Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

PBRM1 Knockdown in RCC Cell Lines

ABSTRACT: PBRM1 was found to be mutated in a high percentage of clear cell RCCs. We performed knockdown of PBRM1 via siRNA and compared with scrambled control in three different RCC cell lines. PBRM1 siRNA and mock treated cell lines were normalized together with 'hypoxic' clear cell renal tumors and normal renal tissue samples from GSE17818.

ORGANISM(S): Homo sapiens

SUBMITTER: Karl Dykema

PROVIDER: E-GEOD-22316 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma.

Varela Ignacio I Tarpey Patrick P Raine Keiran K Huang Dachuan D Ong Choon Kiat CK Stephens Philip P Davies Helen H Jones David D Lin Meng-Lay ML Teague Jon J Bignell Graham G Butler Adam A Cho Juok J Dalgliesh Gillian L GL Galappaththige Danushka D Greenman Chris C Hardy Claire C Jia Mingming M Latimer Calli C Lau King Wai KW Marshall John J McLaren Stuart S Menzies Andrew A Mudie Laura L Stebbings Lucy L Largaespada David A DA Wessels L F A LF Richard Stephane S Kahnoski Richard J RJ Anema John J Tuveson David A DA Perez-Mancera Pedro A PA Mustonen Ville V Fischer Andrej A Adams David J DJ Rust Alistair A Chan-on Waraporn W Subimerb Chutima C Dykema Karl K Furge Kyle K Campbell Peter J PJ Teh Bin Tean BT Stratton Michael R MR Futreal P Andrew PA

Nature 20110119 7331

The genetics of renal cancer is dominated by inactivation of the VHL tumour suppressor gene in clear cell carcinoma (ccRCC), the commonest histological subtype. A recent large-scale screen of ∼3,500 genes by PCR-based exon re-sequencing identified several new cancer genes in ccRCC including UTX (also known as KDM6A), JARID1C (also known as KDM5C) and SETD2 (ref. 2). These genes encode enzymes that demethylate (UTX, JARID1C) or methylate (SETD2) key lysine residues of histone H3. Modification of ...[more]

PMID: 21248752

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Project description:PBRM1 is the 2nd-most frequently inactivated gene in clear cell renal cell cancer (RCC) but the oncogenic mechanisms, and hence methods for correction, are unclear. PBRM1 is a subunit of the PBAF coactivator complex that transcription factors use to reposition nucleosomes (‘open chromatin’) for gene activation. We therefore looked for transcription factors that recruit endogenous PBRM1 in kidney lineage/RCC cells, as a waypoint to identifying pathways impacted by PBRM1 loss. Unbiased immunoprecipitation/mass-spectrometry analyses of the endogenous PBRM1 interactome in kidney lineage cells revealed PAX8, a master transcription factor essential for proximal tubule epithelial fates, as the major transcription factor recruiting PBRM1/PBAF. The reverse analyses of the PAX8 interactome confirmed recruitment specifically of PBRM1/PBAF, and not the functionally similar BAF coactivator complex. More conspicuous in the PAX8 hub in RCC cells, however, were several corepressors, e.g. DNMT1, which oppose coactivators to repress instead of activate genes. Accordingly, key PAX8 target genes, e.g., GATA3, LHX1, WT1, and ~1000 other downstream kidney epithelial genes, but not PAX8 or PAX2, demonstrated loss of the histone lysine 27 acetylation (H3K27ac) activation mark, increase in CpG methylation repression marks, and lower expression in RCC vs normal kidney cortex, with the greatest repression in cases with bi-allelic PBRM1 inactivation. PBRM1 re-introduction into RCC cells, or depletion of the corepressor DNMT1 using siRNA or a clinical drug decitabine, rebalanced composition and function of the PAX8 transcription factor hub to coactivators, to thereby activate terminal epithelial-fates in vitro and in vivo. In sum, PBRM1 loss in RCC cells skews coregulator composition of the PAX8 master transcription factor hub toward corepressors and repression instead of activation of the downstream terminal epithelial-program; this oncogenic action could be reversed by pharmacologic corepressor depletion/inhibition.

Dataset Information

PBRM1 Knockdown in RCC Cell Lines

Publications

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma.

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