Identification of Differential Protein-coding Gene Expressions in Early Phase Lung Adenocarcinoma

Overview

Journal Thorac Cancer

Specialties Oncology
Pulmonary Medicine

Date 2017 Dec 22

PMID 29266838

Citations 4

Authors

Li-Na Zhou

Shi-Cheng Li

Xue-Ying Li

Hong Ge

Hong-Mei Li

Affiliations

Soon will be listed here.

Abstract

Background: The diagnosis of early phase lung adenocarcinoma (LADC) is associated with therapeutic strategy, effect, and survival time. However, the sensitive biomarkers of early phase LADC are still unclear. This study aimed to identify protein-coding genes that can be used as biomarkers of early stage LADC.

Methods: Gene microarray analysis was performed to identify key hub genes that show different expression in lung adenocarcinoma compared to normal tissues. The microarray data of lung adenocarcinoma in stages IA, IB, IIA, IIB, and normal tissues (GSE10072) were downloaded from a free online database, Gene Expression Omnibus (GEO).

Results: A total of 572 differentially expressed genes (DEGs) were identified between early phase lung adenocarcinoma and normal tissues using R software. Database for Annotation, Visualization and Integrated Discovery online tools were used to obtain Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to analyze DEGs. Cytoscape software was used to express the protein-protein interaction network. We found that some cancer-related Gene Ontology terms and pathways (e.g. cell adhesion, cell surface receptor signaling pathway, PI3K-Akt signaling pathway) were significantly enriched in DEGs.

Conclusion: Protein-coding genes JUN, FYN, CAV1, and SFN may play vital roles in the progress of early-stage lung adenocarcinoma. Consequently, through bioinformatics analysis, the key genes could be established to provide more potential references for the therapeutic targets of lung adenocarcinoma.

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References

Ji H, Pang D, Fu S, Jin Y, Yao L, Qi J . Overexpression of focal adhesion kinase correlates with increased lymph node metastasis and poor prognosis in non-small-cell lung cancer. J Cancer Res Clin Oncol. 2012; 139(3):429-35. DOI: 10.1007/s00432-012-1342-8. View

Griesing S, Kajino T, Tai M, Liu Z, Nakatochi M, Shimada Y . Thyroid transcription factor-1-regulated microRNA-532-5p targets KRAS and MKL2 oncogenes and induces apoptosis in lung adenocarcinoma cells. Cancer Sci. 2017; 108(7):1394-1404. PMC: 5497805. DOI: 10.1111/cas.13271. View

Nakamura H, Saji H, Ogata A, Hosaka M, Hagiwara M, Saijo T . cDNA microarray analysis of gene expression in pathologic Stage IA nonsmall cell lung carcinomas. Cancer. 2003; 97(11):2798-805. DOI: 10.1002/cncr.11406. View

Cortez M, Ivan C, Valdecanas D, Wang X, Peltier H, Ye Y . PDL1 Regulation by p53 via miR-34. J Natl Cancer Inst. 2015; 108(1). PMC: 4862407. DOI: 10.1093/jnci/djv303. View

Raymond K, Deugnier M, Faraldo M, Glukhova M . Adhesion within the stem cell niches. Curr Opin Cell Biol. 2009; 21(5):623-9. DOI: 10.1016/j.ceb.2009.05.004. View

Li Q, Xie Y, Wu Y, Li L, Liu Y, Miao X . Sulforaphane inhibits cancer stem-like cell properties and cisplatin resistance through miR-214-mediated downregulation of c-MYC in non-small cell lung cancer. Oncotarget. 2017; 8(7):12067-12080. PMC: 5355326. DOI: 10.18632/oncotarget.14512. View

Schenone S, Brullo C, Musumeci F, Biava M, Falchi F, Botta M . Fyn kinase in brain diseases and cancer: the search for inhibitors. Curr Med Chem. 2011; 18(19):2921-42. DOI: 10.2174/092986711796150531. View

Bender E . Epidemiology: The dominant malignancy. Nature. 2014; 513(7517):S2-3. DOI: 10.1038/513S2a. View

Shen Q, Wang Y, Kokovay E, Lin G, Chuang S, Goderie S . Adult SVZ stem cells lie in a vascular niche: a quantitative analysis of niche cell-cell interactions. Cell Stem Cell. 2008; 3(3):289-300. PMC: 2747473. DOI: 10.1016/j.stem.2008.07.026. View

10.

Lin K, Yang R, Zheng Z, Zhou Y, Geng Y, Hu Y . Sulforaphane-cysteine-induced apoptosis via phosphorylated ERK1/2-mediated maspin pathway in human non-small cell lung cancer cells. Cell Death Discov. 2017; 3:17025. PMC: 5494314. DOI: 10.1038/cddiscovery.2017.25. View

11.

Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M . KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 2015; 44(D1):D457-62. PMC: 4702792. DOI: 10.1093/nar/gkv1070. View

12.

DeNicola G, Chen P, Mullarky E, Sudderth J, Hu Z, Wu D . NRF2 regulates serine biosynthesis in non-small cell lung cancer. Nat Genet. 2015; 47(12):1475-81. PMC: 4721512. DOI: 10.1038/ng.3421. View

13.

Meng Q, Xia Y . c-Jun, at the crossroad of the signaling network. Protein Cell. 2011; 2(11):889-98. PMC: 4875184. DOI: 10.1007/s13238-011-1113-3. View

14.

. The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 2005; 34(Database issue):D322-6. PMC: 1347384. DOI: 10.1093/nar/gkj021. View

15.

Lawrence M, Stojanov P, Polak P, Kryukov G, Cibulskis K, Sivachenko A . Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013; 499(7457):214-218. PMC: 3919509. DOI: 10.1038/nature12213. View

16.

Dennis Jr G, Sherman B, Hosack D, Yang J, Gao W, Lane H . DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 2003; 4(5):P3. View

17.

Gyorffy B, Surowiak P, Budczies J, Lanczky A . Online survival analysis software to assess the prognostic value of biomarkers using transcriptomic data in non-small-cell lung cancer. PLoS One. 2013; 8(12):e82241. PMC: 3867325. DOI: 10.1371/journal.pone.0082241. View

18.

Dy G, Ylagan L, Pokharel S, Miller A, Brese E, Bshara W . The prognostic significance of focal adhesion kinase expression in stage I non-small-cell lung cancer. J Thorac Oncol. 2014; 9(9):1278-84. PMC: 4133746. DOI: 10.1097/JTO.0000000000000248. View

19.

Kajiura K, Masuda K, Naruto T, Kohmoto T, Watabnabe M, Tsuboi M . Frequent silencing of the candidate tumor suppressor TRIM58 by promoter methylation in early-stage lung adenocarcinoma. Oncotarget. 2016; 8(2):2890-2905. PMC: 5356850. DOI: 10.18632/oncotarget.13761. View

20.

Hirai Y, Shimizu Y, Oura S, Yoshimasu T, Ota F, Nakamura R . [The importance of p53 and ras mutation as predictive markers for adjuvant chemotherapy in non-small-cell lung cancer]. Gan To Kagaku Ryoho. 2012; 39(3):381-4. View