Prognostic and Immunomodulatory Roles of BNIP3 in Osteosarcoma Revealed by Integrated Single-Cell and Bulk Transcriptomic Profiling

Abstract

Osteosarcoma is a highly aggressive bone tumor with a complex tumor microenvironment (TME) that contributes to its progression and therapeutic resistance. In this study, we integrated single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq datasets to characterize the TME and identify key prognostic genes in osteosarcoma. Using scRNA-seq data from 16 osteosarcoma samples, we defined eight major cell types within the TME and performed functional enrichment analyses. Through weighted gene co-expression network analysis (WGCNA) focused on an inflammation-related gene signature, we identified the yellow module as the most correlated with inflammation. By intersecting tumor-upregulated genes with WGCNA-derived genes, we identified BNIP3 as the only significant prognostic gene associated with poor survival in both the TARGET and GSE21257 cohorts. Functional annotation revealed that high BNIP3 expression is negatively correlated with immune-related pathways and immune cell infiltration, including T cells, B cells, NK cells, and neutrophils. Additionally, BNIP3-high patients exhibited a reduced sensitivity to several potential therapeutic agents. Our findings highlight BNIP3 as a hazardous gene in osteosarcoma, with important roles in immune evasion and prognosis, suggesting its potential as a therapeutic target.