Emerging roles of circRNAs in the pathological process of myocardial infarction

Wen, Zeng-Jin; Hui, Xin; Wang, Yongchen; Liu, Haowen; Gao, Yanyan; Zhang, Yinfeng

doi:10.1016/j.omtn.2021.10.002

Cited by 41 publications

(24 citation statements)

References 181 publications

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“…The results showed that mRNAs were mainly enriched in autophagy, apoptosis signals, chemokine signaling pathways, and foxo signaling pathways. Previous studies have shown that cardiomyocyte apoptosis and autophagy, inflammation and oxidative stress were the main pathophysiological changes of AMI ( Frangogiannis, 2015 ; Wen et al, 2021 ). Apoptosis and autophagy are the main ways of myocardial cell death in MI, and the balance between them is directly related to cell survival and cardiac function ( Wang et al, 2018 ; Wu et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

“…The foxo signaling pathway induces anti-oxidation, anti-apoptosis, and anti-autophagy to promote the survival of cardiomyocytes under oxidative stress ( Sengupta et al, 2011 ). More and more studies have reported the regulation of circRNA on apoptosis and autophagy, inflammation and oxidative stress in acute myocardial infarction ( Wen et al, 2021 ). Our results suggest that circRNAs in the ceRNA network also participate in AMI through the above-mentioned pathways, and further study of these results will contribute to the discovery of new therapeutic targets.…”

Section: Discussionmentioning

confidence: 99%

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Construction and Bioinformatics Analysis of circRNA-miRNA-mRNA Network in Acute Myocardial Infarction

Zhou

Wang

et al. 2022

Front. Genet.

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Background: Acute myocardial infarction (AMI) is one of the main fatal diseases of cardiovascular diseases. Circular RNA (circRNA) is a non-coding RNA (ncRNA), which plays a role in cardiovascular disease as a competitive endogenous RNA (ceRNA). However, their role in AMI has not been fully clarified. This study aims to explore the mechanism of circRNA-related ceRNA network in AMI, and to identify the corresponding immune infiltration characteristics.Materials and Methods: The circRNA (GSE160717), miRNA (GSE24548), and mRNA (GSE60993) microarray datasets of AMI were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed circRNAs (DEcircRNAs), miRNAs (DEmiRNAs), and mRNAs (DEmRNAs) were identified by the “limma” package. After integrating the circRNA, miRNA and mRNA interaction, we constructed a circRNA-miRNA-mRNA network. The “clusterProfiler” package and String database were used for functional enrichment analysis and protein-protein interaction (PPI) analysis, respectively. After that, we constructed a circRNA-miRNA-hub gene network and validated the circRNAs and mRNAs using an independent dataset (GSE61144) as well as qRT-PCR. Finally, we used CIBERSORTx database to analyze the immune infiltration characteristics of AMI and the correlation between hub genes and immune cells.Results: Using the “limma” package of the R, 83 DEcircRNAs, 54 DEmiRNAs, and 754 DEmRNAs were identified in the microarray datasets of AMI. Among 83 DEcircRNAs, there are 55 exonic DEcircRNAs. Then, a circRNA-miRNA-mRNA network consists of 21 DEcircRNAs, 11 DEmiRNAs, and 106 DEmRNAs were predicted by the database. After that, 10 hub genes from the PPI network were identified. Then, a new circRNA-miRNA-hub gene network consists of 14 DEcircRNAs, 7 DEmiRNAs, and 9 DEmRNAs was constructed. After that, three key circRNAs (hsa_circ_0009018, hsa_circ_0030569 and hsa_circ_0031017) and three hub genes (BCL6, PTGS2 and PTEN) were identified from the network by qRT-PCR. Finally, immune infiltration analysis showed that hub genes were significantly positively correlated with up-regulated immune cells (neutrophils, macrophages and plasma cells) in AMI.Conclusion: Our study constructed a circRNA-related ceRNA networks in AMI, consists of hsa_circ_0031017/hsa-miR-142-5p/PTEN axis, hsa_circ_0030569/hsa-miR-545/PTGS2 axis and hsa_circ_0009018/hsa-miR-139-3p/BCL6 axis. These three hub genes were significantly positively correlated with up-regulated immune cells (neutrophils, macrophages and plasma cells) in AMI. It helps improve understanding of AMI mechanism and provides future potential therapeutic targets.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Construction and Bioinformatics Analysis of circRNA-miRNA-mRNA Network in Acute Myocardial Infarction

Zhou

Wang

et al. 2022

Front. Genet.

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“…In addition to protein-coding transcripts, the transcriptome also consists of many noncoding RNA species, including both small and long noncoding RNAs. The functions of these RNAs have been extensively examined and implicated in important biological pathways [25][26][27][28]. The small noncoding RNAs present a unique opportunity to new therapeutic approaches [29].…”

Section: Transcriptomementioning

confidence: 99%

Decoding the Equine Genome: Lessons from ENCODE

Peng

Petersen

Kalbfleisch

et al. 2021

Genes

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The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has generated data from more than 400 experiments using over 50 tissues, targeting a variety of regulatory features of the equine genome. In this review, we examine how valuable lessons learned from the ENCODE project informed our decisions in the equine FAANG project. We report the current state of the equine FAANG project and discuss how FAANG can serve as a template for future expansion of functional annotation in the equine genome and be used as a reference for studies of complex traits in horse. A well-annotated reference functional atlas will also help advance equine genetics in the pan-genome and precision medicine era.

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“…With sequencing technology development, a huge number of lncRNAs have been identified. LncRNAs, originally considered as junk RNA, are reported to dysregulate in various types of cancer [ 66 ]. Hu et al [ 67 ] found that lncRNA H19 was significantly increased in the plasma of patients with lung cancer, making it a potential biomarker for the auxiliary diagnosis of lung cancer.…”

Section: Introductionmentioning

confidence: 99%

Liquid biopsy in lung cancer: significance in diagnostics, prediction, and treatment monitoring

et al. 2022

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Primary lung cancer is one of the most common malignant tumors in China. Approximately 60% of lung cancer patients have distant metastasis at the initial diagnosis, so it is necessary to find new tumor markers for early diagnosis and individualized treatment. Tumor markers contribute to the early diagnosis of lung cancer and play important roles in early detection and treatment, as well as in precision medicine, efficacy monitoring, and prognosis prediction. The pathological diagnosis of lung cancer in small biopsy specimens determines whether there are tumor cells in the biopsy and tumor type. Because biopsy is traumatic and the compliance of patients with multiple biopsies is poor, liquid biopsy has become a hot research direction. Liquid biopsies are advantageous because they are nontraumatic, easy to obtain, reflect the overall state of the tumor, and allow for real-time monitoring. At present, liquid biopsies mainly include circulating tumor cells, circulating tumor DNA, exosomes, microRNA, circulating RNA, tumor platelets, and tumor endothelial cells. This review introduces the research progress and clinical application prospect of liquid biopsy technology for lung cancer.

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Emerging roles of circRNAs in the pathological process of myocardial infarction

Cited by 41 publications

References 181 publications

Construction and Bioinformatics Analysis of circRNA-miRNA-mRNA Network in Acute Myocardial Infarction

Construction and Bioinformatics Analysis of circRNA-miRNA-mRNA Network in Acute Myocardial Infarction

Decoding the Equine Genome: Lessons from ENCODE

Liquid biopsy in lung cancer: significance in diagnostics, prediction, and treatment monitoring

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