This study reveals two novel subtypes of microsatellite stable colorectal cancer (MSS CRC) through multi-omics analysis and identifies deubiquitinating enzyme USP7 as a key regulator of the tumor immune microenvironment, offering a new strategy to overcome resistance to immunotherapy.
Literature Overview
The article titled 'Immune-related deubiquitylation spectrum of microsatellite stability colorectal cancer reveals USP7 as a potential immunotherapeutic target,' published in the journal Molecular Cancer, reviews the limited efficacy of immune checkpoint inhibitors in microsatellite stable colorectal cancer (MSS CRC). Through multi-omics analysis, the study identifies two novel MSS CRC subtypes—DUB-H and DUB-L—with the DUB-L subtype exhibiting stronger immune infiltration and better prognosis. Further screening reveals that the deubiquitinating enzyme USP7 is specifically upregulated in MSS CRC and significantly associated with the immune-desert phenotype. Mechanistically, USP7 suppresses CD8⁺ T cell infiltration by inhibiting the secretion of T-cell chemokines CXCL9/10/11, thereby shaping an immunosuppressive microenvironment. Targeting USP7 enhances the efficacy of anti–PD-1 therapy, suggesting its potential as a sensitizing target for immunotherapy. The entire section is coherent and logically structured, ending with a Chinese period.Background Knowledge
Colorectal cancer is the third leading cause of cancer-related deaths worldwide, with approximately 85% of cases classified as microsatellite stable (MSS) or mismatch repair–proficient (pMMR). These tumors typically exhibit an 'immune-cold' phenotype—characterized by low tumor mutational burden and insufficient immune cell infiltration—rendering them unresponsive to monotherapy with immune checkpoint inhibitors such as anti–PD-1/PD-L1 antibodies. Although some MSS patients achieve clinical responses through combination therapies, the lack of reliable predictive biomarkers limits the application of precision medicine. In recent years, the classification of tumors into 'hot' and 'cold' has been widely used to explain differences in immunotherapy responses. 'Hot' tumors are rich in T-cell infiltration and display inflammatory gene expression profiles, whereas 'cold' tumors lack immune infiltration and harbor mechanisms of immune escape. Thus, identifying key molecules that drive the 'cold' phenotype has become a research hotspot in overcoming immunotherapy resistance. Deubiquitinating enzymes (DUBs), important enzymes regulating protein stability and signaling pathways, have recently been found to participate in immune regulation. However, their role in modulating the immune microenvironment of MSS CRC remains unclear. This study focuses on the immune-related DUB spectrum, aiming to systematically elucidate their functions in MSS CRC and explore their potential as immunotherapeutic targets, thereby filling a critical gap in this field.
Research Methods and Experiments
The study first analyzed DUB expression differences between MSS and adjacent normal tissues using the TCGA-COAD&READ cohort, integrating single-sample gene set enrichment analysis (ssGSEA) and seven other algorithms (e.g., CIBERSORT, TIMER) to assess immune cell infiltration levels. This allowed the identification of immune-related DUBs (IR-DUBs) significantly correlated with CD8⁺ T and NK cell infiltration. Subsequently, consensus clustering based on five core DUB genes (USP7, USP10, USP36, USP40, BRCC3) was used to classify MSS CRC into subtypes, with stability validated across multiple independent GEO cohorts. USP7 expression patterns and their relationship with the immune microenvironment were confirmed using immunohistochemistry, multiplex immunofluorescence, and single-cell RNA sequencing. Functionally, USP7 was knocked down using shRNA or inhibited pharmacologically with P5091, and its effects on T-cell recruitment, activation, and anti–PD-1 efficacy were evaluated through in vitro chemotaxis assays, co-culture systems, and in vivo tumor-bearing models. Additionally, the associations between USP7 expression and microsatellite status, CMS molecular subtypes, mutation profiles, and patient prognosis were analyzed.Key Conclusions and Perspectives
Research Significance and Prospects
This study systematically maps the immune-related deubiquitinating enzyme landscape in MSS CRC and proposes a novel molecular classification system based on DUB expression that effectively distinguishes immune-active from immune-desert MSS tumors. This provides new insights into the mechanisms of immunotherapy resistance in MSS CRC and offers a potential tool for patient stratification.
The study clarifies the pivotal role of USP7 in shaping the immunosuppressive microenvironment and reveals a novel mechanism by which USP7 limits T-cell infiltration through suppression of chemokine secretion, expanding our understanding of DUB family functions in tumor immune regulation. More importantly, targeting USP7 effectively remodels the tumor immune microenvironment, converting 'cold' tumors into 'hot' ones and significantly enhancing the efficacy of anti–PD-1 therapy, highlighting USP7 as a highly promising target for immunotherapy sensitization.
Future studies could further explore the specific substrates of USP7 and the molecular mechanisms underlying its regulation of chemokine expression, develop more selective USP7 inhibitors, and advance their translational application in the clinic. Additionally, combining USP7 targeting with other immune-modulatory pathways may represent a novel strategy to overcome immunotherapy resistance in MSS CRC.
Conclusion
This study integrates multi-omics data to systematically analyze the relationship between deubiquitinating enzymes and the tumor immune microenvironment in microsatellite stable colorectal cancer (MSS CRC), proposing a novel molecular classification system—DUB-H and DUB-L—based on DUB expression. The DUB-L subtype exhibits stronger immune activation features and better prognosis, whereas the DUB-H subtype displays an immune-desert phenotype. The study focuses on USP7, a deubiquitinating enzyme specifically overexpressed in MSS CRC, and confirms that its high expression is closely associated with reduced immune cell infiltration, suppressed T-cell function, and poor prognosis. Mechanistically, USP7 inhibits the secretion of chemokines such as CXCL9/10/11, thereby impairing CD8⁺ T cell recruitment and activation. Functional experiments demonstrate that knocking down or inhibiting USP7 significantly enhances the efficacy of anti–PD-1 therapy and remodels the tumor immune microenvironment. Clinical sample analyses also show that low USP7 expression correlates with better response to immunotherapy. In summary, this study not only provides a new framework for immune classification of MSS CRC but also identifies USP7 as a key target for overcoming immunotherapy resistance, laying a solid theoretical and experimental foundation for developing novel combination therapeutic strategies.
