Cancer Genetics

Q603
Spring 2014
 Objectives
• Understand that cancer is a genetic disease and a multistep
process.

• Know the types of genes associated with cancer.

• Know fundamentals about cancer pathogenesis, including the

concepts of: oncogene action/activation; the mode(s) of
disease pathogenesis associated with tumor suppressor genes
(e.g., two hit); and, other phenomenon such as microsatellite
instability and the potential role of epigenetics in cancer.

• Know features of the specific disorders discussed in class.

• Understand issues (e.g., ethical) related to genetic testing for

cancer.
 Cancer is a heterogeneous
disease
that will claim more than
560,000
lives in our country this year.
 Cancer is a genetic disease.
• All cancers involve genetic changes

• In addition to genes, there are other

predisposing factors such as
– Infection (virus)
– Radiation
– Carcinogens
– Immunological defects
 Cancer Genes

• Most gene mutations in cancer occur in

somatic cells and are acquired

• However, some mutations do occur in the

germline and may be inherited and passed
on to future generations.
some have high penetrance, others don’t
– Return to concept of mutations that predestine,
predispose or increase susceptibility
Hereditary/familial predisposition for cancer

Br ca, dx 50

Br ca, dx 42 Pr ca, dx 60 Ov ca, dx 58

Br ca, dx 35 Br ca, dx 45

Some families show autosomal dominant inheritance

 Features suggesting an inherited
predisposition to cancer:

• Two or more close relatives affected.

• Early age of onset.
• Cancers of a specific type occurring together
more often than you’d expect by chance
(e.g., breast and ovary).
• Multiple or bilateral cancers occurring in one
person. ∴ probably a genetic factor underlying cancer
 Cancer is a multistep process and is
clonal in nature Like text fig 16-2

numerous hits push the cell towards malignancy

Hits can include both genetic and environmental factors

Genetic factors include mutations in individual genes as well
as chromosomal/cytogenetic changes.
Although a cytogenetic change(s) may sometimes be an early
hit, cytogenetic changes are often acquired as later events in
the evolution to cancer and in progression of disease.
 Mutation types in human cancer
mostly somatic, some germline
or a combo

SOMATIC
MUTATIONS

Futreal et al., 2004

 Chromosomal abnormalities and cancer formation

• Acquired somatic mutations

in a cell line, early in progression
• Represent clonal abnormalities
additional mutations may occur
to a small part of the cell lines

Mullighan et al., 2008

searching for an association of chromosomal abnormalities w/ therapy or prognosis of certain

types of cancer.
Cancer cytogenetics is a field built upon identification of
nonrandom (recurring) chromosome abnormalities in cancer.
 Considerations for Cancer Cytogenetics
can study cytogenetics w/o stimulating division (w/o adding
• Culturing: mitogens)
– no mitogens added
– short-term cultures (24 hr-72 hr)
in the lab mixtures of cells are studied/kept

• Analysis:
– heterogeneous populations
(normal, abnormal cells)
compared to normal
• Tumor chromosomes: poor morphology, more condensed,
fewer bands are visible (normal cells have optimal banding)
Constitutional vs. Cancer Abnormalities
Constitutional karyogram
bands normal
Constitutional vs. Cancer Abnormalities
Cancer karyogram shorter chromosomes, bands
are closer together

loss of 2 excess chrom 3

 Cytogenetic Definitions
• CLONE
A cell population derived from a single progenitor. Two cells
with the same structural rearrangement or additional chromosome,
or three cells with loss of the same chromosome
as cell divides, there are additional changes

• MODAL NUMBER
The most common chromosome number in a tumor population
count the number of chromosomes from numerous tumors

Diploid – 46 chromosomes
Hypodiploid – <46 chromosomes
Near Haploid – close to 23 chromosomes
Hyperdiploid – >46 chromosomes
High Hyperdiploid – ≥55 chromosomes
Pseudodiploid – 46 chromosomes with structural abnormalities
 Cytogenetic Definitions

• STEM LINE (sl)

The most basic clone of a tumor cell population (listed first)

• SIDE LINE begin w/ primary defect then sidelines develop

Subclones derived from the stem line

Cytogenetically related clones are presented in the order of

increased complexity, irrespective of the size of the clone
Example of cancer cytogenetic nomenclature
Stem line (sl) Side line

=stem line
46,XY,t(9;22)(q34;q11.2) 47,XY,t(9;22)(q34;q11.2),+8,i(17)(q10)
translocation of 9 & 22 written as
stem line has this chromosomal
abnormality 47,sl,+8,i(17)(q10)
 Genes involved with controlling
cell proliferation and cell death

Categories / classes of genes

– Oncogenes
– Tumor suppressor genes
– DNA repair/metabolism genes
– Other
balance between cell proliferation & death in normal development

Apoptosis

Text fig 16-1

 Cell Cycle and Checkpoints

numerous checkpoints in
cell cycle where proliferation
can be stopped & DNA
repaired
 Oncogenes
• Dominantly acting gene(s) involved in up-regulating cell growth
and prolifieration
– Identified because of their ability to cause transformation
(promote tumors/cancer) promote tumor development
• Oncogenes are normal genes (proto-oncogenes) that have gone
awry (e.g., become activated)
• Proto-oncogenes: Normal genes involved in some aspect of cell
division or proliferation
normal gene=proto-oncogene

• Growth factors Growth factor receptors

• Signal transduction molecules Nuclear proteins
• Transcriptional regulation Cell cycle related

can interact w/ each other

Oncogenes may act synergistically
 Transformation

genes can act in a dominant way to

promote tumor development.
DNA was extracted from tumors and put into
mouse cells, leading them to grow into foci
rather than a nice monolayer.
Transformed foci put into a mouse led to
tumors in mice ∴ something in DNA was promoting
tumor development (oncogenes)
Oncogenes are dominant at
the cellular level.
Proto-oncogene activation to oncogene
how do proto-oncogenes drive cell proliferation?

Gain of function mutations

• Change in protein structure
– Point mutation (e.g., Ras)
– Hybrid (fusion) proteins
» E.g., Philadelphia chromosome translocation in CML
• Change in expression (levels or site)
– Viral (retroviral) insertion
– Gene Amplification
– Translocation

Mutations in oncogenes are often acquired during the

progression to malignancy. they’re not the first thing starting off
 Normal activation of Ras by receptor tyrosine kinase
Ras is a gene that can be activated to form an oncogene

RAS is responding to signaling molecule that

activates tyrosine kinase. Activation of RAS via GTP (inactive form bound to GDP) makes
RAS a signalling molecule that promotes proliferation.
 E.g., Ras point mutation
Active Ras is bound to GTP—drives cell signaling/proliferation. Normally it’s inactivated by
the cell and goes to a GDP bound Ras. In caner, mutations can occur in RAS (single mutation)
that prevents it from being
inactivated as readily and RAS
is “stuck on”

Activation of an oncogene
via point mutation

Mutations in one of three human RAS genes (K-RAS, H-

RAS or N-RAS) are found in 10-15% of all human cancers
locking RAS in an active state. Dominant ∴ just one hit necessary (p53 requires loss of
both b/c it’s recessive)
 Cytogenetically visible features
another way to activate an oncogene HSRs
• Gene amplification
– May be seen as
• Double minutes (small accessory chromosomes)
• Homogeneously staining regions (HSRs)
chrom. w/ arrows have homogenous
– May result in region where part of DNA was amplified
many times and it contains a proto-oncogene
• Increased gene (proto-oncogene) expression

• Chromosomal translocations
changing a proto-oncogene to
– Often in leukemias an oncogene
 Burkitt lymphoma
• B-cell tumor of the jaw (Most common tumor in
children in equatorial Africa, rare elsewhere)
• Translocations & chromosomal rearrangements driving cell proliferation &
tumor growth
– Myc proto-oncogene, 8q24 Myc on chrom. 8
t(8;14) [Also t(8;22) and t(2;8)] translocations between 8 & 14
or * and 22 or 2&8
– Immunoglobulin genes these chromosomes contain Ig genes, as a result
of translocation, myc is activated
Chromosomes: 2 (kappa light), 14 (heavy chain),
22 (lambda light).

Activation of myc as a result of the

translocation
 Burkitt Lymphoma

Ig gene cluster which has

a nearby enhancer that
promotes Ig proliferation
in b-cells
Enhancer

translocation of myc
to area nearby enhancer
drives proliferation of myc
“derivative 8”
bottom of 8 was put onto bottom of 14, ∴ myc overexpression
and part of 14 was put onto 8.
14, 2, and 22 all have
enhancers by Ig gene
 Chronic myelogenous leukemia
(CML, Clinical case #8)

• Philadelphia chromosome translocation t(9;22) in

90-95% of cases ∴ low locus heterogeneity
proto-
– 9q - abl oncogene
– 22q - BCR (breakpoint cluster region)
• Results in a chimeric protein - ABL at carboxy end
net result is a chimeric
protein produced that
• Increased tyrosine kinase activity has ⇑ tyrosine kinase
activity of ABL protein,
∴ driving proliferation
• Other leukemias have a variety of translocations.
• E.g., Acute lymphocytic leukemia (ALL), t(9;22)
in 10-15% of cases
 some ALL
CML normal 22 w/ BCR BCR: breakpoint
cluster region

normal 9 w/ abl proto-oncogene

on end
in middle of BCR, there’s an exchange w/
chrom 9 ∴ abl brought in

Chimeric gene

Chimeric protein
contains part of BCR and
part of ABL
translocation of 22 onto
9
BCR ABL
Text fig 16-4 Philadelphia chromosome ∴ ⇑ activity of tyrosine
kinase/ABL driving prolif.
 tx of CML is based on knowledge of philadelphia chromosome & chimeric protein
Gleevec, the first specific anti-cancer drug based on a known molecular mechanism

hybrid protein that binds w/ ATP and phosphorylates

target (part of signaling cascade)

Gleevec binds to chimeric protein and blocks

BCR-ABl from phosphorylating substrate
 Amplification

Presence of multiple copies (amplification) of

some proto-oncogenes has been associated
with poor prognosis
(e.g., nmyc in some neuroblastomas).
 HER2/NEU gene
gene (proto-oncogene) was
• Initially identified through DNA transfection studies.
• Epidermal growth factor receptor-like protein.
• Gene is most commonly affected by amplification /
over expression.
• Primary tumors - node-negative breast cancer.
Patients with amplification / over expression of NEU,
have worse prognosis than patients who do not.
∴ test for NEU
– Also may be evaluated in other cancers such as gastric. amplification
– We will return to breast cancer again later in grading/tx

• Herceptin/Trastuzumab (monoclonal antibody) used to

treat HER2-positive tumors. Can increase survival but
cancer may develop resistance. can knock down degree of her w/
herceptin
oncogenes exist in different regions and can interact w/ each other to promote tumor proliferation

Oncogenes may act synergistically

 Inherited mutations in oncogenes
are not common but can occur
usually occur later in progression towards cancer

• Multiple endocrine neoplasia (MEN) type 2.

– Autosomal Dominant (thyroid carcinoma)
– RET proto-oncogene (tyrosine kinase receptor)
– Mutation leads to constitutive kinase activity gain of function
– (Loss of function RET mutations - Hirschsprung disease)
loss of function

• Hereditary papillary renal carcinoma (HPRC).

– Autosomal Dominant
– MET tyrosine kinase receptor gene
– HPRC mutations activate kinase in absence of ligand
∴ “stuck on” in signaling cascade
 Telomeres and Telomerase
• Telomeres
• Ends of chromosomes contain multiple Text copies of
tandemly repeated sequence (TTAGGG)n that is needed
for normal chromosome function / cell division.
helps provide stability and ensure normal function during cell division
• Length tends to decline / shorten with age. Decreases
by about 100 bp per replication. length is maintained by telomerase

• Telomerase
• Needed to maintain structure / length of telomeres.
• Expression of telomerase reappears and/or is
maintained in tumors.
in cells that are proliferating more than they should, telomerase level
comes back up (in cells where they don’t divide much, telomerase levels are normally
lowered)
lomerase is required to maintain the end of chromosome during DNA replic
(Telomeres shorten in each cell division and causes senescence. Many types of cancer have
elevated levels of telomerase, thus increasing the replicative potential of the cell)
telomerase maintain end of chromosomes,
numerous divisions w/ out telomerase leads
to shorter chromosomes eventually into
nothing. Telomerase levels are ⇑ in cancer
cells, ⇑ their reproductive potential
 Tumor suppressor genes
• Normally block abnormal growth and malignant
transformation.
unlike oncogenes,
• Mutations are recessive at the cellular level.
– Two hit theory > Alfred Knudson
(retinoblastoma)
• Mutations can act as dominants at the organismal
level. person has inherited one mutant gene
• Concept of loss of heterozygosity (LOH).
• Many examples. We will only discuss some.
 Retinoblastoma
(Clinical case #34)

• Retinal tumors
• 1/23,000 live births
• Most common eye tumor in
early childhood
• May begin forming prenatally
• Average age of onset 18
months
• Can be inherited as autosomal
dominant trait
• Treat - removal of orbit Text fig C-34
Text fig 16-5
 Retinoblastoma (cont.)
• 40% inherited, 60% sporadic
– 10% of all patients have a history of affected family members
– inherited forms from affected/carrier parent (usually high
penetrance, e.g., null alleles) or germline mutation
one eye • Most new germline mutations are on the paternal allele
• Unilateral (70% of patients) vs bilateral (30% of patients)
both eyes involved
– if bilateral, likely inherited (less likely to be sporadic)
– but, 15% of unilateral have germline mutation
• Unifocal vs multifocal same idea—multiple tumors in same eye of independent
origin more likely to be genetic origin
• Onset age early more likely to be inherited
• Patients have increased risk of other cancers / tumors
– E.g., osteosarcoma —RB mutations also have ⇑ risk for osteosarcoma
 “Two hit hypothesis”

homozygote wild-type heterozygote—one wild-type, one abnormal allele

2nd hit, wipes out one normal allele

multifocal or bilateral disease b/c

more cells are primed for a first hit

unifocal/unilateral more likely

more likely to be later onset b/c two hits have to take place (∴ more
time necessary for hits to occur)
 Comparison of Mendelian
and sporadic forms of
cancers
all are starting (See text fig 16-6)
out as heterozygotes,
second hit led to development
of tumor
 Loss of Heterozygosity (LOH)
• Loss of a normal allele from a region of one
(Definition from text)
chromosome of a pair, allowing a defective allele on the
homologous chromosome to be clinically manifest. A feature of
many cases of retinoblastoma, breast cancer, and other tumors
due to mutation in a tumor-suppressor gene.
• Represents the mutation, inactivation or loss of the remaining wild-type
allele of tumor suppressor gene.
LOH
• Also used to refer to a laboratory analysis of the mechanism of
the second hit . (Remember the discussion of Absence of
heterozygosity and SNP arrays in the Cytogenetics lecture.)
to have LOH, must start out as a heterozygote and one goes away. Some of these lab LOHO
tests are actually Absence of heterozygosity tests
• Loss of heterozygosity can result in loss of a flanking or
intragenic marker.
• Searching for LOH in tumors has been a way to identify the
existence of tumor-suppressor genes.
 Types of Second Hits
marker
what patient
started out with
vs derived/somatic
genotype
diff forms
of LOH copy neutral—normal
number is there but duplication
of mutant chromosome

LOH for RB but not recomb put loss of normal chrom. and only normal chrom
for markers 1 & rb on chrom2 copies of mutant copies is gone

homologues may
mutant rb ∴ no LOH for rb
pair w/ each other &
supression and for flanking marke
recombine
Not LOH for distal Loss of Heterozygosity (LOH) for rb and also for distal
marker(s) marker(s)
Modified text fig 16-7
begin with this then look for evidence of LOH for markers
 normal tumor

person presents w/ tumors and you look

keep heterozygosity
for markers along chromosome in normal
of distal markers
and tumor cells don’t begin w/ heterozygote
mutation—both wild type
LOH of distal marker in first three mechanisms
 Retinoblastoma gene/protein
(RB1)
• Tumor suppressor on chromosome 13
• Protein located primarily in nucleus
• Involved with transcriptional control
• Transgenic mice mutant for Rb die in mid
gestation with defects in erythroposiesis,
cell cycle control and apoptosis ∴ RB is important for cell
cycle control
• RB1 phosphorylation status is important
 RB is a tumor supressor—helps shut down
cell cycle
Retinoblastoma protein (RB) is a negative regulator of cell cycle
RB interacts w/ transcription factor,
Active G1-cdk
holding them tight to prevent them RB can be overridden by activating G1-cyclin
from going onto S. dep. kinase Inactive RB, after cell is
Active RB in
resting cell phosphorylate Rb committed to progression
protein and blocks binding to TF
P" P"
P" P"

Transcription factor (TF)

TF is then allowed to
help transcribe genes
coactivator Transcription of genes important
for cell cycle progression

DNA

TF-binding site
Cyclins (e.g., CYCD1) and cyclin-
dependent kinases (e.g. CDK4)
Phosphorylation of Rb causes it cyclins phosphorylate Rb
to dissociate from other proteins
and allows transcription of
genes to promote cell division

RB blocking
Transcription factors

in a normal cell cycle, RB is then

dephosphorylated and it goes back to
blocking TF
 Some other tumor suppressor genes

Tumor suppressors act at

various locations in cells

other tumor suppresor genes

p16 also acts in nucleus
 • Normally, p16 inhibits the phosphorylation of Rb
by CDK.
• Since phosphorylation of Rb promotes cell
division, p16 inhibition of Rb phosphorylation tumor suppressor gene p16
inhibits cell division (i.e., p16 acts as a tumor blocks cyclin dependent phosphorylation
suppressor). of Rb, allowing it to block cell cycle
• If p16 is missing, Rb is more readily
phosphorylated, thus promoting cell division.

removing p16 allows more phosphorylation

of RB by Cyclin & CDK
 Inactivating mutations of RB and p16 are
commonly found in different cancers
may inherit a mutation in RB or it can happen later
G1 to S transition of cell cycle

a
phosphorylate c
t
RB, shutting it down i
v
e

gene transcription
factor

∴ RB dissociated from TF
 LiFraumeni Syndrome (LFS)
• Cancer families
• History of various types of cancer including soft
tissue sarcomas, breast cancer, brain cancer,
osteosarcoma, leukemia and other neoplasms at an
unusually early age. were caused by mutations of p53

• p53 protein - tumor suppressor gene (TP53)

Inherited mutations in LFS families.
Somatic mutations often in cancer.
Loss of activity relieves a normal block to cell
growth. loss of maintaining block on RB
 p53 / TP53
• Chromosome 17 LOH

• One of the most commonly mutated genes in

human cancer
– E.g., many mutations in colorectal cancer.

• Multiple factor interaction

– E.g., cervical cancer risk associated with human
papillomavirus (HPV).
– If both circumstances are present, p53 mutation
and HPV, the cancer is more aggressive.
 p53 function
**
• DNA-binding protein - Important in cellular response to
DNA damage. Activates transcription of genes that stop
cell division to allow repair of DNA damage. Also
induces apoptosis in cells with irreparable DNA damage.

• DNA damage - if w.t. p53, cells arrest at G1/S checkpoint

if p53 absent, cells not arrested ∴ division continues
(loss of p53 function probably adds to somatic instability of tumors)

TX: • Therapeutics - Tumor cells that regain p53 activity may

be more susceptible to radiation and/or chemotherapy.
cells will go to apoptosis following radiation rather than continuing
to divide

p53 normally in an inactive state.
Damage of DNA leads to activation
of p53 via phosphorylation.
active p53 binds to promoter
region of p21 gene, leading
to production of p21
p21 acts like p16, shuts
down cyclin & CDK—helps
stop cycle
 Apoptosis

—helps anti-apoptotic
activity as well (prevents
senesence) Text fig 16-1
 Neurofibromatosis (Revisited, Types I and II)
Autosomal dominant neurocutaneous pleiotropic syndromes –
tumors and malformations involving the skin and nervous system

Type I: (Most common, Clinical case #29)

– Peripheral Neurofibromatosis or
von Recklinhausen Disease cafe-au-lait, lisch nodules
– Mutation of NF1 gene (encodes
neurofibromin a GTPase
activator)
• Negative regulator of Ras,
Over 500 different mutations
Neurofibromin acts as a
– About 50% are new (de novo)tumor suppressor
mutations b/c it helps shut down RAS
• ~ 80% of de novo are (which promotes cell
paternal (no apparent age proliferation)
effect)
both alleles are inactivated in some patients
Biallelic inactivation of NF1 has been demonstrated in NF1-associated tumors.
(E.g., in Schwann cells or astrocytes)
 NF Type 2 (NF2)

• Central or Acoustic Neurofibromatosis

• Less Common – 1/40,000-50,000
• Clinical features
– Café-au-lait spots (70%) bilateral acoustic neuromas &
multiple meningiomas
– No Lisch nodules **
– Neurofibromas (70%)
– Range of tumors
– Bilateral acoustic schwannomas (acoustic neuromas) CN VIII
• Almost pathognomonic for NF2

• Mutation in NF2 gene

– Merlin / schwannomin diff names for gene
– Tumor suppressor helps regulate progression through cell cycle
– Loss of contact inhibition and cell cycle control
NF2 Schwannomas

Wikipedia

Medscape
 Breast cancer
(Clinical case # 5)

• Breast cancer is a common disorder

• Lifetime risk is ~ 1 in 8.
• 180,000 new cases each year
90% • Sporadic - no family history

10%
• Familial - clustering of cases with or without obvious
Mendelian (e.g., AD) inheritance or early onset
viewed as a multifactorial
– Risk ↑ 3X if one 1o relative affected disorder (even if gene
o
– Risk ↑ 10X if more than one 1 relative affected not identified)
– Risk ↑ if relative has early onset (e.g., < 40y) or bilateral disease

• Perhaps 5 - 10% with mutation in a major gene

• 20% may have a significant genetic component
that has not been identified yet
much of it is unknown

not identified
familial cause
 Breast Cancer

• Two major susceptibility genes, BRCA1

and BRCA2 have been identified.

• Mutations in these genes account for 3-5%

of all breast cancers.
 Breast cancer genes
– BRCA1 (most common cause) (over 1000 mutations)
• Accounts for about 1/2 of familial, Auto Dom cases
• Gene on chromosome 17
• Most mutations frameshift or nonsense
function of protein is significantly knocked out
w/ these mutations
– BRCA2
• Accounts for about 1/3 of familial, Auto Dom cases
• Gene on chromosome 13
• Many mutations missense loss of function of protein w/ these mutations

– BRCA1 and BRCA2

• Involved with genomic stability (e.g., response to d.s. breaks)

– p53 and others can also cause breast cancer (LiFraumeneis has breast cancer)

– Locus Heterogeneity
similar phenotypes due to mutations at 2 or more loci/genes
 Breast ca. risk Ovarian ca. risk
by age 70 by age 70
(Pop risk 10-12%) (Pop risk 1-2%)

BRCA1 In AD families In AD families

this data had an ascertainment vs 10-12% vs 1-2% in
50-85% in gen pop. 15-45% gen pop.
bias b/c those studied were
ones w/ worse cancer Not ↑ male risk
(case-control study)

BRCA2 In families In families

50-85% 10-20%
Male carriers, 6% risk
* BRCA2 – ca. 10-20% of all male breast ca.

In population screen for BRCA1 or BRCA2 carriers, the risk for

breast cancer by age 70 is 45-60%.

Ashkenazi Jews (1/40 carriers): BRCA1: 185del AG, 5382insC - BRCA2: 6174delT
 Colorectal cancer (CRC)

• General lifetime population risk for

colorectal cancer in US is ~ 2-5%
• 150,000+ new cases per year in US - 15%
of cancer
• 57,000 deaths each year
• Most, 65-85%, of colorectal cancer is
sporadic
Etiology of Colorectal Cancer
A small proportion of colorectal cancer is due
to Familial adenomatous polyposis (FAP)
and a subvariant Gardner syndrome.

Familial adenomatous polyposis (FAP)

(Clincal case # 13)
– Also known as Adenomatous polyposis coli (APC).
– Autosomal dominant.
– Heterozygotes develop numerous adenomatous
(benign) polyps in the first two decades of life.
– In almost all cases, one or more polyps becomes
malignant.
– Treat by surgical removal of colon.*
– Relatives/carriers examined by periodic
colonoscopy.
 Text Clinical
Case Study

APC gene produces a protein that

helps drive β-catenin towards degradation.
In absence of APC, β catenin binds
transcription factors and drives cell
proliferation.
∴ APC blocks cell proliferation

APC gene
Tumor
suppressor

Text fig 16-11

 Order of loss: AK-53
K-

loss of blocakade of β catenin

In Individuals without FAP but with adenomatous polyps (sporadic) ,

Nearly 70% have loss of both APC genes in tumor

Text fig 16-13

 HNPCC
Hereditary Non-polyposis Colon Cancer
(Clinical case #19)
AD mutation fo DNA mismatch repair genes. ~80% progress to CRC. Proximal colon is
always involved

• First describe in 1913 by Alfred Warthin, who

identified a clustering of predominantly stomach
and endometrial cancers in the family of his
seamstress (family G).

• Fifty years later, HNPCC was characterized

further by Henry Lynch, as Lynch syndrome.
 HNPCC
• HNPCC accounts for 5-10% of all colorectal cancer (CRC)
– Autosomal dominant
– Increased colorectal cancer risk (80% penetrance)
– Early onset CRC (average age 40-45 years)
Average age in general population 64 yrs early onset suggests inherited
form
– Increased incidence of endometrial and ovarian cancer
– Also increased risk for tumors of:
• Stomach, small intestine, ovary, kidney, brain glioblastoma,
other …
 Amsterdam Criteria
For identifying HNPCC families

(high-risk candidates for molecular genetic testing)

• 3 relatives with CRC.

– 2 of the relatives are first degree

• Two successive generations

• 1 case ofearly
CRC onset
before 50 years of age.
 HNPCC Genetics
caused by Mutations in DNA mismatch repair genes

MSH2 MSH6 MLH1 MLH3 PMS1 PMS2

• Inherit one mutant allele and mutation / LOH of second allele

Second-hit hypothesis
•
** Mutations lead to ineffective DNA repair and microsatellite
instability (MSI).
• Mutations in the MLH1 and MSH2 genes increase the risk
of CRC to 70-82% before the age of 70, as compared to the
general population risk of 2-5%.
• Mutations in the MLH1 and MSH2 genes are associated with
an approximately 42-60% risk of endometrial cancer before the
age of 70.
MSH2—caretaker genes
 Apoptosis

important in maintaining
genomic stability

Text fig 16-1

 Microsatellites and Instability
• Microsatellites important in HNPCC

– Short sequences of DNA repeated in tandem (e.g.,

10-50 times) that vary from individual to individual.
– Are useful as polymorphic markers.
– Stably inherited, low inherent mutation rate.
∴ used in paternal testing, forensics studies

• Microsatellite instability (MSI)

– With defective DNA repair, there is failure to
recognize/repair mismatches and errors occur, resulting
in expansion or contraction of the size of
microsatellites. size of repeat elements change in somatic cells due
to defective DNA repair
 Microsatellite Instability (MSI)
• Found in tumors, not normal tissue.
• Characterized by expansion or contraction of short, repeated DNA
sequences.
• Found in >90% of tumors of patients with HNPCC.
• Found in approximately 15% of sporadic colorectal cancers.
N=normal, T=tumor

2 bands
in normal
tissue=2
chrom.

more
bands
tumors have here
other bands show
up—MSI
Text fig 16-12 due to changes in sizes of microsatellites
 Xeroderma pigmentosum (XP)
(Clinical case # 43)

Classic Autosomal Recessive

Predisposition to cancer and other problems
There are different types - complementation groups
Defective DNA repair

Features common among different forms

Skin involvement, ocular involvement

Heterogeneity
XP with and without CNS degeneration
20% with neurological signs
Frequency: 1 x 10-6 (10X higher Japan, Egypt)

Consanguinity in about 30% of cases

b/c AR
Median onset of symptoms: 1-2 years Text fig C-43
 XP clinical features (cont.)

Skin: Abnormal reaction to sun in most

Severe sunburn, blistering, persistent erythema after
minimal exposure, freckles by age 2
Premalignant lesions
Skin cancer of various types - median onset 8 yrs;
50 yrs younger than general population;
~30 yr reduction in survival (70% survival to age 40)
Skin cancer 2000X greater than in the general
population for patients under 20 yrs.
20X increase in frequency of internal neoplasms

Ocular: photophobia, neoplasms, etc.

Neurologic: progressive deterioration, sensorineural deafness.

Some with early onset.
keep kids out of sun
Defective
DNA
Repair
inability to repair thymidine
dimers in DNA secondary
to UV damage

Protect from
sun exposure!
 Studies with cell-fusion experiments helped to identify
the different types / complementation groups of XP
—became genes

two patients w/ disease. Take

cells from each patient and
fuse together. If patients had
same underlying defect, fusing
them together wouldn’t fix
DNA. If there was a difference,
A+B heterokaryon (combo)
could repair DNA—the two
complemented each other

If A+B Heterokaryon could repair DNA, it

indicated the patients were from different
complementation groups. Implied the existence
of different repair genes.
 DNA Repair
diff complementation groups represent different genes that are important in DNA repair

• The repair pathways are complex and errors at different points

in the pathway may cause the same or similar diseases.

• Many proteins are necessary for DNA repair the clinical

picture may become quite complex.

• Errors in DNA repair can lead to CNS degeneration, immune

deficiency, anemia, skin manifestations, etc.

• XP: Caused by mutations that affect global genome repair or

postreplication repair.

• Cockayne syndrome: A related disorder caused by mutations

that affect transcription coupled repair (TCR).
 Complementation Groups
originally defined by cel fusion studies

XPA DNA damage recognition complementation groups

represent distinct groups
XPB DNA unwinding, 3 -5 helicase that are important in repa

XPC DNA damage recognition

XPD DNA unwinding, 5 -3 helicase
don’t memorize
all. maybe. XPE DNA damage recognition, UV-damaged DNA
XPF Endonuclease, makes 5 incision
XPG Endonuclease, makes 3 incision
XPV DNA synthesis

CSA Transcription coupled repair

CSB Transcription coupled repair
Model for
Nucleotide
Excision
Repair

XPC—protein important in
letting cell recognize original
DNA damage.
In transcription coupled repair,
DNA damage recognition occurs overlap in this section
simultaneously w/ transcription
and uses cockayne syndrome
protein
Gene expression changes and cancer

associated w/ Many diff kinds of cancer

 Epigenetics
Cancer cells show changes of epigenetic marks in their genome

• Global DNA hypomethylation you’re losing methylation in a global sense

– In both benign and malignant neoplasms

– Typically at repetitive sequences (satellite or pericentromeric)
• May add to genomic instability
• May lead to activation of oncogenes or retrotransposons
• May lead to loss of imprinting (LOI) methylation is also important in imprinting
– E.g., LOI of the IGF2/H19 region seen in about 40% of colorectal
cancer oncogenes drive cell-proliferation,
methylation shuts genes down ∴ hypomethalation
of oncogenes/retrotransposons helps drive proliferation
• Hypermethylation
– Tends to be focal at CpG islands some regions show ⇑ methylation
– E.g., Promoter silencing of tumor suppressor genes by
hypermethylation hypermethylation of tumor suppressor gene shuts
it off ∴ it no longer shuts down cell proliferation
(so you can mutate TS genes, delete it, or shut it off)
DNA and epigenetic changes that inactivate tumor-suppressor genes

tumor suppressor gene

is mutated, deleted, or
shut off
Increase in genetic instability/mutation !!
Changes in gene expression !!
 Overview

Malignant transformation is often

a multistep process

A single cancer may involve many

different genes locus heterogeneity &
allelic heterogeneity

A single gene may be involved in

more than one type of cancer
phenotypic heterogeneity
 Obstacles to Widespread DNA Testing for Familial
Cancer Syndromes

can find a mutation but in many cases you don’t know what it’s
going to do

_______________

eg mutation may not lead to 100% risk (mutations w/

incomplete penetrance)

GINA
 Ethical and Social
• Principles
– Respect for Individual Autonomy
• Right of individual for self determination and to control
• This requires that the physician provide sufficient information
to allow the individual to make an informed judgment
– Beneficence
• Doing good for the patient
– Avoid Maleficence
• Do no harm
– Justice
• Ensure that all individuals are treated fairly

• Dilemmas in Medical Genetics

– Genetic Testing
– Privacy of Genetic Information
– Misuse of Genetic Information
– Genetic Screening
• (E.g., Population screening)
 Case 1 - Breast and ovarian cancer

• 36-year old female with strong family history of breast and ovarian
cancer. Her older sister has a 2 bp deletion in BRCA.
• After education/counseling the proband elects to be tested and is
found to have the same mutation as her sister.
• She is deeply concerned and after extensive discussion elects
bilateral prophylactic mastectomy followed a year later by removal
of her ovaries.
• Her 32-year-old sister elects to not undergo testing, fearful of losing
her health insurance if found to be positive.
• Other family members including the proband are deeply concerned
and pressure the physician to talk some sense into her .
 Case 2- APC colon cancer
• Couple and three children (under 18) come for counseling.
• Family history of colon cancer on the father s side indicative of
familial polyposis coli.
• Linkage analysis shows disease in family traveling with B
allele of APC.
• With full informed consent, testing (by linkage analysis) is
carried out on the three children.
– Two children received normal APC allele
– Third child, high likelihood of different father
• Separately, the mother admits the child could have had a
different father but pleads with clinic staff to keep this
confidential.
• Staff simply informed the family that the father s APC
mutation had not been passed on to any children.
 Case 3 – HNPCC colon cancer
• Asymptomatic 25 yr old woman with family history of
colon and endometrial cancer suggestive of HNPCC.
• In a research protocol, a mutation is found in the MSH2
gene in the family.
• She wishes to know her status and after extensive
education about possible outcomes, she is tested and found
to carry the mutation.
• She has an MBA and six months later interviews with and
receives a tentative offer of employment with a major
company.
• She reports her family history in a pre-employment health
survey and the company contacts her physician who copies
and sends her mutation results to the company.
• The employment director withdraws the offer. before GINA,
doesn’t happen
anymore
Indiana Familial Cancer Clinic

Genetic Services for Familial Cancer

Cancer Net:
http://cancernet.nci.nih.gov/
END