Promoter methylation of DNA homologous recombination genes is predictive of the responsiveness to PARP inhibitor treatment in testicular germ cell tumors

Abstract

Testicular germ cell tumors (TGCTs) are the most common cancers in men aged 15–39 years and are divided into two major groups, seminomas and nonseminomas. Novel treatment options are required for these patients, to limit side effects of chemotherapy. We hypothesized that promoter methylation of relevant homologous recombination (HR) genes might be predictive of response to poly‐ADP ribose polymerase inhibitors (PARPis) in TGCTs. We report a study pipeline combining in silico, in vitro, and clinical steps. By using several databases and in silico tools, we identified BRCA1, RAD51C, PALB2, RAD54B, and SYCP3 as the most relevant genes for further investigation and pinpointed specific CpG sites with pronounced negative correlation to gene expression. Nonseminomas displayed significantly higher methylation levels for all target genes, where increased methylation was observed in patients with more differentiated subtypes and higher disease burden. We independently performed second‐line targeted validation in tissue series from TGCT patients. A moderate and/or strong anti‐correlation between gene expression (assessed by RNA‐sequencing) and promoter methylation (assessed by 450k array) was found, for all of the targets. As a proof of concept, we demonstrated the sensitivity of TGCT cell lines to Olaparib, which associated with differential methylation levels of a subset of targets, namely BRCA1 and RAD51C. Our findings support the use of HR genes promoter methylation as a predictor of the therapeutic response to PARPis in patients with TGCT.

The component of the m6A writer complex VIRMA is implicated in aggressive tumor phenotype, DNA damage response and cisplatin resistance in germ cell tumors

“…Overall, we demonstrate that shifts in m 6 A abundance, as well as in expression of related players go along with the process of differentiation in (T) GCTs, and further highlight that VIRMA has an oncogenic role in these tumors, contributing both to tumor aggressiveness and to cisplatin response in NS, in vitro and in vivo, by influencing DNA repair capacity. In future studies we aim to further explore other pathways hypothetically regulated by m 6 A deposition, and evaluate DNA damage response in more detail, following our previous observations in this tumor model [86]. Our data further reinforces investigation of RNA modifications in TGCTs (with VIRMA representing a promising predictive biomarker of patient outcome and therapeutic target, to be confirmed in future studies).…”

Reciprocal epigenetic remodeling controls testicular cancer hypersensitivity to hypomethylating agents and chemotherapy

“…It will be interesting to assess how altering DNMT3B and polycomb components effect these endpoints in TGCT cells in future studies. Another potential mechanism to consider is the direct regulation of DNA damage response and repair gene expression by DNA methylation and polycomb remodeling in TGCT cells as recent reports have shown some genes involved in these pathways can be regulated by DNA methylation in TGCT cells and tumors [41][42][43]. However, we did not detect a clear signal for these family of genes in our transcriptome analyses.…”

Cisplatin for cancer therapy and overcoming chemoresistance

“…Resistance to cisplatin increased in cells which (i) repaired the DNA double strand breaks via the homologous recombination repair pathway, (ii) had reduced expression of the tumour protein 53 binding protein 1 (53BP1), and (iii) inhibited DNA-dependent protein kinase protein (DNA-PKcs) activity that decreased cisplatin cytotoxicity [ 119 ]. Thus, by modulating 53BP1 and, by inhibiting poly (ADP-ribose) polymerase (PARP) activity (which is often used in anticancer salvage therapy), the cisplatin-resistance could be counteracted, and cisplatin given in combination with a PARP inhibitor would be potentially beneficial to cisplatin-refractory patients [ 121 ]. An evaluation of the crosstalk between the immune cell subsets and endogenous DNA damage was linked to chemoresistance in testicular germ cell tumours to cisplatin therapy [ 122 ].…”