Intratumor heterogeneity analysis in lung adenocarcinoma by single-cell RNA sequencing and construction of a prognostic gene signature.

Abstract

e20521 Background: Lung adenocarcinoma (LUAD), at the cellular level, has a high degree of intratumor heterogeneity. Advanced single-cell sequencing technologies have offered tools to analyze intratumor heterogeneity and identify the biomarkers, thereby aiding cancer diagnosis and prediction of the patient prognosis. Methods: From the Gene Expression Omnibus (GEO) (www.ncbi.nlm.nih.gov/geo) database, the single-cell RNA sequencing (scRNA-seq) data from two LUAD and two para-cancerous tissue samples were obtained. We performed a dimensionality reduction and unsupervised clustering to identify the different cell clusters within the tumor tissues. To identify the most relevant modules and important cell subpopulations (clusters) in LUAD tissues, a weighted gene co-expression network analysis (WGCNA) was performed. Subsequently, we classified the LUAD molecular subtypes according to the marker genes of these clusters. The Limma package ( www.bioconductor.org/packages/release/bioc/html/limma ) was used to screen for the differentially expressed genes (DEGs) between the subtypes. Using univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses, the gene signature most significantly associated with the prognosis of LUAD patients was determined. Results: A total of 14 cell clusters belonging to 10 cell types in LUAD was identified. The turquoise module was found to be the most relevant to LUAD among all the modules; cluster 10 (C10) was found to be the most strongly associated with the turquoise module. In The Cancer Genome Atlas (TCGA), patients with LUAD 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. Conclusions: 14 cell clusters co-existed in LUAD, which contributed to its intratumor heterogeneity. In addition, 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. Keywords: single-cell RNA sequencing, lung adenocarcinoma, intratumor heterogeneity, molecular subtypes, prognosis, five-gene signature.