Identification and validation of smoking-related genes in lung adenocarcinoma using an in vitro carcinogenesis model and bioinformatics analysis

Jin Wang,Tao Chen,Xiaofan Yu,Jianxiang Li,Jian Tong,Nan Ouyang,Lirong Tan,Beibei Jia

doi:10.1186/s12967-020-02474-x

Abstract

BackgroundLung cancer is one of the most common carcinomas in the world, and lung adenocarcinoma (LUAD) is the most lethal and most common subtype of lung cancer. Cigarette smoking is the most leading risk factor of lung cancer, but it is still unclear how normal lung cells become cancerous in cigarette smokers. This study aims to identify potential smoking-related biomarkers associated with the progression and prognosis of LUAD, as well as their regulation mechanism using an in vitro carcinogenesis model and bioinformatics analysis.ResultsBased on the integration analysis of four Gene Expression Omnibus (GEO) datasets and our mRNA sequencing analysis, 2 up-regulated and 11 down-regulated genes were identified in both S30 cells and LUAD. By analyzing the LUAD dataset in The Cancer Gene Analysis (TCGA) database, 3 of the 13 genes, viz., glycophorin C (GYPC), NME/NM23 nucleoside diphosphate kinase 1 (NME1) and slit guidance ligand 2 (SLIT2), were found to be significantly correlated with LUAD patients’ smoking history. The expression levels of GYPC, NME1 and SLIT2 in S30 cells and lung cancer cell lines were validated by quantitative PCR, immunofluorescence, and western blot assays. Besides, these three genes are associated with tumor invasion depth, and elevated expression of NME1 was correlated with lymph node metastasis. The enrichment analysis suggested that these genes were highly correlated to tumorigenesis and metastasis-related biological processes and pathways. Moreover, the increased expression levels of GYPC and SLIT2, as well as decreased expression of NME1 were associated with a favorable prognosis in LUAD patients. Furthermore, based on the multi-omics data in the TCGA database, these genes were found to be regulated by DNA methylation.ConclusionIn conclusion, our observations indicated that the differential expression of GYPC, NME1 and SLIT2 may be regulated by DNA methylation, and they are associated with cigarette smoke-induced LUAD, as well as serve as prognostic factors in LUAD patients.

Highlights

Lung cancer is one of the most common carcinomas in the world, and lung adenocarcinoma (LUAD) is the most lethal and most common subtype of lung cancer
Expressed genes in smoke continuously for 30 passages (S30) cells and Gene Expression Omnibus (GEO) datasets Based on the high throughput analysis, a total of 753 differentially expressed genes (DEGs) were identified in cigarette smoke-induced transformed cells (S30) compared with unexposed BEAS-2B cells, including 273 up-regulated and 480 down-regulated genes (Fig. 2a, b)
A total of 11 down-regulated and 2 up-regulated smokingrelated genes were identified by taking the intersection of the DEGs extracted from S30 cells and GEO datasets (Fig. 2f )

Summary

Introduction

Lung cancer is one of the most common carcinomas in the world, and lung adenocarcinoma (LUAD) is the most lethal and most common subtype of lung cancer. There is a significant and positive correlation between cigarette smoke and lung cancer, and the risk of developing lung cancer in smokers is nearly 10 times higher than that in non-smokers [4, 5]. It is still unclear how normal lung cells become cancerous in cigarette smokers

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