Single-Cell Transcriptional States of Human Leukocyte Antigen DR Positive CD4 Positive T Cells Linked to Genetic Susceptibility of Gastric Cancer

Background Gastric cancer (GC) involves complex immune-metabolic crosstalk, but MR-prioritized immunophenotypes and mediating metabolites remain unclear.Methods Two-sample Mendelian randomization (MR) was performed using GWAS summary data for 731 immunophenotypes, 1,400 circulating metabolites, and GC (218,792 European participants). Instruments were selected at p < 1 × 10−5, LD-clumped (r2 < 0.001, 10,000 kb), and filtered for strength (F > 10). IVW served as the primary estimator, with sensitivity and reverse MR analyses. Two-step MR explored metabolite-mediated pathways. Single-cell RNA-seq from 56 samples across three sources was integrated to resolve HLA-DR+ CD4+ T-cell transcriptional states, evaluate GC genetic-risk enrichment via scDRS, and infer cell-cell communication using CellChat.Results Twenty-six immunophenotypes showed candidate associations with GC. HLA-DR expression on HLA-DR+ CD4+ T cells was inversely associated with GC risk (OR = 0.761, 95% CI 0.634–0.912, FDR q = 0.0393). Reverse MR was not FDR-significant, and MR-Egger indicated no directional pleiotropy. Candidate mediation involved bilirubin degradation product C17H18N2O4(2). Single-cell analysis identified five HLA-DR+ CD4+ T-cell subsets; T1 and T5 showed relatively higher GC genetic-susceptibility enrichment, with T5 exhibiting low CytoTRACE scores. These subsets were linked to immune activation and chemokine signaling. The exploratory TIGIT-NECTIN2 signal was not robustly retained after CellChat sensitivity filtering.Conclusion This study suggests a potential inverse association between HLA-DR+ CD4+ T-cell immunophenotypes and GC risk, with bilirubin-related metabolites as a candidate mediating pathway. Subsets T1/T5 provide candidate directions for future GC immune-prevention research.