Medical genetics
Cancer Genetics
Yongbo Wang（王勇波）
2014-12-26
Department of Cellular and Genetic Medicine,
School of Basic Medical Sciences, Fudan University
Outline
1. What Is Cancer?

Introduction of the basic concepts
2. What Causes Cancer?

Genetic underpinnings of cancer

Three types of Cancer Critical Genes

Cancer initiation and progression
3. How to Prevent and Diagnose Cancer?
Utilization the knowledge we learned from
cancer genetics

1. What Is Cancer?
Cancer is the most virulent disease and soon becoming the
leading cause of death worldwide: as many as ca. 1 in 3
individuals develop cancer and 1 in 4 will die of it.

(Percentage of all deaths due to five leading causes of death by year: United States,
1935–2010.)
http://www.cdc.gov/nchs/data/databriefs/db88.htm
An abnormal cell that grows and proliferates out of
control will give rise to tumor or neoplasm.

Benign: as long as the tumor cells do not become
invasive;

Malignant: tumor cells have acquired the ability to
invade surrounding tissues.


A tumor is considered a cancer only if it is malignant.
Metastasis: spread of malignant tumor cells
throughout the body (typically through the blood and
lymphatic system)

There are a large variety types of cancer which are
classified according to the tissue and cell type from which
they derive: carcinoma (arising from epithelial cells), sarcoma
(from connective tissue or muscle cells), leukemia and
lymphoma (from hemopoietic cells), cancers derived from
cells of nervous system etc.

(About 80% of human cancers)
Example: development of cancer of the epithelium of
the uterine cervix
Benign
Malignant
Adapted from Molecular Biology of the Cell 5th edition
Cancer originating from different origin are, in general, very
different diseases.

Incidence and mortality of different cancers in the United States. Data from American Cancer Society , 2004.
Adapted from Molecular Biology of the Cell 5th edition
Part 1 summary
1). The basic concepts
 Benign and malignant tumor
 Cancer cells reproduce without restraint and colonize
other tissues
2). Cancer is a very complex and virulent
disease
 Cancer is becoming the leading cause of death
worldwide.
 There are large variety kinds of cancer which can be
classified by their tissue or cell origin.
 Different types of cancer can be considered as very
different disease.
2. What Causes Cancer?
• Chemical Exposure
– Behavior (Tobacco smoke -> lung cancer)
– Environmental (polychlorinated biphenyl, (PCBs))
– Occupational (coal tar, asbestos, aniline dye)
– Diet (aflatoxin -> liver cancer)
• Radiation (UV -> xeroderma pigmentosum, ionizing)
• Infection
– Viruses (Epstein–Barr virus (EBV) -> lymphoma, hepatitis
B -> liver cancer, papilloma -> cervical cancer etc)
• Inherited familial cancer syndromes
• Mutations and/or chromosomal abnormalities
Most, if not all, of these causes have their genetic
underpinning linked with cancer.
Aflatoxin B can directly reacting with on DNA and
induce mutations

- Is a toxin from mold that grows on grain and peanuts when
stored in humid tropical conditions;
- and a contributory cause of live cancer in the tropics with a
characteristic mutations in TP53.

Rous sarcoma virus (RSV)
- First characterized in 1910 by F. Peyton Rous from a chicken
tumor, later named the Rous sarcoma virus;
- mid-1970s, Michael Bishop & Harold Varmus (Nobel Prize
1989) demonstrated normal animal cells contain non-cancer
causing genes (c-Src) closely related to viral oncogenes (v-Src).
Normal
Transformed
Animal Fibroblast
Cancer Arises From Malfunction of Genes:
mutations and/or aberrant expression

Proto-oncogenes and oncogenes

Tumor suppressor genes

DNA repair genes
Germline vs. Somatic mutations
Germline mutations
Parent
Mutation
in egg or
sperm
Child
All cells in
affected
offspring
inherited from parents and
present in egg or sperm
 Cause
inherited
cancerpredisposing syndromes
 Account for ~ 5% of all cancers

Somatic mutations
Somatic
mutation (eg,
breast, lung
etc)
Are not heritable
 Occur in specific tissues
 Responsible for the majority,
possibly all, types of cancers

Proto-oncogenes and oncogenes
Proto-oncogene: genes which are involved in the promotion of
cell division and proliferation, in which gain of function mutation
can drive a cell toward cancer;

Oncogenes: mutation, overactive or overexpressed forms of
proto-oncogenes.


Gain of function; dominant at cellular level.
“Accelerator”
Functions of Cellular Proto-Oncogenes
1. Secreted Growth Factors
2. Growth Factor Receptors
3. Cytoplasmic
Signal Transduction
Proteins
4. Nuclear
Proteins:
Transcription
Factors
5. Cell Cycle
Genes
6. Anti-apoptosis
Genes
Examples of Oncogenes
• RAS - GTPase - activated in many cancers
• c-MYC –Transcription factor - overexpressed in
colon cancer, amplified in lung, rearranged in
lymphoma
• RET - Tyrosine kinase - multiple endocrine
adenomatosis type 2A (MEN2A)
• MET - Tyrosine kinase - hereditary papillary renal
cancer
• CDK4 – Cell cycle - familial melanoma
• BCR/ABL - Tyrosine kinase - chronic myeloid
leukemia t(9;22)
• BCL2 – Anti-apoptosis- follicular lymphoma
t(14;18)
Activation mechanisms of proto-oncogenes
(proto-oncogene --> oncogene)

Activation via chromosomal translocation
Diagrammatic representation of
9:22 chromosomal translocation
seen in chronic myeloid leukemia
(CML), the formation of BCR-ABL
oncogene and its detection by FISH.

(Encoded activated tyrosine kinase)
Adapted from Molecular Biology of the Cell 5th edition and
http://www.slh.wisc.edu/clinical/cytogenetics/fish/
Fluorescent in Situ Hybridization (FISH)
• Certain chromosomal
translocations are easily
detected by FISH
• Fluorescent in Situ
Hybridization
– probes on different
chromosomes labeled
with distinct Fluorophore.

Activation via gene amplification
chromosomal changes and amplification in MYC gene in cancer cells
(eg. neuroblastoma, lung cancer etc) resulting in double minute
chromosomes.


Activation by point mutation
Point mutations in RAS genes resulting in reduced intrinsic GTPase activity
have been identified in several tumors, including pancreatic, colorectal, lung
and bladder cancer.

Point mutations producing
constitutively active form of
RAS, promoting cell growth.

S. Schubbert, K. Shannon, and G. Bollag. Nat Rev Cancer, 2007. 7(4): 295-308.
Tumor Suppressor Genes
Normally exerts a negative effect on cell division and
proliferation.
 Recessive at cellular level.
 Loss of function in both alleles result in uncontrolled
cell division and tumor formation - ‘Loss of
Heterozygosity’ and ‘Two Hit Hypothesis’.

“Brakes”
Examples of tumor suppressor genes
Disorders in which gene is
affected
Gene (locus)
Function
Familial
Sporadic
DCC (18q)
cell surface
interactions
unknown
Colorectal cancer
WT1 (11p)
transcription
Wilm’s tumor
lung cancer
Rb1 (13q)
transcription
retinoblastoma
small-cell lung
carcinoma
p53 (17p)
transcription
Li-Fraumeni
syndrome
breast, colon, &
lung cancer
BRCA1(17q)
BRCA2 (13q)
transcriptional
regulator/DNA
repair
breast
cancer
breast/ovarian
tumors
Mechanisms Leading to Loss of
Heterozygosity
Normal allele
Mutant allele
Loss of normal allele
Chromosome
loss
Deletion
Unbalanced
Loss and
Mitotic
translocation reduplication recombination
Point
mutation
Retinoblastoma
• Retinoblastoma - tumor of retinal stem
cell
• Affects 1 in 20, 000 live-born infants
• Average age at presentaion
– unilateral 26 months
– bilateral 8 months
• Males and Females equally affected
• Occurs in familial (~40%) and sporadic
(~60%) forms
• Familial more likely to be bilateral,
younger
• RB1 gene on chr 13 (first tumor
suppressor gene discovered)
Genetic Features of Heritable Retinoblastoma
Knudson Two Hıt hypothesıs
Familial RB (%30)
Rb
Rb
Rb
LOH
Tumor cells
Rb Rb
Normal cells
Rb
Inactivation of a tumor suppressor gene
requires two mutations, inherited
mutation and somatic mutation.
LOH: Loss of Heterozygosity
Normal cells
Genetic Features of Sporadic Retinoblastoma
Knudson Two Hıt hypothesıs
Normal
Cells
RB
RB
RB
RB
RB
Mutation
RB
LOH
Tumor cells
Inactivation of a tumor
suppressor gene
requires two somatic
mutations.
Heritable vs Nonheritable Retinoblastoma
Inherited
Sporadic
Family history
Often positive, but affected
child may represent a new
mutation
No affected relatives
Average age at
presentation
8 months
24 months
Tumor
distribution
Usually bilateral and multifocal Unilateral
Increased risk for
other primary
tumors
Osteosarcoma, other sarcomas,
None
melanoma, bladder cancer
Mutational origin One germline and one somatic Both somatic
The RB1 Gene
• Encodes Rb protein which is involved in cell cycle
regulation;
• mutations of Rb have also been identified in various other
cancers, including osteosarcomas, small-cell lung
carcinomas, bladder, breast, pancreatic and prostate
cancers.
Long-Term Survival of Children With
Heritable Retinoblastoma
35
No Radiotherapy
30
Mortality 25
(%)
20
15
10
Radiotherapy
5
0
1
10
20
30
Years after diagnosis
40
Eng C et al. J Natl Can Instit 85:1121, 1993
TP53 tumor suppressor gene
TP53 resides in Chr. 17 and encodes a protein p53
with molecular weight 53 kDa.

‘Guardian of the genome’: Loss of function
mutations in TP53 are the most common genetic
changes observed in human cancer, with mutations
found in > 50% of all tumors.

Germline mutations in TP53 cause the inherited
cancer predisposing condition known as ‘LiFraumeni
syndrome’,
a
rare
autosomal

dominant syndrome characterized by neoplasms at multiple
sites,
including
breast
cancer,
soft
tissue
sarcomas, brain tumors, osteosarcoma, leukemia,
and adrenocortical carcinoma.
Modes of action of the p53 tumor suppressor
When mutated:
 Not essential for
normal development;
(G1 -> S arrest)
 cells with DNA damage
continue cell cycle;
 escape apoptosis;
 genetic instability and
accumulate mutations;
 resistance to drugs and
irradiation.
(regulate BCL2 pathway)
Adapted from Molecular Biology of the Cell 5th edition
DNA Repair Genes
These are genes that
ensure each strand of
genetic
information
is
accurately copied during cell
division of the cell cycle.

Mutations in DNA repair
genes lead to an increase in
the frequency of mutations
in other genes, such as
proto-oncogenes and tumor
suppressor genes.

BRCA1/2 in Breast/ovarian cancer
• Breast cancer affects 1 in 10 women and represents 31% of
cancers in women (~185,000 women diagnosed each year).
• ~5% of breast cancers are hereditary, with age of onset earlier
than sporadic forms (mutations at 2 alleles).
• Inherited breast/ovarian cancer is an autosomal dominant
condition and occurs as a result of mutations in DNA repair genes:
BRCA1 (Chr17) and/or BRCA2 (Chr13).
• BRCA1 is important for homologous recombination, cellular
repair of DNA damage, and transcription of mRNA.
• Mutations in BRCA1 also are involved in ovarian cancer.
• BRCA2 plays a role in timing of mitosis in the cell cycle.
BRCA mutation and the risk of
breast/ovarian cancer
http://www.myriad.com/patients-families/disease-info/breast-cancer/
Human Non-Polyposis Colon Cancer (HNPCC)
•2-3% of all colorectal cancer (CRC) cases.
• Autosomal dominant, high penetrance.
• Typical age of cancer onset is 40-50 years.
• High lifetime risk of CRC and other cancers beginning age 20.
• Caused by mutations or deletions in mismatch repair (MMR)
genes MSH2, MLH1, MSH6, (PMS2) , with 90% of detectable
mutations in MSH2 and MLH1
• Tumor formation requires mutation at the second allele.
• All four genes have homologs in yeast.
• DNA blood tests are available for all four genes.
Cancer Risks in HNPCC
100
80
Colorectal 78%
60
% with
cancer 40
Endometrial 43%
Stomach 19%
Biliary tract 18%
Urinary tract 10%
Ovarian 9%
20
0
0
20
40
60
80
Age (years)
Aarnio M et al. Int J Cancer 64:430, 1995
Tumor initiates from a single founding cell
Schematic illustration of tumor clonal evolution.
Adapted from Molecular Biology of the Cell 5th edition
Age dependent colon cancer incidence
Tumor progress with accumulation of mutations:
one mutation is often not sufficient to cause cancer
(c) Lung cancer
Part 2 summary
1). Cancer as a genetic disease
Both external and intrinsic causes demonstrate genetic
changes linked with cancer.
2). Cancer Arises From Malfunction of Genes
Definition, cellular functions, mechanisms of action in
cancer and representative examples of:
 Proto-oncogenes and oncogenes
 Tumor suppressor genes
 DNA repair genes
3). Tumor initiates from a single founding cell and
progress with the accumulation of cancer gene
mutations.
3. How to prevent and diagnose cancer?
For cancers with known causes:
Liver cancer: vaccine to hepatitis B; diet without cancer
inducing chemicals


Lung cancer: away from smoking tobacco

Cervical cancer - ‘Pap’ test

Colon cancer: colonoscopy

Genetic testing for heritable cancer
-BRCA1/2 in breast and ovarian cancer
-APC in familial adenomatous polyposis
-Sets of cancer predisposing genes
Prevention and early stage detection is far more
effective than treatment!
Human Papilloma Virus & Cervical Cancer
• Caused by HPV and clinically detected by ‘Pap’ test and HPV
Screening.
• Types 16 and 18: Cause 70% of cervical cancer.
• HPV Types 6 and 11: cause 90% of genital warts.
• GARDASIL Vaccine to HPV.
• Risk Factors: smoking, having many children, and human
immunodeficiency virus (HIV) infection.
Genetic test for breast cancer
‘The Angelina Effect’
In 2013, actress Angelina Jolie announced that she had undergone a
preventive double mastectomy because she was a BRCA1 gene
mutation carrier, which puts her at very high risk for breast and
ovarian cancer. Jolie also had a family history of these cancers.

Cancer Death Rates in U.S.
MALE
FEMALE
from American Cancer Society
Revolution of DNA sequencing technologies
I: Sanger sequencing
ABI 3730
700-1000 nt
96/384 well
II: Next generation sequencing
Illumina HiSeq2000
2007-~
2*100 nt * 800M = 160G
Ion Proton ABI
2010-~
200 nt * 60 M = ~12G
Solid ABI
2007-~
(out of market )
454 Roche
2005~present
1000 nt*1M=1000M
(out of market in 2016)
III: Single molecule (third generation) sequencing
The PacBio™ RS
2010-~
2000 nt * 50000
Nanopore GridION
2012-~
> 4000 nt read length
Sequencing cost decreases very rapidly
Francis Collins
Craig Venter
Human
Genome
project
1990-2003
>2 billion $
J. Watson’s
genome
Jan-May, 2007
1 million $
Personal genome
Day-Week
2014
<1000$
Personal genome
Hour
near future
<100$
van Dijk, E.L., et al. Trends in Genetics. 2014,30(9): 418-426.
Cancer genomics with evolving DNA sequencing
Directly screen sets of cancer disposing genes with affordable
cost
 Construct the catalogue of cancer causing genes for each major
cancer type
 Comprehensively profile the gene expression and epigenetic
modification changes in cancer

More effectively detect tumor in early stage and accurately
classify cancer subtypes
 Devise targeted therapy
 Monitor the drug response and prognosis


Personalized medicine in cancer prevention and treatment
Catalogue of cancer critical genes

Direct comparison of tumor and normal condition via large scale sequencing
International Cancer Genome
Consortium (ICGC)
https://icgc.org/
The Cancer Genome Atlas (TCGA)
http://cancergenome.nih.gov/
Cancer Genome Project (CGP)
http://www.sanger.ac.uk/researc
h/projects/cancergenome/
Adapted from Vogelstein et al. 2013. Science
Example: Mutation landscape in breast cancer
Polyak, K. and O. Metzger Filho. Cancer cell, 2012, 22(4): 562-562.
Part 3 summary
1). Effective prevention and early detection have
been developed for cancers with known causes.
2). Revolutions in DNA sequencing technologies
greatly impute cancer genetic testing and targeted
therapy, which will eventually lead to personalized
medicine in cancer prevention, diagnosis and
treatment in the near future.
Take-home message
1. What Is Cancer?

Malignant tumor and a complex disease
2. What Causes Cancer?
Cancer is a genetic disease caused
malfunction of genes
 Three types of Cancer Critical Genes
 Cancer initiation and progression

by
3. How to Prevent and Diagnose Cancer?
Utilization the knowledge we learned from
cancer genetics
