Immune-related deubiquitylation spectrum of microsatellite stability colorectal cancer reveals USP7 as a potential immunotherapeutic target.

The efficacy of immune checkpoint inhibitors (ICIs) in microsatellite stable colorectal cancer (MSS CRC) remains limited, highlighting an urgent need for predictive biomarkers. Through multi-omics analysis, we identified two novel MSS CRC subtypes, termed DUB-H and DUB-L. The DUB-L subtype exhibited an inflamed tumor immune microenvironment, a superior response to immune therapy, and better recurrence-free survival (RFS) compared to DUB-H. The classifier gene USP7 was selected as a gene of interest due to its specific expression profile, which is highly expressed in MSS CRC but not in microsatellite instability-high (MSI-H) tumors, and strongly correlated with suppressed immune infiltration. Large-scale clinical analyses confirmed associations between high USP7 expression, microsatellite stability, specific consensus molecular subtypes (CMS), and unfavorable prognosis. Single-cell analysis and multiplex immunofluorescence validated an immune-desert phenotype in USP7-high MSS tumors. Mechanistically, USP7 knockdown in MSS CRC cells enhances the secretion of T-cell-recruiting chemokines (CXCL9/10/11), promoting CD8⁺ T cell recruitment and cytotoxicity in vitro. In vivo experiments demonstrated that USP7 blockade enhanced the efficacy of anti-PD-1 treatment in MSS CRC models by remodeling the tumor immune microenvironment, increasing infiltration and function of CD8⁺ T and NK cells. Consistently, low USP7 expression is associated with a better response to anti-PD-1 therapy. Overall, we propose a novel DUB-based classification system for MSS CRC and demonstrate that targeting USP7 may overcome immunotherapy resistance by converting immunologically “cold” tumors into “hot” ones. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12943-025-02502-8.