Cancer genetics and Genomes

06-13-2014

Clinical features of human cancer

n
n

Tumor location --- liver, kidney, colon, brain, etc.

Cancer types --- carcinomas, leukemias, lymphomas
(according to the cell type from which they derive)
Tumor histology --- dysplasia, adenoma, cancer
(grade of tumor differentiation)
Tumor stage --- early, late, metastasis
(sequence of lesions)

Benign and Malignant tumor

n

benign--the neoplastic cells remain

clustered together in a single mass.
malignant-- the neoplastic cells have the
ability to invade surrounding tissue,
which implies to break loose, enter the
bloodstream or lymphatic vessels, and
form secondary tumors at other sites in
the body.

Cancer as a micro-evolutionary process

n

Cancer cells, by definition, proliferate in defiance

of normal controls and are able to invade and
colonize surrounding tissues.
Most cancers are thought to originate from a
single cell that has undergone a somatic mutation,
but the progeny of this cells must undergo further
changes, probably requiring several additional
mutations, before they become cancerous.

Changes when a cell becomes cancer cell

>

Immortalization:
indefinite growth and establishment of cell line
Immortalized cells are not tumorigenic; but are:
anchorage- and growth factor-dependent; densitydependent inhibition monolayer

>

Transformation:
deviation from normal growth requirements and
constrains; still depends on anchorage and serum
growth factors, inhibits by density

>

Metastasis: invasion of normal tissues

Genes and Cancer

Viruses
Chemicals

Heredity

Radiation

Chromosomes
Contain Long
Strings of Genes

Genetic contribution in cancer biology

n

Oncogenes and tumor suppressor genes

Immortalization and the role of telomeres

DNA damage and survival

Cellular process

The genetic basis of human cancer

n
n

Cancer is a genetic disease

Different kinds of genes have been
implicated in initiating the cancer process
(cell proliferation, contact inhibition, cell
cycle regulators, programmed cell death
machinery, repairing mutations)
Different types of mutations are
responsible for causing cancer

Inherited syndromes
predisposing to human cancer
n

Heritable tendencies to cancer have been

demonstrated in about >1% of total cancer
cases
Most of familial cancer is inherited as
autosomal dominant Mendelian traits
Other familial cancers display the inheritance
characteristics of autosomal recessive traits
(defect in DNA repair or replication)

Heredity Can Affect Many Types of Cancer

General features of hereditary cancer syndrome

n
n
n
n
n
n

Same or linked forms of cancer in two or more

close relatives
Earlier than usual cancer onset in one or more
relatives
Bilateral cancer in paired organs
Multiple primary tumors in the same individual
Specific constellation of tumors are part of
known cancer syndrome
Evidence of autosomal dominant transmission of
cancer susceptibility

Cancer-predisposition syndrome
n

It provides a unique opportunity to identify and

study genes that when dysfunctional lead to the
development of cancer
Investigations of inherited cancer genes have
contributed substantially to our understanding of
the somatic mutations present in sporadic
cancers, as well as function of cell signaling
pathways
Allelic variation and modifier genes involved in
phenotypic difference among patients

Genes associated with human Cancer

The control of cell proliferation

n

Proliferate genes -- help to promote cell growth and

the assembly of the cell-cycle control system and to
drive the cell past the G1 checkpoint

Antiproliferate genes -- help to apply the brakes that

halt the control system and cause it to be dismantled

Oncogenes
n

Definition -- the mutation in a proliferation gene

that causes its product to be over-expressed or
hyperactive results in excessive cell proliferation
characteristic of cancer

The changes from proto-oncogenes to oncogenes

have a dominant effect

These are gain-of-function mutations of protooncogenes

Many oncogenes have been tracked down by their

presence in transforming retroviruses

Viruses contribute to the current concept of cancer biology

A proto-oncogene can be made oncogenic

in many ways
n

Gene mutation --- point mutations are frequently

detected in the ras family of proto-oncogenes (K-ras,
H-ras, and N-ras in bladder carcinoma)
Gene amplification --- gene amplification refers to
the expansion in copy number of a gene within the
genome of a cell (N-myc in neuroblastoma)
Chromosome re-arrangement --- recurring
chromosomal re-arrangements are often detected in
hematologic malignancies as well as in some solid
tumors (c-abl in CML)
Insertional mutagenesis --- proviral DNA integrates
into cellular chromosomes near transcriptional
regulation sites (c-myc in ALV-induced lymphoma)

Growth factor receptor kinases can be

mutated to oncogenes
n

v-erbB: Change in N-terminal domain or C-terminal

deletion(removal of transformation inhibitory activity)

erbB2: mutation in transmembrane domain

c-fms: extracellular domain mutation, C-terminal mutation

Figure 1 EGFR signaling and related pathways

Harris, T. J. R. & McCormick, F. (2010) The molecular pathology of cancer

Nat. Rev. Clin. Oncol. doi:10.1038/nrclinonc.2010.41

Oncogenes :Mutant Forms of Proto-Oncogenes

Inactive growth factor receptor

Inactive intracellular
signaling protein

Signaling protein from active oncogene

Activated gene
regulatory protein

Transcription

Cell proliferation driven by

internal oncogene signaling

Normal Growth-Control Pathway

Growth factor
Receptor
Signaling enzymes
Transcription
factors
Cell nucleus

DNA

Cell proliferation

Oncogenes & Signal Transduction Cascades

Common features of all oncogene protein functions
Capable of triggering general changes in cell
phenotypes
Possible transformation signal transduction pathway:
Growth factors activates growth factor
receptor (tyrosine kinase) pass to Ras kinase
cascade (serine/threonine kinase) Transcription
factor(s)

Nat Rev Cancer 2011

Activation of oncogenes by chromosome translocation

Example: Translocation of Bcr-Abl Genes

9

9
(q+)

Ph
22
bcr

(22q)
bcr-abl

abl

Fusion protein
with tyrosine
kinase activity

Tumor suppressor genes

n
n

Definition -- tumor suppressor genes are

antiproliferation genes found in normal cells
The mutations in tumor suppressor genes are
usually recessive in their effects on the individual
cell
For an ordinary diploid cell both copies of a tumor
suppressor gene must be lost or inactivated to
bring about the loss of growth control
These loss-of-function mutations makes a cell
released from the normal proliferation restraints
and enabled to divide as a cancer cell

Tumor Suppressor Genes Act Like a Brake Pedal

Tumor Suppressor
Gene Proteins
Growth factor
Receptor

Signaling
enzymes
Cell nucleus

Transcription
factors
DNA

Cell proliferation

Cloned tumor suppressor genes

n
n
n
n
n
n
n
n

DNA-binding transcription factors (p53 and WT1)

Modulators of transcriptional regulation (RB, APC,
possibly BRCA1)
Inhibitor of kinases for cell-cycle progression
(p16)
Cell structural component (NF2)
Phosphatases (PTEN and MMAC1)
Potential mediator of mRNA processing (VHL)
Genes in signaling pathways ras (NF1), TGF-B
(DPC4) and hedgehog (Patched)
DNA repair and genomic stability (MSH2, MLH1,
p53, possibly BRCA1 and BRCA2)

These heritable syndromes represent natures ultimate

mutagenesis experiment and clearly establish the responsible
target genes as critical growth regulations in the
pathogenesis of specific human cancers

Familial cancer syndromes with

Mendelian inheritance
n

Autosomal dominant inheritance activated oncogene (RET, MET)

Autosomal dominant inheritance loss of a tumor-suppressor gene (RB1,

WT1, VHL, NF1, NF2, APC , etc.)

Autosomal dominant inheritance loss of DNA repair gene (TP53,

BRCA1, BRCA2, MSH2, MLH1, etc.)

Autosomal dominant inheritance interference with apoptosis (FAS,

FASL)
Autosomal recessive inheritance abnormal genome integrity (ATM,
BLM, XPB, FANCA, etc.)

DNA repair processes and links to the cell-cycle checkpoint control

Knudsons two-hit theory of carcinogenesis

n

A cell can initiate a tumor only when it contains two

damaged alleles; therefore a person who inherits one
copy of a mutant retinoblastoma gene must
experience a second, somatic mutation in one or more
retinoblasts to develop one or more retinoblastomas.
Two somatic mutations can also occur in a single
retinoblast of a non-predisposed fetus, producing
sporadic retinoblastoma

Alfred G. Knudson Jr.

Single mutation event

Two inactivating mutations

Genomic instability as the cause of tumorigenesis

Chromosomal instability

Abnormal chromosome behavior

n
n
n

An elevated spontaneous aberration frequency

An elevated level of spontaneous sister
chromatid exchanges
Clonal or recurrent stable chromosome
rearrangements

Loss of heterozygosity in human cancer

n
n

n
n

Loss of heterozygosity (LoH) occurs in all types of

solid tumors
LoH results in the cellular absence of functional
tumor suppressor gene product and in the growth
of that cell into a tumor
LoH is limited to a few specific regions of the
genome
LoH--loss of the normal functional allele at a
heterozygous locus
shared regions of loss of heterozygosity likely
reflect common mechanisms of tumorigenesis

LoH screening identifies locations of TS genes

n

applied to paired samples of DNA from

the tumors and normal tissue of patients

analogous to cytogenetic analysis

may have greater resolution

may identify parental chromosomes

Tumor suppressor mechanisms

Cancer as a complex genetic trait

Multiple genetic variants involved in cancer
susceptibility
>> nature of sequence changes for different
traits >> functional domains of the protein
n

Knowledge of genetic interactions for cancer

pathway
>> more sophisticated statistical approaches are
necessary to uncover the locations of multiple
weak susceptibility alleles
n

Cell 2002

Cancer Tends to Involve Multiple Mutations

Benign tumor cells
grow only locally and
cannot spread by
invasion or metastasis

Malignant cells invade

neighboring tissues, enter
blood vessels, and
metastasize to different sites

Time
Mutation
Cells
inactivates proliferate
suppressor
gene

Mutations
Proto-oncogenes
inactivate
mutate to
DNA repair oncogenes
genes

More mutations,
more genetic
instability,
metastatic
disease

Acquisition of somatic mutations in cancer genomes

2009 Nature

Multiple genetic changes in carcinogenesis

n

Tumor progression usually takes many years,

reflects the operation of evolution by mutation and
natural selection among somatic cells
Genetic changes lead the conversion from normal
cells to transformed cells: 6-7 events over 20-40
years
Cancer of a given type do not all have mutations in a
standard set of genes

Colorectal cancer
n Leading

cancer/Large number
(epidemiology)
n Familial vs. sporadic
n Tumorigenesis (duration and severity)
n Survival rate
n Sampling/solid tumor

90

A genetic model for tumorigenesis

n

Allelotype of colorectal carcinomas (widespread deletion,

Science 1989)

Genes involved in chromosomal instability

Multistep basis of tumorigenesis

Accumulation, rather than order, is the most important

feature of the progression of colorectal tumors

The genetic basis of colorectal cancer:

insights into critical pathways of tumorigenesis

The APC/ -catenin pathway

The DNA mismatch repair pathway

The TGF-/SMAD pathway

Additional genetic events in colorectal

tumorigenesis

Gastroenterology 2000

Familial Adenomatous Polyposis (FAP)

Hereditary Nonpolyposis Colorectal Cancer (HNPCC)

Cancer genomic era

2010 Nature

Cancer epigenomics
n

Identified a large number of genes that are hypermethylated in a tumor-specific manner

Most genes are located in chromosomal regions known to
undergo frequent loss of heterozygosity in cancers
Many genes identified encode components of pathways
that have been implicated in cancer

The dynamics of gene silencing in human cancer

Genetically mediated loss
of gene function
---no functional protein
n

Epigenetically mediated
loss of gene function
---A variable decrease in
protein production
n

Modifications in gene expression that are controlled by heritable but potentially

reversible changes in DNA methylation and/or chromatin structure
Changes to the genome that dont affect DNA sequence
Defined as nonmutational cellular information

Epigenetic and genetic interaction

in tumorigenesis
n

Epigenetic events --- promoter CpG

island hypermethylation cause gene
silencing in cancer
Genetic events --- inactivation of
tumor-suppressor genes in cancer

Genetic landmarks in cancer research

n
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Chromosomal aberrations were the cause of cancer (Boveris

predictions, 1902-1914)
Discovery of the philadelphia chromosome, t(9;22) (1960)
Knudsons two-hit hypothesis (1971)
Discovery of cellular proto-oncogenes (1976)
Activated oncogenes in tumor DNA (1979)
Identification of p53 in a complex with viral proteins (1979)
LOH mapping, cloning and identification of RB tumor-suppressor
gene (1983-1986)
The era of TP53 tumor-suppressor (1993 Molecule of the year)
Identification of APC, MSH2, BRCA1 genes (1991-1994)
Cloning of the telomerase gene (1997-1998)
Genomic era to define the complete molecular anatomy of
tumor cells (1997-present)
Post-genomic era

The development of cancer research

n

Cytogenetic techniques

Recombinant DNA technology

DNA transfection experiments

Linkage analysis/ Association

studies

Genomic techniques

From mutants gain powers

30 years on

Nat Rev Cancer 2009

Integrating functional and structural cancer genomics

Overview of cancer functional genomics

NRG 2011

From cancer genomics to personalized medicine

Figure?6 Therapeutic Targeting of the Hallmarks of Cancer Drugs that interfere with each of the acquired capabilities necessary for
tumor growth and progression have been developed and are in clinical trials or in some cases approved for clinical use in t...

The practical value of mutation analysis

n

Identification of hot-spot regions and

natural mutants is essential to define
crucial regions in an unknown protein
( negative result for large genes, sitespecific alteration, etc.)
Analysis of variations can also lead to the
definition of risk factors
( different mutations for different risks)

In the Future
n
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Significantly mutated genes

Distinguishing driver from passenger
mutations
Integrative and pathway analysis
Functional validation of significantly mutated
genes