Multi-Omics profiling identify NNMT in tumor endothelium as a key regulator of CD8⁺ T cell exhaustion via the TGF signaling pathway

BACKGROUND: CD8⁺ T cell exhaustion is a defining feature of the immunosuppressive TME in ccRCC. METHODS: We employed a multi-omics driven pipeline to nominate Nicotinamide N-methyltransferase (NNMT) as a high-confidence therapeutic target in ccRCC. This computational prediction was validated through bulk RNA-seq, single-cell RNA sequencing, and spatial transcriptomics to delineate NNMT-associated molecular and cellular programs. While the discovery phase highlighted endothelial-specific NNMT overexpression, we further validated the functional consequences of NNMT modulation using Caki-1 and A498 cell lines to model the downstream signaling cascades. Functional assays assessed impacts on proliferation, apoptosis, cytokine secretion (IL-6, IL-1β, TNF-α), and TGF-β pathway activity. Immune infiltration and T cell exhaustion signatures were evaluated across TCGA cohorts. RESULTS: Multi-omics profiling revealed that NNMT is specifically overexpressed in tumor-associated endothelial cells enriched for active TGF-β signaling and inflammatory cues. High NNMT expression strongly correlated with CD8⁺ T cell exhaustion, elevated apoptotic signaling, and immunosuppressive cytokine production. In functional validation, NNMT knockdown suppressed TGF-β activity, reduced pro-inflammatory cytokines, and restored CD8⁺ T cell infiltration and effector function. Mechanistically, NNMT loss shifted the BAX/Bcl-2 ratio toward apoptosis and increased cleaved caspase-3. Spatial transcriptomics confirmed that NNMT⁺ endothelial cells form an immunosuppressive niche in direct contact with exhausted T cells. We also found that I-BET-762, I-BET-151, PFI-1, and BMS-387032 can target and inhibit NNMT to reduce CD8⁺ T cell exhaustion. CONCLUSION: We establish NNMT as a central metabolic-immune hub that orchestrates TGF-β-mediated CD8⁺ T cell dysfunction and endothelial reprogramming in ccRCC.