Abstract 3458: An epigenomic next-generation sequencing approach to identify predictive markers for PARP inhibitor response in breast cancer cells.
Authors: De Meyer Tim , Trooskens Geert , Wibbe Mascha K. , Bartmann Sebastian B. , van Engeland Manon , Van Criekinge Wim , Tjan-Heijnen Vivianne C. , Knüchel Ruth , Veeck Jürgen 
Published: August 2014

Abstract
Background: Inhibition of poly(ADP-ribose)-polymerase-1 (PARP1) leads to synthetic lethality in BRCA-associated breast cancer cells, and is a promising novel treatment strategy for hereditary BRCA-mutated tumors. Since BRCA1/2 germline mutations are relatively infrequent, our study aims at a systematic identification of epigenetic aberrations that may predict PARP inhibitor (PARib) response in sporadic breast cancer cells.
Methods: Genome-wide DNA methylation was assessed in nine malignant and one non-malignant (MCF10A) breast cell line (BCL) by MBD-isolated genome sequencing (MiGS). Sensitivity to the PARib AG14361 was determined by viability and clonogenicity assays before and after global DNA demethylation in vitro, and confirmed with the PARib AZD-2281 (olaparib). Correlation analyses of DNA methylation with PARib sensitivity identified potentially predictive candidate genes and microRNAs. By incubation with increasing concentrations of AG14361 we generated an isogenic PARib resistant BCL originally sensitive to AG14361.
Results: BCL clustered in three sensitivity groups (sensitive, intermediate, resistant) independent of hormone receptor status, but associated with PARP1 level (p=0.042). BRCA1 mutated (MDA-MB-436) and BRCA1 methylated (UACC3199) BCL were most sensitive to PARib. After global DNA demethylation sensitive BCL acquired resistance while resistant BCL were modestly sensitized. MCF10A cells did not shift PARib resistance after DNA demethylation. Correlation of MiGS profiles with PARib sensitivity identified 382 genes and seven microRNAs with exclusive promoter/exon1 methylation in sensitive BCL, while 313 genes and one microRNA were affected in resistant BCL. Artificially mediating resistance to BRCA1 methylated cells did neither hypomethylate the BRCA1 promoter nor induce BRCA1 expression, but significantly reduce cell proliferation. Gene ontology analyses revealed that methylation of WNT, ErbB, SHH, and mTOR signaling genes was significantly enriched in PARib resistant cells, while PARib sensitive cells exhibited methylation in DNA repair genes.
Conclusions: Aberrant DNA methylation seems to be involved in PARib sensitivity/resistance in BCL. By epigenomic analyses we identified several potential candidate genes beyond BRCA1 that might modulate PARib sensitivity/resistance in breast cancer, implying that more patients than currently anticipated may benefit from this drug class. Their expression, DNA methylation and net effect on cancer pathways are currently validated in BCL and explored in primary breast cancer tissues.
Citation Format: Tim De Meyer, Geert Trooskens, Mascha K. Wibbe, Sebastian B. Bartmann, Manon van Engeland, Wim Van Criekinge, Vivianne C. Tjan-Heijnen, Ruth Knüchel, Jürgen Veeck. An epigenomic next-generation sequencing approach to identify predictive markers for PARP inhibitor response in breast cancer cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3458. doi:10.1158/1538-7445.AM2013-3458