Prognostic molecular subtype reveals the heterogeneity of tumor immune microenvironment in gastric cancer

Gastric cancer (GC) remains a leading cause of cancer-related deaths and exhibits considerable heterogeneity among patients. Thus, accurate classifications are essential for predicting prognosis and developing personalized therapeutic strategies. To address this, we retrospectively analyzed multi-omics data from 359 GC samples, incorporating transcriptomic RNA (mRNA), DNA methylation, mutation data, and clinical parameters. Using ten clustering algorithms, we integrated these datasets to classify GC into molecular subtypes. The robustness of our clustering approach was externally validated using an independent cohort generated from different sequencing technologies, and we characterized the heterogeneity of each subtype. Our analysis identified three distinct molecular subtypes of GC, designated CS1, CS2, and CS3. These subtypes exhibited significant differences in survival outcomes, activation of cancer-related pathways, immune microenvironment composition, genomic alterations, and responses to immunotherapy and chemotherapy. Notably, Cathepsin V (CTSV) was significantly downregulated in the immunologically active and highly responsive CS3 subtype, while it was upregulated in the immunologically exhausted CS2 subtype. These findings suggest that CTSV could serve as both a prognostic marker and a molecular classifier. Furthermore, this study provides the first evidence of CTSV's high expression in GC and its potential role in tumor progression. The novel clustering approach, based on ten clustering algorithms and comprehensive analysis of multi-omics data in gastric cancer, can guide prognosis, characterize different clinical and biological features, and elucidate the tumor immune microenvironment, providing insights into the intratumor heterogeneity of GC and potential novel therapeutic strategies. Additionally, CTSV emerges as a prognostic marker linked to tumor immunity and disease progression, which lays the foundation for improved stratification strategies and the development of targeted therapeutic approaches in GC.