La biologia dei meccanismi di riparo del DNA

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La biologia dei meccanismi di riparo del DNA

Nicola Normanno

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

(2)

An overview of types of DNA damage and causal agents

Helleday Nat Rev Genetics 2014

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How the cell copes with damaged DNA

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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

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Mechanisms of single strand DNA break repair

• Nucleic acid excision repair (NER): removes short single- stranded DNA segment around the lesion and repairs mutations resulting from UV light and hydrocarbons

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Mechanisms of single strand DNA break repair

• Mismatch repair (MMR): recognizes and corrects mismatched bases that can result from DNA replication and recombination

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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

(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

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Homologous recombination (HR)

Toss & Cortesi J Cancer Sci Ther 2013

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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

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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 pathway¹

– 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;28:2512–19

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DNA damage

PARP

Formation of single strand DNA break (SSB)

Repair of of SSB by Base Excision Repair

Mechanism of synthetic lethality

between BRCA deficiency and PARP inhibition

Banerjee, Kaye and Ashworth (2010)

Courtesy of S.Banerjee

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DNA damage

PARP

PARP inhibition Impairs base excision repair SSB persists

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DNA damage

PARP

DNA replication: Replication fork arrests at SSB Formation of double strand breaks (DSBs) or

replication fork collapse

Normal cell with functional HR

pathway

HR-mediated DNA repair

CELL SURVIVAL

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DNA damage

PARP

DNA replication: Replication fork arrests at SSB Formation of double strand breaks (DSBs) or

replication fork collapse)

Normal cell with functional HR

pathway

HR-mediated DNA repair

Impaired HR-mediated

DNA repair

TUMOUR-SELECTIVE CELL DEATH (Synthetic Lethality))

CELL DEATH

HR-deficient tumour cell (BRCA deficient)

CELL SURVIVAL

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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…

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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

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Differences between patients with BRCA1/BRCA2-mutated tumors and

sporadic tumors

Davies Nat Med 2017

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Copy number signatures in HGSOC

Macintyre Nat Genetics 2018

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Mi-OncoSeq<br />Michigan Oncology Sequencing Program

Presented By Erin Cobain at 2017 ASCO Annual Meeting

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Mi-OncoSeq<br />MET500 Demographics

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Mi-OncoSeq<br />

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Mi-OncoSeq: Case Example #2

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Patient survival and response to pembrolizumab across 12 different tumor types with mismatch

repair deficiency

Le Science 2017

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-100 #

-90 -80 -70 -60 -50 -40 -30 -20 -10 0 10 20 30 40 50

Infantile fibrosarcoma Soft tissue sarcoma Thyroid

Salivary gland

Melanoma Breast Lung Appendix

Gastrointestinal stromal tumour Colon

Pancreas

Cholangiocarcinoma

Larotrectinib - Efficacy Across Tumour Types – Integrated Data Set

Congenital mesoblastic nephroma Unknown primary

Bone sarcoma

93.2

#

*

Maximum change in tumoursize (%)

‡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

Investigator response assessments, as of 30 July 2018

Integrated^‡ (n=109) ORR (95% CI)^† 81% (72‒88%) Best response^†

PR 63%

CR 17%

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There appears to be significant correlation between TMB and patient response to anti–PD-L1/PD-1 therapy

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):2500-2501.

Merkel cell

Median no. of coding somatic mutations per Mb 50

40

10

0

1 10 20 30 40 50

ORR (%) ₃₀

20

Melanoma

Noncolorectal (dMMR)

Cutaneous squamous cell

Colorectal (dMMR)

Renal cell Anal Cervical Hepatocellular Mesothelioma

Sarcoma

Uveal

Pancreatic Germ cell Colorectal (pMMR) Breast

Adrenocortical Prostate

GlioblastomaOvarianEndometrialHead and neckOesophagogastricNSCLC (nonsquamous)NSCLC (squamous)Small cell lung Urothelial

ORR (no. of patients evaluated)

TMB (no. of tumours analysed)

50 100 500 1000

100 1000 10,000

Correlation between TMB and ORR in 27 tumour types

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

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The major classes of genomic alterations that give rise to cancer

Modified from McConaill JCO 2010 EGFR

BRAF KRAS NRAS BRCA1/2 ERBB2 PIK3CA AKT1 MAP2K1 STK11 FGFR1-3 IDH1

EML4-ALK ROS-1 RET

NTRK1-2-3 FGFR1-2-3 ERBB2

EGFR MET Sequencing,

qPCR, NGS etc.

FISH, Immunohistochemistry qPCR, NGS

MSI

MET ex14 skipping TMB

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DCA N. 89 del 05/11/2018

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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

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Genomics-Driven Oncology

Garraway JCO 2013

Surgeon Endoscopist

Radiologist

Surgeon Endoscopist

Radiologist

Medical Oncologist

Pathologist, Molecular Biologist, Geneticist Medical

Oncologist

SurgeonRadiotherapist