An Epigenetically Remodeled EMT–Inflammatory Clone Associated with Spatial Immune Exclusion in Clear Cell Renal Cell Carcinoma

Clear cell renal cell carcinoma (ccRCC) exhibits intra-tumoral heterogeneity and spatial complexity that restrict immune infiltration, yet the malignant populations driving spatial immune exclusion remain elusive. We integrated scRNA-seq, paired scATAC-seq, spatial transcriptomics, and multiple bulk cohorts to identify the malignant subpopulation driving ccRCC progression. Multi-omics analyses, including malignancy inference, epigenomic profiling, cell–cell communication, and spatial modeling, characterized its molecular features and clinical relevance. We identified a malignant subpopulation co-activating epithelial–mesenchymal transition (EMT) and inflammatory programs, termed the aggressive EMT–inflammatory clone (AEIC). AEIC exhibited pronounced genomic instability, enhanced stemness, and poor prognosis across multicenter cohorts (p < 0.001). Chromatin accessibility revealed a MAZ/RUNX1-centered network driving key AEIC signature genes such as TGFBI and COL6A2. Cell–cell communication analysis suggested AEIC interacts with NK_CD16− cells via the COL6A2–(ITGA1+ITGB1) axis. Spatial analyses showed AEIC-enriched regions forming an extracellular matrix-rich barrier associated with NK_CD16− cell exclusion, M2-like macrophage polarization, and increased genomic instability. Finally, an AEIC-derived 16-gene signature stratified prognosis across independent cohorts and was associated with distinct drug-sensitivity patterns, including increased predicted sensitivity to Bortezomib and AZD4547. Overall, AEIC is associated with spatial and epigenetic remodeling in ccRCC, and the AEIC-derived signature supports prognostic stratification and further exploration of potential therapeutic vulnerabilities associated with the AEIC phenotype.