title: RNA-seq analysis of lung adenocarcinomas reveals different gene expression profiles between smoking and nonsmoking patients.
abstract: Lung adenocarcinoma is caused by the combination of genetic and environmental effects, and smoking plays an important role in the disease development. Exploring the gene expression profile and identifying genes that are shared or vary between smokers and nonsmokers with lung adenocarcinoma will provide insights into the etiology of this complex cancer. We obtained RNA-seq data from paired normal and tumor tissues from 34 nonsmoking and 34 smoking patients with lung adenocarcinoma (GEO: GSE40419). R Bioconductor, edgeR, was adopted to conduct differential gene expression analysis between paired normal and tumor tissues. A generalized linear model was applied to identify genes that were differentially expressed in nonsmoker and smoker patients as well as genes that varied between these two groups. We identified 2273 genes that showed differential expression with FDR < 0.05 and |logFC| >1 in nonsmoker tumor versus normal tissues; 3030 genes in the smoking group; and 1967 genes were common to both groups. Sixty-eight and 70% of the identified genes were downregulated in nonsmoking and smoking groups, respectively. The 20 genes such as SPP1, SPINK1, and FAM83A with largest fold changes in smokers also showed similar large and highly significant fold changes in nonsmokers and vice versa, showing commonalities in expression changes for adenocarcinomas in both smokers and nonsmokers for these genes. We also identified 175 genes that were significantly differently expressed between tumor samples from nonsmoker and smoker patients. Gene expression profile varied substantially between smoker and nonsmoker patients with lung adenocarcinoma. Smoking patients overall showed far more complicated disease mechanism and have more dysregulation in their gene expression profiles. Our study reveals pathogenetic differences in smoking and nonsmoking patients with lung adenocarcinoma from transcriptome analysis. We provided a list of candidate genes for further study for disease detection and treatment in both smoking and nonsmoking patients with lung adenocarcinoma.
authors.affiliation: Department of Biomedical Data Science, Dartmouth College, 74 College Street, Vail 716A, Hanover, NH, 03755, USA.
authors.forename: Yafang
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Biomedical Data Science, Dartmouth College, 74 College Street, Vail 716A, Hanover, NH, 03755, USA.
authors.forename: Xiangjun
authors.initials: X
authors.lastname: Xiao
authors.affiliation: Department of Biomedical Data Science, Dartmouth College, 74 College Street, Vail 716A, Hanover, NH, 03755, USA.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Ji
authors.affiliation: Department of Genetics, Center for Genetics and Genomics, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 1010, Houston, 77030, TX, USA.
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.affiliation: Department of Biomedical Data Science, Dartmouth College, 74 College Street, Vail 716A, Hanover, NH, 03755, USA. Christopher.I.Amos@Dartmouth.edu.
authors.forename: Christopher I
authors.initials: CI
authors.lastname: Amos
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics* / Q000473:pathology; D000077192:Adenocarcinoma of Lung; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology; D009363:Neoplasm Proteins / Q000096:biosynthesis* / Q000235:genetics; D012313:RNA / Q000235:genetics; D012907:Smoking / Q000235:genetics* / Q000473:pathology; D059467:Transcriptome / Q000235:genetics
chemical_list: D009363:Neoplasm Proteins; D012313:RNA
keywords: Expression analysis; Lung adenocarcinoma; Lung cancer; RNA-seq; Smoking