Dataset Information

Whole genome characterisation of chemoresistant ovarian cancer [Illumina_450K_Methylation]

ABSTRACT: Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1. Genomic DNA (500ng) was bisulfite converted using EZ DNA methylation Kit (Zimo Research) following the manufacturer’s protocol with modification for Illumina Infinium Methyaltion arrays. Samples were hybridized to Infinium Human Methylation 450K BeadChips (Illumina) according to the manufacturer’s protocol. Arrays were scanned on Iscan (Illumina). Data was background corrected, normalized to internal controls and QC was performed at the probe and sample level. COMBAT was used to remove batch effects (Johnson et al., 2007). Contributor: The Australian Ovarian Cancer Study Group

ORGANISM(S): Homo sapiens

SUBMITTER: Greg Young Jason Ellul Senel Idrisoglu Kathryn Alsop Sian Fereday Paul Waring Chris Mitchell Angelika N Christ Joy Hendley Patricia O'Brien Orla McNally Michael Friedlander Elizabeth L Christie Huei San Ravikiran Vedururu Timothy J Bruxner Felicity Newell Matthew Anderson Scott Wood Michael C Quinn Barsha Poudel Qinying Xu Karin S Kassahn Ernst Lengyel Emma Markham Catherine Kennedy George Au-Yeung Robert Brown Jodie Leditschke Timothy P Holloway Shivashankar H Nagaraj Stephen Kazakoff San Leong Nicola Waddell Peter J Wilson Ann M Patch Kelly Quek Dale W Garsed David K Miller Dariush Etemadmoghadam Andrea Jewell J L Fink Paul Harnett Hani Gabra Mark Shackleton Stephen Cordner David D Bowtell Peter J Bailey Heather Thorne Yoke E Chiew Linda Mileshkin John V Pearson Prue Cowin Anne Hamilton Darrin F Taylor Charlotte Wilhelm-Benartzi Richard W Tothill Nathan Hall Conrad Leonard Ehsan Nourbakhsh Nick Waddell Andrew Lonie Ann-Marie Patch Gisela Mir Arnau Katia Nones Ronny Drapkin Ed Curry Kate Strachan Sean M Grimmond Craig Nourse Jan Pyman Suzanne Manning Euan Stronach Ivon Harliwong Joshy George Collin Stewart Michael Quinn Anna deFazio Walid Azar Jillian Hung Nadia Traficante Maria A Doyle Oliver Holmes Timothy Semple

PROVIDER: E-GEOD-65820 | ArrayExpress | 2015-05-19

SECONDARY ACCESSION(S): GSE65820PRJNA275137

REPOSITORIES: GEO, ArrayExpress

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Project description:INTRODUCTION: BRCA1 or BRCA2 germline mutations increase the risk of developing breast cancer. Tumour cells from germline mutation carriers have frequently lost the wild-type allele. This is predicted to result in genomic instability where cell survival depends upon dysfunctional checkpoint mechanisms. Tumorigenic potential could then be acquired through further genomic alterations. Surprisingly, somatic BRCA mutations are not found in sporadic breast tumours. BRCA1 methylation has been shown to occur in sporadic breast tumours and to be associated with reduced gene expression. We examined the frequency of BRCA1 methylation in 143 primary sporadic breast tumours along with BRCA1 copy number alterations and tumour phenotype. METHODS: Primary sporadic breast tumours were analysed for BRCA1alpha promoter methylation by methylation specific PCR and for allelic imbalance (AI) at BRCA1 and BRCA2 loci by microsatellite analysis and TP53 (also known as p53) mutations by constant denaturing gel electrophoresis. The BRCA1 methylated tumours were analysed for BRCA1 copy alterations by fluorescence in situ hybridisation and BRCA1 expression by immunostaining. RESULTS: BRCA1 methylation was found in 13/143 (9.1%) sporadic breast tumours. The BRCA1 methylated tumours were significantly associated with estrogen receptor (ER) negativity (P = 0.0475) and displayed a trend for BRCA1 AI (P = 0.0731) as well as young-age at diagnosis (< or = 55; P = 0.0898). BRCA1 methylation was not associated with BRCA2 AI (P = 0.5420), although a significant association was found between BRCA1 AI and BRCA2 AI (P < 0.0001).Absent/markedly reduced BRCA1 expression was observed in 9/13 BRCA1 methylated tumours, most of which had BRCA1 deletion. An elevated TP53 mutation frequency was found among BRCA1 methylated tumours (38.5%) compared with non-methylated tumours (17.2%). The BRCA1 methylated tumours were mainly of tumour grade 3 (7/13) and infiltrating ductal type (12/13). Only one methylated tumour was of grade 1. CONCLUSION: BRCA1 methylation is frequent in primary sporadic breast tumours. We found an indication for BRCA1 methylation to be associated with AI at the BRCA1 locus. Almost all BRCA1 methylated tumours with absent/markedly reduced BRCA1 expression (8/9) displayed BRCA1 deletion. Thus, epigenetic silencing and deletion of the BRCA1 gene might serve as Knudson's two 'hits' in sporadic breast tumorigenesis. We observed phenotypic similarities between BRCA1 methylated and familial BRCA1 tumours, based on BRCA1 deletion, TP53 mutations, ER status, young age at diagnosis and tumour grade.

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