Comprehensive analysis of liquid-liquid phase separation-related genes in osteosarcoma: implications for prognosis,...

Liquid-liquid phase separation (LLPS) contributes to osteosarcoma (OS) regulatory mechanisms. This investigation focused on evaluating the predictive potential of LLPS-related genes (LRGs) for OS.

LRGs were obtained from the data resource of LLPS (DrLLPS) database. Transcriptome data from OS patients were downloaded from The Cancer Genome Atlas (TCGA)-Target and Gene Expression Omnibus (GEO) databases, and differentially expressed genes (DEGs) and key module genes for OS were identified through differential expression analysis and weighted gene co-expression network analysis (WGCNA). Univariate Cox regression and machine learning, including least absolute shrinkage and selection operator (LASSO), random forest (RF), and XGBoost, were used to identify hub differentially expressed LRGs (DELRGs), and their predictive value was assessed. Single-gene gene set enrichment analysis (GSEA), immune infiltration, and drug sensitivity analyses were conducted. In vitro experiments verified bioinformatics results.

By intersecting DEGs, key module genes, and LRGs, 221 DELRGs were obtained. Four genes (MRPL12, GCA, ABLIM1, and MAGED1) were identified as hub DELRGs with excellent predictive value in OS. Single-gene GSEA highlighted the regulatory roles of hub DELRGs in OS. Neutrophils were significantly correlated with all four hub DELRGs. These genes were extensively correlated with drug sensitivity. MRPL12 levels were upregulated, while MAGED1, ABLIM1, and GCA levels were downregulated in OS cells, consistent with bioinformatics-predicted expression and prognostic significance of GCA and MRPL12. MRPL12 knockdown or GCA overexpression inhibited the malignant phenotypes of U2OS cells.

This study identified four hub DELRGs for OS prognosis, offering insight into LLPS in OS pathogenesis.