Identification and Validation of Dilated Cardiomyopathy-Related Genes via Bioinformatics Analysis

Wang, Lijun; Qiu, Bai‐Quan; Yuan, Mingming; Zou, Hua-Xi; Gong, Chengwu; Huang, Huang; Lai, Songqing; Liu, Jichun

doi:10.2147/ijgm.s350954

Cited by 5 publications

(5 citation statements)

References 56 publications

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“…Another miRNA found to be significantly downregulated in kidneys upon HFD feeding in our study was miR-551b-3p. miR-551b-3p has been reported to be involved in different types of cancers [ 51 , 52 , 53 ], and in the pathogenesis of cardiomyopathy [ 54 ]. Interestingly, circulating miR-551b-3p has been found to be downregulated in patients with childhood obesity [ 55 ], while, on the other hand, it was upregulated in adipose tissue of obese individuals [ 56 ].…”

Section: Discussionmentioning

confidence: 99%

microRNA Expression Profile in Obesity-Induced Kidney Disease Driven by High-Fat Diet in Mice

Eritja,

Caus,

Belmonte

et al. 2024

Nutrients

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Obesity is one of the main causes of chronic kidney disease; however, the precise molecular mechanisms leading to the onset of kidney injury and dysfunction in obesity-associated nephropathy remain unclear. The present study aimed to unveil the kidney microRNA (miRNA) expression profile in a model of obesity-induced kidney disease in C57BL/6J mice using next-generation sequencing (NGS) analysis. High-fat diet (HFD)-induced obesity led to notable structural alterations in tubular and glomerular regions of the kidney, increased renal expression of proinflammatory and profibrotic genes, as well as an elevated renal expression of genes involved in cellular lipid metabolism. The miRNA sequencing analysis identified a set of nine miRNAs differentially expressed in the kidney upon HFD feeding, with miR-5099, miR-551b-3p, miR-223-3p, miR-146a-3p and miR-21a-3p showing the most significant differential expression between standard diet (STD) and HFD mice. A validation analysis showed that the expression levels of miR-5099, miR-551b-3p and miR-146a-3p were consistent with NGS results, while Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses revealed that these three validated miRNAs modulated target genes involved in metabolic and adipocytokine pathways, fatty acid and lipid metabolism, and inflammatory, senescence and profibrotic pathways. Our results suggest that differentially expressed miRNAs play pivotal roles in the intricate pathophysiology of obesity-associated kidney disease and could potentially create novel treatment strategies to counteract the deleterious effects of obesity on kidney function.

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Section: Discussionmentioning

confidence: 99%

microRNA Expression Profile in Obesity-Induced Kidney Disease Driven by High-Fat Diet in Mice

Eritja,

Caus,

Belmonte

et al. 2024

Nutrients

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“…DMR-related genes were thought to substantially enrich GO terms with a corrected P -value < 0.05. The statistical enrichment of DMR-related genes in KEGG pathways was examined using KOBAS software ( 17 ).…”

Section: Methodsmentioning

confidence: 99%

Immunity of turbot Induced by inactivated vaccine of Aeromonas salmonicida from the perspective of DNA methylation

Lin²,

Liu³

et al. 2023

Front. Immunol.

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IntroductionDNA methylation was one of the most important modification in epigenetics and played an important role in immune response. Since the introduction of Scophthalmus maximus, the scale of breeding has continued to expand, during which diseases caused by various bacteria, viruses and parasites have become increasingly serious. Therefore, the inactivated vaccines have been widely researched and used in the field of aquatic products with its unique advantages. However, the immune mechanism that occurred in turbot after immunization with inactivated vaccine of Aeromonas salmonicida was not clear.MethodsIn this study, differentially methylated regions (DMRs) were screened by Whole Genome Bisulfite Sequencing (WGBS) and significantly differentially expressed genes (DEGs) were screened by Transcriptome sequencing. Double luciferase report assay and DNA pull-down assay were further verified the DNA methylation state of the gene promoter region affected genes transcriptional activity after immunization with inactivated vaccine of Aeromonas salmonicida.ResultsA total of 8149 differentially methylated regions (DMRs) were screened, in which there were many immune-related genes with altered DNA methylation status. Meanwhile, 386 significantly differentially expressed genes (DEGs) were identified, many of which were significantly enriched in Toll-like receptor signaling pathway, NOD-like receptor signaling pathway and C-type lectin receptor signaling pathway. Combined analysis of WGBS results and RNA-seq results, a total of 9 DMRs of negatively regulated genes are located in the promoter region, including 2 hypermethylated genes with lower expression and 7 hypomethylated genes with higher expression. Then, two immune-related genes C5a anaphylatoxin chemotactic receptor 1-like (C5ar1-Like) and Eosinophil peroxidase-like (EPX-Like), were screened to explore the regulation mechanism of DNA methylation modification on their expression level. Moreover, the DNA methylation state of the gene promoter region affected genes transcriptional activity by inhibiting the binding of transcription factors, which lead to changes in the expression level of the gene.DiscussionWe jointly analyzed WGBS and RNA-seq results and revealed the immune mechanism that occurred in turbot after immunized with inactivated vaccine of A. salmonicida from the perspective of DNA methylation.

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“…Based on the differentially expressed miRNAs, the upstream TFs were predicted using TransmiR v2.0 database ( http://www.cuilab.cn/transmir ), an easy-accessible public tool, which integrates experimentally verified TF-miRNA regulatory relationships from the publications ( 27 ). In addition, the downstream target genes of miRNAs were also predicted using miRWalk database ( http://mirwalk.umm.uni-heidelberg.de/ ), which is freely available and presents validated and predicted information on miRNA-target interaction ( 28 ).…”

Section: Methodsmentioning

confidence: 99%

“…In addition, the downstream target genes of miRNAs were also predicted using miRWalk database (http://mirwalk. umm.uni-heidelberg.de/), which is freely available and presents validated and predicted information on miRNA-target interaction (28).…”

Section: Inhibition Of Mir-142-3p and Overexpression Of Drd2 In Vivomentioning

confidence: 99%

Natural emodin reduces myocardial ischemia/reperfusion injury by modulating the RUNX1/miR‑142‑3p/DRD2 pathway and attenuating inflammation

Zhang

Qin

et al. 2022

Exp Ther Med

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Acute myocardial infarction is one of the leading causes of death worldwide. Although timely reperfusion could attenuate myocardial ischemia injury and reduce mortality, it causes severe secondary injury to the myocardium known as myocardial ischemia/reperfusion injury (MIRI) with unmet clinical needs. Emodin has a protective effect on MIRI in rodents. However, the precise mechanism underlying its pharmacological effect remains poorly understood. Accordingly, the present study used mRNA and microRNA (miRNA) sequencing based on MIRI mouse models to determine the mechanism involved. Emodin was found to prevent MIRI and attenuate the inflammation of myocardium in the MIRI model. In addition, by using an interdisciplinary approach, the present study uncovered that emodin suppressed the runt-related transcription factor 1 (RUNX1), which is a transcription factor of miR-142-3p, in either MIRI or the hypoxia/reoxygenation injury model. Furthermore, miR-142-3p can negatively regulate dopamine receptor D2 (DRD2), which acted as an anti-inflammatory factor to suppress NF-κB-dependent inflammation and prevent MIRI. These results were demonstrated by both cellular hypoxia/reoxygenation and mouse MIRI models. Overall, the present study provided an unrevealed molecular mechanism for emodin function. Emodin could inhibit NF-κB-triggered inflammation in MIRI by regulating the RUNX1/miR-142-3p/DRD2 pathway. Therefore, the RUNX1/miR-142-3p/DRD2 pathway presented a novel target for MIRI treatment, and the application of emodin in clinical practice may improve the treatment of MIRI.

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Identification and Validation of Dilated Cardiomyopathy-Related Genes via Bioinformatics Analysis

Cited by 5 publications

References 56 publications

microRNA Expression Profile in Obesity-Induced Kidney Disease Driven by High-Fat Diet in Mice

microRNA Expression Profile in Obesity-Induced Kidney Disease Driven by High-Fat Diet in Mice

Immunity of turbot Induced by inactivated vaccine of Aeromonas salmonicida from the perspective of DNA methylation

Natural emodin reduces myocardial ischemia/reperfusion injury by modulating the RUNX1/miR‑142‑3p/DRD2 pathway and attenuating inflammation

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