Integrated single-cell and bulk RNA-seq analysis identifies BCAA metabolism-related prognostic signatures in head and...

Impaired metabolism of branched-chain amino acids (BCAAs) has been linked to cancer progression; however, the specific mechanisms underlying BCAA metabolism in head and neck squamous cell carcinoma (HNSCC) remain unclear. This study aimed to identify prognostic genes associated with BCAA metabolism in HNSCC and elucidate their functional roles.

HNSCC-related datasets (TCGA-HNSCC, GSE65858, GSE41613, GSE103322, and GSE140042) were analyzed, and candidate genes were identified by intersecting differentially expressed genes from differential expression analysis with key module genes associated with BCAA metabolism-related gene (BCAA-MRG) scores from weighted gene coexpression network analysis. Prognostic genes were subsequently selected to construct a risk model using univariate Cox regression analysis, proportional hazards testing, and least absolute shrinkage and selection operator regression. Independent prognostic analysis, enrichment analysis, and immune microenvironment assessment were subsequently performed. Moreover, single-cell RNA sequencing (scRNA-seq) and pseudotime analysis were used to evaluate prognostic gene expression at the cellular level. RT-qPCR was used to validate gene expression levels in HNSCC tissues.

SMS, PRDX6, GSTO1, and ADA were identified as prognostic genes for the risk model. The HNSCC samples were stratified into a high-risk group (HRG) and a low-risk group (LRG), with LRG showing notably better survival outcomes. A nomogram model based on risk score and age demonstrated excellent predictive performance for patients with HNSCC. Furthermore, enrichment analysis revealed that the pentose phosphate pathway and fructose and mannose metabolism were substantially associated with HNSCC progression. Differences in the infiltration levels of 20 immune cell types (including plasmacytoid dendritic cells, mast cells, and T follicle helper cells) and the expression of 10 immune checkpoints (such as CD276, CD27, and CD40) were observed between HRG and LRG. Epithelial cells, which exhibited higher expression of prognostic genes, were highlighted as key cells. Notably, the expression trends of these genes varied across different cell differentiation stages. RT-qPCR validation revealed that SMS, GSTO1, and ADA were highly expressed in the tumor group, whereas PRDX6 showed no significant difference between the tumor and normal tissues.

A four-gene BCAA metabolism-related signature (SMS, PRDX6, GSTO1, ADA) was identified that stratifies patients with HNSCC into distinct risk groups with different survival and immune microenvironments. The model suggests BCAA-immune interactions, specifically in epithelial cells, provide preliminary insights for prognosis and therapy. Nevertheless, these conclusions are mainly based on computational predictions, and the small RT-qPCR cohort limits experimental validation strength; thus, further studies are needed to confirm these findings.