Keratin gene expression signature predicts prognosis and immunotherapy efficacy in lung adenocarcinoma

Abstract

Keratins (KRTs) are intermediate filament proteins expressed in epithelial cells and serve as diagnostic cancer biomarkers. They serve pivotal roles in tumor progression and metastasis, but their prognostic value in lung adenocarcinoma (LUAD) and relationship with the tumor immune microenvironment remain unclear. Gene expression of KRTs in The Cancer Genome Atlas (TCGA)-LUAD was analyzed; candidate genes were selected using LASSO and random forest. An XGBoost classifier with SHAP interpretation distinguished tumor from normal tissues. Prognostic models were developed using 101 algorithms with 10-fold cross-validation and validated in two independent GEO cohorts. Immune cell composition and pathway activity were assessed by CIBERSORT, MCP-counter, ssGSEA and GSEA; the TIDE score estimated potential immunotherapy response. Functional validation of KRT81 was performed via shRNA knockdown in LUAD cell lines, followed by proliferation, apoptosis and migration assays. A KRT-based diagnostic and prognostic signature was established. The XGBoost model achieved high accuracy (TCGA AUC=0.996; GSE31210 AUC=0.860); SHAP identified KRT81 as a key contributor. A four-gene prognostic model (KRT27, KRT80, KRT16, KRT81) stratified patients into high- and low-risk groups. The risk score was associated with advanced tumor stage and independently predicted overall survival (multivariate HR=2.16, 95% CI 1.43–3.28, P=2.0×10-4). High-risk tumors enriched proliferation/stroma pathways (cell cycle, DNA repair, ECM-receptor interaction, focal adhesion, p53 signaling); low-risk tumors enriched immune pathways. Immune profiling revealed reduced T/B cell infiltration, increased endothelial cells and higher T-cell exclusion scores in high-risk patients, indicating an immunosuppressive microenvironment. Higher risk scores also associated with chemotherapy resistance. Functional validation confirmed that shRNA-mediated KRT81 knockdown reduced LUAD cell proliferation, migration and invasion, while promoting apoptosis. These findings link KRT expression to clinical outcomes, the tumor microenvironment and therapeutic response in LUAD, suggesting roles for KRTs in cancer progression, chemotherapy resistance and predictive potential for immunotherapy response. This study provides new insights for prognostic evaluation and therapeutic decision-making in LUAD.