The Nature of Cancer

Understanding Cancer Genomics

Edyta Borkowska
Department of Clinical Genetics
Medical University of Lodz
3 Sterling Street 91-425 Lodz Poland

Materials from:
National Cancer Institute
Biology of the Cancer Robert Weinberg

Przykadowy kariotyp ludzki.

Centromer
6

10
q

11

12

13

14

15

Chromosom 5
16

17

18

21

22

X Y

19

20

Geny

Start site
Promoter

Exon 1

Splice sites
Intron

Exon 2

Stop site
Intron

Exon 3

5 end

3 end
Exon 1

Exon 2
mRNA

Exon 3

Regiony niekodujce

Gen 1

Biako 1
Region niekodujcy
Biako 2

Gen 2
Exon
Noncoding
intron

Region niekodujacy

Gen - mRNA - Biako

Rybosomy
Jdro komrkowe
Narastanie
acucha
biakowego
mRNA

Biako

C
G
G
A

mRNA

G
C
C
U

G
C
C
T

switched-on

RNA Processing przed Translacj

DNA

Exon

Intron

Exon

Intron
Transkrypcja

Primary
mRNA
Processing

Mature
mRNA
Translacja
Biako

Exon

Kod trjkowy
Kodony s zbudowane z 3 nukleotydw
64 moliwe kodony

kodon (AUG) koduje

methionine i startuje
translacj wszystkich
biaek

61 kodonw kodujcych
20 aminokwasw
(kod zdegenerowany)

AUG

GCA

Methionina

Alanina

3 ckodony stop
Zatrzymuj translacj biaek

UAA

UAG

UGA

Mutacje

A mutation is a change in the normal base pair sequence

Najczciej uywane do zdefiniowania zmiany, ktra

upoledza funkcj kodowanego biaka

Mutacje: somatyczne i germline

Mutacje somatyczne

Mutacje germline

Nie wystpuj w kom. germinalnych

W kom. jajowych lub plemnikach

Nie dziedzicza si

Dziedzicz si

Przyczyna nowotworow dziedzicznych

niedziedziczne

Somatic mutation
(e.g., breast)

Mutation in egg All cells affected

or sperm
in offspring

Tumors Are Clonal

Normal
cell
First
mutation
Second
mutation
Third
mutation
Fourth or
later mutation

Malignant cells

Mitosis and Somatic Mutations

Example: one pair of
chromosomes

2N
Nuclear
membrane
2N

2N

4N

Centromere

Microtubules

Meiosis and Germline Mutations

Example: one pair of
chromosomes

4N
Ova (or sperm)
N

N
N

Nuclear
membrane

Homologous
chromosomes form
a bivalent

2N
Crossing over has
occurred

Recombination: Crossing Over

Synapsis

Crossing over

Chromosomes after crossing

over

De Novo Mutations
No family history of hereditary cancer

New mutation in
germ cell

Affected offspring

De novo mutations common in:

Familial adenomatous polyposis
Multiple endocrine neoplasia 2B
Hereditary retinoblastoma

30%
50%
50%

Point Mutations
GU UC G AU UGA

DNA
Normal

mRNA
C A AG C T A A C T
GU U C G C U U GA

Missense

CAAG C GAA C T
GU U C C G C G A U U G A

Frameshift insertion

CA A G G C G C T A A C T
GU UC UUG A

Frameshift deletion

CA A G AA C T
GUU UA G

Nonsense

CAAAC T

C
T

Frameshift Mutations
Normal

AUG

A AG

UUU

GG C

GCA

UUG

GAA

Methionine

Lysine

Phenylalanine

Glycine

Alanine

Leucine

Glutamine

C AU

UG G

tRNA
Protein

Frameshift

AUG

A AG

UUG

GCG

Methionine

Lysine

Leucine

Alanine

tRNA
Protein

AA

Splice-Site Mutations

DNA Exon 1

Altered
mRNA

Intron

Exon 1

Exon 2

Intron

Exon 2

Exon 3

Exon 3

DNA Exon 1

Altered
mRNA

Intron

Exon 2

Exon 1

Intron

Exon 3

Exon 3

Regulatory Mutations
Normal expression

Overexpression

Her2 protein

Her2 protein

Messenger
RNA

Chromosome 17
Her2 gene

Her2 gene amplification

SNPs: Frequently Occurring

Genetic Variants
Most of the population

At least 1 percent of the population

G to C

SNP site
Common
sequence

Variant
sequence

Functional protein

Functional protein

Large Deletions or Insertions

SKY chromosome painting: breast cancer

Normal SKY chromosomes are not

multicolored.
Chromosomes in breast cancer
appear multicolored because they
have exchanged genetic material.

Example: Translocation of Bcr-Abl Genes

9

9
(q+)

Ph
22

bcr

(22q)
bcr-abl

abl

Fusion protein
with tyrosine
kinase activity

Cancer-Associated Mutations

Oncogenes
Tumor suppressor genes
DNA repair genes
Carcinogen
activating genes
deactivating genes
Cell cycle genes
Cell cycle checkpoint genes
Cell death genes
Cell signaling genes
Cellular differentiation genes
Cellular senescence genes
Metastasis/invasion genes

Genotypes and Phenotypes

A phenotype is the physical
manifestation of an inherited
trait or disease
A genotype is the
genetic make up of a
person

In cancer, both genotype and phenotype keep changing over time

Alleles

Dominant
allele

Normal
allele

Recessive
allele

Aa

aa

Aa

aa

Damaged
allele

Aa

aa

Same Allele, Different Locus,

Different Phenotype
5

Cysteine-rich domain
Transmembrane domain
Tyrosine kinase 1

Tyrosine kinase 2
Activating mutations: MEN 2A/B
3

Different Locus, Different Allele,

Same Phenotype
Chromosome 17

Chromosome 13
Allele
(gene)
Locus (spot
on gene)

Allele
(gene)
Locus (spot
on gene)

BRCA1

Hereditary breast and ovarian cancer

BRCA2

Penetrance
Genotype and phenotype
present
Genotype and
phenotype absent
Genotype present,
phenotype (disease) absent

Factors Influencing Penetrance

Modifier genes
Carcinogens

Estrogen

Repair enzyme
Response to DNA
damage

Hormonal/
reproductive
factors

Age-Related Penetrance

100
80

HNPCC
mutation
carriers

Affected 60
with
colorectal
cancer (%) 40
20

General
population

20

40

60

80

Age
Percentage of individuals with altered
mismatch repair gene who develop cancer

Epigenetic Factors and Penetrance

Inactive mRNA
Gene

Primary RNA
transcript

Translational control
mRNA

RNA transport
control

RNA processing control

Transcriptional control

DNA

Translational control

mRNA
ribosome

Active mRNA

A lot can happen between

transcription and translation

Inactive
protein

Protein activity
control

Protein

Phosphorylation

Active
protein

Epigenetic Example:
Methylation Alters Gene Expression
CpG island

Me

Gene

Me

HDAC

CpG island
becomes
methylated

Methyl-binding
proteins

Me

Me
Gene inactivated

HDAC modifies chromatin

Imprinting Alters Gene Expression

Gene 1

Me

Gene 1

Me

Me

Gene 2

Me
Paternal chromosome
II

Gene 2
Maternal
chromosome II

Active gene
Imprinted gene

Carrier Frequency
Example: carrier frequency=20%

Prevalence of an altered disease-linked allele in a given population

Prevalence and Founder Effect

Founder

Original population

Marked population
decrease, migration, or
isolation

Generations later

Example: Founder Effect in

Ashkenazi Jewish Population
An estimated 1 in 40 Ashkenazi Jews carries a
BRCA1 or BRCA2 mutation

BRCA1
185delAG
Prevalence = ~1%

5382insC
Prevalence = ~0.15%

BRCA2
6174delT
Prevalence = ~1.5%

Mutations in
Cancer Susceptibility Genes: BRCA1
On chromosome 17

Protein has role in

genomic stability

Autosomal dominant
transmission

~500 different mutations

reported

Nonsense/Frameshift
Missense
Splice-site

Mutations in
Cancer Susceptibility Genes: BRCA2
On chromosome 13

Protein has role in

genomic stability

Autosomal dominant
transmission

~300 different mutations

reported

Nonsense/Frameshift
Missense

Autosomal Dominant Inheritance

Equally transmitted by
men and women
No skipped generations
Each child has a 50%
chance of
inheriting
the mutation

Normal
Affected

Examples of
Dominantly Inherited Cancer Syndromes

Cancer Susceptibility:
Incomplete Penetrance and Phenocopies

Normal
Susceptible carrier
Carrier, affected with
cancer
Sporadic cancer

Example: BRCA1-Linked
Hereditary Breast and Ovarian Cancer

92

73

Breast,
dx 45, d. 89

68

Ovary,
dx 59,
d. 62

Noncarrier
BRCA1-mutation carrier
Affected with cancer

86

Breast,
dx 36

Breast,
dx 59

Autosomal Recessive Inheritance

Two germline mutations

(one from each parent)
to develop disease
Equally transmitted by
men and women

Noncarrier
Nonaffected carrier
Affected carrier

Some Recessively Inherited

Cancer Syndromes

X-Linked Inheritance
Mutant genes are on the
X (sex) chromosome

Women must inherit two

mutated copies to be affected
All men who inherit the
mutation are affected
(only one X chromosome)

Carrier female
Affected male
Normal male
Normal female

Other Genetic Conditions

Linked to Increased Cancer Risk

Normal Cell Growth: The Cell Cycle

2 homologous pairs are shown

G1 (cell growth)

M (mitosis)
Oncogenes

G2

Tumor
suppressor
genes

DNA repair
genes
S (synthesis)

Abnormal Cell Growth: Oncogenes

Normal genes
(regulate cell
growth)

1st mutation
(leads to accelerated
cell division)

Proto-oncogene to oncogene

Tumor Suppressor Genes

Tumor suppressor genes

Normal genes
(regulate cell
growth)

Tumor suppressor genes

1st mutation
(leads to accelerated
cell division)

Active oncogene

Mutations in Tumor Suppressor Genes

Tumor suppressor genes
Normal genes (regulate
cell growth)

Tumor suppressor genes

Active oncogene

1st mutation (susceptible

carrier)

No brakes!
2nd mutation or loss
(leads to cancer)

No brakes!

Active oncogene

Two-Hit Hypothesis

No cancer

Germline mutation
Somatic mutation

Cancer

If first hit is a germline

mutation, second somatic
mutation more likely to
enable cancer

Heterozygous Condition

Normal allele

Mutant allele

Loss of normal allele

Chromosome loss

Deletion

Unbalanced
translocation

Loss and
reduplication

Mitotic
recombination

Point
mutation

Loss of Heterozygosity

Normal
allele

Mutant
allele

CANCER SUSCEPTIBILITY GENES

Heterozygous condition: normal

gene balances the mutated gene

Germline mutation