Enhancer reprogramming establishes ETS1-RUNX1-FOSL1 as an oncogenic and immunosuppressive transcriptional circuitry in gallbladder carcinoma

Background: Gallbladder carcinoma (GBC) is a highly aggressive malignancy with poor prognosis and limited therapeutic options. Enhancers and super-enhancers (SEs) are critical regulators of cell type-specific transcription and oncogenic programs, yet their roles in GBC progression remain poorly defined. Objective: We aimed to map enhancer and SE reprogramming in GBC and identify master transcription factors (TFs) driving these transcriptional programs. Design: Chromatin immunoprecipitation sequencing and RNA sequencing were performed on normal, inflammatory, and tumorous gallbladder tissues, as well as GBC cell lines. Integrative analyses of enhancer remodeling, TF motif enrichment, expression, and transcriptional connectivity were conducted to identify SE-driven master TFs. Functional assays and immunohistochemistry were used to evaluate their oncogenic and immunomodulatory functions. Results: GBC exhibited extensive enhancer and SE reprogramming relative to non-tumorous gallbladder tissues, with gained enhancers and SEs preferentially enriched in oncogenic pathways. ETS1, RUNX1, and FOSL1 were identified as SE-driven master TFs that form an interconnected regulatory circuitry co-occupying SEs, including those of CD274 (encoding PD-L1), to promote oncogenic transcription and immune evasion. Perturbation of this circuitry suppressed GBC cell proliferation, migration, and tumor growth in vitro and in vivo . Clinically, elevated expression of these master TFs correlated with reduced CD8 + T cell infiltration, poorer patient survival, and diminished responsiveness to immunotherapy in GBC. Conclusion: This study delineates enhancer and SE reprogramming during gallbladder malignant transformation, identifies an ETS1-RUNX1-FOSL1 master TF circuitry, and highlights FOSL1 as a key driver of oncogenic transcription and immune evasion, providing mechanistic, prognostic, and therapeutic insights into GBC.