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Odogwu NM, Hagen C, Nelson TJ. Transcriptome studies of congenital heart diseases: identifying current gaps and therapeutic frontiers. Front Genet 2023; 14:1278747. [PMID: 38152655 PMCID: PMC10751320 DOI: 10.3389/fgene.2023.1278747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/16/2023] [Indexed: 12/29/2023] Open
Abstract
Congenital heart disease (CHD) are genetically complex and comprise a wide range of structural defects that often predispose to - early heart failure, a common cause of neonatal morbidity and mortality. Transcriptome studies of CHD in human pediatric patients indicated a broad spectrum of diverse molecular signatures across various types of CHD. In order to advance research on congenital heart diseases (CHDs), we conducted a detailed review of transcriptome studies on this topic. Our analysis identified gaps in the literature, with a particular focus on the cardiac transcriptome signatures found in various biological specimens across different types of CHDs. In addition to translational studies involving human subjects, we also examined transcriptomic analyses of CHDs in a range of model systems, including iPSCs and animal models. We concluded that RNA-seq technology has revolutionized medical research and many of the discoveries from CHD transcriptome studies draw attention to biological pathways that concurrently open the door to a better understanding of cardiac development and related therapeutic avenue. While some crucial impediments to perfectly studying CHDs in this context remain obtaining pediatric cardiac tissue samples, phenotypic variation, and the lack of anatomical/spatial context with model systems. Combining model systems, RNA-seq technology, and integrating algorithms for analyzing transcriptomic data at both single-cell and high throughput spatial resolution is expected to continue uncovering unique biological pathways that are perturbed in CHDs, thus facilitating the development of novel therapy for congenital heart disease.
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Affiliation(s)
- Nkechi Martina Odogwu
- Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States
| | - Clinton Hagen
- Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States
| | - Timothy J. Nelson
- Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States
- Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, United States
- Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States
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Babakhanzadeh E, Danaei H, Abedinzadeh M, Ashrafzadeh HR, Ghasemi N. Association of miR-146a and miR196a2 genotype with susceptibility to idiopathic recurrent pregnancy loss in Iranian women: A case-control study. Int J Reprod Biomed 2021; 19:725-732. [PMID: 34568733 PMCID: PMC8458919 DOI: 10.18502/ijrm.v19i8.9620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 08/04/2020] [Accepted: 12/21/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Recurrent pregnancy loss (RPL) is the most common complaint of pregnancy in females with a prevalence of 5%. Numerous documents have shown that single nucleotide polymorphisms are able to change miRNA transcription and/or maturation, which may alter the incidence of disorders such as RPL. OBJECTIVE To assess the relationship of miR-146aC > G (rs2910164) and miR-196a2T > C (rs11614913) with RPL susceptibility in Iranian women. MATERIALS AND METHODS Blood samples were collected from 214 women who had experienced at least two consecutive spontaneous miscarriages (case) and 147 normal individuals without a history of miscarriage (control). MiR-146aC > G and miR-196a2T > C genotypes were evaluated via the restriction fragment length polymorphism technique. RESULTS The genotypes incidence did not show a significant difference in pre-miR-146aC > G polymorphism CC vs CG + GG (p = 0.854; OR = 0.933; 95% CI) and CC + CG vs GG (p = 0.282; OR = 1.454; 95% CI). Also, no significant difference was observed between pre-miR-196a2T > C polymorphism TT vs TC + CC (p = 0.862; OR = 0.938; 95% CI) and TT + TC vs CC and (p = 0.291; OR = 1.462; 95% CI) in both the case and control groups. CONCLUSION The results showed that although the distribution of miR-146aC > G and miR-196a2T > C was different between the unknown RPL and control groups, these variances were not statistically significant.
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Affiliation(s)
- Emad Babakhanzadeh
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hamid Danaei
- Abortion Research Centre, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Abedinzadeh
- Abortion Research Centre, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hamid Reza Ashrafzadeh
- Abortion Research Centre, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Nasrin Ghasemi
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Abortion Research Centre, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Lim TB, Foo SYR, Chen CK. The Role of Epigenetics in Congenital Heart Disease. Genes (Basel) 2021; 12:genes12030390. [PMID: 33803261 PMCID: PMC7998561 DOI: 10.3390/genes12030390] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/23/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023] Open
Abstract
Congenital heart disease (CHD) is the most common birth defect among newborns worldwide and contributes to significant infant morbidity and mortality. Owing to major advances in medical and surgical management, as well as improved prenatal diagnosis, the outcomes for these children with CHD have improved tremendously so much so that there are now more adults living with CHD than children. Advances in genomic technologies have discovered the genetic causes of a significant fraction of CHD, while at the same time pointing to remarkable complexity in CHD genetics. For this reason, the complex process of cardiogenesis, which is governed by multiple interlinked and dose-dependent pathways, is a well investigated process. In addition to the sequence of the genome, the contribution of epigenetics to cardiogenesis is increasingly recognized. Significant progress has been made dissecting the epigenome of the heart and identified associations with cardiovascular diseases. The role of epigenetic regulation in cardiac development/cardiogenesis, using tissue and animal models, has been well reviewed. Here, we curate the current literature based on studies in humans, which have revealed associated and/or causative epigenetic factors implicated in CHD. We sought to summarize the current knowledge on the functional role of epigenetics in cardiogenesis as well as in distinct CHDs, with an aim to provide scientists and clinicians an overview of the abnormal cardiogenic pathways affected by epigenetic mechanisms, for a better understanding of their impact on the developing fetal heart, particularly for readers interested in CHD research.
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Affiliation(s)
- Tingsen Benson Lim
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Sik Yin Roger Foo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Ching Kit Chen
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Division of Cardiology, Department of Paediatrics, Khoo Teck Puat-National University Children’s Medical Institute, National University Health System, Singapore 119228, Singapore
- Correspondence:
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Wang S, Cao N. Uncovering potential differentially expressed miRNAs and targeted mRNAs in myocardial infarction based on integrating analysis. Mol Med Rep 2020; 22:4383-4395. [PMID: 33000230 PMCID: PMC7533449 DOI: 10.3892/mmr.2020.11517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/25/2020] [Indexed: 01/08/2023] Open
Abstract
Myocardial infarction (MI) is one of the leading causes of death globally. The aim of the present study was to find valuable microRNAs (miRNAs/miRs) and target mRNAs in order to contribute to our understanding of the pathology of MI. miRNA and mRNA data were downloaded for differential expression analysis. Then, a regulatory network between miRNAs and mRNAs was established, followed by function annotation of target mRNAs. Thirdly, prognosis and diagnostic analysis of differentially methylated target mRNAs were performed. Finally, an in vitro experiment was used to validate the expression of selected miRNAs and target mRNAs. A total of 19 differentially expressed miRNAs and 1,007 differentially expressed mRNAs were identified. Several regulatory interaction pairs between miRNA and mRNAs were identified, such as hsa-miR-142-2p-long-chain-fatty-acid-CoA ligase 1 (ACSL1), hsa-miR-15a-3p-nicotinamide phosphoribosyltransferase (NAMPT), hsa-miR-33b-5p-regulator of G-protein signaling 2 (RGS2), hsa-miR-17-3p-Jun dimerization protein 2 (JDP2), hsa-miR-24-1-5p-aquaporin-9 (AQP9) and hsa-miR-34a-5p-STAT1/AKT3. Of note, it was demonstrated that ACSL1, NAMPT, RGS2, JDP2, AQP9, STAT1 and AKT3 had diagnostic and prognostic values for patients with MI. In addition, STAT1 was involved in the ‘chemokine signaling pathway’ and ‘Jak-STAT signaling pathway’. AKT3 was involved in both the ‘MAPK signaling pathway’ and ‘T cell receptor signaling pathway’. Reverse transcription-quantitative PCR validation of hsa-miR-142-3p, hsa-miR-15a-3p, hsa-miR-33b-5p, ACSL1, NAMPT, RGS2 and JDP2 expression was consistent with the bioinformatics analysis. In conclusion, the identified miRNAs and mRNAs may be involved in the pathology of MI.
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Affiliation(s)
- Shiai Wang
- Department of Cardiology, Jinan Jigang Hospital, Jinan, Shandong 250000, P.R. China
| | - Na Cao
- Department of Cardiology, Jinan Jigang Hospital, Jinan, Shandong 250000, P.R. China
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Dueñas A, Expósito A, Aranega A, Franco D. The Role of Non-Coding RNA in Congenital Heart Diseases. J Cardiovasc Dev Dis 2019; 6:E15. [PMID: 30939839 PMCID: PMC6616598 DOI: 10.3390/jcdd6020015] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/24/2019] [Accepted: 03/26/2019] [Indexed: 12/13/2022] Open
Abstract
Cardiovascular development is a complex developmental process starting with the formation of an early straight heart tube, followed by a rightward looping and the configuration of atrial and ventricular chambers. The subsequent step allows the separation of these cardiac chambers leading to the formation of a four-chambered organ. Impairment in any of these developmental processes invariably leads to cardiac defects. Importantly, our understanding of the developmental defects causing cardiac congenital heart diseases has largely increased over the last decades. The advent of the molecular era allowed to bridge morphogenetic with genetic defects and therefore our current understanding of the transcriptional regulation of cardiac morphogenesis has enormously increased. Moreover, the impact of environmental agents to genetic cascades has been demonstrated as well as of novel genomic mechanisms modulating gene regulation such as post-transcriptional regulatory mechanisms. Among post-transcriptional regulatory mechanisms, non-coding RNAs, including therein microRNAs and lncRNAs, are emerging to play pivotal roles. In this review, we summarize current knowledge on the functional role of non-coding RNAs in distinct congenital heart diseases, with particular emphasis on microRNAs and long non-coding RNAs.
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Affiliation(s)
- Angel Dueñas
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain.
| | - Almudena Expósito
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain.
| | - Amelia Aranega
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain.
| | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain.
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Zhou K, Yue P, Ma F, Yan H, Zhang Y, Wang C, Qiu D, Hua Y, Li Y. Interpreting the various associations of MiRNA polymorphisms with susceptibilities of cardiovascular diseases: Current evidence based on a systematic review and meta-analysis. Medicine (Baltimore) 2018; 97:e10712. [PMID: 29794746 PMCID: PMC6393131 DOI: 10.1097/md.0000000000010712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND To interpret the various associations between miRNA polymorphisms and cardiovascular diseases (CVD). METHODS Literature search has identified relevant studies up to June 2016. A meta-analysis was performed followed the guidelines from the Cochrane review group and the PRISMA statement. Studies were identified by searching the Cochrane Library, EMBASE, PUBMED and WHO clinical trials registry center. A meta-analysis has been done with a fixed/random-effect model using STATA 14.0, which also has been used to estimate the publication bias and meta-regression. RESULTS The results from 11 case-control studies were included. The miR-146a G/C makes a contribution to the causing of CVD as recessive genetic model. And the miR-499 G/A raised the risks of cardiomyopathy, however it could still accelerate the procedure of CVD combined with myocardial infraction. At this point, we consider that it could deepen the adverse of outcomes from coronary artery disease (CAD), but it's hard to draw an association between miR-499 G/A and CAD. At last the miR-196a2 T/C demonstrated a contrary role between development problem and metabolic issues, which protects the development procedure and impairs the metabolism to cause different disease phenotypes. CONCLUSION Despite inter-study variability, the polymorphisms from miR-146a, miR-499 and miR-196a2 have impacts on cardiovascular disease. Each type of miRNA has individual role in either cardiac development or the origins of CVD.
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Affiliation(s)
- Kaiyu Zhou
- Department of Pediatrics, West China Second University Hospital, Sichuan University
- Ministry of Education Key Laboratory of Women and Children's Diseases and Birth Defects, West China Second University Hospital, Sichuan University
- Program for Changjiang Scholars and Innovative Research Team in University, West China Second University Hospital, Sichuan University
| | - Peng Yue
- Department of Pediatrics, West China Second University Hospital, Sichuan University
- Ministry of Education Key Laboratory of Women and Children's Diseases and Birth Defects, West China Second University Hospital, Sichuan University
- West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Fan Ma
- Department of Pediatrics, West China Second University Hospital, Sichuan University
- Ministry of Education Key Laboratory of Women and Children's Diseases and Birth Defects, West China Second University Hospital, Sichuan University
- West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Hualin Yan
- Department of Pediatrics, West China Second University Hospital, Sichuan University
- Ministry of Education Key Laboratory of Women and Children's Diseases and Birth Defects, West China Second University Hospital, Sichuan University
- West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Yi Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University
- Ministry of Education Key Laboratory of Women and Children's Diseases and Birth Defects, West China Second University Hospital, Sichuan University
| | - Chuan Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University
- Ministry of Education Key Laboratory of Women and Children's Diseases and Birth Defects, West China Second University Hospital, Sichuan University
| | - Dajian Qiu
- Department of Pediatrics, West China Second University Hospital, Sichuan University
- Ministry of Education Key Laboratory of Women and Children's Diseases and Birth Defects, West China Second University Hospital, Sichuan University
| | - Yimin Hua
- Department of Pediatrics, West China Second University Hospital, Sichuan University
- Ministry of Education Key Laboratory of Women and Children's Diseases and Birth Defects, West China Second University Hospital, Sichuan University
- Program for Changjiang Scholars and Innovative Research Team in University, West China Second University Hospital, Sichuan University
| | - Yifei Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University
- Ministry of Education Key Laboratory of Women and Children's Diseases and Birth Defects, West China Second University Hospital, Sichuan University
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Fan PC, Chen CC, Chen YC, Chang YS, Chu PH. MicroRNAs in acute kidney injury. Hum Genomics 2016; 10:29. [PMID: 27608623 PMCID: PMC5016954 DOI: 10.1186/s40246-016-0085-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 08/31/2016] [Indexed: 12/19/2022] Open
Abstract
Acute kidney injury (AKI) is an important clinical issue that is associated with significant morbidity and mortality. Despite research advances over the past decades, the complex pathophysiology of AKI is not fully understood. The regulatory mechanisms underlying post-AKI repair and fibrosis have not been clarified either. Furthermore, there is no definitively effective treatment for AKI. MicroRNAs (miRNAs) are endogenous single-stranded noncoding RNAs of 19~23 nucleotides that have been shown to be crucial to the post-transcriptional regulation of various cellular biological functions, including proliferation, differentiation, metabolism, and apoptosis. In addition to being fundamental to normal development and physiology, miRNAs also play important roles in various human diseases. In AKI, some miRNAs appear to act pathogenically by promoting inflammation, apoptosis, and fibrosis, while others may act protectively by exerting anti-inflammatory, anti-apoptotic, anti-fibrotic, and pro-angiogenic effects. Thus, miRNAs have not only emerged as novel biomarkers for AKI; they also hold promise to be potential therapeutic targets.
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Affiliation(s)
- Pei-Chun Fan
- Kidney Research Center, Department of Nephrology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Chun Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yung-Chang Chen
- Kidney Research Center, Department of Nephrology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Pao-Hsien Chu
- Division of Cardiology, Department of Internal Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taipei, Taiwan. .,Healthcare Center, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taipei, Taiwan. .,Heart Failure Center, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taipei, Taiwan. .,Department of Cardiology, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, 199 Tung Hwa North Road, Taipei, 105, Taiwan.
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