Gene expression profiling reveals genes and transcription factors associated with dilated and ischemic cardiomyopathies.
OBJECTIVE
Dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM) can cause heart failure, and this study aims to identify genes and transcription factors (TFs) associated with DCM and ICM.


METHODS
Gene expression dataset GSE42955 was generated from GEO database, and it contained 12 DCM, 12 ICM, and 5 control samples. Differentially expressed genes (DEGs) were identified between DCM (or ICM) and controls. Gene functions were investigated, and their associations were analyzed using Enrichmentmap plugin in Cytoscape. Protein-protein interactions (PPIs) between DEGs were determined, and DEGs with high degree were defined as key DEGs. Potential TFs of key DEGs were predicted using iRegulon plugin. Common DEGs were found, and their functional interactions were investigated using GeneMANIA.


RESULTS
A total of 362 and 300 DEGs were respectively identified for DCM and ICM in comparison with controls, and these DEGs mainly participated in similar functions about extracellular region, membrane, immune process, and defense response. PPI networks were respectively constructed for DCM and ICM, and 26 key DEGs (e.g. CXCL10, IL6, TLR3, and VCAM1) were found, which might be targeted by 35 TFs (e.g. IRF1). Besides, 47 common up-regulated DEGs were found, which participated in 14 pathways like Apoptosis, Collagen formation, as well as 127 common down-regulated DEGs that involved in 20 pathways like Adaptive immune system, Interferon γ signaling (e.g. IRF1, VCAM1), and Toll-like receptor signaling pathway (e.g. CXCL10, IL6, TLR3).


CONCLUSIONS
DCM and ICM may share similar mechanism, and TFs (e.g. IRF1) play crucial roles in their development via regulating gene expression.
Department of Pharmacy, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
Aiqing
A
Qiao
School of Chemical Engineering and Technology, Tianjin University, Tianjin, China; Department of Pharmacy, Tianjin Union Medical Center, Tianjin, China.
Zhenying
Z
Zhao
Department of Pharmacy, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
Hui
H
Zhang
Emergency Department, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
Zhenyu
Z
Sun
Department of Pharmacy, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China. Electronic address: cuixiao999@163.com.
Xiao
X
Cui
D002311:Cardiomyopathy, Dilated / Q000235:genetics*; D019295:Computational Biology; D030541:Databases, Genetic; D015536:Down-Regulation; D020869:Gene Expression Profiling; D006801:Humans; D017202:Myocardial Ischemia / Q000235:genetics*; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics*; D015854:Up-Regulation
D014157:Transcription Factors
Differentially expressed gene; Dilated cardiomyopathy; Functional interaction; Ischemic cardiomyopathy; Transcription factor