SWI/SNF Alterations Define a Chromatin-Dependent Subtype of Urothelial Carcinoma

Feng, B.-J.; Fatema, K.; Nix, D. A.; Atkinson, A.; Caparas, C.; Stubben, C. J.; Lum, D. H.; Parnell, T. J.; Carroll, C.; Grass, G. D.; Graham, L.; Singer, E. A.; Nepple, K. G.; Manojlovic, Z.; Kauffman, E.; King, J. M.; Ghodoussipour, S.; Hensley, P.; Viscuse, P. V.; Ayanambakkam, A.; Churchman, M. L.; Swami, U.; Agarwal, N.; Cairns, B.; Gupta, S.

doi:10.64898/2026.08.05.743022

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bioRxiv · 10.64898/2026.08.05.743022

SWI/SNF Alterations Define a Chromatin-Dependent Subtype of Urothelial Carcinoma

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Abstract

PurposeSWI/SNF (BAF) chromatin remodeling complex alterations are common in urothelial carcinoma, yet no biomarker-directed therapeutic strategies have been established for this population. We investigated whether BAF alterations delineate a biologically distinct, therapeutically actionable urothelial carcinoma subtype. Experimental DesignWe performed integrative genomic and transcriptomic analyses of 792 urothelial carcinoma tumors from the Oncology Research Information Exchange Network (ORIEN) and validated findings in the TCGA-BLCA cohort. Mechanistic studies incorporated RNA sequencing and ATAC-seq following histone deacetylase (HDAC) inhibition. Functional dependencies were assessed using patient-derived xenograft organoids and cell line models. Clinical relevance was explored in a biomarker-enriched investigator-initiated trial. ResultsApproximately half of urothelial carcinoma tumors exhibited BAF alterations, defining a previously unrecognized chromatin-altered molecular subtype characterized by activation of proliferative programs, loss of lineage identity, and altered metabolic signaling. This subtype was enriched for transcriptomic programs associated with HDAC inhibitor sensitivity and depleted of HDAC inhibitor resistance signatures. Mechanistically, HDAC inhibition induced widespread chromatin remodeling with reduced accessibility at AP-1 and TEAD-associated regions, and downregulation of E2F- and MYC-driven transcriptional networks. Functional studies confirmed enhanced HDAC inhibition sensitivity in ARID1A-mutated cell lines and a patient-derived organoid model. Early clinical observations demonstrated a durable responder treated with HDAC inhibitors and immunotherapy. ConclusionsBAF alterations define a chromatin-dependent tumor state in urothelial carcinoma that is selectively vulnerable to HDAC inhibition. Integrating genomic, epigenomic, functional, and early clinical evidence, these findings provide a rationale for biomarker-enriched clinical trials and HDAC inhibitor-based combination strategies in urothelial carcinoma.

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Feng, B.-J., Fatema, K., Nix, D. A., Atkinson, A., Caparas, C., Stubben, C. J., Lum, D. H., Parnell, T. J., Carroll, C., Grass, G. D., Graham, L., Singer, E. A., Nepple, K. G., Manojlovic, Z., Kauffman, E., King, J. M., Ghodoussipour, S., Hensley, P., Viscuse, P. V., Ayanambakkam, A., Churchman, M. L., Swami, U., Agarwal, N., Cairns, B., Gupta, S.. 2026-08-06. SWI/SNF Alterations Define a Chromatin-Dependent Subtype of Urothelial Carcinoma. https://doi.org/10.64898/2026.08.05.743022

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