A palmitoylation-associated three-gene signature predicts prognosis, immune features, and drug sensitivity in gastric cancer: functional validation of CTHRC1
Abstract
Gastric cancer (GC) is a heterogeneous malignancy that requires improved molecular tools for prognostic stratification. Protein palmitoylation regulates membrane localization and signaling, but the clinical relevance of palmitoylation-related genes (PRGs) in GC remains unclear. Gene Expression Omnibus, The Cancer Genome Atlas, and GeneCards data were integrated to identify PRGs. Differential expression analysis, weighted gene co-expression network analysis, and three machine-learning algorithms were used to select key genes. Diagnostic and prognostic performance was evaluated in TCGA-STAD, platform-specific GEO cohorts, and an institutional cohort of 80 paired tissues. Immune infiltration, single-cell RNA sequencing, immunotherapy-related indices, and GDSC-based drug sensitivity were analyzed. CTHRC1 was further examined using clinical specimens, cell assays, and xenografts. Thirteen differentially expressed PRGs were identified, and SERPINE1, CTHRC1, and EGR1 were selected. The integrated diagnostic model achieved AUCs of 0.935 in TCGA-STAD, 1.000 in GSE54129, and 0.916 in GSE118916, respectively. The three-gene score stratified overall survival in the total, training, and testing TCGA-STAD cohorts and in GSE84437, GSE236522, and the institutional cohort. It remained independently associated with survival in multivariable analysis. High-risk tumors showed increased stromal and immune scores, altered immune-cell composition, higher checkpoint expression, and higher TIDE scores. Single-cell analysis localized SERPINE1 and CTHRC1 mainly to fibroblast-related compartments. CTHRC1 knockdown reduced GC-cell proliferation, clonogenicity, migration, invasion, and xenograft growth while increasing apoptosis. The SERPINE1/CTHRC1/EGR1 signature provides prognostic and immune-stromal information in GC, and the experiments support a tumor-promoting role for CTHRC1. The findings define a palmitoylation-associated transcriptional framework but do not establish a palmitoylation-dependent mechanism.