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:Multiple DNA methylation changes have been associated with the acquisition of drug resistance; however it remains uncertain how many of these changes may represent critical DNA methylation drivers of chemoresistance. Using genome-wide DNA methylation profiling across 27,578 CpG sites on Illumina HumanMethylation27 bead array we identified loci at 4092 genes becoming hypermethylated in the chemoresistant A2780/cp70 ovarian tumour cell line compared to the parental sensitive A2780 line. Hypermethylation at CpG islands (CGI) is often associated with transcriptional silencing, however only 245 of these hypermethylated genes become down-regulated in A2780/cp70 as measured by microarray expression profiling. Treatment with the demethylating agent Decitabine induces re-sensitisation to cisplatin and resulted in re-expression of 41 of the down-regulated genes in cisplatin-resistant cells at the time point when re-sensitisation occurs. 13 of the 41 genes were consistently hypermethylated in two further independent cisplatin-resistant A2780 cell derivatives. Nine out of the 13 genes (ARHGDIB, ARMCX2, COL1A, FLNA, FLNC, MEST, MLH1, NTS, PSMB9) acquired methylation at CpG sites in ovarian tumours at relapse following chemotherapy or chemoresistant cell lines derived at the time of patient relapse. Furthermore, 5/13 candidate genes acquired methylation in drug-resistant in vivo-derived ovarian cancer sustaining (side population) cells. Therefore, this small set of genes are potential key drivers of chemoresistance and should be further evaluated as predictive biomarkers, both to existing chemotherapies, but also to epigenetic therapies used to modulate drug resistance. Array-based methylation profiling was performed using the Infinium HumanMethylation27 BeadChip in two cisplatin sensitive cell lines and three cisplatin resistant cell lines derived in vitro, four pairs of cisplatin sensitive and resistant cell lines derived in vivo, 7 pairs of tumour tissues obtained from patients before chemotherapy and at disease relapse, 2 pairs of IGROV1 SP and NSP cells. The reproducibility of the Infinium HumanMethylation27 BeadChips was evaluated using biological and technical replicates of matched chemosensitive/chemoresistant ovarian cancer cell lines PEO1/PEO4. Differential methylation cutoff was estimated from two biological replicates by bootstrap resampling.