Genome-wide methylation profiling of ovarian cancer patient-derived xenografts treated with the demethylating agent decitabine identifies novel epigenetically regulated genes and pathways.

Tushar Tomar,Nicolette G Alkema,Rieks L Hoekman,Steven De Jong,G Bea A Wisman,Gert Jan Meersma,Ate Gj Van Der Zee,Harry G Klip

doi:10.1186/s13073-016-0361-5

Abstract

BackgroundIn high-grade serous ovarian cancer (HGSOC), intrinsic and/or acquired resistance against platinum-containing chemotherapy is a major obstacle for successful treatment. A low frequency of somatic mutations but frequent epigenetic alterations, including DNA methylation in HGSOC tumors, presents the cancer epigenome as a relevant target for innovative therapy. Patient-derived xenografts (PDXs) supposedly are good preclinical models for identifying novel drug targets. However, the representativeness of global methylation status of HGSOC PDXs compared to their original tumors has not been evaluated so far. Aims of this study were to explore how representative HGSOC PDXs are of their corresponding patient tumor methylome and to evaluate the effect of epigenetic therapy and cisplatin on putative epigenetically regulated genes and their related pathways in PDXs.MethodsGenome-wide analysis of the DNA methylome of HGSOC patients with their corresponding PDXs, from different generations, was performed using Infinium 450 K methylation arrays. Furthermore, we analyzed global methylome changes after treatment of HGSOC PDXs with the FDA approved demethylating agent decitabine and cisplatin. Findings were validated by bisulfite pyrosequencing with subsequent pathway analysis. Publicly available datasets comprising HGSOC patients were used to analyze the prognostic value of the identified genes.ResultsOnly 0.6–1.0 % of all analyzed CpGs (388,696 CpGs) changed significantly (p < 0.01) during propagation, showing that HGSOC PDXs were epigenetically stable. Treatment of F3 PDXs with decitabine caused a significant reduction in methylation in 10.6 % of CpG sites in comparison to untreated PDXs (p < 0.01, false discovery rate <10 %). Cisplatin treatment had a marginal effect on the PDX methylome. Pathway analysis of decitabine-treated PDX tumors revealed several putative epigenetically regulated pathways (e.g., the Src family kinase pathway). In particular, the C-terminal Src kinase (CSK) gene was successfully validated for epigenetic regulation in different PDX models and ovarian cancer cell lines. Low CSK methylation and high CSK expression were both significantly associated (p < 0.05) with improved progression-free survival and overall survival in HGSOC patients.ConclusionsHGSOC PDXs resemble the global epigenome of patients over many generations and can be modulated by epigenetic drugs. Novel epigenetically regulated genes such as CSK and related pathways were identified in HGSOC. Our observations encourage future application of PDXs for cancer epigenome studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-016-0361-5) contains supplementary material, which is available to authorized users.

Highlights

In high-grade serous ovarian cancer (HGSOC), intrinsic and/or acquired resistance against platinumcontaining chemotherapy is a major obstacle for successful treatment
We comparatively analyzed all DNA methylation probes based on genomic compartment (Fig. 1b), CpG context (Fig. 1c), CpG island content (Fig. 1d), and HIL CpG classes (high-density CpG island (HC), intermediatedensity CpG island (IC), and non-island (LC)) based on CpG enrichment [38]
We show that genome-wide DNA methylation in HGSOC Patient-derived xenograft (PDX) models is largely stable during propagation in mice

Summary

Introduction

In high-grade serous ovarian cancer (HGSOC), intrinsic and/or acquired resistance against platinumcontaining chemotherapy is a major obstacle for successful treatment. Effective treatment of cancer relies on the identification of key molecular targets of cancer growth and subsequent development of therapeutic agents against these targets This in turn mainly depends on preclinical research and predictive model systems. Patient-derived xenografts (PDXs), i.e., patient tumor tissues transplanted directly into immune-deficient mice, have appeared as better representative preclinical models [10]. They recapitulate the histological type and maintain the genomic features and reminiscent heterogeneity of corresponding patients’ primary tumors [11,12,13]. Only a few small studies in other tumor types have compared genome-wide DNA methylation of PDXs with their corresponding solid patient tumors [17,18,19]

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