Integrated multi-omics analysis reveals PTM networks as key regulators of colorectal cancer progression and immune evasion.

Colorectal cancer (CRC) is a leading cause of cancer mortality, with treatment resistance often driven by molecular heterogeneity and an immunosuppressive tumor microenvironment (TME). Post-translational modifications (PTMs) regulate key oncogenic processes, but their comprehensive role in CRC progression and immune evasion remains unexplored. We integrated multi-omics data from bulk RNA-seq (GEO/TCGA, n = 1,783), single-cell transcriptomics (41,143 cells), and Mendelian randomization. Differential expression, GSVA, and machine learning (LASSO/SVM/Random Forest) were used to identify PTM-associated signatures. Functional validation included spatial transcriptomics, and immune profiling. Multi-omics analysis identified dysregulation in 80% of PTM pathways in CRC, with ubiquitination sustaining Wnt/β-catenin signaling and GALNT6-mediated glycosylation driving immune evasion through PD-L1 stabilization and CD8 + T cell exclusion. Single-cell analysis revealed GALNT6-specific enrichment in immune-excluded goblet cells (p < 0.05). Machine learning derived a 5-gene PTM Activity Signature (CCNB1IP1, GALNT6, NEDD4L, PSMD14, UBE2C) that distinguish between patients with diseases and those without (AUC = 1.00). GALNT6 was validated as a causal risk factor (OR = 1.10, 95%CI:1.01-1.18), with its inhibition synergizing with anti-PD-1 to enhance CD8 + T cell infiltration (p < 0.01). This study establishes PTM networks as central regulators of CRC progression and immune resistance. The PTM-AS framework enables precision subtyping, while GALNT6 emerges as a novel therapeutic target for overcoming immunotherapy resistance.