Abstract Background: Metastatic castration-resistant prostate cancer (mCRPC) is a heterogeneous disease and often comprise molecularly distinct subtypes that differ in prognosis and therapeutic response. Super-Enhancers (SEs) are large enhancer clusters that robustly drive expression of genes controlling developmental processes and cell identity. In this study, we developed an epigenetic-based framework to determine whether mCRPC harbors subtype-specific SE programs that may reactivate distinct developmental transcriptional programs and define molecularly subtypes of disease progression. Methods: We developed a computational workflow, Super-Enhancer Analysis for Lineages (SEAL), to map SE landscapes, classify tumor subtypes and identify subtype-specific SE-driven genes. Using ROSE analysis on H3K27ac ChIP-seq data from the LuCaP and MURAL PDX mCRPC series, we constructed an integrated SE atlas. Molecular subtypes were defined through consensus clustering of SE regions and further characterized by genomic, transcriptional, and clinical features. We integrated matched RNA sequencing data to identify top-ranked SE-driven transcription factors, which were further evaluated via loss- and gain-of-function studies as well as ChIP-seq and RNA-seq analyses to define their cistromes, transcriptomes, and interacting networks. Results: We identified five distinct SE programs in mCRPC: three AR-positive subtypes (AR-1, AR-2, AR-3) and two AR-independent subtypes (NEPC-like and DNPC-like). Among the three AR-driven subtypes, AR-1 and AR-2 displayed aggressive tumor features, enriched for cell cycle, EMT, and hypoxia pathways. Each subtype exhibited a distinct SE-driven transcriptional program. Notably, we identified TWIST1, HNF1A, and TBX10 as key SE-driven transcription factors in AR-1, AR-2, and AR-3 subtypes, respectively. Among these, HNF1A, a critical transcription factor involved in hepatic development and metabolic regulation, was exclusively expressed in the AR-2 subtype. HNF1A silencing significantly reduced proliferation in vitro and in vivo and markedly suppressed glycolytic activity. AR-2 tumors produced high levels of secreted albumin, a well-established HNF1A hepatic target, which was decreased upon HNF1A silencing. ChIP-seq and RNA-seq analyses revealed that HOXB13 co-occupied HNF1A-mediated enhancers and cooperatively regulated the hepatic transcriptional programs. Conversely, HNF1A overexpression in AR-3 cells induced the expression of hepatic markers, enhanced proliferation and migration, and recapitulated features of the AR-2 subtype, indicating that HNF1A acts as a driver of hepatic lineage reprogramming. Conclusions: Our study reveals a novel HOXB13-HNF1A transcriptional axis that governs a previously undefined hepatic reprogramming in a subset of AR-driven mCRPC tumors. These findings establish a SE-based molecular classification of mCRPC and highlight HNF1A as a key regulator of metabolic and lineage programs, with potential implications for precision therapy and biomarker development in advanced prostate cancer. Citation Format: Mingyu Liu, Songqi Zhang, Nolan D. Patten, Jared G. Lourie, Xiaolin Zi, Kai Zou, Shuai Gao, Kourosh Zarringhalam, Changmeng Cai. Super-enhancer landscape analysis reveals a HOXB13-HNF1A transcriptional axis driving hepatic reprogramming in castration-resistant prostate cancer abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86 (2Suppl): Abstract nr PR015.
Liu et al. (Tue,) studied this question.