Dual regulation of CDH3 by NAT10-mediated ac4C modification and USP19-mediated deubiquitination promotes colorectal cancer progression and immune evasion

Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, largely driven by its aggressive progression and potent immune evasion capabilities. Unraveling the molecular mechanisms underlying CRC tumorigenesis and immunosuppression is therefore critical for identifying novel diagnostic and therapeutic targets. An integrative approach combining bioinformatics analysis, weighted gene co-expression network analysis (WGCNA), and machine learning algorithms was utilized to identify key CRC biomarkers. Functional roles were evaluated by assessing cell viability, proliferation, migration, and tube formation. Immunomodulatory effects were examined via co-culture systems with peripheral blood mononuclear cells (PBMCs), CD8 + T cells, and THP-1-derived macrophages to quantify cytokine secretion (tumor necrosis factor-α [TNF-α], interferon-γ [IFN-γ]), CD8 + T cell apoptosis, and M2 macrophage polarization. In vivo tumorigenicity and lung metastasis models using HCT-116 cells validated the in vitro findings. Underlying regulatory mechanisms were investigated via ac4C RNA immunoprecipitation (RIP), RNA pull-down, and dual-luciferase reporter assays. Co-immunoprecipitation (Co-IP) and ubiquitination assays were employed to assess protein–protein interactions and K48-linked deubiquitination. Cadherin 3 (CDH3) was pinpointed as a critical CRC biomarker, and it was significantly upregulated in CRC tissues and cells (P < 0.05). Moreover, CDH3 was correlated with adverse patient prognosis (P < 0.05). Functionally, CDH3 silencing in CRC cells suppressed cell proliferation, migration, and angiogenesis (P < 0.05). Immunologically, CDH3 knockdown enhanced anti-tumor immunity by reducing CD8 + T cell apoptosis, elevating TNF-α and IFN-γ secretion from PBMCs, and inhibiting M2 macrophage polarization (P < 0.05). Mechanistically, N-acetyltransferase 10 (NAT10)-mediated ac4C modification stabilized CDH3 mRNA (P < 0.05), while ubiquitin specific peptidase 19 (USP19) interacted with CDH3 to remove K48-linked ubiquitin chains (P < 0.05), thereby preventing its protein degradation. Notably, CDH3 overexpression partially reversed the suppressive effects of NAT10 or USP19 knockdown on malignant phenotypes and in vitro immune escape, as well as on in vivo tumor growth and metastatic colonization (P < 0.05). CDH3 drove CRC progression and contributed to immune evasion in vitro through dual regulation by NAT10-dependent mRNA acetylation and USP19-mediated protein deubiquitination. Targeting the NAT10/USP19-CDH3 axis represents a promising candidate therapeutic strategy for CRC, although further validation in immunocompetent models is warranted. • CDH3 was identified as a crucial upregulated biomarker correlating with poor prognosis in CRC. • CDH3 silencing suppressed CRC cell proliferation, migration, and angiogenesis while enhancing anti-tumor immunity. • NAT10-mediated ac4C modification stabilized CDH3 mRNA in CRC cells. • USP19 prevented CDH3 protein degradation by removing K48-linked ubiquitin chains in CRC cells. • CDH3 overexpression rescued the suppressive effects of NAT10 or USP19 knockdown on CRC progression and immune evasion.