DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer

Riikka J Lund,Kaisa Huhtinen,Olli Carpén,Riitta Lahesmaa,Juha Rantala,Jussi Salmi,Elizabeth V Nguyen,Robert Moulder,David R Goodlett

doi:10.1038/s41598-017-01624-4

Abstract

High-grade serous ovarian cancer is the most common ovarian cancer type. Although the combination of surgery and platinum-taxane chemotherapy provide an effective treatment, drug resistance frequently occurs leading to poor outcome. In order to clarify the molecular mechanisms of drug resistance, the DNA methylation and transcriptomic changes, associated with the development of drug resistance in high-grade serous ovarian cancer, were examined from patient derived malignant ascites cells. In parallel with large-scale transcriptome changes, cisplatin resistance was associated with loss of hypermethylation at several CpG sites primarily localized in the intergenic regions of the genome. The transcriptome and CpG methylome changes in response to cisplatin treatment of both sensitive and resistant cells were minimal, indicating the importance of post-translational mechanisms in regulating death or survival of the cells. The response of resistant cells to high concentrations of cisplatin revealed transcriptomic changes in potential key drivers of drug resistance, such as KLF4. Among the strongest changes was also induction of IL6 in resistant cells and the expression was further increased in response to cisplatin. Also, several other components of IL6 signaling were affected, further supporting previous observations on its importance in malignant transformation and development of drug resistance in ovarian cancer.

Highlights

The molecular mechanisms leading to drug resistance can be heterogeneous and complex[4]
We have further investigated the potential mechanisms associated with drug resistance by comparing cisplatin responses in sensitive and resistant patient derived HGSOC cell lines with next-generation sequencing based applications
237 (16%) sites were methylated at higher levels in the resistant cell line and had lower methylation levels in the sensitive line

Summary

Introduction

The molecular mechanisms leading to drug resistance can be heterogeneous and complex[4]. DNA methylation and transcriptional changes associated with drug resistance have been detected in several genomic sites in both cell lines and patient samples[5,6,7,8]. Methylation and transcriptional silencing of the MLH1 gene have been repeatedly associated with cisplatin resistance[8, 9]. Several candidate driver genes for cisplatin resistance have been identified, further studies are required to clarify the heterogeneity of the drug resistance mechanisms and clinical significance of the findings. We have further investigated the potential mechanisms associated with drug resistance by comparing cisplatin responses in sensitive and resistant patient derived HGSOC cell lines with next-generation sequencing based applications. We have used Reduced Representation Bisulfite Sequencing (RRBS) together with messenger RNA sequencing (mRNA-seq) for unbiased identification of the DNA methylation changes at single nucleotide resolution in the CpG rich regions of the genome in correlation with genome-wide transcriptome changes

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