The relationship between LncRNAs and lung adenocarcinoma as well as their ceRNA network

Article type: Research Article

Authors: Zhao, Yuxin^{a; 1} | Ma, Shuwen^{a; 1} | Cui, Zhigang^c | Li, Sixuan^{a; b} | Chen, Yao^a | Yin, Yu^a | Yin, Zhihua^{a; b; d; *}

Affiliations: [a] China Medical University, Shenyang North New Area, Shenyang, Liaoning, China | [b] Department of Epidemiology, School of Public Health, China Medical University, Shenyang, Liaoning, China | [c] School of Nursing, China Medical University, Shenyang, Liaoning, China | [d] Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang North New Area, Shenyang, Liaoning, China

Correspondence: [*] Corresponding author: Zhihua Yin, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China. Tel.: +86 18900910228; E-mail: [email protected].

Note: [1] These authors contributed equally to this work and should be considered co-first authors.

Abstract: BACKGROUND: More and more studies have shown that long non-coding RNA (LncRNA) as a competing endogenous RNA (ceRNA) plays an important role in lung cancer. Therefore, we analyzed the RNA expression profiles of 82 lung cancer patients which were all from Gene Expression Omnibus (GEO). METHODS: Firstly, we used BLASTN (evalue = 1e-10) to annotate the gene sets, performed in-group correction and batched normalization of the three data sets with R. Secondly, we used the limma and sva packages to compare tumor tissues with normal tissues. Then through WGCNA, we obtained the 4 gene modules most related to the trait. RESULTS: We intersected the genes of above 4 modules with the differential expression genes: 28 LncRNAs (up: 5, down: 23) and 265 mRNAs (up:11, down: 254). Based on these genes, we picked up 6 LncRNAs (CCDC39, FAM182A, SRGAP3-AS2, ADAMTS9-AS2, AC020907.2, SFTA1P), then set and visualized the LncRNA-miRNA-mRNA ceRNA network with 12 miRNAs related to 12 mRNAs. Finally, we performed downstream analysis of 265 mRNAs by Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Protein-Protein Interaction (PPI) network. CONCLUSION: After analyzing, we think this study provides a new direction for basic and clinical research related to LAD, and is expected to provide new targets for early diagnosis, prognostic evaluation and clinical treatment of lung cancer.

Keywords: Lung adenocarcinoma, GEO, LncRNA, ceRNA, WGCNA

DOI: 10.3233/CBM-203078

Journal: Cancer Biomarkers, vol. 31, no. 2, pp. 165-176, 2021