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Kozhevnikova MV, Belenkov YN. [Biomarkers in Heart Failure: Current and Future]. ACTA ACUST UNITED AC 2021; 61:4-16. [PMID: 34112070 DOI: 10.18087/cardio.2021.5.n1530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 01/29/2021] [Indexed: 11/18/2022]
Abstract
Heart failure (HF) is the ending of practically all cardiovascular diseases and the reason for hospitalization of 49% of patients in a cardiological hospital. Available instrumental diagnostic methods and biomarkers not always allow verification of HF, particularly in patients with preserved left ventricular ejection fraction. Prediction of chronic HF in patients with risk factors faces great difficulties. Currently, natriuretic peptides (NUP) are widely used for the diagnosis, prognosis and management of patients with HF and are included in clinical guidelines for diagnosis and treatment of HF. Following multiple studies, the understanding of NUP significance has changed. This resulted in a need for new biomarkers to improve the insight into the process of HF and to personalize the treatment by better individual phenotyping. In addition, current technologies, such as transcriptomic, proteomic and metabolomic analyses, provide identification of new biomarkers and better understanding of features of the HF pathogenesis. The aim of this study was to discuss recent reports on NUP and novel, most promising biomarkers in respect of their possible use in clinical practice.
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Affiliation(s)
- M V Kozhevnikova
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow
| | - Yu N Belenkov
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow
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Chair SY, Chan JYW, Waye MMY, Liu T, Law BMH, Chien WT. Exploration of Potential Genetic Biomarkers for Heart Failure: A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18115904. [PMID: 34072866 PMCID: PMC8198957 DOI: 10.3390/ijerph18115904] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/12/2022]
Abstract
Patients with heart failure (HF) often present with signs and symptoms that are often nonspecific and with a wide differential diagnosis, making diagnosis and prognosis of HF by clinical presentation alone challenging. Our knowledge on genetic diversity is rapidly evolving with high-throughput DNA sequencing technology, which makes a great potential for genetic biomarker development. The present review attempts to provide a comprehensive review on the modification of major genetic components in HF patients and to explore the potential application of these components as clinical biomarkers in the diagnosis and in monitoring the progress of HF. The literature search was conducted using six databases, resulting in the inclusion of eighteen studies in the review. The findings of these studies were summarized narratively. An appraisal of the reporting quality of the included studies was conducted using a twelve-item checklist adapted from the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) checklist. The findings showed that changes in genetic components in patients with HF compared to healthy controls could be noninvasive diagnostic or prognostic tools for HF with higher specificity and sensitivity in comparison with the traditional biomarkers. This review provided evidence for the potential of developing genetic biomarkers of HF.
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Affiliation(s)
- Sek-Ying Chair
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
- Asia-Pacific Genomic and Genetic Nursing Centre, The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Judy-Yuet-Wa Chan
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
- Correspondence:
| | - Mary-Miu-Yee Waye
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
- The Croucher Laboratory for Human Genomics, The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Ting Liu
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
| | - Bernard-Man-Hin Law
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
| | - Wai-Tong Chien
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
- Asia-Pacific Genomic and Genetic Nursing Centre, The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
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Abstract
This review provides a comprehensive overview of the past 25+ years of research into the development of left ventricular assist device (LVAD) to improve clinical outcomes in patients with severe end-stage heart failure and basic insights gained into the biology of heart failure gleaned from studies of hearts and myocardium of patients undergoing LVAD support. Clinical aspects of contemporary LVAD therapy, including evolving device technology, overall mortality, and complications, are reviewed. We explain the hemodynamic effects of LVAD support and how these lead to ventricular unloading. This includes a detailed review of the structural, cellular, and molecular aspects of LVAD-associated reverse remodeling. Synergisms between LVAD support and medical therapies for heart failure related to reverse remodeling, remission, and recovery are discussed within the context of both clinical outcomes and fundamental effects on myocardial biology. The incidence, clinical implications and factors most likely to be associated with improved ventricular function and remission of the heart failure are reviewed. Finally, we discuss recognized impediments to achieving myocardial recovery in the vast majority of LVAD-supported hearts and their implications for future research aimed at improving the overall rates of recovery.
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Affiliation(s)
| | | | - Gabriel Sayer
- Cardiovascular Research Foundation, New York, NY (D.B.)
| | - Nir Uriel
- Cardiovascular Research Foundation, New York, NY (D.B.)
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54
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A Brief Review on the Biology and Effects of Cellular and Circulating microRNAs on Cardiac Remodeling after Infarction. Int J Mol Sci 2021; 22:ijms22094995. [PMID: 34066757 PMCID: PMC8125864 DOI: 10.3390/ijms22094995] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 01/21/2023] Open
Abstract
Despite advances in diagnostic, prognostic, and treatment modalities, myocardial infarction (MI) remains a leading cause of morbidity and mortality. Impaired cellular signaling after an MI causes maladaptive changes resulting in cardiac remodeling. MicroRNAs (miRNAs/miR) along with other molecular components have been investigated for their involvement in cellular signaling in the pathogenesis of various cardiac conditions like MI. miRNAs are small non-coding RNAs that negatively regulate gene expression. They bind to complementary mRNAs and regulate the rate of protein synthesis by altering the stability of their targeted mRNAs. A single miRNA can modulate several cellular signaling pathways by targeting hundreds of mRNAs. This review focuses on the biogenesis and beneficial effects of cellular and circulating (exosomal) miRNAs on cardiac remodeling after an MI. Particularly, miR-1, -133, 135, and -29 that play an essential role in cardiac remodeling after an MI are described in detail. The limitations that will need to be addressed in the future for the further development of miRNA-based therapeutics for cardiovascular conditions will also be discussed.
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Galluzzo A, Gallo S, Pardini B, Birolo G, Fariselli P, Boretto P, Vitacolonna A, Peraldo-Neia C, Spilinga M, Volpe A, Celentani D, Pidello S, Bonzano A, Matullo G, Giustetto C, Bergerone S, Crepaldi T. Identification of novel circulating microRNAs in advanced heart failure by next-generation sequencing. ESC Heart Fail 2021; 8:2907-2919. [PMID: 33934544 PMCID: PMC8318428 DOI: 10.1002/ehf2.13371] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/22/2021] [Accepted: 04/06/2021] [Indexed: 12/20/2022] Open
Abstract
Aims Risk stratification in patients with advanced chronic heart failure (HF) is an unmet need. Circulating microRNA (miRNA) levels have been proposed as diagnostic and prognostic biomarkers in several diseases including HF. The aims of the present study were to characterize HF‐specific miRNA expression profiles and to identify miRNAs with prognostic value in HF patients. Methods and results We performed a global miRNome analysis using next‐generation sequencing in the plasma of 30 advanced chronic HF patients and of matched healthy controls. A small subset of miRNAs was validated by real‐time PCR (P < 0.0008). Pearson's correlation analysis was computed between miRNA expression levels and common HF markers. Multivariate prediction models were exploited to evaluate miRNA profiles' prognostic role. Thirty‐two miRNAs were found to be dysregulated between the two groups. Six miRNAs (miR‐210‐3p, miR‐22‐5p, miR‐22‐3p, miR‐21‐3p, miR‐339‐3p, and miR‐125a‐5p) significantly correlated with HF biomarkers, among which N‐terminal prohormone of brain natriuretic peptide. Inside the cohort of advanced HF population, we identified three miRNAs (miR‐125a‐5p, miR‐10b‐5p, and miR‐9‐5p) altered in HF patients experiencing the primary endpoint of cardiac death, heart transplantation, or mechanical circulatory support implantation when compared with those without clinical events. The three miRNAs added substantial prognostic power to Barcelona Bio‐HF score, a multiparametric and validated risk stratification tool for HF (from area under the curve = 0.72 to area under the curve = 0.82). Conclusions This discovery study has characterized, for the first time, the advanced chronic HF‐specific miRNA expression pattern. We identified a few miRNAs able to improve the prognostic stratification of HF patients based on common clinical and laboratory values. Further studies are needed to validate our results in larger populations.
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Affiliation(s)
- Alessandro Galluzzo
- Department of Medical Sciences, University of Turin, Turin, Italy.,A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy.,Ospedale Sant'Andrea, Vercelli, Italy
| | - Simona Gallo
- Department of Oncology, University of Turin, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Barbara Pardini
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy.,Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Piero Fariselli
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Paolo Boretto
- Department of Medical Sciences, University of Turin, Turin, Italy.,A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy
| | - Annapia Vitacolonna
- Department of Oncology, University of Turin, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Caterina Peraldo-Neia
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy.,Laboratory of Cancer Genomics, Fondazione Edo ed Elvo Tempia, Biella, Italy
| | | | - Alessandra Volpe
- Department of Medical Sciences, University of Turin, Turin, Italy.,A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy
| | - Dario Celentani
- Department of Medical Sciences, University of Turin, Turin, Italy.,A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy
| | - Stefano Pidello
- Department of Medical Sciences, University of Turin, Turin, Italy.,A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy
| | | | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy.,A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy
| | - Carla Giustetto
- Department of Medical Sciences, University of Turin, Turin, Italy.,A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy
| | - Serena Bergerone
- A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy
| | - Tiziana Crepaldi
- Department of Oncology, University of Turin, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
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Qiu X, Lin J, Liang B, Chen Y, Liu G, Zheng J. Identification of Hub Genes and MicroRNAs Associated With Idiopathic Pulmonary Arterial Hypertension by Integrated Bioinformatics Analyses. Front Genet 2021; 12:667406. [PMID: 33995494 PMCID: PMC8117102 DOI: 10.3389/fgene.2021.636934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
Objective The aim of this study is the identification of hub genes associated with idiopathic pulmonary arterial hypertension (IPAH). Materials and Methods GSE15197 gene expression data was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified by screening IPAH patients and controls. The 5,000 genes with the greatest variances were analyzed using a weighted gene co-expression network analysis (WGCNA). Modules with the strongest correlation with IPAH were chosen, followed by a functional enrichment analysis. Protein–protein interaction (PPI) networks were constructed to identify hub gene candidates using calculated degrees. Real hub genes were found from the overlap of DEGs and candidate hub genes. microRNAs (miRNAs) targeting real hub genes were found by screening miRNet 2.0. The most important IPAH miRNAs were identified. Results There were 4,395 DEGs identified. WGCNA indicated that green and brown modules associated most strongly with IPAH. Functional enrichment analysis showed that green and brown module genes were mainly involved in protein digestion and absorption and proteoglycans in cancer, respectively. The top ten candidate hub genes in green and brown modules were identified, respectively. After overlapping with DEGs, 11 real hub genes were identified: EP300, MMP2, CDH2, CDK2, GNG10, ALB, SMC2, DHX15, CUL3, BTBD1, and LTN1. These genes were expressed with significant differences in IPAH versus controls, indicating a high diagnostic ability. The miRNA–gene network showed that hsa-mir-1-3p could associate with IPAH. Conclusion EP300, MMP2, CDH2, CDK2, GNG10, ALB, SMC2, DHX15, CUL3, BTBD1, and LTN1 may play essential roles in IPAH. Predicted miRNA hsa-mir-1-3p could regulate gene expression in IPAH. Such hub genes may contribute to the pathology and progression in IPAH, providing potential diagnostic and therapeutic opportunities for IPAH patients.
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Affiliation(s)
- Xue Qiu
- Department of Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jinyan Lin
- The First Clinical Medical School, Guangxi Medical University, Nanning, China
| | - Bixiao Liang
- The First Clinical Medical School, Guangxi Medical University, Nanning, China
| | - Yanbing Chen
- The First Clinical Medical School, Guangxi Medical University, Nanning, China
| | - Guoqun Liu
- The First Clinical Medical School, Guangxi Medical University, Nanning, China
| | - Jing Zheng
- Department of Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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57
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Examining the evidence for extracellular RNA function in mammals. Nat Rev Genet 2021; 22:448-458. [PMID: 33824487 DOI: 10.1038/s41576-021-00346-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
Abstract
The presence of RNAs in the extracellular milieu has sparked the hypothesis that RNA may play a role in mammalian cell-cell communication. As functional nucleic acids transfer from cell to cell in plants and nematodes, the idea that mammalian cells also transfer functional extracellular RNA (exRNA) is enticing. However, untangling the role of mammalian exRNAs poses considerable experimental challenges. This Review discusses the evidence for and against functional exRNAs in mammals and their proposed roles in health and disease, such as cancer and cardiovascular disease. We conclude with a discussion of the forward-looking prospects for studying the potential of mammalian exRNAs as mediators of cell-cell communication.
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58
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A critical approach for successful use of circulating microRNAs as biomarkers in cardiovascular diseases: the case of hypertrophic cardiomyopathy. Heart Fail Rev 2021; 27:281-294. [PMID: 33656618 DOI: 10.1007/s10741-021-10084-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules that act as major regulators of gene expression at the post-transcriptional level. As the potential applications of miRNAs in the diagnosis and treatment of human diseases have become more evident, many studies of hypertrophic cardiomyopathy (HCM) have focused on the systemic identification and quantification of miRNAs in biofluids and myocardial tissues. HCM is a hereditary cardiomyopathy caused by mutations in genes encoding proteins of the sarcomere. Despite overall improvements in survival, progression to heart failure, stroke, and sudden cardiac death remain prominent features of living with HCM. Several miRNAs have been shown to be promising biomarkers of HCM; however, there are many challenges to ensuring the validity, consistency, and reproducibility of these biomarkers for clinical use. In particular, miRNA testing may be limited by pre-analytical and analytical caveats, making our interpretation of results challenging. Such factors that may affect miRNA testing include sample type selection, hemolysis, platelet activation, and renal dysfunction. Therefore, researchers should be careful when developing appropriate standards for the design of miRNA profiling studies in order to ensure that all results provided are both accurate and reliable. In this review, we discuss the application of miRNAs as biomarkers for HCM.
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The double face of miR-320: cardiomyocytes-derived miR-320 deteriorated while fibroblasts-derived miR-320 protected against heart failure induced by transverse aortic constriction. Signal Transduct Target Ther 2021; 6:69. [PMID: 33597502 PMCID: PMC7890065 DOI: 10.1038/s41392-020-00445-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/03/2020] [Accepted: 11/30/2020] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) are aberrantly expressed in the pathophysiologic process of heart failure (HF). However, the functions of a certain miRNA in different cardiac cell types during HF are scarcely reported, which might be covered by the globe effects of it on the heart. In the current study, Langendorff system was applied to isolate cardiomyocytes (CMs) and cardiac fibroblasts (CFs) from transverse aortic constriction (TAC)-induced mice. Slight increase of miR-320 expression was observed in the whole heart tissue of TAC mice. Interestingly, miR-320 was significantly elevated in CMs but decreased in CFs from TAC mice at different time points. Then, recombinant adeno-associated virus 9 with cell-type-specific promoters were used to manipulate miR-320 expressions in vivo. Both in vitro and in vivo experiments showed the miR-320 overexpression in CMs exacerbated cardiac dysfunction, whereas overexpression of miR-320 in CFs alleviated cardiac fibrosis and hypertrophy. Mechanically, downstream signaling pathway analyses revealed that miR-320 might induce various effects via targeting PLEKHM3 and IFITM1 in CMs and CFs, respectively. Moreover, miR-320 mediated effects could be abolished by PLEKHM3 re-expression in CMs or IFITM1 re-expression in CFs. Interestingly, miR-320 treated CFs were able to indirectly affect CMs function, but not vice versa. Meanwhile, upstream signaling pathway analyses showed that miR-320 expression and decay rate were rigorously manipulated by Ago2, which was regulated by a cluster of cell-type-specific TFs distinctively expressed in CMs and CFs, respectively. Together, we demonstrated that miR-320 functioned differently in various cell types of the heart during the progression of HF.
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Galectin-3 and sST2 as Prognosticators for Heart Failure Requiring Extracorporeal Life Support: Jack n' Jill. Biomolecules 2021; 11:biom11020166. [PMID: 33513858 PMCID: PMC7911521 DOI: 10.3390/biom11020166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 11/18/2022] Open
Abstract
Extracorporeal life support provides perfusion for patients with heart failure to allow time for recovery, function as a bridge for patients to heart transplantation, or serve as destination therapy for long term mechanical device support. Several biomarkers have been employed in attempt to predict these outcomes, but it remains to be determined which are suitable to guide clinical practice relevant to extracorporeal life support. Galectin-3 and soluble suppression of tumorigenicity-2 (sST2) are two of the more promising candidates with the greatest supporting evidence. In this review, we address the similarities and differences between galectin-3 and sST2 for prognostic prediction in adults and children with heart failure requiring extracorporeal life support and highlight the significant lack of progress in pediatric biomarker discovery and utilization.
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Abstract
The discovery that all cells secrete extracellular vesicles (EVs) to shuttle proteins and nucleic acids to recipient cells suggested they play an important role in intercellular communication. EVs are widely distributed in many body fluids, including blood, cerebrospinal fluid, urine and saliva. Exosomes are nano-sized EVs of endosomal origin that regulate many pathophysiological processes including immune responses, inflammation, tumour growth, and infection. Healthy individuals release exosomes with a cargo of different RNA, DNA, and protein contents into the circulation, which can be measured non-invasively as biomarkers of healthy and diseased states. Cancer-derived exosomes carry a unique set of DNA, RNA, protein and lipid reflecting the stage of tumour progression, and may serve as diagnostic and prognostic biomarkers for various cancers. However, many gaps in knowledge and technical challenges in EVs and extracellular RNA (exRNA) biology, such as mechanisms of EV biogenesis and uptake, exRNA cargo selection, and exRNA detection remain. The NIH Common Fund-supported exRNA Communication Consortium was launched in 2013 to address major scientific challenges in this field. This review focuses on scientific highlights in biomarker discovery of exosome-based exRNA in cancer and its possible clinical application as cancer biomarkers.
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Affiliation(s)
- Christine Happel
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aniruddha Ganguly
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute at the National Institutes of Health, Bethesda, MD 20892, USA
| | - Danilo A Tagle
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
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The Degree of Cardiac Remodelling before Overload Relief Triggers Different Transcriptome and miRome Signatures during Reverse Remodelling (RR)-Molecular Signature Differ with the Extent of RR. Int J Mol Sci 2020; 21:ijms21249687. [PMID: 33353134 PMCID: PMC7766898 DOI: 10.3390/ijms21249687] [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: 11/09/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
This study aims to provide new insights into transcriptome and miRome modifications occurring in cardiac reverse remodelling (RR) upon left ventricle pressure-overload relief in mice. Pressure-overload was established in seven-week-old C57BL/6J-mice by ascending aortic constriction. A debanding (DEB) surgery was performed seven weeks later in half of the banding group (BA). Two weeks later, cardiac function was evaluated through hemodynamics and echocardiography, and the hearts were collected for histology and small/bulk-RNA-sequencing. Pressure-overload relief was confirmed by the normalization of left-ventricle-end-systolic-pressure. DEB animals were separated into two subgroups according to the extent of cardiac remodelling at seven weeks and RR: DEB1 showed an incomplete RR phenotype confirmed by diastolic dysfunction persistence (E/e' ≥ 16 ms) and increased myocardial fibrosis. At the same time, DEB2 exhibited normal diastolic function and fibrosis, presenting a phenotype closer to myocardial recovery. Nevertheless, both subgroups showed the persistence of cardiomyocytes hypertrophy. Notably, the DEB1 subgroup presented a more severe diastolic dysfunction at the moment of debanding than the DEB2, suggesting a different degree of cardiac remodelling. Transcriptomic and miRomic data, as well as their integrated analysis, revealed significant downregulation in metabolic and hypertrophic related pathways in DEB1 when compared to DEB2 group, including fatty acid β-oxidation, mitochondria L-carnitine shuttle, and nuclear factor of activated T-cells pathways. Moreover, extracellular matrix remodelling, glycan metabolism and inflammation-related pathways were up-regulated in DEB1. The presence of a more severe diastolic dysfunction at the moment of pressure overload-relief on top of cardiac hypertrophy was associated with an incomplete RR. Our transcriptomic approach suggests that a cardiac inflammation, fibrosis, and metabolic-related gene expression dysregulation underlies diastolic dysfunction persistence after pressure-overload relief, despite left ventricular mass regression, as echocardiographically confirmed.
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63
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Florio MC, Magenta A, Beji S, Lakatta EG, Capogrossi MC. Aging, MicroRNAs, and Heart Failure. Curr Probl Cardiol 2020; 45:100406. [PMID: 30704792 PMCID: PMC10544917 DOI: 10.1016/j.cpcardiol.2018.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 12/23/2018] [Indexed: 12/12/2022]
Abstract
Aging is a major risk factor for heart failure, one of the leading causes of death in Western society. The mechanisms that underlie the different forms of heart failure have been elucidated only in part and the role of noncoding RNAs is still poorly characterized. Specifically, microRNAs (miRNAs), a class of small noncoding RNAs that can modulate gene expression at the posttranscriptional level in all cells, including myocardial and vascular cells, have been shown to play a role in heart failure with reduced ejection fraction. In contrast, miRNAs role in heart failure with preserved ejection fraction, the predominant form of heart failure in the elderly, is still unknown. In this review, we will focus on age-dependent miRNAs in heart failure and on some other conditions that are prevalent in the elderly and are frequently associated with heart failure with preserved ejection fraction.
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64
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Zhang L, Xu RL, Liu SX, Dong SH, Zhao XX, Zhang BL. Diagnostic value of circulating microRNA-19b in heart failure. Eur J Clin Invest 2020; 50:e13308. [PMID: 32663314 DOI: 10.1111/eci.13308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/16/2020] [Accepted: 05/27/2020] [Indexed: 12/23/2022]
Abstract
OBJECTIVE For differentiating heart failure (HF) with preserved ejection fraction (HFpEF) from HF with reduced EF (HFrEF), N-terminal prohormone brain natriuretic peptide (NT-proBNP) is less accurate. Decreased expression of microRNA-19b (miR-19b) is associated with increased cardiac-fibrosis. We aim to evaluate the value of miR-19b in diagnosing HFrEF patients. METHOD We included 200 HF patients and 100 healthy controls. Intergroup comparisons of miR-19b were made and correlation between miR-19b and NT-proBNP was analysed. Diagnostic values of NT-proBNP and miR-19b for HF patients versus controls and HFrEF versus HFpEF were obtained by ROC analysis and described by area under curve (AUC), sensitivity and specificity. RESULTS HFrEF patients (0.87, 95% CI 0.37-1.45) had significantly lower miR-19b level than HFpEF group (1.32, 95% CI 0.63-2.51) and the controls (1.82, 95% CI 0.37-1.45) (both P < .001). There was a remarkable negative correlation between miR-19b and NT-proBNP (P < .001). The additional use of miR-19b did not improve the accuracy of NT-proBNP alone in diagnosing HF patients from the controls (both AUC = 0.98, 95%CI 0.97-0.99). However, as for distinguishing the HFpEF from HFrEF, miR-19b and NT-proBNP yielded a significantly higher AUC than NT-proBNP alone (0.85, 95% CI 0.80-0.90 vs. 0.66, 95% CI 0.58-0.74) (P < .001), and the sensitivity for diagnosing HFrEF was raised from 58% to 77% and the specificity from 75% to 79%. CONCLUSIONS On top of NT-proBNP, miR-19b added the value in diagnosing HFrEF. But in view of satisfactory accuracy of NT-proBNP in predicting HF from the healthy volunteers, miR-19b did not provide incremental value.
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Affiliation(s)
- Liang Zhang
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Rong-Liang Xu
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Su-Xuan Liu
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Shao-Hua Dong
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xian-Xian Zhao
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Bi-Li Zhang
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
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65
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Peterlin A, Počivavšek K, Petrovič D, Peterlin B. The Role of microRNAs in Heart Failure: A Systematic Review. Front Cardiovasc Med 2020; 7:161. [PMID: 33195446 PMCID: PMC7593250 DOI: 10.3389/fcvm.2020.00161] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/31/2020] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs are highly investigated for their role in the pathogenesis of cardiovascular diseases. Nevertheless, evidence for clinical implementation is still lacking. In our systematic review, we evaluated the potential of microRNAs as pathophysiological and diagnostic biomarkers of heart failure. We identified 72 differentially expressed microRNA molecules among groups of heart failure patients and control groups by searching the PubMed database. We did not identify a substantial overlap of differentially expressed microRNAs among different studies; only five microRNAs (miR-1228, miR-122, miR-423-5p, miR-142-3p, and exosomal miR-92b-5p) were differentially expressed in more than one included study. Gene set enrichment analysis, based on the gene targets of microRNAs presented in the included studies, showed that gene targets of differentially expressed microRNAs were enriched in the MAPK, TGFβ, PI3K-Akt, and IL-2 signaling pathways, as well as apoptosis pathway, p53 activity regulation, and angiogenesis pathway. Results of our systematic review show that there is currently insufficient support for the use of any of the presented microRNAs as pathophysiological or prognostic biomarkers in the clinical setting.
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Affiliation(s)
- Ana Peterlin
- Faculty of Medicine, Institute of Histology and Embryology, University of Ljubljana, Ljubljana, Slovenia
| | - Karolina Počivavšek
- Department of Cardiovascular Surgery, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Danijel Petrovič
- Faculty of Medicine, Institute of Histology and Embryology, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
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66
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Shao X, Zhang X, Yang L, Zhang R, Zhu R, Feng R. Integrated analysis of mRNA and microRNA expression profiles reveals differential transcriptome signature in ischaemic and dilated cardiomyopathy induced heart failure. Epigenetics 2020; 16:917-932. [PMID: 33016206 DOI: 10.1080/15592294.2020.1827721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Cardiac remodelling is widely accepted as a common characteristic for many heart diseases, especially in heart failure (HF). Ischaemic cardiomyopathy (ICM) and dilated cardiomyopathy (DCM) are associated with cardiac remodelling. Both mRNA and microRNA are potential diagnostic markers and therapeutic targets of cardiac remodelling in HF. However, the mechanisms of microRNA-mRNA joint regulation in HF are still unclear. In this study, 3 gene expression profiles from patients with and without HF were analysed to harvest shared differentially expressed genes (microRNA and mRNA) with significant major biological function. Moreover, key genes highly related to ICM and DCM-induced HF were screened out through a Weighted Genes Co-Expression Network Analysis (WGCNA). Based on microRNA-mRNA analysis, several microRNAs and target genes were identified. Combined with pathway analysis, we found that miR-542-3p and its target gene CILP were likely involved in the regulation of TGF-β signalling pathway in ICM induced HF. Collectively, the microRNA-mRNA interaction network analysis revealed that miR-542-3p-CILP as mediator of TGF-β signalling pathway might be a new mechanism to mediate ICM induced HF. This study provides certain novel targets for diagnosis and therapeutic treatment of ICM- and DCM-induced HF.
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Affiliation(s)
- Xiuli Shao
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
| | - Xiaolin Zhang
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
| | - Lei Yang
- Tianjin Customs, Technical Center for Safety of Industrial Products, Tianjin, China
| | - Ruijia Zhang
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
| | - Rongli Zhu
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
| | - Rui Feng
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
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67
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de Gonzalo-Calvo D, Vea A, Bär C, Fiedler J, Couch LS, Brotons C, Llorente-Cortes V, Thum T. Circulating non-coding RNAs in biomarker-guided cardiovascular therapy: a novel tool for personalized medicine? Eur Heart J 2020; 40:1643-1650. [PMID: 29688487 PMCID: PMC6528150 DOI: 10.1093/eurheartj/ehy234] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/22/2017] [Accepted: 04/06/2018] [Indexed: 02/06/2023] Open
Abstract
Current clinical guidelines emphasize the unmet need for technological innovations to guide physician decision-making and to transit from conventional care to personalized cardiovascular medicine. Biomarker-guided cardiovascular therapy represents an interesting approach to inform tailored treatment selection and monitor ongoing efficacy. However, results from previous publications cast some doubts about the clinical applicability of biomarkers to direct individualized treatment. In recent years, the non-coding human transcriptome has emerged as a new opportunity for the development of novel therapeutic strategies and biomarker discovery. Non-coding RNA (ncRNA) signatures may provide an accurate molecular fingerprint of patient phenotypes and capture levels of information that could complement traditional markers and established clinical variables. Importantly, ncRNAs have been identified in body fluids and their concentrations change with physiology and pathology, thus representing promising non-invasive biomarkers. Previous publications highlight the translational applicability of circulating ncRNAs for diagnosis and prognostic stratification within cardiology. Numerous independent studies have also evaluated the potential of the circulating non-coding transcriptome to predict and monitor response to cardiovascular treatment. However, this field has not been reviewed in detail. Here, we discuss the state-of-the-art research into circulating ncRNAs, specifically microRNAs and long non-coding RNAs, to support clinical decision-making in cardiovascular therapy. Furthermore, we summarize current methodological and conceptual limitations and propose future steps for their incorporation into personalized cardiology. Despite the lack of robust population-based studies and technical barriers, circulating ncRNAs emerge as a promising tool for biomarker-guided therapy.
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Affiliation(s)
- David de Gonzalo-Calvo
- Biomedical Research Institute Sant Pau (IIB Sant Pau), Av. Sant Antoni Maria Claret 167, Pavelló del Convent, Barcelona, Spain.,Institute of Health Carlos III, CIBERCV, Av. Monforte de Lemos 5, Madrid, Spain.,Institute of Molecular and Translational Therapeutic Strategies (IMTTS), IFB-Tx, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany.,Institute of Biomedical Research of Barcelona (IIBB)-Spanish National Research Council (CSIC), C/ Rosselló 161, Barcelona, Spain
| | - Angela Vea
- Biomedical Research Institute Sant Pau (IIB Sant Pau), Av. Sant Antoni Maria Claret 167, Pavelló del Convent, Barcelona, Spain
| | - Christian Bär
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), IFB-Tx, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany
| | - Jan Fiedler
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), IFB-Tx, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany
| | - Liam S Couch
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), IFB-Tx, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany.,National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, UK
| | - Carlos Brotons
- Biomedical Research Institute Sant Pau (IIB Sant Pau), Sardenya Primary Health Care Center, C/ Sardenya 466, Barcelona, Spain
| | - Vicenta Llorente-Cortes
- Biomedical Research Institute Sant Pau (IIB Sant Pau), Av. Sant Antoni Maria Claret 167, Pavelló del Convent, Barcelona, Spain.,Institute of Health Carlos III, CIBERCV, Av. Monforte de Lemos 5, Madrid, Spain.,Institute of Biomedical Research of Barcelona (IIBB)-Spanish National Research Council (CSIC), C/ Rosselló 161, Barcelona, Spain
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), IFB-Tx, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany.,National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, UK.,Excellence Cluster REBIRTH, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany
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68
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miRNALoc: predicting miRNA subcellular localizations based on principal component scores of physico-chemical properties and pseudo compositions of di-nucleotides. Sci Rep 2020; 10:14557. [PMID: 32884018 PMCID: PMC7471944 DOI: 10.1038/s41598-020-71381-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/07/2020] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are one kind of non-coding RNA, play vital role in regulating several physiological and developmental processes. Subcellular localization of miRNAs and their abundance in the native cell are central for maintaining physiological homeostasis. Besides, RNA silencing activity of miRNAs is also influenced by their localization and stability. Thus, development of computational method for subcellular localization prediction of miRNAs is desired. In this work, we have proposed a computational method for predicting subcellular localizations of miRNAs based on principal component scores of thermodynamic, structural properties and pseudo compositions of di-nucleotides. Prediction accuracy was analyzed following fivefold cross validation, where ~ 63–71% of AUC-ROC and ~ 69–76% of AUC-PR were observed. While evaluated with independent test set, > 50% localizations were found to be correctly predicted. Besides, the developed computational model achieved higher accuracy than the existing methods. A user-friendly prediction server “miRNALoc” is freely accessible at https://cabgrid.res.in:8080/mirnaloc/, by which the user can predict localizations of miRNAs.
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69
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Yao J, Wu DC, Nottingham RM, Lambowitz AM. Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling. eLife 2020; 9:e60743. [PMID: 32876046 PMCID: PMC7518892 DOI: 10.7554/elife.60743] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Human plasma contains > 40,000 different coding and non-coding RNAs that are potential biomarkers for human diseases. Here, we used thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) combined with peak calling to simultaneously profile all RNA biotypes in apheresis-prepared human plasma pooled from healthy individuals. Extending previous TGIRT-seq analysis, we found that human plasma contains largely fragmented mRNAs from > 19,000 protein-coding genes, abundant full-length, mature tRNAs and other structured small non-coding RNAs, and less abundant tRNA fragments and mature and pre-miRNAs. Many of the mRNA fragments identified by peak calling correspond to annotated protein-binding sites and/or have stable predicted secondary structures that could afford protection from plasma nucleases. Peak calling also identified novel repeat RNAs, miRNA-sized RNAs, and putatively structured intron RNAs of potential biological, evolutionary, and biomarker significance, including a family of full-length excised intron RNAs, subsets of which correspond to mirtron pre-miRNAs or agotrons.
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Affiliation(s)
- Jun Yao
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
| | - Douglas C Wu
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
| | - Ryan M Nottingham
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
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70
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Tosar JP, Cayota A. Extracellular tRNAs and tRNA-derived fragments. RNA Biol 2020; 17:1149-1167. [PMID: 32070197 PMCID: PMC7549618 DOI: 10.1080/15476286.2020.1729584] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 01/08/2023] Open
Abstract
Fragmentation of tRNAs generates a family of small RNAs collectively known as tRNA-derived fragments. These fragments vary in sequence and size but have been shown to regulate many processes involved in cell homoeostasis and adaptations to stress. Additionally, the field of extracellular RNAs (exRNAs) is rapidly growing because exRNAs are a promising source of biomarkers in liquid biopsies, and because exRNAs seem to play key roles in intercellular and interspecies communication. Herein, we review recent descriptions of tRNA-derived fragments in the extracellular space in all domains of life, both in biofluids and in cell culture. The purpose of this review is to find consensus on which tRNA-derived fragments are more prominent in each extracellular fraction (including extracellular vesicles, lipoproteins and ribonucleoprotein complexes). We highlight what is becoming clear and what is still controversial in this field, in order to stimulate future hypothesis-driven studies which could clarify the role of full-length tRNAs and tRNA-derived fragments in the extracellular space.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit, Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Department of Medicine, University Hospital, Universidad de la República, Montevideo, Uruguay
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71
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Williams AL, Khadka VS, Anagaran MCT, Lee K, Avelar A, Deng Y, Shohet RV. miR-125 family regulates XIRP1 and FIH in response to myocardial infarction. Physiol Genomics 2020; 52:358-368. [PMID: 32716698 DOI: 10.1152/physiolgenomics.00041.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are powerful regulators of protein expression. Many play important roles in cardiac development and disease. While several miRNAs and targets have been well characterized, the abundance of miRNAs and the numerous potential targets for each suggest that the vast majority of these interactions have yet to be described. The goal of this study was to characterize miRNA expression in the mouse heart after coronary artery ligation (LIG) and identify novel mRNA targets altered during the initial response to ischemic stress. We performed small RNA sequencing (RNA-Seq) of ischemic heart tissue 1 day and 3 days after ligation and identified 182 differentially expressed miRNAs. We then selected relevant mRNA targets from all potential targets by correlating miRNA and mRNA expression from a corresponding RNA-Seq data set. From this analysis we chose to focus, as proof of principle, on two miRNAs from the miR-125 family, miR-125a and miR-351, and two of their potential mRNA targets, Xin actin-binding repeat-containing protein 1 (XIRP1) and factor inhibiting hypoxia-inducible factor (FIH). We found miR-125a to be less abundant and XIRP1 more abundant after ligation. In contrast, the related murine miRNA miR-351 was substantially upregulated in response to ischemic injury, and FIH expression correspondingly decreased. Luciferase reporter assays confirmed direct interactions between these miRNAs and targets. In summary, we utilized a correlative analysis strategy combining miRNA and mRNA expression data to identify functional miRNA-mRNA relationships in the heart after ligation. These findings provide insight into the response to ischemic injury and suggest future therapeutic targets.
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Affiliation(s)
- Allison Lesher Williams
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Vedbar S Khadka
- Bioinformatics Core, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Ma C T Anagaran
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Katie Lee
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Abigail Avelar
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Youping Deng
- Bioinformatics Core, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Ralph V Shohet
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
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72
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Das S, Shah R, Dimmeler S, Freedman JE, Holley C, Lee JM, Moore K, Musunuru K, Wang DZ, Xiao J, Yin KJ. Noncoding RNAs in Cardiovascular Disease: Current Knowledge, Tools and Technologies for Investigation, and Future Directions: A Scientific Statement From the American Heart Association. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2020; 13:e000062. [DOI: 10.1161/hcg.0000000000000062] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background:
The discovery that much of the non–protein-coding genome is transcribed and plays a diverse functional role in fundamental cellular processes has led to an explosion in the development of tools and technologies to investigate the role of these noncoding RNAs in cardiovascular health. Furthermore, identifying noncoding RNAs for targeted therapeutics to treat cardiovascular disease is an emerging area of research. The purpose of this statement is to review existing literature, offer guidance on tools and technologies currently available to study noncoding RNAs, and identify areas of unmet need.
Methods:
The writing group used systematic literature reviews (including MEDLINE, Web of Science through 2018), expert opinion/statements, analyses of databases and computational tools/algorithms, and review of current clinical trials to provide a broad consensus on the current state of the art in noncoding RNA in cardiovascular disease.
Results:
Significant progress has been made since the initial studies focusing on the role of miRNAs (microRNAs) in cardiovascular development and disease. Notably, recent progress on understanding the role of novel types of noncoding small RNAs such as snoRNAs (small nucleolar RNAs), tRNA (transfer RNA) fragments, and Y-RNAs in cellular processes has revealed a noncanonical function for many of these molecules. Similarly, the identification of long noncoding RNAs that appear to play an important role in cardiovascular disease processes, coupled with the development of tools to characterize their interacting partners, has led to significant mechanistic insight. Finally, recent work has characterized the unique role of extracellular RNAs in mediating intercellular communication and their potential role as biomarkers.
Conclusions:
The rapid expansion of tools and pipelines for isolating, measuring, and annotating these entities suggests that caution in interpreting results is warranted until these methodologies are rigorously validated. Most investigators have focused on investigating the functional role of single RNA entities, but studies suggest complex interaction between different RNA molecules. The use of network approaches and advanced computational tools to understand the interaction of different noncoding RNA species to mediate a particular phenotype may be required to fully comprehend the function of noncoding RNAs in mediating disease phenotypes.
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73
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Coelho-Lima J, Mohammed A, Cormack S, Jones S, Ali A, Panahi P, Barter M, Bagnall A, Ali S, Young D, Spyridopoulos I. Kinetics Analysis of Circulating MicroRNAs Unveils Markers of Failed Myocardial Reperfusion. Clin Chem 2020; 66:247-256. [PMID: 31672851 DOI: 10.1373/clinchem.2019.308353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/17/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Failed myocardial reperfusion occurs in approximately 50% of patients with ST-elevation myocardial infarction (STEMI) treated with primary percutaneous coronary intervention (PPCI). It manifests as microvascular obstruction (MVO) on cardiac magnetic resonance (CMR) imaging. Although prognostically important, MVO is not routinely screened for. Our aim was to investigate the kinetics of circulating short noncoding ribonucleic acids [microRNAs (miRNAs)] following PPCI and their association with MVO in STEMI patients. METHODS Screening of 2083 miRNAs in plasma from STEMI patients with (n = 6) and without (n = 6) MVO was performed by next-generation sequencing. Two candidate miRNAs were selected and quantified at 13 time points within 3 h postreperfusion in 20 STEMI patients by reverse transcription and quantitative PCR. Subsequently, these 2 miRNAs were measured in a "validation" STEMI cohort (n = 50) that had CMR imaging performed at baseline and 3 months post-PPCI to evaluate their association with MVO. RESULTS miR-1 and miR-133b were rapidly released following PPCI in a monophasic or biphasic pattern. Both miRNAs were enriched in circulating microparticles. A second miR-1 peak (90-180 min postreperfusion) seemed to be associated with a higher index of microvascular resistance. In addition, miR-1 and miR-133b levels at 90 min post-PPCI were approximately 3-fold (P = 0.001) and 4.4-fold (P = 0.008) higher in patients with MVO, respectively. Finally, miR-1 was significantly increased in a subgroup of patients with worse left ventricular (LV) functional recovery 3 months post-PPCI. CONCLUSIONS miR-1 and miR-133b levels increase within 3 h of PPCI. They are positively associated with MVO and worse LV functional recovery post-PPCI.
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Affiliation(s)
- Jose Coelho-Lima
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ashfaq Mohammed
- Department of Cardiology, Freeman Hospital, Newcastle upon Tyne, UK
| | - Suzanne Cormack
- Department of Cardiology, Freeman Hospital, Newcastle upon Tyne, UK
| | - Samuel Jones
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Adnan Ali
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Pedram Panahi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Matt Barter
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Alan Bagnall
- Department of Cardiology, Freeman Hospital, Newcastle upon Tyne, UK.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Simi Ali
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - David Young
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ioakim Spyridopoulos
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.,Department of Cardiology, Freeman Hospital, Newcastle upon Tyne, UK
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74
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Dang H, Ye Y, Zhao X, Zeng Y. Identification of candidate genes in ischemic cardiomyopathy by gene expression omnibus database. BMC Cardiovasc Disord 2020; 20:320. [PMID: 32631246 PMCID: PMC7336680 DOI: 10.1186/s12872-020-01596-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Ischemic cardiomyopathy (ICM) is one of the most usual causes of death worldwide. This study aimed to find the candidate gene for ICM. METHODS We studied differentially expressed genes (DEGs) in ICM compared to healthy control. According to these DEGs, we carried out the functional annotation, protein-protein interaction (PPI) network and transcriptional regulatory network constructions. The expression of selected candidate genes were confirmed using a published dataset and Quantitative real time polymerase chain reaction (qRT-PCR). RESULTS From three Gene Expression Omnibus (GEO) datasets, we acquired 1081 DEGs (578 up-regulated and 503 down-regulated genes) between ICM and healthy control. The functional annotation analysis revealed that cardiac muscle contraction, hypertrophic cardiomyopathy, arrhythmogenic right ventricular cardiomyopathy and dilated cardiomyopathy were significantly enriched pathways in ICM. SNRPB, BLM, RRS1, CDK2, BCL6, BCL2L1, FKBP5, IPO7, TUBB4B and ATP1A1 were considered the hub proteins. PALLD, THBS4, ATP1A1, NFASC, FKBP5, ECM2 and BCL2L1 were top six transcription factors (TFs) with the most downstream genes. The expression of 6 DEGs (MYH6, THBS4, BCL6, BLM, IPO7 and SERPINA3) were consistent with our integration analysis and GSE116250 validation results. CONCLUSIONS The candidate DEGs and TFs may be related to the ICM process. This study provided novel perspective for understanding mechanism and exploiting new therapeutic means for ICM.
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Affiliation(s)
- Haiming Dang
- Department of cardiac surgery, Capital medical university, Beijing Anzhen hospital, Beijing, China
| | - Yicong Ye
- Department of cardiology, Capital medical university, Beijing Anzhen hospital, No.2, Anzhen Road, Chaoyan District, Beijing, 100029, China
| | - Xiliang Zhao
- Department of cardiology, Capital medical university, Beijing Anzhen hospital, No.2, Anzhen Road, Chaoyan District, Beijing, 100029, China
| | - Yong Zeng
- Department of cardiology, Capital medical university, Beijing Anzhen hospital, No.2, Anzhen Road, Chaoyan District, Beijing, 100029, China.
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75
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Sadat-Ebrahimi SR, Aslanabadi N. Role of MicroRNAs in Diagnosis, Prognosis, and Treatment of Acute Heart Failure: Ambassadors from Intracellular Zone. Galen Med J 2020; 9:e1818. [PMID: 34466598 PMCID: PMC8343948 DOI: 10.31661/gmj.v9i0.1818] [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: 12/31/2019] [Revised: 01/24/2020] [Accepted: 02/06/2020] [Indexed: 12/12/2022] Open
Abstract
Acute heart failure (AHF) is one of the burdensome diseases affecting a considerable proportion of the population. Recently, it has been demonstrated that micro-ribonucleic acids (miRNAs) can exert diagnostic, prognostic, and therapeutic roles in a variety of conditions including AHF. These molecules play essential roles in HF-related pathophysiology, particularly, cardiac fibrosis, and hypertrophy. Some miRNAs namely miRNA-423-5p are reported to have both diagnostic and prognostic capabilities. However, some studies suggest that combination of biomarkers is a much better way to achieve the highest accuracy such as the combination of miRNAs and N-terminal pro b-type Natriuretic Peptide (NT pro-BNP). Therefore, this review discusses different views towards various roles of miRNAs in AHF.
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Affiliation(s)
- Seyyed-Reza Sadat-Ebrahimi
- Cardiovascular Research Center, Madani Heart Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Naser Aslanabadi
- Cardiovascular Research Center, Madani Heart Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Correspondence to: Naser Aslanabadi, Professor of Cardiology, Cardiovascular Research Center, Madani Heart Center, Tabriz University of Medical Sciences, Tabriz, Iran Telephone Number: +989143110844 Email Address:
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76
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Meiri E, Volinsky N, Dromi N, Kredo-Russo S, Benjamin H, Tabak S, Marmor H, Motin M, Lebanony D, Lithwick-Yanai G, Kadosh E, Kreader C, Grosman-Rimon L, Amir O. Differential expression of microRNA in serum fractions and association of Argonaute 1 microRNAs with heart failure. J Cell Mol Med 2020; 24:6586-6595. [PMID: 32400052 PMCID: PMC7299714 DOI: 10.1111/jcmm.15306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 08/01/2019] [Accepted: 03/30/2020] [Indexed: 12/15/2022] Open
Abstract
The serum or plasma microRNA (miRNA) molecules have been suggested as diagnostic and prognostic biomarkers, in various pathological conditions. However, these molecules are also found in different serum fractions, such as exosomes and Argonaute (Ago) protein complexes. Ago1 is the predominant Ago protein expressed in heart tissue. The objective of the study was to examine the hypothesis that Ago1‐associated miRNAs may be more relevant to cardiac disease and heart failure compared with the serum. In total, 84 miRNA molecules were screened for their expression in the whole serum, exosomes and Ago1, and Ago2 complexes. Ago1‐bound miR‐222‐3p, miR‐497‐5p and miR‐21‐5p were significantly higher, and let‐7a‐5p was significantly lower in HF patients compared with healthy controls, whereas no such difference was observed for those markers in the serum samples among the groups. A combination of these 4 miRNAs into an Ago1‐HF score provided a ROC curve with an AUC of 1, demonstrating clear discrimination between heart failure patients and healthy individuals. Ago1 fraction might be a better and more specific platform for identifying HF‐related miRNAs compared with the whole serum.
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Affiliation(s)
- Eti Meiri
- Rosetta Genomics Ltd, Rehovot, Israel
| | - Natalia Volinsky
- Division of Cardiovascular Medicine, Baruch Padeh Medical Center, Poriya, Israel.,The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Nir Dromi
- Rosetta Genomics Ltd, Rehovot, Israel
| | | | | | | | | | | | | | | | | | | | - Liza Grosman-Rimon
- Division of Cardiovascular Medicine, Baruch Padeh Medical Center, Poriya, Israel.,The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Offer Amir
- Division of Cardiovascular Medicine, Baruch Padeh Medical Center, Poriya, Israel.,The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
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Kmecova Z, Veteskova J, Lelkova-Zirova K, Bies Pivackova L, Doka G, Malikova E, Paulis L, Krenek P, Klimas J. Disease severity-related alterations of cardiac microRNAs in experimental pulmonary hypertension. J Cell Mol Med 2020; 24:6943-6951. [PMID: 32395887 PMCID: PMC7299706 DOI: 10.1111/jcmm.15352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/24/2020] [Accepted: 04/01/2020] [Indexed: 12/16/2022] Open
Abstract
Right ventricular (RV) failure is the primary cause of death in pulmonary arterial hypertension (PAH). We hypothesized that heart‐relevant microRNAs, that is myomiRs (miR‐1, miR‐133a, miR‐208, miR‐499) and miR‐214, can have a role in the right ventricle in the development of PAH. To mimic PAH, male Wistar rats were injected with monocrotaline (MCT, 60 mg/kg, s.c.); control group received vehicle. MCT rats were divided into two groups, based on the clinical presentation: MCT group terminated 4 weeks after MCT administration and prematurely terminated group (ptMCT) displaying signs of terminal disease. Myocardial damage genes and candidate microRNAs expressions were determined by RT‐qPCR. Reduced blood oxygen saturation, breathing disturbances, RV enlargement as well as elevated levels of markers of myocardial damage confirmed PH in MCT animals and were more pronounced in ptMCT. MyomiRs (miR‐1/miR‐133a/miR‐208a/miR‐499) were decreased and the expression of miR‐214 was increased only in ptMCT group (P < 0.05). The myomiRs negatively correlated with Fulton index as a measure of RV hypertrophy in MCT group (P < 0.05), whereas miR‐214 showed a positive correlation (P < 0.05). We conclude that the expression of determined microRNAs mirrored the disease severity and targeting their pathways might represent potential future therapeutic approach in PAH.
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Affiliation(s)
- Zuzana Kmecova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
| | - Jana Veteskova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
| | - Katarina Lelkova-Zirova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
| | - Lenka Bies Pivackova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
| | - Gabriel Doka
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
| | - Eva Malikova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
| | - Ludovit Paulis
- Institute of Pathophysiology, Faculty of Medicine, Comenius University, Bratislava, Slovakia.,Institute of Normal and Pathological Physiology, Centre of Experimental Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Krenek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
| | - Jan Klimas
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
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Tang R, Long T, Lui KO, Chen Y, Huang ZP. A Roadmap for Fixing the Heart: RNA Regulatory Networks in Cardiac Disease. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 20:673-686. [PMID: 32380417 PMCID: PMC7210385 DOI: 10.1016/j.omtn.2020.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/16/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023]
Abstract
With the continuous development of RNA biology and massive genome-wide transcriptome analysis, more and more RNA molecules and their functions have been explored in the last decade. Increasing evidence has demonstrated that RNA-related regulatory networks play an important role in a variety of human diseases, including cardiovascular diseases. In this review, we focus on RNA regulatory networks in heart disease, most of which are devastating conditions with no known cure. We systemically summarize recent discoveries of important new components of RNA regulatory networks, including microRNAs, long non-coding RNAs, and circular RNAs, as well as multiple regulators that affect the activity of these networks in cardiac physiology and pathology. In addition, this review covers emerging micropeptides, which represent short open reading frames (sORFs) in long non-coding RNA transcripts that may modulate cardiac physiology. Based on the current knowledge of RNA regulatory networks, we think that ongoing discoveries will not only provide us a better understanding of the molecular mechanisms that underlie heart disease, but will also identify novel biomarkers and therapeutic targets for the diagnosis and treatment of cardiac disease.
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Affiliation(s)
- Rong Tang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Tianxin Long
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Kathy O Lui
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR 999077, China
| | - Yili Chen
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Zhan-Peng Huang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China.
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Variations of circulating miRNA in paediatric patients with Heart Failure supported with Ventricular Assist Device: a pilot study. Sci Rep 2020; 10:5905. [PMID: 32246041 PMCID: PMC7125126 DOI: 10.1038/s41598-020-62757-7] [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: 11/12/2019] [Accepted: 03/18/2020] [Indexed: 01/13/2023] Open
Abstract
Circulating miRNAs (c-miRNAs) are promising biomarkers for HF diagnosis and prognosis. There are no studies on HF pediatric patients undergoing VAD-implantation. Aims of this study were: to examine the c-miRNAs profile in HF children; to evaluate the effects of VAD on c-miRNAs levels; to in vitro validate putative c-miRNA targets. c-miRNA profile was determined in serum of HF children by NGS before and one month after VAD-implant. The c-miRNA differentially expressed were analyzed by real time-PCR, before and at 4 hrs,1,3,7,14,30 days after VAD-implant. A miRNA mimic transfection study in HepG2 cells was performed to validate putative miRNA targets selected through miRWalk database. Thirteen c-miRNAs were modified at 30 days after VAD-implant compared to pre-VAD at NSG, and, among them, six c-miRNAs were confirmed by Real-TimePCR. Putative targets of the validated c-miRNAs are involved in the hemostatic process. The in vitro study confirmed a down-regulatory effect of hsa-miR-409-3p towards coagulation factor 7 (F7) and F2. Of note, all patients had thrombotic events requiring pump change. In conclusion, in HF children, the level of six c-miRNAs involved in the regulation of hemostatic events changed after 30 days of VAD-treatment. In particular, the lowering of c-miR-409-3p regulating both F7 and F2 could reflect a pro-thrombotic state after VAD-implant.
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80
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Wong LL, Zou R, Zhou L, Lim JY, Phua DCY, Liu C, Chong JPC, Ng JYX, Liew OW, Chan SP, Chen YT, Chan MMY, Yeo PSD, Ng TP, Ling LH, Sim D, Leong KTG, Ong HY, Jaufeerally F, Wong R, Chai P, Low AF, Lund M, Devlin G, Troughton R, Cameron VA, Doughty RN, Lam CSP, Too HP, Richards AM. Combining Circulating MicroRNA and NT-proBNP to Detect and Categorize Heart Failure Subtypes. J Am Coll Cardiol 2020; 73:1300-1313. [PMID: 30898206 DOI: 10.1016/j.jacc.2018.11.060] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/29/2018] [Accepted: 11/06/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND Clinicians need improved tools to better identify nonacute heart failure with preserved ejection fraction (HFpEF). OBJECTIVES The purpose of this study was to derive and validate circulating microRNA signatures for nonacute heart failure (HF). METHODS Discovery and validation cohorts (N = 1,710), comprised 903 HF and 807 non-HF patients from Singapore and New Zealand (NZ). MicroRNA biomarker panel discovery in a Singapore cohort (n = 546) was independently validated in a second Singapore cohort (Validation 1; n = 448) and a NZ cohort (Validation 2; n = 716). RESULTS In discovery, an 8-microRNA panel identified HF with an area under the curve (AUC) 0.96, specificity 0.88, and accuracy 0.89. Corresponding metrics were 0.88, 0.66, and 0.77 in Validation 1, and 0.87, 0.58, and 0.74 in Validation 2. Combining microRNA panels with N-terminal pro-B-type natriuretic peptide (NT-proBNP) clearly improved specificity and accuracy from AUC 0.96, specificity 0.91, and accuracy 0.90 for NT-proBNP alone to corresponding metrics of 0.99, 0.99, and 0.93 in the discovery and 0.97, 0.96, and 0.93 in Validation 1. The 8-microRNA discovery panel distinguished HFpEF from HF with reduced ejection fraction with AUC 0.81, specificity 0.66, and accuracy 0.72. Corresponding metrics were 0.65, 0.41, and 0.56 in Validation 1 and 0.65, 0.41, and 0.62 in Validation 2. For phenotype categorization, combined markers achieved AUC 0.87, specificity 0.75, and accuracy 0.77 in the discovery with corresponding metrics of 0.74, 0.59, and 0.67 in Validation 1 and 0.72, 0.52, and 0.68 in Validation 2, as compared with NT-proBNP alone of AUC 0.71, specificity 0.46, and accuracy 0.62 in the discovery; with corresponding metrics of 0.72, 0.44, and 0.57 in Validation 1 and 0.69, 0.48, and 0.66 in Validation 2. Accordingly, false negative (FN) (81% Singapore and all NZ FN cases were HFpEF) as classified by a guideline-endorsed NT-proBNP ruleout threshold, were correctly reclassified by the 8-microRNA panel in the majority (72% and 88% of FN in Singapore and NZ, respectively) of cases. CONCLUSIONS Multi-microRNA panels in combination with NT-proBNP are highly discriminatory and improved specificity and accuracy in identifying nonacute HF. These findings suggest potential utility in the identification of nonacute HF, where clinical assessment, imaging, and NT-proBNP may not be definitive, especially in HFpEF.
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Affiliation(s)
- Lee Lee Wong
- Cardiovascular Research Institute, National University Health System, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ruiyang Zou
- Bioprocessing Technology Institute, A*STAR, Singapore; MiRXES Pted Ltd, Singapore
| | - Lihan Zhou
- Bioprocessing Technology Institute, A*STAR, Singapore; MiRXES Pted Ltd, Singapore
| | - Jia Yuen Lim
- Cardiovascular Research Institute, National University Health System, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | - Jenny P C Chong
- Cardiovascular Research Institute, National University Health System, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jessica Y X Ng
- Cardiovascular Research Institute, National University Health System, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Oi Wah Liew
- Cardiovascular Research Institute, National University Health System, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Siew Pang Chan
- Cardiovascular Research Institute, National University Health System, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yei-Tsung Chen
- Cardiovascular Research Institute, National University Health System, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Life Sciences and Institute of Genome Sciences National Yang-Ming University, Taipei, Taiwan
| | | | - Poh Shuan D Yeo
- Department of Cardiology, Tan Tock Seng Hospital, Singapore; Apex Heart Clinic, Gleneagles Hospital, Singapore
| | - Tze Pin Ng
- Department of Psychological Medicine, National University of Singapore, Singapore
| | - Lieng H Ling
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cardiac Department, National University Health System, Singapore
| | - David Sim
- National Heart Centre, Singhealth, Singapore
| | - Kui Toh G Leong
- Department of Cardiology, Changi General Hospital, Singapore
| | - Hean Y Ong
- Department of Cardiology, Khoo Teck Puat Hospital, Singapore
| | - Fazlur Jaufeerally
- Duke-NUS Graduate Medical School, Singapore; Department of Internal Medicine, Singapore General Hospital, Singapore
| | - Raymond Wong
- Cardiac Department, National University Health System, Singapore; National University Heart Centre, National University Hospital, Singapore
| | - Ping Chai
- Cardiac Department, National University Health System, Singapore; National University Heart Centre, National University Hospital, Singapore
| | - Adrian F Low
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cardiac Department, National University Health System, Singapore
| | - Mayanna Lund
- Middlemore Hospital, Otahuhu, Auckland, New Zealand
| | | | - Richard Troughton
- Christchurch Heart Institute, University of Otago, Christchurch, New Zealand
| | - Vicky A Cameron
- Christchurch Heart Institute, University of Otago, Christchurch, New Zealand
| | - Robert N Doughty
- Heart Health Research Group, University of Auckland, Auckland, New Zealand
| | - Carolyn S P Lam
- National Heart Centre Singapore and Duke-National University of Singapore, Singapore
| | - Heng Phon Too
- Bioprocessing Technology Institute, A*STAR, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Arthur Mark Richards
- Cardiovascular Research Institute, National University Health System, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cardiac Department, National University Health System, Singapore; Christchurch Heart Institute, University of Otago, Christchurch, New Zealand.
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Shah RV, Das S, Lewis GD. Circulating MicroRNAs: New Avenues for Heart Failure Classification? J Am Coll Cardiol 2020; 73:1314-1316. [PMID: 30898207 DOI: 10.1016/j.jacc.2018.10.091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 10/23/2018] [Indexed: 10/27/2022]
Affiliation(s)
- Ravi V Shah
- Cardiology Division of the Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Saumya Das
- Cardiology Division of the Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Gregory D Lewis
- Cardiology Division of the Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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82
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Abstract
Cardiovascular diseases are one of the most common causes of death in both developing and developed countries worldwide. Even though there have been improvements in primary prevention, the prevalence of cardiovascular diseases continues to increase in recent years. Hence, it is crucial to both investigate the molecular pathophysiology of cardiovascular diseases in-depth and find novel biomarkers regarding the early and proper prevention and diagnosis of these diseases. MicroRNAs, or miRNAs, are endogenous, conserved, single-stranded non-coding RNAs of 21-25 nucleotides in length. miRNAs have important roles in various cellular events such as embryogenesis, proliferation, vasculogenesis, apoptosis, cell growth, differentiation, and tumorigenesis. They also have potential roles in the cardiovascular system, including angiogenesis, cardiac cell contractility, control of lipid metabolism, plaque formation, the arrangement of cardiac rhythm, and cardiac cell growth. Circulating miRNAs are promising novel biomarkers for purposes of the diagnosis and prognosis of cardiovascular diseases. Cell or tissue specificity, stability in serum or plasma, resistance to degradative factors such as freeze-thaw cycles or enzymes in the blood, and fast-release kinetics, provide the potential for miRNAs to be surrogate markers for the early and accurate diagnosis of disease and for predicting middle- or long-term prognosis. Moreover, it may be a logical approach to combine miRNAs with traditional biomarkers to improve risk stratification and long-term prognosis. In addition to their efficacy in both diagnosis and prognosis, miRNA-based therapeutics may be beneficial for treating cardiovascular diseases using novel platforms and computational tools and in combination with traditional methods of analysis. microRNAs are promising, novel therapeutic agents, which can affect multiple genes using different signaling pathways. miRNAs therapeutic modulation techniques have been used in the settings of atherosclerosis, acute myocardial infarction, restenosis, vascular remodeling, arrhythmias, hypertrophy and fibrosis, angiogenesis and cardiogenesis, aortic aneurysm, pulmonary hypertension, and ischemic injury. This review presents detailed information about miRNAs regarding structure and biogenesis, stages of synthesis and functions, expression profiles in serum/plasma of living organisms, diagnostic and prognostic potential as novel biomarkers, and therapeutic applications in various diseases.
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Affiliation(s)
| | - Mehmet Demir
- Department of Cardiology, University of Health Sciences, Bursa Yüksek İhtisas Research and Training Hospital, Bursa, Turkey
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83
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The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research. Cell 2020; 177:231-242. [PMID: 30951667 DOI: 10.1016/j.cell.2019.03.023] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Extracellular RNA Communication Consortium (ERCC) was launched to accelerate progress in the new field of extracellular RNA (exRNA) biology and to establish whether exRNAs and their carriers, including extracellular vesicles (EVs), can mediate intercellular communication and be utilized for clinical applications. Phase 1 of the ERCC focused on exRNA/EV biogenesis and function, discovery of exRNA biomarkers, development of exRNA/EV-based therapeutics, and construction of a robust set of reference exRNA profiles for a variety of biofluids. Here, we present progress by ERCC investigators in these areas, and we discuss collaborative projects directed at development of robust methods for EV/exRNA isolation and analysis and tools for sharing and computational analysis of exRNA profiling data.
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84
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Butler AE, Ramachandran V, Sathyapalan T, David R, Gooderham NJ, Benurwar M, Dargham SR, Hayat S, Hani Najafi-Shoushtari S, Atkin SL. microRNA Expression in Women With and Without Polycystic Ovarian Syndrome Matched for Body Mass Index. Front Endocrinol (Lausanne) 2020; 11:206. [PMID: 32411089 PMCID: PMC7199502 DOI: 10.3389/fendo.2020.00206] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 03/24/2020] [Indexed: 12/22/2022] Open
Abstract
Background: Despite several authors who have hypothesized that alterations of small noncoding RNAs (miR) are implicated in the etiopathogenesis of polycystic ovarian syndrome (PCOS), contrasting findings have been reported so far. Discrepancies in body mass index (BMI) levels may account for these differences; therefore, the aim of the present study was to determine whether miR differed in serum samples collected from age- and BMI-matched control and PCOS women. Methods: In a cross-sectional study, miR were measured using quantitative polymerase chain reaction in 29 women with anovulatory PCOS women and 29 control women who were in the follicular phase of their menstrual cycle, from the local biobank. Results: One hundred seventy-six miR were detected, of which 15 miR passed the false discovery rate (FDR; p < 0.05) that differed between PCOS and control women. There was no association of the top 9 miR (p < 0.02) (miR-486-5p, miR-24-3p, miR-19b-3p, miR-22-3p, miR-19a-3p, miR-339-5p, miR-185-5p, miR-101-3p, miR-let-7i-5p) with BMI, androgen levels, insulin resistance, or antimullerian hormone (AMH) in either PCOS or normal women. Ingenuity pathway assessment showed the pathways were interrelated for abnormalities of the reproductive system. Conclusion: When the confounding influence of weight was accounted for, miR levels differed between anovulatory PCOS women and control women in the follicular phase of the menstrual cycle. Interestingly, the differing miR were associated with the pathways of reproductive abnormalities but did not associate with AMH or metabolic parameters.
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Affiliation(s)
- Alexandra E. Butler
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
- *Correspondence: Alexandra E. Butler ;
| | - Vimal Ramachandran
- Division of Research, Weill Cornell Medical College-Qatar, Qatar Foundation, Education City, Doha, Qatar
| | - Thozhukat Sathyapalan
- Academic Diabetes, Endocrinology and Metabolism, Hull York Medical School, University of Hull, Hull, United Kingdom
| | - Rhiannon David
- Department of Surgery & Cancer, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Nigel J. Gooderham
- Department of Surgery & Cancer, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Manasi Benurwar
- Division of Research, Weill Cornell Medical College-Qatar, Qatar Foundation, Education City, Doha, Qatar
| | - Soha R. Dargham
- Division of Research, Weill Cornell Medical College-Qatar, Qatar Foundation, Education City, Doha, Qatar
| | - Shahina Hayat
- Division of Research, Weill Cornell Medical College-Qatar, Qatar Foundation, Education City, Doha, Qatar
| | - S. Hani Najafi-Shoushtari
- Division of Research, Weill Cornell Medical College-Qatar, Qatar Foundation, Education City, Doha, Qatar
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, United States
| | - Stephen L. Atkin
- Division of Research, Weill Cornell Medical College-Qatar, Qatar Foundation, Education City, Doha, Qatar
- Royal College of Surgeons Ireland, Busaiteen, Bahrain
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85
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Syed SN, Frank AC, Raue R, Brüne B. MicroRNA-A Tumor Trojan Horse for Tumor-Associated Macrophages. Cells 2019; 8:E1482. [PMID: 31766495 PMCID: PMC6953083 DOI: 10.3390/cells8121482] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRs) significantly contribute to the regulation of gene expression, by virtue of their ability to interact with a broad, yet specific set of target genes. MiRs are produced and released by almost every cell type and play an important role in horizontal gene regulation in the tumor microenvironment (TME). In the TME, both tumor and stroma cells cross-communicate via diverse factors including miRs, which are taking central stage as a therapeutic target of anti-tumor therapy. One of the immune escape strategies adopted by tumor cells is to release miRs as a Trojan horse to hijack circulating or tumor-localized monocytes/macrophages to tune them for pro-tumoral functions. On the other hand, macrophage-derived miRs exert anti-tumor functions. The transfer of miRs from host to recipient cells depends on the supramolecular structure and composition of miR carriers, which determine the distinct uptake mechanism by recipient cells. In this review, we provide a recent update on the miR-mediated crosstalk between tumor cells and macrophages and their mode of uptake in the TME.
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Affiliation(s)
- Shahzad Nawaz Syed
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (S.N.S.); (A.-C.F.); (R.R.)
| | - Ann-Christin Frank
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (S.N.S.); (A.-C.F.); (R.R.)
| | - Rebecca Raue
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (S.N.S.); (A.-C.F.); (R.R.)
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (S.N.S.); (A.-C.F.); (R.R.)
- Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology, 60596 Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, 60590 Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe-University Frankfurt, 60596 Frankfurt, Germany
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86
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Miklas JW, Clark E, Levy S, Detraux D, Leonard A, Beussman K, Showalter MR, Smith AT, Hofsteen P, Yang X, Macadangdang J, Manninen T, Raftery D, Madan A, Suomalainen A, Kim DH, Murry CE, Fiehn O, Sniadecki NJ, Wang Y, Ruohola-Baker H. TFPa/HADHA is required for fatty acid beta-oxidation and cardiolipin re-modeling in human cardiomyocytes. Nat Commun 2019; 10:4671. [PMID: 31604922 PMCID: PMC6789043 DOI: 10.1038/s41467-019-12482-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 09/10/2019] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial trifunctional protein deficiency, due to mutations in hydratase subunit A (HADHA), results in sudden infant death syndrome with no cure. To reveal the disease etiology, we generated stem cell-derived cardiomyocytes from HADHA-deficient hiPSCs and accelerated their maturation via an engineered microRNA maturation cocktail that upregulated the epigenetic regulator, HOPX. Here we report, matured HADHA mutant cardiomyocytes treated with an endogenous mixture of fatty acids manifest the disease phenotype: defective calcium dynamics and repolarization kinetics which results in a pro-arrhythmic state. Single cell RNA-seq reveals a cardiomyocyte developmental intermediate, based on metabolic gene expression. This intermediate gives rise to mature-like cardiomyocytes in control cells but, mutant cells transition to a pathological state with reduced fatty acid beta-oxidation, reduced mitochondrial proton gradient, disrupted cristae structure and defective cardiolipin remodeling. This study reveals that HADHA (tri-functional protein alpha), a monolysocardiolipin acyltransferase-like enzyme, is required for fatty acid beta-oxidation and cardiolipin remodeling, essential for functional mitochondria in human cardiomyocytes.
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Affiliation(s)
- Jason W Miklas
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Elisa Clark
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Shiri Levy
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA, 98195, USA
| | - Damien Detraux
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA, 98195, USA
| | - Andrea Leonard
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
| | - Kevin Beussman
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
| | - Megan R Showalter
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA, 95616, USA
| | - Alec T Smith
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Peter Hofsteen
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Pathology, University of Washington, Seattle, WA, 98109, USA
| | - Xiulan Yang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Pathology, University of Washington, Seattle, WA, 98109, USA
| | - Jesse Macadangdang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Tuula Manninen
- Helsinki University Hospital, 00290, Helsinki, Finland
- Research Programs Unit, Stem Cells and Metabolism, University of Helsinki, 00290, Helsinki, Finland
| | - Daniel Raftery
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington, Seattle, WA, 98109, USA
| | - Anup Madan
- Covance Genomics Laboratory, Redmond, WA, 98052, USA
| | - Anu Suomalainen
- Helsinki University Hospital, 00290, Helsinki, Finland
- Research Programs Unit, Stem Cells and Metabolism, University of Helsinki, 00290, Helsinki, Finland
- Neuroscience Center, University of Helsinki, 00290, Helsinki, Finland
| | - Deok-Ho Kim
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, 98109, USA
- Department of Pathology, University of Washington, Seattle, WA, 98109, USA
- Department of Medicine/Cardiology, University of Washington, Seattle, WA, 98109, USA
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA, 95616, USA
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nathan J Sniadecki
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
- Department of Pathology, University of Washington, Seattle, WA, 98109, USA
| | - Yuliang Wang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Hannele Ruohola-Baker
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA, 98195, USA.
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87
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Soler-Botija C, Gálvez-Montón C, Bayés-Genís A. Epigenetic Biomarkers in Cardiovascular Diseases. Front Genet 2019; 10:950. [PMID: 31649728 PMCID: PMC6795132 DOI: 10.3389/fgene.2019.00950] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/05/2019] [Indexed: 12/16/2022] Open
Abstract
Cardiovascular diseases are the number one cause of death worldwide and greatly impact quality of life and medical costs. Enormous effort has been made in research to obtain new tools for efficient and quick diagnosis and predicting the prognosis of these diseases. Discoveries of epigenetic mechanisms have related several pathologies, including cardiovascular diseases, to epigenetic dysregulation. This has implications on disease progression and is the basis for new preventive strategies. Advances in methodology and big data analysis have identified novel mechanisms and targets involved in numerous diseases, allowing more individualized epigenetic maps for personalized diagnosis and treatment. This paves the way for what is called pharmacoepigenetics, which predicts the drug response and develops a tailored therapy based on differences in the epigenetic basis of each patient. Similarly, epigenetic biomarkers have emerged as a promising instrument for the consistent diagnosis and prognosis of cardiovascular diseases. Their good accessibility and feasible methods of detection make them suitable for use in clinical practice. However, multicenter studies with a large sample population are required to determine with certainty which epigenetic biomarkers are reliable for clinical routine. Therefore, this review focuses on current discoveries regarding epigenetic biomarkers and its controversy aiming to improve the diagnosis, prognosis, and therapy in cardiovascular patients.
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Affiliation(s)
- Carolina Soler-Botija
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain
- CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Carolina Gálvez-Montón
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain
- CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Antoni Bayés-Genís
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain
- CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
- Cardiology Service, HUGTiP, Badalona, Spain
- Department of Medicine, Barcelona Autonomous University (UAB), Badalona, Spain
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88
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Mushtaque RS, Hameed S, Mushtaque R, Idrees M, Siraj F. Role of Cardio-Specific Micro-Ribonucleic Acids and Correlation with Cardiac Biomarkers in Acute Coronary Syndrome: A Comprehensive Systematic Review. Cureus 2019; 11:e5878. [PMID: 31772848 PMCID: PMC6837270 DOI: 10.7759/cureus.5878] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Acute coronary syndrome (ACS) is an acute and severe manifestation of coronary artery disease (CAD); thus, timely diagnosis can save a life. Commonly, cardiac troponin T (CTnT), cardiac troponin I (CTnI) or creatine kinase muscle/brain subtype (CK-MB) have been used as cardiac biomarkers to assess ACS with certain limitations, such as increased time to rise for diagnosis and increased levels in the patients with chronic kidney disease (CKD). Recently, micro-ribonucleic acids (miRNAs) have become potential candidates as biomarkers for cardiac ischemia due to their remarkable stability and reproducibility. Certain miRNAs, for instance, miR-1, miR-133a/b, miR-208a/b, and miR-499a, strongly increase in the serum or plasma of patients with acute cardiac ischemia, making them as cardio-specific miRNAs and prospective biomarkers in ACS. This literature review gives enlightenment about the regulation of cardio-specific miRNA in acute myocardial ischemia (AMI) and correlation with common cardiac biomarkers and time at which they increase in the blood.
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Affiliation(s)
- Raja S Mushtaque
- Internal Medicine, Jinnah Postgraduate Medical Center, Karachi, PAK
| | | | - Rabia Mushtaque
- Cardiology, National Institute of Cardiovascular Diseases (NICVD), Karachi, PAK
| | | | - Farah Siraj
- Internal Medicine, Chandka Medical College Hospital, Larkana, PAK
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89
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Abstract
Systems medicine is a holistic approach to deciphering the complexity of human physiology in health and disease. In essence, a living body is constituted of networks of dynamically interacting units (molecules, cells, organs, etc) that underlie its collective functions. Declining resilience because of aging and other chronic environmental exposures drives the system to transition from a health state to a disease state; these transitions, triggered by acute perturbations or chronic disturbance, manifest as qualitative shifts in the interactions and dynamics of the disease-perturbed networks. Understanding health-to-disease transitions poses a high-dimensional nonlinear reconstruction problem that requires deep understanding of biology and innovation in study design, technology, and data analysis. With a focus on the principles of systems medicine, this Review discusses approaches for deciphering this biological complexity from a novel perspective, namely, understanding how disease-perturbed networks function; their study provides insights into fundamental disease mechanisms. The immediate goals for systems medicine are to identify early transitions to cardiovascular (and other chronic) diseases and to accelerate the translation of new preventive, diagnostic, or therapeutic targets into clinical practice, a critical step in the development of personalized, predictive, preventive, and participatory (P4) medicine.
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Affiliation(s)
- Kalliopi Trachana
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Rhishikesh Bargaje
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Gustavo Glusman
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Nathan D Price
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Sui Huang
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.).,Department of Biological Sciences, University of Calgary, Alberta, Canada (S.H.)
| | - Leroy E Hood
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
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90
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Eguchi S, Takefuji M, Sakaguchi T, Ishihama S, Mori Y, Tsuda T, Takikawa T, Yoshida T, Ohashi K, Shimizu Y, Hayashida R, Kondo K, Bando YK, Ouchi N, Murohara T. Cardiomyocytes capture stem cell-derived, anti-apoptotic microRNA-214 via clathrin-mediated endocytosis in acute myocardial infarction. J Biol Chem 2019; 294:11665-11674. [PMID: 31217281 DOI: 10.1074/jbc.ra119.007537] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 06/17/2019] [Indexed: 01/10/2023] Open
Abstract
Extracellular vesicles (EVs) have emerged as key mediators of intercellular communication that have the potential to improve cardiac function when used in cell-based therapy. However, the means by which cardiomyocytes respond to EVs remains unclear. Here, we sought to clarify the role of exosomes in improving cardiac function by investigating the effect of cardiomyocyte endocytosis of exosomes from mesenchymal stem cells on acute myocardial infarction (MI). Exposing cardiomyocytes to the culture supernatant of adipose-derived regenerative cells (ADRCs) prevented cardiomyocyte cell damage under hypoxia in vitro. In vivo, the injection of ADRCs into the heart simultaneous with coronary artery ligation decreased overall cardiac infarct area and prevented cardiac rupture after acute MI. Quantitative RT-PCR-based analysis of the expression of 35 known anti-apoptotic and secreted microRNAs (miRNAs) in ADRCs revealed that ADRCs express several of these miRNAs, among which miR-214 was the most abundant. Of note, miR-214 silencing in ADRCs significantly impaired the anti-apoptotic effects of the ADRC treatment on cardiomyocytes in vitro and in vivo To examine cardiomyocyte endocytosis of exosomes, we cultured the cardiomyocytes with ADRC-derived exosomes labeled with the fluorescent dye PKH67 and found that hypoxic culture conditions increased the levels of the labeled exosomes in cardiomyocytes. Chlorpromazine, an inhibitor of clathrin-mediated endocytosis, significantly suppressed the ADRC-induced decrease of hypoxia-damaged cardiomyocytes and also decreased hypoxia-induced cardiomyocyte capture of both labeled EVs and extracellular miR-214 secreted from ADRCs. Our results indicate that clathrin-mediated endocytosis in cardiomyocytes plays a critical role in their uptake of circulating, exosome-associated miRNAs that inhibit apoptosis.
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Affiliation(s)
- Shunsuke Eguchi
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Mikito Takefuji
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Teruhiro Sakaguchi
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Sohta Ishihama
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Yu Mori
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Takuma Tsuda
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Tomonobu Takikawa
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Tatsuya Yoshida
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Koji Ohashi
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Yuuki Shimizu
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Ryo Hayashida
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Kazuhisa Kondo
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Yasuko K Bando
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Noriyuki Ouchi
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Toyoaki Murohara
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
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91
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Lu D, Thum T. RNA-based diagnostic and therapeutic strategies for cardiovascular disease. Nat Rev Cardiol 2019; 16:661-674. [PMID: 31186539 DOI: 10.1038/s41569-019-0218-x] [Citation(s) in RCA: 212] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/03/2019] [Indexed: 12/17/2022]
Abstract
Cardiovascular diseases are the leading cause of death globally and are associated with increasing financial expenditure. With the availability of next-generation sequencing technologies since the early 2000s, non-coding RNAs such as microRNAs, long non-coding RNAs and circular RNAs have been assessed as potential therapeutic targets for numerous diseases, including cardiovascular diseases. In this Review, we summarize current approaches employed to screen for novel coding and non-coding RNA candidates with diagnostic and therapeutic potential in cardiovascular disease, including next-generation sequencing, functional high-throughput RNA screening and single-cell sequencing technologies. Furthermore, we highlight viral-based delivery tools that have been widely used to evaluate the therapeutic utility of both coding and non-coding RNAs in the context of cardiovascular disease. Finally, we discuss the potential of using oligonucleotide-based molecular products such as modified RNA, small interfering RNA and RNA mimics/inhibitors for the treatment of cardiovascular diseases. Given that many non-coding RNAs have not yet been functionally annotated, the number of potential RNA diagnostic and therapeutic targets for cardiovascular diseases will continue to expand for years to come.
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Affiliation(s)
- Dongchao Lu
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany. .,Cardior Pharmaceuticals GmbH, Hannover Medical School, Hannover, Germany. .,National Heart and Lung Institute, Imperial College London, London, UK.
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92
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Wong RK, MacMahon M, Woodside JV, Simpson DA. A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma. BMC Genomics 2019; 20:446. [PMID: 31159762 PMCID: PMC6547578 DOI: 10.1186/s12864-019-5826-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Circulating microRNAs (miRNAs) are attractive non-invasive biomarkers for a variety of conditions due to their stability and altered pathophysiological expression levels. Reliable detection of global expression profiles is required to maximise miRNA biomarker discovery. Although developments in small RNA-Seq technology have improved detection of plasma-based miRNAs, the low RNA content and sequencing bias introduced during library preparation remain challenging. In this study we compare commercially available RNA extraction methods using MagnaZol (Bioo Scientific) or miRNeasy (QIAGEN) and three library preparation methods - CleanTag (TriLink), NEXTflex (Bioo Scientific) and QIAseq (QIAGEN) - which aim to address one or both of these issues. RESULTS Different RNA extractions and library preparation protocols result in differential detection of miRNAs. A greater proportion of reads mapped to miRNAs in libraries prepared with MagnaZol RNA than with miRNeasy RNA. Libraries prepared using QIAseq demonstrated the greatest miRNA diversity with many more very low abundance miRNAs detected (~ 2-3 fold more with < 10 reads), whilst CleanTag detected the fewest individual miRNAs and considerably over-represented miR-486-5p. Libraries prepared with QIAseq had the strongest correlation with RT-qPCR quantification. Analysis of unique molecular indices (UMIs) incorporated in the QIAseq protocol indicate that little PCR bias is introduced during small RNA library preparation. CONCLUSIONS Small RNAs were consistently detected using all RNA extraction and library preparation protocols tested, but with some miRNAs at significantly different levels. Choice of the most suitable protocol should be informed by the relative importance of minimising the total sequencing required, detection of rare miRNAs or absolute quantification.
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Affiliation(s)
- Ryan K.Y. Wong
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7BL UK
| | - Meabh MacMahon
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7BL UK
| | - Jayne V. Woodside
- Nutrition Group, Institute for Global Food Security (Centre for Public Health), School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Institute of Clinical Science A (First Floor), Grosvenor Road, Belfast, BT12 6BJ UK
| | - David A. Simpson
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7BL UK
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93
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Akat KM, Lee YA, Hurley A, Morozov P, Max KE, Brown M, Bogardus K, Sopeyin A, Hildner K, Diacovo TG, Neurath MF, Borggrefe M, Tuschl T. Detection of circulating extracellular mRNAs by modified small-RNA-sequencing analysis. JCI Insight 2019; 5:127317. [PMID: 30973829 DOI: 10.1172/jci.insight.127317] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Extracellular mRNAs (ex-mRNAs) potentially supersede extracellular miRNAs (ex-miRNAs) and other RNA classes as biomarkers. We performed conventional small-RNA-sequencing (sRNA-seq) and sRNA-seq with T4 polynucleotide kinase (PNK) end-treatment of total exRNA isolated from serum and platelet-poor EDTA, ACD, and heparin plasma to study the effect on ex-mRNA capture. Compared to conventional sRNA-seq PNK-treatment increased the detection of informative ex-mRNAs reads up to 50-fold. The exRNA pool was dominated by hematopoietic cells and platelets, with additional contribution from the liver. About 60% of the 15- to 42-nt reads originated from the coding sequences, in a pattern reminiscent of ribosome-profiling. Blood sample type had a considerable influence on the exRNA profile. On average approximately 350 to 1,100 distinct ex-mRNA transcripts were detected depending on plasma type. In serum, additional transcripts from neutrophils and hematopoietic cells increased this number to near 2,300. EDTA and ACD plasma showed a destabilizing effect on ex mRNA and non-coding RNA ribonucleoprotein complexes compared to other plasma types. In a proof-of-concept study, we investigated differences between the exRNA profiles of patients with acute coronary syndrome (ACS) and healthy controls. The improved tissue resolution of ex mRNAs after PNK-treatment enabled us to detect a neutrophil-signature in ACS that escaped detection by ex miRNA analysis.
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Affiliation(s)
| | | | - Arlene Hurley
- Center for Translational Science, The Rockefeller University, New York, New York, USA
| | | | | | | | | | | | - Kai Hildner
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Kussmaul Campus for Medical Research, Erlangen, Bavaria, Germany
| | - Thomas G Diacovo
- Departments of Pediatrics and Cell Biology and Pathology, Columbia University Medical Center, New York, New York, USA
| | - Markus F Neurath
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Kussmaul Campus for Medical Research, Erlangen, Bavaria, Germany
| | - Martin Borggrefe
- First Department of Medicine, University Medical Center Mannheim, Faculty of Medicine Mannheim, University of Heidelberg, European Center for AngioScience, and DZHK (German Center for Cardiovascular Research), partner site Heidelberg/Mannheim, Mannheim, Baden-Wuerttemberg, Germany
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94
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Rozowsky J, Kitchen RR, Park JJ, Galeev TR, Diao J, Warrell J, Thistlethwaite W, Subramanian SL, Milosavljevic A, Gerstein M. exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling. Cell Syst 2019; 8:352-357.e3. [PMID: 30956140 DOI: 10.1016/j.cels.2019.03.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/31/2019] [Accepted: 03/06/2019] [Indexed: 01/09/2023]
Abstract
Small RNA sequencing has been widely adopted to study the diversity of extracellular RNAs (exRNAs) in biofluids; however, the analysis of exRNA samples can be challenging: they are vulnerable to contamination and artifacts from different isolation techniques, present in lower concentrations than cellular RNA, and occasionally of exogenous origin. To address these challenges, we present exceRpt, the exRNA-processing toolkit of the NIH Extracellular RNA Communication Consortium (ERCC). exceRpt is structured as a cascade of filters and quantifications prioritized based on one's confidence in a given set of annotated RNAs. It generates quality control reports and abundance estimates for RNA biotypes. It is also capable of characterizing mappings to exogenous genomes, which, in turn, can be used to generate phylogenetic trees. exceRpt has been used to uniformly process all ∼3,500 exRNA-seq datasets in the public exRNA Atlas and is available from genboree.org and github.gersteinlab.org/exceRpt.
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Affiliation(s)
- Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Robert R Kitchen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jonathan J Park
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Timur R Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - James Diao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - William Thistlethwaite
- Bioinformatics Research Laboratory, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
| | - Sai L Subramanian
- Bioinformatics Research Laboratory, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
| | - Aleksandar Milosavljevic
- Bioinformatics Research Laboratory, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA.
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95
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Xu EG, Khursigara AJ, Li S, Esbaugh AJ, Dasgupta S, Volz DC, Schlenk D. mRNA-miRNA-Seq Reveals Neuro-Cardio Mechanisms of Crude Oil Toxicity in Red Drum ( Sciaenops ocellatus). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:3296-3305. [PMID: 30816040 DOI: 10.1021/acs.est.9b00150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) present in crude oil can cause global gene dysregulation and developmental impairment in fish. However, the mechanisms that alter gene regulation are not well understood. In this study, larval red drum ( Sciaenops ocellatus) were exposed to water accommodated fractions of source oil (6.8, 13.7, and 35.9 μg/L total PAHs) and weathered slick oil (4.7, 8.1, and 18.0 μg/L total PAHs) from the Deepwater Horizon (DWH) oil spill. The global mRNA-microRNA functional networks associated with the toxicity of DWH oil were explored by next-generation sequencing and in-depth bioinformatics analyses. Both source and slick oil significantly altered the expression of miR-18a, miR-27b, and miR-203a across all exposure concentrations. Consistent with the observed concentration-dependent morphological changes, the target mRNAs of these microRNAs were predominantly involved in neuro-cardio system development processes and associated key signaling pathways such as axonal guidance signaling, cAMP-response-element-binding protein signaling in neurons, calcium signaling, and nuclear-factor-of-activated T cells signaling in cardiac hypertrophy. The results indicated that the developmental toxicity of crude oil may result from the abnormal expression of microRNAs and associated target genes, especially for the nervous system. Moreover, we provide a case study for systematic toxicity evaluation leveraging mRNA-microRNA-seq data using nonmodel species.
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Affiliation(s)
- Elvis Genbo Xu
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
- Department of Chemical Engineering , McGill University , Montreal , Quebec H3A 0C5 , Canada
| | - Alexis J Khursigara
- Marine Science Institute , University of Texas at Austin , Austin , Texas 78373 , United States
| | - Shuying Li
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
- Institute of Pesticide and Environmental Toxicology , Zhejiang University , Hangzhou 310058 , P. R. China
| | - Andrew J Esbaugh
- Marine Science Institute , University of Texas at Austin , Austin , Texas 78373 , United States
| | - Subham Dasgupta
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
| | - David C Volz
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
| | - Daniel Schlenk
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
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96
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Sadik N, Cruz L, Gurtner A, Rodosthenous RS, Dusoswa SA, Ziegler O, Van Solinge TS, Wei Z, Salvador-Garicano AM, Gyorgy B, Broekman M, Balaj L. Extracellular RNAs: A New Awareness of Old Perspectives. Methods Mol Biol 2019; 1740:1-15. [PMID: 29388131 DOI: 10.1007/978-1-4939-7652-2_1] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Extracellular RNA (exRNA) has recently expanded as a highly important area of study in biomarker discovery and cancer therapeutics. exRNA consists of diverse RNA subpopulations that are normally protected from degradation by incorporation into membranous vesicles or by lipid/protein association. They are found circulating in biofluids, and have proven highly promising for minimally invasive diagnostic and prognostic purposes, particularly in oncology. Recent work has made progress in our understanding of exRNAs-from their biogenesis, compartmentalization, and vesicle packaging to their various applications as biomarkers and therapeutics, as well as the new challenges that arise in isolation and purification for accurate and reproducible analysis. Here we review the most recent advancements in exRNA research.
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Affiliation(s)
- Noah Sadik
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lilian Cruz
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alessandra Gurtner
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Rodosthenis S Rodosthenous
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sophie A Dusoswa
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands.,Amsterdam Infection & Immunity Institute, VU University Medical Center, Amsterdam, The Netherlands.,Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Olivia Ziegler
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Thomas Sebastiaan Van Solinge
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,NeuroDiscovery Center, Harvard Medical School, Boston, MA, USA.,Department of Neurosurgery, VU University Medical Center, Amsterdam, The Netherlands
| | - Zhiyun Wei
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Bence Gyorgy
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Marike Broekman
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Neurosurgery, Brain Center Rudolf Magnus University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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97
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The presence of extracellular microRNAs in the media of cultured Drosophila cells. Sci Rep 2018; 8:17312. [PMID: 30470777 PMCID: PMC6251921 DOI: 10.1038/s41598-018-35531-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 11/07/2018] [Indexed: 12/26/2022] Open
Abstract
While regulatory RNA pathways, such as RNAi, have commonly been described at an intracellular level, studies investigating extracellular RNA species in insects are lacking. In the present study, we demonstrate the presence of extracellular microRNAs (miRNAs) in the cell-free conditioned media of two Drosophila cell lines. More specifically, by means of quantitative real-time PCR (qRT-PCR), we analysed the presence of twelve miRNAs in extracellular vesicles (EVs) and in extracellular Argonaute-1 containing immunoprecipitates, obtained from the cell-free conditioned media of S2 and Cl.8 cell cultures. Next-generation RNA-sequencing data confirmed our qRT-PCR results and provided evidence for selective miRNA secretion in EVs. To our knowledge, this is the first time that miRNAs have been identified in the extracellular medium of cultured cells derived from insects, the most speciose group of animals.
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98
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Oatmen KE, Toro-Salazar OH, Hauser K, Zellars KN, Mason KC, Hor K, Gillan E, Zeiss CJ, Gatti DM, Spinale FG. Identification of a novel microRNA profile in pediatric patients with cancer treated with anthracycline chemotherapy. Am J Physiol Heart Circ Physiol 2018; 315:H1443-H1452. [DOI: 10.1152/ajpheart.00252.2018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Anthracycline chemotherapy (AC) is associated with decline in left ventricular ejection fraction (LVEF), yet the mechanisms remain unclear. Although changes in microRNAs (miRs) have been identified in adult cardiovascular disease, miR profiles in pediatric patients with AC have not been well studied. The goal of this study was to examine miR profiles (unbiased array) in pediatric patients with AC compared with age-matched referent normal patients. We hypothesize that pediatric patients with AC will express a unique miR profile at the initiation and completion of therapy and will be related to LVEF. Serum was collected in pediatric patients (10–22 yr, n = 12) with newly diagnosed malignancy requiring AC within 24–48 h after the initiation of therapy (30–60 mg/m2) and ~1 yr after completing therapy. A custom microarray of 84 miRs associated with cardiovascular disease was used (quantitative RT-PCR) and indexed to referent normal profiles (13–17 yr, n = 17). LVEF was computed by cardiac MRI. LVEF fell from AC initiation at ~1 yr after AC completion (64.28 ± 1.78% vs. 57.53 ± 0.95%, respectively, P = 0.004). Of the 84 miRs profiled, significant shifts in 17 miRs occurred relative to referent normal ( P ≤ 0.05). Moreover, the functional domain of miRs associated with myocardial differentiation and development fell over threefold at the completion of AC ( P ≤ 0.05). Moreover, eight miRs were significantly downregulated after AC completion in those patients with the greatest decline in LVEF (≥10%, P < 0.05). This study demonstrates, for the first time, that changes in miR expression occur in pediatric patients with AC. These findings suggest that miRs are a potential strategy for the early identification of patients with AC susceptible to left ventricular dysfunction. NEW & NOTEWORTHY Although anthracycline chemotherapy (AC) is effective for a number of pediatric cancers, an all too often consequence of AC is the development of left ventricular failure. The present study identified that specific shifts in the pattern of microRNAs, which regulate myocardial growth, function, and viability, occurred during and after AC in pediatric patients, whereby the magnitude of this shift was associated with the degree of left ventricular failure.
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Affiliation(s)
- Kelsie E. Oatmen
- University of South Carolina School of Medicine, Columbia, South Carolina
| | | | - Kristine Hauser
- Connecticut Children’s Medical Center, Hartford, Connecticut
| | - Kia N. Zellars
- University of South Carolina School of Medicine, Columbia, South Carolina
| | - Kathryn C. Mason
- University of South Carolina School of Medicine, Columbia, South Carolina
- William Jennings Bryan Dorn Veterans Affairs Medical Center, Columbia, South Carolina
| | - Kan Hor
- Nationwide Children’s Hospital, Columbus, Ohio
| | - Eileen Gillan
- Connecticut Children’s Medical Center, Hartford, Connecticut
| | | | | | - Francis G. Spinale
- University of South Carolina School of Medicine, Columbia, South Carolina
- William Jennings Bryan Dorn Veterans Affairs Medical Center, Columbia, South Carolina
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99
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Ageing alters the severity of Sunitinib-induced cardiotoxicity: Investigating the mitogen activated kinase kinase 7 pathway association. Toxicology 2018; 411:49-59. [PMID: 30393206 DOI: 10.1016/j.tox.2018.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 09/28/2018] [Accepted: 10/24/2018] [Indexed: 02/07/2023]
Abstract
Anti-cancer drug Sunitinib is linked to adverse cardiovascular events, which have shown to involve mitogen activated kinase kinase 7 (MKK7) pathway. Sunitinib-induced cardiotoxicity in 3, 12 and 24 months old male Sprague-Dawley rats and MKK7 expression and activation was investigated using the Langendorff perfused heart model followed by Western blot analysis. Cardiac function and infarct size were measured during/after 125 min of Sunitinib treatment. Left ventricular cardiac samples were analysed by qRT-PCR for expression of MKK7 mRNA and cardiac injury associated microRNAs. Infarct size was increased in all Sunitinib treated age groups. Haemodynamic alterations were observed following Sunitinib administration. Left ventricular developed pressure (LVDP) was decreased in all age groups, while heart rate (HR) was decreased in 3 and 12 months groups. Sunitinib treatment decreased the expression of miR-27a in all age groups, while miR-133a and miR-133b levels were increased in 3 months and decreased in 24 months groups. MKK7 mRNA and p-MKK7 levels were decreased in the 3 months group after Sunitinib treatment. MKK7 mRNA level was increased in 24 months group and p-MKK7 levels were increased in 12 months group following Sunitinib treatment. This study highlights the importance and impact of ageing and anti-cancer therapy-induced cardiotoxicity.
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100
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Turchinovich A, Baranova A, Drapkina O, Tonevitsky A. Cell-Free Circulating Nucleic Acids as Early Biomarkers for NAFLD and NAFLD-Associated Disorders. Front Physiol 2018; 9:1256. [PMID: 30294278 PMCID: PMC6158334 DOI: 10.3389/fphys.2018.01256] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/20/2018] [Indexed: 12/16/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the worldwide most common cause of chronic liver pathology, which prevalence strongly correlates with the increasing incidence of diabetes, obesity and metabolic syndrome in the general population. Simple steatosis, the earliest NAFLD stage, usually remains asymptomatic, and appropriate changes in the lifestyle, as well as the diet, can reverse the affected liver into the healthy state. The potential of simple steatosis to progress into severe fibrotic stages and to facilitate carcinogenesis necessitates timely NAFLD detection and risk stratification in community-based healthcare settings. Since their initial discovery a decade ago, extracellular circulating miRNAs have been found in all human biological fluids including blood and shown to hold great promises as non-invasive biomarkers. Normally, intracellular miRNAs participate in the regulation of gene expression, but once released by dying/dead cells they remain highly stable in the extracellular environment for prolonged periods. Therefore, circulating miRNA profiles can reflect the ongoing pathogenic processes in body's tissues and organs, and enable highly sensitive non-invasive diagnosis of multiple disorders. A non-urgent character of the NAFLD-related decision-making justifies the use of chronic liver diseases as an excellent test case for examining the practical utility of circulating miRNAs as biomarkers for longitudinal monitoring of human health. In this review, we summarize the state-of-the-art in the field of early diagnosis of NAFLD using circulating blood miRNAs, and stress the necessity of additional experimental validation of their diagnostic potential. We further emphasize on the potential diagnostics promises of other cell-free RNA species found in human biological fluids.
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Affiliation(s)
- Andrey Turchinovich
- SciBerg e.Kfm, Mannheim, Germany
- Molecular Epidemiology C080, German Cancer Research Center, Heidelberg, Germany
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, United States
- Research Center for Medical Genetics, Moscow, Russia
- Atlas Biomed Group, Moscow, Russia
| | - Oksana Drapkina
- Federal State Institution National Research Center for Preventive Medicine, Moscow, Russia
| | - Alexander Tonevitsky
- Department of Cell Biology, Higher School of Economics, Moscow, Russia
- art photonics GmbH, Berlin, Germany
- SRC Bioclinicum, Moscow, Russia
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