Single-Cell eQTL-Guided Mendelian Randomization Reveals a Dual-Axis Immune Evasion Mechanism and Therapeutic Targets in Esophageal Cancer

Background: The tumor microenvironment (TME) drives esophageal cancer (EC) progression and immune evasion, yet immune cell-type-specific genetic regulatory candidates associated with EC susceptibility remain incompletely characterized. This study aimed to prioritize immune cell-specific genetic regulatory candidates associated with EC susceptibility. Methods: We integrated single-cell expression quantitative trait loci (sc-eQTL) data with East Asian EC genome-wide association studies (GWAS; n = 160,589) to perform Mendelian randomization (MR). MR-prioritized candidates were further evaluated using tumor single-cell expression profiling, in silico perturbation analysis, The Cancer Genome Atlas Program (TCGA) transcriptomic correlations, phenome-wide association studies (PheWAS), and drug-repositioning analysis. Results: MR prioritized 18 gene–cell type pairs representing 16 immune cell-associated candidate genes (F-statistics >10), all of which remained significant within the prioritized candidate set after Benjamini–Hochberg correction. These findings supported a novel putative dual-axis immune evasion model. The TNFSF13B-associated inflammatory component showed monocyte-enriched tumor expression and transcriptomic associations with myeloid-derived suppressor cell (MDSC) markers CD33 (R = 0.63) and ITGAM (R = 0.47). Simultaneously, SLC25A29 showed CD8 effector memory T/NK-context MR signals but adipocyte-enriched tumor expression, suggesting a stromal metabolic–immune crosstalk hypothesis. In silico perturbation further linked SLC25A29 to CD8+ T cell effector-related programs, including GZMK. PheWAS did not identify evident severe pleiotropic safety signals for these hubs. Drug repositioning nominated TNFSF13B-directed agents, including belimumab, as testable repurposing candidates requiring further validation. Conclusions: This sc-eQTL-guided framework prioritizes immune cell-associated candidate genes and generates testable hypotheses linking germline genetic regulation, tumor single-cell expression localization, and TME remodeling in EC.