Pan-Cancer Landscape of TMEM9 With Experimental Validation in Head and Neck Squamous Cell Carcinoma

Transmembrane protein 9 (TMEM9) has been implicated in tumor progression, but its pan-cancer diagnostic, prognostic, and immunological relevance remains incompletely characterized.

TMEM9 expression, diagnostic and prognostic value, genetic alterations, functional states, and immune associations were systematically evaluated using TCGA, GTEx, and complementary public cancer databases. Experimental validation was primarily performed in HNSC models using Western blotting, colony-formation, wound-healing, Transwell, and xenograft assays, with additional exploratory validation in RCC models.

TMEM9 showed good-to-high diagnostic performance in 15 evaluable cancer cohorts, with particularly high AUCs in CHOL (1.000), KICH (0.970), LIHC (0.949), and THYM (0.925), whereas BRCA also showed strong discriminatory performance (AUC = 0.890). Higher TMEM9 expression was associated with unfavorable survival in several cancers, although its prognostic relevance varied by tumor type. TMEM9 expression was also associated with cancer-related pathways, functional states, immune cell infiltration, and immunoregulatory gene expression in a context-dependent manner. Experimentally, TMEM9 knockdown suppressed colony formation, wound closure, migration, and invasion in HNSC cells and inhibited FaDu xenograft growth. Similar inhibitory effects were additionally observed in exploratory RCC models.

TMEM9 exhibits cancer-type-dependent diagnostic, prognostic, and immunological associations, whereas functional experiments support a tumor-promoting role for TMEM9 in HNSC. Exploratory RCC experiments suggest that this effect may also occur in selected renal cancer cellular contexts.