System analysis based on T-cell exhaustion-related genes identifies PTPRT as a promising diagnostic and prognostic biomarker for gastric cancer

• Published in: Scientific reports Vol. 14; no. 1; pp. 21049 - 13
• Main Authors: Wu, Jianli, Li, Le, Cheng, Zhenyun
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group 09.09.2024; Nature Publishing Group UK; Nature Portfolio
• Subjects: Adenocarcinoma; Apoptosis; Bioinformatics; Biomarkers; Cancer immunotherapy; CD8 antigen; Cell surface; Fibroblast growth factor 1; Flow cytometry; Gastric cancer; Gene expression; Genes; Genomic analysis; Immune microenvironment; Immune response; Lymphocytes T; Metastases; PD-1 protein; Prognosis; PTPRT; Single-nucleotide polymorphism; T-cell exhaustion; Tumor necrosis factor-α; Tumors; Variance analysis; γ-Interferon
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-72135-2

Multiple investigations have demonstrated the crucial involvement of T-cell exhaustion (TEX) in anti-tumor immune response and their strong correlation with prognosis. This study aimed at creating a strong signature using TEX for gastric cancer through bioinformatics analysis and experimental validation. We utilized data from The Cancer Genome Atlas (TCGA) databases to retrieve RNA-seq data from patients with stomach adenocarcinoma (STAD). Genes related to TEX were discovered using gene set variance analysis (GSVA) and weighted gene correlation network analysis (WGCNA). Subsequently, prognostic signature based on TEX was developed using LASSO-Cox analysis. Relationship between key genes and immune cells were examined. Finally, biological function of a key TEX-related gene PTPRT in gastric cancer was verified by in vivo experiment. A total of 29 TEX-related biomarkers were screened by WGCNA and random forest. Among them, five core signatures (PTPRT, CAV2, PPIH, PRDM2, and FGF1), further identified by LASSO-Cox, were considered as strong predictors of prognosis for gastric cancer and associated with immune infiltration. PTPRT gene had the largest number of SNPs, with the most mutation types. In vivo experiments revealed that PTPRT overexpression significantly inhibited tumor malignant progression and accelerated apoptosis through stimulating the secretion of killer cytokines such as TNF-α and IFN-γ. In addition, flow cytometry revealed that PTPRT overexpression alleviated TEX by increasing the abundance of CD8+ T cells, with inhibition of cell surface PD-1 and Tim-3. The predictive prognostic value of TEX gene expression levels was evaluated in patients with gastric cancer, providing a new perspective for precision immuno-oncology studies.