La biologia dei meccanismi di riparo del DNA

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1 ISTITUTO NAZIONALE PER LO STUDIO E LA CURA DEI TUMORI FONDAZIONE G. Pascale NAPOLI SC Biologia Cellulare e Bioterapie CENTRO RICERCHE ONCOLOGICHE MERCOGLIANO (AV) Laboratorio di Farmacogenomica La biologia dei meccanismi di riparo del DNA Nicola Normanno

2 An overview of types of DNA damage and causal agents Helleday Nat Rev Genetics 2014

3 How the cell copes with damaged DNA

4 Mechanisms of single strand DNA break repair Base excision repair (BER): is important for removing damaged bases by a DNA glycosylase and it is involved in the damage induced by radiation and alkylating agents Toss & Cortesi J Cancer Sci Ther 2013

5 Mechanisms of single strand DNA break repair Nucleic acid excision repair (NER): removes short singlestranded DNA segment around the lesion and repairs mutations resulting from UV light and hydrocarbons Helleday Nat Rev Genetics 2014

6 Mechanisms of single strand DNA break repair Mismatch repair (MMR): recognizes and corrects mismatched bases that can result from DNA replication and recombination Helleday Nat Rev Genetics 2014

7 Mechanisms of double-strand DNA breaks repair Homologous recombination (HR): provides accurate recombination using a sister chromatid as a template, maintaining genomic stability. However, due to the need for a sister chromatid, HR is limited to the S-phase and G2-phase of cell cycle Helleday Nat Rev Genetics 2014

8 Mechanisms of double-strand DNA breaks repair Nonhomologous end joining (NHEJ): plays a crucial role in minimizing DNA damage in both G0 and G1 phases of cell cycle, when HR cannot be supplied. Moreover, when a defect occurs in one of the enzymes involved in HR, the DSBs are repaired from error prone mechanisms, mostly NHEJ, resulting in increased risk of new chromosomal defects and thus the development of cancer

9 Homologous recombination (HR) Toss & Cortesi J Cancer Sci Ther 2013

10 BRCA mutations are associated with sensitivity to platinum-based therapy Patients carrying a BRCA mutation appear to show a favourable response to platinum-based therapy

11 BRCA-mutant tumors are sensitive to targeted therapy via PARP inhibition In women with ovarian cancer and BRCA mutation, tumour cells are characterised by homologous recombination repair deficiency (HRD) PARP inhibitors are a class of targeted treatments that act on the DNA repair pathway 1 PARP inhibition can result in selective tumour cell death in BRCA1/2 mutation carriers with ovarian cancer 1,2 1. Liu JF, et al. Gynecol Oncol 2014;133:362 9; 2. Fong PC, et al. J Clin Oncol 2010;28:

12 Mechanism of synthetic lethality between BRCA deficiency and PARP inhibition DNA damage Formation of single strand DNA break (SSB) Repair of of SSB by Base Excision Repair Banerjee, Kaye and Ashworth (2010) PARP Courtesy of S.Banerjee

13 Mechanism of synthetic lethality between BRCA deficiency and PARP inhibition DNA damage Formation of single strand DNA break (SSB) Repair of of SSB by Base Excision Repair Banerjee, Kaye and Ashworth (2010) PARP inhibition PARP Impairs base excision repair SSB persists Courtesy of S.Banerjee

14 Mechanism of synthetic lethality between BRCA deficiency and PARP inhibition DNA damage Formation of single strand DNA break (SSB) Repair of of SSB by Base Excision Repair Banerjee, Kaye and Ashworth (2010) PARP inhibition DNA replication: Replication fork arrests at SSB Formation of double strand breaks (DSBs) or replication fork collapse PARP Impairs base excision repair SSB persists Normal cell with functional HR pathway CELL SURVIVAL HR-mediated DNA repair Courtesy of S.Banerjee

15 Mechanism of synthetic lethality between BRCA deficiency and PARP inhibition DNA damage Formation of single strand DNA break (SSB) Repair of of SSB by Base Excision Repair Banerjee, Kaye and Ashworth (2010) PARP inhibition DNA replication: Replication fork arrests at SSB Formation of double strand breaks (DSBs) or replication fork collapse) PARP Impairs base excision repair SSB persists Normal cell with functional HR pathway HR-deficient tumour cell (BRCA deficient) CELL SURVIVAL HR-mediated DNA repair TUMOUR-SELECTIVE CELL DEATH (Synthetic Lethality)) Impaired HR-mediated DNA repair CELL DEATH Courtesy of S.Banerjee

16 Seminal Hypothesis (synthetic letality) If you treat cells with impaired HR (i.e. BRCA1/2 defective) they should rely on low-fidelity NHEJ (errore-prone) machinery to repair DNA damage

17 Genetic Mutations Beyond BRCA Mutations May Lead to Homologous Recombination Deficiency Data from Cancer Genome Atlas (TCGA) demonstrates that approximately 50% of high grade serous ovarian cancers have aberrations in HR repair

18 Differences between patients with BRCA1/BRCA2-mutated tumors and sporadic tumors Davies Nat Med 2017

19 Copy number signatures in HGSOC Macintyre Nat Genetics 2018

20 Mi-OncoSeq<br />Michigan Oncology Sequencing Program Presented By Erin Cobain at 2017 ASCO Annual Meeting

21 Mi-OncoSeq<br />MET500 Demographics Presented By Erin Cobain at 2017 ASCO Annual Meeting

22 Mi-OncoSeq<br /> Presented By Erin Cobain at 2017 ASCO Annual Meeting

23 Mi-OncoSeq: Case Example #2 Presented By Erin Cobain at 2017 ASCO Annual Meeting

24 Patient survival and response to pembrolizumab across 12 different tumor types with mismatch repair deficiency Le Science 2017

25 Maximum change in tumour size (%) Larotrectinib - Efficacy Across Tumour Types Integrated Data Set * Infantile fibrosarcoma Soft tissue sarcoma Thyroid Salivary gland Melanoma Breast Appendix Lung Gastrointestinal stromal tumour Colon Pancreas Cholangiocarcinoma Congenital mesoblastic nephroma Unknown primary Bone sarcoma Integrated (n=109) ORR (95% CI) 81% (72 88%) Best response PR 63% CR 17% # # Investigator response assessments, as of 30 July 2018 Includes 9 unconfirmed PRs pending confirmation; does not include 13 patients continuing on study and awaiting initial response assessment *Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy; #Surgical CR; RECIST 1.1. Note: Two patients not shown here. These patients discontinued treatment prior to any post-baseline tumour measurements CR, complete response; ORR, objective response rate; PR, partial response. 1. Lassen UN, et al. Presented at: ESMO 2018 Congress; October 19-23, 2018; Munich, Germany. Abstract 4090

26 ORR (%) There appears to be significant correlation between TMB and patient response to anti PD-L1/PD-1 therapy Investigation overview: literature review to identify data to explore the relationship between TMB and response to anti PD-L1/ PD-1 therapy Parameters: a literature search yielded studies reporting ORR and studies that met all of these criteria: Only monotherapy anti PD-L1/PD-1 as the treatment Minimum of 10 patients enrolled PD-L1 positive or negative patients enrolled TMB assessment: evaluated using a comprehensive genomic profiling assay provided by Foundation Medicine; defined as the median number of coding somatic mutations Merkel cell Median no. of coding somatic mutations per Mb Significant correlation (P<0.001) between TMB and ORR was observed dmmr=mismatch repair deficient; Mb=megabase; no.=number; NSCLC=non-small cell lung cancer; ORR=overall response rate; PD-1=programmed death receptor-1; PD-L1=programmed death ligand 1; pmmr=mismatch repair proficient; TMB=tumour mutational burden. Yarchoan M et al. N Engl J Med. 2017;377(25): Uveal Mesothelioma Correlation between TMB and ORR in 27 tumour types Sarcoma Renal cell Anal Cervical Hepatocellular Adrenocortical Pancreatic Germ cell Ovarian Glioblastoma Prostate Breast NSCLC (nonsquamous) Head and neck Endometrial Colorectal (pmmr) Noncolorectal (dmmr) Melanoma Urothelial NSCLC (squamous) Small cell lung Oesophagogastric Cutaneous squamous cell Colorectal (dmmr) ORR (no. of patients evaluated) TMB (no. of tumours analysed) ,000 26

27 The major classes of genomic alterations that give rise to cancer FISH, Immunohistochemistry qpcr, NGS Sequencing, qpcr, NGS etc. MSI MET ex14 skipping TMB EGFR BRAF KRAS NRAS BRCA1/2 ERBB2 PIK3CA AKT1 MAP2K1 STK11 FGFR1-3 IDH1 ERBB2 EGFR MET EML4-ALK ROS-1 RET NTRK1-2-3 FGFR1-2-3 Modified from McConaill JCO 2010

28 DCA N. 89 del 05/11/2018

29 Rete regionale della oncogenetica Identificare i bisogni della popolazione della regione Campania con riferimento alla problematica delle neoplasie ereditarie Stabilire i percorsi per il counseling genetico ed i test di laboratorio, definendo le modalità di interazione tra oncologo, genetista e laboratorio di biologia molecolare Organizzare una rete laboratoristica regionale che condivida metodologie di analisi e di interpretazione e schemi di refertazione Definire programmi di sorveglianza sanitaria per i soggetti ad alto rischio, portatori di alterazioni genetiche predisponenti al cancro Garantire la massima integrazione tra tutte le professionalità coinvolte nella gestione dei soggetti a rischio e nel trattamento di pazienti con neoplasie legate ad alterazioni genetiche

30 Genomics-Driven Oncology Surgeon Endoscopist Radiologist Surgeon Endoscopist Radiologist Medical Oncologist Medical Oncologist Medical Oncologist Pathologist, Molecular Biologist, Geneticist Surgeon Radiotherapist Garraway JCO 2013