Bioinformatics Analysis and Identification of Genes and Pathways in Ischemic Cardiomyopathy.
bioinformatics analysis
differential expressed genes
ischemic cardiomyopathy
Journal
International journal of general medicine
ISSN: 1178-7074
Titre abrégé: Int J Gen Med
Pays: New Zealand
ID NLM: 101515487
Informations de publication
Date de publication:
2021
2021
Historique:
received:
27
07
2021
accepted:
08
09
2021
entrez:
29
9
2021
pubmed:
30
9
2021
medline:
30
9
2021
Statut:
epublish
Résumé
Ischemic cardiomyopathy (ICM) is considered to be the most common cause of heart failure, with high prevalence and mortality. This study aimed to investigate the different expressed genes (DEGs) and pathways in the pathogenesis of ICM using bioinformatics analysis. The control and ICM datasets GSE116250, GSE46224 and GSE5406 were collected from the gene expression omnibus (GEO) database. DEGs were identified using limma package of R software, and co-expressed genes were identified using Venn diagrams. Then, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to explore the biological functions and signaling pathways. Protein-protein interaction (PPI) networks were assembled with Cytoscape software to identify hub genes related to the pathogenesis of ICM. RT-PCR of Heart tissues (n=2 for non-failing controls and n=4 for ischemic cardiomyopathy patients) was used to validate the bioinformatic results. A total of 844 DEGs were screened from GSE116250, of which 447 were up-regulated genes and 397 were down-regulated genes, respectively. A total of 99 DEGs were singled out from GSE46224, of which 58 were up-regulated genes and 41 were down-regulated genes, respectively. Thirty DEGs were screened from GSE5406, including 10 genes with up-regulated expression and 20 genes with down-regulated expression. Five up-regulated and 3 down-regulated co-expressed DEGs were intersected in three datasets. GO and KEGG pathway analyses revealed that DEGs are mainly enriched in collagen fibril organization, protein digestion and absorption, AGE-RAGE signaling pathway and other related pathways. Collagen alpha-1(III) chain (COL3A1), collagen alpha-2(I) chain (COL1A2) and lumican (LUM) are the three hub genes in all three datasets through PPI network analysis. The expression of 5 DEGs (SERPINA3, FCN3, COL3A1, HBB, MXRA5) in heart tissues by qRT-PCR results was consistent with our GEO analysis, while expression of 3 DEGs (ASPN, LUM, COL1A2) was opposite with GEO analysis. These findings from this bioinformatics network analysis investigated key hub genes, which contributed to better understanding the mechanism and new therapeutic targets of ICM.
Identifiants
pubmed: 34584445
doi: 10.2147/IJGM.S329980
pii: 329980
pmc: PMC8464396
doi:
Types de publication
Journal Article
Langues
eng
Pagination
5927-5937Informations de copyright
© 2021 Cao et al.
Déclaration de conflit d'intérêts
The authors declare that they have no competing interests.
Références
Cell Tissue Res. 2016 Sep;365(3):563-81
pubmed: 27324127
Sci Rep. 2019 Jun 24;9(1):9206
pubmed: 31235849
Biochem Biophys Res Commun. 2017 Jan 22;482(4):1304-1311
pubmed: 27939890
J Mol Cell Cardiol. 2015 Jul;84:70-80
pubmed: 25886697
Eur J Heart Fail. 2020 May;22(5):789-799
pubmed: 32020756
Methods Mol Biol. 2016;1375:207-21
pubmed: 25971912
Cardiology. 2020;145(3):187-198
pubmed: 31968347
Front Oncol. 2020 May 15;10:605
pubmed: 32500021
Circ Res. 2017 Nov 10;121(11):1279-1290
pubmed: 28923793
Front Cell Dev Biol. 2020 May 29;8:377
pubmed: 32548117
Cell Biol Int. 2019 Sep 9;:
pubmed: 31498521
Rev Esp Cardiol (Engl Ed). 2017 Oct;70(10):832-840
pubmed: 28215921
Circ Res. 2019 Jun 21;125(1):117-146
pubmed: 31219741
BMC Bioinformatics. 2017 Sep 2;18(1):389
pubmed: 28865426
Nat Rev Cardiol. 2011 Jan;8(1):30-41
pubmed: 21060326
Circ Res. 2019 May 24;124(11):1520-1535
pubmed: 31120824
JACC Cardiovasc Imaging. 2011 Jan;4(1):98-108
pubmed: 21232712
Nat Rev Cardiol. 2016 Jun;13(6):368-78
pubmed: 26935038
Front Biosci (Landmark Ed). 2019 Jun 1;24:1178-1189
pubmed: 31136974
Mol Cell Endocrinol. 2018 Feb 5;461:248-255
pubmed: 28919298
Med Sci Monit. 2019 Mar 27;25:2246-2256
pubmed: 30916045
Ann Med. 2001 Feb;33(1):7-21
pubmed: 11310942
Circ Res. 2013 Aug 30;113(6):646-59
pubmed: 23989710
Cardiovasc Res. 2002 Jul;55(1):76-82
pubmed: 12062710
Exp Biol Med (Maywood). 2002 May;227(5):301-14
pubmed: 11976400
Aging (Albany NY). 2020 May 11;12(9):8605-8621
pubmed: 32392178
Circulation. 2006 Sep 19;114(12):1269-76
pubmed: 16952980
Cell Death Dis. 2019 Feb 6;10(2):109
pubmed: 30728352
J Am Coll Cardiol. 2000 Mar 1;35(3):569-82
pubmed: 10716457
Circulation. 1997 May 20;95(10):2448-54
pubmed: 9170409
Circulation. 2014 Mar 4;129(9):1009-21
pubmed: 24429688
Carcinogenesis. 2012 Sep;33(9):1797-805
pubmed: 22696596
Circulation. 2017 Mar 7;135(10):e146-e603
pubmed: 28122885
J Am Coll Cardiol. 2012 Jan 24;59(4):359-70
pubmed: 22261158
J Mol Cell Cardiol. 2007 Apr;42(4):870-83
pubmed: 17343875