Genetic Predisposition to Cancer

Dr. Jordi Surralls, Jan 2015

Topics:
1. Familiar cancer versus cancer predisposition syndromes
2. DNA repair pathways and human disease
3. Targeting DNA repair in cancer therapeutics. Synthetic lethality
4. Genetic strategies to identify cancer susceptibility genes
5. Bench to beadside research in Fanconi anemia

16 FEBRUARY 2001 VOL 291 SCIENCE

DNA damage response

DNA damage response

From: http://www.sigmaaldrich.com/technical-documents/articles/biofiles/dna-damage-and-repair.html

Cell cycle during DNA damage response

From the following article:

The impact of a negligent G2/M checkpoint on genomic instability and cancer
induction
Markus Lbrich & Penny A. Jeggo
Nature Reviews Cancer 7, 861-869 (November 2007)

From the following article:

DNA repair dysregulation from cancer driver to therapeutic target
Nicola J. Curtin
Nature Reviews Cancer 12, 801-817 (December 2012)

From the following article:

How nucleotide excision repair protects against cancer
Errol C. Friedberg
Nature Reviews Cancer 1, 22-33

Sources of DNA damage and their repair

From the following article:

DNA repair dysregulation from cancer driver to therapeutic target
Nicola J. Curtin
Nature Reviews Cancer 12, 801-817 (December 2012)

Main DNA lesions and corresponding DNAdamage-repair pathways

Postel-Vinay, S. et al. (2012) The potential of exploiting DNA-repair defects for optimizing lung cancer treatment
Nat. Rev. Clin. Oncol. doi:10.1038/nrclinonc.2012.3

Mutations in DNA repair genes

Defective DNA repair
Genomic instability

Cell death or Cancer

Somatic level:
sporadic cancer in
the general
population

Germinal level: cancer

predisposition DNA
repair syndromes

Disease evolution in Fanconi Anemia

Kutler et al., Blood, 2003

Mutations in DNA repair genes

Defective DNA repair
Genomic instability

Cell death or Cancer

Somatic level:

Germinal level:

1 mutation

1 mutation

Breast cancer risk in BRCA2 mutation carriers

Angelina Jolie is a BRCA mutation carrier

Familiar cancer

DNA repair pathways

Direct repair
-Transferases
-Photolyases
Double Strand Break (DSB) repair
-Non-homologous end joining (NHEJ)
-Homologous recombination (HR)
Base excision repair (BER)
-short patch BER
-long patch BER
Nucleotide excision repair (NER)
-Global genome NER (GG-NER)
-Transcription coupled NER (TC-NER)
Mismatch repair (MMR)
ICL repair (Fanconi anemia/BRCA pathway)

DNA repair pathways

Direct repair
-Transferases
-Photolyases
Double Strand Break (DSB) repair
-Non-homologous end joining (NHEJ)
-Homologous recombination (HR)
Base excision repair (BER)
-short patch BER
-long patch BER
Nucleotide excision repair (NER)
-Global genome NER (GG-NER)
-Transcription coupled NER (TC-NER)
Mismatch repair (MMR)
ICL repair (Fanconi anemia/BRCA pathway)

O6-alquil G (A:T)
O4-alquil T (C:G)

O6-metilguanina metiltransferasa (O6-MGMT)

DNA repair pathways

Direct repair
-Transferases
-Photolyases
Double Strand Break (DSB) repair
-NHEJ
-HR
Base excision repair (BER)
-short patch BER
-long patch BER
Nucleotide excision repair (NER)
-Global genome NER (GG-NER)
-Transcription coupled NER (TC-NER)
Mismatch repair (MMR)
ICL repair (Fanconi anemia/BRCA pathway)

DSB repair by NHEJ and homologous recombination

From the following article:

Chromatin dynamics and the preservation of genetic information
Jessica A. Downs, Michel C. Nussenzweig & Andr Nussenzweig
Nature 447, 951-958(21 June 2007)

DSB repair by NHEJ and homologous recombination

From the following article:

Charity begins at home: non-coding RNA functions in DNA repair
Dipanjan Chowdhury, Young Eun Choi & Marie Eve Brault
Nature Reviews Molecular Cell Biology 14, 181-189 (March 2013)

HRR:
http://www.youtube.com/watch?v=y_OWCU5HwMU
NHEJ:
http://www.youtube.com/watch?v=jOrm-sK-Yjg

Origin of DNA double strand breaks (DSB)

Ataxia telangiectasia (ATM)

Nijmegen breakage syndrome (NBS1)

Bloom syndrome (BLM)

Seckle syndrome (ATR)

Severe immunodeficient syndromes

NHEJ can be error prone

From: http://www.sigmaaldrich.com/technical-documents/articles/biofiles/dna-damage-and-repair.html

Gene editing with engineered nucleases is

based on DSB repair (TALEN, CRISPR)

From: http://www.toolgen.com/html/kor/technology/gen_eng_nuc.php

From the following article:

Tumour-suppressor function in the nervous system
Suzanne J. Baker & Peter J. McKinnon
Nature Reviews Cancer 4, 184-196 (March 2004)

DNA repair pathways

Direct repair
-Transferases
-Photolyases
Double Strand Break (DSB) repair
-Non-homologous end joining (NHEJ)
-Homologous recombination (HR)
Base excision repair (BER)
-short patch BER
-long patch BER
Nucleotide excision repair (NER)
-Global genome NER (GG-NER)
-Transcription coupled NER (TC-NER)
Mismatch repair (MMR)
ICL repair (Fanconi anemia/BRCA pathway)

Base excision repair (BER)

Glicosilasa:
corte enlace glicoslico
entre la base y la ribosa
deja un sitio AP

AP endonucleasa:
rompe la cadena en el
extremo 5 del sitio AP

DNA pol:
rellena el hueco
elimina el grupo ribosa-fosfato
(actividad liasa)

Complejo XRCC1-ligasaIII:
sellado de la mella

Many DNA glycosilases

BER: two pathways

Base excision repair (BER)

From: http://www.sigmaaldrich.com/technical-documents/articles/biofiles/dna-damage-and-repair.html

BER (SP)
http://www.youtube.com/watch?v=72oT6N90iWc

BER (LP)
http://www.youtube.com/watch?v=g4khROaOO6c&list
=PLF3FFAE8A8BD9C140

DNA repair pathways

Direct repair
-Transferases
-Photolyases
Double Strand Break (DSB) repair
-Non-homologous end joining (NHEJ)
-Homologous recombination (HR)
Base excision repair (BER)
-short patch BER
-long patch BER
Nucleotide excision repair (NER)
-Global genome NER (GG-NER)
-Transcription coupled NER (TC-NER)
Mismatch repair (MMR)
ICL repair (Fanconi anemia/BRCA pathway)

Nucleotide excision repair (NER)

UV

recognition
dual incision

excision

DNA synthesis
ligation

Xeroderma pigmentosum (XP)

Early Stages of Global Genome

Repair

Initial Steps of TranscriptionCoupled NER

Final Steps of Eukaryotic NER

NER (GG)
http://www.youtube.com/watch?v=bgUH9NfO2QM

NER and human disease

From the following article:

DNA repair deficiency and neurological disease
Peter J. McKinnon
Nature Reviews Neuroscience 10, 100-112 (February 2009)

Xeroderma pigmentosum

Cockayne syndrome

NER
GGR
Xeroderma pigmentosum

Skin cancer

TCR
Cockayne syndrome

No cancer!

DNA repair pathways

Direct repair
-Transferases
-Photolyases
Double Strand Break (DSB) repair
-Non-homologous end joining (NHEJ)
-Homologous recombination (HR)
Base excision repair (BER)
-short patch BER
-long patch BER
Nucleotide excision repair (NER)
-Global genome NER (GG-NER)
-Transcription coupled NER (TC-NER)
Mismatch repair (MMR)
ICL repair (Fanconi anemia/BRCA pathway)

DNA pol have proof-reading activity

The Escherichia coli Methyl-Directed

Mismatch Repair Reaction
The overall repair reaction can be divided into several
steps:
mismatch-dependent incision of the unmethylated
strand at a hemi-methylated GATC site.
Excision of that portion of the incised strand spanning
the single-strand break and the mispair.
Repair of the ensuing gap by DNA synthesis and
ligation.

Human mismatch repair (MMR) pathway

From the following article:

AID and mismatch repair in antibody diversification
Alberto Martin & Matthew D. Scharff
Nature Reviews Immunology 2, 605-614 (August 2002)

MMR
http://www.youtube.com/watch?v=HYS6EKnQcv0
http://www.youtube.com/watch?v=dgPh1qigv7s

Microsatellite instability

Distinct molecular pathways for the development of

defective DNA MMR and MSI-H in colon cancer

Sinicrope, F. A. (2010) DNA mismatch repair and adjuvant chemotherapy in sporadic colon cancer
Nat. Rev. Clin. Oncol. doi:10.1038/nrclinonc.2009.235

DNA repair pathways

Direct repair
-Transferases
-Photolyases
Double Strand Break (DSB) repair
-Non-homologous end joining (NHEJ)
-Homologous recombination (HR)
Base excision repair (BER)
-short patch BER
-long patch BER
Nucleotide excision repair (NER)
-Global genome NER (GG-NER)
-Transcription coupled NER (TC-NER)
Mismatch repair (MMR)
ICL repair (Fanconi anemia/BRCA pathway)

Interstrand crosslink repair (ICLR)

Fork stalling

Unhooking

Translesion sythesis

Recombination

Fanconi anemia

FA-A

FA-C

DNA repair as a therapeutic target

Postel-Vinay, S. et al. (2012) The potential of exploiting DNA-repair defects for optimizing lung cancer treatment
Nat. Rev. Clin. Oncol. doi:10.1038/nrclinonc.2012.3

DNA repair pathways involved in repairing toxic DNA

lesions formed by cancer treatments

Helleday et al. Nature Reviews Cancer 8, 193-204 (March 2008)

Synthetic lethality in cancer treatment

From the following article:

DNA repair dysregulation from cancer driver to therapeutic target
Nicola J. Curtin
Nature Reviews Cancer 12, 801-817 (December 2012)

Synthetic lethality in cancer treatment

http://www.missiontherapeutics.com/index.php/research-and-development/science/synthetic-lethality

Synthetic lethality in cancer treatment

DNA-repair biomarkers and therapeutic implication

Postel-Vinay, S. et al. (2012) The potential of exploiting DNA-repair defects for optimizing lung cancer treatment
Nat. Rev. Clin. Oncol. doi:10.1038/nrclinonc.2012.3

NER in cancer and as target in cancer treatment

From the following article:

DNA repair dysregulation from cancer driver to therapeutic target
Nicola J. Curtin
Nature Reviews Cancer 12, 801-817 (December 2012)

BER in cancer and as target in cancer treatment

From the following article:

Nicola J. Curtin
Nature Reviews Cancer 12, 801-817 (December 2012)

MMR in cancer and as target in cancer treatment

From the following article:

DNA repair dysregulation from cancer driver to therapeutic target
Nicola J. Curtin
Nature Reviews Cancer 12, 801-817 (December 2012)

MMR in cancer and as target in cancer treatment

From the following article:

DNA repair dysregulation from cancer driver to therapeutic target
Nicola J. Curtin
Nature Reviews Cancer 12, 801-817 (December 2012)

DSB repair in cancer and as target in cancer treatment

From the following article:

DNA repair dysregulation from cancer driver to therapeutic target
Nicola J. Curtin
Nature Reviews Cancer 12, 801-817 (December 2012)

Synthetic lethality in tumors from BRCA1 and BRCA2

mutation carriers treated with PARP inhibitors

Nature Medicine 17, 283284 (2011)

Nature Biotechnology 29,373374(2011)

Mechanism of synthetic lethality between BRCA

deficiency and PARP inhibition

Banerjee, S. et al. (2010) Making the best of PARP inhibitors in ovarian cancer
Nat. Rev. Clin. Oncol. doi:10.1038/nrclinonc.2010.116

BRCAness and PARP inhibitors

Effects of PARP inhibition on BRCA2-mutant cells

- PARP inhibitor

+ PARP inhibitor

Banerjee, S. et al. (2010) Making the best of PARP inhibitors in ovarian cancer
Nat. Rev. Clin. Oncol. doi:10.1038/nrclinonc.2010.116

CT scans of two patients with advanced ovarian

cancer after PARPi therapy

Banerjee, S. et al. (2010) Making the best of PARP inhibitors in ovarian cancer
Nat. Rev. Clin. Oncol. doi:10.1038/nrclinonc.2010.116

Examples of DDR inhibitors in clinical use or in development

Nature 481, 287294 (19 January 2012)

Experiments to be done:
UV sensitivity of XP deficient skin cells
Abnormal repair kinetics of UV-light induced
DNA damage in XP deficient skin cells
Chemotherapy induced cell cycle arrest in
tumor cells deficient in the FA pathway on ICL
repair
PARP inhibition for selective killing of BRCA1
deficient tumor cells
Homologous recombination repair of DSB

Experiments to be done:
UV sensitivity of XP deficient skin cells
Abnormal repair kinetics of UV-light induced
DNA damage in XP deficient skin cells
Chemotherapy induced cell cycle arrest in
tumor cells deficient in the FA pathway on ICL
repair
PARP inhibition for selective killing of BRCA1
deficient tumor cells
Homologous recombination repair of DSB

Experiments to be done:
UV sensitivity of XP deficient skin cells
Abnormal repair kinetics of UV-light induced
DNA damage in XP deficient skin cells
Chemotherapy induced cell cycle arrest in
tumor cells deficient in the FA pathway on ICL
repair
PARP inhibition for selective killing of BRCA1
deficient tumor cells
Homologous recombination repair of DSB

% of cells containing 66-4P P foci

90%

60%

30%

0
0

8
12
16
Time (h) after UV irradiation

20

24

Experiments to be done:
UV sensitivity of XP deficient skin cells
Abnormal repair kinetics of UV-light induced
DNA damage in XP deficient skin cells
Chemotherapy induced cell cycle arrest in
tumor cells deficient in the FA pathway on ICL
repair
PARP inhibition for selective killing of BRCA1
deficient tumor cells
Homologous recombination repair of DSB

FA-A Patient

Healthy Donor

- MMC

+ MMC

G1: 74.8%
G2+M: 15.0%

G1: 70.8%
G2+M: 21.8%

G1: 80.6%
G2+M: 11.9%

G1: 36.2%
G2+M: 56.4%

+ FANCA

G1: 83.8%
G2+M: 10.4%

+ FANCA

G1: 66.8%
G2+M: 29.5%

Experiments to be done:
UV sensitivity of XP deficient skin cells
Abnormal repair kinetics of UV-light induced
DNA damage in XP deficient skin cells
Chemotherapy induced cell cycle arrest in
tumor cells deficient in the FA pathway on ICL
repair
PARP inhibition for selective killing of BRCA1
deficient tumor cells
Homologous recombination repair of DSB

Experiments to be done:
UV sensitivity of XP deficient skin cells
Abnormal repair kinetics of UV-light induced
DNA damage in XP deficient skin cells
Chemotherapy induced cell cycle arrest in
tumor cells deficient in the FA pathway on ICL
repair
PARP inhibition for selective killing of BRCA1
deficient tumor cells
Homologous recombination repair of DSB

HR repair assay
HR proficiency using DR-GFP system: