Identification of differentially expressed protein-coding genes in lung adenocarcinomas

Abstract

Lung adenocarcinoma accounts for a high proportion of lung cancers. Though efforts have been made to develop new and effective treatments for this disease, the mortality rate remains high. Gene expression microarrays facilitate the study of lung cancer at the molecular level. The present study aimed to detect differentially expressed protein-coding genes to identify novel biomarkers and therapeutic targets for lung adenocarcinoma. Aberrations in gene expression in lung adenocarcinoma were determined by analysis of mRNA microarray datasets from the Gene Expression Omnibus database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, protein-protein interaction (PPI) networks and statistical analysis were used to identify the biological functions of the differentially expressed genes (DEGs). The results of the bioinformatics analysis were subsequently validated using reverse transcription-quantitative PCR. A total of 303 DEGs were identified in lung adenocarcinomas, and they were enriched in a number of cancer-associated GO terms and KEGG pathways. DNA topoisomerase 2α (TOP2A), cell division cycle protein homolog 20 (CDC20), mitotic checkpoint serine/threonine protein kinase BUB1 (BUB1) and mitotic spindle assembly checkpoint protein MAD2A (MAD2L1) exhibited the highest degree of interaction in the PPI network. Survival analysis performed using Kaplan-Meier curves and Cox regression indicated that these four genes were all significantly associated with the survival of patients with lung adenocarcinomas. In conclusion, TOP2A, CDC20, BUB1 and MAD2L1 may be key protein-coding genes that may serve as biomarkers and therapeutic targets in lung adenocarcinomas.

Keywords: DNA topoisomerase 2α; bioinformatics analysis; biomarkers; cell division cycle protein homolog 20; lung adenocarcinoma; mitotic checkpoint serine/threonine protein kinase BUB1; mitotic spindle assembly checkpoint protein MAD2L1.

Figure 1.

Top seven Kyoto Encyclopedia of Genes and Genomes pathways enriched by the differentially expressed protein-coding genes in lung adenocarcinoma. eNOS, nitric oxide synthase 3; NOSTRIN, nitric oxide synthase trafficking; GPCR, G protein-coupled receptor.

Figure 2.

Gene Ontology terms enriched by the differentially expressed protein-coding genes in lung adenocarcinoma in the categories (A) biological process, (B) cellular component and (C) molecular function.

Figure 3.

Protein-protein interaction network for differentially expressed protein-coding genes in lung adenocarcinoma generated using the Search Tool for the Retrieval of Interacting Genes/proteins and Cytoscape software. Proteins with a high degree of interaction (indicated in red) were considered key genes, including TOP2A, CDC20, BUB1 and MAD2L1. BUB1, mitotic checkpoint serine/threonine protein kinase BUB1; TOP2A, DNA topoisomerase 2α; CDC20, cell division cycle protein homolog 20; MAD2L1, mitotic spindle assembly checkpoint protein MAD2A.

Figure 4.

Influence of high/low expression of key genes on overall survival. (A) TOP2A, (B) BUB1, (C) CDC20 and (D) MAD2L1 are significantly associated with overall survival in patients with lung adenocarcinoma, as indicated by Kaplan-Meier curves and the log-rank test. TOP2A, DNA topoisomerase 2α; BUB1, mitotic checkpoint serine/threonine protein kinase BUB1; CDC20, cell division cycle protein homolog 20; MAD2L1, mitotic spindle assembly checkpoint protein MAD2A; HR, hazard ratio.

Figure 5.

(A) DNA topoisomerase 2α and (B) mitotic checkpoint serine/threonine protein kinase BUB1 were identified to be overexpressed in LUAD tissues. Red corresponds to the tumor group and gray corresponds to the normal group. *P<0.05. LUAD, lung adenocarcinoma; T, tumor tissues; N, normal lung tissues.

Figure 6.

Expression of (A) TOP2A and (B) mitotic checkpoint serine/threonine protein kinase BUB1 in different stages of lung cancer. TOP2A, DNA topoisomerase 2α.

Figure 7.

Validation of the protein expression levels of (A) DNA topoisomerase 2α and (B) mitotic checkpoint serine/threonine protein kinase BUB1 in lung adenocarcinoma tissues using the Oncomine and HPA databases.

Figure 8.

(A) TOP2A, (B) BUB1, (C) CDC20 and (D) MAD2L1 were confirmed to be significantly upregulated in lung cancer tissues compared to normal tissues based on reverse transcription-quantitative PCR analysis. *P<0.05, **P<0.01, ***P<0.001 vs. normal group. TOP2A, DNA topoisomerase 2α; BUB1, mitotic checkpoint serine/threonine protein kinase BUB1; CDC20, cell division cycle protein homolog 20; MAD2L1, mitotic spindle assembly checkpoint protein MAD2A.