FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity

Mutations in the pioneer transcription factor FOXA1 occur in 10%-40% of prostate cancers and broadly alter chromatin accessibility. In a cohort of 874 primary and metastatic tumors, we confirm frequent Wing2 missense mutations and indels, as well as C-terminal truncating frameshifts. To define their functional impact, we performed single-nucleus multiome profiling in mouse prostate organoids expressing representative alleles, including overexpressed wild-type FOXA1. Each subgroup produces distinct chromatin and transcriptional changes, but all perturb epithelial lineage specification. Indel mutants promote basal-like states, whereas C-terminal truncations, Wing2 missense mutations, and elevated wild-type FOXA1 drive secretory L1-like luminal fates. Integrated RNA-seq, ATAC-seq, and ChIP-seq reveal that L1-like specification involves a hybrid androgen receptor/FOXA1 motif and cooperation with POU2F1. In vivo, these same alleles, combined with Trp53/Pten loss, shift tumor histology from basal-like to secretory luminal phenotypes.