Constructing a Prognostic Gene Signature for Lung Adenocarcinoma Based on Weighted Gene Co-Expression Network Analysis and Single-Cell Analysis

PURPOSE: Lung adenocarcinoma (LUAD) has a high degree of intratumor heterogeneity. Advanced single-cell RNA sequencing (scRNA-seq) technologies have offered tools to analyze intratumor heterogeneity, which improves the accuracy of identifying biomarkers based on single-cell expression data, and thus helps in predicting prognosis of cancer patients and assisting decision-makings for cancer treatment. PATIENTS AND METHODS: ScRNA-seq data containing two LUAD and two para-cancerous tissue samples were included to identify different cell clusters in tumor tissues. To identify the most relevant modules and important cell subpopulations (clusters) in LUAD tissues, weighted gene co-expression network analysis (WGCNA) was performed. Subsequently, LUAD molecular subtypes were constructed by unsupervised consensus clustering based on genes in key modules. Using differential analysis, univariate Cox regression analysis, and least absolute shrinkage and selection operator (LASSO) regression analysis, a prognostic model of LUAD was established. RESULTS: A total of 14 cell clusters belonging to 10 cell types in LUAD were identified. The turquoise module was the most relevant to LUAD among all the modules; cluster 10 (C10, lung epithelial cells) was found to be the most strongly associated with the turquoise module. LUAD samples were divided into two groups of distinct molecular subtypes. Based on the 165 shared genes between the turquoise module and C10, 511 DEGs between the two molecular subtypes were obtained, and five of them were selected to construct the gene signature, which was validated to be an independent prognostic marker of LUAD. CONCLUSION: Fourteen cell clusters co-existed in LUAD, which contributed to its intratumor heterogeneity. Two molecular subtypes of LUAD were identified and a five-gene signature was developed and validated to be significantly associated with prognostic and clinical characteristics of LUAD patients.