Identifying ceRNA Networks Associated With the Susceptibility and Persistence of Atrial Fibrillation Through Weighted Gene Co-Expression Network Analysis

Liu, Yaozhong; Liu, Na; Bai, Fan; Liu, Qiming

doi:10.3389/fgene.2021.653474

Cited by 11 publications

(6 citation statements)

References 61 publications

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“…Considering the CD8A and CD4 gene markers, as well as a high number of TCR clonotypes, it is plausible that IRF4 is associated with an intensified T-cell response, leading to cardiac damage. In this line, IRF4 exhibits correlations with LINC00964 and LINC00528, both of which have already been implicated in heart diseases (47,48). MIAT, a lncRNA previously linked to CCC (13) and present in our network, is also overexpressed in CCC6 patient.…”

Section: Discussionmentioning

confidence: 67%

Exploring global and specific pathogenic mechanisms in Chronic Chagas Cardiomyopathy through multi-omics integration

Brochet,

Kalil,

Procaccio

et al. 2023

Preprint

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Chagas disease is a neglected disease from South America caused by a parasite, Trypanosoma cruzi. While most of infected people remains asymptomatic, around 30% develop Chronic Chagas Cardiomyopathy (CCC), a very lethal cardiomyopathy characterized by an exacerbate inflammatory response. The last few years, our team has set up multiple omics analysis. Briefly, we have pointed the over-expression of many genes involved in the Th1 lymphocyte response, as well as some epigenetic features potentially involved in their regulation, including miRNA, lncRNA and methylation site. Moreover, some mitochondria mutation seems to predispose to the development of CCC. In order to understand and characterize the impact of genetic and epigenetic elements on the pathogenic process associated to CCC, we have performed here a multi-omics integration, combining transcriptomic, methylomic, miRNomic and mitochondria sequencing. We have identified two distinct pathogenic pathways that vary among patients with chronic Chagas cardiomyopathy (CCC). One pathway is primarily influenced by IRF4, a transcription factor known for its involvement in the development of both B and T cells, while the other is driven by TLR signaling. Notably, genes related to B cells play a role in both of these processes. Additionally, we have detected certain similarities in the B cell receptors of all CCC patients, which may potentially contribute to autoimmunity. While further analysis is necessary to validate these findings, they collectively enhance our understanding of the pathogenic mechanisms associated with CCC.

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Section: Discussionmentioning

confidence: 67%

Exploring global and specific pathogenic mechanisms in Chronic Chagas Cardiomyopathy through multi-omics integration

Brochet,

Kalil,

Procaccio

et al. 2023

Preprint

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“…Moreover, an increasing number of reports indicate that lncRNAs can regulate protein-coding genes in mammals through the ceRNA network ( 27 ), where lncRNAs function as miRNA sponges to upregulate the expression of their targets ( 28 ). For instance, Liu et al identified LINC00964 as a key lncRNA in AF susceptibility- and persistence-associated ceRNA networks ( 29 ). By integrating three microarray datasets and construction of a ceRNA network, the study by Wu et al discovered that HCG11, KRBOX1-AS1, ACBD5 and RAD52 may compete with WEE1 for has-miR-17-5p to affect the development of AF ( 30 ).…”

Section: Discussionmentioning

confidence: 99%

Construction and Analysis of the lncRNA-miRNA-mRNA Network Based on Competing Endogenous RNA in Atrial Fibrillation

Zhang

Huang

et al. 2022

Front. Cardiovasc. Med.

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BackgroundAccumulated studies have revealed that long non-coding RNAs (lncRNAs) play critical roles in human diseases by acting as competing endogenous RNAs (ceRNAs). However, functional roles and regulatory mechanisms of lncRNA-mediated ceRNA in atrial fibrillation (AF) remain unknown. In the present study, we aimed to construct the lncRNA-miRNA-mRNA network based on ceRNA theory in AF by using bioinformatic analyses of public datasets.MethodsMicroarray data sets of GSE115574 and GSE79768 from the Gene Expression Omnibus database were downloaded. Twenty-one AF right atrial appendage (RAA) samples and 22 sinus rhythm (SR) subjects RAA samples were selected for subsequent analyses. After merging all microarray data and adjusting for batch effect, differentially expressed genes were identified. Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out. A ceRNA network was constructed.ResultA total of 8 lncRNAs and 43 mRNAs were significantly differentially expressed with fold change >1.5 (p < 0.05) in RAA samples of AF patients when compared with SR. GO and KEGG pathway analysis showed that cardiac muscle contraction pathway were involved in AF development. The ceRNA was predicted by co-expressing LOC101928304/ LRRC2 from the constructional network analysis, which was competitively combined with miR-490-3p. The expression of LOC101928304 and LRRC were up-regulated in myocardial tissue of patients with AF, while miR-490-3p was down-regulated.ConclusionWe constructed the LOC101928304/miR-490-3p/LRRC2 network based on ceRNA theory in AF in the bioinformatic analyses of public datasets. The ceRNA network found from this study may help improve our understanding of lncRNA-mediated ceRNA regulatory mechanisms in the pathogenesis of AF.

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“…ceRNAs act as key mediators in the progression of different types of cancer[ 46 ]. Although the ceRNA network has been established in HCC, other novel ceRNA mechanisms need to be elucidated[ 47 - 50 ].…”

Section: Discussionmentioning

confidence: 99%

Delineation of a SMARCA4-specific competing endogenous RNA network and its function in hepatocellular carcinoma

Zhang¹,

Sun²,

Wu³

et al. 2022

World J Clin Cases

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BACKGROUND Hepatocellular carcinoma (HCC) is a common malignancy worldwide, and the mortality rate continues to rise each year. SMARCA4 expression has been associated with poor prognosis in various types of cancer; however, the specific mechanism of action of SMARCA4 in HCC needs to be fully elucidated. AIM To explore the specific mechanism of action of SMARCA4 in HCC. METHODS Herein, the expression level of SMARCA4 as well as its association with HCC prognosis were evaluated using transcriptome profiling and clinical data of 18 different types of cancer collected from The Cancer Genome Atlas database. Furthermore, SMARCA4-high and -low groups were identified. Thereafter, gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to identify the function of SMARCA4, followed by construction of a SMARCA4-specific competing endogenous RNA (ceRNA) network using starBase database. The role of SMARCA4 in immunotherapy and its association with immune cells were assessed using correlation analysis. RESULTS It was observed that SMARCA4 was overexpressed and negatively correlated with prognosis in HCC. Further, SMARCA4 expression was positively associated with tumor mutational burden, microsatellite stability, and immunotherapy efficacy. The SNHG3/THUMP3-AS1-miR-139-5p-SMARCA4 ceRNA network was established and could be assumed to serve as a stimulatory mechanism in HCC. CONCLUSION The findings of this study demonstrated that SMARCA4 plays a significant role in progression and immune infiltration in HCC. Moreover, a ceRNA network was detected, which was found to be correlated with poor prognosis in HCC. The findings of this study could contribute towards the identification of predictive markers for immunotherapy and a novel mechanism of action for HCC treatment.

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Identifying ceRNA Networks Associated With the Susceptibility and Persistence of Atrial Fibrillation Through Weighted Gene Co-Expression Network Analysis

Cited by 11 publications

References 61 publications

Exploring global and specific pathogenic mechanisms in Chronic Chagas Cardiomyopathy through multi-omics integration

Exploring global and specific pathogenic mechanisms in Chronic Chagas Cardiomyopathy through multi-omics integration

Construction and Analysis of the lncRNA-miRNA-mRNA Network Based on Competing Endogenous RNA in Atrial Fibrillation

Delineation of a SMARCA4-specific competing endogenous RNA network and its function in hepatocellular carcinoma

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