Identification of candidate genes in ischemic cardiomyopathy by gene expression omnibus database

Abstract

Background Ischemic cardiomyopathy (ICM) is one of the most usual causes of death worldwide. This study aimed to find the candidate gene for ICM. Methods We studied differentially expressed genes (DEGs) in ICM compared to healthy control. According to these DEGs, we carried out the functional annotation, protein-protein interaction (PPI) network and transcriptional regulatory network constructions. The expression of selected candidate genes were confirmed using a published dataset and Quantitative real time polymerase chain reaction (qRT-PCR). Results From three Gene Expression Omnibus (GEO) datasets, we acquired 1081 DEGs (578 up-regulated and 503 down-regulated genes) between ICM and healthy control. The functional annotation analysis revealed that cardiac muscle contraction, hypertrophic cardiomyopathy, arrhythmogenic right ventricular cardiomyopathy and dilated cardiomyopathy were significantly enriched pathways in ICM. SNRPB, BLM, RRS1, CDK2, BCL6, BCL2L1, FKBP5, IPO7, TUBB4B and ATP1A1 were considered the hub proteins. PALLD, THBS4, ATP1A1, NFASC, FKBP5, ECM2 and BCL2L1 were top six transcription factors (TFs) with the most downstream genes. The expression of 6 DEGs (MYH6, THBS4, BCL6, BLM, IPO7 and SERPINA3) were consistent with our integration analysis and GSE116250 validation results. Conclusions The candidate DEGs and TFs may be related to the ICM process. This study provided novel perspective for understanding mechanism and exploiting new therapeutic means for ICM.

Identification of Core Gene Biomarkers in Patients With Hypertrophic Cardiomyopathy

“…Recently, the development of second-generation sequencing technologies, such as targeted gene sequencing, whole exon sequencing (WES) and whole genome sequencing appeared, these technologies can help to identify more HCM patients and discover more gene mutations. Integrated microarrays analysis from different data sets will obtain genome-wide expression pro ling with more samples which will increase the statistical power than an individual microarray [28]. Screening DEGs and biological pathways that are abnormally expressed in the pathogenesis of HCM through bioinformatics analysis would shed light on the diagnosis and treatment of HCM [29].…”

Differentiation and subpopulation composition of VEGFR2+ cells in the blood and bone marrow in ischemic cardiomyopathy

“…In the bone marrow, the levels of ВВЕДЕНИЕ Ишемическая кардиомиопатия (ИКМП) является осложненной формой хронической ишемической болезни сердца (ИБС) и служит одной из наиболее частых причин смертности во всем мире от сердечно-сосудистых заболеваний [1]. ИКМП характеризуется дилатацией камер сердца, гипертрофией (преимущественно левого желудочка) и снижением насосной функции сердца с формированием хронической сердечной недостаточности [2]. Считается, что в основе развития ИКМП лежит нарушение сократительной функции миокарда вследствие коронарной микрососудистой дисфункции, которая является триггером распространенной ишемии и гибернации миокарда, некроза и апоптоза кардиомиоцитов с последующим фиброзированием и ремоделированием желудочков [1,2].…”

Integrated Strategies of Diverse Feature Selection Methods Identify Aging-Based Reliable Gene Signatures for Ischemic Cardiomyopathy

“…Accumulated evidence demonstrates that numerous fetal and immediate-early genes present deregulation in ICM ( Dang et al, 2020 ). However, genetic causes and molecular mechanisms underlying ICM progression remain partially clarified ( Suffee et al, 2020 ).…”

“…Evidence suggests that gene signatures exert critical roles in diverse diseases that depend on the leapfrog advance of sequencing technologies ( Li et al, 2020 ). For instance, Dang et al proposed deregulated genes in ICM and their upstream transcription factors ( Dang et al, 2020 ). Wang et al reported that transcriptome profile analyses uncovered PHLDA1 as a candidate molecular signature for ICM ( Wang et al, 2018 ).…”