Genomic instability. Amin Mahpour

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1 Genomic instability Amin Mahpour 1

2 Some questions to ponder What is Genomic instability? What factors contribute to the genomic integrity? How we identify these aberrations? 2

3 PART I: MOLECULAR BIOLOGY OF GENOMIC INTEGRITY 3

4 Instability, a hallmark of Cancer Hallmarks of Cancer: The Next Generation. Hanahan, weinberg. 4

5 Cell Cycle G1 Restriction point Interphase S Mitosis G2 5

6 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. 6

7 Chromosomal Instability Spindle Assembly Checkpoint Centrosome number and geometry 7

8 Microsatellite instability Replication slippage CACACA CACACA CACACACACACACACA CACACACACACACACA Mismatch repair failure 8

9 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 9

10 Gatekeeper genes tightly control cell cycle progression Environmental factors DNA Damage ROS, Oxidative reagents Base dehydration Replication stress Telomere attrition Aberrant Homologous recombination GKGs Cell Cycle arrest Cell Cycle or differentiation Repair Senescence or Apoptosis 10

11 Retinoblastoma protein G1/M CDKs Rb E2F Hypo- methylated state G1 phase G1/M CDKs Rb E2F Hyper- methylated state G2 phase E2F G1/S phase Genes that are essential for replication 11

12 P53, the guardian of genome Ubiquitin MDM Proteosome Normal Genotoxic stress Damage P53 kinases P53 Cytosol Nucleus p21 XPC MDM2 MDMX PUMA BAX 12

13 DNA damage checkpoint Double strand break Alkylated nucleotide Replication stress ATM ATR p53 CHK2! BRCA1 CHK1! apoptosis! repair! Cell cycle arrest 13

14 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 14

15 Special Case of BRCA1 Non Homologous End Joining (NHEJ) Homologous Recombination(HR) Deletion ATM BRCA1 15

16 PARP1 inhibitors can be used in BRCA1 mutated cancers Single strand break(ssb) Double strand break(dsb) PARP inhibitors PARP ATM Apoptosis BRCA1 16

17 Oncogenes and instability Growth factors / Trophic factors Survival Signal Proliferation signal Master transcription factors and Pro- survival gene expression 17

18 Replication is regulated under normal condition S phase Licensing factors Replicons Replicons S phase Replicons 18

19 Oncogenes promote DNA replication Oncogenic signal Replicons S phase Replicons 19

20 Oncogenes and local replication Growth and survival advantage (e.g. Myc) 20

21 Replication Stress 21

22 Telomere attrition contribute to genomic instability DNA replication Telomeres Telomerase p53 ALT Crisis Apoptosis End to end fusion elomerase OE Anaphase breakage End to end fusion 22

23 Chromothripsis Normal Chromosome Catastrophic event Pulverized Chromosome Repair Rearranged Chromosome Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development. Cell

24 PART II: IDENTIFICATION OF GENOMIC INSTABILITY 24

25 Cytogenetic - Karyotyping 25

26 Fluorescent In Situ Hybridization(FISH) PNA Probe fluorophore Photo: Swiss perinatal institute 26

27 Spectral Karyotyping (SKY) Photo: Autism Spectrum Disorder in a Girl with a De Novo X;19 Balanced Translocation. Hindawi

28 Microarray Comparative Genomic Hybridization(M-CGH) Photo: Agilent 28

29 Utilization of CGH in cancer High frequency of PTEN, PI3K, and AKT abnormalities in T- cell acute lymphoblastic leukemia. Blood

30 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). 30

31 Further reading! The biology of cancer. R. A. Weinberg. Garland Science (2 nd edition). Chapter 8: prb and control of cell cycle clock Genomic instability and cancer: an introduction. Zhiyuan shen. JMCB (2011) 31

32 Thank you In science truth always wins Max F. Perutz 32