Download Genomic instability - Roswell Park Cancer Institute

Genomic instability
Amin Mahpour
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Some questions to ponder
• What is Genomic instability?
• What factors contribute to the genomic integrity?
• How we identify these aberrations?
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PART I:
MOLECULAR BIOLOGY OF
GENOMIC INTEGRITY
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Instability, a hallmark of Cancer
Hallmarks of Cancer: The Next Generation. Hanahan, weinberg.
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Cell Cycle
G1
Restriction point
S
Interphase
Mitosis
G2
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Forms of instability
• Chromosomal Instability(CIN)
– Microscopic changes in the Karyotype
• Chromosomal gain or lost (Aneuploidy)
• Chromosomal translocation
– Can be studied by Cytogenetics techniques
• Microsatellite Instability(MSI or MIN)
– More subtle changes affecting short repeats in the genome.
– Require molecular techniques(i.e. PCR) to identify them
• Mutations, small deletions and other forms of
aberrations.
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Chromosomal Instability
Spindle Assembly Checkpoint Centrosome number and geometry 7
Microsatellite instability
Replication slippage
CACACA
CACACACACACACACA
CACACA
CACACACACACACACA
Mismatch repair failure
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Tumor suppressors are vital for genomic
integrity
• Tumor suppressor genes(TSG)
– Gatekeepers (control cell cycle progression)
• Rb, CDK/Cyclin inhibitors (CKIs)
• p53
– Caretakers (are involved in DNA repair)
• Telomerase
• PARPs
• ATM/ATR, CHKs
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Gatekeeper genes tightly control cell cycle
progression
Environmental factors
DNA Damage •
•
•
•
•
ROS, Oxidative reagents Base dehydration Replication stress Telomere attrition Aberrant Homologous recombination Cell Cycle or differentiation
GKGs
Cell Cycle arrest
Repair
Senescence or Apoptosis
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Retinoblastoma protein
G1/M CDKs
G1/M CDKs
G1 phase
Rb
Rb
E2F
E2F
Hypo-­‐methylated state
Hyper-­‐methylated state
G1/S phase
G2 phase
E2F
E2F
Genes that are essential for replication
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P53, the guardian of genome
Ubiquitin
Proteosome
MDM
Normal
Cytosol
P53
Genotoxic stress
Nucleus
Damage
P53 kinases
p21 XPC MDM2 MDMX
PUMA BAX
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DNA damage checkpoint
Double strand break
Alkylated nucleotide
Replication stress
p53
ATM
ATR
CHK2
CHK1
!
BRCA1
!
apoptosis
!
!
repair Cell cycle arrest
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Caretakers repair various DNA lesions
• Mismatch repair(MMR)
– MutS, MutL, RPA, Polymerase delta, Ligase
• Base Excision repair(BER)
– DNA glycosylases, Polymerase beta
• Nucleotide Excision Repair(NER)
– XPA, XPG, RPA, TFIIH, XPF/ERCC1, Ligase
• Homologous Repair(HR)
– BRCA1, BRCA2, etc…
• Non-Homologous Repair(NHR)
– Ku70, Ku80, DNAPK, Ligase III and IV
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Special Case of BRCA1
Non Homologous End Joining (NHEJ)
Deletion
Homologous Recombination(HR)
ATM
BRCA1
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PARP1 inhibitors can be used in BRCA1
mutated cancers
Single strand break(SSB)
Double strand break(DSB)
PARP inhibitors
PARP
ATM
BRCA1
Apoptosis
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Oncogenes and instability
ors t
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f
c
rophi
T
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Survival Signal
Proliferation signal
Master transcription factors and Pro-­‐survival gene expression
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Replication is regulated under normal
condition
Licensing factors
S phase
Replicons
Replicons
S phase
Replicons
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Oncogenes promote DNA replication
Oncogenic signal
Replicons
S phase
Replicons
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Oncogenes and local replication
Growth and survival advantage (e.g. Myc)
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Replication Stress
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Telomere attrition contribute to genomic
instability
DNA replication
Telomeres
ALT
Telomerase
Crisis
p53
Apoptosis
End to end fusion
Telomerase OE
Anaphase breakage
End to end fusion
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Chromothripsis
Normal Chromosome
Catastrophic event
Pulverized Chromosome
Repair
Rearranged Chromosome
Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development. Cell 2011
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PART II:
IDENTIFICATION OF
GENOMIC INSTABILITY
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Cytogenetic - Karyotyping
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Fluorescent In Situ Hybridization(FISH)
fluorophore
PNA Probe
Photo: Swiss perinatal institute
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Spectral Karyotyping (SKY)
Photo: Autism Spectrum Disorder in a Girl with a De Novo X;19 Balanced Translocation. Hindawi 2012
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Microarray Comparative Genomic
Hybridization(M-CGH)
Photo: Agilent
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Utilization of CGH in cancer
High frequency of PTEN, PI3K, and AKT abnormalities in T-­‐cell acute lymphoblastic leukemia. Blood. 2009
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Next-generation sequencing(NGS)
• Best way to analyze genomic instability is to
sequence the cancer genome.
• Exome sequencing has been used to analyzed
Lung, glioblastoma and many other cancers.
• The data is publicly available through TCGA and
other sequencing consortium.
• Whole genome sequencing is expensive, but
provides more details about cancer genome(e.g.
Noncoding and promoter sequence).
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Further reading!
• The biology of cancer. R. A. Weinberg. Garland Science
(2nd edition).
– Chapter 8: pRb and control of cell cycle clock
• Genomic instability and cancer: an introduction. Zhiyuan
shen. JMCB (2011)
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Thank you
“In science truth always wins” Max F. Perutz
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