Identification and Validation of Three-Gene Signature in Lung Squamous Cell Carcinoma by Integrated Transcriptome and Methylation Analysis

Abstract

Since DNA methylation (DNAm) is associated with the carcinogenesis of various cancers, this study aimed to explore potential DNAm prognostic signatures of lung squamous cell carcinoma (LUSC). First, transcriptomic and methylation profiles of LUSC were obtained from The Cancer Genome Atlas database (TCGA). DNAm-related genes were screened by integrating DNAm and transcriptome profiles via MethylMix package. Subsequently, a prognostic signature was conducted with the least absolute shrinkage and selector operation (LASSO) Cox analysis. This signature combined with the clinicopathological parameters was then utilized to construct a prognostic nomogram via the rms package. A signature based on three DNAm-related genes claudin 1 (CLDN1), ATP-binding cassette subfamily C member 5 (ABCC5), and cystatin A (CSTA) that were hypomethylated and upregulated in LUSC was constructed. Univariate and multivariate Cox regression analysis suggested that this signature, combined with age and TNM.N stage, was significantly correlated with survival rate. Time-dependent receiver operating characteristics and calibration curves suggested the nomogram constructed with age and TNM.N stage variables could accurately evaluate the 3- and 5-year outcome of LUSC. Finally, the average mRNA and protein expression levels of CLDN1, ABCC5, and CSTA in LUSC were verified to be significantly higher than those in paracancerous tissues. Moreover, silencing CLDN1, ABCC5, and CSTA expressions could significantly reduce the carcinogenesis of the A549 cell line. The DNAm-driven prognostic signature consists of CLDN1, ABCC5, and CSTA incorporated with age and TNM. N stage could facilitate the prediction outcome of LUSC.

MMP12 serves as an immune cell–related marker of disease status and prognosis in lung squamous cell carcinoma

“…Lung cancer is one of the deadliest malignancies in the world and is the primary cause of death among cancer patients ( Siegel, Miller & Jemal, 2020 ; Mridha et al., 2022 ; Adams et al., 2023 ). Lung squamous cell carcinoma (LUSC) belongs to non-small-cell lung cancer (NSCLC), and clinical statistics show that the number of patients with LUSC accounts for about 30% of patients with NSCLC ( Li et al., 2022a ; Ding et al., 2022 ; Chen et al., 2022a ; Pan et al., 2022 ). In recent years, conventional platinum-based two-drug therapy and combination chemotherapy have remained the first-line treatments for advanced LUSC.…”