Integrated transcriptomics identifies HIF1A and GSTP1 as biomarkers for cutaneous squamous cell carcinoma

Cutaneous squamous cell carcinoma (cSCC) is one of the most common skin malignancies with limited reliable biomarkers for early detection and prognosis. This study integrated bulk and single‑cell transcriptomic data to identify post‑translational modification-related key genes and to characterise cellular and immune alterations in cSCC.

Publicly available cSCC datasets and post-translational modification-related genes (PTMRGs) were analysed. Single-cell analysis identified key cell populations and differentially expressed genes (DEGs), which were intersected with bulk DEGs, weighted gene co‑expression network modules, and PTMRGs. Candidate genes were prioritised using five feature selection algorithms, validated by quantitative real-time polymerase chain reaction (qRT-PCR) and receiver operating characteristic (ROC) analysis [area under the curve (AUC) >0.7]. Functional exploration included predictive modelling, SHapley Additive Explanations (SHAP) interpretation, immune infiltration analysis, protein interaction mapping, drug prediction with molecular docking, intercellular communication inference, and pseudotime trajectory analysis.

Keratinocytes were identified as the key cell population, yielding 999 single-cell-differentially expressed genes (sc-DEGs). Bulk analysis detected 5,771 DEGs and 17 co‑expression modules; intersection yielded 19 candidate genes. Multi‑method feature selection nominated HIF1A, UBC, and GSTP1; validation retained HIF1A and GSTP1 as final diagnostic markers (upregulated in cSCC; AUCs >0.7). A least absolute shrinkage and selection operator (LASSO) classifier achieved the best performance. SHAP highlighted HIF1A and GSTP1 as dominant contributors. HIF1A was predicted to be nuclear, GSTP1 mitochondrial; both correlated positively with macrophages, natural killer (NK) cells, and neutrophils. Drug prediction and docking identified camptothecin, hydroquinone, and resveratrol with favorable binding (e.g., HIF1A-camptothecin -8.7 kcal/mol; GSTP1-camptothecin -8.6 kcal/mol). Cell-cell signaling was enhanced in cSCC [vascular endothelial growth factor (VEGF), endothelin (EDN) pathways; elevated MIF-(CD74+CXCR4) and MIF-(CD74+CD44)]. Keratinocyte pseudotime revealed progression from normal to metastatic states with concordant keratinocyte‑related gene programs.

HIF1A and GSTP1 are promising diagnostic biomarkers for cSCC, linked to altered immune landscapes, enhanced intercellular signaling, and potential druggable interactions.