Extended Data Fig. 5: PBRM1 loss is associated with gain in NF-κB activity across various models. | Nature Cell Biology

Extended Data Fig. 5: PBRM1 loss is associated with gain in NF-κB activity across various models.

From: PBRM1-deficient PBAF complexes target aberrant genomic loci to activate the NF-κB pathway in clear cell renal cell carcinoma

Extended Data Fig. 5

a) BETA analysis with P-values calculated by Kolmogorov-Smirnov test. b) Gene expression changes of selected NF-κB targets after PBRM1 expression in 786-O PBRM1 KO cells. c-h) Enrichment of TNFa_signaling_via_NF-κB geneset in c) 786-O PBRM1 KO cells expressing empty vector or PBRM1, d) 769-P cells expressing sgRNA against non-targeting control or PBRM1), e) PBRM1-deficient NCC432 and f) PBRM1-deficient A704 cells expressing empty vector or PBRM1, g) genetic mouse model with VHL single knockout or double knockout of PBRM1 and VHL (DKO) and h) TCGA data (KIRC) of tumors deficient or proficient in PBRM1. P-values were calculated by Kolmogorov-Smirnov test and q value was adjusted for multiple hypotheses testing using gene permutation. i) Heatmap shows all the significantly upregulated genes of the TNFa_signaling_via_NF-κB geneset in the PBRM1-deficient TCGA KIRC samples relative to PBRM1-proficient samples. P-value computed by Wald test. j) Normalized gene expression of selected upregulated NF-κB targets in NCC432 expressing empty vector control or wildtype PBRM1 after TNFα stimulation for 6 hours measured by RT-qPCR (n = 3 technical replicates representative of 2 biological replicates). Data are presented as mean values + /- s.d. *p < 0.05, ** p < 0.01 (two-sided t-test). k-m) Enrichment of the Hallmark geneset inflammatory response in k) 786-O PBRM1 KO cells expressing empty vector or PBRM1, l) PBRM1-deficient NCC432 cells expressing empty vector or PBRM1 and m) genetic mouse model with VHL single knockout or double knockout of PBRM1 and VHL (DKO). P values were calculated by Kolmogorov-Smirnov test and q value was adjusted for multiple hypotheses testing using gene permutation. n) Gene expression changes of NF-κB target genes after shRNA-mediated knockdown of NF-κB subunits measured by RT-qPCR (n = 3 technical replicates). *p < 0.05, ** p < 0.01, *** p < 0.001, ****p < 0.0001 (two-sided t-test). Data are presented as mean values + /- s.d. o) Overlap of RELA targets defined by RELA ChIP occupancy and decreased expression after shRELA (p < 0.05 and log2FC < -0.5) with downregulated genes after PBRM1 restoration in PBRM1-KO 786-O cells (p < 0.05 and |log2FC | > 0.3). P value of the overlap was computed by hypergeometric test.

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