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Lecture 7
Cancer Genetics and
Genomics

Cancer is not a single disease, it is used to describe
the more virulent forms of neoplasia, a disease
process characterized by uncontrolled cellular
proliferation leading to a mass or tumor (neoplasm).
 For a neoplasm to be a cancer, however, it must also
be malignant, which means its growth is no longer
controlled and the tumor is capable of progression by
(1) invading neighboring tissues, (2) spreading
(metastasizing) to more distant sites, or both.
 Tumors that do not invade or metastasize are not
cancerous but are referred to as benign tumors.

There are three main forms of cancer:
– sarcomas, in which the tumor has arisen in
mesenchymal tissue, such as bone, muscle, or
connective tissue, or in nervous system tissue;
– carcinomas, which originate in epithelial
tissue, such as the cells lining the intestine,
bronchi, or mammary ducts; and
– hematopoietic and lymphoid malignant
neoplasms, such as leukemia and lymphoma,
which spread throughout the bone marrow,
lymphatic system, and peripheral blood.

Within each of the major groups, tumors are
classified by site, tissue type, histological
appearance, and degree of malignancy.
GENETIC BASIS OF CANCER
 Neoplasia is an abnormal accumulation of
cells that occurs because of an imbalance
between cellular proliferation and cellular
attrition.
 Cells proliferate as they pass through the
cell cycle and undergo mitosis. Attrition,
due to programmed cell death, removes
cells from a tissue.
The Genetic Basis of Cancer
Regardless of whether a cancer occurs
sporadically in an individual, as a result of
somatic mutation, or repeatedly in many
individuals in a family as a hereditary trait,
cancer is a genetic disease.
Genes in which mutations cause cancer fall
into two distinct categories: oncogenes and
tumor-suppressor genes (TSGs). TSGs in
turn are either "gatekeepers" or
"caretakers".
 An oncogene is a mutant allele of a protooncogene, a class of normal cellular proteincoding genes that promote growth and survival of
cells.
 Oncogenes facilitate malignant transformation by
stimulating proliferation or inhibiting apoptosis.
 Oncogenes encode proteins such as:
– proteins in signaling pathways for cell proliferation
– transcription factors that control the expression of
growth-promoting genes
– inhibitors of programmed cell death machinery
 Gatekeeper TSGs control cell growth.
Gatekeeper genes block tumor development by
regulating the transition of cells through
checkpoints ("gates") in the cell cycle or by
promoting programmed cell death and, thereby,
controlling cell division and survival.
 Loss-of-function mutations of gatekeeper genes
lead to uncontrolled cell accumulation. Gatekeeper
TSGs encode:
– regulators of various cell-cycle checkpoints
– mediators of programmed cell death
Caretaker TSGs protect the integrity of the
genome. Loss of function of caretaker genes
permits mutations to accumulate in
oncogenes and gatekeeper genes, which, in
concert, go on to initiate and promote
cancer. Caretaker TSGs encode:
– proteins responsible for detecting and repairing
mutations
– proteins involved in normal chromosome
disjunction during mitosis
– components of programmed cell death
machinery
 Tumor initiation. Different types of genetic
alterations are responsible for initiating cancer.
These include mutations such as:
– activating or gain-of-function mutations, including gene
amplification, point mutations, and promoter mutations,
that turn one allele of a proto-oncogene into an
oncogene
– ectopic and heterochronic mutations of protooncogenes
– chromosome translocations that cause misexpression
of genes or create chimeric genes encoding proteins
with novel functional properties
– loss of function of both alleles, or a dominant negative
mutation of one allele, of TSGs.

Tumor progression. Once initiated, a cancer
progresses by accumulating additional genetic
damage, through mutations or epigenetic
silencing, of caretaker genes that encode the
machinery that repairs damaged DNA and
maintains cytogenetic normality.
 A further consequence of genetic damage is
altered expression of genes that promote
vascularization and the spread of the tumor
through local invasion and distant metastasis.

Some tumor-suppressor genes directly regulate proto-oncogene
function (gatekeepers); others act more indirectly by maintaining
genome integrity and correcting mutations during DNA replication
and cell division (caretakers). Activation of an antiapoptotic gene
allows excessive accumulation of cells, whereas loss of function of
apoptotic genes has the same effect. Activation of oncogenes or
antiapoptotic genes is dominant. Mutations in tumor-suppressor genes
are recessive; when both alleles are mutated or inactivated, cell
growth is unregulated or genomic integrity is compromised. Loss of
pro-apoptotic genes may occur through loss of both alleles or through
a dominant negative mutation in one allele.

The development of cancer (oncogenesis) results
from mutations in one or more of the vast array of
genes that regulate cell growth and programmed cell
death.
 When cancer occurs as part of a hereditary cancer
syndrome, the initial cancer-causing mutation is
inherited through the germline and is therefore
already present in every cell of the body.
 Most cancers, however, are sporadic because the
mutations occur in a single somatic cell, which then
divides and proceeds to develop into the cancer.
 It is not surprising that somatic mutations can cause
cancer. Large numbers of cell divisions are required
to produce an adult organism of an estimated 1014
cells from a single-cell zygote.
Given a frequency of 10-10 replication errors per base
of DNA per cell division, and an estimated 1015 cell
divisions during the lifetime of an adult, replication
errors alone result in thousands of new DNA
mutations in the genome in every cell of the organism.
 Genome and chromosome mutations add to the
mutational burden.
 The genes mutated in cancer are not inherently more
mutable than other genes. Many mutations doubtlessly
occur in somatic cells and cause one cell among many
to lose function or die, but they have no phenotypic
effects because the loss of one cell is masked by the
vast majority of healthy cells in an organ or tissue.
 What distinguishes oncogenic mutations is that, by
their very nature, they allow even one mutant cell to
develop into a life-threatening disease.

Micro-RNA genes

The catalogue of genes involved in cancer also
includes genes that are transcribed into noncoding
RNAs from which regulatory microRNAs
(miRNAs) are generated.
 There are at least 250 miRNAs in the human
genome that carry out RNA-mediated inhibition of
the expression of their target protein-coding genes,
either by inducing the degradation of their targets'
mRNAs or by blocking their translation.
 Approximately 10% of miRNAs have been found to
be either greatly overexpressed or down-regulated in
various tumors, and are referred to as oncomirs.

One example is the 100-fold overexpression of the
miRNA miR-21 in glioblastoma multiforme, a
highly malignant form of brain cancer.
 Overexpression of some miRNAs can suppress the
expression of tumor-suppressor gene targets,
whereas loss of function of other miRNAs may
allow overexpression of the oncogenes they
regulate.
 Since each miRNA may regulate as many as 200
different gene targets, overexpression or loss of
function of miRNAs may have widespread
oncogenic effects because many genes will be
dysregulated.
Initiation and Progression of Cancer

Once it is initiated, a cancer progresses by
accumulating additional genetic damage
through mutations in caretaker genes
encoding the cellular machinery that repairs
damaged DNA and maintains cytogenetic
normality.
 Damage to these genes produces an everwidening cascade of mutations in an
increasing assortment of the genes that
control cellular proliferation and repair
DNA damage.

In this way, the original clone of neoplastic
cells serves as a reservoir of genetically
unstable cells, referred to as cancer stem
cells. These give rise to multiple
sublineages of varying degrees of
malignancy, each carrying a set of
mutations that are different from but overlap
with mutations carried in other sublineages.
 In this sense, cancer is fundamentally a
"genetic" disease, and mutations are central
to its etiology and progression.

A paradigm for the development of cancer, as
illustrated in Figure 16-2, provides a useful
conceptual framework for considering the role
of genetic changes in cancer.
 It is a general model that probably applies to
many if not most cancers, although it is best
elucidated in the case of colon cancer.

Figure 16-2. Stages in the evolution of cancer. Increasing degrees
of abnormality are associated with sequential loss of tumorsuppressor genes from several chromosomes and activation of
proto-oncogenes, with or without a concomitant defect in DNA
repair. Multiple lineages carrying somewhat different mutational
spectra and epigenetic changes are likely, particularly once
metastatic disease appears.
Cancer in Families

Many forms of cancer have a higher
incidence in relatives of patients than in the
general population.
 Most prominent among these familial forms
of cancer are the nearly 50 mendelian
hereditary cancer syndromes in which the
risk of cancer is very high and the
approximately 100 additional mendelian
disorders listed in Online Inheritance in
Man that predispose to cancer.

Extensive epidemiological studies have shown,
however, that some families have an above-average
risk of cancer even in the absence of an obvious
mendelian inheritance pattern.
 For example, an increased incidence of cancer, in
the range of 2- to 3-fold, has been observed in firstdegree relatives of probands with most forms of
cancer, which suggests that many cancers are
complex traits resulting from both genetic and
environmental factors.
 Thus, a family history of cancer in multiple firstdegree or second-degree relatives of a patient
should arouse the physician's suspicion of increased
cancer risk in the patient.

Although individuals with a hereditary cancer
syndrome represent probably less than 5% of all
patients with cancer, identification of a genetic basis
for their disease has great importance both for clinical
management of these families and for understanding
cancer in general.
 First, the relatives of individuals with strong
hereditary predispositions, which are most often due
to mutations in a single gene, can be offered testing
and counseling to provide appropriate reassurance or
more intensive monitoring and therapy, depending on
the results of testing.
 Second, as is the case with many common diseases,
understanding the hereditary forms of the disease
provides crucial insights into disease mechanisms that
go far beyond the rare hereditary forms themselves.
ONCOGENES
 An oncogene is a mutant gene whose altered
function or expression results in abnormal
stimulation of cell division and proliferation.
 The mutation can be an activating gain-of-function
mutation in the coding sequence of the oncogene
itself, a mutation in its regulatory elements, or an
increase in its genomic copy number, leading to
unregulated heterochronic or ectopic function of
the oncogene product.
 Oncogenes have a dominant effect at the cellular
level; that is, when it is activated or
overexpressed, a single mutant allele is sufficient
to initiate the change in phenotype of a cell from
normal to malignant.

Activated oncogenes encode proteins that act in
many steps in the pathway that controls cell
growth, including growth factors that stimulate
cell division, the receptors and cytoplasmic
proteins that transduce these signals, the
transcription factors that respond to the
transduced signals, and the proteins that
counteract programmed cell death (apoptosis).

Fig 16-3. Mechanisms of
tumorigenesis by
oncogenes of various
classes. Unregulated
growth factor signaling
may be due to mutations
in genes encoding
growth factors
themselves (1), their
receptors (2), or
intracellular signaling
pathways (3).
Downstream targets of
growth factors include
transcription factors (4),
whose expression may
become unregulated.
Both telomerase (5) and
antiapoptotic proteins
that act at the
mitochondria (6) may
interfere with cell death
and lead to
tumorigenesis.
Table 16-1. Mechanisms of Activation of Proto-oncogenes
Mechanism
Type of Gene Activated
Result
Regulatory mutation
Growth factor genes
Increased expression
Structural mutation
Growth factor receptors,
signal-transducing proteins
Allows autonomy of
expression
Translocation, retroviral
insertion, gene amplification
Transcription factors
Overexpression
Regulatory mutation,
Oncomirs
translocation, retroviral insertion
Overexpression, downregulates tumor-suppressor
genes
Deletion, inactivating mutation
Loss of expression, upregulates oncogenes
Oncomirs
TUMOR-SUPPRESSOR GENES

Whereas the proteins encoded by oncogenes
promote cancer, mutations in tumor-suppressor
genes (TSGs) contribute to malignancy by a
different mechanism, that is, through loss of
function of both alleles of the gene.
 TSGs are highly heterogeneous. Some truly
suppress tumors by regulating the cell cycle or
causing growth inhibition by cell-cell contact;
TSGs of this type are gatekeepers because they
regulate cell growth directly.

Other TSGs, the caretakers, are involved in
repairing DNA damage and maintaining
genomic integrity. Loss of both alleles of
genes that are involved in repairing DNA
damage or chromosome breakage leads to
cancer indirectly by allowing additional
secondary mutations to accumulate either in
proto-oncogenes or in other TSGs.
Table 16-3. Selected Tumor-Suppressor Genes
Gene
Gene product and possible
function sporadic
Gatekeepers
DISORDERS IN WHICH THE GENE IS
AFFECTED
Familial
Sporadic
RB1
p110
Cell cycle regulation
Retinoblastoma
Retinoblastoma, small
cell lung carcinomas,
breast cancer
TP53
p53
Cell cycle regulation
Li-Fraumeni
syndrome
Lung cancer, breast
cancer, many others
DCC
Dcc-receptor
Decreases cell survival in the
absence of survival signal from its
netrin ligands
None known
Colorectal cancer
VHL
Vhl
Forms part of a cytoplasmic
destruction complex with APC that
normally inhibits induction of
blood vessel growth when oxygen
is present
von HippelLindau syndrome
Clear cell renal
carcinoma
Gene
Gene product and
possible function
sporadic
Caretakers
DISORDERS IN WHICH THE GENE IS
AFFECTED
Familial
Sporadic
BRCA1,
BRCA2
Brca1, Brca2
Chromosome repair in
response to doublestranded DNA breaks
Familial breast
and ovarian
cancer
Breast cancer, ovarian
cancer
MLH1,
MSH2
Mlh1, Msh2
Repair nucleotide
mismatches between
strands of DNA
Hereditary
nonpolyposis
colon cancer
Colorectal cancer
The Two-Hit Origin of Cancer

The existence of TSG mutations leading to cancer
was originally proposed in the 1960s to explain
why certain tumors can occur in both hereditary
and sporadic forms.
 For example, it was suggested that the hereditary
form of the childhood cancer retinoblastoma
might be initiated when a cell in a person
heterozygous for a germline mutation in a tumorsuppressor retinoblastoma gene, required to
prevent the development of the cancer, undergoes
a second, somatic event that inactivates the other
allele.

As a consequence of this second somatic event,
the cell loses function of both alleles, giving rise
to a tumor. The second hit is most often a somatic
mutation, although loss of function without
mutation, such as occurs with transcriptional
silencing, has also been observed in some cancer
cells.
 In the sporadic form of retinoblastoma, both
alleles are also inactivated, but in this case, the
inactivation results from two somatic events
occurring in the same cell.

The "two-hit" model is now widely accepted as
the explanation for many familial cancers besides
retinoblastoma, including familial polyposis coli,
familial breast cancer, neurofibromatosis type 1
(NF1), hereditary nonpolyposis colon carcinoma,
and a rare form of familial cancer known as LiFraumeni syndrome.
 In all of these syndromes, the second hit is often
but not always a mutation.
 Silencing due to epigenetic changes such as DNA
methylation, associated with a closed chromatin
configuration and loss of accessibility of the DNA
to transcription factors, is another important,
alternative molecular mechanism for loss of
function of a TSG.

Because an alteration in gene function due to
methylation is stably transmitted through mitosis,
it behaves like a mutation; because there is no
change in the DNA itself, however, the alteration
is referred to as an epigenetic rather than a genetic
change.
 Epigenetic silencing of gene expression is a
normal phenomenon that explains such widely
diverse phenomena as X inactivation, genomic
imprinting, and regulation of a specialized
repertoire of gene expression in the development
and maintenance of differentiation of specific
tissues.
Gatekeeper Tumor-Suppressor Genes in
Autosomal Dominant Cancer Syndromes
Retinoblastoma
 Retinoblastoma, the prototype of diseases caused
by mutation in a TSG, is a rare malignant tumor of
the retina in infants, with an incidence of about 1
in 20,000 births.
 Diagnosis of a retinoblastoma must usually be
followed by removal of the affected eye, although
smaller tumors, diagnosed at an early stage, can be
treated by local therapy so that vision can be
preserved.

About 40% of cases of retinoblastoma are of the
heritable form, in which the child inherits one mutant
allele at the retinoblastoma locus (RB1) through the
germline.
 A somatic mutation or other alteration in a single
retinal cell leads to loss of function of the remaining
normal allele, thus initiating development of a tumor.
 The disorder is inherited as a dominant trait because
the large number of primordial retinoblasts and their
rapid rate of proliferation make it very likely that a
somatic mutation will occur in one or more of the
more than 106 retinoblasts.

Since the chance of the second hit in the heritable
form is so great, the hit occurs frequently in more
than one cell, and thus heterozygotes for the
disorder are often affected with multiple tumors,
often affecting both eyes.
 On the other hand, the occurrence of the second
hit is a matter of chance and does not occur 100%
of the time; the penetrance of retinoblastoma,
therefore, although high, is not complete.

The other 60% of cases of retinoblastoma are
nonheritable (sporadic); in these cases, both RB1
alleles in a single retinal cell have been inactivated
independently.
 Because two hits in the same cell is a rare event,
there is usually only a single clonal tumor and the
retinoblastoma is found in one eye only.
 Although sporadic retinoblastoma usually occurs
in one place in one eye only, 15% of patients with
unilateral retinoblastoma have the heritable type
but by chance develop a tumor in only one eye.
 Another difference between hereditary and
sporadic tumors is that the average age at onset of
the sporadic form is in early childhood, later than
in infants with the heritable form.

Figure 16-5
Retinoblastoma
in a young girl,
showing as a
white reflex in
the affected eye
when light
reflects directly
off the tumor
surface.
Loss of Heterozygosity

Geneticists studying DNA polymorphisms in the
region close to the RB1 locus made an unusual but
highly significant genetic discovery when they
analyzed the alleles seen in tumor tissue from
retinoblastoma patients.
 Individuals with retinoblastoma who were
heterozygous at polymorphic loci near RB1 in
normal tissues, such as in their white blood cells,
had tumors that contained alleles from only one of
their two chromosome 13 homologues, revealing a
loss of heterozygosity (LOH) in the region of the
gene.

In familial cases, the retained chromosome
13 markers were the ones inherited from the
affected parent, that is, the one with the
abnormal RB1 allele. Thus, LOH
represented the second hit of the remaining
allele.
 LOH may occur by interstitial deletion, but
there are other mechanisms, such as mitotic
recombination or nondisjunction.
 LOH is the most common mutational
mechanism by which the function of the
remaining normal RB1 allele is disrupted in
heterozygotes.

When LOH is not seen, the second hit is
usually a second somatic gene mutation or,
occasionally, transcriptional inactivation of
a nonmutated allele through methylation.
 LOH is a feature of a number of other
tumors, both heritable and sporadic, and is
often considered evidence for the existence
of a TSG, even when that gene is unknown.

Figure 16-6 Comparison of mendelian and sporadic
forms of cancers such as retinoblastoma and familial
polyposis of the colon.

Figure 16-7 Chromosomal mechanisms that could lead to identical
DNA markers at or near a tumor-suppressor gene in an individual
heterozygous for an inherited germline mutation. The figure depicts
the events that constitute the "second hit" that leads to retinoblastoma.
Local events such as mutation, gene conversion, or transcriptional
silencing, however, could cause loss of function of both RB1 genes
without producing LOH. + is the normal allele, rb the mutant allele.

The RB1 gene maps to chromosome 13, in
band 13q14. In a small percentage of
patients with retinoblastoma, the first
mutation is a cytogenetically detectable
deletion or translocation of this portion of
chromosome 13.
 Such chromosomal changes, if they also
disrupt genes adjacent to RB1, may lead to
dysmorphic features in addition to
retinoblastoma.
Li-Fraumeni syndrome

There are rare "cancer families" in which there is a
striking history of many different forms of cancer
(including several kinds of bone and soft tissue
sarcoma, breast cancer, brain tumors, leukemia,
and adrenocortical carcinoma), affecting a number
of family members at an unusually early age,
inherited in an autosomal dominant pattern.
 This highly variable phenotype is known as the
Li-Fraumeni syndrome (LFS). Because the TSG
TP53, encoding the protein p53, is inactivated in
the sporadic forms of many of the cancers found
in LFS, TP53 was considered a candidate for the
gene defective in LFS.

DNA analysis of several families with LFS has
now confirmed this hypothesis; affected members
in more than 70% of families with LFS carry a
mutant form of the TP53 gene as a germline
mutation.
 As seen also in retinoblastoma, one of the two
mutations necessary to inactivate the TP53 gene is
present in the germline in familial LFS, whereas in
many sporadic cancers, both mutations are
somatic events.

Figure 16-8 A pedigree of the Li-Fraumeni
syndrome, in which breast cancer, sarcomas,
and other malignant tumors have occurred.
Ages at diagnosis are shown.

The p53 protein is a DNA-binding protein that
appears to be an important component of the
cellular response to DNA damage.
 In addition to being a transcription factor that
activates the transcription of genes that stop cell
division and allow repair of DNA damage, p53
also appears to be involved in inducing apoptosis
in cells that have experienced irreparable DNA
damage.
 Loss of p53 function, therefore, allows cells with
damaged DNA to survive and divide, thereby
propagating potentially oncogenic mutations. The
TP53 gene can therefore be considered to also be a
gatekeeper TSG.