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

Mutations in the pioneer transcription factor FOXA1, found in 10-40% of human prostate cancers, alter global chromatin accessibility and promote growth in prostate cells. Through analysis of a novel cohort of 874 primary and metastatic prostate tumors with somatic FOXA1 mutations, we confirm the high frequency of missense mutations (n=339) and indels (n=335) in the Wing2 region of the Forkhead domain, as well as frameshift mutations that truncate the C-terminus (n=287). To investigate the transcriptomic consequences of each mutation subgroup as well as elevated levels of wild-type FOXA1 (WT) (a fourth well documented subgroup), we performed single nucleus multiome sequencing in primary mouse organoids following inducible expression of representative alleles. Whereas each mutant induced distinct transcriptomic and DNA accessibility features, a prominent feature of all mutants was perturbed epithelial lineage specification, ranging from basal-like fates in cells expressing indel mutants to secretory (L1-like) luminal fates in cells expressing C-terminal truncation, missense mutations or excess WT. Integrated RNA-seq, ATAC-seq and ChIP-seq analysis of L1-like fate specification revealed enrichment of a composite androgen receptor-FOXA1 hybrid motif and cooperativity with the Oct family transcription factor POU2F1. Importantly, L1-like fate specification is seen in vivo tumorigenicity assays where, in combination with Trp53 / Pten loss, expression of these mutants results in a histologic switch from basal-like to secretory luminal histology.