Identification of targets of clinical FOXA1 mutants involved in EMT and immune suppression in prostate cancer.

FOXA1 is a critical transcription factor in prostate cancer (PCa) progression, functioning as a pioneer factor for the androgen receptor (AR). Its expression is elevated in advanced stages of PCa and plays a central role in oncogenic reprogramming. Recurrent coding mutations in the forkhead DNA-binding domain (FKHD) of FOXA1 become increasingly prevalent in drug-resistant metastatic PCa, particularly clustering in the Wing2 region of FKHD. While recent studies demonstrated that these mutations promote PCa progression, the downstream targets of FKHD mutants remain poorly understood. In this study, we employed three analytical approaches to elucidate these targets: (i) traditional transcriptomic analyses, (ii) chromatin structure-based super-enhancer (SE) profiling, and (iii) immune deconvolution. We identified HPSE, an enzyme that degrades heparan sulfate, as a druggable target activated by FKHD mutants both in vitro and in vivo. SE profiling further revealed that FKHD mutants can reprogram the SE landscape, with FOXP1 emerging as a consistently SE-driven and upregulated gene across multiple FOXA1 mutants. Additionally, FOXA1 mutations were associated with immune suppression in PCa patient samples, and B2M, a key gene in antigen processing and presentation, was notably downregulated in FKHD-mutant tumors. Together, our findings provide distinct insights into how FOXA1 FKHD mutations drive PCa progression and highlight potential therapeutic targets in tumors harboring these mutations.