CD109 is associated with an immunosuppressive microenvironment and M2 macrophage polarization: pan-cancer analysis and functional validation

BACKGROUND: CD109 is a glycosylphosphatidylinositol‑anchored glycoprotein implicated in tumor progression and physiological homeostasis. Although aberrant CD109 expression has been reported in multiple malignancies, its prognostic relevance across cancer types and its potential immunomodulatory roles remain incompletely characterized. METHODS: We performed an integrative pan-cancer analysis of CD109 using RNA sequencing data from the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) databases. CD109 expression, genetic alterations, survival associations, and immune infiltration patterns were systematically assessed. Single-cell RNA sequencing (scRNA-seq) data from non-small cell lung cancer (NSCLC) cohorts were analyzed to define cellular CD109 distribution. Functional validation was performed using siRNA-mediated CD109 knockdown in A549 lung adenocarcinoma cells, followed by macrophage co-culture experiments, flow cytometry, qPCR, ELISA, and migration assays. RESULTS: CD109 was markedly upregulated in 15 tumor types and showed heterogeneous prognostic associations across cancers. Elevated CD109 expression was associated predominantly with unfavorable survival in several tumor types, whereas opposite prognostic associations were observed in a subset of cancers. Bioinformatic analysis revealed that high CD109 expression was associated with an immunosuppressive tumor immune microenvironment, characterized by the enrichment of M2-like tumor-associated macrophages (TAMs) and activation of oncogenic signaling axes. Single-cell profiling showed that CD109 was predominantly expressed in malignant cells and a subset of M2 macrophages. Consistent with these clinical and computational insights, functional validation in an in vitro lung cancer model showed that CD109 knockdown in A549 cells significantly suppressed tumor migration and was associated with a shift in macrophage polarization away from a pro-tumorigenic M2 phenotype toward an anti-tumor M1 state. CONCLUSIONS: Our study highlights CD109 as a context-dependent biomarker with tumor type specific prognostic relevance and links its expression to immunosuppressive features of the tumor immune microenvironment. These findings suggest that CD109 warrants further investigation as a potential therapeutic target, particularly in tumor contexts characterized by macrophage-associated immunosuppression, although the macrophage-related functional effects observed here were validated in a lung cancer model and require further investigation in additional tumor types.