TIMP1 and PKM drive immunosuppression and metabolic remodeling to promote colorectal cancer progression through integrated multi-omics analysis.

The majority of colorectal cancers (CRC) exhibit low tumor mutational burden and an "immune-cold" microenvironment, with immune evasion initiating as early as the precancerous stage. This characteristic significantly limits the clinical efficacy of immunotherapy. Therefore, this study aimed to identify key targets and mechanisms underlying immune evasion in CRC through integrated multi-omics analysis. Transcriptomic analysis identified 1341 differentially expressed immune evasion-related genes (IERGs), with 674 up-regulated and 647 down-regulated. Among these, 11 core transcription factors (TFs), including HDAC2 and E2F1, cooperatively drove the up-regulation of IERGs and were significantly associated with increased infiltration of immunosuppressive cells (MDSCs and M2-TAMs). Integrated analysis revealed tissue inhibitor of metalloproteinases 1 (TIMP1) as a key effector molecule, whose high expression was associated with shortened overall survival and resistance to immunotherapy, and was involved in interferon signaling pathways. Single-cell RNA sequencing and T cell killing assay confirmed that TIMP1 significantly impaired the tumor-killing capacity and IFN-γ secretion of CD8+ T cells. Furthermore, post-translational modification (PTM) analysis identified pyruvate kinase muscle (PKM) as a cross-omics core regulatory node, with its mRNA and protein levels significantly up-regulated in CRC and correlated with poor prognosis. Five altered PTM sites on PKM (e.g., pS37) were also identified. AlphaFold3 structural prediction indicated a binding free energy of -8.4 kcal/mol for the PKM-lactate dehydrogenase A (LDHA) complex, and Co-IP experiment further confirmed their physical interaction. Functionally, treatment with a PKM inhibitor significantly suppressed lactate production. This study reveals that TIMP1 promotes immunosuppression and PKM-LDHA drives metabolic reprogramming in CRC.