Supplementary Tables from Targeting Bromodomain and Extra-Terminal (BET) Family Proteins in Castration-Resistant Prostate Cancer (CRPC)

Supplementary Tables 1 to 10 Supplementary Table 1: Cell lines ATCC - american type culture collection, FBS - fetal bovine serum, CSS - charcoal stripped serum, * - LNCaP95 cells were kindly provided by Drs. Alan K Meeker and Jun Luo (Johns Hopkins University, Baltimore, Maryland, USA), NA - non-applicable, ^ - phenol red free, BPE/EGF - bovine pituitary extract and human recombinant epidermal growth factor. Supplementary Table 2: ON-TARGETplus siRNA pools for gene expression knock down Supplementary Table 3: TaqMan probes for qRT-PCR analysis Supplementary Table 4: Primary antibodies for western blot analysis Supplementary Table 5: AR regulated genes included in AR activity score Supplementary Table 6: Patient baseline characteristics at prostate cancer diagnosis N - number, SD - standard deviation, IQR - interquartile range, NR - not recorded, PSA - prostate specific antigen, NA - non-applicable. ^5 patient without PSA values; one value >2000 (analyzed as 2000) *All cases adenocarcinoma 1Student's t-test 2Fisher's Exact Test 3Wilcoxon Rank-Sum Test Supplementary Table 7: Cellular pathways regulated by I-BET151 treatment Cellular pathways annotated by CellMap (C), Reactome (R), KEGG (K), NCI PID (N), Panther (P) and BioCarta (B) with p value <0.005 and false discovery rate (FDR) <0.05 are shown. Supplementary Table 8: Alternative splicing events in response to I-BET151 treatment SE - skipped exons, A5SS - alternative 5′ splice sites, A3SS - alternative 3′ splice sites, MXE - mutually exclusive exons, RI - retained introns, FDR - false discovery rate, NRCD - normalized reads count difference. All genes with normalized reads count difference (NRCD) >0.2 and <-0.2, and false discovery rate (FDR) <0.05 highlighted in blue. Supplementary Table 9: Patient derived organoids derived from CRPC biopsies harboring AR aberrations. CRPC - castration resistant prostate cancer, AR - androgen receptor, CN - copy number, AR-V7 androgen receptor variant 7, AR-FL - androgen receptor full length, SPOP - substrate-binding adaptor speckle-type POZ protein, IHC - immunohistochemistry H-score. *Mutational, CN analysis or IHC performed on same patient but alternative metastatic biopsy Supplementary Table 10: Patient baseline characteristics at prostate cancer diagnosis. N - number, SE - standard error, NR - not recorded, PSA - prostate specific antigen. *one patient received curative therapy (with oligo-metastatic disease) ^one patient received docetaxel in hormone sensitive setting 1Fisher's Exact Test 2Wilcoxon Rank-Sum Test