Distinct Patterns of mRNA and lncRNA Expression Differences Between Lung Squamous Cell Carcinoma and Adenocarcinoma

Abstract

This study aimed to assess mRNA and lncRNA expression differences between lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD). Cancer tissues were obtained from three LUSC and three LUAD patients, followed by RNA-seq. Differentially expressed mRNAs (DE-mRNAs) and lncRNAs (DE-lncRNAs) were identified between LUSC and LUAD, after which functional enrichment analysis and protein–protein interaction (PPI) network construction was performed on DEGs. Coexpression analysis of lncRNA-gene and prediction of DEG-related miRNAs as well as function enrichment analysis, and construction of competing endogenous RNAs (ceRNA) regulatory network were then conducted. Moreover, survival analysis on differentially expressed RNAs was performed based on data downloaded from The Cancer Genome Atlas (TCGA) database. In this study, 518 DEGs and 117 DE-lncRNAs were identified between LUSC and LUAD. The DEGs were mainly associated with cell adhesion, PI3K-Akt signaling pathway, and focal adhesion. PPI network analysis indicated several genes with highest connectivity, such as CCND1. DE-lncRNAs that coexpressed with DEGs were also associated with tight junction and DE-lncRNAs that had more corepressed relationships with DEGs included GSEC, NKX2-1-AS1, LINC01415, and LINC00839. Moreover, the genes and lncRNAs with higher connectivity in the ceRNA network included NEAT1, SLC5A3, LINC00839, ETV1, CMTM4, and SNX30. Several genes were significantly related to the survival of patients with LUSC and LUAD, including ETV1, RTKN2, SNX30, PAK2, and CCND1. Genes and lncRNAs associated with cell junction have specific patterns in two major histological subtypes of NSCLC. GSEC, NKX2-1-AS1, NEAT1, CCND1, and ETV1 may be potential novel biomarkers for personalized treatment strategies of NSCLC.