Immune Microenvironment Dynamics and Therapeutic Targets in GIST Revealed by Multi-Omics and Functional Validation

The tumour immune microenvironment (TIME) significantly influences the progression and treatment response of gastrointestinal stromal tumours (GIST), but the causal mechanisms and therapeutic targets remain incompletely understood. We integrated multi-omics analyses, including Mendelian randomization analysis of 731 immune cell phenotypes to assess their causal relationship with GIST, mediation analysis to identify plasma metabolite mediators, single-cell RNA sequencing (scRNA-seq) to characterise TIME heterogeneity and bulk RNA-seq to screen for differentially expressed genes. Using the GIST-882 cell and CD8⁺ T cell co-culture model, combined with functional assays such as proliferation, migration, invasion and protein uptake tracing, we validated the roles of candidate genes MYBL1 and AIF1L. Additionally, we evaluated their combined effects with PD-1 inhibitors. Mendelian randomization analysis identified 18 immune cell phenotypes with causal relationships to GIST (10 risk factors and 8 protective factors) and 4 mediating plasma metabolites. scRNA-seq revealed dynamic remodelling of the TIME. We identified genes that progressively increased or decreased from peritumoral tissues to primary tumours and metastatic tumours, and were positively correlated with PD-1 expression. The inhibitory effects of these genes on GIST malignant phenotypes were dependent on CD8⁺ T cells, and their proteins were taken up by T cells. Knockdown of MYBL1 or overexpression of AIF1L exhibited synergistic anti-tumour effects when combined with PD-1 blockade. Mendelian randomization analysis identified 18 immune cell phenotypes with causal relationships to GIST (10 risk factors and 8 protective factors) and 4 mediating plasma metabolites. scRNA-seq revealed dynamic remodelling of the TIME. We identified genes that progressively increased or decreased from peritumoral tissues to primary tumours and metastatic tumours, and were positively correlated with PD-1 expression. The inhibitory effects of these genes on GIST malignant phenotypes were dependent on CD8⁺ T cells, and their proteins were taken up by T cells. Knockdown of MYBL1 or overexpression of AIF1L exhibited synergistic anti-tumour effects when combined with PD-1 blockade. This study investigates changes in the immune microenvironment during GIST progression and identifies MYBL1 and AIF1L as key mediators regulating CD8⁺ T cell function and PD-1 response, providing new strategies for combined immunotherapy in GIST.