Hypermethylation and global remodelling of DNA methylation is associated with acquired cisplatin resistance in testicular germ cell tumours

ABSTRACT

Testicular germ cell tumours (TGCTs) respond well to cisplatin-based therapy. However, cisplatin resistance and poor outcomes do occur. It has been suggested that a shift towards DNA hypermethylation mediates cisplatin resistance in TGCT cells, although there is little direct evidence to support this claim. Here we utilized a series of isogenic cisplatin-resistant cell models and observed a strong association between cisplatin resistance in TGCT cells and a net increase in global CpG and non-CpG DNA methylation spanning regulatory, intergenic, genic and repeat elements. Hypermethylated loci were significantly enriched for repressive DNA segments, CTCF and RAD21 sites and lamina associated domains, suggesting that global nuclear reorganization of chromatin structure occurred in resistant cells. Hypomethylated CpG loci were significantly enriched for EZH2 and SUZ12 binding and H3K27me3 sites. Integrative transcriptome and methylome analyses showed a strong negative correlation between gene promoter and CpG island methylation and gene expression in resistant cells and a weaker positive correlation between gene body methylation and gene expression. A bidirectional shift between gene promoter and gene body DNA methylation occurred within multiple genes that was associated with upregulation of polycomb targets and downregulation of tumour suppressor genes. These data support the hypothesis that global remodelling of DNA methylation is a key factor in mediating cisplatin hypersensitivity and chemoresistance of TGCTs and furthers the rationale for hypomethylation therapy for refractory TGCT patients.

KEYWORDS:

• Cisplatin
• testicular germ cell tumour
• DNA methylation
• chemoresistance

Acknowledgments

We would like to thank Daniel Weisenberger and Kendra Bergen at the Molecular Genomics/Methylation Core at the University of Southern California for performing Infinium MethylationEPIC beadchip array assays and members of the Roy J. Carver Biotechnology Center and the University of Illinois, including Dr. Alvaro Hernandez and Chris Wright for RNA-sequencing.

Disclosure statement

The authors declare no conflict of interest.

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Funding

This research was funded by the National Institutes of Health [Grants R01-CACA211875 (MJS) and R03CA223709 (MJS)]; a Reach Grant from the Alex’s Lemonade Stand Foundation (MJS); and an ASCO Conquer Cancer Career Development Award (CA).