Multi-omics analysis of GBP2 as a prognostic and immune-associated biomarker in papillary thyroid carcinoma

Background: Guanylate-binding protein 2 (GBP2) is dysregulated in several malignancies and participates in immune regulation. This study aimed to characterize its expression, prognostic relevance, cellular distribution, immune associations, and biological role in papillary thyroid carcinoma (PTC).

Methods: We integrated multi-omics data from TCGA-THCA, GEO, and the Human Protein Atlas (HPA). The TCGA-THCA cohort primarily comprises differentiated thyroid carcinoma, with PTC as the predominant histologic subtype; single-cell RNA-sequencing (scRNA-seq) data from PTC samples were also analyzed. Kaplan–Meier survival analysis and univariable and multivariable Cox regression were used to evaluate the prognostic association of GBP2. ESTIMATE, CIBERSORT, and TIMER2.0 were used to assess associations between GBP2 and the tumor immune microenvironment and immune-cell infiltration. Immune-checkpoint expression and immunophenoscores from The Cancer Immunome Atlas (TCIA) were used to characterize immune-related phenotypes. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were performed to explore potential functions. scRNA-seq data were used to characterize the PTC microenvironment and cell-type-specific GBP2 expression, identify GBP2-associated differentially expressed genes, and infer potential intercellular communication with CellChat. Finally, GBP2 was transiently silenced with small interfering RNA (siRNA) in TPC-1 cells, followed by CCK-8, wound-healing, Transwell invasion, and flow-cytometric apoptosis assays.

Results: GBP2 mRNA and protein expression were higher in PTC than in normal thyroid tissue. Patients with high GBP2 expression had longer overall survival (OS), and multivariable Cox regression showed an adjusted association between GBP2 expression and a lower risk of death (hazard ratio [HR], 0.23; 95% confidence interval [CI], 0.08–0.65; P=0.006). GBP2 expression was negatively associated with age and clinical stage and positively associated with N stage. Stratified survival analyses and interaction testing did not indicate a significant interaction between GBP2 and N stage. High GBP2 expression was associated with higher immune and stromal scores and with infiltration by several immune-cell populations, including CD8+ T cells, B cells, and dendritic cells. GBP2-related genes were enriched in T-cell activation, antigen processing and presentation, and interferon-response pathways. scRNA-seq analysis showed that GBP2 was detectable in T cells, malignant thyrocytes, and myeloid cells, with the highest average expression in T cells. In malignant thyrocytes, higher GBP2 expression was associated with enrichment of MHC-complex and immune-related functions. CellChat suggested a potential HLA-A/B/C/E–CD8A/B communication pattern between GBP2-high malignant thyrocytes and CD8+ T cells; this finding requires experimental validation. In TPC-1 cells, GBP2 knockdown increased CCK-8 signals, wound closure, and invasive capacity and reduced apoptosis.

Conclusions: In predominantly PTC cohorts, high GBP2 expression is associated with longer OS and an immune-inflamed tumor microenvironment. GBP2 may therefore serve as a candidate biomarker for prognostic and immune-phenotype studies in PTC. Its mechanistic role in tumor cells and the immune microenvironment requires further validation.