Machine learning-driven development of a novel unfolded protein response-related gene signature for predicting lung adenocarcinoma patient prognosis.

Abstract

Lung adenocarcinoma (LUAD) is the most common lung cancer histological subtype. Although the unfolded protein response (UPR) has been linked to various human diseases, its role in LUAD remains unclear. To identify UPR-related genes, we applied various methods, including weighted gene co-expression network analysis, differential expression analysis, and multivariate Cox regression. Ten machine learning algorithms were used to construct a UPR-related signature (UPRRS), which was validated using multiple public LUAD datasets. The UPRRS was integrated into a nomogram used in clinical practice for prognosis prediction. We also evaluated predicted drug sensitivity patterns across different risk subgroups. We identified 33 UPR-associated hub genes. A UPRRS was developed through systematic evaluation of 101 machine-learning combinations, exhibiting stable prognostic performance across multiple cohorts. Integration of the UPRRS into a nomogram facilitated the construction of a quantitative prognostic model. Significant differences in biological processes and tumor microenvironment immune cell infiltration were observed between the high- and low-risk UPRRS groups. All five UPRRS genes (ALDH2, FKBP4, KLF4, LAIR1, SIDT2) were validated at the protein level in LUAD cell lines, and FKBP4 was further confirmed by IHC in clinical tissues. Functional experiments showed that FKBP4 knockdown inhibited proliferation, migration, and invasion of A549 and H1975 cells, supporting a potential role for FKBP4 in LUAD progression. Our UPRRS provides a promising tool for prognostic stratification and may offer additional insights into tumor immune microenvironment characterization and therapeutic response prediction in LUAD.