Integrative multi-omics analysis identifies a PTM-related immune signature and IRF9 as a driver in ccRCC

Clear cell renal cell carcinoma (ccRCC) exhibits marked heterogeneity and variable benefit from immune checkpoint inhibitors (ICIs). Post-translational modifications (PTMs) regulate immune signaling and tumor behavior, yet PTM-informed biomarkers for ccRCC remain underexplored.

We intersected immune-related genes, PTM-related genes, and differentially expressed genes in TCGA-KIRC to derive candidates and built a prognostic model across TCGA and E-MTAB-1980 using multiple algorithms, selecting a random survival forest-based post-translational modification-related signature (PTMRS) with the best performance. Prognostic value and independence were evaluated by time-dependent ROC, Kaplan-Meier, and multivariate Cox analyses. Tumor immune context was profiled by immune infiltration scores, immune checkpoints, and TIDE to infer dysfunction/exclusion and ICI response. Genomic features (driver mutations, pathway alterations, tumor mutational burden) and an external ICI cohort (IMvigor210) were analyzed. Single-cell RNA-seq with CellChat, trajectory, and UCell assessed cell-cell communication and PTMRS distribution across immune subsets. Experimental validation included IHC and qPCR of IRF9, loss- and gain-of-function assays (Transwell, wound healing, CCK-8, colony, EdU), and molecular dynamics to explore IRF9 compound binding.

We established a five-gene PTMRS that robustly stratified prognosis in training, testing, and external cohorts and remained an independent predictor. High-PTMRS tumors displayed immunosuppressive features, including greater infiltration of Tregs/MDSCs/macrophages, higher expression of immunosuppressive checkpoints, and elevated TIDE scores with lower predicted ICI responsiveness. High PTMRS associated with alterations in oncogenic pathways and higher TMB. In IMvigor210, high PTMRS linked to inferior outcomes and non-response. Single-cell analyses showed PTMRS enrichment in Tregs and exhausted CD8⁺ T cells and dense immune communication networks. Among PTMRS genes, IRF9 was upregulated in ccRCC tissues and cell lines. Knockdown of IRF9 curtailed invasion, migration, and proliferation, whereas overexpression enhanced these phenotypes.

PTMRS is a PTM-informed immune signature that reflects an immunosuppressive tumor microenvironment, improves prognostic stratification, and indicates ICI benefit in ccRCC. Experimental data pinpoint IRF9 as a functional driver and potential therapeutic target within this PTM-immunity axis.