Identifying Obstructive Sleep Apnea Syndrome-Associated Genes and Pathways Through Weighted Gene Coexpression Network Analysis

Overview

Journal Comput Math Methods Med

Publisher Hindawi

Specialty Medical Informatics

Date 2022 Feb 8

PMID 35132330

Authors

Yan Li

Li Li

Hua Zhao

Xiwen Gao

Shanqun Li

Affiliations

Soon will be listed here.

Abstract

Background: Obstructive sleep apnea syndrome (OSAS) is the most common type of sleep apnea disorder. The disease seriously affects the patient's respiratory system. At present, the prognosis of the disease is poor and there is a lack of effective treatments. Therefore, it is urgent to explore its pathogenesis and treatment methods.

Method: We downloaded a set of expression profile data from GSE75097 related to OSAS based on the Gene Expression Omnibus (GEO) database and selected the representative differentially expressed genes (DEGs) from the sample of the GSE75097 dataset. WGCNA was used to find genes related to OSAS and obtain coexpression modules. The Gene Ontology (GO) function and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were used to analyze genes from key modules. Finally, Cytoscape software was used to construct a protein-protein interaction (PPI) network and analyze the hub genes.

Result: We obtained a total of 7565 DEGs. Through WGCNA, we got four coexpression modules and the modules most related to OSAS were green-yellow, magenta, purple, and turquoise, and we screened out eight hub genes (DDX46, RNF115, COPA, FBXO4, PA2G4, NHP2L1, CDC20, and PCNA). GO and KEGG analyses indicated that the key modules were mainly enriched in tRNA modification, nucleobase metabolic process, DNA ligation, regulation of cellular component movement, basal transcription factors, Huntington disease, and vitamin digestion and absorption.

Conclusion: These pathways and hub genes can facilitate understanding the molecular mechanism of OSAS and provide a meaningful reference for finding biological targets of OSAS treatment.

Citing Articles

Construction of a mitochondrial dysfunction related signature of diagnosed model to obstructive sleep apnea.

Liu Q, Hao T, Li L, Huang D, Lin Z, Fang Y Front Genet. 2022; 13:1056691.

PMID: 36468038 PMC: 9714559. DOI: 10.3389/fgene.2022.1056691.

References

Adjamian P, Hall D, Palmer A, Allan T, Langers D . Neuroanatomical abnormalities in chronic tinnitus in the human brain. Neurosci Biobehav Rev. 2014; 45:119-33. PMC: 4148481. DOI: 10.1016/j.neubiorev.2014.05.013. View

Stavrou V, Bardaka F, Karetsi E, Daniil Z, Gourgoulianis K . Brief Review: Ergospirometry in Patients with Obstructive Sleep Apnea Syndrome. J Clin Med. 2018; 7(8). PMC: 6111535. DOI: 10.3390/jcm7080191. View

Luo Z, Ye X, Shou F, Cheng Y, Li F, Wang G . RNF115-mediated ubiquitination of p53 regulates lung adenocarcinoma proliferation. Biochem Biophys Res Commun. 2020; 530(2):425-431. DOI: 10.1016/j.bbrc.2020.05.061. View

Guigo R, de Hoon M . Recent advances in functional genome analysis. F1000Res. 2019; 7. PMC: 6305211. DOI: 10.12688/f1000research.15274.1. View

Parker-Cote J, Rizer J, Vakkalanka J, Rege S, Holstege C . Challenges in the diagnosis of acute cyanide poisoning. Clin Toxicol (Phila). 2018; 56(7):609-617. DOI: 10.1080/15563650.2018.1435886. View

Kaur H, Singh P . Rationally designed molecules for resurgence of cyanide mitigated cytochrome c oxidase activity. Bioorg Chem. 2018; 82:229-240. DOI: 10.1016/j.bioorg.2018.10.045. View

de Lima F, Mazzotti D, Tufik S, Bittencourt L . The role inflammatory response genes in obstructive sleep apnea syndrome: a review. Sleep Breath. 2015; 20(1):331-8. DOI: 10.1007/s11325-015-1226-7. View

van Vlymen J, Fu W, White P, KLEIN K, Griffin J . Use of the cuffed oropharyngeal airway as an alternative to the laryngeal mask airway with positive-pressure ventilation. Anesthesiology. 1999; 90(5):1306-10. DOI: 10.1097/00000542-199905000-00014. View

Zhang B, Horvath S . A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2006; 4:Article17. DOI: 10.2202/1544-6115.1128. View

10.

Maspero C, Giannini L, Galbiati G, Rosso G, Farronato G . Obstructive sleep apnea syndrome: a literature review. Minerva Stomatol. 2015; 64(2):97-109. View

11.

Del Giacco L, Cattaneo C . Introduction to genomics. Methods Mol Biol. 2011; 823:79-88. DOI: 10.1007/978-1-60327-216-2_6. View

12.

Zhang L, Lu Q, Chang C . Epigenetics in Health and Disease. Adv Exp Med Biol. 2020; 1253:3-55. DOI: 10.1007/978-981-15-3449-2_1. View

13.

Gulotta G, Iannella G, Vicini C, Polimeni A, Greco A, de Vincentiis M . Risk Factors for Obstructive Sleep Apnea Syndrome in Children: State of the Art. Int J Environ Res Public Health. 2019; 16(18). PMC: 6765844. DOI: 10.3390/ijerph16183235. View

14.

Athanasios A, Charalampos V, Vasileios T, Ashraf G . Protein-Protein Interaction (PPI) Network: Recent Advances in Drug Discovery. Curr Drug Metab. 2017; 18(1):5-10. DOI: 10.2174/138920021801170119204832. View

15.

Maughan R, Shirreffs S . Muscle Cramping During Exercise: Causes, Solutions, and Questions Remaining. Sports Med. 2019; 49(Suppl 2):115-124. PMC: 6901412. DOI: 10.1007/s40279-019-01162-1. View

16.

Hall A, Saiers J, Baud F . Which cyanide antidote?. Crit Rev Toxicol. 2009; 39(7):541-52. DOI: 10.1080/10408440802304944. View

17.

Lo Bue A, Salvaggio A, Insalaco G . Obstructive sleep apnea in developmental age. A narrative review. Eur J Pediatr. 2020; 179(3):357-365. DOI: 10.1007/s00431-019-03557-8. View

18.

Liu O, Kiema M, Beter M, Yla-Herttuala S, Laakkonen J, Kaikkonen M . Hypoxia-Mediated Regulation of Histone Demethylases Affects Angiogenesis-Associated Functions in Endothelial Cells. Arterioscler Thromb Vasc Biol. 2020; 40(11):2665-2677. DOI: 10.1161/ATVBAHA.120.315214. View

19.

Gui H, Gong Q, Jiang J, Liu M, Li H . Identification of the Hub Genes in Alzheimer's Disease. Comput Math Methods Med. 2021; 2021:6329041. PMC: 8302378. DOI: 10.1155/2021/6329041. View

20.

Chen Y, Chen Y, Chang Y, Wang H, Liu W, Chong S . Expression and Left Atrial Remodeling in the Incidence of Atrial Fibrillation in Patients with Obstructive Sleep Apnea Syndrome. Biomedicines. 2021; 9(10). PMC: 8533106. DOI: 10.3390/biomedicines9101463. View