Professional Documents
Culture Documents
Full Chapter Cancer Stem Cells Methods and Protocols Methods in Molecular Biology 2777 Papaccio PDF
Full Chapter Cancer Stem Cells Methods and Protocols Methods in Molecular Biology 2777 Papaccio PDF
https://textbookfull.com/product/cancer-cytogenetics-methods-and-
protocols-methods-in-molecular-biology-1541-desconocido/
https://textbookfull.com/product/hepatic-stem-cells-methods-and-
protocols-naoki-tanimizu/
https://textbookfull.com/product/skin-stem-cells-methods-and-
protocols-kursad-turksen/
https://textbookfull.com/product/stem-cell-renewal-and-cell-cell-
communication-methods-and-protocols-methods-in-molecular-
biology-2346-kursad-turksen-editor/
Neurobiology Methods and Protocols Methods in Molecular
Biology 2746 Sebastian Dworkin
https://textbookfull.com/product/neurobiology-methods-and-
protocols-methods-in-molecular-biology-2746-sebastian-dworkin/
https://textbookfull.com/product/xylem-methods-and-protocols-
methods-in-molecular-biology-2722-javier-agusti/
https://textbookfull.com/product/teratogenicity-testing-methods-
and-protocols-methods-in-molecular-biology-2753-luis-felix/
https://textbookfull.com/product/mucins-methods-and-protocols-
methods-in-molecular-biology-2763-1st-edition-kameyama/
https://textbookfull.com/product/computational-stem-cell-biology-
methods-and-protocols-patrick-cahan/
Methods in
Molecular Biology 2777
Federica Papaccio
Gianpaolo Papaccio Editors
Cancer
Stem Cells
Methods and Protocols
Second Edition
METHODS IN MOLECULAR BIOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, UK
Second Edition
Edited by
Federica Papaccio
Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno,
Baronissi, Italy
Gianpaolo Papaccio
Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
Editors
Federica Papaccio Gianpaolo Papaccio
Department of Medicine, Surgery and Department of Experimental Medicine
Dentistry “Scuola Medica Salernitana” University of Campania “Luigi Vanvitelli”
University of Salerno Naples, Italy
Baronissi, Italy
This Humana imprint is published by the registered company Springer Science+Business Media, LLC, part of Springer
Nature.
The registered company address is: 1 New York Plaza, New York, NY 10004, U.S.A.
This second edition of the book Cancer Stem Cells: Methods and Protocols follows the
great success of its first edition, published in 2018.
In this second edition, a great effort has been made to provide readers with all the
scientific advances in methods and protocols related to cancer stem cells. They will, there-
fore, find both the most important updated chapters from the previous edition and new
chapters on hot topics.
The aim of the book is always to try to be a comprehensive collection of all methods,
protocols, and procedures used for the identification, characterization, and selection of
cancer stem cells. The new chapters focus on the latest technologies that have improved
our knowledge in this field. Among the newly included chapters, we feature contributions
on organoids, machine learning, nanoparticles, and other recent advances.
Regarding the topics of the new chapters, we believe that organoids, in particular,
represent a great challenge, and the related techniques are of great importance for cancer
stem cells thanks to the many applications they can have. At this point, it is very important to
be rigorous and understand the difference between spheroids and organoids.
We hope that the hard work we put into producing this book will be useful to scientists
who want to read it.
v
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 Cancer Stem Cells: Current Challenges and Future Perspectives . . . . . . . . . . . . . . 1
Muhammad Vaseem Shaikh, Stefan Custers, Alisha Anand,
Petar Miletic, Chitra Venugopal, and Sheila K. Singh
2 Immunohistochemistry for Cancer Stem Cell Detection: Principles
and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Giuseppa Zannini, Renato Franco, and Federica Zito Marino
3 Isolating Cancer Stem Cells from Solid Tumors . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Vitale Del Vecchio, Marcella La Noce, and Virginia Tirino
4 Surface Markers for the Identification of Cancer Stem Cells . . . . . . . . . . . . . . . . . . 51
Tasfik Ul Haque Pronoy, Farhadul Islam, Vinod Gopalan,
and Alfred King-yin Lam
5 CD44-Based Detection of CSCs: CD44 Immunodetection
by Flow Cytometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Lornella Seeneevassen, Anissa Zaafour, and Christine Varon
6 ALDH Activity Assay: A Method for Cancer Stem Cell (CSC)
Identification and Isolation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Vitale Del Vecchio, Marcella La Noce, and Virginia Tirino
7 In Vitro Tumorigenic Assay: A Tumor Sphere Assay for Cancer
Stem Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Amani Yehya, Hisham Bahmad, and Wassim Abou-Kheir
8 Multicellular Tumoroids for Investigating Cancer Stem-Like
Cells in the Heterogeneous Tumor Microenvironment . . . . . . . . . . . . . . . . . . . . . . 99
Kathleen M. Burkhard and Geeta Mehta
9 Generation, Expansion, and Biobanking of Gastrointestinal
Patient-Derived Organoids from Tumor and Normal Tissues. . . . . . . . . . . . . . . . . 123
Manuel Cabeza-Segura, Blanca Garcia-Mico, Andrés Cervantes,
and Josefa Castillo
10 Prostate Cancer Organoids for Tumor Modeling and Drug Screening. . . . . . . . . 135
Amani Yehya, Fatima Ghamlouche, Sana Hachem, and Wassim Abou-
Kheir
11 Mimicking the Tumor Niche: Methods for Isolation, Culture,
and Characterization of Cancer Stem Cells and Multicellular Spheroids. . . . . . . . 145
Laura De Lara-Peña, Cristiano Farace, Andrea Pisano,
Julia Lopez de Andrés, Grazia Fenu, Federica Etzi,
Carmen Griñán-Lison, Juan Antonio Marchal, and Roberto Madeddu
vii
viii Contents
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Contributors
ix
x Contributors
Abstract
Despite major advances in health care including improved diagnostic tools, robust chemotherapeutic
regimens, advent of precision, adjuvant and multimodal therapies, there is a major proportion of patients
that still go on to experience tumor progression and recurrence. Cancer stem cells (CSCs) are shown to be
responsible for tumor persistence and relapse. This subpopulation of cancer cells possess normal stem
cell like traits of self-renewal, proliferation, and multilineage differentiation. Currently, they are isolated and
enriched based on the cell surface markers that can be detected and sorted through fluorescence and
magnetic-based cell sorting. In this chapter, we review the current challenges and limitations often
encountered in CSC research, including the identification of universal markers, therapy resistance, and
new drug development. Current and future perspectives are discussed to address these challenges including
utilization of cutting-edge technologies such as next-generation sequencing to elucidate the genome,
epigenome, and transcriptome on a single-cell level and genome-wide CRISPR-Cas9 screens to identify
novel pathway-based targeted therapies. Further, we discuss the future of precision medicine and the need
for the improvement of clinical trial designs.
Key words Cancer stem cells, Tumor initiating cells, Standard of care, Intratumoral heterogeneity,
Cell surface makers, Fluorescent activated cell sorting, CRISPR-Cas9 system, Single cell RNA
sequencing, Minimal residual disease.
1 Introduction
Muhammad Vaseem Shaikh and Stefan Custers contributed equally with all other contributors.
Federica Papaccio and Gianpaolo Papaccio (eds.), Cancer Stem Cells: Methods and Protocols, Methods in Molecular Biology,
vol. 2777, https://doi.org/10.1007/978-1-0716-3730-2_1,
© The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2024
1
2 Muhammad Vaseem Shaikh et al.
The concept of the CSC has progressed from being a highly specu-
lative and intensively debated concept to a fairly defined and better
understood biological entity in many tumor types, including AML,
breast, brain, colon, lung, and other cancers. Despite the advances
made in understanding CSCs, many challenges lie ahead and will be
discussed below.
2.1 The CSC CSCs by definition are a subset of tumor cells that contain both
Definition Is a self-renewal and multilineage differentiation capacities that fuel
Functional Trait Rather tumor initiation, treatment resistance, and recurrence [22]. This
than a Specific Cell definition is based on the shared functional tumor-initiation trait
among CSCs. Considering that CSC phenotypes are complex, vary
between tumors, and are affected by abnormalities arising from
neoplastic transformation, defining CSCs outside the scope of the
shared functional trait of tumor initiation can be difficult
[23]. Importantly, this functional CSC definition can make data
interpretation complex as the gold standard assay for CSC identifi-
cation is in vivo serial transplantation, a functional read-out which
can underestimate total CSC numbers and has a bias towards more
malignant CSC types. Moreover, serial implantation risks isolating
artifacts and may limit true heterogeneity of the original tumor.
Due to this limiting effect a more refined definition has been
proposed: CSCs are tumor cells that can be proven to generate
long-term progeny, either by direct engraftment or genetic
tracing [22].
2.2 Molecular Historically, CSCs have been isolated by Hoechst staining, utilizing
Markers Used to the ATP-binding cassette (ABC) transporter protein family, which
Identify the CSC Do Not was later replaced and standardized by fluorescence-activated cell
Specifically Nor sorting (FACS) based on cell surface markers. Although marker-
Uniformly Mark CSCs based CSC isolation is easier to perform, the markers used are not
always reliable, leading to challenges in CSC identification and data
interpretation [22].
First, the markers currently used do not specifically identify
CSCs, as these markers play central roles in normal stem cell biol-
ogy and are also expressed in other normal cell types. For some
markers, CSC specificity can be achieved by targeting splice var-
iants. For example, full-length CD144 is widely expressed, while
the CD44v6 splice variant is more indicative of CSCs [24–26]. The
use of marker combinations has alleviated this problem to some
extent; however, the lack of specificity remains a hurdle for reliable
CSC detection [22, 23]. On top of this, markers may have roles in
other mechanisms, which may be favorably selected for during
in vivo serial transplantation. For example, CD44, CD90, and
CD34 are involved in cell adhesion and attachment and are thus
4 Muhammad Vaseem Shaikh et al.
2.3 The Origins of One of the most debated topics of the CSC is its cell of origin.
CSCs Tumors are the result of genetic and epigenetic alterations accu-
mulated over many years. The presence of stem cell markers seems
indicative of a stem cell origin. Another possibility is that CSCs arise
from transit-amplifying/progenitor cells that increase mutational
burden during multistep tumorigenesis and introduce their
acquired mutations into corresponding stem cell pools via a process
of spontaneous dedifferentiation [23, 35, 36].
Cancer Stem Cells: Current Challenges and Future Perspectives 5
3 Future Perspectives
Fig. 1 Schematic representation of target discovery for the development of CSC-specific therapies
3.2 Genome-Wide Comprehensive genetic studies in the past two decades have
CRISPR Screens emphasized and helped us understand correlations between the
disease phenotype and the mutations seen in cancers; however,
gene editing technologies that could allow us to study the driving
forces of cancer and correct mutations in the genome were needed
to drive further breakthroughs in precision medicine. Discovery of
zinc finger nucleases (ZFNs) [60], TALE domains in transcription
activator-like effector nucleases (TALENs) [61], and CRISPR/Cas
(clustered regularly interspaced palindromic repeats/CRISPR-
associated) technology have allowed for the precise editing of the
eukaryotic genome. The CRISPR/Cas system has revolutionized
the gene editing technology due to its ability to precisely manipu-
late genes even if they are silenced or in a dense location and have
allowed for ease of design, affordability, and scalability compared to
other techniques [62, 63]. With the advent of genome-wide loss-
of-function (LOF) and gain-of-function (GOF) single-guide RNA
(sgRNA) libraries, it is now possible to screen and discover new
therapeutic vulnerabilities in CSCs.
LOF screens are carried out by using genome-wide knockdown
libraries, in the presence or absence of therapies in order to identify
the fitness genes and biological processes that make the cells resis-
tant. Shalem et al. [64] constructed a genome-wide CRISPR/Cas9
knockout library (GecKO) and employed it to mice for genes that
confer resistance to a human melanoma cell line when treated with
vemurafenib. Hart et al. [65] developed an improved CRISPR loss-
of-function library known as the Toronto KnockOut (TKO) library
targeting over 18,000 genes, identifying ~2000 fitness genes which
is 4–5 times more than RNAi screens. Chen et al. [66] employed a
genome-wide CRISPR LOF screen (mGeCKOa) comprising
67,405 sgRNAs targeting 20,611 protein-coding genes and 1175
microRNA precursors to study the evolution of cancer and metas-
tasis in a mouse model.
LOF screens have been routinely used to discover novel and
adjuvant therapeutic targets as well as studying the TIME. CRISPR
LOF screen conducted on CSCs from patient-derived colon cancer
lines identified 44 essential genes including genes involved in the
cholesterol biosynthesis pathway. The authors validated these find-
ings by demonstrating enhanced antitumor efficacy in vivo when
treated with combinatorial treatment with cholesterol biosynthesis
inhibitors and 5-FU [67]. Wei et al. [68] discovered loss of
Regnase-1 led to increased fitness in CD8 + Tcells, prolonging
their persistence and their ability to infiltrate and fight cancer
cells. Recently, CRISPR Cas9 screens carried out on GSCs
10 Muhammad Vaseem Shaikh et al.
3.3 Precision Pathway-based medicines have been developed using our deeper
Medicine understanding of cancer biology from the genomic, proteomic, and
functional data generated from CRISPR screens and single-cell
sequencing. These therapies could not only target aberrant cellular
populations but also help to spare healthy cells. Imatinib, which
targets gain-of-function mutations in the genes encoding platelet-
derived growth factor receptor-α (PDGFRα) in gastrointestinal
stromal tumors, was the first clinical success story for targeted
cancer treatment [75].
Since then, several targeted therapies have been designed
against CSCs owing to the increased clinical significance of target-
ing these functionally important cells. Hedgehog signaling pathway
expression is correlated with chemoresistance, metastatic spread,
and CSC maintenance. Hh regulates the target gene expression
through the transmembrane protein Smoothened (Smo)
[76]. Glasdegib, vismodegib, and sonidegib showed significant
Cancer Stem Cells: Current Challenges and Future Perspectives 11
[89, 90]. Based on our understanding of the TIME, over the past
decade, novel immunotherapeutic strategies such as immune
checkpoint inhibitors and CAR-T cell therapy have emerged. In a
first of its kind study, Vora et al. carried out a head-to-head com-
parison of three immunotherapeutic modalities (antibodies, bispe-
cific T cell engagers [BITEs], and CAR-T) targeting CD133 on
GSCs and found the CAR-T-based treatment modality to be most
efficacious [91]. Several immune checkpoint inhibitors including
CTLA4 (ipilimumab) [92], PD-1 (cemiplimab) [93], and PDL-1
(avelumab) [94] have been evaluated clinically in various cancers
and have shown efficacy. CD19 and CD22 CAR-T cell therapy have
shown clinical success in liquid tumors [95–97] and several trials
testing their efficacy are underway for solid tumors
(NCT02915445, NCT02465983, NCT03585764).
3.4 Clinical Trial Improved therapeutic regimens have allowed complete remission in
Design patients with most cancers and thereby improving prognosis
[98, 99]. Complete remission is defined as reduction in the tumor
burden by 99% as measured by advanced radiological techniques
(PET, CT, or MRI) [100]. However, small therapy-resistant sub-
populations of tumor cells survive aggressive treatment regimens to
drive tumor recurrence [101, 102]. These cells are traditionally
called “minimal residual disease” (MRD) [103]. Recent studies
indicate that tumor recurrence is not driven by innate mutational
mechanisms [104, 105], rather by enrichment of a small population
of cells (CSCs) that are inherently resistant to anticancer therapy
[102, 106].
There are several conceptual advantages of treating patients at
MRD rather than waiting for clinical relapse to initiate further
therapy: first, the fact that cancer which is characterized by exten-
sive ITH will be at its lowest subclonal complexity and most homo-
geneous state which would increase the likelihood of designing a
tailored drug, targeting a rare minority of CSCs enriched at MRD
[107]. Additionally, due to the decrease in tumor burden there is
also reduction in the ability of the cells to remodel the surrounding
environment, or reprogram the TIME leading to a chemoprotec-
tive milieu [108]. Moreover, at MRD patients are clinically well and
generally off SoC therapy and hence more likely to tolerate any
potential therapeutic side effects compared to being treated at
relapse [109].
Identification, characterization, validation, and developing tar-
geted therapies against MRD will allow for the development of
precision treatment modalities that would most likely improve
patient outcomes and may lead to a potential cure [110]. Unfortu-
nately, it comes with a new set of clinical and technical challenges in
sampling, especially in solid tumors wherein repeated invasive pro-
cedures would lead to patient discomfort and reduce clinical appli-
cability [111]. To overcome this situation there is a need to develop
Cancer Stem Cells: Current Challenges and Future Perspectives 13
References
11. Greaves M, Maley CC (2012) Clonal evolu- characterization of human colorectal cancer
tion in cancer. Nature 481(7381):306–313 stem cells. Proc Natl Acad Sci U S A
12. Steinbichler TB, Dudás J, Skvortsov S, 104(24):10158–10163
Ganswindt U, Riechelmann H, Skvortsova II 25. Al-Hajj M, Wicha MS, Benito-Hernandez A,
(2018) Therapy resistance mediated by cancer Morrison SJ, Clarke MF (2003) Prospective
stem cells. Semin Cancer Biol 53:156–167 identification of tumorigenic breast cancer
13. Baisiwala S, Hall RR, Saathoff MR, cells. Proc Natl Acad Sci U S A 100(7):
Shireman J, Park C, Budhiraja S et al (2020) 3983–3988
LNX1 modulates Notch1 signaling to pro- 26. Snyder EL, Bailey D, Shipitsin M, Polyak K,
mote expansion of the glioma stem cell popu- Loda M (2009) Identification of CD44v6+/
lation during Temozolomide therapy in CD24- breast carcinoma cells in primary
glioblastoma. Cancers 12(12):E3505 human tumors by quantum dot-conjugated
14. Walcher L, Kistenmacher AK, Suo H, Kitte R, antibodies. Lab Investig 89(8):857–866
Dluczek S, Strauß A et al (2020) Cancer stem 27. Kemper K, Grandela C, Medema JP (2010)
cells—origins and biomarkers: perspectives Molecular identification and targeting of
for targeted personalized therapies. Front colorectal cancer stem cells. Oncotarget
Immunol 11:1280 1(6):387–395
15. Bonnet D, Dick JE (1997) Human acute 28. Ginestier C, Hur MH, Charafe-Jauffret E,
myeloid leukemia is organized as a hierarchy Monville F, Dutcher J, Brown M et al
that originates from a primitive hematopoietic (2007) ALDH1 is a marker of normal and
cell. Nat Med 3(7):730–737 malignant human mammary stem cells and a
16. Al-Hajj M, Wicha MS, Benito-Hernandez A, predictor of poor clinical outcome. Cell Stem
Morrison SJ, Clarke MF (2003) Prospective Cell 1(5):555–567
identification of tumorigenic breast cancer 29. Deng S, Yang X, Lassus H, Liang S, Kaur S, Ye
cells. Proc Natl Acad Sci 100(7):3983–3988 Q et al (2010) Distinct expression levels and
17. Singh SK, Hawkins C, Clarke ID, Squire JA, patterns of stem cell marker, aldehyde dehy-
Bayani J, Hide T et al (2004) Identification of drogenase isoform 1 (ALDH1), in human
human brain tumour initiating cells. Nature epithelial cancers. PLoS One 5(4):e10277
432(7015):396–401 30. Ginestier C, Wicinski J, Cervera N,
18. Eramo A, Lotti F, Sette G, Pilozzi E, Monville F, Finetti P, Bertucci F et al (2009)
Biffoni M, Di Virgilio A et al (2008) Identifi- Retinoid signaling regulates breast cancer
cation and expansion of the tumorigenic lung stem cell differentiation. Cell Cycle 8(20):
cancer stem cell population. Cell Death Differ 3297–3302
15(3):504–514 31. Kemper K, Sprick MR, de Bree M,
19. Ma S, Chan KW, Hu L, Lee TKW, Wo JYH, Scopelliti A, Vermeulen L, Hoek M et al
Ng IOL et al (2007) Identification and char- (2010) The AC133 epitope, but not the
acterization of tumorigenic liver cancer stem/ CD133 protein, is lost upon cancer stem cell
progenitor cells. Gastroenterology 132(7): differentiation. Cancer Res 70(2):719–729
2542–2556 32. Mak AB, Blakely KM, Williams RA, Penttil€a
20. Li C, Heidt DG, Dalerba P, Burant CF, PA, Shukalyuk AI, Osman KT et al (2011)
Zhang L, Adsay V et al (2007) Identification CD133 protein N-glycosylation processing
of pancreatic cancer stem cells. Cancer Res contributes to cell surface recognition of the
67(3):1030–1037 primitive cell marker AC133 epitope. J Biol
21. Schatton T, Murphy GF, Frank NY, Chem 286(47):41046–41056
Yamaura K, Waaga-Gasser AM, Gasser M 33. Sun Y, Kong W, Falk A, Hu J, Zhou L, Pollard
et al (2008) Identification of cells initiating S et al (2009) CD133 (Prominin) negative
human melanomas. Nature 451(7176): human neural stem cells are clonogenic and
345–349 tripotent. PLoS One 4(5):e5498
22. Medema JP (2013) Cancer stem cells: the 34. Yi JM, Tsai HC, Glöckner SC, Lin S, Ohm JE,
challenges ahead. Nat Cell Biol 15(4): Easwaran H et al (2008) Abnormal DNA
338–344 methylation of CD133 in colorectal and glio-
23. Pattabiraman DR, Weinberg RA (2014) Tack- blastoma tumors. Cancer Res 68(19):
ling the cancer stem cells – what challenges do 8094–8103
they pose? Nat Rev Drug Discov 13(7): 35. Chaffer CL, Brueckmann I, Scheel C, Kaestli
497–512 AJ, Wiggins PA, Rodrigues LO et al (2011)
24. Dalerba P, Dylla SJ, Park IK, Liu R, Wang X, Normal and neoplastic nonstem cells can
Cho RW et al (2007) Phenotypic spontaneously convert to a stem-like state.
Cancer Stem Cells: Current Challenges and Future Perspectives 15
Proc Natl Acad Sci U S A 108(19): stem cells by high-throughput screening. Cell
7950–7955 138(4):645–659
36. Gupta PB, Fillmore CM, Jiang G, Shapira SD, 47. Farmer P, Bonnefoi H, Anderle P,
Tao K, Kuperwasser C et al (2011) Stochastic Cameron D, Wirapati P, Becette V et al
state transitions give rise to phenotypic equi- (2009) A stroma-related gene signature pre-
librium in populations of cancer cells. Cell dicts resistance to neoadjuvant chemotherapy
146(4):633–644 in breast cancer. Nat Med 15(1):68–74
37. Borovski T, Verhoeff JJC, ten Cate R, 48. Kurrey NK, Jalgaonkar SP, Joglekar AV, Gha-
Cameron K, de Vries NA, van Tellingen O nate AD, Chaskar PD, Doiphode RY et al
et al (2009) Tumor microvasculature sup- (2009) Snail and slug mediate radioresistance
ports proliferation and expansion of glioma- and chemoresistance by antagonizing
propagating cells. Int J Cancer 125(5): p53-mediated apoptosis and acquiring a
1222–1230 stem-like phenotype in ovarian cancer cells.
38. Friedmann-Morvinski D, Bushong EA, Ke E, Stem Cells 27(9):2059–2068
Soda Y, Marumoto T, Singer O et al (2012) 49. Venugopal C, Hallett R, Vora P,
Dedifferentiation of neurons and astrocytes Manoranjan B, Mahendram S, Qazi MA et al
by oncogenes can induce gliomas in mice. (2015) Pyrvinium targets CD133 in human
Science 338(6110):1080–1084 glioblastoma brain tumor–initiating cells.
39. Vermeulen L, De Sousa E, Melo F, van der Clin Cancer Res 21(23):5324–5337
Heijden M, Cameron K, de Jong JH, Bor- 50. Sica A, Allavena P, Mantovani A (2008) Can-
ovski T et al (2010) Wnt activity defines cer related inflammation: the macrophage
colon cancer stem cells and is regulated by connection. Cancer Lett 267(2):204–215
the microenvironment. Nat Cell Biol 12(5): 51. Garziera M, Roncato R, Montico M, De
468–476 Mattia E, Gagno S, Poletto E et al (2019)
40. Scheel C, Eaton EN, Li SHJ, Chaffer CL, New challenges in tumor mutation heteroge-
Reinhardt F, Kah KJ et al (2011) Paracrine neity in advanced ovarian cancer by a targeted
and autocrine signals induce and maintain next-generation sequencing (NGS) approach.
mesenchymal and stem cell states in the Cell 8(6):E584
breast. Cell 145(6):926–940 52. Sathe A, Grimes SM, Lau BT, Chen J,
41. Bruna A, Greenwood W, Le Quesne J, Suarez C, Huang RJ et al (2020) Single-cell
Teschendorff A, Miranda-Saavedra D, Rueda genomic characterization reveals the cellular
OM et al (2012) TGFβ induces the formation reprogramming of the gastric tumor microen-
of tumour-initiating cells in claudinlow breast vironment. Clin Cancer Res 26(11):
cancer. Nat Commun 3(1):1055 2640–2653
42. Chen J, Li Y, Yu TS, McKay RM, Burns DK, 53. Sun G, Li Z, Rong D, Zhang H, Shi X, Yang
Kernie SG et al (2012) A restricted cell popu- W et al (2021) Single-cell RNA sequencing in
lation propagates glioblastoma growth after cancer: applications, advances, and emerging
chemotherapy. Nature 488(7412):522–526 challenges. Mol Ther Oncolytics 21:183–206
43. Roesch A, Fukunaga-Kalabis M, Schmidt EC, 54. Tang F, Barbacioru C, Wang Y, Nordman E,
Zabierowski SE, Brafford PA, Vultur A et al Lee C, Xu N et al (2009) mRNA-Seq whole-
(2010) A temporarily distinct subpopulation transcriptome analysis of a single cell. Nat
of slow-cycling melanoma cells is required for Methods 6(5):377–382
continuous tumor growth. Cell 141(4): 55. Navin N, Kendall J, Troge J, Andrews P,
583–594 Rodgers L, McIndoo J et al (2011) Tumour
44. Grimm M, Krimmel M, Polligkeit J, evolution inferred by single-cell sequencing.
Alexander D, Munz A, Kluba S et al (2012) Nature 472(7341):90–94
ABCB5 expression and cancer stem cell 56. Aceto N, Bardia A, Miyamoto DT, Donald-
hypothesis in oral squamous cell carcinoma. son MC, Wittner BS, Spencer JA et al (2014)
Eur J Cancer 48(17):3186–3197 Circulating tumor cell clusters are oligoclonal
45. Moitra K, Lou H, Dean M (2011) Multidrug precursors of breast cancer metastasis. Cell
efflux pumps and cancer stem cells: insights 158(5):1110–1122
into multidrug resistance and therapeutic 57. Lei B, Zhang XY, Zhou JP, Mu GN, Li YW,
development. Clin Pharmacol Ther 89(4): Zhang YX et al (2016) Transcriptome
491–502 sequencing of HER2-positive breast cancer
46. Gupta PB, Onder TT, Jiang G, Tao K, stem cells identifies potential prognostic
Kuperwasser C, Weinberg RA et al (2009) marker. Tumour Biol 37(11):14757–14764
Identification of selective inhibitors of cancer
16 Muhammad Vaseem Shaikh et al.
58. Chung W, Eum HH, Lee HO, Lee KM, Lee CRISPR–Cas9 screen identifies ifenprodil as
HB, Kim KT et al (2017) Single-cell RNA-seq an adjunct to sorafenib for liver cancer treat-
enables comprehensive tumour and immune ment. Cancer Res 81(24):6219–6232
cell profiling in primary breast cancer. Nat 71. Decker CE, Young T, Pasnikowski E, Chiu J,
Commun 8:15081 Song H, Wei Y et al (2019) Genome-scale
59. Zhang K, Erkan EP, Jamalzadeh S, Dai J, CRISPR activation screen uncovers tumor-
Andersson N, Kaipio K et al (2022) Longitu- intrinsic modulators of CD3 bispecific anti-
dinal single-cell RNA-seq analysis reveals body efficacy. Sci Rep 9(1):20068
stress-promoted chemoresistance in meta- 72. Joung J, Kirchgatterer PC, Singh A, Cho JH,
static ovarian cancer. Sci Adv 8(8):eabm1831 Nety SP, Larson RC et al (2022) CRISPR
60. Bibikova M, Beumer K, Trautman JK, Carroll activation screen identifies BCL-2 proteins
D (2003) Enhancing gene targeting with and B3GNT2 as drivers of cancer resistance
designed zinc finger nucleases. Science to T cell-mediated cytotoxicity. Nat Commun
300(5620):764–764 13(1):1606
61. Boch J, Scholze H, Schornack S, Landgraf A, 73. Wang D, Prager BC, Gimple RC, Aguilar B,
Hahn S, Kay S et al (2009) Breaking the code Alizadeh D, Tang H et al (2021) CRISPR
of DNA binding specificity of TAL-type III screening of CAR T cells and cancer stem
effectors. Science 326(5959):1509–1512 cells reveals critical dependencies for cell-
62. Knight SC, Xie L, Deng W, Guglielmi B, Wit- based therapies. Cancer Discov 11(5):
kowsky LB, Bosanac L et al (2015) Dynamics 1192–1211
of CRISPR-Cas9 genome interrogation in liv- 74. Ramaker RC, Hardigan AA, Gordon ER,
ing cells. Science 350(6262):823–826 Wright CA, Myers RM, Cooper SJ (2021)
63. Zhang F, Wen Y, Guo X (2014) CRISPR/ Pooled CRISPR screening in pancreatic can-
Cas9 for genome editing: progress, implica- cer cells implicates co-repressor complexes as a
tions and challenges. Hum Mol Genet 23 cause of multiple drug resistance via regula-
(R1):R40–R46 tion of epithelial-to-mesenchymal transition.
64. Shalem O, Sanjana NE, Hartenian E, Shi X, BMC Cancer 21(1):632
Scott DA, Mikkelson T et al (2014) Genome- 75. Dagher R, Cohen M, Williams G,
scale CRISPR-Cas9 knockout screening in Rothmann M, Gobburu J, Robbie G et al
human cells. Science 343(6166):84–87 (2002) Approval summary: imatinib mesylate
65. Hart T, Chandrashekhar M, Aregger M, in the treatment of metastatic and/or unre-
Steinhart Z, Brown KR, MacLeod G et al sectable malignant gastrointestinal stromal
(2015) High-resolution CRISPR screens tumors. Clin Cancer Res 8(10):3034–3038
reveal fitness genes and genotype-specific can- 76. Zhao Y, Tong C, Jiang J (2007) Hedgehog
cer liabilities. Cell 163(6):1515–1526 regulates smoothened activity by inducing a
66. Chen S, Sanjana NE, Zheng K, Shalem O, conformational switch. Nature 450(7167):
Lee K, Shi X et al (2015) Genome-wide 252–258
CRISPR screen in a mouse model of tumor 77. Sekulic A, Migden MR, Oro AE, Dirix L,
growth and metastasis. Cell 160(6): Lewis KD, Hainsworth JD et al (2012) Effi-
1246–1260 cacy and safety of vismodegib in advanced
67. Gao S, Soares F, Wang S, Wong CC, Chen H, basal-cell carcinoma. N Engl J Med 366(23):
Yang Z et al (2021) CRISPR screens identify 2171–2179
cholesterol biosynthesis as a therapeutic target 78. Norsworthy KJ, By K, Subramaniam S,
on stemness and drug resistance of colon can- Zhuang L, Del Valle PL, Przepiorka D et al
cer. Oncogene 40(48):6601–6613 (2019) FDA approval summary: glasdegib for
68. Wei J, Long L, Zheng W, Dhungana Y, Lim newly diagnosed acute myeloid leukemia. Clin
SA, Guy C et al (2019) Targeting REGNASE- Cancer Res 25(20):6021–6025
1 programs long-lived effector T cells for can- 79. Quail DF, Taylor MJ, Postovit LM (2012)
cer therapy. Nature 576(7787):471–476 Microenvironmental regulation of cancer
69. MacLeod G, Bozek DA, Rajakulendran N, stem cell phenotypes. Curr Stem Cell Res
Monteiro V, Ahmadi M, Steinhart Z et al Ther 7(3):197–216
(2019) Genome-wide CRISPR-Cas9 screens 80. Hoffman LM, Fouladi M, Olson J, Daryani
expose genetic vulnerabilities and mechanisms VM, Stewart CF, Wetmore C et al (2015)
of Temozolomide sensitivity in glioblastoma Phase I trial of weekly MK-0752 in children
stem cells. Cell Rep 27(3):971–986.e9 with refractory central nervous system malig-
70. Xu F, Tong M, Tong CSW, Chan BKC, Chu nancies: a pediatric brain tumor consortium
HY, Wong TL et al (2021) A combinatorial study. Childs Nerv Syst 31(8):1283–1289
Cancer Stem Cells: Current Challenges and Future Perspectives 17
Every limb and member of the body is made for some good
purpose.
The eye is made to see with; the ear is made to hear with; the
nose is made to smell with; the mouth is made to eat and speak with.
The feet are made to run and walk with; the hands are made to
work with, to write with, and to do many other things.
But do you think children’s hands were ever made to strike their
brothers, or sisters, or playmates? Were your little hands ever made
to snatch away things from each other?
Who gave you hands? God gave them. Did he give you hands to
steal with? Did God give you hands that you might throw stones at
geese, or dogs, or hens, or cows, or any other innocent animals?
Did God give you hands to injure or wound any of the creatures
he has made?
Take care of your little hands, then, my children! Take care that
the hands God has given, do nothing that God disapproves.
Nuts to Crack.
“What are you writing such a thundering big hand for, Patrick?”
“Why, do you see, my grandmother is deaf, and I am writing a loud
lether to her.”
1.D. The copyright laws of the place where you are located also
govern what you can do with this work. Copyright laws in most
countries are in a constant state of change. If you are outside
the United States, check the laws of your country in addition to
the terms of this agreement before downloading, copying,
displaying, performing, distributing or creating derivative works
based on this work or any other Project Gutenberg™ work. The
Foundation makes no representations concerning the copyright
status of any work in any country other than the United States.
1.E.6. You may convert to and distribute this work in any binary,
compressed, marked up, nonproprietary or proprietary form,
including any word processing or hypertext form. However, if
you provide access to or distribute copies of a Project
Gutenberg™ work in a format other than “Plain Vanilla ASCII” or
other format used in the official version posted on the official
Project Gutenberg™ website (www.gutenberg.org), you must, at
no additional cost, fee or expense to the user, provide a copy, a
means of exporting a copy, or a means of obtaining a copy upon
request, of the work in its original “Plain Vanilla ASCII” or other
form. Any alternate format must include the full Project
Gutenberg™ License as specified in paragraph 1.E.1.
• You pay a royalty fee of 20% of the gross profits you derive from
the use of Project Gutenberg™ works calculated using the
method you already use to calculate your applicable taxes. The
fee is owed to the owner of the Project Gutenberg™ trademark,
but he has agreed to donate royalties under this paragraph to
the Project Gutenberg Literary Archive Foundation. Royalty
payments must be paid within 60 days following each date on
which you prepare (or are legally required to prepare) your
periodic tax returns. Royalty payments should be clearly marked
as such and sent to the Project Gutenberg Literary Archive
Foundation at the address specified in Section 4, “Information