Nuclear proteomics identifies TEAD4 as an IFN-γ-responsive regulator of pathogenic synovial fibroblast programs

Abstract Difficult-to-treat rheumatoid arthritis (D2T RA) remains a major unmet clinical challenge despite advances in targeted therapies. Recent single-cell and spatial transcriptomic studies identified synovial fibroblast (SF) subsets associated with multidrug-resistant disease states. Transcriptome-based inference approaches have been used to further characterize pathogenic fibroblast subsets by identifying candidate master transcriptional regulators. However, their accuracy is limited by the context-dependent relationship between transcription factors and their target genes. Here, we applied nuclear proteomics using data-independent acquisition mass spectrometry (DIA-MS) to identify transcription factors regulated in cytokine-stimulated rheumatoid arthritis synovial fibroblasts (RASFs). Nuclear DIA-MS identified TEAD4 as a transcription factor selectively induced by IFN-γ signaling. Transcriptomic and functional analyses demonstrated that TEAD4 regulates gene programs associated with multidrug-resistant fibroblast subsets, including TGF-β-associated fibroblast activation programs. Comparative perturbation analyses showed that TEAD family members exhibit both redundant and distinct functions and regulate transcriptional programs that only partially overlap with those controlled by YAP/TAZ. Pharmacologic inhibition of TEAD activity suppressed fibroblast proliferation and migration in vitro and attenuated arthritis severity in the collagen-induced arthritis model without impairing antigen-specific immune responses. Together, these findings identify TEAD signaling as a therapeutically targetable pathway in rheumatoid arthritis and provide a mechanistic framework linking inflammatory and profibrotic fibroblast activation.