Extended Data Fig. 8: Bortezomib abrogates RELA occupancy and selectively targets PBRM1 deficiency.
a) Colony formation of 786-O cells with and without PBRM1 treated with DMSO or NF-κB inhibitor, Bay 11-7085. b) Single sample gene-set enrichment (ssGSEA) of TNFa signaling via NF-κB in 786-O PBRM1 WT or KO cells treated with DMSO or 0.005 μM bortezomib (n = 3 biological replicates). Data are presented as median + /- 25%. Lower whisker is smallest observation greater than or equal to 25% quantile - 1.5 * interquantile range (IQR). Upper whisker represents the largest observation less than or equal to 75% + 1.5 * IQR. Amount of normalized RELA protein in the c) input or d) co-immunoprecipitated with SMARCA4 from 3 independent runs. Data are presented as mean values + /- s.d. e) Tornado plots of RELA and SMARCA4 ChIP-seq signals in parental 786-O or PBRM1-KO 786-O cells treated with DMSO or 0.005 μM bortezomib for 9 hours. f) Kaplan-Meier curves of NSG mice bearing 786-O isogenic cells treated with PBS vehicle control or 0.5 mg/kg bortezomib (WT: n = 10 PBS arm, median survival = 39 days, n = 10 bortezomib arm, median survival = 52 days, HR = 4.1, p = 3E-6, log rank test; KO: n = 10 PBS arm, median survival = 35 days, n = 10 bortezomib arm, median survival = 66 days, HR = 4.1, p = 3E-6, log rank test). g) Kaplan-Meier curves of NSG mice bearing NCC432 isogenic cells treated with PBS vehicle control or 0.5 mg/kg bortezomib (EV: n = 16 PBS arm, median survival = 42 days, n = 14 bortezomib arm, median survival = 49 days, HR = 2.5, p = 0.0009, log rank test; PBRM1: n = 12 PBS arm, median survival = 55 days, n = 14 bortezomib arm, median survival = 58 days, HR = 0.9, p = 0.7, log rank test). h) 786-O PBRM1 WT or KO cells were screened against the high-specific SGC epigenetic probe collection and cell viability was measured by colony formation after 1 week of treatment relative to DMSO control.
