SETDB2 induces abnormal SHP-1 splicing and promotes immunosuppression in hepatocellular carcinoma

The clinical application of targeted therapy and immune checkpoint inhibitors (ICIs) has significantly improved the survival prognosis of patients with hepatocellular carcinoma (HCC). However, due to the high heterogeneity of HCC, the response rate to immunotherapy is still low, and there is an urgent need to identify reliable biomarkers and potential therapeutic targets to improve the therapeutic benefit. In this study, a patient-derived xenograft (PDX) model of HCC was constructed to compare and analyze the tumor tissues of the immunotherapy responder group and the non-responder group. RNA sequencing and proteomics combined analysis found that histone H3K9 trimethyltransferase SETDB2 was highly expressed in the non-responder group. Functional experiments showed that SETDB2 deficiency could significantly inhibit tumorigenesis, enhance CD8⁺ T cell infiltration, and improve the immune microenvironment. Further mechanistic studies found that SETDB2 shut down the chromatin structure of the promoter region of the splicing factor SRSF1 through H3K9me3 modification, inhibiting its expression, thereby leading to a decrease in the proportion of functional spliceosomes of the immune regulatory factor SHP-1. After the activity of SHP-1 was weakened, the JAK/STAT3 signaling pathway was continuously activated, leading to an enhanced tumor immunosuppressive phenotype. SETDB2 overexpression also promoted the polarization of tumor-associated macrophages M2 and inhibited the function of effector T cells, leading to a decrease in immunotherapy response. This study systematically revealed that SETDB2 regulates SRSF1 expression through an epigenetic mechanism mediated by H3K9me3, thereby driving the SHP-1 spliceosome deviation, activating STAT3 signaling and reshaping the key pathway of the immune microenvironment. The SETDB2/SRSF1/SHP-1/STAT3 axis plays a core role in HCC immune escape, providing a new perspective on the mechanism of resistance to immunotherapy in liver cancer, and providing a theoretical basis and potential biomarkers for the combined epigenetic targeted intervention strategy of ICIs.