Copy-number amplification drives IFI30 overexpression and coordinated immune activation, identifying a novel diagnostic and therapeutic target in gastric adenocarcinoma

Abstract

Interferon-γ-inducible protein 30 (IFI30, also known as lysosomal thiol reductase, GILT) plays a key role in antigen processing by reducing disulfide bonds. However, its biological significance in gastric cancer (GC) has not been systematically elucidated. This study integrated pan-cancer multi-omics data, including transcriptomics (TCGA-STAD, GEO), genomics (whole-exome somatic mutations, copy number alterations), immune profiling, single-cell RNA sequencing, and transcription factor prediction to comprehensively characterize the dysregulation of IFI30 in GC. Downstream pathway involvement was inferred through weighted gene co-expression network analysis (WGCNA), gene set enrichment analysis (GSEA), and phosphoproteomic correlation mapping. The immune microenvironment was analyzed using CIBERSORTx, TIMER2.0, and re-annotated spatial transcriptomics. Multi-omics interrogation revealed that IFI30 is markedly up-regulated in gastric adenocarcinoma (STAD) relative to normal gastric mucosa. Across TCGA-GTEx and three validation cohorts, IFI30 mRNA and protein levels were significantly higher in tumours, with robust diagnostic performance (AUC = 0.92). Copy-number amplification—not point mutation—was the principal genomic driver of over-expression and was accompanied by heightened genome instability and co-occurrence of TP53 and PIK3CA alterations. Single-cell RNA-seq pinpointed IFI30 enrichment in dendritic cells, CD8⁺ T cells and macrophages, forming dense ligand-receptor networks that link innate and adaptive immunity. WGCNA and pathway analyses showed that IFI30-high tumours converge on antigen presentation, cytokine/chemokine, JAK–STAT and NF-κB signalling while activating epithelial-mesenchymal transition, cell-cycle and hypoxia programmes. IFI30 correlated strongly with multiple steps of the cancer–immunity cycle and with PD-L1, SPI1, FOXP3 and IRF1 expression. Pharmacogenomic profiling indicated resistance to MAPK- and cell-cycle inhibitors yet increased sensitivity to EGFR and PI3K/AKT blockade. IFI30-based signatures outperformed TIDE, TMB and PD-L1 in predicting immune-checkpoint-blockade response and were enriched in MSI-H tumours. In vitro, IFI30 protein was abundant in six gastric-cancer cell lines, and shRNA-mediated knock-down curtailed proliferation. Collectively, these findings establish IFI30 as a genomically driven, immunologically active and therapeutically actionable biomarker in gastric cancer. IFI30 is a copy-number–driven oncogenic and immunomodulatory gene that is markedly over-expressed in gastric adenocarcinoma. Its high expression integrates tumor-intrinsic programs (cell cycle, EMT, hypoxia) with tumor-extrinsic immune activation, predicts differential drug sensitivities, and outperforms established biomarkers in forecasting response to immune-checkpoint blockade—particularly in MSI-high disease. These findings nominate IFI30 as a promising diagnostic marker and therapeutic target.