Inactivation of the PBRM1 tumor suppressor gene amplifies the HIF-response in VHL ^−/− clear cell renal carcinoma

Abstract

Most clear cell renal carcinomas (ccRCCs) are initiated by somatic inactivation of theVHLtumor suppressor gene. TheVHLgene product, pVHL, is the substrate recognition unit of an ubiquitin ligase that targets the HIF transcription factor for proteasomal degradation; inappropriate expression of HIF target genes drives renal carcinogenesis. Loss of pVHL is not sufficient, however, to cause ccRCC. Additional cooperating genetic events, including intragenic mutations and copy number alterations, are required. Common examples of the former are loss-of-function mutations of thePBRM1andBAP1tumor suppressor genes, which occur in a mutually exclusive manner in ccRCC and define biologically distinct subsets of ccRCC.PBRM1encodes the Polybromo- and BRG1-associated factors-containing complex (PBAF) chromatin remodeling complex component BRG1-associated factor 180 (BAF180). Here we identified ccRCC lines whose ability to proliferate in vitro and in vivo is sensitive to wild-type BAF180, but not a tumor-associated BAF180 mutant. Biochemical and functional studies linked growth suppression by BAF180 to its ability to form a canonical PBAF complex containing BRG1 that dampens the HIF transcriptional signature.

Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma

“…4A and table S5, A and B). As expected, the hallmark hypoxia gene set was up-regulated in A704 BAF180−/− vs. A704 BAF180wt cell lines (family-wise error rate - FWER q=0.071) (table S5A) (19). Across the more refined “founder” gene sets describing these five significantly enriched hallmark gene sets, the most strongly enriched gene set in PBAF-deficient cell lines was the KEGG cytokine-cytokine receptor interaction gene set (FWER q=0.0020 for A704 BAF180−/− vs. A704 BAF180wt and q=0.023 for A704 BAF180wt, BRG1−/− vs. A704 BAF180wt ) (Fig.…”

“…The PBAF complex suppresses the hypoxia transcriptional signature in VHL −/− ccRCC (18, 19) but its effects on tumor-immune interactions have not been thoroughly studied. To explore the potential impact of this complex on the immunophenotype of ccRCC, we analyzed previously reported whole transcriptome sequencing (RNA-seq) data from A704 ccRCC cell lines with perturbations in the PBAF complex (19). Loss of BAF180 or the related PBAF subunit BRG1, encoded by the gene SMARCA4 , prevent formation of the intact PBAF complex (19).…”

“…To explore the potential impact of this complex on the immunophenotype of ccRCC, we analyzed previously reported whole transcriptome sequencing (RNA-seq) data from A704 ccRCC cell lines with perturbations in the PBAF complex (19). Loss of BAF180 or the related PBAF subunit BRG1, encoded by the gene SMARCA4 , prevent formation of the intact PBAF complex (19). We performed gene expression analyses of BAF180-null (A704 BAF180−/− ) cell lines vs. PBAF-wildtype (A704 BAF180wt ) cell lines, as well as BRG1-null (A704 BAF180wt, BRG1−/− ) cell lines vs. PBAF-wildtype (A704 BAF180wt ) cell lines (Fig.…”

VHL Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma

“…Besides VHL, mutations in other genes such as PBRM1, SETD2, ARID1A, SMARCA4, JARID1C, and KDM6A/UTX have been reported in ccRCC (47,85), and these are likely to augment VHL's core transcriptional effects (86), contributing to heterogeneity in disease phenotypes (87) and progression patterns (88). Using the example of 786-O cells, at least two other mutations in these cells may have a direct impact on chromatin-MLL3 (p.A3902G) and gain-of-function TP53 mutations (p.R248W).…”

Genetic and metabolic hallmarks of clear cell renal cell carcinoma

“…Varela, et al demonstrated that suppression of PBRM1 through siRNA resulted in enhanced proliferation, colony formation, and migration of several ccRCC cell lines in vitro , consistent with a tumor suppressive function in renal carcinoma [38]. Interestingly, Gao, et al did not recapitulate these in vitro findings, but found that PBRM1 suppression by CRISPR did promote subcutaneous tumor growth in an on-target fashion [39]. Inactivating or truncating mutations in JARID1C (also known as KDM5C ), a histone H3 lysine 4 demethylase, and UTX (KMD6A) a histone H3 lysine 27 demethylase were identified in another study as positively selected for in ccRCC compared to other cancers [40], [41].…”