Pan-cancer multi-omics dissection of podosome-related genes reveals their dual roles in tumor invasion and immune modulation

Podosomes and their cancer-specific counterparts, invadopodia, are pivotal organelles facilitating extracellular matrix (ECM) degradation and tumor invasion. However, the pan-cancer landscape and clinical implications of podosome-related genes (PRGs) remain largely unexplored. We conducted a systematic pan-cancer analysis of six core PRGs—MMP9, NCK1, RHOA, SH3PXD2A, SRC, and STIM1—across 33 tumor types utilizing multi-dimensional datasets from TCGA, GTEx, GDSC, TIDE, and CancerSEA. We integrated expression profiles with somatic mutations, DNA methylation, and copy number variations (CNV) to delineate their regulatory landscape. A podosome activity score was constructed via ssGSEA, and single-cell RNA-seq (scRNA-seq) data were leveraged to resolve cell-type specificity. We further evaluated associations with immune checkpoints, tumor-infiltrating lymphocytes (TILs), and immunotherapy response predictors. Finally, Colon Adenocarcinoma (COAD) was selected for integrative transcriptomic analysis and experimental validation of the hub gene MMP9. Our analysis revealed that PRGs are extensively dysregulated across tumor types, driven by distinct epigenetic and genomic alterations. Elevated podosome scores correlated with advanced tumor stage, poor prognosis, and an immunosuppressive microenvironment characterized by high TGFB1 expression and T-cell exclusion. Single-cell profiling identified that podosome activity was predominantly enriched in monocytes, endothelial cells, and mast cells, highlighting their role in immune remodeling and angiogenesis. Functionally, PRGs were strongly associated with epithelial–mesenchymal transition (EMT), metastasis, and drug sensitivity, particularly to targeted agents like dasatinib. In COAD, integrated network analysis and in vitro assays confirmed MMP9 as a central driver promoting cancer cell migration and invasion. This study provides the first comprehensive pan-cancer functional atlas of PRGs. Our findings elucidate the dual roles of PRGs in driving tumor invasion and modulating the immune microenvironment, nominating them as promising biomarkers and therapeutic targets for precision oncology.