Integrative Epigenetic and Gene Expression Analysis of Renal Tumor Progression to Metastasis

Abstract

The Cancer Genome Atlas (TCGA) and other large-scale genomic data pipelines have been integral to the current understanding of the molecular events underlying renal cell carcinoma (RCC). These data networks have focused mostly on primary RCC, which often demonstrates indolent behavior. However, metastatic disease is the major cause of mortality associated with RCC and data sets examining metastatic tumors are sparse. Therefore, a more comprehensive analysis of gene expression and DNA methylome profiling of metastatic RCC in addition to primary RCC and normal kidney was performed. Integrative analysis of the methylome and transcriptome identified over 30 RCC-specific genes whose mRNA expression inversely correlated with promoter methylation, including several known targets of hypoxia inducible factors. Notably, genes encoding several metabolism-related proteins were identified as differentially regulated via methylation including hexokinase 2, aldolase C, stearoyl-CoA desaturase, and estrogen-related receptor-γ (ESRRG), which has a known role in the regulation of nuclear-encoded mitochondrial metabolism genes. Several gene expression changes could portend prognosis in the TCGA cohort. Mechanistically, ESRRG loss occurs via DNA methylation and histone repressive silencing mediated by the polycomb repressor complex 2. Restoration of ESRRG in RCC lines suppresses migratory and invasive phenotypes independently of its canonical role in mitochondrial metabolism. Collectively, these data provide significant insight into the biology of aggressive RCC and demonstrate a novel role for DNA methylation in the promotion of HIF signaling and invasive phenotypes in renal cancer.

PRDM16 suppresses HIF-targeted gene expression in kidney cancer

“…As a positive control, we identified increased 5mC enrichment in RCC (as compared with matched normal kidney) of the promoter of ESSRG , a gene that we recently reported to be methylated in RCC (Fig. S2, B and C; Nam et al, 2019). Collectively, these data demonstrate that the PRDM16 promoter region is methylated in RCC.…”

“…As noted previously, PRDM16 has a prominent role in brown fat metabolism and has previously been shown to induce expression of the mitochondrial metabolism-related transcription factors in adipocytes including PGC-1α and ERR-γ (encoded by PPARGC1A and ESRRG ) as well as uncoupling protein 1 ( UCP1 ; Kajimura et al, 2008; Seale et al, 2007, 2008). Notably, the expression of PPARGC1A and ESRRG has previously been shown to be reduced in RCC (LaGory et al, 2015; Nam et al, 2019). We therefore assessed the effects of PRDM16 on the expression of these factors in RCC cells via stable transduction in RCC cells.…”

“…We recently reported an integrative genomic analysis of DNA methylation and gene expression landscapes of kidney cancer that included three sample groups: normal kidney ( n = 9), primary RCC ( n = 9), and metastatic RCC tissue deposits ( n = 26; Nam et al, 2019). We analyzed the transcriptomes of the deposited data (series GSE105261) using GEO2R (National Center for Biotechnology Information [NCBI]) and identified the top 250 most differentially expressed genes (regardless of directionality) based on the F-statistic, an analysis that combines t-statistics for all pairwise comparisons when more than two sample groups are present (Table S1).…”

Targeting the Immune system and Epigenetic Landscape of Urological Tumors

“…Also, several promoter-methylated genes involved in the various hallmarks of cancer are found in RCC, including the ones related to angiogenesis (in which VHL is included), metabolism, apoptosis and cell cycle, among others [95]. Agents targeting specific epigenetic aberrations have also shown anti-neoplastic activity in RCC, including the EZH2 inhibitor GSK126, which suppressed migration and invasion [96], and various HDAC inhibitors, alone or in combination with routinely used agents [97][98][99][100][101]. Moreover, similar to BlCa, these latter inhibitors also showed the ability to reverse resistance to currently used agents such as mTOR inhibitors [102].…”

ESRRG promoter hypermethylation as a diagnostic and prognostic biomarker in laryngeal squamous cell carcinoma

“…Similar to its role in female tumors, ESRRG has been reported to be a tumor suppressor in prostate cancer, a male cancer, inducing p21 and p27 expression to arrest the cell cycle . Recently, Nam et al reported that ESRRG plays a canonical role in renal cell carcinoma (RCC). The study found that ESRRG loss occurred via DNA methylation and histone repressive silencing mediated by the polycomb repressor complex 2 (PRC2), and ESRRG restoration in RCC lines suppressed the migratory and invasive phenotypes.…”