/WHSC1: Gene coding for the Wolf-Hirschhorn syndrome candidate 1 protein (also known as multiple myeloma
SET domain [MMSET]). Ubiquitously expressed in early development, WHSC1 protein contains four domains present in other
proteins implicated in development: a PWWP domain, an HMG box, a SET domain, and a PHD-type zinc finger. The gene is
involved in t(4;14)(p16.3;q32) chromosomal translocation found in approximately 15% of multiple myelomas.
Modifiable signal-transducing target: Signal-transducing molecules are efficient and powerful targets that can predict
disease outcome and therapy response. Modifiable signal-transducing targets are particularly helpful because of their
multisubstrate/multifunctional signalling cascade modifications.
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Molecular interaction network: Molecular interactions (e.g. protein–protein and protein–DNA) made possible as a result
of advances in high-throughput technologies are visualised as a network of interactions using software tools that have been
developed to visualise and analyse large-scale data. The network is visualised with molecules as nodes and molecular interactions
as edges, with “force-directed layout algorithms” used to visualise the molecular interaction network. Some programs used
are InterViewer, Pajek, Tulip, and Cytoscape. Increasingly, Web-based application programs (e.g. WebInterViewer, Ingenuity
Pathway Analysis) are used to produce molecular interaction networks of “good quality,” because multiple molecular interaction
networks for shared molecules and for interactions shared by all or some of the networks can be searched.
Monoclonal antibody: An antibody that is secreted from a single clone of an antibody-forming cell. Large quantities of
monoclonal antibodies are produced from hybridomas, which are produced by fusing single antibody-forming cells to tumour
cells. The process is initiated when a mouse is immunised initially against a particular antigen, stimulating the production of
antibodies targeted to different epitopes of the antigen. Antibody-forming cells are subsequently isolated from the spleen. By
fusing each antibody-forming cell to tumour cells, hybridomas can be generated each with a different specificity and targeted
against a different epitope of the antigen.
Monocyte chemoattractant protein-1: The chemokine (C-C motif) ligand 2 (CCL2) is also referred to as monocyte
chemotactic protein-1 (MCP1) and small inducible cytokine A2. CCL2 is a small cytokine that belongs to the CC chemokine
family. CCL2 recruits monocytes, memory T cells, and dendritic cells to the sites of inflammation produced by either tissue
injury or infection.
Monocytic leukaemia zinc-finger protein: Monocytic leukaemia zinc-finger protein (MOZ), a transcriptional coactivator
and member of the MYST family of histone acetyltransferases, is the target of recurrent translocations in acute myeloid
leukaemia. Moz is a MYST family coactivator with histone acetyltransferase activity.
MOZ-related factor (MORF): Showing a very close homology to MOZ throughout its length, MORF preferentially acetylates
histones H3 and H4 and has an N-terminal transcriptional repression region containing zinc-finger motifs.
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MSH3: DNA mismatch repair protein, MutS Homologue 3 (MSH3) is a human homologue of the bacterial mismatch repair
protein MutS that participates in the mismatch repair (MMR) system. MSH3 typically forms the heterodimer MutSβ with MSH2
in order to correct long insertion/deletion loops and base–base mispairs in microsatellites during DNA synthesis. Deficient
capacity for MMR is found in approximately 15% of colorectal cancers, and somatic mutations in the MSH3 gene can be
found in nearly 50% of MMR-deficient colorectal cancers.
MTG16: MTG16 is a transcriptional corepressor that forms complexes implicated in colon cancer development. MTG16
can only interact with DNA by forming complexes with other proteins, such as Kaiso, that can directly bind DNA. While both
proteins have been shown to target known cancer pathways, such as the Wnt pathway, Kaiso may work by interacting with
MTG16 and targeting the MTG16 repression complexes to specific promoter.
mTOR: The mammalian target of rapamycin belongs to a protein complex (along with raptor and GβL) that is used by cells to
sense nutrients in the environment. mTOR is a serine/threonine kinase that is activated by Akt and regulates protein synthesis
on the basis of nutrient availability. It was discovered when rapamycin, a drug used in transplantation, was shown to block cell
growth presumably by blocking the action of mTOR (Figure 45).
MUC-1: A transmembrane-anchored mucin-type glycoprotein, MUC-1 is present on the surface of normal epithelial cells
of organs such as the breast, ovary, pancreas, and colon. It is also a tumour marker because it is overexpressed in similar
malignant tissues. Structurally, MUC-1 has an extracellular carbohydrate-rich domain, a transmembrane, and a cytoplasmic
domain. Human MUC-1, a membrane-bound glycoprotein, is a major component of the ductal cell surface of normal
glandular cells probably involved in intercell adhesion. MUC-1 is overexpressed and aberrantly glycosylated in carcinoma
cells, promoting tumour metastases and inducing immune suppression.
Multidrug-resistance protein (MRP): In tumour cell lines, multidrug resistance is often associated with an ATP-dependent
decrease in cellular drug accumulation which is attributed to the overexpression of certain ATP-binding cassette (ABC)
transporter proteins. ABC proteins that confer drug resistance include (but are not limited to) P-glycoprotein (gene symbol
ABCB1), the multidrug resistance protein 1 (MRP1, gene symbol ABCC1), MRP2 (gene symbol ABCC2), and the breast cancer
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Figure 45. mTOR signalling.

Publishers Ltd: Nature Reviews Clinical
Oncology 2010; 7 (4): 209-219.
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resistance protein (BCRP, gene symbol ABCG2). In addition to their role in drug resistance, there is substantial evidence that
these efflux pumps have overlapping functions in tissue defence. Collectively, these proteins are capable of transporting a vast
and chemically diverse array of toxicants including bulky lipophilic cationic, anionic, and neutrally charged drugs and toxins
as well as conjugated organic anions that encompass dietary and environmental carcinogens, pesticides, metals, metalloids,
and lipid peroxidation products.
MUM-3: Recognised by autologous cytotoxic T cells on melanoma cells, MUM-3 is an antigen that is ubiquitously expressed
and is homologous with the RNA helicase gene family.
Mutations: Alterations of genetic material which are not normally silent; point mutations refer to exchanges, deletions,
or insertions of single bases in a DNA sequence, and chromosomal mutations describe alterations of blocks of genes or
sequences through translocations, deletions, etc. Mutations in coding sequences of genes may alter the amino acid sequence
of a protein and thus alter its “meaning” (missense mutations). Mutations shifting the reading frame of a gene usually result
in no protein being produced at all or in the production of a completely incorrect protein chain (frameshift mutations). Some
mutations may produce new premature stop codons leading to the formation of (usually useless) truncated protein chains
(nonsense mutations). Mutations can also hit promoter elements and thus interfere with the regulation of gene transcription.
Germline mutations are present in gonadal cells and are thus passed on to the progeny of an individual; they are present in all
cells of an individual and therefore need to be distinguished from silent polymorphisms. Somatic mutations hit single specific
somatic cells in an individual; if they are suitable to confer a growth advantage to such a cell, they may produce the basis for
clonal neoplastic growth, a basic principle of cancer development.
MutL homologue 1 (MLH1): The DNA mismatch-repair enzyme, MLH1 is responsible for overall fidelity of DNA replication.
Myb: A proto-oncogene whose protein product is a transcriptional activator. Its transcriptional activity is enhanced by
acetylation, which increases its DNA-binding activity. Myb normally regulates the proliferation and differentiation of certain
types of cell; improper regulation of or by this protein is associated with oncogenic transformation.
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MYBL2: Gene coding for v-myb myeloblastosis viral oncogene homologue (avian)-like 2 protein, which is a member of
the Myb family of proteins. The expressed protein, phosphorylated during the S phase of the cell cycle by cyclin A/cyclin-
dependent kinase, possesses activator and repressor activities. It activates cyclin D1 and the insulin-like growth factor-
binding protein 5 genes.
MYCN: N-myc proto-oncogene protein also known as N-Myc or basic helix–loop–helix protein 37 (bHLHe37), is a protein
that in humans is encoded by the MYCN gene. The MYCN gene is a member of the MYC family of transcription factors and
encodes a protein with a basic helix–loop–helix (bHLH) domain. This protein is located in the cell nucleus and must dimerise
with another bHLH protein in order to bind DNA. Amplification and overexpression of N-Myc can lead to tumourigenesis.
Excess N-Myc is associated with a variety of tumours, most notably neuroblastomas, where patients with amplification of the
N-Myc gene tend to have poor outcomes.
Myogenin: A muscle-specific transcription factor that can induce myogenesis in a variety of cell types in tissue culture.
Myogenin is a member of the basic helix–loop–helix gene family.
MYST: Named for its original members MOZ, Ybf2/Sas3, Sas2, and Tip60, this family of histone acetyltransferases (HATs)
are grouped based on their close sequence homology and the occurrence of a particular acetyltransferase homology region
of the GNAT superfamily of HATs.
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N N-CoR and SMRT corepressors: N-CoR and SMRT are non-DNA-binding corepressors originally shown to be important
for transcriptional repression by unliganded nuclear hormone receptors. These corepressors can in fact confer repression on
a variety of transcription factors, including AP-1, NF-κB, Pit-1, and STAT5. The two proteins are components of a variety of
multiprotein complexes that contain histone deacetylases (e.g. Rpd3p or Hda1p) — these appear to repress transcription by
deacetylating lysine residues in the N-terminal tails of histones. Regulation seems to occur at several levels. Phosphorylation
of the corepressor can stimulate or block association with transcription factors, depending on the kinase, and vice versa. In
addition, it can modulate the subcellular localisation of the corepressor and its ability to form distinct corepressor complexes.
The importance of these corepressors for normal cell function is illustrated by human genetic diseases such as resistance to
thyroid hormone (RTH) and acute promyelocytic leukaemia (APL), both of which inappropriately activate N-CoR/SMRT.
N-terminal: The end of a polypeptide chain that has an amino acid with a free amino group; proteins are synthesised starting
from the N-terminal amino acid.
Natural killer (NK) cells: NK cells belong to the innate immune system and are specialised to kill target cells that are either
infected with viruses or are host cells that have become cancerous. CD56 is a surface marker specific to NK cells (Figure 46).
Neuropilin 1 (NRP-1): A coreceptor for VEGF, but distinct from the tyrosine kinase VEGFR family of receptors. NRP-1
augments the binding affinity of the ligand for the tyrosine kinase VEGFR. It is also present on tumour cells and may function
independently of the other VEGFRs. It was initially discovered as a neuronal repulsion factor involved in embryological neuronal
guidance.
NG2: NG2, or neural/glial antigen 2, is a rat integral membrane proteoglycan found in the plasma membrane of many diverse
cell types. This single-pass transmembrane molecule may be plasma membrane-bound or secreted and associated with
the extracellular matrix. It plays a role in functions such as cell adhesion, cell–cell and cell–ECM communication, migration
and metastasis, proliferation, and axonal growth, guidance, and regeneration. NG2-positive cells include oligodendrocyte
progenitor cells (OPCs) and other progenitor cell populations, such as chondroblasts, myoblasts, and pericytes, as well as
several different tumours including glioblastoma multiforme and melanoma.
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Figure 46. NK cells and immune responses to tumour cells.
CD8+T cell Dendritic cell

(CTL) Tumour Ag uptake and generation of
Ag presentation Ag-specific immune
Helping CTL
generation
Ag-specific CTL
response
IFN-γ
IFN-γ Stress ligand
CD4+T cell Danger signal?
NK cell
(Helper T cell)
Immune pressure
Activation
Cytokines Maturation
NK1.1+ T cell Activation
(NKT cell)
B cell
Glycolipid ligand/CD1 Dendritic cell Tumour cells
IL-12
Anti-tumour Abs
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NKT cells: Natural killer T (NKT) cells are a heterogeneous group of T cells that share properties of both T cells and natural
killer cells. Many of these cells recognise the non-polymorphic CD1d molecule, an antigen-presenting molecule that binds self
and foreign lipids and glycolipids. NKT cells are a subset of T cells that co-express an αβ T-cell receptor, but also express a
variety of molecular markers that are typically associated with NK cells, such as NK1.1. Upon activation, NKT cells are able to
produce large quantities of interferon gamma, IL-4, and granulocyte-macrophage colony-stimulating factor, as well as multiple
other cytokines and chemokines (such as IL-2, interleukin-13, interleukin-17, interleukin-21, and TNF-alpha).
Nonreceptor tyrosine kinases: Cellular tyrosine kinases (TKs) that are not membrane-spanning TK receptors.
Nonsense mutation: A mutation that changes a codon that codes for an amino acid into a stop codon, therefore terminating
translation.
Noxa: A pro-apoptotic member of the Bcl-2 family, which contains the Bcl-2 homology 3 (BH3) region, but lacks other BH
domains. Noxa functions as an early response gene and a mediator of p53-induced apoptosis. In human cells, Noxa is also
designated as PMA-induced protein 1 or APR.
NPM1: Gene coding for nucleophosmin (also called nucleolar phosphoprotein B23 [numatrin]), which is mainly localised in the
nucleolus of the nucleus. It contains an N-terminus oligomerisation domain, a metal-binding site, two acid-rich domains, and
two nuclear localisation signals in the C-terminus of the protein. It is an RNA-binding phosphoprotein involved in the assembly
of ribosomal proteins into ribosomes and the transport of ribonucleoproteins between the cellular compartments. The gene is
involved in several tumour-associated chromosomal translocations.
NRAS: An isoform of Ras. The Ras gene family consists of H-Ras, N-Ras, and K-Ras. The Ras proteins are typically small
triphosphate-binding proteins, and are the common upstream molecule of several signalling pathways that play a key role in
signal transduction, which results in cellular proliferation and transformation.
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Nuclear factor kappa B (NF-κB): NF-κB is a transcriptional factor involved in the transcriptional activation of genes that
regulate different cellular processes. Its nuclear location is restricted by its interaction with an inhibitor, I-kappa B, which
sequesters it in the cytoplasm. When I-kappa B is phosphorylated and degraded in response to different stimuli, NF-κB
becomes free to enter the nucleus (Figure 47).
Figure 47. N
F-κB target genes involved in cancer development and progression.
Inf lammation Proliferation

TNF, IL-1, IL-8, MIP2, MCP1, Cyclin D1, Cyclin E, CDK2,
iNOS, COX2, ICAM1, ELAM1 MYC, TNF, IL-1, IL-6
Survival
Cell death and BFL1, GADD45β, BCL-2, BCL-XL,
anti-proliferative effects NF-кB TRAF1/2, XIAP, cIAP1/2, FLIP,
FasL, Fas and DR4/5, A20, IEX-1L, survivin, telomerase,
p53, p2Waf1/Cipl MnSOD
Tumour promotion
Angiogenesis
and metastasis Reprinted by permission from
CXCL1/8, IL-1/6,
uPA, MMP2/9, VCAM1, ICAM1, Macmillan Publishers Ltd:
VEGF, IL-8, HIF1α, TNF
ELAM1, KAL1, COX2, iNOS Nat Rev Drug Discov 2009; 8: 33-40.
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Nuclear receptor corepressor (N-CoR): A transcriptional corepressor.
Nucleoside: A purine or pyrimidine base linked to a sugar molecule (ribose or deoxyribose); adenosine, guanosine, cytidine,
thymidine, and uridine.
Nucleosome: A nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in
sequence around eight histone protein cores. Nucleosomes form the fundamental repeating units of eukaryotic chromatin,
which is used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it. Nucleosomes
are folded through a series of successively higher order structures to eventually form a chromosome; this both compacts DNA
and creates an added layer of regulatory control, which ensures correct gene expression. Nucleosomes are thought to carry
epigenetically inherited information in the form of covalent modifications of their core histones.
Nucleotide excision repair (NER): Nucleotides are organic molecules that serve as the monomers, or subunits, of nucleic
acids like DNA and RNA. The building blocks of nucleic acids, nucleotides are composed of a nitrogenous base, a five-
carbon sugar (ribose or deoxyribose), and at least one phosphate group. Thus a nucleoside plus a phosphate group yields a
nucleotide. Nucleotides serve to carry packets of energy within the cell in the form of the nucleoside triphosphates (ATP, GTP,
CTP, and UTP), playing a central role in metabolism. In addition, nucleotides participate in cell signalling (cGMP and cAMP),
and are incorporated into important cofactors of enzymatic reactions (e.g. coenzyme A, FAD, FMN, NAD, and NADP+).
Null: Complete loss of function phenotype. This term is used in reference to the mutation or inactivation of specific genes,
resulting in complete absence of protein expression.
NY-ESO-1: NY-ESO-1 is emerging as one of the most important tumour antigens so far discovered. It is also known as CTAG1b
or cancer/testis antigen 1B, which is very rare in healthy individuals. Frequently, it causes spontaneous immunogenicity in
cancer patients.
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O Oligomerisation: The forming of a compound (polymer) by the combination of relatively few smaller molecules (monomers).
Oligonucleotide: A short chain of nucleotides with a specific sequence; mostly designed and synthesised in vitro; used for
hybridisation of blots or as primers for the polymerase chain reaction.
Omi: Omi/HtrA2, along with Smac and cytochrome C, is released from the mitochondria into the cytoplasm upon disruption
of the outer mitochondrial membrane during apoptosis. Omi/HtrA2 also induces apoptosis in a caspase-dependent manner.
Oncogene: The normal counterparts of these genes known as proto-oncogenes regulate cell proliferation and differentiation.
Structural defects/mutations of these genes alter these important features and may help to promote tumour growth; oncogenes
are dominant tumour-producing genes since the mutation of one allele/copy in a cell is usually sufficient to produce the
respective phenotype; ras and myc are examples of oncogenes mutated in human cancer; many oncogene products are
growth factors or growth factor receptors.
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P p14ARF: A protein product of the alternative reading frame of the human INK4a locus, p14ARF is a tumour-suppressor protein
(actually a cell cycle kinase inhibitor) and acts through p53-dependent and p53-independent pathways. In p53-dependent
pathways, by inhibiting cell cycle kinase, p14ARF leads to elevated levels of MDM2 and arrests cell cycle progression at both
the G1 and G2/M phases. In response to oncogenic stimuli, p14ARF acts by attenuating MDM2-mediated degradation of
p53.
p15INK4b: A specific cell cycle regulator that inhibits the G1 phase of the cell cycle by inhibiting the kinase activity of cyclin-
dependent kinases 4 and 6. The gene is inactivated by homozygous deletion, point mutation, or methylation in various
tumours.
p16: Also known as p16INK4, p16 binds to cyclin-dependent kinases 4 and 6, thereby preventing their interaction with cyclin
D. It thus behaves as a negative regulator of proliferation and arrests cells in the G0/G1 phase of the cell cycle.
p21: Also known as cyclin-dependent kinase inhibitor 1 or CDK-interacting protein 1, p21 is a protein that in humans is
encoded by the CDKN1A gene located on chromosome 6. It is a potent cyclin-dependent kinase inhibitor.
p27: A gene that belongs to the family of cell cycle regulators, typically known as cyclin-dependent kinase inhibitors. It has a
DNA sequence similar to other members of the family, which include the p21 and p57 genes.
p38/MAPK signalling pathway: p38 MAPKs (α, β, γ, and δ) are members of the MAPK family that are activated by a
variety of environmental stresses and inflammatory cytokines. Stress signals are delivered to this cascade by members of
small GTPases of the Rho family (Rac, Rho, Cdc42). As with other MAPK cascades, the membrane-proximal component is
a MAPKKK, typically a MEKK or a mixed lineage kinase (MLK). The MAPKKK phosphorylates and activates MKK3/5, the p38
MAPK kinase. MKK3/6 can also be activated directly by ASK1, which is stimulated by apoptotic stimuli. P38 MAK is involved
in regulation of Hsp27 and MAPKAP-2 and several transcription factors including ATF2, STAT1, the Max/Myc complex, MEF-
2, ELK-1, and indirectly CREB via activation of MSK1 (Figure 48).
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Figure 48. p38 MAPK signalling pathway.
Reprinted by permission from http://atlasgeneticsoncology.org/
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P38α: Activated by stress and proinflammatory cytokines, P38α belongs to the family of MAPKs and is involved in pathways
that mediate cell proliferation, differentiation, and survival.
p53: Tumour protein p53 (a molecular mass of 53 kDa – hence its name), also known as p53, cellular tumour antigen p53,
phosphoprotein p53, tumour suppressor p53, antigen NY-CO-13, or transformation-related protein 53 (TRP53), is a protein
crucial in multicellular organisms, where it prevents cancer formation, thus, functions as a tumour suppressor. As such,
p53 has been described as “the guardian of the genome” because of its role in conserving stability by preventing genome
mutation. TP53 gene is the most frequently mutated gene (>50%) in human cancer, indicating that the TP53 gene plays a
crucial role in preventing cancer formation. TP53 gene encodes proteins that bind to DNA and regulate gene expression to
prevent mutations of the genome. p53 has many mechanisms of anticancer function, and plays a role in apoptosis, genomic
stability, and inhibition of angiogenesis. In its anti-cancer role, p53 works through several mechanisms:
• It can activate DNA repair proteins when DNA has sustained damage. Thus, it may be an important factor in ageing
• It can arrest growth by holding the cell cycle at the G1/S regulation point on DNA damage recognition (if it holds the cell
here for long enough, the DNA repair proteins will have time to fix the damage and the cell will be allowed to continue the
cell cycle)
• It can initiate apoptosis – programmed cell death – if DNA damage proves to be irreparable (Figure 49, Figure 50).
p57: Belonging to and functioning like other members in the family of cell cycle regulators known as cyclin-dependent kinase
inhibitors, p57 binds to cyclin–CDK complexes, leading to cell cycle arrest. However, unlike other cyclin-dependent kinase
inhibitors, p57 functions in a cell type-specific manner.
p70S6 kinase: Responsible for the mitogen-dependent stimulation of the ribosomal protein S6, which regulates the initiation
of translation or protein synthesis.
p70S6K/RPS6KA1: Gene that expresses a kinase that catalyses the phosphorylation of the S6 protein, a component of the
40S subunit of the eukaryotic ribosome, which plays a key role in protein synthesis. p70S6K and RPS6KA1 are alternative
names given to the same gene.
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Figure 49. Three-dimensional structure of p53 in its tetrameric form.
The p53 pathway.
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Figure 50. p53 tumour suppression.

Nat Rev Cancer 2001; 1: 68-76.
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p73: A relative of p53, p73 encodes a p53-like protein with a DNA-binding domain that corresponds to that seen in p53. Like
p53, p73 is a transcriptional activator and is associated with cell cycle regulation. However, p73 differs from p53 in its inability
to respond to DNA damage.
p300: A non-DNA-binding transcriptional coactivator. It interacts with transcriptional activators as well as repressors to
influence cellular processes of growth, terminal differentiation, and apoptosis. p300 has histone acetyltransferase activity.
p-4EBP: Phosphorylated form of 4EBP. An inhibitor of the eukaryotic initiation factor 4E (eIF-4E), 4EBP is responsible for cell
cycle arrest. Phosphorylation of 4EBP disrupts its ability to bind eIF-4E, thereby enhancing cap-dependent translation initiation.
PAK-JNKK-JNK/JNK activation pathway: A cascade of proteins originally identified as those involved in the activation (by
phosphorylating critical residues) of the activation domain of c-Jun, a component of a transcriptional complex. These kinases
have also been known to be activated in stress-activated pathways.
Pentaplex: A variation of multiplexing or multiplex polymerase chain reaction (PCR) that simultaneously amplifies two or more
regions of DNA by virtue of adding more than one primer set to the amplification reaction mixture. In pentaplex PCR, five
different segments of DNA are amplified.
pERK: ERK is a downstream enzyme of the MAP kinase pathway that is directly activated by Raf to pERK. In case of Raf
inhibition, as with sorafenib, the level of pERK serves as a surrogate of this inhibition and may be correlated to response to therapy.
P-glycoprotein (Pgp): Also known as ABCB1, is a member of the ATP-binding cassette (ABC) transporters, which are divided
into seven subfamilies. ABCB1 is a member of the MDR/TAP subfamily and is involved in multidrug resistance. The protein
behaves as a pump and is responsible for the efflux of xenobiotic compounds from the cell, thereby decreasing drug levels in
multidrug-resistant cells. Resistance to chemotherapeutic agents in cancer is often due to the presence of this transporter.
PHD domain: A conservative zinc finger-type motif found in plant homeodomains, the PHD domain has been observed as
part of transcriptional corepressor proteins (e.g. KAP1), which assist in transcriptional repression.
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Phenotype: The overall appearance of an organism, or the observable expression of a specific trait, determined by its
genotype and environmental factors.
pHER-2: Phosphorylated (activated) form of HER-2.
Phosphatase and tensin homologue (PTEN): PTEN is a tumour-suppressor gene with a gamut of regulatory activities.
The gene product is a multifunctional molecule. The predominant activity identified for PTEN is its lipid phosphatase activity
that converts inositol trisphosphates into inositol bisphosphates, thus inhibiting survival and proliferative pathways that are
activated by inositol trisphosphates. PTEN acts to maintain arrest in the G1 phase of the cell cycle and enable apoptosis
through an Akt-dependent mechanism (Figure 51).
Phosphatidylinositol kinase: Generic name for enzymes that phosphorylate phosphatidylinositol.
Phospho-Akt: The phosphorylated form of Akt, which is the activated form of the molecule.
Phospho-EGFR: Phosphorylated (i.e. activated) form of EGFR.
Phospho-ERK: The phosphorylated form of ERK, which is the activated form of the molecule.
Phosphoinositide-dependent kinase 1 (PDK1): An activator of Akt, it interacts with phosphoinositides through its
pleckstrin-homology domain, resulting in its recruitment (along with Akt) to the plasma membrane, where it becomes activated
(phosphorylated). Once activated, it activates Akt.
Phospho-MAPK: Phosphorylated (activated) form of MAPK.
Phospho-mTOR: Phosphorylated form of mTOR.
Phospho-p70S6 kinase: Phosphorylated (active) form of p70S6 kinase.
Phospho-PDGFR: The phosphorylated form of PDGFR, which is the activated form of the receptor.
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Figure 51. The PI3K-PTEN signalling network.

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Phosphorylation: Refers to the addition of phosphate groups from a high-energy compound such as ATP on to small
molecules (e.g. phosphoinositides) or amino acid residues (e.g. serine, threonine, or tyrosine) in proteins. The process is
regulated by enzymes called kinases, which add phosphate groups, and enzymes called phosphatases, which remove
phosphate groups. The phosphorylation states of individual components in a signal-transduction pathway often control the
activity of these components, thereby contributing to the overall activation state of signal-transduction pathways.
Phosphothioate-linked antisense oligonucleotide: Phosphothioate is the substitution of one oxygen atom with suphur
in the internucleotide linkage. The phosphothioate modification renders the oligonucleotide more resistant to nuclease
degradation without adversely affecting hybridisation to complementary sequences.
Phosphotyrosine-binding domain: A three-dimensional motif present in proteins that binds to the regions of receptors that
have been tyrosine phosphorylated. Thus, tyrosine phosphorylated regions of receptors can be viewed as docking stations
for other proteins.
PI3K: Phosphatidylinositol-4,5-bisphosphate 3-kinase (also called phosphatidylinositide-3-kinases, phosphatidylinositol-3-
kinases, PI 3-kinases, PI(3)Ks), PI3Ks are a family of enzymes involved in cellular functions such as cell growth, proliferation,
differentiation, motility, survival, and intracellular trafficking, which in turn are involved in cancer. PI3Ks are a family of related
intracellular signal transducer enzymes capable of phosphorylating the 3 position hydroxyl group of the inositol ring of
phosphatidylinositol (PtdIns). The pathway, with oncogene PIK3CA and tumour suppressor PTEN, is implicated in insensitivity
of cancer tumours to insulin and IGF1, in calorie restriction. The class IA PI 3-kinase p110α is mutated in many cancers. Many
of these mutations cause the kinase to be more active (Figure 52).
PI3K/AKT pathway: Signal-transduction pathways involving the signalling molecules phosphatidylinositol-3-kinase (PI3K)
and Akt, where PI3K generates phosphorylated inositides at the cell membrane which are required for the recruitment and
activation of Akt, a transforming serine/threonine kinase involved in cell survival.
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Figure 52. Schematic of signalling through the phosphatidylinositol-3-kinase (PI3K)-Akt pathway.

Nature Reviews Drug Discovery 2005; 4 (12): 988-1004.
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PI3K-AKT-mTOR: The PI3K/AKT/MTOR pathway is an intracellular signalling pathway important in regulating the cell cycle.
Therefore, it is directly related to cellular quiescence, proliferation, cancer, and longevity. PI3K activation phosphorylates and
activates AKT, localising it in the plasma membrane. AKT can have a number of downstream effects such as activating CREB,
inhibiting p27, localising FOXO in the cytoplasm, activating PtdIns-3ps, and activating mTOR which can effect transcription
of p70 or 4EBP1. There are many known factors that enhance the PI3K/AKT pathway including EGF, shh IGF-1, insulin, and
CaM. The pathway is antagonised by various factors including PTEN, GSK3B, and HB9. In many cancers, this pathway is
overactive, thus reducing apoptosis and allowing proliferation. This pathway is necessary, however, to promote growth and
proliferation over differentiation of adult stem cells, neural stem cells specifically.
PI3K-PTEN-AKT pathway: A key signalling pathway involved in the regulation of cell growth. Dysregulated signalling of this
pathway may be associated with activating mutations of PI3K-related genes. Analyses of these mutations reveal that they
increase the PI3K signal, stimulate downstream Akt signalling, promote growth factor-independent growth, and increase cell
invasion and metastasis.
PIK3CA: The catalytic subunit of phosphatidylinositol-3-kinase involved in the generation of PIP3 which, in turn, leads to
the activation of Akt and other oncogenic kinases. Mutations in the PIK3CA gene have been found in a number of cancers,
including ovarian, breast, colon, and lung carcinomas.
PIK3R3: Gene coding for the regulatory unit of phosphatidylinositol-3-kinase.
PIM-1: An oncogene that encodes for a serine/threonine kinase, PIM-1 plays a role in signal transduction in haematopoietic
cells by suppressing apoptosis, cell cycle progression, and transcriptional regulation via chromatin silencing. In all these
processes, functions of key target proteins are affected when PIM-1 phosphorylates critical serine/threonine residues.
PKC theta (PRKCQ): A member of the protein kinase C family. PKC theta is highly expressed by T cells, interstitial cells of
Cajal, and gastrointestinal stromal tumours.
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Placenta growth factor (PlGF): A protein with significant sequence homology to the VEGF family of proteins, PlGF has
significant expression in the placenta of the developing embryo and is also present on endothelial cells, where its activity
contributes to angiogenesis induction and endothelial cell permeability.
Plasmid: Circular double-stranded DNA which can a) take up foreign DNA fragments of up to 10 kb, and b) replicate in
bacteria; essential tool for cloning procedures, and to generate large amounts of specific DNA fragments for manipulation.
Plasminogen activator inhibitor (PAI-1): PAI-1 is a serine protease inhibitor, and an inhibitor of uPA and tPA. Together with
other members of the uPA system it is involved in extracellular matrix degradation, stimulation of cell migration, and control of
cell adhesion, which are important for invasion and metastasis in cancer. Official gene symbol: SERPINE1 (Figure 53).
PLAT: Gene coding for the tissue plasminogen activator, which is used in patients for its anticoagulant activity to prevent the
onset of ischaemic stroke. Native tissue-type plasminogen activator (tPA) is a serine proteinase that is activated by plasmin.
tPA has homologies present in other proteins such as fibronectin and epidermal growth factor.
Platelet-derived growth factor: A family of proteins that regulate cell growth and division. PDGF is a potent mitogen for
cells of mesenchymal origin, including smooth muscle cells and glial cells. PDGFs are mitogenic during early developmental
stages, driving the proliferation of undifferentiated mesenchyme and some progenitor populations. During later maturation
stages, PDGF signalling has been implicated in tissue remodelling and cellular differentiation, and in inductive events involved
in patterning and morphogenesis (Figure 54).
Platelet-derived growth factor receptors: Platelet-derived growth factor receptors (PDGFRs) are cell surface tyrosine
kinase receptors for members of the platelet-derived growth factor (PDGF) family. PDGF subunits A and B are important
factors regulating cell proliferation, cellular differentiation, cell growth, development, and many diseases including cancer.
There are two forms of the PDGFR, alpha and beta, each encoded by a different gene. Depending on which growth factor is
bound, PDGFR homo- or heterodimerises.
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Figure 53. PAI-1 structure.
PAI-1 is a serine protease inhibitor that functions as the principal inhibitor of tissue
plasminogen activator (tPA) and urokinase (uPA).
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Figure 54. Signal transduction by PDGF family kinases.

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PLZF-RARα: A translocation [t(11;17)(q23;q21)] seen in promyelocytic leukaemia, the PLZF gene (encoding the promyelocytic
leukaemia zinc-finger protein) juxtaposes alongside the RAR gene (encoding a retinoic acid receptor). The chimeric protein is
a transcriptional repressor.
PML-RARα: The acute promyelocytic leukaemia chromosomal translocation t(15;17) generates a PML/RARα chimeric gene
whose chimeric protein product associates with corepressor molecules in the absence of all-trans retinoic acid.
Poly (ADP-ribose) polymerase (PARP): A family of proteins involved in a number of cellular processes involving mainly
DNA repair and programmed cell death. The PARP family comprises 17 members (10 putative). They have all very different
structures and functions in the cell. One important function of PARP is assisting in the repair of single-strand DNA breaks
(Figure 55).
Polycomb group (PcG) proteins: The polycomb group (PcG) proteins are a family of proteins responsible for cellular
differentiation during development via transcriptional repression. The polycomb group was first described in Drosophila as
a locus involved in the silencing of Hox gene expression. Many PcG proteins achieve this control of gene expression via
catalysing H3K27 methylation. These proteins have been the subject of intense study as it is clear that they are vital for
maintenance of cell-type identity, differentiation, and disease by creating and maintaining repressive chromatin environments.
Overexpression of PcG proteins correlates with the severity and invasiveness of several cancer types.
Polymerase chain reaction restriction fragment: A procedure to determine single nucleotide polymorphisms (SNPs) on
the basis of the different DNA sequence. The small genetic change or variation in the genetic code for a given SNP means
that the concrete DNA region becomes a target for a given restriction enzyme; that restriction enzyme does not recognise the
sequence in the absence of the change, or vice versa. When digesting the amplified DNA fragment with the given restriction
enzyme, different sized DNA fragments are obtained depending on the SNP presence or absence.
Polymorphic DNA markers: Naturally occurring DNA sequence differences among individuals at particular genomic sites
that can be used as genetic markers and are commonly referred to as polymorphisms.
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Figure 55. Structural and functional characteristics of PARP1.

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Polymorphism: A phenotypically silent sequence variation in the DNA producing many different alleles in a given population
(for comparison: the ABO blood group system is a good example; ABO blood groups are distributed in a given population
with particular frequencies and are phenotypically silent). Point polymorphisms are characterised through variations in DNA
sequences which are specifically recognised as cleavage sites by restriction enzymes; these restriction fragment length
polymorphisms (RFLP) create new or destroy preexisting recognition sequences; variable-number-of-tandem-repeat
(VNTR) polymorphisms or minisatellites are composed of repetitive tandem repeats of short blocks of 20–30 nucleotides,
usually between genes or exons in noncoding DNA; microsatellites are composed of di-, tri-, or tetranucleotide repeat
sequences. Polymorphisms are important genetic markers in human genetics, used for gene mapping and cloning, linkage
studies, and in cancer to detect loss of heterozygosity at loci harbouring tumour-suppressor genes, etc.
Polysomy: A condition in which an otherwise diploid organism has at least one more chromosome than normal; there may
be three or more copies of the chromosome rather than the expected two copies.
PPARγ: An orphan nuclear receptor belonging to the nuclear hormone receptor family termed peroxisome proliferator
activated receptors (PPARs), which are ligand-dependent proteins that stimulate gene transcription. PPARs are activated by
peroxisome proliferators (e.g. clofibric acid, nafenopin, and some fatty acids). Like other nuclear hormone receptors, PPARγ
isoforms heterodimerise with the RXR (retinoid X receptor) alpha receptor. Synthetic PPARγ ligands include thiazolidinediones,
which are known to improve insulin sensitivity.
pRB: Phosphorylated form of RB, the retinoblastoma susceptibility gene product. Phosphorylated RB has important ramifications
for cell cycle progression. In the phosphorylated state, RB is unable to bind to the transcriptional factor E2F (also important for
cell cycle regulation). This results in an excess of free E2F, which can then induce transcription of genes involved in cell cycle
progression. Hence, phosphorylation of RB allows cells to progress through the G1 checkpoint into S phase of the cell cycle.
Predictive markers: A marker which can be used to identify subpopulations of patients who are most likely to respond to
a given therapy.
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Prenylation: Post-translational lipid modification involving the covalent addition of either farnesyl (15-carbon moiety) or
geranylgeranyl (20-carbon moiety) hydrophobic prenyl lipids to a conserved cysteine residue near the C-terminus of a protein.
Farnesyltransferases and geranylgeranyltransferases are the respective enzymes that catalyse these reactions.
Primer: A primer is a short oligonucleotide sequence that can specifically anneal to single-strand DNA according to its
sequence complementarity; after annealing it leaves a free 3＇end to which DNA polymerase can attach nucleotides and thus
direct the synthesis of a new complementary DNA strand.
PRKCQ: Gene that codes for protein kinase C theta, a member of the family of serine-specific and threonine-specific protein
kinases that are activated by calcium and the second messenger, diacylglycerol.
Proangiogenic factors: Involved in the process of angiogenesis, proangiogenic factors constitute growth factors and
cytokines, including vascular endothelial growth factors (VEGFs), platelet-derived growth factor (PDGF), fibroblast growth
factor (FGF), transforming growth factor-alpha (TGF-α), epidermal growth factor (EGF), hepatocyte growth factor (HGF),
angiopoietins (Ang), and interleukin 8.
Pro-caspase 9: The inactive form of caspase 9 that has to be proteolytically cleaved to the active caspase 9, which activates
caspase 3, leading to DNA fragmentation and cell death. Phosphorylation of pro-caspase 9 by Akt inhibits the proteolytic
processing of pro-caspase 9.
Progesterone receptor: The progesterone receptor (PR, also known as NR3C3 or nuclear receptor subfamily 3, group C,
member 3), is a protein found inside cells. It is activated by the steroid hormone progesterone. In humans, PR is encoded
by a single PGR gene residing on chromosome 11q22; it has two main forms, A and B, that differ in their molecular weight.
Progesterone is necessary to induce the progesterone receptors. When no binding hormone is present, the carboxyl terminal
inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. Progesterone
antagonists prevent the structural reconfiguration. After progesterone binds to the receptor, restructuring with dimerisation follows
and the complex enters the nucleus and binds to DNA. There transcription takes place, resulting in formation of messenger RNA
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that is translated by ribosomes to produce specific proteins. Like estrogen receptors, progesterone receptors are also nuclear
proteins that are activated by the hormone progesterone in breast cancer cells that are hormone-dependent.
Prognostic factor: A measurable patient characteristic that is associated with the subsequent course of disease (whether
or not therapy is administered). The identification of a prognostic factor does not necessarily imply a cause-and-effect
relationship. However, within a suitable outcome model, the measurement of a prognostic factor contributes to an estimate of
an outcome probability (e.g. the probability of disease-free survival within a given time interval).
Prognostic marker: A marker that predicts the prognosis of a patient (e.g. the likelihood of relapse, progression, and/or
death) independent of future treatment effects. A factor can be both prognostic and predictive.
Prognostic model: A combination of patient, tumour, and treatment characteristics that predicts outcome of individual
patients.
Programmed cell death 5 (PDCD5): This gene encodes a protein expressed in tumour cells during apoptosis independent
of the apoptosis-inducing stimuli. Before apoptosis induction, this gene product is distributed in both the nucleus and
cytoplasm. Once apoptosis is induced, the level of this protein increases and, by relocation from the cytoplasm, it accumulates
in the nucleus. Although its exact function is not defined, this protein is thought to play an early and universal role in apoptosis.
PDCD5 is also called TFAR19 (TF1 cell apoptosis-related gene 19).
Proline-directed protein kinase FA (PDPK FA): PDPK FA is a signal-transducing molecule. It is essential for the development
of highly malignant phenotypes and rapid cancer progression. PDPK FA targets a wide spectrum of oncogenic downstream
molecules in a cascading manner.
Promoter: Promoter sequences are DNA sequences that define where transcription of a gene by RNA polymerase begins.
Promoter sequences are typically located directly upstream or at the 5’ end of the transcription initiation site. RNA polymerase
and the necessary transcription factors bind to the promoter sequence and initiate transcription. Promoter sequences define
the direction of transcription and indicate which DNA strand will be transcribed; this strand is known as the sense strand.
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Many eukaryotic genes have a conserved promoter sequence called the TATA box, located 25 to 35 base pairs upstream
of the transcription start site. Transcription factors bind to the TATA box and initiate the formation of the RNA polymerase
transcription complex, which promotes transcription.
Promoter hypermethylation: Methylation of the promoter region of a gene can lead to DNA silencing as a consequence
of the inability of activating transcriptional factors to bind to the promoter region, a process important in gene transcription.
In addition, repressor complexes may be attracted to sites of promoter methylation, leading to the formation of inactive
chromatin structures.
Promyelocytic leukaemia zinc finger (PLZF): A transcription factor with nine Krüppel-like C2H2 zinc fingers at the
C-terminus and a POZ (pox virus and zinc-finger) domain at the N-terminus of the protein. The POZ domain mediates
dimerisation and transcriptional repression. Expressed during development in the central nervous system and the limb buds,
PLZF is expressed in CD34+ progenitor cells and in undifferentiated haematopoietic cells in adults.
Pro-Ras: Ras protein to which proline has been added, making the protein more hydrophobic and allowing for its targeting
to a hydrophobic region in cell membranes. The first step in this process is the farnesylation of Ras.
Protease-activated receptors: There are four known protease-activated receptors (PARs), numbered from one to four.
These receptors are members of the seven transmembrane G-protein-coupled receptor superfamily, and are expressed
throughout the body. PARs are activated by the action of serine proteases such as thrombin (acts on PARs 1, 3, and 4) and
trypsin (PAR 2). These enzymes cleave the N-terminus of the receptor, which in turn acts as a tethered ligand. In the cleaved
state, part of the receptor itself acts as the agonist, causing a physiological response. Most of the PAR family act through the
actions of G-proteins i (cAMP inhibitory), 12/13 (Rho and Ras activation), and q (calcium signalling) to cause cellular actions.
Proteasomes: Proteasomes are protein complexes inside all eukaryotes and archaea, and in some bacteria, and their main
function is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that
help such reactions are called proteases. Proteasomes are part of a major mechanism by which cells regulate the concentration of
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particular proteins and degrade misfolded proteins. The degradation process yields peptides of about seven to eight amino acids
long, which can then be further degraded into shorter amino acid sequences and used in synthesising new proteins. Proteins are
tagged for degradation with a small protein called ubiquitin. The tagging reaction is catalysed by enzymes called ubiquitin ligases.
Once a protein is tagged with a single ubiquitin molecule, this is a signal to other ligases to attach additional ubiquitin molecules.
The result is a polyubiquitin chain that is bound by the proteasome, allowing it to degrade the tagged protein.
Protein kinase: A protein kinase is a kinase enzyme that modifies other proteins by chemically adding phosphate groups to
them (phosphorylation). Phosphorylation usually results in a functional change of the target protein (substrate) by changing
enzyme activity, cellular location, or association with other proteins. The human genome contains about 500 protein kinase
genes and they constitute about 2% of all human genes. Up to 30% of all human proteins may be modified by kinase activity,
and kinases are known to regulate the majority of cellular pathways, especially those involved in signal transduction.
Protein kinase C: Protein kinase C, also known as PKC, is a family of protein kinase enzymes that are involved in controlling the
function of other proteins through the phosphorylation of hydroxyl groups of serine and threonine amino acid residues on these
proteins. PKC enzymes in turn are activated by signals such as increases in the concentration of diacylglycerol (DAG) or calcium
ions (Ca2+). Hence PKC enzymes play important roles in several signal transduction cascades. A multiplicity of functions have
been ascribed to PKC. Recurring themes are that PKC is involved in receptor desensitisation, in modulating membrane structure
events, in regulating transcription, in mediating immune responses, and in regulating cell growth. These functions are achieved by
PKC-mediated phosphorylation of other proteins. However, the substrate proteins present for phosphorylation vary, since protein
expression is different between different kinds of cells. Thus, effects of PKC are cell-type-specific.
Protein synthesis: Protein biosynthesis is the process whereby biological cells generate new proteins; it is balanced by the
loss of cellular proteins via degradation or export. Translation, the assembly of amino acids by ribosomes, is an essential part
of the biosynthetic pathway, along with generation of messenger RNA (mRNA), aminoacylation of transfer RNA (tRNA), co-
translational transport, and post-translational modification. Protein biosynthesis is strictly regulated at multiple steps. They are
principally during transcription (phenomena of RNA synthesis from DNA template) and translation (phenomena of amino acid
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assembly from RNA).The cistron DNA is transcribed into a variety of RNA intermediates. The last version is used as a template
in synthesis of a polypeptide chain. Protein will often be synthesised directly from genes by translating mRNA. When a protein
must be available on short notice or in large quantities, a protein precursor is produced. A proprotein is an inactive protein
containing one or more inhibitory peptides that can be activated when the inhibitory sequence is removed by proteolysis
during posttranslational modification. A preprotein is a form that contains a signal sequence (an N-terminal signal peptide)
that specifies its insertion into or through membranes, i.e. targets them for secretion. The signal peptide is cleaved off in the
endoplasmic reticulum. Preproproteins have both sequences (inhibitory and signal) still present.
Protein transduction domain: Protein transduction domains (PTDs) are small peptides that are able to carry larger
molecules such as oligonucleotides, peptides, full-length proteins, 40 nm iron nanoparticles, bacteriophages, and even 200
nm liposomes across cellular membranes. There are two general classes of PTDs described, including positively charged
transduction domains (cationic) and protein leader sequence-derived domains (hydrophobic), both able to transduce a wide
variety of cell types.
Protein tyrosine kinase: Generic name for enzymes that phosphorylate tyrosine molecules in proteins.
Protein tyrosine phosphatase receptor gamma (PTPRG): A tumour-suppressor gene frequently deleted in renal cell
carcinoma and lung cancer, PTPRG codes for a protein belonging to the protein tyrosine phosphatase family. Members belonging
to this family regulate cellular processes of growth, differentiation, mitosis, and oncogenic transformation. The protein coded
by this protein possesses an extracellular region, a single transmembrane region, and two tandem intracytoplasmic catalytic
domains, and has the enzymatic activity of removing phosphate groups from proteins that regulate biological processes.
pTAT motif: An 11 amino acid sequence present in the transcriptional transactivator Tat of the human immunodeficiency
virus type 1 that acts as a protein transduction domain (PTD). Engineering proteins containing the pTAT motif allows for their
efficient targeting to the cellular nucleus.
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PTPRN2: A putative tumour-suppressor gene coding for protein tyrosine phosphatase, receptor type, N polypeptide 2, also
referred to as islet cell antigen-related protein tyrosine phosphatase (IAP), phogrin or protein tyrosine phosphatase, receptor-
type pi (PTPR Pi). The enzyme coded by PTPRN2 removes phosphate groups from tyrosine residues in proteins and is a
known autoantigen in type I insulin-dependent diabetes mellitus (IDDM).
PTPRO: Receptor-type tyrosine-protein phosphatase O (PTPRO) is an enzyme that in humans is encoded by the PTPRO
gene. This gene encodes a receptor-type protein tyrosine phosphatase containing a single intracellular catalytic domain with
a characteristic signature motif. The gene product, which has a transmembrane domain, is an integral membrane protein.
Several alternatively spliced transcript variants, some of which encode different isoforms of the protein, have been described.
These variants exhibit tissue-specific expression. Gene silencing of PTPRO has been seen in tumours, including lung cancer.
The enzyme coded by PTPRO removes phosphate groups from tyrosine residues in proteins.
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R Rab: The Rab family of proteins is a member of the Ras superfamily of monomeric G proteins. Approximately 70 types
of Rabs have now been identified in humans. Rab GTPases regulate many steps of membrane traffic, including vesicle
formation, vesicle movement along actin and tubulin networks, and membrane fusion. These processes make up the route
through which cell surface proteins are trafficked from the Golgi to the plasma membrane and are recycled. Surface protein
recycling returns proteins to the surface whose function involves carrying another protein or substance inside the cell, such as
the transferrin receptor, or serves as a means of regulating the number of a certain type of protein molecules on the surface.
Like other GTPases, Rabs switch between two conformations, an inactive form bound to GDP (guanosine diphosphate), and
an active form bound to GTP (guanosine triphosphate). Rab effectors are very heterogeneous, and each Rab isoform has
many effectors through which it carries out multiple functions.
RAD54: DNA repair and recombination protein RAD54-like belongs to the DEAD-like helicase superfamily, and shares similarity
with Saccharomyces cerevisiae Rad54, a protein known to be involved in the homologous recombination and repair of DNA.
This protein has been shown to play a role in homologous recombination-related repair of DNA double-strand breaks. The
binding of this protein to double-strand DNA induces a DNA topological change, which is thought to facilitate homologous
DNA pairing, and stimulate DNA recombination. RAD54 is one of the key proteins necessary for homologous recombination
and DNA repair in many organisms. Without functional RAD54, tumour development is more likely.
Raf: Raf proteins (Raf-1, A-Raf, B-Raf) are intermediate to Ras and MAPK in the cellular proliferative pathway. Raf proteins are
typically activated by Ras via phosphorylation, and activated Raf proteins in turn activate MAPK via phosphorylation. However,
Raf proteins may also be independently activated by other kinases.
Raf kinase: Raf kinases are a family of three serine/threonine-specific protein kinases that are related to retroviral oncogenes.
The mouse sarcoma virus 3611 contains a Raf kinase-related oncogene that enhances fibrosarcoma induction. RAF is
an acronym for Rapidly Accelerated Fibrosarcoma. Raf kinases participate in the RAS-RAF-MEK-ERK signal transduction
cascade, also referred to as the mitogen-activated protein kinase (MAPK) cascade. Activation of RAF kinases requires
interaction with RAS-GTPases.The three RAF kinase family members are: (1) A-Raf, (2) B-Raf, and (3) C-Raf (Raf-1). Raf can
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be mutated or overexpressed in certain types of cancer. Raf kinase is a target of inhibition by sorafenib. The regulation of Raf
is complex and involves the integration of other signalling pathways as well as intramolecular interactions, phosphorylation,
dephosphorylation, and protein–protein interactions.
Ran: Ran (RAs-related nuclear protein), also known as GTP-binding nuclear protein Ran, is a protein that in humans is
encoded by the RAN gene. Ran is a small 25-kDa protein that is involved in transport into and out of the cell nucleus during
interphase and also involved in mitosis. It is a member of the Ras superfamily. Ran is essential for the translocation of RNA
and proteins through the nuclear pore complex. The Ran protein has also been implicated in the control of DNA synthesis
and cell cycle progression, as mutations in Ran have been found to disrupt DNA synthesis. Ran is the major regulator that
controls the bidirectional transport of macromolecules between the nucleus and the cytoplasm of cells through the nuclear
pore complex in nuclear membranes.
Rapamycin binding protein: Intracellular protein that binds immunosuppressants such as rapamycin and tacrolimus. The
complex binds to and inhibits the serine/threonine kinase activity of mTOR.
Ras: The Ras gene family consists of H-Ras, N-Ras, and K-Ras. The Ras proteins are typically small triphosphate-binding
proteins, and are the common upstream molecule of several signalling pathways that play a key role in signal transduction,
which results in cellular proliferation and transformation.
Ras association domain family member 1A (RASSF1A): One of the most commonly epigenetically silenced tumour-
suppressor genes in human cancer that controls the cell cycle and apoptosis.
Ras homologue enriched in brain (Rheb): A conserved member of the Ras superfamily of G proteins, Rheb promotes
cell growth. Rheb activity can be blocked by rapamycin, an inhibitor of mTOR. Thus Rheb is involved in mTOR signalling, a
pathway involved in nutrient-mediated signalling.
Ras-MAP kinase cascade: Signal-transduction pathway involving Ras and MAP kinase. The pathway is generally involved
in proliferative and survival signals.
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Ras pathway: A signal-transduction pathway involving the signalling molecules Ras, Raf, and ERK, where activated Ras
activates Raf, which then activates MEK (MAPK/ERK kinase) and thereby ERK. Generally, the involvement of these molecules
results in enhanced cell survival and/or proliferation.
Ras-Raf-ERK pathway: Signal-transduction pathways involving the signalling molecules Ras, Raf, and ERK, where activated
Ras activates Raf, which then activates MEK (MAPK/ERK kinase) and thereby ERK. Generally, the involvement of these
molecules results in enhanced cell survival and/or proliferation. Activating mutations of Raf have been discovered in some
human tumours such as melanoma and non-small cell lung cancer.
RAS-RAF-MEK-ERK pathway: Signalling pathways involving Ras, Raf, MEK, and ERK (Figure 56).
RB: The first tumour-suppressor gene identified in children with hereditary retinoblastomas, its phosphorylation state has
important implications for cell cycle progression. Hypophosphorylated RB tightly binds the transcriptional factor E2F (also
important for cell cycle regulation), thus preventing E2F-mediated cell cycle entry.
Reading frame: The sequence of base triplets in mRNA placed between the start and the stop codon of a gene; a precise
topographical localisation of the start of gene transcription is essential for the successful production of a protein; mutations
altering this feature are known as frameshift mutations; an open reading frame is a nucleotide sequence that, when divided
into triplet codons, contains no termination codon.
Rearrangement: Refers to juggling, reshuffling, and shifting of DNA sequences or fragments within a gene or between two
genes resulting in reassembly and altered gene structure; gene rearrangements are a physiological way to create diversity in
antigen receptor genes; they may also play an important role in cancer, for example in chromosomal translocations.
Receptor tyrosine kinase: Transmembrane protein with intrinsic ability to transfer phosphate groups to tyrosine residues
contained in cellular substrates.
RecQ1: The protein encoded by this gene is a member of the RecQ DNA helicase family, which comprises enzymes involved
in various types of DNA repair.
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Figure 56. The RAS-RAF-MEK-ERK signalling pathway.
Reprinted by permission from the American Association for Cancer Research: C. Pratilas et al.
Targeting the Mitogen-Activated Protein Kinase Pathway: Physiological Feedback and
Drug Response. Clin Cancer Res 2010; 16 (13): 3329-3334.
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Regulatory associated protein of mTOR (raptor): Raptor is a scaffold protein that enhances the ability of mTOR to
activate 4E-BP1 and p70S6 kinase. Raptor binds to, but does not alter the catalytic activity of, mTOR. However, by also
binding 4E-BP1 and p70S6 kinase, raptor increases the ability of mTOR to phosphorylate p70S6 kinase.
RELA: Transcription factor p65, also known as nuclear factor NF-kappaB p65 subunit, is a protein that in humans is encoded
by the RELA gene. RELA, also known as p65, is a REL-associated protein involved in NF-κB heterodimer formation, nuclear
translocation, and activation. NF-κB is an essential transcription factor complex involved in all types of cellular processes,
including cellular metabolism, chemotaxis, etc. Phosphorylation and acetylation of RELA are crucial post-translational
modifications required for NF-κB activation. RELA has also been shown to modulate immune responses, and activation of
RELA is positively associated with multiple types of cancer.
Retinoic acid receptor alpha: Retinoic acid receptor alpha (RAR-α), also known as NR1B1 (nuclear receptor subfamily 1,
group B, member 1), is a nuclear receptor that in humans is encoded by the RARA gene. Retinoid signalling is transduced
by two families of nuclear receptors, retinoic acid receptor (RAR) and retinoid X receptor (RXR), which form RXR/RAR
heterodimers. In the absence of ligand, DNA-bound RXR/RARA represses transcription by recruiting the corepressors
NCOR1, SMRT (NCOR2), and histone deacetylase. When ligand binds to the complex, it induces a conformational change
allowing the recruitment of coactivators, histone acetyltransferases, and the basic transcription machinery. Translocations that
always involve rearrangement of the RARA gene are a cardinal feature of acute promyelocytic leukaemia. The most frequent
translocation is t(15,17)(q21;q22), which fuses the RARA gene with the PML gene.
Retinoic acid receptor beta-2 (RARβ2) gene: RARβ is expressed from two distinct promoters, both of which have distinct
CpG islands. RARβ2 is expressed in adult tissues and hypermethylated in a number of cancer cells. Studies in cell lines
indicate that sensitivity to the effects of retinoic acid is lost when RARβ expression is suppressed.
Retinoid receptors: Nuclear receptors for retinoic acid. The functional receptor is a heterodimer of closely related retinoic
acid receptor (RAR) and retinoid X receptor (RXR).
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Retroviral vector: Artificial DNA construct derived from a retrovirus, used to insert genetic material into cells.
Reverse transcriptase: An enzyme naturally present in retroviruses which permits the synthesis of a complementary
DNA copy (cDNA) from single-stranded RNA; the enzyme needs a primer to start DNA synthesis; copying RNA into DNA,
it “reverses” the traditional dogmatic unidirectional pathway from DNA to RNA to protein.
Rho: A family of related proteins that share structural similarity with Ras proteins. They contain a GTPase activity and can bind
GTP and GDP. The binding of GTP and GDP is regulated by guanine nucleotide exchange factors (Figure 57).
RhoB: Ras-like small protein with GTPase activity involved in a variety of cellular processes, including cell cycle progression,
cellular transformation, and apoptosis. Specific prenylation of Rho proteins is required for Rho functions.
RhoC: RhoC (Ras homologue gene family, member C) is a small (~21 kDa) signalling G protein (more specifically a GTPase), and
is a member of the Rac subfamily of the Rho family of GTPases. It is encoded by the gene RHOC. It is prenylated at its C-terminus,
and localises to the cytoplasm and plasma membrane. It cycles between inactive GDP-bound and active GTP-bound states and
functions as molecular switches in signal transduction cascades. Rho proteins promote reorganisation of the actin cytoskeleton and
regulate cell shape and motility. RhoC can activate formins such as mDia1 and FMNL2 to remodel the cytoskeleton. Overexpression
of RhoC is associated with cell proliferation and causing tumours to become malignant. It causes degradation and reconstruction
of the extracellular matrix (ECM) which helps cells escape the tissue they are currently in. It enhances cell motility, giving it the ability
to become invasive. It has also been found to enhance the creation of angiogenic factors such as VEGF.
Rhodopsin-like receptors: Rhodopsin-like receptors are a family of proteins that comprise the largest group of G protein-
coupled receptors (GPCRs).The rhodopsin-like GPCRs themselves represent a widespread protein family that includes
hormones, neurotransmitters, and light receptors, all of which transduce extracellular signals through interaction with guanine
nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid
sequences of the receptors are very similar and are believed to adopt a common structural framework comprising seven
transmembrane (TM) helices.
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Figure 57. Involvement of RHO proteins at different stages of tumour progression.
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Ribonucleotide reductase (RRM1): A gene that encodes the regulatory subunit of ribonucleotide reductase and is a
molecular target of gemcitabine.
Ribosomal protein, large, PO (RPLPO): Sometimes used as a reference or “housekeeping” gene for normalisation of
reverse transcriptase polymerase chain reaction data.
Ribosomal proteins: Proteins that assemble in an ordered fashion to form the functional ribosome. Ribosomes in eukaryotes
are made of large 60S subunits (an ordered assembly of the L proteins) and small 40S subunits (an ordered assembly of the
S proteins), forming the functional 80S initiation complex with the mRNA. The number of L and S ribosomal subunits differs
in different species (Figure 58).
Ribosomal S6 kinase (S6K): Also called p90rsk, it belongs to the class of AGC family of serine/threonine protein kinases,
which also includes protein kinase C and protein kinase B. Its activity is regulated by phosphorylation/dephosphorylation
events, which occur in response to various stimuli. The two forms of S6K, S6Kα and S6Kβ, have cytoplasmic and nuclear
variants and have the highest sequence homology in the kinase and kinase extension domains.
rIL-2: Recombinant interleukin 2.
RIZ1: RIZ gene encodes two protein products, RIZ1 and RIZ2, which differ for a motif present in the N-terminal domain.
This motif, defined as PR domain and lacking in RIZ2 protein, is structurally related to a similar domain present in the myeloid
leukaemia gene MDS1-EVI1 and in the transcription repressor differentiation factor PRDI-BF1yBLIMP1. The RIZ1 isoform is
lost or expressed at reduced levels in cancer cells. RIZ1 expression is associated with cell cycle arrest.
RNA polymerase II: The multiprotein complex which carries out transcription, reading the DNA template to yield mRNA.
RNase H: Enzyme that cleaves RNA in RNA–DNA hybrids.
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Figure 58. Different steps in the pathway to ribosome production that can lead to cancer, when deregulated.
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ROS1: ROS1 is a receptor tyrosine kinase that has been shown to undergo genetic rearrangements in a variety of human cancers,
including glioblastoma, non-small cell lung cancer (NSCLC), cholangiocarcinoma, ovarian cancer, gastric adenocarcinoma,
colorectal cancer, inflammatory myofibroblastic tumour, angiosarcoma, and epithelioid haemangioendothelioma. These
rearrangements create fusion proteins in which the kinase domain of ROS1 becomes constitutively active and drives cellular
proliferation (Figure 59).
Rosa-26 mice: Developed from murine embryonic stem cells infected with a retroviral gene trap containing the genes for
neomycin and beta-galactosidase (lacZ), Rosa-26 mouse strains express lacZ in all haematopoietic cells and cells in all tissues
of the embryo. The strain is thus exquisitely suited for chimeric analysis.
RUNX: Mammalian homologues of the Drosophila genes runt and lozenge, members of the RUNX family function as master
regulators of haematopoiesis and osteogenesis. They code for the α subunit of the transcription factor, PEBP2/CBF (the β
subunit consists of the non-RUNX protein, PEBP2β).
RUNX1/MTG8: The t(8;21) chromosomal translocation commonly seen in acute myeloid leukaemia results in the expression
of the fusion protein RUNX1/MTG8, which behaves as a transcriptional repressor.
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Figure 59. ROS1 fusion proteins in cancer.
3´ ROS1 5´ Fusion partners

Variable region
FIG (GOPC)
(exon 32-35)
Conserved region SLC34A2, CD74, SDC4,

(includes kinase TPM3, EZR, LRIG3,
domain) KDELR2, CCDC6,
YWHAE, TFG, CEP85L
Plasma membrane
ESYT1 Invasion
Cytosol
SHP2
Golgi
RAS PI3K JAK
apparatus
MEK AKT STAT
ERK
Proliferation and survival

Reprinted by permission from Clin Cancer Res 2013; 19: 4040-4045
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S SCUBE2: Gene coding for signal peptide, CUB domain, EGF-like 2 protein, an endothelial cell-associated, secreted
glycoprotein.
SDHA: This protein is one of the four components of the enzymatic mitochondrial complex II which is involved in the
mitochondrial respiratory chain. It is considered a housekeeping gene because of its essential function in cells.
Selectin: Expressed principally on leukocytes and endothelial cells, selectins are cell adhesion molecules that play an important
role in host defence mechanisms. Selectins bind to carbohydrate molecules on cells, resulting in weak binding. Thus, selectin-
mediated interactions between leukocytes and endothelial cells facilitate rolling of the leukocytes along the endothelium. E
(endothelial)-selectins and P (platelet)-selectins are largely redundant molecules on endothelial cells. L (leukocyte)-selectins
act as homing receptors for leukocytes.
Semaphorin: Belongs to a family of secreted and transmembrane proteins that serve as repulsive signals in axonal and
neuronal development. These proteins may also play a role in endothelial cell guidance.
Serine protease: Enzymes that are involved in breakdown of proteins. Although unchanged after the enzymatic reaction, at
the catalytic site of the enzyme is an essential serine molecule that is intimately involved in the enzymatic reaction.
Serine/threonine kinase: Generic name for enzymes that phosphorylate serine and/or threonine molecules in proteins.
Serpina 5: Also known as PAI3 or PCI, serpina 5 is a tumour-suppressor gene that is a member of the superfamily of serine
protease inhibitors. Serpina 5 inhibits several plasma proteases involved in blood coagulation, including uPA.
SET domain: An acronym for Su(var)39, Enhancer of zeste, Trithorax, SET domains are protein–protein interaction domains
found in proteins that modulate chromatin structure (e.g. members of the Polycomb and Trithorax family). The SET domain
is associated with a methyltransferase activity and interacts with several proteins including N-terminal tails of histones and
components of nucleosome-remodelling factors.
Short hairpin RNA; short-interfering hairpin (shRNA): shRNA contains sense and antisense sequences from a target
gene connected by a loop, and is expressed in mammalian cells from a vector by a pol III–type promoter. The shRNA is
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transported from the nucleus into the cytoplasm, where Dicer processes it. Once in the cell, the shRNA can decrease the
expression of a gene with complementary sequences by RNAi.
Short-interfering RNA (siRNA): siRNA is used in RNA silencing, a method that allows one to “knock down” expression of
genes in a sequence-specific fashion. Although RNA silencing occurs naturally to protect organisms from aberrant transcription,
it is now being exploited to silence genes implicated in diseases and to determine the functions of various genes.
Short interspersed elements (SINEs): SINEs are sequences that are repeated, unblocked, and dispersed throughout the
genome. They make up roughly 20% of the human genome and are useful as markers for organism classification. An ALU
repeat sequence is an example of a SINE.
SHP1: Gene that codes for a haematopoietic-specific protein tyrosine phosphatase.
Signal transduction: The interaction of a growth factor (ligand) with its receptor on a cell activates a specific cascade of
intracellular biological events ultimately responsible for a particular biological response; a growth factor often activates a
receptor tyrosine kinase; an activated receptor kinase will in turn phosphorylate “second messenger” molecules in the cell that
travel to the nucleus and result in transcriptional activation of genes and inactivation of others, as requested.
Signalling lymphocytic activation molecule (SLAM): Also called CD150, SLAM is found on activated T cells, B cells,
macrophages, and dendritic cells. SLAM is a costimulator in T-cell receptor (TCR)-induced T-cell proliferation and controls
the production of Th1 cytokines. It also mediates intracellular protein tyrosine phosphorylation signals by binding with SLAM-
associated protein (SAP) (Figure 60).
Sin3: Sin3 is a master transcriptional scaffold and corepressor capable of transcriptional silencing via associated histone
deacetylases (HDACs). The core Sin3–HDAC complex interacts with a wide variety of repressors and corepressors, providing
flexibility and expanded specificity in modulating chromatin structure and transcription. As a result, the Sin3–HDAC complex
is involved in an array of biological and cellular processes, including cell cycle progression, genomic stability, embryonic
development, and homeostasis. Abnormal recruitment of this complex or alteration of its enzymatic activity has been
implicated in neoplastic transformation.
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Figure 60. SLAM-mediated regulation of T helper 2 cytokine production.

Nat Rev Immunol 2006; 6: 56-66.
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Single nucleotide polymorphism (SNP): Genetic polymorphisms are natural variations in the genomic DNA sequence
present in greater than 1% of the population, with SNP representing DNA variations in a single nucleotide. SNPs are being widely
used to better understand disease processes, thereby paving the way for genetic-based diagnostics and therapeutics.
SIRT2: NAD-dependent deacetylase sirtuin-2 is an enzyme that in humans is encoded by the SIRT2 gene. Also known as
sirtuin or silent mating type information 2-homologue, SIRT2 is an NAD-dependent deacetylase (NDAC) that regulates gene
silencing, cell cycle, and DNA damage repair.
SMAC: Diablo homologue is a mitochondrial protein that in humans is encoded by the DIABLO gene. DIABLO is also
referred to as second mitochondria-derived activator of caspases or SMAC. SMAC is a mitochondrial protein that promotes
cytochrome-c dependent activation by eliminating the effect of inhibitor of apoptosis protein (IAP) – a protein that negatively
regulates apoptosis, programmed cell death. SMAC is normally a mitochondrial protein, but it is found in the cytosol when a
cell is primed for apoptosis during the final execution step of caspase activation. SMAC is the second protein in the apoptosis
link, along with cytochrome c, that promotes apoptosis by activating caspases. SMAC is an inhibitor of apoptosis protein
(IAP)-binding protein. This mitochondrial protein enters the cytosol when cells undergo apoptosis, and it moderates the
caspase inhibition of IAPs.
SP1: Transcription factor Sp1, also known as specificity protein 1, is a protein that in humans is encoded by the SP1
gene. The protein encoded by this gene is a zinc-finger transcription factor that binds to GC-rich motifs of many promoters.
The encoded protein is involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune
responses, response to DNA damage, and chromatin remodelling. Post-translational modifications such as phosphorylation,
acetylation, glycosylation, and proteolytic processing significantly affect the activity of this protein, which can be an activator
or a repressor.
Splice site mutation: A mutation that changes the specific sites at which the splicing of an intron takes place.
Splicing: Refers to the removal of introns and joining of exon sequences in primary RNA at transcription.
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Src: The cellular homologue of v-src (viral-src), it is a nonreceptor tyrosine kinase with pleiotropic activities. Typically activated
by growth factor receptors, c-Src mediates the processes of survival and proliferation. It is generally activated in several
epithelial tumours (Figure 61).
Src-homology 2 (SH2): Modules of approximately 100 amino acids, SH2 domains are motifs in proteins that bind to
phosphotyrosine regions (within a specific sequence context) of activated tyrosine kinase receptors. This conserved sequence
was first identified between the oncoproteins Src and Fps.
STAT: Present in the cytoplasm in their inactive form, STAT (signal transducer and activator of transcription) proteins are
transcription factors that become activated after recruitment to an activated receptor complex at the cell surface. Following
activation, STAT proteins form homo- or heterodimers and, as such, translocate to the nucleus where they induce unique
gene expression programmes by binding to specific DNA-response elements in the promoters of target genes. Currently
seven STAT proteins have been identified in mammalian cells (Figure 62).
STAT5β-RARα: A fusion protein that acts as a transcriptional repressor, where the self-association domain of STAT5 is
retained in the fusion protein and is necessary to induce aberrant transcriptional repression of target genes by retinoic acid
receptor alpha (RARα), which is critical for leukaemogenesis.
Stem-cell factor (SCF): A growth factor that stimulates the proliferation, differentiation, and survival of haematopoietic cells,
SCF is a ligand for c-Kit.
STK15: STK15 or Aurora A kinase, also known as serine/threonine-protein kinase 6, is an enzyme that in humans is encoded by
the AURKA gene. Aurora A is a member of a family of mitotic serine/threonine kinases. It is implicated with important processes
during mitosis and meiosis whose proper function is integral for healthy cell proliferation. Aurora A is activated by one or more
phosphorylations and its activity peaks during the G2 phase to M phase transition in the cell cycle. Dysregulation of Aurora A may
lead to cancer because Aurora A is required for the completion of cytokinesis. If the cell begins mitosis, duplicates its DNA, but is
then not able to divide into two separate cells it becomes an aneuploid – containing more chromosomes than normal. Aneuploidy is
a trait of many cancerous tumours. Ordinarily, Aurora A expression levels are kept in check by the tumour suppressor protein p53.
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Figure 61. Structure of Src and Src family kinases.
Src plays a key role in several signal transduction pathways.
Annals of Oncology 2008; 19 (8): 1379-1386.
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Figure 62. STAT3 signalling allows crosstalk between
Tumour cell
tumour cells and dendritic cells, forming an STAT3P*
immunosuppressive network.
VEGF, IL-6
and IL-10
STAT3P*
HPC
STAT3P*
iMC pDC
VEGF
and
bFGF
IL-10
Endothelial cell STAT3P* STAT3P*
STAT3P*
Immature TReg cell CD8+ T cell
dendritic cell
Tumour vascularisation ↓ MHC class II
↓ CD80 and
CD86 Immunosuppression
↓ IL-12

Nat Rev Immunol 2007; 7: 41-51. Dendritic
cell NK cell
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sTNF-RII: Soluble form of tumour necrosis factor-receptor II.
Stress kinase signalling: Pathways activated by stress signals, which are extracellular in nature and varied (e.g. hypoxia,
exposure to high salt, ionising radiation, osmotic shock), including cell survival pathways that involve the signalling molecules,
p38-MAPK and JNK/SAPK.
Suppressor of cytokine signalling (SOCS): The SOCS gene may have regulatory roles in T-cell differentiation. It is also
postulated to negatively regulate activated T cells. Absence of the gene permits activated T cells to make interferon gamma.
Surface-enhanced laser desorption and ionisation–time of flight mass spectrometry (SELDI-TOF-MS): A powerful
analytic tool that profiles proteins in a biological sample. In contrast to cDNA microarrays, SELDI uses aluminium chips
(1 to 2 mm in diameter) that are spotted with baits to capture proteins. The baits vary and may consist of affinity resins, small
molecules, antibodies, DNA, or enzymes. Analysts apply crude biological samples to the chip, allowing the baits to capture
appropriate molecules that bind to their surfaces. After extensive washes, the analytes are laser desorbed from the chip,
ionised, and analysed by mass spectroscopy. Mass spectral fingerprints are thus obtained. Proteomic researchers are using
the technique to understand the involvement of specific proteins in the disease process or to define/follow biomarkers for
diseases.
Survivin: A protein encoded by the BIRC5 gene. It is a member of the inhibitor of apoptosis family. The survivin protein
functions to inhibit caspase activation, thereby leading to negative regulation of apoptosis or programmed cell death.
Swi/Snf: Chromatin-remodelling multiprotein complexes, Swi/Snf complexes are involved in global transcriptional activation
because of their ability to bind DNA, disrupt nucleosomes, and provide transcription factors with access to nucleosomal DNA.
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T TAp73: TP73 isoforms, which contain the DNA-binding, the oligomerisation, and transactivation domains. TAp73 proteins
largely mimic p53 suppressor functions in experimental systems and are capable of inducing cell cycle arrest and cell death
in response to DNA damage.
Target of methylation-induced silencing (TMS1): A CpG island-associated gene that is hypermethylated and silenced in
cells overexpressing DNA cytosine-5-methyltransferase-1. The gene codes for a protein containing a COOH-terminal caspase
recruitment domain (CARD), but is structurally dissimilar to other CARD proteins.
TBP: Gene coding for the TATA box-binding protein, a transcription initiation factor. TBP plays a key role in the activation and
regulation of eukaryotic promoters that occurs when it binds to TATA elements in promoter regions, initiating the assembly of
a pre-initiation complex involving RNA polymerase II and several initiation factors.
T-cell receptor: The T cell receptor or TCR is a molecule found on the surface of T lymphocytes (or T cells) that is responsible
for recognising antigens bound to major histocompatibility complex (MHC) molecules. The binding between TCR and antigen
is of relatively low affinity and is degenerate: that is, many TCR recognise the same antigen and many antigens are recognised
by the same TCR. The TCR is composed of two different protein chains (that is, it is a heterodimer). In 95% of T cells, this
consists of an alpha (α) and beta (β) chain, whereas in 5% of T cells this consists of gamma and delta (γ/δ) chains. This ratio
changes during ontogeny and in disease states. When the TCR engages with antigenic peptide and MHC (peptide/MHC),
the T lymphocyte is activated through signal transduction, that is, a series of biochemical events mediated by associated
enzymes, coreceptors, specialised adaptor molecules, and activated or released transcription factors. A disulphide-linked
heterodimer of highly variable α and β chains in complex with CD3 molecules on T-cell surfaces. In some subsets of T cells,
disulphide-linked highly variable δ and γ chains are in complex with CD3 molecules. Thus, T cells carrying these receptors are
designated as either α:β or δ:γ T cells, respectively.
TCRγδ: T cells bearing the γδ T-cell receptor, typically contribute to host defence mechanisms at epithelial surfaces.
TEL: TEL is a subset of the ETS family of transcription repressors.
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Telomerase: Also called telomere terminal transferase, it is an enzyme made of protein and RNA subunits. Its role is to
elongate chromosomes by adding telomeric sequences to the end of existing chromosomes.
Telomeres: A tandem array of short DNA sequences that occur at the physical ends of chromosomes, telomeres have
addressed the issue of the inability of DNA polymerases to replicate the ends of DNA strands. As a result, during the course
of replication, telomeres in somatic cells shorten with each cell division.
TEL-RUNX1: The most common gene rearrangement associated with childhood cancer and is a result of the chromosomal
translocation t(12;21) seen in paediatric acute lymphoid leukaemia. The fusion protein functions as a transcriptional repressor.
TERT: Catalytic subunit of telomerase reverse transcriptase.
TF1 cell apoptosis-related gene 19 (TFAR19): This gene encodes a protein expressed in tumour cells during apoptosis
independent of the apoptosis-inducing stimuli. Before apoptosis induction, this gene product is distributed in both the nucleus
and cytoplasm. Once apoptosis is induced, the level of this protein increases and, by relocation from the cytoplasm, it
accumulates in the nucleus. Although its exact function is not defined, this protein is thought to play an early and universal role
in apoptosis. TFAR19 is also called PDCD5 (programmed cell death 5).
TFIIE: Transcriptional factor IIE has multiple roles in transcription initiation. It recruits TFIIH, a protein complex with subunits
having DNA helicase activities.
TFRC: Gene coding for the transferrin receptor, which mediates cellular uptake of iron.
TG4010: A second-generation modified vaccinia virus Ankara harbouring nucleotide sequences encoding MUC-1 and
interleukin 2 (IL-2). It has been engineered to retain its immunogenicity, but is replication defective in mammals. IL-2 production
by this vaccinia virus potentiates cell-mediated and humoral responses. It is the ability to target MUC-1 and coexpression of
IL-2 in the vaccine vector providing local release and improved T-cell priming that are believed to be the advantages of this
vaccine. TG4010 is being studied for its potential to treat a variety of cancer types.
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TGF-β receptor: TGF-β receptors are single pass serine/threonine kinase receptors. They exist in several different isoforms
that can be homo- or heterodimeric. The number of characterised ligands in the TGFβ superfamily far exceeds the number
of known receptors, suggesting the promiscuity that exists between the ligand and receptor interactions. TGFs (transforming
growth factors) are involved in paracrine signalling and can be found in many different tissue types, including brain, heart,
kidney, liver, and testes. Overexpression of TGF can induce renal fibrosis, causing kidney disease, as well as diabetes, and
ultimately end-stage renal disease. Recent developments have found that using certain types of protein antagonists against
TGF-β receptors can halt, and in some cases reverse, the effects of renal fibrosis. Three TGF-β receptor types can be
distinguished by their structural and functional properties. Receptor types I and II have similar ligand-binding affinities and can
be distinguished from each other only by peptide mapping. Both receptor types I and II have a high affinity for TGF-β1 and low
affinity for TGF-β2. TGF-β receptor type III has a high affinity for both TGF-β1 and -β2 and in addition TGF-β1.2.
TGF-β type II receptor: In response to ligand-dependent activation, transforming growth factor-beta type II receptors form
heterooligomeric complexes, which have serine/threonine kinase activity. Activated TGF-β type II receptor initiates signal
transduction by transphosphorylating the type I receptor.
Thioredoxin: Thioredoxin is a class of small redox proteins known to be present in all organisms. It plays a role in many important
biological processes, including redox signalling. In humans, it is encoded by the TXN gene. Loss-of-function mutation of either of
the two human thioredoxin genes is lethal at the four-cell stage of the developing embryo.
Thioredoxin-binding protein 2 (TBP2): Involved in the binding of thioredoxin, leading to reduced levels of thioredoxin in cells.
Thymine: A pyrimidine base.
Tie2: An endothelial cell receptor tyrosine kinase, Tie2 activates cell migration processes on activation by angiopoietin. Having
overlapping activities with VEGFR, Tie2 may be involved in capillary sprouting that is seen in a mature vasculature.
Tissue factor pathway inhibitor (TFPI): A de-novo regulator of coagulation activated by tissue factor, it contains protease
inhibitor domains for the inhibition of factor Xa and VIIa/tissue factor complex.
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Tissue inhibitor of metalloproteinases (TIMP): A family of secreted proteins, TIMPs 1–4 are matrix metalloproteinase
(MMP) inhibitors modulating the activity of soluble, matrix-bound, and cell-associated MMPs of extracellular matrix proteins
(e.g. collagenases, stromelysins, and gelatinases) during the processes of tissue remodelling, inflammation, and tumour
invasion and metastases. Except for TIMP4, TIMPs show a wide tissue distribution.
Tissue microarray: Used to analyse the expression of genes of interest simultaneously in multiple tissue samples, tissue
microarrays consist of hundreds of individual tissue samples placed on slides ranging from 2 to 3 mm in diameter. Using
conventional histochemical and molecular detection techniques, tissue microarrays are powerful tools to evaluate the
expression of genes of interest in tissue samples. In cancer research, tissue microarrays are used to analyse the frequency
of a molecular alteration in different tumour types, to evaluate prognostic markers, and to test potential diagnostic markers.
TNF-related apoptosis-inducing ligand: TNF-related apoptosis-inducing ligand (TRAIL) is a protein functioning as a ligand
that induces the process of cell death called apoptosis. TRAIL is a cytokine that is produced and secreted by most normal
tissue cells. It causes apoptosis primarily in tumour cells, by binding to certain death receptors. TRAIL binds to the death
receptors DR4 (TRAIL-RI) and DR5 (TRAIL-RII). The process of apoptosis is caspase-8-dependent. Caspase-8 activates
downstream effector caspases including procaspase-3, -6, and -7, leading to activation of specific kinases. TRAIL also
binds the receptors DcR1 and DcR2, which do not contain a cytoplasmic domain (DcR1) or contain a truncated death
domain (DcR2). DcR1 functions as a TRAIL-neutralising decoy-receptor. The cytoplasmic domain of DcR2 is functional and
activates NF-κB. In cells expressing DcR2, TRAIL binding therefore activates NF-κB, leading to transcription of genes known
to antagonise the death signalling pathway and/or to promote inflammation.
Topoisomerase I: An enzyme that acts on the topology of native DNA by changing the supercoiled structure of DNA.
Topoisomerase I makes a nick in one DNA strand, twists it around the other, and religates the nicked strand.
Topoisomerase II: An enzyme that catalyses the ATP-dependent transport of one segment of DNA duplex through another
DNA duplex; topoisomerases change the topology of DNA by controlling the essential functions of separating intertwined
daughter chromosomes.
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TRAIL-R: Death receptors used by the ligand TRAIL. TRAIL-R1 (also called DR4) and TRAIL-R2 (also called DR5), the
principal receptors for TRAIL, have an intracellular death domain responsible for mediating apoptosis. In addition, TRAIL-
R3 and TRAIL-R4, lacking the death domain, are decoy receptors and inhibit apoptosis. The decoy TRAIL receptors are
abundantly present in normal cells, perhaps regulating apoptosis.
Transactivation: Induction of the transcription by a transcription factor binding to DNA and activating adjacent proteins.
Transcription: Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA (mRNA)
by the enzyme RNA polymerase. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary
language. The two can be converted back and forth from DNA to RNA by the action of the correct enzymes. During transcription,
a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary
transcript. Transcription proceeds in the following general steps: 1. One or more sigma factor protein binds to the RNA polymerase
holoenzyme, allowing it to bind to promoter DNA. 2. RNA polymerase creates a transcription bubble, which separates the two
strands of the DNA helix. This is done by breaking the hydrogen bonds between complementary DNA nucleotides. 3. RNA
polymerase adds matching RNA nucleotides to the complementary nucleotides of one DNA strand. 4. RNA sugar-phosphate
backbone forms with assistance from RNA polymerase to form an RNA strand. 5. Hydrogen bonds of the untwisted RNA–DNA
helix break, freeing the newly synthesised RNA strand. 6. If the cell has a nucleus, the RNA may be further processed. This may
include polyadenylation, capping, and splicing. 7. The RNA may remain in the nucleus or exit to the cytoplasm through the nuclear
pore complex.The stretch of DNA transcribed into an RNA molecule is called a transcription unit and encodes at least one gene.
If the gene transcribed encodes a protein, messenger RNA (mRNA) will be transcribed; the mRNA will in turn serve as a template
for the protein’s synthesis through translation. Alternatively, the transcribed gene may encode for either noncoding RNA (such as
microRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), or other enzymatic RNA molecules called ribozymes. Overall, RNA helps
synthesise, regulate, and process proteins; it therefore plays a fundamental role in performing functions within a cell.
Transcription factors: Proteins which through direct or indirect interaction with regulator DNA sequences (promoters
or enhancers) exert a profound impact on gene transcription; they may stimulate or sometimes inhibit gene transcription;
alterations of transcription factors are frequent in cancer (for example, as a consequence of chromosomal translocations in
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lymphoma) and thus important in carcinogenesis; four types of transcription factors are known: 1) helix–turn–helix, 2) helix–
loop–helix, 3) leucine zippers, and 4) zinc fingers.
Transcriptional activator: Proteins with conserved, structural motifs or domains that positively modulate the transcriptional
machinery of cells. Transcriptional activators recruit other molecules called “coactivators” to the transcriptional machinery.
Transcriptional factor AP-2 alpha (TFAP): Regulates cell proliferation, differentiation, and cell death. In the absence of
AP-2, the deregulated expression of critical genes involved in metastases and invasion, including c-Kit, MUC-18, thrombin
receptor, and MMP-2, is responsible for the progression to the metastatic phenotype through processes involved in resistance
to apoptosis, adhesion to endothelial cells, and increased angiogenesis and invasion.
Transcriptional regulatory complexes: Complexes of proteins that regulate the transcriptional activity in cells. Specific
regulatory sequences exist in genes or in mRNAs that bind specific transcriptional factors. TFIIA, B, and C, for example, are
transcriptional factors regulating RNA polymerase II activity. The number and type of regulatory elements can vary in each
gene or mRNA, giving rise to a combination of transcriptional factors, each exerting different regulatory control. Transcriptional
complexes are also unique for different cell types.
Transcriptional repressors: Proteins with conserved, structural motifs or domains that negatively modulate the transcriptional
machinery of cells. Transcriptional repressors recruit other molecules called “corepressors” to the transcriptional machinery.
Transcriptome: The complete expressed product of the entire genome in a particular cell, tissue, or biofluid at a specific
point in time.
Transduction: The transfer of genetic material by a viral vector into a cell.
Transformation: This term may create some confusion since it is used for two quite different processes: incorporation of
foreign (usually eukaryotic) DNA into bacteria in gene cloning protocols; and alteration of the geno- and phenotype of somatic
cells in carcinogenesis, usually associated with clonal expansion of cells that have switched from normal proliferation and
differentiation to altered neoplastic behaviour including unrestrained growth.
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Transforming growth factor alpha: Transforming growth factor alpha (TGF-α) is a protein that in humans is encoded by
the TGFA gene. As a member of the epidermal growth factor (EGF) family, TGF-α is a mitogenic polypeptide. The protein
becomes activated when binding to receptors capable of protein kinase activity for cellular signalling. TGF-α is a transforming
growth factor that is a ligand for the epidermal growth factor receptor, which activates a signalling pathway for cell proliferation,
differentiation, and development. This protein may act as either a transmembrane-bound ligand or a soluble ligand. This gene
has been associated with many types of cancers, and it may also be involved in some cases of cleft lip/palate. TGF-α can be
produced in macrophages, brain cells, and keratinocytes. TGF-α induces epithelial development. Considering that TGF-α is
a member of the EGF family, the biological actions of TGF-α and EGF are similar. For instance, TGF-α and EGF bind to the
same receptor. When TGF-α binds to EGFR it can initiate multiple cell proliferation events. Cell proliferation events that involve
TGF-α bound to EGFR include wound healing and embryogenesis. TGF-α is also involved in tumourigenesis and is believed
to promote angiogenesis.
Transforming growth factor beta: A tumour-suppressing cytokine with growth-inhibitory effects in epithelial cells,
transforming growth factor beta (TGF-β) may also act as a tumour promoter by eliciting an epithelial-to-mesenchymal
transition. TGF-β inactivates several proteins involved in cell cycle progression and thereby exerts its growth-inhibitory effects
on epithelial cells by causing them to arrest in the G1 phase of the cell cycle (Figure 63).
Translation: Refers to the production of a specific polypeptide sequence from mRNA.
Translocation: In a chromosomal translocation a chromosomal segment moves from one chromosome to another and a
new chromosome is formed; example: t(14;18)(q32;q21) describes a translocation between chromosomes 14 and 18 with
breakpoints on the long arm of chromosome 14 in band 32 and on the long arm of chromosome 18 in band 21; the t(14;18)
is an example of a translocation that leads to overexpression of an involved gene (BCL-2) through deregulation; other types of
translocations, for example t(9;22) in CML create fusion genes (e.g. the BCR-ABL fusion gene in CML) with profoundly altered
expression and function.
Transphosphorylation: An activated receptor acting as a stimulus to phosphorylate another receptor in the cell in the
absence of a second stimulus.
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Figure 63. T
GF-β signalling in tumour cells determines micro-environmental modification.
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TrkA: A gene encoding the tyrosine kinase TrkA receptor. TrkA binds to neurotrophins and serves as the high-affinity receptor
for the nerve growth factor, required for normal development of the peripheral nervous system as well as the function of central
forebrain neurons. Neurotrophin-3 and neurotrophin-4/5, but not brain-derived neurotrophic factor, are also ligands for TrkA.
TrkB: Gene encoding TrkB, a member of the neurotrophic tyrosine receptor kinase family. This kinase is a membrane-bound
receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. Signalling through this
kinase leads to cell differentiation. It plays an important role in maintaining neuronal cell populations in the neocortex of adults.
The neurotrophins, NT4 and NT5, and the brain-derived neurotrophic factor are the ligands for TrkB.
TUBB: Tubulin beta chain is a protein that in humans is encoded by the TUBB gene.
Tuberin: A protein product of the tuberous sclerosis 2 (TSC2) tumour-suppressor gene, tuberin is a phosphoprotein that
negatively regulates the phosphatidylinositol pathway. Tuberin possesses a GTPase activity and functions along with hamartin
to convert Rheb to the inactive GDP-bound form.
Tuberous sclerosis protein 1 and 2 (TSC1 and TSC2): Also known as hamartin and tuberin, they form a protein complex.
The encoding two genes are TSC1 and TSC2. The complex is known as a tumour suppressor.
Tumour-associated antigens: Proteins associated with tumours that elicit an immune response in tumour-bearing subjects.
Tumour necrosis factor-alpha (TNF-α): A cytokine with pleiotropic activities, TNF-α (originally called cachexin) is secreted
by several types of cells (e.g. macrophages, monocytes, neutrophils, T cells) and in response to a variety of stimuli (e.g.
interferons, IL-2, platelet-activating factor). It acts as a cytolytic and cytostatic agent on several cell types. In addition, by
promoting thrombotic processes, TNF-α is significantly involved in pathological processes, including venous thomboses and
arteriosclerosis. It is also a potent activator of angiogenesis in vivo (Figure 64).
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Figure 64. Potential targets for the inhibition of TNF-α signalling pathways or protein
expression.

Nat Drug Discov 2003; 2: 736-746.
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Tumour-suppressor genes: A tumour-suppressor gene, or anti-oncogene, is a gene that protects a cell from one step on
the path to cancer. When this gene mutates to cause a loss or reduction in its function, the cell can progress to cancer, usually
in combination with other genetic changes. The loss of these genes may be even more important than proto-oncogene/
oncogene activation for the formation of many kinds of human cancer cells. Tumour-suppressor genes can be grouped into
categories including caretaker genes, gatekeeper genes, and landscaper genes; the classification schemes are evolving as
medicine advances, learning from fields including molecular biology, genetics, and epigenetics. Tumour-suppressor genes
or, more precisely, the proteins for which they code, either have a dampening or repressive effect on the regulation of the cell
cycle or promote apoptosis, and sometimes do both. The functions of tumour-suppressor proteins fall into several categories
including the following: 1. Repression of genes that are essential for the continuing of the cell cycle. If these genes are not
expressed, the cell cycle does not continue, effectively inhibiting cell division. 2. Coupling the cell cycle to DNA damage.
As long as there is damaged DNA in the cell, it should not divide. If the damage can be repaired, the cell cycle can continue.
3. If the damage cannot be repaired, the cell should initiate apoptosis (programmed cell death) to remove the threat it poses
for the greater good of the organisms produced. 4. Some proteins involved in cell adhesion prevent tumour cells from
dispersing, block loss of contact inhibition, and inhibit metastasis. These proteins are known as metastasis suppressors. DNA
repair proteins are usually classified as tumour suppressors as well, as mutations in their genes increase the risk of cancer, for
example mutations in HNPCC, MEN1, and BRCA. Furthermore, increased mutation rate from decreased DNA repair leads to
increased inactivation of other tumour suppressors and activation of oncogenes.
Tumour-suppressor proteins: Proteins expressed by tumour-suppressor genes.
TUNEL staining: A procedure for detecting apoptotic cells. Because DNA fragmentation is a hallmark of apoptosis, the
TdT-mediated dUTP-biotin nick end-labelling (TUNEL) uses the enzyme deoxynucleotidyltransferase (TdT) to directly label the
fragmented DNA ends. The apoptotic cells can then either be quantified using flow cytometry or visualised in tissue sections
by using colourimetric reagents.
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TWIST2: A bHLH transcriptional factor important in neural and limb development. Its oncogenic properties are associated
with its antagonistic effects on p53-induced apoptosis.
Tyrosine kinase domain: The three-dimensional structural motif in proteins having tyrosine kinase activity.
Tyrosine kinase receptors: Receptors belonging to the tyrosine kinase family (e.g. EGFR, PDGFR) are activated through the
auto- or transphosphorylation of tyrosine residues in the cytoplasmic region of the receptors in an ATP-dependent manner.
Tyrosine kinases: A tyrosine kinase is an enzyme that can transfer a phosphate group from ATP to a protein in a cell.
It functions as an “on” or “off” switch in many cellular functions. Tyrosine kinases are a subclass of protein kinase. The
phosphate group is attached to the amino acid tyrosine on the protein. Tyrosine kinases are a subgroup of the larger class
of protein kinases that attach phosphate groups to other amino acids (serine and threonine). Phosphorylation of proteins by
kinases is an important mechanism in communicating signals within a cell (signal transduction) and regulating cellular activity,
such as cell division. Protein kinases can become mutated, stuck in the “on” position, and cause unregulated growth of the
cell, which is a necessary step for the development of cancer. Therefore, kinase inhibitors, such as imatinib, are often effective
cancer treatments.
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U Ubiquitin: Ubiquitin is a small (8.5-kDa) regulatory protein that has been found in almost all tissues (ubiquitously) of eukaryotic
organisms. There are four genes in the human genome that produce ubiquitin: UBB, UBC, UBA52, and RPS27A (Figure 65).
Ubiquitylation: Ubiquitylation (ubiquitination) is a post-translational modification (an addition to a protein after it has been
made) where ubiquitin is attached to a substrate protein. The addition of ubiquitin can affect proteins in many ways: It can
signal for their degradation via the proteasome, alter their cellular location, affect their activity, and promote or prevent protein
interactions. Ubiquitylation is carried out in three main steps: activation, conjugation, and ligation, performed by ubiquitin-
activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s), respectively. The result of this
sequential cascade binds ubiquitin to lysine residues on the protein substrate via an isopeptide bond or to the amino group of
the protein’s N-terminus via a peptide bond.
UDP-glucuronosyltransferase 1A1 (UGT1A1): An isoform of uridine-diphosphoglucuronate (UDG) glucuronosyltransferases,
UGT1A1 is responsible for the glucuronidation of bilirubin, xenobiotic compounds, and endogenous steroids. Variants of
UGT1A1 are known to affect the glucuronidation of SN-38, the active metabolite of irinotecan.
UGT1A1H28: An allele of UGT1A1 with seven TA repeats in the promoter region of the UGT1A1 gene. The variant allele is
associated with a reduced expression of UGT1A1, leading to reduced glucuronidation of metabolites such as SN-38, which
accumulates and leads to toxicities such as diarrhoea and leucopenia during irinotecan therapy.
uPAR: The Urokinase receptor, also known as uPA receptor or uPAR or CD87 (Cluster of Differentiation 87), is multidomain
glycoprotein tethered to the cell membrane with a glycosylphosphatidylinositol (GPI) anchor. uPAR was originally identified as a
saturable binding site for urokinase on the cell surface. Besides the primary ligand urokinase, uPAR interacts with several other
proteins, among others: vitronectin, the uPAR associated protein (uPARAP), and the integrin family of membrane proteins.
uPAR is a part of the plasminogen activation system, which in the healthy body is involved in tissue reorganisation events such
as mammary gland involution and wound healing. However the components of the plasminogen activation system have been
found to be highly expressed in many malignant tumours, indicating that tumours are able to hijack the system, and use it in
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metastasis. Thus inhibitors of the various components of the plasminogen activation system have been sought as possible
anticancer drugs. uPAR has been involved in various other non-proteolytic processes related to cancer, such as cell migration,
cell cycle regulation, and cell adhesion.
Uridine–cytidine kinase: An enzyme involved in the nucleotide metabolism pathway, it catalyses the formation of uridine
monophosphate from uridine and GTP. This enzyme belongs to the family of transferases, specifically those transferring
phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this
enzyme class is ATP:uridine 5’-phosphotransferase. Other names in common use include pyrimidine ribonucleoside kinase,
uridine-cytidine kinase, uridine kinase (phosphorylating), and uridine phosphokinase. This enzyme participates in pyrimidine
metabolism.
Urokinase-type plasminogen activator (uPA): A molecule with chemotactic activity when bound to its receptor, uPAR.
Soluble uPA or uPA bound to uPAR also generates plasmin, which degrades extracellular matrix components leading to invasion
and metastasis. The chemotactic activity is responsible for cell recruitment, which occurs in inflammation, neoangiogenesis,
and cancer invasiveness.
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Figure 65. Ubiquitin conjugation.
E3
26S proteasome
E2
Substrate
E1
Ub
O– S S
Ub
O = C O = C O = C
Ub
Ub Ub Ub Ub ADP Degraded
Ub ATP substrate
ATP AMP
Ub
DUB
Ub
Ub Substrate
Ub
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V Vascular cell adhesion molecule (VCAM): A member of the superfamily of immunoglobulin-like molecules, VCAM is
expressed on endothelial cells and regulates leukocyte migration across blood vessels. The molecule is a transmembrane
protein that binds to a cytoskeletal protein within the cell and to the same (homophilic) or a different (heterophilic) protein
present on another cell. It is also an anchor for the developing vasculature during angiogenesis.
Vascular cell adhesion molecule-1: Vascular cell adhesion protein 1, also known as vascular cell adhesion molecule-1
(VCAM-1) or cluster of differentiation 106 (CD106), is a protein that in humans is encoded by the VCAM1-gene. VCAM-1
functions as a cell adhesion molecule. The VCAM-1 gene contains six or seven immunoglobulin domains, and is expressed
on both large and small blood vessels only after the endothelial cells are stimulated by cytokines. It is alternatively spliced into
two known RNA transcripts that encode different isoforms in humans. The gene product is a cell surface sialoglycoprotein, a
type I membrane protein that is a member of the Ig superfamily. The VCAM-1 protein mediates the adhesion of lymphocytes,
monocytes, eosinophils, and basophils to vascular endothelium. It also functions in leukocyte–endothelial cell signal
transduction, and it may play a role in the development of atherosclerosis and rheumatoid arthritis. Upregulation of VCAM-1
in endothelial cells by cytokines occurs as a result of increased gene transcription (e.g. in response to tumour necrosis factor-
alpha [TNF-α] and interleukin 1 [IL-1]) and through stabilisation of messenger RNA (mRNA) (e.g. interleukin 4 [IL-4]). The
promoter region of the VCAM-1 gene contains functional tandem NF-κB (nuclear factor-kappaB) sites.
Vascular endothelial growth factor (VEGF): VEGF is a subfamily of growth factors: the platelet-derived growth factor family of
cystine-knot growth factors. They are important signalling proteins involved in both vasculogenesis (the de-novo formation of the
embryonic circulatory system) and angiogenesis (the growth of blood vessels from pre-existing vasculature). VEGF is a cytokine
that mediates numerous functions of endothelial cells including proliferation, migration, invasion, survival, and permeability. VEGF is
also known as vascular permeability factor. VEGF naturally occurs as a glycoprotein and is critical for angiogenesis. Many tumours
overexpress VEGF, which correlates with poor prognosis. VEGF-A, -B, -C, -D, and -E are members of the larger family of VEGF-
related proteins. All members of the VEGF family stimulate cellular responses by binding to tyrosine kinase receptors (the VEGFRs)
on the cell surface, causing them to dimerise and become activated through transphosphorylation, although to different sites,
times, and extents. The VEGF receptors have an extracellular portion consisting of seven immunoglobulin-like domains, a single
transmembrane spanning region, and an intracellular portion containing a split tyrosine-kinase domain (Figure 66).
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Figure 66. The VEGF family.
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Vascular endothelial growth factor receptor (VEGFR): VEGFRs are transmembrane tyrosine kinase receptors to which the
VEGF ligand binds. VEGFR-1 (also called FLT1) and VEGFR-2 (also called KDR/Flk-1 [murine homologue]) are expressed on
endothelial cells, while VEGFR-3 (also called FLT4) is expressed on cells of the lymphatic and vascular endothelium. VEGFR-2 is
thought to be principally responsible for angiogenesis and for the proliferation of endothelial cells. Typically, most VEGFRs have
seven extracellular immunoglobulin-like domains, responsible for VEGF binding, and an intracellular tyrosine kinase domain.
Vasculogenesis: Early development of the vascular system whereby new capillaries are formed. According to two separate
proposals, the mechanisms that explain vasculogenesis are related to the sprouting of new capillaries from newly formed
vessels (capillaries or veins) or new capillaries arising de novo from mesoderm-derived angioblasts.
VEGF-trap: Now engineered as a composite decoy receptor, the parental VEGF-trap was generated by fusing the first three
immunoglobulin (Ig) domains of VEGFR-1 to the constant region (Fc) of human IgG1. More potent VEGF-traps combine the
Fc domain of human IgG1 with Ig domains from VEGFR-1 and VEGFR-2, thereby effectively preventing VEGF from binding
to any of its cellular receptors.
v-ErbB: The ErbB family of proteins contains four receptor tyrosine kinases, structurally related to the epidermal growth
factor receptor (EGFR), its first discovered member. In humans, the family includes HER-1 (EGFR, ErbB1), HER-2 (Neu,
ErbB2), HER-3 (ErbB3), and HER-4 (ErbB4). The gene symbol, ErbB, is derived from the name of a viral oncogene to which
these receptors are homologous: erythroblastic leukaemia viral oncogene. Insufficient ErbB signalling in humans is associated
with the development of neurodegenerative diseases, such as multiple sclerosis and Alzheimer’s disease, while excessive
ErbB signalling is associated with the development of a wide variety of types of solid tumour. v-ErbBs are homologous to
EGFR, but lack sequences within the ligand binding ectodomain. ErbB-1 is overexpressed in many cancers. Drugs such
as panitumumab, cetuximab, gefitinib, erlotinib, and afatinib are used to inhibit it. It has recently been shown that acquired
resistance to cetuximab and gefitinib can be linked to hyperactivity of ErbB-3. This is linked to an acquired overexpression
of c-MET, which phosphorylates ErbB-3, which in turn activates the AKT pathway. ErbB-2 (HER-2) is often overexpressed in
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breast cancer, and is targeted by the drug trastuzumab (Herceptin). Only one-third of the women respond to trastuzumab.
While the mechanism of resistance has not yet been elucidated, it has been shown that patients with ER+/HER-2+ compared
with ER–/HER-2+ breast cancers may actually benefit more from drugs that inhibit the PI3K/AKT molecular pathway.
Viral Abl: Abelson murine leukaemia viral oncogene homologue 1, also known as ABL1, is a protein that, in humans, is
encoded by the ABL1 gene (previous symbol ABL) located on chromosome 9. c-Abl is sometimes used to refer to the version
of the gene found within the mammalian genome, while v-Abl refers to the viral gene. The ABL1 proto-oncogene encodes
a cytoplasmic and nuclear protein tyrosine kinase that has been implicated in processes of cell differentiation, cell division,
cell adhesion, and stress response. Activity of ABL1 protein is negatively regulated by its SH3 domain, and deletion of the
SH3 domain turns ABL1 into an oncogene. The DNA-binding activity of the ubiquitously expressed ABL1 tyrosine kinase is
regulated by CDC2-mediated phosphorylation, suggesting a cell cycle function for ABL1.
Von Hippel-Lindau tumour suppressor: The Von Hippel–Lindau tumour suppressor, also known as pVHL, is a protein
that in humans is encoded by the VHL gene. Mutations of the VHL gene are associated with Von Hippel–Lindau disease.
Von Hippel–Lindau syndrome is a dominantly inherited hereditary cancer syndrome predisposing to a variety of malignant
and benign tumours of the eye, brain, spinal cord, kidney, pancreas, and adrenal glands. A germline mutation of this gene
is the basis of familial inheritance of VHL syndrome. Individuals with VHL syndrome inherit one mutation in the VHL protein
that causes the protein’s normal function to be lost or altered. Over time, sporadic mutation in the second copy of the VHL
protein can lead to carcinomas, in particular haemangioblastomas affecting the liver and kidneys, renal (and vaginal) clear cell
adenocarcinomas.
Molecular Biology
212
W Wild-type: Wild-type (abbreviation wt) refers to the phenotype of the typical form of a species as it occurs in nature.
XIAP: X-linked inhibitor of apoptosis protein (XIAP), also known as inhibitor of apoptosis protein 3 (IAP3) and baculoviral IAP
X
repeat-containing protein 4 (BIRC), is a protein that stops apoptotic cell death. In humans, this protein (XIAP) is produced by a
gene named XIAP gene located on the X chromosome. XIAP is a member of the inhibitor of apoptosis family of proteins (IAP).
IAPs were initially identified in baculoviruses, but XIAP is one of the homologous proteins found in mammals. It is so-called
because it was first discovered by a 273 base pair site on the X chromosome.
XIAP-interacting protein 1 (XAF1): A protein that can antagonise the anticaspase activity of XIAP and is regulated in
expression by interferons. Cancer cells express less XAF1 than normal cells, suggesting that this pro-apoptotic protein may
have tumour-suppressor function.
X-ray repair cross-complementing group 1: The X-ray repair cross-complementing group 1 (XRCC1) protein, which is
encoded by the XRCC1 gene, is an important component of the base excision repair (BER) pathway.
ZAP-70: Involved in T-cell activation and differentiation signals. Early events in the activation of the T-cell receptor (CD3/TCR)
Z
are the activation of nonreceptor tyrosine kinases (e.g. the Src family) leading to the phosphorylation of immunoreceptor,
tyrosine-based activation motifs (ITAMs) in the cytoplasmic domains of the CD3/TCR ξ chains. The phosphorylation of
ITAMs is responsible for the recruitment and activation of ξ-associated protein (ZAP)-70 via its SH2 domain, with subsequent
recruitment and activation of other proteins.
Molecular Biology
213
Zinc-finger motif: A zinc finger is a small protein structural motif that is characterised by the co-ordination of one or more
zinc ions in order to stabilise the fold. Proteins that contain zinc fingers (zinc-finger proteins) are classified into several different
structural families. Unlike many other clearly defined supersecondary structures such as Greek keys or β hairpins, there are
a number of unique types of zinc fingers, each with a unique three-dimensional architecture. A particular zinc-finger protein’s
class is determined by this three-dimensional structure, but it can also be recognised based on the primary structure of the
protein or the identity of the ligands co-ordinating the zinc ion. In spite of the large variety of these proteins, however, the
vast majority typically function as interaction modules that bind DNA, RNA, proteins, or other small, useful molecules, and
variations in structure serve primarily to alter the binding specificity of a particular protein.
Molecular Biology
214
Molecular Biology
215
ESMO Glossary in
Molecular Techniques
216
A Antisense oligonucleotides
Small synthetic nucleotide sequences designed to be complementary to specific DNA or RNA sequences; they may be
targeted to inhibit selectively the transcription or translation of a gene.
Apoptosis assays
Apoptosis, also termed type I cell death, is defined by characteristic changes in the nuclear morphology, including chromatin
condensation and fragmentation, overall cell shrinkage, blebbing of the plasma membrane and formation of apoptotic bodies
that contain nuclear or cytoplasmic material.
Apoptosis assays include: nucleic acid stains, DNA strand breaks detection, membrane asymmetry detection, protease
activity (e.g. caspases), mitochondrial stains (Figure 1).
Apoptotic index
The percentage of apoptotic cells in a given biological specimen. The apoptotic index can be determined in several ways,
including TUNEL and caspase 3 cleavage assays.
Array-based comparative genomic hybridisation (array-based CGH)

Array-based comparative genomic hybridisation is a method that uses microarrays to probe changes in chromosomal DNA,
thereby identifying precise areas in which genetic changes occur in cancer cells.
217
Figure 1. Apoptosis-related cellular and molecular changes.
Apoptotic cell
Plasma membrane
Cytoplasm
Mitochondrion
∆ψm↓ Cytochrome c
Smac/DIABLO
Annexin V
Ca2+
DNA fragmentation
Caspase cascade Nucleus
Phosphatidylserine
Source of information: 2014 Enzo Life Sciences, Inc.
218
Automated quantitative protein expression analysis (AQUA)
This technology overcomes limitations associated with traditional “brown stain” immunohistochemistry (IHC). In traditional
IHC, protein expression is reported on a quantised scale such as 0, 1, 2, 3. Biological material rarely is expressed in such
neatly quantised packets, but rather is expressed on a continuous scale. AQUA is a method of computerised interpretation
of fluorescence IHC images that allows protein expression to be automatically assigned to subcellular compartments and
expressed on a continuous scale.
Bioinformatics
B
Bioinformatics or computational biology is the use of techniques from applied mathematics, informatics, statistics, and
computer science to solve biological problems.
Biomarker
A functional biochemical or molecular indicator of a biological or disease process that has predictive, diagnostic, and/or
prognostic utility.
Biomarker classifiers
A diagnostic or prognostic classifier based on biomarker components. The classifier is used to select or stratify patients for
treatment. The biomarker components need not be validated measures of disease status, as used in the sense of the US
Food and Drug Administration agency for surrogate end points or early detection biomarkers.
Bispecific monoclonal antibody

A modified monoclonal antibody that has two binding arms, one to a tumour antigen and the other to a hapten.
219
Bisulphite sequence analysis
DNA treated with sodium bisulphite prior to sequence determination converts unmethylated cytosines in DNA to deoxyruracils,
leaving methylated cytosines unchanged. The pattern of methylated cytosines in the final sequence of the DNA is assessed
by polymerase chain reaction using specific primers followed by sequence analysis.
Capillary gel electrophoresis
C
A method for separating biopolymers (e.g. DNA and polypeptides) in a capillary filled with a network of cross-linked or
entangled linear polymers (sieving matrix) with an applied electric field.
cDNA
cDNA (complementary DNA) is a DNA copy synthesised from mRNA. The enzyme used is reverse transcriptase an RNA-
dependent DNA polymerase isolated from a retrovirus (AMV or MMLV). As with other polymerases, a short double-stranded
sequence is needed at the 3’ end of the mRNA which acts as a start point for the polymerase. It is often used in gene cloning
or as gene probes or in the creation of a cDNA library.
cDNA microarray
Also known as biochip, DNA chip, or gene array, cDNA microarray technology allows for identification of gene expression
levels in a biological sample. cDNAs or oligonucleotides, each representing a given gene, are immobilised on a small chip or
nylon membrane, tagged, and serve as probes that will indicate whether they are expressed in biological samples of interest.
Thus, the simultaneous expression of thousands of genes can be monitored simultaneously.
220
Cell culture Tissue
To cultivate living cells that are maintained in vitro in artificial media of serum
and nutrients for experiments in controlling diseases, such as cancer.
Primary cultures are obtained from tissues and usually have a short half-life.
However, cancer cells can propagate and give rise to continuous cell lines A piece of tissue is
(Figure 2). dispersed into a suspension
of individual cells
Figure 2. Culture of animal cells. The cells are plated

in a culture dish in
nutrient medium
Cell suspension
Liquid medium
Primary
culture
The cells in this primary culture
attach to the dish and grow until they
cover the culture dish surface
The cells can then be removed from

the culture dish and replated at a lower
density to form a secondary culture
Secondary
Source of information: Cooper GM. The Cell: A Molecular Approach; 2nd edition. Sunderland, MA:
culture
Sinauer Associates; 2000.
221
Cell cycle analysis
Cell cycle analysis is a method in cell biology that employs flow cytometry to distinguish cells in different phases of the cell
cycle. Before analysis, the cells are permeabilised and treated with a fluorescent dye that stains DNA quantitatively, usually
propidium iodide (PI). The fluorescence intensity of the stained cells at certain wavelengths will therefore correlate with the
amount of DNA they contain. As the DNA content of cells duplicates during the S phase of the cell cycle, the relative amount of
cells in the G0 phase and G1 phase (before S phase), in the S phase, and in the G2 phase and M phase (after S phase) can be
determined, as the fluorescence of cells in the G2/M phase will be twice as high as that of cells in the G0/G1 phase (Figure 3).
Figure 3. The cell cycle phases (A) and diploid DNA histogram measured by flow cytometry (B).
A B
M PHASE
mitosis
(nuclear G0-G1
division) cytokinesis
G2 PHASE (cytoplasmic
M division)
G2
Cell number
Part A: Reprinted by permission from: Alberts B, et al.
INTERPHASE Molecular Biology of the Cell, 4th edition. New York:
Garland Science; 2002.
S G1 G2-M
S PHASE S Part B: Source of information:
G1 PHASE
(DNA replication) Purdue University Cytometry Laboratories.
Fluorescence intensity
Cell cycle phases A DNA histogram
222
Cell proliferation/viability assays
In general, two parameters are used to measure the health of cells: cell viability and/or cell proliferation. In almost all cases,
these parameters are measured by assaying for vital functions that are characteristic of healthy cells.
Cell Viability
Cell viability can be defined as the number of healthy cells in a sample. Whether the cells are actively dividing or are quiescent
is not distinguished.
Cell Proliferation
Cell proliferation is the measurement of the number of cells that are dividing in a culture.
Chromogenic in situ hybridisation (CISH)

A process in which a labelled complementary DNA or RNA strand is used to localise a specific DNA or RNA sequence in a
tissue specimen. CISH methodology may be used to evaluate gene amplification, gene deletion, chromosomal translocation,
and chromosome number.
Circulating markers including circulating tumour cells

The concept of a circulating tumour marker applies to a secreted chemical product of a tumour cell such that the concentration
of the chemical in the blood may in some way represent a quantifiable assessment of the tumour burden at that time. One
example is the measurement of serum or plasma circulating free DNA (cfDNA) concentration. The cfDNA probably derives
from necrosis and apoptosis, although this is not completely clear. The cfDNA represents an important source of tumour DNA
that can be used for molecular profiling by using different molecular biology techniques. Proteins or protein fragments may be
released into the circulation from cancers and detected by surface-enhanced laser desorption-ionisation time-of-flight mass
spectroscopy (SELDI-TOF).
223
Figure 4. S
chematic representation of tumour dissemination and clinical relevance of circulating tumour
cell biomarkers.
Apoptosis, dormancy
or colonization and
Circulating tumour cell proliferation
dissemination into the
Intravasation peripheral blood Extravasation
Extracellular Mesenchymal-
matrix to-epithelial
transition
Basement
Circulating tumour cells (CTCs) are membrane
rare cells that are shed from primary Extracellular

matrix breakdown
and metastatic tumour deposits Circulating tumour cell enrichment,
detection and characterization methods
into the peripheral circulation, and
Second site reinvasion
represent a means of performing into the bloodstream
non-invasive tumour sampling. Micrometastases

at second site
Overt
metastases
Markers of primary cancer detection
Indeed, enumeration of CTCs and prognosis
• CK19 RT-PCR; breast cancer Markers of metastatic potential
before and after therapy has shown • CK20 IHC; colorectal cancer • Anti-CK-8, -18, -19 and CD45 antibodies;
that CTC burden correlates with • Beta-catenin mutations; liver cancer
• Survivin RT-PCR ELISA;
breast cancer
• hTERT,CK19, CK20, CEA RT-PCR;
prognosis in patients with tumours non-small-cell lung cancer Molecular profiling of circulating
tumour cells
colorectal cancer
• FGF2, CY19, MUC1 secretion (EPISPOT);
of certain etiology. Moreover, • Mutations and SNP analysis prostate cancer
• Methylation analysis
studies have demonstrated the Markers for selection of • CGH
(neo)adjuvant therapy • Gene expression (RT-PCR and qPCR)
potential of molecular analysis of • Adna test (EpCAM, MUC1 and • miRNA Metastatic treatment response markers
• FISH
CTCs in monitoring and predicting ERBB2 transcripts); breast cancer
• Survivin RT-PCR ELISA; • IF
• ERBB2 status; breast cancer
• RAS mutation status; colorectal cancer
response to therapy in patients colorectal cancer, gastric cancer
• ERG rearrangements, PSA;
• Protein expression, secretion
• IHC
• IGF-IR, IF; prostate cancer
• EGFR mutation status;
(Figure 4). prostate cancer non-small-cell lung cancer
Source of information: Future Oncology 2011; 7(7): 849-871. Future Medicine Ltd.
224
Classifiers
A mathematical function that assigns a specimen to a class based on the values of a set of component variables or
features. The classes are predefined and often represent diagnostic categories or prognostic categories. Developing a
completely specified classifier involves determining which features should be included as components, what mathematical
form to use for combining the values of the different features, what values to use for the parameters of the mathematical
form, and what cutoff values to use for converting a continuous function into a discrete classification. Some classifiers
are based on the level of expression of a single protein or the presence of a specific DNA polymorphism. With gene
expression profiling, classifiers may contain dozens of components, representing the level of expression of genes that
are selected from tens of thousands of candidate genes. A completely defined classifier will select patients and stratify
patients for therapy and needs to be validated independently of the study used to develop it.
Cloning
In biology, cloning is the process of producing similar populations of genetically identical individuals that occurs in nature
when organisms such as bacteria, insects or plants reproduce asexually.
Cloning in biotechnology refers to processes used to create copies of DNA fragments (molecular cloning), cells (cell cloning)
or organisms.
Molecular cloning refers to the process of making multiple molecules. Cloning is commonly used to amplify DNA fragments
containing whole genes, but it can also be used to amplify any DNA sequence such as promoters, non-coding sequences
and randomly fragmented DNA (Figure 5).
225
Molecular cloning
Figure 5. Molecular cloning.
Construction of
a chimera
Vector DNA fragment
Transport into
the host cell
Multiplication
Division of host cell
Cell divisions
resulting in a clone
6111103 Copyright © motifolio.com

Reprinted by permission from: Motifolio, Inc.
226
Clustering
Organisation of data consisting of many variables (multivariate data) into classes with similar patterns. Hierarchical clustering
creates a dendrogram based on pairwise similarities in gene expression within a set of samples. Samples within a cluster are
more similar to one another than to samples outside the cluster. The vertical length of branches in the tree represents the
extent of similarity between the samples. Thus, the shorter the branch length, the fewer the differences between the samples.
Comparative genomic hybridisation (CGH)

A molecular cytogenetic method of screening tumour samples for genetic changes showing characteristic patterns for
copy number changes (mutations cannot be detected by CGH) at chromosomal and subchromosomal levels. Alterations
in patterns are classified as DNA gains and losses. The method consists of isolating DNA from tumours and healthy tissues
(reference) and labelling each with a different “colour” or fluor. The two samples are then mixed and hybridised to normal
metaphase chromosomes. In the case of array or matrix CGH, the hybridisation mixing is done on a slide with thousands
of DNA probes. The detection system is varied, but basically determines the colour ratio along the chromosomes to
determine DNA regions that might be gained or lost in tumour samples (Figure 6).
227
Figure 6. M
icroarray-based
Step 1 Patient Control Step 2 Array CGH: The Complete Process comparative genomic
DNA DNA hybridisation (aCGH)
Steps 1-3 Patient and control DNA are labelled with fluorescent dyes process.
and applied to the microarray
Step 4 Patient and control DNA compete to attach, or hybridise, to

the microarray
Step 3
Step 5 The microarray scanner measures the fluorescent signals
Step 6 Computer software analyses the data and generates a plot
Step 5 Step 6
Step 4 HYBRIDISATION
DNA dosage loss
COMPUTER DATA PLOT

SOFTWARE (Chromosome 7)
Equal DNA DNA
hybridisation dosage loss dosage gain Reprinted by permission from: Macmillan Publishers Ltd:
Nat Educ 2008; 1: 45.
228
Copy number arrays and Figure 7. Strategies for SNP genotyping by primer extension using
SNP arrays microarrays.
SNP1 SNP2 SNP3
Copy number analysis usually refers to (AA) (CG) (CC)
the process of analysing data produced

by a test for DNA copy number variation a
T G
T A T A G C C G G C G C
in a patient’s sample. Such analysis +

Extension
SNP1 SNP2 SNP3
helps detect chromosomal copy number PCR products

+ DNA polymerase
C A
Mix of labelled
variation that may cause or may increase ddNTPs
5′ 5′ 5′ 5′ 5′ 5′ AA CG CC
the risks of various critical disorders.

Copy number variation can be detected b
with various types of tests such as 5′
5′
+ T A C A G C C G A C G C
SNP1 SNP2 SNP3
5′
fluorescent in situ hybridisation (FISH), 5′
Transcribed RNA
C
Once labelled
Extension
comparative genomic hybridisation (CGH) + reverse transcriptase + unlabelled dNTPs AA CG CC
and high-resolution array-based tests 5′ 5′ 5′ 5′ 5′ 5′

c
based on array comparative genomic 5′
hybridisation (aCGH) and single nucleotide SNP1

T
SNP1
G T T G C G G
SNP1 SNP2 SNP3
polymorphism (SNP) array technologies. SNP2

5′
G Capture
5′ AA CG CC
In molecular biology and bioinformatics, C
3′ 3′ 3′ 3′ 3′ 3′
an SNP array is a type of DNA microarray Products of primer

extension in solution
which is used to detect polymorphisms
within a population. An SNP, a variation at
a single site in DNA, is the most frequent Reprinted by permission from: Nat Rev Genet 2001; 2(12): 930-942.
type of variation in the genome (Figure 7).
229
Cytofluorimetric dimer assay
An indirect cytofluorimetric assay, which allows the recognition of T cells with peptide-specific T-cell receptors. These cells are
recognised because of their ability to bind the target cognate peptide, which is previously conjugated to a chimeric, dimeric
molecule composed by the Fc portion of a mouse immunoglobulin and the binding site of HLA-A(*)02.01 molecules.
Cytogenetic–morphological correlations
Studies that correlate cytogenetic findings in tumour cells to tumour morphology. Cytogenetically, the structure of the
chromosome is analysed for chromosomal aberrations using cytogenetics such as fluorescence in situ hybridisation and
comparative genomic hybridisation. Tumour morphology is typically determined by a clinical pathologist using histochemical
techniques.
Denaturing gradient gel electrophoresis (DGGE)
D
DGGE is a rapid mutation-scanning technology that is based on the melting characteristics of double-stranded DNA. Based
on the fact that identical DNA molecules, which differ by only one nucleotide within a low melting domain, will have different
melting temperatures, DGGE is typically performed on polymerase chain reaction products. In the procedure, double-
stranded DNA is electrophoresed through an acrylamide gel containing a gradient of denaturant, which increases in the
direction of electrophoresis. When appropriate denaturing conditions exist, the DNA molecules melt (melting domain). When
the characteristic melting temperature is achieved, the amplicon melts and a single band is observed. Mismatched DNA
(mutations) will retard the movement of the DNA through the gel, with sequence differences of one base having the ability to
significantly alter the stability of the melting domains, and more than one band will be observed (Figure 8).
230
Figure 8. D
enaturing gradient gel
DGGE: Denaturing Gradient Gel Electrophoresis
electrophoresis (DGGE).
Extract DNA from each Add GC clamp
Samples from different community (anchors DNA together once it is denatured)
microbial communities
PCR fragment
GC clamp
Denatured PCR fragment

GC clamp
Each lane represents one microbial community
–
Denaturing gradient
Shared genes amongst communities

Change
Unique genes within communities
+
Courtesy: Wikipedia.
231
Densitometric
Densitometric analysis measures the optical density of the bands appearing in blotting techniques (Northern, Southern,
Western, etc.) in order to semiquantify gene, mRNA, or protein expression.
Differential methylation hybridisation (DMH)

A high-throughput microarray technique designed to identify changes in DNA methylation patterns commonly observed
in cancer and other disease states. The DMH methodology comprises three fundamental components: the arraying of
CpG island clones on glass slides, the preparation of the sample amplicons under investigation (using methylation-sensitive
endonucleases, which digest non-methylated DNA, while leaving methylated DNA intact), and the hybridisation of amplicon
targets on to the CpG island microarray.
ELISpot
E
Enzyme-linked immunospot that is exquisitely sensitive to assay minute amounts of mediators that are produced by cells.
Typically, cells are deposited on a membrane coated with an antibody specific for a given protein. The protein of interest is
captured directly around the secreting cell and is detected with an antibody specific for a different epitope. Coupled with
colorimetry, the cells are visualised by specialised plate readers. Thus, the molecule is assayed before it is diluted in the
supernatant, captured by receptors of adjacent cells, or degraded.
232
Epigenetics
Epigenetics is the study of heritable
changes that are not caused by
changes in the DNA sequence.
The term also refers to the changes
themselves: functionally relevant
changes to the genome that do not
involve a change in the nucleotide
sequence. Examples of mechanisms
that produce such changes are DNA
methylation and histone modification,
each of which alters how genes
are expressed without altering the
underlying DNA sequence (Figure 9).
Figure 9. Epigenetic
modifications that
regulate transcription
or translation.
Reprinted by permission from: Nat Rev Cardio 2010; 7(9): 510-519.
233
Expression profiling
Gene expression profiling is a technique used in molecular biology to query the expression of thousands of genes
simultaneously. In the context of cancer, gene expression profiling has been used to more accurately classify tumours.
The information derived from gene expression profiling often has an impact on predicting the patient’s clinical outcome.
Expression signature classifiers

A diagnostic or prognostic classifier in which the components are genes defined from microarray approaches, which
have shown differential expression in patients responding to or likely to respond to (as a function of risk category) a given
therapeutic intervention and, therefore, have utility in future studies to determine clinical outcomes in patients. Classifiers
have to be validated in independent studies and have to have a high negative predictive value to justify withholding a
potentially curative therapy.
FISH
F
Fluorescence in situ hybridisation is a technique to assign genes to particular chromosomes or to determine the gene
copy number in particular cells; DNA probes are hybridised to fixed preparations of metaphase cells or interphase
nuclei, and labelling is visualised by counter-staining with avidin or other reagents; the method matches genetic studies
with morphology; and it produces beautiful pictures.
234
Flow cytometry Figure 10. Complex object parametric analyser and sorter.
Analysis of biological material via detection of the Fluorescently labelled
light-absorbing or fluorescing properties of cells, or of bead or organism population
subcellular fractions such as chromosomes, as they pass
in a narrow stream through a laser beam. Cells are usually
stained with monoclonal antibodies conjugated with
fluorescent dyes to allow phenotypic characterisation Aqueous
through flow cytometric analysis. Flow cytometry can be sheath flow
used with automated sorting devices to sort successive
droplets of a stream into different fractions, depending nc
e
on the fluorescence emitted by each droplet (Figure 10). sce
ore
Flu
Dual laser excitation
Size &
Analysis
Optical density
Non-destructive
Air sorting
Diverter valve
Un-tagged objects to waste

Dispensing
Tagged objects sorted into microwells
for further analysis
Reprinted by permission from: Union Biometrica.
235
Functional validation
Functional validation assays demonstrate how genetic differences have a measurable phenotypic effect that can be correlated
with a specific disease.
Functional validation assays can be classified into molecular and biological assays.
Molecular functional validation is performed in vitro and is intended to characterise gene function by employing biochemical
assays such as: mRNA expression, transcript/protein localisation, protein–DNA interaction, protein–protein interaction.
Biological functional validation is performed in living cells or organisms, building evidence of a gene’s importance, because it
demonstrates the relationship between a genetic entity and the phenotype visible at the cellular level or above. Some of the
biological approaches include human cell lines, animal models and human patients.
Gelatin zymography
G
A technique that allows for assaying the enzymatic activity of a protein suspected of being a protease, including proteins
belonging to the class of MMPs. Typically, the sample suspected of containing the proteases is electrophoresed in
polyacrylamide gels containing the substrate (type III gelatin or b-casein) that can be degraded by these enzymes, the SDS
removed after electrophoresis, and the proteolytic proteins visualised as clear bands against the Coomassie blue-stained
protein background.
Gene expression analysis

Technique for the simultaneous quantification of the mRNA expression level of thousands of genes. It can be performed using
microarrays, RT-PCR, or other technologies for measuring gene expression.
236
Gene expression arrays Figure 11. Gene-expression analysis of tumours.
Gene arrays are solid supports upon which a a Reference RNA Tumour RNA b c
collection of gene-specific nucleic acids have
been placed at defined locations, either by Multidimensional-scaling plot
spotting or direct synthesis. In array analysis, cDNA

a nucleic acid-containing sample is labelled Statistical analysis
Hybridisation
and then allowed to hybridise with the gene- of probe to
microarray
specific targets on the array. (In the literature,
the term “target” can refer to either the nucleic
acids attached to the array or the labelled
nucleic acid of the sample. Here, the nucleic
acids attached to arrays are called “targets”,
whereas the labelled nucleic acids comprising d e
the sample are called “probes”.) Based on the

amount of probe hybridised to each target
spot, information is gained about the specific
nucleic acid composition of the sample.
Using array analysis, the expression profiles Donor paraffin block Recipient paraffin block Tissue microarray
of normal and tumour tissues, treated and
untreated cell cultures, developmental
stages of an organism or tissue, and different
tissues can be compared (Figure 11). Reprinted by permission from: Nat Rev Cancer 2001; 1(2): 151-157.
237
Gene expression profile
The expression of a set of genes in a biological sample (e.g. blood, tissue) using microarray, RT-PCR, or other technology
capable of measuring gene expression.
Genomics
The scientific discipline in which multiple genes, gene products, or regions of the genome are analysed via large-scale, high-
throughput molecular approaches directed to DNA and RNA. The definition is a deviation from the original term, which meant
an analysis of the whole genome.
Genotyping
The process used for obtaining the genotype of a given gene. Typically, polymerase chain reaction-based methods are used.
However, in the case of single nucleotide polymorphism genotyping, microarray platforms are used routinely. Genotyping data
serves several purposes, including a means to determine genetic diversity, to identify important genetic traits, and in forensic
and population studies. It is used increasingly in determining paternity of offspring. From a somatic point of view (within a
tumour), genotyping is used to determine loss of heterozygosity.
238
H High-throughput interference technologies Figure 12. S
ummary schematic of siRNA
High-throughput screening (HTS) is a method for scientific HTS strategies.
experimentation especially used in drug discovery and relevant to the PolIII
PolIII
fields of biology and chemistry. Using robotics, data processing and Synthesised PCR-product
control software, liquid handling devices, and sensitive detectors, HTS siRNA
allows a researcher to quickly conduct millions of chemical, genetic, or PolIII PolIII
pharmacological tests.
Viral
Multiparametric assays generate biological activity profiles that provide Plasmid vector
valuable insight into complex disease models. The use of multiple assay
measurements in RNA interference (RNAi) HTS provides biological Prepare siRNA library
signatures produced by knocking down individual genes via RNAi.
RNAi can be realised using RNA sequences that are able to “silence”
expression of target sequences such as small interfering RNA (siRNA) Pooled libraries Arrayed libraries
(Figure 12).
Transfect Transfect
or infect or infect
Run assay
& identify
active wells
Run assay
& select for
Reprinted by permission from: Oncogene 2004; 23(51): 8392-8400. phenotype
239
Hybridisation
Annealing or base pairing of two single-stranded RNA and/or DNA molecules with specific binding of single nucleic acid
strands to form a double strand according to their complementary sequences. Both DNA–DNA binding and DNA–RNA
binding are possible; hybridisation of nucleic acids placed on blots or in solution with labelled molecular probes is an important
principle of looking at gene structure or gene expression.
Immunoblotting
I
Probing for cellular proteins blotted on to a nylon membrane using antibodies specific to the protein of interest. Cellular proteins
are first separated on the basis of molecular weights using gel electrophoresis. The proteins from the gel are then transferred
on to a nylon membrane either by diffusion or using an electric field. The cellular proteins on the gel are probed with the primary
antibody specific to the protein of interest. The antigen–antibody complex is then detected using a secondary detection system.
Immunohistochemical analyses
Techniques used to evaluate the levels and patterns of expression of protein on cells or tissue specimens located on flat slides.
Immunohistochemistry
The application of antigen–antibody interactions to histochemical techniques. Typically, a tissue section is mounted on a slide and
is incubated with antibodies (polyclonal or monoclonal) specific to the antigen (primary reaction). The antigen–antibody signal is
then amplified using a second antibody conjugated to a complex of peroxidase–antiperoxidase (PAP), avidin–biotin–peroxidase
(ABC), or avidin–granzyme–biotin alkaline phosphatase. In the presence of substrate and chromogen, the enzyme forms a
coloured deposit at the sites of antibody–antigen binding. Immunofluorescence is an alternative approach to visualise antigens.
In this technique, the primary antigen–antibody signal is amplified using a second antibody conjugated to a fluorochrome. On
ultraviolet light absorption, the fluorochrome emits its own light at a longer wavelength (fluorescence), thus allowing localisation
of antibody–antigen complexes.
240
Immunophenotyping Figure 13. S
chematic summary of a standard
A way to identify cells based on their immunoprecipitation assay.
surface antigens. This assay, applying
a panel of different fluorochrome- Cell lysate or Incubation with
conjugated antibodies, is used to protein mixture antibody-coupled resin
diagnose specific types of leukaemia
and lymphoma.
Immunoprecipitation
Immunoprecipitation is the technique
of precipitating a protein antigen out
of solution using an antibody that
Coupled antibody Spin and wash Elute
specifically binds to that particular
protein. This process can be used to
Antigen
isolate and concentrate a particular
protein from a sample containing
many thousands of different proteins.
Immunoprecipitation requires that
the antibody be coupled to a solid
substrate at some point in the
procedure (Figure 13). Analyse
Reprinted by permission from: Thermo Fisher Scientific, copyrighted 2014.
241
Immunoscintigraphy
An imaging scintigraphic procedure that uses a radiolabelled antibody as the radiopharmaceutical for the detection of an
antigen expressed by a lesion.
Knock out experiments
K
Particularly suitable to develop animal models of autosomal recessive diseases where both alleles of a gene of interest must
be inactivated; the goal of the method is to replace a specific gene of interest with one that is inactive, altered, or irrelevant;
it works based on the principle of homologous recombination between the gene and a vector which a) contains sequences
flanking the locus of interest, b) does not contain the gene of interest, and c) contains marker genes to identify and select cells
that have successfully incorporated the vector; knock out techniques can be used to determine whether a single genetic locus
is responsible for a given disease, for example to determine the significance of cytokines or growth factors, and to generate
models to look at the phenotypic effects of particular disrupted genes associated particularly with loss of function.
Laser-capture microdissection
L
A method for isolating pure cells of interest from specific microscopic regions of tissue sections.
242
M Metabolomics Figure 14. The metabolome.
Metabolomics is the study of the complete collection of
metabolites present in a cell or tissue under a particular set DNA polymerases +
other DNA enzymes THE PROTEOME
of conditions (= the metabolome) generating a biochemical
profile. RNA polymerases
+ other
RNA enzymes
The metabolome refers to the complete set of small- splicosome
mRNA ribosome
tRNA
molecule chemicals found within a biological sample. DNA complex
rRNA
replication
The biological sample can be a cell, a cellular organelle, THE TRANSCRIPTOME
an organ, a tissue, a tissue extract, a biofluid or an entire DNA RNA PROTEIN
organism (Figure 14). THE
GENOME ribosomal
proteins
ribozymes
nuclear
membrane
metabolic
nucleotides nucleotides amino acids substrates ions
THE METABOLOME
ENVIRONMENT
cell in organism
organism in ecosystem
Source of information: University of California.
243
Metaphase comparative genomic hybridisation (M-CGH)
A relatively new molecular cytogenetic technique that detects DNA sequence copy number changes throughout the genome
in a single hybridisation. The method is based on co-hybridisation of differentially labelled tumour and normal DNA to human
metaphase chromosomes. Alterations, classified as DNA gains and losses, reveal a characteristic pattern that includes
mutations at chromosomal and subchromosomal levels. Gains and losses of DNA sequences of approximately 2 to 20 Mb
can be detected by this method.
2-Methoxyethyl backbone
Third-generation oligonucleotides used in antisense technology. The methoxyethyl backbone substitutes for the conventional
phosphodiester backbone found in oligonucleotides, RNA, and DNA.
Methylation-specific polymerase chain reaction (MSP)

MSP is a method to identify methylated cytosine bases in genomic DNA. Bisulphite treatment deaminates unmethylated
cytosine residues into thymidine bases; methylation prevents deamination. Primers specific for methylated and unmethylated
DNA sequences are then used in a polymerase chain reaction to amplify respective sequences.
Microarray
A multiplex lab-on-a-chip, 2D array on a solid substrate that assays large amounts of biological material using high-throughput
screening methods. Types of microarrays include DNA microarrays, such as cDNA microarrays, oligonucleotide microarrays,
and SNP microarrays; MMChips, for surveillance of microRNA populations; protein microarrays and peptide microarrays, for
detailed analyses or optimisation of protein–protein interactions; tissue microarrays; cellular microarrays; chemical compound
microarrays; and antibody microarrays.
244
Microarray-based comparative genomic hybridisation (array-CGH)
Array-based comparative genomic hybridisation is a method that uses microarrays to probe changes in chromosomal DNA,
thereby identifying precise areas in which genetic changes occur in cancer cells.
Microarray expression profiling

Gene expression profiles using microarray technology.
Microarray transcriptional profiling

The use of arrays of immobilised cDNAs or oligonucleotides representing gene sequences upon which RNA from various cell
types is hybridised and detected. In this manner, the expression of thousands of genes expressed in a given cell type can be
measured simultaneously.
Microchip arrays
Also known as DNA chip technology or GeneChip assays, provide a new strategy for gene structure and expression
screenings with great potential. Two types of DNA chips are currently most popular: oligonucleotide chips and cDNA chips.
“Oligo” Chips: multiple oligonucleotide probe arrays are defined based on their ability to hybridise to target loci or genes of
interest. The probes synthesised are arranged as large arrays of short multiple perfect-match or mismatch oligonucleotides
covering both the wild-sequence as well as multiple sequence variants of a gene or a specific mRNA. The sequences are
placed on a glass wafer about 1 cm2 in size (with each probe in a predefined position) and packaged into a plastic cartridge
which also serves as hybridisation chamber. Thus, oligonucleotide arrays on the chip represent the sequence of genes or the
sequences of a cDNA of interest. cDNA Chips: instead of defined oligonucleotide sequences, cDNA sequences (for example,
derived from mRNA libraries of cell samples of interest) are aligned on the chip surface to form rows and columns with defined
localisation. For the detection of gene sequences or gene expression patterns, sample nucleic acids are fluorescently labelled
and hybridised to an appropriate array of cDNA or oligo sequences on the chip. After hybridisation and washing, specifically
245
bound DNA or mRNA sequences from the samples are detected on the array by scanning of fluorescence signal intensity.
Hybrids produced by a perfect match between an oligo and sample DNA or mRNA yield higher fluorescence intensity relative
to other target:probe hybrids in the set. The software records and prints average hybrid intensity as well as sequence data. The
time from purified sample DNA to complete sequence data analysis is little more than 3–4 hours. DNA microchips are useful
to screen samples for DNA mutations, for example germline mutations of a tumour-suppressor gene in hereditary cancer,
or somatic gene mutations in cancers such as translocations, oncogene point mutations etc. Gene expression screening in
tumours may also be achieved comparing mRNA from tumour and homologous normal tissue (differential display screening),
or by comparing different types of neoplasms. Gene expression profiles have been shown to define “new” clinical entities in a
variety of tumours, including lymphomas and breast cancers (Figure 15).
Figure 15. Steps required in a microarray experiment.
Courtesy: Wikipedia.
246
MicroRNAs
Endogenous noncoding RNAs approximately 22 nucleotides long that regulate gene silencing by post-transcriptional
mechanisms such as cleavage or translational repression.
Mixed lymphocyte-peptide culture (MLPC)/tetramer/cloning

In this cytotoxic T lymphocyte (CTL)-monitoring approach, peripheral blood mononuclear cells are incubated with the target
antigenic peptide in limiting dilution conditions. Expanded antigen-specific CTLs are then identified by tetramers (tetrameric
arrays of soluble class I major histocompatibility complex–peptide complexes) and cloned for further characterisation.
Molecular cytogenetics
Cytogenetic studies that probe the molecular makeup of chromosomes. Several techniques have been developed that
have advanced the field of molecular cytogenetics, including fluorescence in situ hybridisation and array-based comparative
genomic hybridisation.
Molecular profiling
With the advent of bioinformatics, molecular profiling is a new discipline that uses a variety of approaches to generate a global
view of mRNA, protein patterns, and DNA alterations in various cell types. Thus, molecular profiles of disease processes may
be seen as distinct from normal cells, and therapeutic approaches may be tailored based on molecular profiles.
Molecular signature
Molecular signatures or “gene-expression signatures” are a key feature in many studies that use microarray data in cancer
research. They refer to signatures as genes that are co-ordinately expressed in samples related by some identifiable criterion
such as cell type, differentiation state, or signalling response. Molecular signatures are often used to model patients’ clinically
247
Figure 16. G
eneration of transgenic and knock-in/
knockout mouse models.
relevant information (e.g. prognosis, survival time, etc.)
as a function of the gene expression data, but instead of A Transgenic B Knock-in or knockout mouse
using individual genes as predictors, the predictors are the
signature components or “metagenes”. Recombinant DNA TK Targeting vector
Mouse models DNA injected to Gene targeted in embryonic

male pronucleus of stem (ES) cells through
The mouse model is a strain of mouse used in basic and fertilised oocyte homologous recombination
translational research as it has specific characteristics that
resemble a human disease, or has natural mutations similar Targeted ES cells
to human mutations. selected and expanded
Genetic mouse models in cancer research are used in Injected oocyte Targeted ES cells
validating gene functions, identifying novel cancer genes develops into early injected into early
mouse embryo mouse embryo
and tumour biomarkers, gaining insight into the molecular
and cellular mechanisms underlying tumour initiation and
multistage processes of tumourigenesis, and providing better Embryo implanted Embryo implanted
into uterus of into uterus of
clinical models in which to test novel therapeutic strategies. pseudopregant pseudopregnant
mouse mouse
Genetically engineered mice include transgenic mice,
Chimeric mouse
knockout mice, and knock-in mice (Figure 16). born and mated
with normal mouse
Reprinted by permission from: J Investig Dermatol Symp Proc 2005; 10(1): 37-46. Transgenic mouse Knock-in or knockout mouse
248
MTT assay
The MTT assay is a colorimetric assay for assessing cell metabolic activity. NAD(P)H-dependent cellular oxidoreductase
enzymes may, under defined conditions, reflect the number of viable cells present. These enzymes are capable of reducing
the tetrazolium dye MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide to its insoluble formazan, which has
a purple colour. Other closely related tetrazolium dyes including XTT, MTS, and the WSTs are used in conjunction with
the intermediate electron acceptor, 1-methoxy phenazine methosulphate (PMS). With WST-1, which is cell-impermeable,
reduction occurs outside the cell via plasma membrane electron transport. Tetrazolium dye assays can also be used to
measure cytotoxicity (loss of viable cells) or cytostatic activity (shift from proliferation to quiescence) of potential medicinal
agents and toxic materials.
Nearest-neighbour classification
N
Used to classify a patient specimen based on the genes selected as being differentially expressed between the diagnostic or
prognostic classes. The vector of expression levels (i.e. the expression profile) for the specimen to be classified is compared
to each expression profile for a training set of specimens, based on a defined distance function between pairs of profiles. The
distance function utilises only those selected genes. The specimen to be classified is predicted to be in the same class as that
in the training set to which it is closest.
Next-generation sequencing
Next-generation sequencing (NGS) platforms perform parallel sequencing, during which millions of fragments of DNA from a
single sample are sequenced in unison. NGS technology facilitates high-throughput sequencing.
The term “next generation” has most often been applied to DNA sequencing in comparisons of new technologies to Sanger
sequencing. The advance from ~400 base pairs per run to millions of base pairs per run and from single-digit coverage to up
to ~1,000× coverage represents a technological increase in orders of magnitude (Figure 17).
249
Figure 17. Basic workflow for NGS experiments. Non-random X-chromosome inactivation
(HUMARA assay)
Tumours arise from a single genetically altered cell.
Consequently, detection of monoclonality, a genetic similarity
among the cells in a tumour mass, can be used to distinguish
neoplastic from polyclonal or hyperplastic lesions. Clonality
can be established based on X-chromosome inactivation
analysis. During early embryonic development of mammalian
female embryos, one of the two X-chromosomes in each cell
is randomly deactivated by the methylation of deoxycytosine
residues. Once established, genetic imprinting retains
X-chromosome inactivation through all subsequent cell
divisions. The cells in a clonal tumour all show inactivation of
the same copy of the X-chromosome. One common assay
detects this inactivation by examining inactivation of the
human androgen receptor (HUMARA) on the X-chromosome.
Reprinted by permission from: Cancer Prev Res (Phila) 2012; 5(7): 887-900.
250
O Oligonucleotide arrays
Mini-DNA microarrays, an important tool in research into genomes. They are small, high-density arrays, containing tens of
thousands of synthetic oligonucleotides. They differ in many details but do share the essential simplicity of the experimental
design of DNA microarrays.
Oligonucleotide microarray chips

In oligonucleotide microarrays, short DNA oligonucleotides are spotted on to the array. The main feature of oligonucleotide
microarray is that each gene is normally represented by more than one probe: the ensemble of probes mapping to different
regions of the gene is usually called a probe set. Commercial oligonucleotide chips are available with an oligonucleotide
representation of tens of thousands genes, covering an entire genome.
PCR/qPCR
P
Polymerase chain reaction (PCR) is a laboratory technique used to amplify DNA or RNA sequences.
PCR is a method where an enzyme (thermostable DNA polymerase, originally isolated in 1960s from the bacterium Thermus
aquaticus, growing in hot lakes of Yellowstone Park, USA) amplifies a short, specific part of the template DNA (amplicon)
in cycles. In every cycle the number of short specific sections of DNA is doubled, leading to an exponential amplification of
targets.
If RNA is used as a template (e.g. in case of gene expression studies or detection of RNA viruses), RNA needs to be reverse
transcribed into DNA (also termed complementary DNA or cDNA) (Figure 18).
251
qPCR Figure 18. Amplification of DNA using the PCR technique.
Nucleic acid (DNA, RNA) quantification
A
can be performed via real-time PCR or 5′
quantitative PCR (qPCR). The method +DNA polymerase
HEAT TO +dATP DNA
is so-called because the amplification of SEPARATE HYBRIDIZATION +dGTP SYNTHESIS
OF PRIMERS +dCTP FROM
DNA with a polymerase chain reaction Double-stranded
DNA
STRANDS
+dTTP PRIMERS
(PCR) is monitored in real time (qPCR 5′
cyclers constantly scan qPCR plates). STEP 1 STEP 2 STEP 3
FIRST CYCLE
Pharmacodynamics B Separate DNA
Separate DNA
strands and DNA synthesis
strands and DNA synthesis anneal primer
A study of the biochemical and Separate DNA anneal primer
physiological effects of drugs on the strands and add
primer
DNA synthesis
body and the mechanisms of drug

action and the relationship between
drug concentration and effect. DNA oligonucleotide
etc.
primers
Region of
double-stranded
chromosomal
DNA to be
amplified
FIRST CYCLE SECOND CYCLE THIRD CYCLE

(producing two double-stranded (producing four double-stranded (producing eight double-stranded
DNA molecules) DNA molecules) DNA molecules)
Reprinted by permission from: Alberts B, et al. Molecular Biology of the Cell, 4th edition. New York: Garland Science; 2002.
252
Pharmacogenetics
Pharmacogenetics is the study of inherited genetic differences in drug metabolic pathways which can affect individual responses
to drugs, both in terms of therapeutic effect as well as adverse effects. The term pharmacogenetics is often used interchangeably
with the term pharmacogenomics which also investigates the role of acquired and inherited genetic differences in relation to drug
response and drug behaviour through a systematic examination of genes, gene products, and inter- and intra-individual variation
in gene expression and function. In oncology, pharmacogenetics historically is the study of germline mutations (e.g. single-
nucleotide polymorphisms affecting genes coding for liver enzymes responsible for drug deposition and pharmacokinetics).
Pharmacogenomics
Pharmacogenomics (a portmanteau of pharmacology and genomics) is the study of the role of genetics in drug response. It deals
with the influence of acquired and inherited genetic variation on drug response in patients by correlating gene expression or single-
nucleotide polymorphisms with drug absorption, distribution, metabolism, and elimination, as well as drug receptor target effects.
Pharmacokinetics
A branch of pharmacology that studies the relationship between drug exposure level, time course of exposure, and the overall
response of an organism. Although it is largely applied to drugs, it is also applicable to other compounds such as nutrients, toxins,
hormones, etc. Pharmacokinetics is subdivided into absorption and disposition (distribution, metabolism, and excretion) and is
generally referred to as ADME (absorption, distribution, metabolism, excretion). With respect to drugs administered, all processes
occur in tandem once a drug dose is administered. In clinical trials, phase I studies will typically study pharmacokinetics and
safety of the drug.
253
Protein assays beyond IHC (next-generation Figure 19. MSIHC analysis.
immunohistochemistry)
Traditional IHC has allowed assessment of a single protein’s
expression in a binary manner using chromogens such
as DAB3 or, at best, in a continuous and quantifiable way
with quantitative immunofluorescence (QIF) of as many as
seven proteins or, with new cycling methods, over a dozen
antigens.
The combination of mass spectroscopy with
immunohistochemistry (MSIHC) allows highly multiplexed,
non-overlapping measurement of 60 or more analytes per
submicrometre field, thus allowing direct quantitative imaging
of tissue samples.
The ability to multiplex within a pixel will allow assessment
of multiple antibodies to the same protein in the same real
estate (Figure 19).
Reprinted by permission from:
Nat Methods 2014; 11(4): 381-383.
254
Tissue
dissection
(Step 1)
Protein/RNA/DNA extraction, quantification

1–3 mm
A
A B
and qualitative analysis Tissue
processing B
EXTRACTION (Steps 2–8) FFPE tissue processing (Steps 9–27)
A B
DNA/RNA extraction is the purification of DNA/RNA from
biological samples. Homogenization
in dry/wet ice
(Steps 32–35)
Protein purification is a series of processes intended to
H&E evaluation
isolate proteins from a complex mixture, usually cells, tissues QIAshredder (Steps 28–31)
homogenization >70% cellularity
or whole organisms. (Steps 36–38)
Other potential applications
for FFPE blocks
Methods exist for simultaneous extraction of DNA, RNA and � Immunohistochemistry (IHC)
proteins from samples (Figure 20). DNA binding

(Steps 39,40)
AllPrep
column
� In situ hybridization (ISH)
Acid phenol- Protein

chloroform precipitation
mirVana
Figure 20. Schematic workflow for obtaining Column washes
(Steps 41–43)
extraction
(Steps 48–54)
filter (Step 56A(i–vi))
+1/3 EtOH
immediate flanking sections and (Step 55B(i))
simultaneous extraction of nucleic acids Filter washes

(Step 55B(ii–v))
+2/3 EtOH
(Step 55B(vii))
mirVana
filter
and proteins from the same samples. Filter washes

(Step 55B(viii))
Protein
DNA elution mRNA elution ncRNA elution resuspension
(Steps 44–47) (Step 55B(vi)) (Step 55B(viii)) (Step 56A
(vii–ix))
Genomic DNA mRNA ncRNA Proteins
• Next-generation sequencing • RNA-seq • miRNA-seq • Western blotting
(whole genome, exome and
applications
• Expression • Expression • 2D gel
Potential
deep sequencing)
• Sanger sequencing microarrays microarrays electrophoresis
• SNP arrays (copy number • qRT-PCR • qRT-PCR • Mass spectrometry
and genotyping)
• Northern • Northern
• DNA methylation blotting blotting
Reprinted by permission from: Nat Protocols 2013; 8(11): 2240-2255. • Southern blotting
255
QUANTIFICATION
In molecular biology, quantification of nucleic acids is commonly performed to determine the average concentrations of DNA
or RNA present in a mixture, as well as their purity. Reactions that use nucleic acids often require particular amounts and purity
for optimum performance. There are several methods to establish the concentration of a solution of nucleic acids, including
spectrophotometric quantification and UV fluorescence in presence of a DNA dye.
Proteins can also be determined by different methods based on spectrophotometry. Quantitative proteomics is an analytical
chemistry technique for determining the amount of proteins in a sample. Rather than just providing lists of proteins identified
in a certain sample, quantitative proteomics yields information about differences between samples.
QUALITATIVE ANALYSIS
Qualitative analysis of nucleic acids may comprise chromatin and epigenetics analysis, computational methods, gel
electrophoresis, genomics, microarray technology, mutagenesis analysis, Northern blotting, nucleic acid amplification,
polymerase chain reaction (PCR), protein–nucleic acid interaction, DNA repair analysis, and Southern blotting.
Qualitative analysis of proteins may comprise protein detection, protein–protein interactions analysis, protein–DNA interactions,
computational analysis, protein structural alignment, protein ontology, mass spectrometry, protein sequencing, proteomics,
peptide mass fingerprinting, ligand binding assay, and Eastern blotting.
Proteomic studies
With the proteome-indicating proteins expressed by a genome of an individual, protein informatics or proteomics is a growing
field that uses technologies like electrophoresis and mass spectrometry to identify and quantify cellular proteins that may be
expressed, even in small amounts, and to determine their role in the physiological and pathophysiological conditions of an
individual.
256
R RNA interference (siRNA, shRNA), transfection and re-expression
RNA interference
RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression, typically by causing the
destruction of specific mRNA molecules.
Two types of small ribonucleic acid (RNA) molecule – microRNA (miRNA) and small interfering RNA (siRNA) – are central to
RNA interference. RNA interference has an important role in defending cells against parasitic nucleotide sequences – viruses
and transposons.
A small hairpin RNA or short hairpin RNA (shRNA) is a sequence of RNA that makes a tight hairpin turn that can be used to
silence target gene expression via RNAi.
RNAi transfection
Gene silencing by RNAi is a powerful research tool for studying gene function in mammalian cells. Therefore, successful RNAi
experimentation is dependent upon the highly efficient delivery of the siRNA into cells by transfection of stable and functional
siRNA molecules.
RNAi re-expression
As miRNA expression seems to be altered in many human diseases, including cancer, re-expressing lost miRNA in a cell can
influence cellular processes, because miRNAs regulate a vast number of genes and pathways (Figure 21).
257
Figure 21. MicroRNA re-expression as differentiation therapy in cancer.
Reprinted by permission from: J Clin Invest 2009; 119(8): 2119-2123.
258
S Sanger sequencing Figure 22. DNA sequencing by the Sanger procedure.
3′ 5′
Sanger sequencing is a method of DNA T G A C G C T T G T C A
sequencing based on the selective 5′

A C T
3′
incorporation of chain-terminating Radioactive primer DNA synthesis in presence of
dideoxynucleotides by DNA polymerase chain-terminating dideoxynucleotides
during in-vitro DNA replication.

ddG ddA ddC ddT
In Sanger sequencing, the DNA to be

sequenced serves as a template for DNA A C T G C G A A C A G A C T G C G A A C A A C T G C G A A C A C T G C G A A C A G T
synthesis. Four individual DNA synthesis A C T G C G A C T G C G A A A C T G C

reactions are performed. The four
A C T G A C T G C G A
reactions include normal A, G, C and T
deoxynucleotide triphosphates (dNTPs).
Following synthesis, the products of the
A, G, C and T reactions are individually P P P
Electrophoresis
loaded into four lanes of a single gel and O G A C T

Autoradiography
separated using gel electrophoresis, a 5′

C O Base
method that separates DNA fragments H H Fragment
T
G
by their sizes. The bands of the gel are 3′ 2′
migration
A
detected, and then the sequence is H H C
A Sequence of
read from the bottom of the gel to the A complementary strand
2′, 3′ Dideoxynucleotide G
top, including bands in all four lanes C
(Figure 22). G
Source of information: Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland, MA: Sinauer Associates; 2000.
259
Spectral karyotyping
A new method for karyotyping that uses fluorescent dyes that bind to specific regions of chromosomes, spectral karyotyping
has been used to detect chromosomal translocations not recognisable by traditional binding methods. Because a series
of specific probes, each with varying amounts of the dyes, are used, different pairs of chromosomes have unique spectral
characteristics. An interferometer recognises slight variations in colour undetectable to the human eye and assigns an easy-
to-distinguish colour to each pair of chromosomes, generating a digital image. Thus, pairing of the chromosomes is simpler
as homologous pairs are the same colour, and aberrations and crossovers are more easily recognisable.
Transfection
T
Incorporation of foreign DNA in eukaryotic cells by any means (in contrast to transduction), i.e. through viral infection,
microinjection, and other techniques, usually in cell culture; foreign DNA may be transiently or permanently (stably) incorporated
in the host genome.
Transgenic animal
An animal which has grown from a fertilised oocyte where a foreign DNA construct was introduced (usually via microinjection);
all cells of the experimental animal will contain the foreign DNA, which can also be passed on to the progeny of the animal; an
important model to study the in-vivo function of mutated genes (for example oncogenes etc.) in carcinogenesis; in contrast
to knock out animals, transgenic mice are particularly suitable to study effects of dominant rather than recessive mutations in
genes (gain of function disease).
260
V Vector
In molecular cloning, a vector is a DNA molecule used as a vehicle to artificially carry foreign genetic material into another
cell, where it can be replicated and/or expressed. A vector containing foreign DNA is termed recombinant DNA. The four
major types of vectors are plasmids, viral vectors, cosmids, and artificial chromosomes. Of these, the most commonly used
vectors are plasmids. Common to all engineered vectors are an origin of replication, a multicloning site, and a selectable
marker. The vector itself is generally a DNA sequence that consists of an insert (transgene) and a larger sequence that
serves as the “backbone” of the vector. The purpose of a vector which transfers genetic information to another cell is
typically to isolate, multiply, or express the insert in the target cell. Vectors called expression vectors (expression constructs)
specifically are for the expression of the transgene in the target cell, and generally have a promoter sequence that drives
expression of the transgene. Simpler vectors called transcription vectors are only capable of being transcribed but not
translated: they can be replicated in a target cell but not expressed, unlike expression vectors. Transcription vectors are
used to amplify their insert. Insertion of a vector into the target cell is usually called transformation for bacterial cells and
transfection for eukaryotic cells, although insertion of a viral vector is often called transduction.
261
W Western/Northern/Southern blot Figure 23. Western blotting, or immunoblotting.
The blotting methods consist of four separate steps: A ELECTROTRANSFER B ANTIBODY DETECTION
electrophoretic separation of protein or of nucleic acid Incubate with
fragments in the sample; transfer to and immobilisation Ab1 (Y) and then wash excess Ab1
on membranes; binding of analytical probe to target
molecule on paper; and visualisation of bound probe.
Three types of blotting techniques are commonly Electric
current
used for visualising particular macromolecules:
Western blot
The Western blot (alternatively, immunoblot) is used to
detect specific proteins in a given sample of tissue SDS-polyacrylamide gel Porous Incubate with enzyme-linked
homogenate or extract (Figure 23). membrane Ab2 (Y) and then wash excess Ab2,
sheet and then activate colour reaction
Northern blot C DEVELOPMENT
Northern blot is a technique used to study gene
expression by detection of RNA (or isolated mRNA) Add
substrate
in a sample.
Southern blot
Southern blot is a method used to check for the
presence of a DNA sequence in a DNA sample.
Reprinted by permission from: Lodish H, et al. Molecular Cell Biology, 4th edition.
New York: W. H. Freeman; 2000.
262
X Xenograft
A surgical graft of tissue from one species to an unlike species (or genus or family).
Yeast artificial chromosomes
Y
Yeast artificial chromosomes (YACs) are genetically engineered chromosomes derived from the DNA of the yeast,
Saccharomyces cerevisiae, which is then ligated into a bacterial plasmid. By inserting large fragments of DNA, from
100–1000 kb, the inserted sequences can be cloned and physically mapped using a process called chromosome walking.
The primary components of a YAC are the ARS, centromere, and telomeres from S. cerevisiae. Additionally, selectable
marker genes, such as antibiotic resistance and a visible marker, are utilised to select transformed yeast cells. Without
these sequences, the chromosome will not be stable during extracellular replication, and would not be distinguishable from
colonies without the vector.
263
Acknowledgements:
We would like to thank Dr Teresa Troiani for her assistance in the selection of images; Yosef Yarden, PhD, for ideas pairing
the structure of the gene with its mechanistic network; Mr Andrea Norsa for the cover page design, which is a redesigned
image of the structure of Src, published in the ESMO flagship journal Annals of Oncology; and Dr Svetlana Jezdic, Mrs Claire
Bramley, and Keith McGregor, PhD, for their assistance in the editorial process. An online glossary prepared by the Journal of
Clinical Oncology was consulted during the revision process of the Glossary in Molecular Biology of Cancer.
264
Prepared by the
ESMO Translational
Research and Personalised
Medicine Working Group
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Prof. Andrés Cervantes-Ruiperez, MD, PhD

Prof. S. Gail Eckhardt, MD, PhD

Prof. Heinz-Josef Lenz, MD, FACP

Desamparados Roda Perez, MD

Prof. Aldo Scarpa, MD, PhD

Prof. Konstantinos Syrigos, MD, PhD

Reprinted by permission from

Reprinted by permission from

Figure 6. ABC transporters and multidrug resistance.

Reprinted by permission from Macmillan Publishers Ltd:

a Base excision repair b Mismatch repair

DNA glycosylase MSH2

A A Reprinted by permission from Macmillan Publishers Ltd:

Reprinted by permission from Macmillan

Reprinted by permission from Macmillan Publishers Ltd:

Reprinted by permission from Macmillan Publishers Ltd:

Reprinted by permission from Trends Immunol 2014; 35: 631–640.

Reprinted by permission from Macmillan

Reprinted by permission from Macmillan Publishers Ltd:

Reprinted by permission from Macmillan Publishers Ltd:

Stromal Cytochrome C: A protein present in

CpG island shore CpG island Gene body

Reprinted by permission from Macmillan Publishers Ltd:

DAG, 1,2-diacylglycerol; IP3, inositol 1,3,5-triphosphate;

Clin Cancer Res 2006; 12: 5268-5272.

Growth factors Integrins

SOS Ras SOS Pax Tal

Roman-Blas et al. Arthritis Research & Therapy 2009; 11: 241.

Reprinted by permission from Macmillan Publishers Ltd:

d Multicellular 3D invasion strands

Reprinted by permission from Macmillan Publishers Ltd:

Reprinted by permission from Carcinogenesis 2008; 29: 244-251.

The New England Journal of Medicine 2007; 357 (1): 39-51.

Drosophila Mouse embryo

BX-C ANT-C HoxB

Clin Cancer Res 2010; 16 (9): 2512-2517.

Reprinted by permission from Macmillan Publishers Ltd:

Natural killer cell Expansion

Reprinted by permission from Macmillan Publishers Ltd:

JIP, JNK-interacting protein;

Reprinted by permission from Macmillan Publishers Ltd:

GSK-3 β-catenin K-RAS MUTANT β-catenin

K-RAS INDEPENDENT CELL K-RAS DEPENDENT CELL

a Tumour angiogenesis – increased tumour growth

Tumour cell Unprocessed

b Tumour lymphangiogenesis – increased lymphatic metastasis

Stromal cell VEGFR3

Reprinted by permission from Macmillan Publishers Ltd:

TCR TGF-β Tumour

IAP family (survivin) a

A-Raf, MEKK1-4, MEKK1-4, TpI2,

MAPKK MEK1/2 MKK4/7 MKK3/6 MEK5

JNK1/2/3 p38 MAPK ERK5

Growth Inflammation Growth Source of information: Cold Spring Harb

Reprinted by permission from

Reprinted by permission from Macmillan Publishers Ltd:

Reprinted by permission from Macmillan

CD8+T cell Dendritic cell

Inf lammation Proliferation

Reprinted by permission from http://atlasgeneticsoncology.org/

Figure 6. ABC transporters and multidrug resistance.

Step 4 Patient and control DNA compete to attach, or hybridise, to

Step 6 Computer software analyses the data and generates a plot