PBRM1 Regulates the Expression of Genes Involved in Metabolism and Cell Adhesion in Renal Clear Cell Carcinoma

Abstract

Polybromo-1 (PBRM1) is a component of the PBAF (Polybromo-associated-BRG1- or BRM-associated factors) chromatin remodeling complex and is the second most frequently mutated gene in clear-cell renal cell Carcinoma (ccRCC). Mutation of PBRM1 is believed to be an early event in carcinogenesis, however its function as a tumor suppressor is not understood. In this study, we have employed Next Generation Sequencing to profile the differentially expressed genes upon PBRM1 re-expression in a cellular model of ccRCC. PBRM1 re-expression led to upregulation of genes involved in cellular adhesion, carbohydrate metabolism, apoptotic process and response to hypoxia, and a downregulation of genes involved in different stages of cell division. The decrease in cellular proliferation upon PBRM1 re-expression was confirmed, validating the functional role of PBRM1 as a tumor suppressor in a cell-based model. In addition, we identified a role for PBRM1 in regulating metabolic pathways known to be important for driving ccRCC, including the regulation of hypoxia response genes, PI3K signaling, glucose uptake, and cholesterol homeostasis. Of particular novelty is the identification of cell adhesion as a major downstream process uniquely regulated by PBRM1 expression. Cytoskeletal reorganization was induced upon PBRM1 reexpression as evidenced from the increase in the number of cells displaying cortical actin, a hallmark of epithelial cells. Genes involved in cell adhesion featured prominently in our transcriptional dataset and overlapped with genes uniquely regulated by PBRM1 in clinical specimens of ccRCC. Genes involved in cell adhesion serve as tumor suppressor and maybe involved in inhibiting cell migration. Here we report for the first time genes linked to cell adhesion serve as downstream targets of PBRM1, and hope to lay the foundation of future studies focusing on the role of chromatin remodelers in bringing about these alterations during malignancies.

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

“…A recent study suggested that BAF180 augments the hypoxic response, in contrast to our findings (22). Although we do not understand this discrepancy, the authors of that study used Caki-2 cells engineered to produce wild-type BAF180.…”

“…Consistent with a recent report, inducible expression of wildtype BAF180 suppressed the proliferation of Caki-2 cells (SI Appendix, Fig. S3 E and F) (22). However, this effect was not specific to wild-type BAF180 because it was also observed with BAF180 (Q1298*; SI Appendix, Fig.…”

“…S5 and S6). Similar findings have been observed by others (22). We do not fully understand the discrepancy between our findings and those reported by Varela et al.…”

The epigenetic landscape of renal cancer

“…Reports of PBRM1 expression levels in RCC and of its association with poor patient survival are contradictory 146,147 . The precise mechanisms that underlie the oncogenic contribution of PBRM1 mutations in RCC remain to be clarified; however, in addition to its role in regulating genes that control proliferation, such as p21 CIP1 , PBRM1 also regulates the expression of cell-adhesion and cell-signalling molecules such as E-cadherin [148][149][150] (and as such, the subcellular distribution of β-catenin) as well as sister chromatid cohesion 151 . Thus, correct expression of PBRM1 is likely to have important roles in pathways that are frequently dysregulated in cancer and in maintenance of genomic integrity, which is a barrier to tumourigenicity 152 .…”

Choosing the right cell line for renal cell cancer research

“…The ACHN cell line expresses the protein, but harbors a heterozygous nonsense mutation, while 786-O, 769-P, Caki-1, and A-498 express wild-type PBRM1 [133, 134]. The PBRM1 mutation is also reported in Caki-2 and A-704 lines; loss-of-function gene mutations in A-704 and the deletion in exon 17 of the PBRM1 gene in Caki-2 [135] results in no protein expression [133, 134, 136]. Mutations have also been detected in OS-RC-2 and RCC-ER (see Additional file 1: Table S1 for ref) cell lines; however, the former was reported to express PBRM1 protein [133].…”