Establishment and analysis of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA identifies functional genes in heart failure

Ma, Xudan; Zhang, Qi‐Jun; Zhu, Haihong; Huang, Kefeng; Pang, Weina; Zhang, Qin

doi:10.3934/mbe.2021201

Cited by 11 publications

(5 citation statements)

References 51 publications

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“…Also, miR-19, miR-181, miR-125, and miR-30 levels were associated with myocardium levels during the development of diabetic cardiomyopathy and failing hearts ( 33 , 36 ), and the miR-30 and miR-19 families were frequently reported to be dysregulated in patients with the acute coronary syndrome (ACS) ( 37 ). Consistent with other studies ( 34 , 36 ), miR-140 was dysregulated in our study in TGA patients with HF compared to TGA patients without HF, suggesting that miR-140 may play an important role in the pathogenesis of TGA. Additionally, miR-502 was dysregulated in patients with chronic congestive heart failure (CHF) ( 38 ) and reported as a biomarker in coronary artery disease (CAD) ( 37 ).…”

Section: Discussionsupporting

confidence: 92%

Expression profiling analysis reveals key microRNA–mRNA interactions in patients with transposition of the great arteries and systemic left and right ventricles

Abu‐Halima

Wagner

Rishik

et al. 2023

Front. Cardiovasc. Med.

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BackgroundPatients with transposition of the great arteries (TGA) have different connected systemic chambers and this determines the long-term morbidities and survival. Limited findings have been reported to systematically identify miRNA and mRNA expression levels in such cohorts of patients. In this study, we aimed to characterize miRNAs, mRNAs, and miRNA–mRNA interaction networks in patients with TGA, with a systemic left (LV) and right ventricle (RV).Materials and methodsLarge panel of human miRNA and mRNA microarrays were conducted to determine the genome-wide expression profiles in the blood of 16 TGA-RV patients, 16 TGA-LV patients, and 16 age and gender-matched controls. Using real-time quantitative PCR (RT-qPCR), the differential expression level of a single miRNA was validated. Enrichment analyses of altered miRNA and mRNA expression levels were identified using bioinformatics tools.ResultsAltered miRNA and mRNA expression levels were observed between TGA-RV and TGA-LV patients, together or separated, compared to controls. Among the deregulated miRNAs and mRNAs, 39 and 101 miRNAs were identified as significantly differentially expressed in patients with TGA (both TGA-RV and TGA-LV) and TGA-RV, when compared to matched controls. Furthermore, 51 miRNAs were identified as significantly differentially expressed in patients with TGA-RV when compared to patients with TGA-LV. RT-qPCR relative expression level was highly consistent with microarray analysis results. Similarly, 36 and 164 mRNAs were identified as significantly differentially expressed in patients with TGA (both TGA-RV and TGA-LV) and TGA-RV, when compared to matched controls. Additionally, miR-140-3p showed a higher expression level in patients with overt heart failure (FC = 1.54; P = 0.001) and miR-502-3p showed a higher expression level in patients died due to cardiac death (FC = 1.41; P = 0.011). Integrative analysis resulted in 21 and 23 target genes with higher and lower expression levels, respectively (r ≥ 0.50 and P < 0.05). These target genes (i.e., 21 and 23 target genes) showed an inverse direction of regulation with miRNA and exhibited a miRNA binding site position within the 3′UTR of the target gene.ConclusionOur findings provide new insights into a potential molecular biomarker(s) for patients with TGA that may guide better risk stratification and the development of novel targeting therapies. Future studies are needed to investigate the potential significance of miRNAs and mRNAs in TGA-related cardiovascular diseases.

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Section: Discussionsupporting

confidence: 92%

Expression profiling analysis reveals key microRNA–mRNA interactions in patients with transposition of the great arteries and systemic left and right ventricles

Abu‐Halima

Wagner

Rishik

et al. 2023

Front. Cardiovasc. Med.

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“…It has been demonstrated that lncRNAs and miRNAs have powerful effects on regulating the expression of mRNAs by a competing mechanism. 21–23 Therefore, ceRNA network is useful for explaining the interactions between miRNA, lncRNA and mRNAs. According to the KEGG analysis, the upregulated genes that enriched in the PPAR signaling pathway, such as ACOX1, ACSL1, ANGPTL4, CD36, EHHADH, GK, and HMGCS2, were integrated in the ceRNA network that constructed based on miRanda predication (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…MiRNAs can downregulate their targeted mRNAs via base paring at the 3′-untranslated regions. 21–23 In this study, the generally used analysis tool, miRanda, was randomly chosen for predicting miRNA–lncRNA interaction (anticorrelated) or miRNA–mRNA interaction (anticorrelated) (with a score ≥140 and an energy ≤−10). 35 Furthermore, the predicted data were further predicted by four databases including Targetscan, miRWalk3.0, miRDB, and miRTarBase.…”

Section: Methodsmentioning

confidence: 99%

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The polysaccharide–peptide complex from mushroom Cordyceps militaris ameliorates atherosclerosis by modulating the lncRNA–miRNA–mRNA axis

Miao

Yin

et al. 2022

Food Funct.

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“…As a consequence, the role of circRNA-associated ceRNA networks and their regulatory mechanisms are of immense significance. Although ceRNA networks corresponding to atrial fibrillation, heart failure, and colon cancer have been constructed in numerous studies [31][32][33], little information is available on the UC-related ceRNA network. In this research, we innovatively generated a characteristic circRNA-miR-NA-mRNA network associated with UC, which was composed of 403 circRNA nodes, 5 miRNA nodes, 138 mRNA nodes, and 559 edges.…”

Section: Discussionmentioning

confidence: 99%

Reconstruction and Differential Expression Profiling Core Target Analyses of the circRNA-miRNA-mRNA Network Based on Competitive Endogenous RNAs in Ulcerative Colitis

Chen

Zhang

et al. 2022

Evidence-Based Complementary and Alternative Medicine

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Ulcerative colitis (UC) is a common autoimmune disease worldwide. Circular RNA (circRNA) is a type of noncoding ribonucleic acids (ncRNAs). In addition to their roles in numerous biological processes, circRNAs are also linked to a vast range of diseases including UC. Although previous studies have examined many circRNAs, the physiological and pathological roles of the circRNA-associated competing endogenous RNA (ceRNA) network in UC remain unclear. Thus, we constructed a circRNA-miRNA-mRNA network based on the ceRNA hypothesis by analyzing data from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI-GEO) database. Genes with higher degree values than others in the ceRNA network were selected as central nodes when constructing the corresponding core subnetworks. To fully understand the biological function of the ceRNA network, we entered all differentially expressed mRNAs (DEmRNAs) from the ceRNA network into the Database for Annotation and Integrated Discovery (DAVID), which was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. We further entered DEmRNAs into the STRING database for protein-protein interaction (PPI) network analysis. The results elucidated that the ceRNA network comprised 403 circRNA nodes, 5 miRNA nodes, 138 mRNA nodes, and 559 edges. Three core ceRNA subnetworks centered on hsa-miR-342-3p, hsa-miR-199a-5p, and hsa-miR-142-3p were reconstructed in this study. GO and KEGG enrichment analyses identified 167 enriched GO categories and 14 enriched KEGG pathway terms. The core PPI network was composed of 15 core targets, of which CD44, HIF1A, and MMP2 were the most significant. In summary, 3 hub miRNAs (hsa-miR-342-3p, hsa-miR-199a-5p, hsa-miR-142-3p) and 3 hub genes (CD44, HIF1A, and MMP2) might play an important role in the development of UC. These hub nodes, first proposed here, might also be used as potential diagnostic markers and therapeutic targets.

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Establishment and analysis of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA identifies functional genes in heart failure

Cited by 11 publications

References 51 publications

Expression profiling analysis reveals key microRNA–mRNA interactions in patients with transposition of the great arteries and systemic left and right ventricles

Expression profiling analysis reveals key microRNA–mRNA interactions in patients with transposition of the great arteries and systemic left and right ventricles

The polysaccharide–peptide complex from mushroom Cordyceps militaris ameliorates atherosclerosis by modulating the lncRNA–miRNA–mRNA axis

Reconstruction and Differential Expression Profiling Core Target Analyses of the circRNA-miRNA-mRNA Network Based on Competitive Endogenous RNAs in Ulcerative Colitis

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