Molecular profiling and prognostic significance of gastric cancer subtypes based on extracellular vesicle-related characteristics

Abstract

Gastric cancer (GC) is a molecularly heterogeneous disease. This study aims to explore whether endocytosis pathway-associated genes and immune checkpoint-related features were linked to GC subtypes and prognosis. Public transcriptomic datasets from TCGA and GEO were analyzed. ssGSEA was applied to predefined endocytosis-related gene sets, and NMF was used to identify molecular subtypes. Survival, tumor microenvironment features, tumor mutation burden, microsatellite instability, and differentially expressed genes were evaluated. A three-gene prognostic model was developed and assessed through retrospective internal and external validation across public cohorts for prognostic association only. Two endocytosis-related subtypes were identified. The Group 1 subtype showed higher pathway activity, more immunosuppressive microenvironmental features, higher expression of selected immune checkpoint-related markers, and poorer survival. The Group 2 subtype showed lower pathway activity and more favorable outcomes. A three-gene signature (NRP1, SERPINE1, and MISP3) stratified patients into higher-risk and lower-risk groups across retrospective cohorts. Higher-risk cases were associated with worse overall survival and enrichment of epithelial-mesenchymal transition- and immune evasion-related pathways. This retrospective cross-cohort validation suggests that the prognostic signal was not restricted to a single dataset, but it does not demonstrate prospective clinical validity, analytical validity, or readiness for clinical implementation. Endocytosis-related molecular patterns may be associated with distinct biological and prognostic features in GC. The identified subtypes and prognostic signature should be interpreted as exploratory, hypothesis-generating findings that warrant further prospective, functional, and assay-level validation.