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Pisklova M, Osmak G. Unveiling MiRNA-124 as a biomarker in hypertrophic cardiomyopathy: An innovative approach using machine learning and intelligent data analysis. Int J Cardiol 2024; 410:132220. [PMID: 38815672 DOI: 10.1016/j.ijcard.2024.132220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is a widespread hereditary cardiac pathology characterized by thickened heart walls and rearrangement of cardiomyocytes. Despite extensive research, the mechanisms underlying HCM development remain poorly understood, impeding the development of effective therapeutic and diagnostic strategies. Recent studies have suggested a polygenic nature of HCM development alongside monogenic forms. Transcriptomic profiling is a valuable tool for investigating such diseases. In this study, we propose a novel approach to study regulatory microRNAs (miRNAs) in the context of HCM, utilizing state-of-the-art data analysis tools. METHODS AND RESULTS Our method involves applying the Monte Carlo simulation and machine learning algorithm to transcriptomic data to generate high-capacity classifiers for HCM. From these classifiers, we extract key genes crucial for their performance, resulting in the identification of 16 key genes. Subsequently, we narrow down the pool of miRNAs by selecting those that may target the greatest number of key genes within the best models. We particularly focused on miR-124-3p, which we validated to have an association with HCM on an independent dataset. Subsequent investigation of its function revealed involvement of miR-124-3p in the RhoA signaling pathway. CONCLUSIONS In this study we propose a new approach to analyze transcriptomic data to search for microRNAs associated with a disease. Using this approach for transcriptomic profiling data of patients with HCM, we identified miR-124-3p as a potential regulator of the RhoA signaling pathway in the pathogenesis of HCM.
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Affiliation(s)
- Maria Pisklova
- E.I. Chazov National Medical Research Center for Cardiology, Academician Chazov st. 15a, 121552 Moscow, Russia; Pirogov Russian National Research Medical University, Ostrovitianov st. 1, 117997 Moscow, Russia
| | - German Osmak
- E.I. Chazov National Medical Research Center for Cardiology, Academician Chazov st. 15a, 121552 Moscow, Russia; Pirogov Russian National Research Medical University, Ostrovitianov st. 1, 117997 Moscow, Russia.
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Machado HC, Bispo S, Dallagiovanna B. miR-6087 Might Regulate Cell Cycle–Related mRNAs During Cardiomyogenesis of hESCs. Bioinform Biol Insights 2023; 17:11779322231161918. [PMID: 37020502 PMCID: PMC10069004 DOI: 10.1177/11779322231161918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/16/2023] [Indexed: 04/03/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that act as negative regulators of gene expression at the post-transcriptional level, promoting mRNA degradation or translation repression. Despite the well-described presence of miRNAs in various human tissues, there is still a lack of information about the relationship between miRNAs and the translation regulation in human embryonic stem cells (hESCs) during cardiomyogenesis. Here, we investigate RNA-seq data from hESCs, focusing on distinct stages of cardiomyogenesis and searching for polysome-bound miRNAs that could be involved in translational regulation. We identify miR-6087 as a differentially expressed miRNA at latest steps of cardiomyocyte differentiation. We analyzed the coexpression pattern between the differentially expressed mRNAs and miR-6087, evaluating whether they are predicted targets of the miRNA. We arranged the genes into an interaction network and identified BLM, RFC4, RFC3, and CCNA2 as key genes of the network. A post hoc analysis of the key genes suggests that miR-6087 could act as a regulator of the cell cycle in hESC during cardiomyogenesis.
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Affiliation(s)
- Hellen Cristine Machado
- Laboratory of Basic Stem-Cell Biology,
Instituto Carlos Chagas – FIOCRUZ-PR, Curitiba, Brazil
| | - Saloe Bispo
- Laboratory of Molecular and Systems
Biology of Trypanosomatids, Instituto Carlos Chagas – FIOCRUZ-PR, Curitiba,
Brazil
| | - Bruno Dallagiovanna
- Laboratory of Basic Stem-Cell Biology,
Instituto Carlos Chagas – FIOCRUZ-PR, Curitiba, Brazil
- Bruno Dallagiovanna, Laboratory of Basic
Stem-Cell Biology, Instituto Carlos Chagas – FIOCRUZ-PR, Rua Professor Algacyr
Munhoz Mader, 3775, Curitiba 81350-010, Brazil.
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The expression profiling of serum miR-92a, miR-134 and miR-375 in acute ischemic stroke. Future Sci OA 2022; 8:FSO829. [PMID: 36874371 PMCID: PMC9979103 DOI: 10.2144/fsoa-2022-0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/17/2023] [Indexed: 02/22/2023] Open
Abstract
Aim To investigate the expression profile and diagnostic potentials of serum miR-92a, 134, and 375 in acute ischemic stroke (AIS) patients. Materials & methods Serum miRs-92a, 134, and 375 expression profiles were estimated by qRT-PCR for 70 AIS patients, age-matched with 25 control subjects. Their diagnostic potential was estimated by ROC analysis. Results Down-expression of miR-92a and miR-375 was found (56; 96.5%; -1.86 ± 1.36; and 53; 91.4%; -1.63 ± 1.38, respectively), while miR-134 showed a predominant upregulation (46; 79.3%; 0.853 ± 1.34). The diagnostic accuracy was the highest for miR-92a and miR-375 (area under the curve = 0.9183 and 0.898, respectively), with greater specificity for miR-375 (Sp = 96%). Conclusion Serum miR-92a and miR-375 could be promising early detective biomarkers of AIS.
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Pisklova M, Osmak G, Favorova O. Regulation of SMAD Signaling Pathway by miRNAs Associated with Myocardial Fibrosis: In silico Analysis of Target Gene Networks. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:832-838. [PMID: 36171647 DOI: 10.1134/s0006297922080144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 06/16/2023]
Abstract
Hypertrophic cardiomyopathy (HCM) is a hereditary heart disease caused by mutations in the sarcomere genes, which is accompanied by myocardial fibrosis leading to progressive heart failure and arrhythmias. Recent studies suggest that the HCM development involves dysregulation of gene expression. Among the molecules involved in this process are microRNAs (miRNAs), which are short non-coding RNAs. Typically, one miRNA regulates several target genes post-transcriptionally, hence, it might be difficult to determine the role of a particular miRNA in the disease pathogenesis. In this study, using the PubMed database, we selected 15 miRNAs whose expression is associated with myocardial fibrosis, one of the critical pathological processes in HCM. We then used an earlier developed algorithm to search in silico for the signaling pathways regulated by these miRNAs and found that ten of them participate in the regulation of the TGF-β/SMAD signaling pathway. At the same time, among the SMAD signaling pathway genes, the target of the most identified miRNAs was the MYC gene, which is involved in the development of fibrosis in some tissues. In our earlier work, we found that the TGF-β/SMAD pathway is also regulated by a set of other miRNAs associated with the myocardial hypertrophy in HCM. The fact that two sets of miRNAs identified in two independent bioinformatic studies are involved in the regulation of the same signaling pathway indicates that the SMAD signaling cascade is indeed a key element in the regulation of pathological processes in HCM. The obtained data might contribute to understanding pathological processes underlying HCM development.
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Affiliation(s)
- Maria Pisklova
- Chazov National Medical Research Center of Cardiology, Moscow, 121552, Russia.
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - German Osmak
- Chazov National Medical Research Center of Cardiology, Moscow, 121552, Russia
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Olga Favorova
- Chazov National Medical Research Center of Cardiology, Moscow, 121552, Russia
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
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Matveeva NA, Baulina NM, Kiselev IS, Titov BV, Favorova OO. MiRNA miR-375 as a Multifunctional Regulator of the Cardiovascular System. Mol Biol 2022. [DOI: 10.1134/s0026893322020078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Orzeł-Gajowik K, Milewski K, Zielińska M. Insight into microRNAs-Mediated Communication between Liver and Brain: A Possible Approach for Understanding Acute Liver Failure? Int J Mol Sci 2021; 23:224. [PMID: 35008650 PMCID: PMC8745738 DOI: 10.3390/ijms23010224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 01/11/2023] Open
Abstract
Acute liver failure (ALF) is a life-threatening consequence of hepatic function rapid loss without preexisting liver disease. ALF may result in a spectrum of neuropsychiatric symptoms that encompasses cognitive impairment, coma, and often death, collectively defined as acute hepatic encephalopathy. Micro RNAs are small non-coding RNAs that modulate gene expression and are extensively verified as biomarker candidates in various diseases. Our systematic literature review based on the last decade's reports involving a total of 852 ALF patients, determined 205 altered circulating miRNAs, of which 25 miRNAs were altered in the blood, regardless of study design and methodology. Selected 25 miRNAs, emerging predominantly from the analyses of samples obtained from acetaminophen overdosed patients, represent the most promising biomarker candidates for a diagnostic panel for symptomatic ALF. We discussed the role of selected miRNAs in the context of tissue-specific origin and its possible regulatory role for molecular pathways involved in blood-brain barrier function. The defined several common pathways for 15 differently altered miRNAs were relevant to cellular community processes, indicating loss of intercellular, structural, and functional components, which may result in blood-brain barrier impairment and brain dysfunction. However, a causational relationship between circulating miRNAs differential expression, and particular clinical features of ALF, has to be demonstrated in a further study.
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Affiliation(s)
| | | | - Magdalena Zielińska
- Department of Neurotoxicology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Str., 02-106 Warsaw, Poland; (K.O.-G.); (K.M.)
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Osmak G, Baulina N, Kiselev I, Favorova O. MiRNA-Regulated Pathways for Hypertrophic Cardiomyopathy: Network-Based Approach to Insight into Pathogenesis. Genes (Basel) 2021; 12:genes12122016. [PMID: 34946964 PMCID: PMC8701189 DOI: 10.3390/genes12122016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 12/26/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common hereditary heart disease. The wide spread of high-throughput sequencing casts doubt on its monogenic nature, suggesting the presence of mechanisms of HCM development independent from mutations in sarcomeric genes. From this point of view, HCM may arise from the interactions of several HCM-associated genes, and from disturbance of regulation of their expression. We developed a bioinformatic workflow to study the involvement of signaling pathways in HCM development through analyzing data on human heart-specific gene expression, miRNA-target gene interactions, and protein-protein interactions, available in open databases. Genes regulated by a pool of miRNAs contributing to human cardiac hypertrophy, namely hsa-miR-1-3p, hsa-miR-19b-3p, hsa-miR-21-5p, hsa-miR-29a-3p, hsa-miR-93-5p, hsa-miR-133a-3p, hsa-miR-155-5p, hsa-miR-199a-3p, hsa-miR-221-3p, hsa-miR-222-3p, hsa-miR-451a, and hsa-miR-497-5p, were considered. As a result, we pinpointed a module of TGFβ-mediated SMAD signaling pathways, enriched by targets of the selected miRNAs, that may contribute to the cardiac remodeling in HCM. We suggest that the developed network-based approach could be useful in providing a more accurate glimpse on pathological processes in the disease pathogenesis.
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Affiliation(s)
- German Osmak
- Laboratory of Functional Genomics of Cardiovascular Disorders, National Medical Research Center for Cardiology, 121552 Moscow, Russia; (N.B.); (I.K.); (O.F.)
- Laboratory of Medical Genomics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Correspondence:
| | - Natalia Baulina
- Laboratory of Functional Genomics of Cardiovascular Disorders, National Medical Research Center for Cardiology, 121552 Moscow, Russia; (N.B.); (I.K.); (O.F.)
- Laboratory of Medical Genomics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Ivan Kiselev
- Laboratory of Functional Genomics of Cardiovascular Disorders, National Medical Research Center for Cardiology, 121552 Moscow, Russia; (N.B.); (I.K.); (O.F.)
- Laboratory of Medical Genomics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Olga Favorova
- Laboratory of Functional Genomics of Cardiovascular Disorders, National Medical Research Center for Cardiology, 121552 Moscow, Russia; (N.B.); (I.K.); (O.F.)
- Laboratory of Medical Genomics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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Zubkova E, Evtushenko E, Beloglazova I, Osmak G, Koshkin P, Moschenko A, Menshikov M, Parfyonova Y. Analysis of MicroRNA Profile Alterations in Extracellular Vesicles From Mesenchymal Stromal Cells Overexpressing Stem Cell Factor. Front Cell Dev Biol 2021; 9:754025. [PMID: 34869342 PMCID: PMC8634878 DOI: 10.3389/fcell.2021.754025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/29/2021] [Indexed: 11/13/2022] Open
Abstract
Mesenchymal stem/stromal cells (MSCs) represent a promising tool to treat cardiovascular diseases. One mode of action through which MSCs exert their protective effects is secretion of extracellular vesicles (EVs). Recently, we demonstrated that rat adipose-derived MSC-overexpressing stem cell factor (SCF) can induce endogenous regenerative processes and improve cardiac function. In the present work, we isolated EVs from intact, GFP- or SCF-overexpressing rat MSC and analyzed microarray datasets of their miRNA cargo. We uncovered a total of 95 differentially expressed miRNAs. We did not observe significant differences between EVs from GFP-MSC and SCF-MSC that may indicate intrinsic changes in MSC after viral transduction. About 80 miRNAs were downregulated in EVs from both SCF- or GFP-MSC. We assembled the miRNA-based network and found several nodes of target genes among which Vim Sept3 and Vsnl1 are involved in regulation of cellular migration that is consistent with our previous EVs data. Topological analyses of the network also revealed that among the downregulated miRNA-rno-miRNA-128-3p that regulates plenty of targets is presumably associated with chemokine signaling pathways. Overall, our data suggest that genetic modification of MSC has a great impact on their miRNA composition and provide novel insights into the regulatory networks underlying EV effects.
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Affiliation(s)
- Ekaterina Zubkova
- Federal State Budgetary Institution (FSBI), "National Medical Research Center of Cardiology," Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Irina Beloglazova
- Federal State Budgetary Institution (FSBI), "National Medical Research Center of Cardiology," Ministry of Health of the Russian Federation, Moscow, Russia
| | - German Osmak
- Federal State Budgetary Institution (FSBI), "National Medical Research Center of Cardiology," Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Alexander Moschenko
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, Russia
| | - Mikhail Menshikov
- Federal State Budgetary Institution (FSBI), "National Medical Research Center of Cardiology," Ministry of Health of the Russian Federation, Moscow, Russia
| | - Yelena Parfyonova
- Federal State Budgetary Institution (FSBI), "National Medical Research Center of Cardiology," Ministry of Health of the Russian Federation, Moscow, Russia
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