Methylomes of renal cell lines and tumors or metastases differ significantly with impact on pharmacogenes

Abstract

Current therapies for metastatic clear cell renal cell carcinoma (ccRCC) show limited efficacy. Drug efficacy, typically investigated in preclinical cell line models during drug development, is influenced by pharmacogenes involved in targeting and disposition of drugs. Here we show through genome-wide DNA methylation profiling, that methylation patterns are concordant between primary ccRCC and macro-metastases irrespective of metastatic sites (rs ≥ 0.92). However, 195,038 (41%) of all investigated CpG sites, including sites within pharmacogenes, were differentially methylated (adjusted P < 0.05) in five established RCC cell lines compared to primary tumors, resulting in altered transcriptional expression. Exemplarily, gene-specific analyses of DNA methylation, mRNA and protein expression demonstrate lack of expression of the clinically important drug transporter OCT2 (encoded by SLC22A2) in cell lines due to hypermethylation compared to tumors or metastases. Our findings provide evidence that RCC cell lines are of limited benefit for prediction of drug effects due to epigenetic alterations. Similar epigenetic landscape of ccRCC-metastases and tumors opens new avenue for future therapeutic strategies.

The epigenetic landscape of renal cancer

“…Epigenetic changes, which depend on the type of treatment and the tissue-specific microenvironment, are likely to drive much of the metastatic process. Metastasising tumours undergo branched evolution at a genetic level, resulting in many cases where the metastasis is no longer genetically identical to the primary tumour 235,236 ; however, genome-wide methylation analyses have revealed that primary renal tumours and resulting metastases remain remarkably similar at the level of DNA methylation 237 . Persistent similarities between primary and metastatic tumours might present good opportunities for the development of novel therapies.…”

“…The heterogeneity of mutations within tumours, which results in different subclones that evolve differently, is a major obstacle to clinical translation 235,236,238,239 . Intratumour heterogeneity of DNA methylation might, however, not be as pronounced as intratumour heterogeneity of genomic changes.…”

Interethnic DNA Methylation Difference and Its Implications in Pharmacoepigenetics

“…Of the CpG sites located close to the ADME genes, 35 (6,8,9 and 227) CpG sites were identified as E-CpGs located in 24 (5, 6, 7 and 109) ADME genes (Supplementary Table 5) in the BRCA (COAD, HNSC, UCEC and HapMap) dataset.…”

“…For example, ∼60% of human genes contain CGIs in their promoter regions, and the hypermethylation of these CGIs suppresses gene expression [4]. Numerous studies have reported that DNA methylation variants are associated with complex traits [1,5] and treatment responses, particularly cancer treatments [6][7][8]. For example, the hypermethylation of the promoter of the DNA repair gene MGMT can be used to predict an improved clinical response to alkylating agents in glioma patients [9].…”

Response to Comment on “Epigenetic activation of the drug transporter OCT2 sensitizes renal cell carcinoma to oxaliplatin”

“…However, the specificity and selectivity of KEK to OCT2 are not convincing based on their reported data. In their recent publication, they showed that KEK detected two bands in OCT2-transfected HEK293 cells, and the molecular mass was not shown (5). In their earlier publication, they presented data that KEK detected multiple and smear bands 80 kDa in OCT2-transfected Madin-Darby canine kidney (MDCK) cells and~90 kDa in kidney tissues (6).…”