Extended Data Fig. 1: Functional essentiality and recurrent alterations of FOXA1 in AR+ prostate cancer.
From: Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer
a–c, AR (a) and FOXA1 (b) mRNA (qPCR) and (c) protein expression in a panel of prostate cancer cells (n = 3 technical replicates). Mean ± s.e.m. is shown and dots are individual data points. d–f, Growth curves of AR+ prostate cancer cells treated with non-targeting control (siNC), AR- or FOXA1-targeting siRNAs (25 nM at day 0 and 1; n = 6 biological replicates). Immunoblots confirm knockdown of FOXA1 protein in LNCaP and LAPC4 72 h after siRNA treatment. For all gel source data, see Supplementary Fig. 1. g, Crystal-violet stain of AR− DU145 prostate cancer and LNCaP (control) cells treated with siNC, AR- or FOXA1-targeting siRNAs. Results represent 3 independent experiments (n = 2 biological replicates). h, Averaged proliferation z-scores for 6 independent FOXA1-targeting sgRNAs extracted from publically available CRISPR Project Achilles data (BROAD Institute) in prostate and breast cancer cells. HPRT1 and AR data serve as negative and positive controls, respectively. Mean ± s.e.m. is shown; dots are proliferative z-scores for independent sgRNAs. i, Ranked depletion or enrichment of sgRNA read counts from GeCKO-V2 CRISPR knockout screen in LNCaP cells (at day 30) relative to the input sample. Only a subset of genes—including essential controls, chromatin modifiers and transcription factors—is visualized. j, Recurrence of FOXA1 mutations across TCGA, MSK-IMPACT and SU2C cohorts. k, Density of break ends (RNA-seq chimeric junctions) within overlapping 1.5-Mb windows along chr14 in mCRPC tumours. l, Whole-genome sequencing (WGS) of seven mCRPC index cases with distinct patterns of FOXA1 translocations (Tlocs) and duplications (Dups), nominated by RNA-seq (WA46, WA37, WA57 and MO_1584) or whole-exome sequencing (MO_1778, SC_9221 and MO_1637). m, Concordance of RNA-seq (chimeric junctions) and whole-exome-sequencing-based FOXA1 locus rearrangements calls (mCRPC cohort). CNV, copy-number variation. n, Frequency of FOXA1 locus rearrangements in mCRPC based on RNA-seq and whole-exome sequencing.
