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Varsha KK, Yang X, Cannon AS, Zhong Y, Nagarkatti M, Nagarkatti P. Identification of miRNAs that target Fcγ receptor-mediated phagocytosis during macrophage activation syndrome. Front Immunol 2024; 15:1355315. [PMID: 38558807 PMCID: PMC10981272 DOI: 10.3389/fimmu.2024.1355315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
Macrophage activation syndrome (MAS) is a life-threatening complication of systemic juvenile arthritis, accompanied by cytokine storm and hemophagocytosis. In addition, COVID-19-related hyperinflammation shares clinical features of MAS. Mechanisms that activate macrophages in MAS remain unclear. Here, we identify the role of miRNA in increased phagocytosis and interleukin-12 (IL-12) production by macrophages in a murine model of MAS. MAS significantly increased F4/80+ macrophages and phagocytosis in the mouse liver. Gene expression profile revealed the induction of Fcγ receptor-mediated phagocytosis (FGRP) and IL-12 production in the liver. Phagocytosis pathways such as High-affinity IgE receptor is known as Fc epsilon RI -signaling and pattern recognition receptors involved in the recognition of bacteria and viruses and phagosome formation were also significantly upregulated. In MAS, miR-136-5p and miR-501-3p targeted and caused increased expression of Fcgr3, Fcgr4, and Fcgr1 genes in FGRP pathway and consequent increase in phagocytosis by macrophages, whereas miR-129-1-3p and miR-150-3p targeted and induced Il-12. Transcriptome analysis of patients with MAS revealed the upregulation of FGRP and FCGR gene expression. A target analysis of gene expression data from a patient with MAS discovered that miR-136-5p targets FCGR2A and FCGR3A/3B, the human orthologs of mouse Fcgr3 and Fcgr4, and miR-501-3p targets FCGR1A, the human ortholog of mouse Fcgr1. Together, we demonstrate the novel role of miRNAs during MAS pathogenesis, thereby suggesting miRNA mimic-based therapy to control the hyperactivation of macrophages in patients with MAS as well as use overexpression of FCGR genes as a marker for MAS classification.
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Affiliation(s)
| | | | | | | | | | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina School of Medicine, Columbia, SC, United States
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2
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Polo-Generelo S, Rodríguez-Mateo C, Torres B, Pintor-Tortolero J, Guerrero-Martínez JA, König J, Vázquez J, Bonzón-Kulichenco E, Padillo-Ruiz J, de la Portilla F, Reyes JC, Pintor-Toro JA. Serpine1 mRNA confers mesenchymal characteristics to the cell and promotes CD8+ T cells exclusion from colon adenocarcinomas. Cell Death Discov 2024; 10:116. [PMID: 38448406 PMCID: PMC10917750 DOI: 10.1038/s41420-024-01886-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/08/2024] Open
Abstract
Serine protease inhibitor clade E member 1 (SERPINE1) inhibits extracellular matrix proteolysis and cell detachment. However, SERPINE1 expression also promotes tumor progression and plays a crucial role in metastasis. Here, we solve this apparent paradox and report that Serpine1 mRNA per se, independent of its protein-coding function, confers mesenchymal properties to the cell, promoting migration, invasiveness, and resistance to anoikis and increasing glycolytic activity by sequestering miRNAs. Expression of Serpine1 mRNA upregulates the expression of the TRA2B splicing factor without affecting its mRNA levels. Through transcriptional profiling, we found that Serpine1 mRNA expression downregulates through TRA2B the expression of genes involved in the immune response. Analysis of human colon tumor samples showed an inverse correlation between SERPINE1 mRNA expression and CD8+ T cell infiltration, unveiling the potential value of SERPINE1 mRNA as a promising therapeutic target for colon tumors.
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Affiliation(s)
- Salvador Polo-Generelo
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - Cristina Rodríguez-Mateo
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - Belén Torres
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - José Pintor-Tortolero
- Colorectal Surgery Unit, Department of General and Digestive Surgery, Virgen del Rocío University Hospital, IBIS, CSIC, University of Sevilla, Sevilla, Spain
| | - José A Guerrero-Martínez
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Jesús Vázquez
- Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
| | - Elena Bonzón-Kulichenco
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Javier Padillo-Ruiz
- Hepatobiliary Surgery Unit, Department of General and Digestive Surgery, Virgen del Rocío University Hospital, IBIS, CSIC, University of Sevilla, Sevilla, Spain
| | - Fernando de la Portilla
- Colorectal Surgery Unit, Department of General and Digestive Surgery, Virgen del Rocío University Hospital, IBIS, CSIC, University of Sevilla, Sevilla, Spain
| | - José C Reyes
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - José A Pintor-Toro
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain.
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3
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Huang W, Paul D, Calin GA, Bayraktar R. miR-142: A Master Regulator in Hematological Malignancies and Therapeutic Opportunities. Cells 2023; 13:84. [PMID: 38201290 PMCID: PMC10778542 DOI: 10.3390/cells13010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/29/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
MicroRNAs (miRNAs) are a type of non-coding RNA whose dysregulation is frequently associated with the onset and progression of human cancers. miR-142, an ultra-conserved miRNA with both active -3p and -5p mature strands and wide-ranging physiological targets, has been the subject of countless studies over the years. Due to its preferential expression in hematopoietic cells, miR-142 has been found to be associated with numerous types of lymphomas and leukemias. This review elucidates the multifaceted role of miR-142 in human physiology, its influence on hematopoiesis and hematopoietic cells, and its intriguing involvement in exosome-mediated miR-142 transport. Moreover, we offer a comprehensive exploration of the genetic and molecular landscape of the miR-142 genomic locus, highlighting its mutations and dysregulation within hematological malignancies. Finally, we discuss potential avenues for harnessing the therapeutic potential of miR-142 in the context of hematological malignancies.
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Affiliation(s)
- Wilson Huang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (W.H.); (G.A.C.)
| | - Doru Paul
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA;
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (W.H.); (G.A.C.)
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Recep Bayraktar
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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4
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Mohammadi-Kordkhayli M, Sahraian MA, Ghorbani S, Mansouri F, Talebi F, Noorbakhsh F, Saboor-Yaraghi AA. Vitamins A and D Enhance the Expression of Ror-γ-Targeting miRNAs in a Mouse Model of Multiple Sclerosis. Mol Neurobiol 2023; 60:5853-5865. [PMID: 37353624 DOI: 10.1007/s12035-023-03427-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/05/2023] [Indexed: 06/25/2023]
Abstract
Autoreactive T cells, particularly those characterized by a Th17 phenotype, exert significant influence on the pathogenesis of multiple sclerosis (MS). The present study aimed to elucidate the impact of individual and combined administration of vitamin A and D on neuroinflammation, and microRNAs (miRNAs) involved in T helper (Th)17 development, utilizing a murine model of experimental autoimmune encephalomyelitis (EAE). EAE was induced in C57BL/6 mice, and 3 days prior to immunization, intraperitoneal injections of vitamins A and D or their combination were administered. Th17 cell percentages were determined in splenocytes utilizing intracellular staining and flow cytometry. Furthermore, the expression of Ror γ-t, miR-98-5p and Let-7a-5p, was measured in both splenocytes and spinal cord tissues using RT-PCR. Treatment with vitamin A and D resulted in a reduction in both disease severity in EAE mice. Treated mice showed a decreased frequency of Th17 cells and lower expression levels of IL17 and Ror γ-t in splenocytes and spinal cord. The spinal cord tissues and splenocytes of mice treated with vitamins A, D, and combined A+D showed a significant upregulation of miR-98-5p and Let-7a-5p compared to the EAE group. Statistical analysis indicated a strong negative correlation between miR-98-5p and Let-7a-5p levels in splenocytes and Ror-t expression. Our findings indicate that the administration of vitamins A and D exerts a suppressive effect on neuroinflammation in EAE that is associated with a reduction in the differentiation of T cells into the Th17 phenotype and is mediated by the upregulation of miR-98-5p and Let-7a-5p, which target the Ror γ-t.
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Affiliation(s)
- Marziyeh Mohammadi-Kordkhayli
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Alberta, Canada
| | - Mohammad Ali Sahraian
- Sina MS Research Center, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Samira Ghorbani
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Alberta, Canada
| | - Fatemeh Mansouri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Farideh Talebi
- Immunoregulation Research Center, Shahed University, Tehran, Iran
| | - Farshid Noorbakhsh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ali Akbar Saboor-Yaraghi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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5
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Hackl LM, Fenn A, Louadi Z, Baumbach J, Kacprowski T, List M, Tsoy O. Alternative splicing impacts microRNA regulation within coding regions. NAR Genom Bioinform 2023; 5:lqad081. [PMID: 37705830 PMCID: PMC10495541 DOI: 10.1093/nargab/lqad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/04/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that bind to target sites in different gene regions and regulate post-transcriptional gene expression. Approximately 95% of human multi-exon genes can be spliced alternatively, which enables the production of functionally diverse transcripts and proteins from a single gene. Through alternative splicing, transcripts might lose the exon with the miRNA target site and become unresponsive to miRNA regulation. To check this hypothesis, we studied the role of miRNA target sites in both coding and non-coding regions using six cancer data sets from The Cancer Genome Atlas (TCGA) and Parkinson's disease data from PPMI. First, we predicted miRNA target sites on mRNAs from their sequence using TarPmiR. To check whether alternative splicing interferes with this regulation, we trained linear regression models to predict miRNA expression from transcript expression. Using nested models, we compared the predictive power of transcripts with miRNA target sites in the coding regions to that of transcripts without target sites. Models containing transcripts with target sites perform significantly better. We conclude that alternative splicing does interfere with miRNA regulation by skipping exons with miRNA target sites within the coding region.
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Affiliation(s)
- Lena Maria Hackl
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
| | - Amit Fenn
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Zakaria Louadi
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Campusvej 50, 5230 Odense, Denmark
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Olga Tsoy
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
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6
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Saulle I, Garziano M, Cappelletti G, Limanaqi F, Strizzi S, Vanetti C, Lo Caputo S, Poliseno M, Santantonio TA, Clerici M, Biasin M. Salivary miRNA Profiles in COVID-19 Patients with Different Disease Severities. Int J Mol Sci 2023; 24:10992. [PMID: 37446170 DOI: 10.3390/ijms241310992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
The oral mucosa is the first site of SARS-CoV-2 entry and replication, and it plays a central role in the early defense against infection. Thus, the SARS-CoV-2 viral load, miRNAs, cytokines, and neutralizing activity (NA) were assessed in saliva and plasma from mild (MD) and severe (SD) COVID-19 patients. Here we showed that of the 84 miRNAs analyzed, 8 were differently expressed in the plasma and saliva of SD patients. In particular: (1) miRNAs let-7a-5p, let-7b-5p, and let-7c-5p were significantly downregulated; and (2) miR-23a and b and miR-29c, as well as three immunomodulatory miRNAs (miR-34a-5p, miR-181d-5p, and miR-146) were significantly upregulated. The production of pro-inflammatory cytokines (IL-1β, IL-2, IL-6, IL-8, IL-9, and TNFα) and chemokines (CCL2 and RANTES) increased in both the saliva and plasma of SD and MD patients. Notably, disease severity correlated with NA and immune activation. Monitoring these parameters could help predict disease outcomes and identify new markers of disease progression.
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Affiliation(s)
- Irma Saulle
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Micaela Garziano
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Gioia Cappelletti
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Fiona Limanaqi
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Sergio Strizzi
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Claudia Vanetti
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Sergio Lo Caputo
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Mariacristina Poliseno
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Teresa Antonia Santantonio
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy
- Don C. Gnocchi Foundation, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Foundation, Via A. Capecelatro 66, 20148 Milan, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
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7
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Wongdontri C, Jaree P, Somboonwiwat K. PmKuSPI is regulated by pmo-miR-bantam and contributes to hemocyte homeostasis and viral propagation in shrimp. FISH & SHELLFISH IMMUNOLOGY 2023; 137:108738. [PMID: 37031922 DOI: 10.1016/j.fsi.2023.108738] [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: 01/26/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 05/22/2023]
Abstract
The Kunitz-type serine protease inhibitor (KuSPI) is a low molecular weight protein that plays a role in modulating a range of biological processes. In Penaeus monodon, the PmKuSPI gene has been found to be highly expressed in the white spot syndrome virus (WSSV)-infected shrimp and is predicted to be regulated by a conserved microRNA, pmo-miR-bantam. We reported that, despite being upregulated at the transcriptional level, the PmKuSPI protein was also upregulated after WSSV infection. Silencing the PmKuSPI gene in healthy shrimp had no effect on phenoloxidase activity or apoptosis but resulted in a delay in the mortality of WSSV-infected shrimp as well as a reduction in the total hemocyte number and WSSV copies. According to an in vitro luciferase reporter assay, the pmo-miR-bantam bound to the 3'UTR of the PmKuSPI gene as predicted. In accordance with the loss of function studies using dsRNA-mediated RNA interference, the administration of the pmo-miR-bantam mimic into WSSV-infected shrimp lowered the expression of the PmKuSPI transcript and the PmKuSPI protein, as well as the WSSV copy number. According to these results, the protease inhibitor PmKuSPI is posttranscriptionally controlled by pmo-miR-bantam and plays a role in hemocyte homeostasis, which in turn affects shrimp susceptibility to WSSV infection.
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Affiliation(s)
- Chantaka Wongdontri
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phayathai Rd., Bangkok, Thailand
| | - Phattarunda Jaree
- Center of Applied Shrimp Research and Innovation, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phayathai Rd., Bangkok, Thailand.
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Prinz R. Nothing in evolution makes sense except in the light of code biology. Biosystems 2023; 229:104907. [PMID: 37207840 DOI: 10.1016/j.biosystems.2023.104907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023]
Abstract
This article highlights the potential contribution of biological codes to the course and dynamics of evolution. The concept of organic codes, developed by Marcello Barbieri, has fundamentally changed our view of how living systems function. The notion that molecular interactions built on adaptors that arbitrarily link molecules from different "worlds" in a conventional, i.e., rule-based way, departs significantly from the law-based constraints imposed on livening things by physical and chemical mechanisms. In other words, living and non-living things behave like rules and laws, respectively, but this important distinction is rarely considered in current evolutionary theory. The many known codes allow quantification of codes that relate to a cell, or comparisons between different biological systems and may pave the way to a quantitative and empirical research agenda in code biology. A starting point for such an endeavour is the introduction of a simple dichotomous classification of structural and regulatory codes. This classification can be used as a tool to analyse and quantify key organising principles of the living world, such as modularity, hierarchy, and robustness, based on organic codes. The implications for evolutionary research are related to the unique dynamics of codes, or ´Eigendynamics´ (self-momentum) and how they determine the behaviour of biological systems from within, whereas physical constraints are imposed mainly from without. A speculation on the drivers of macroevolution in light of codes is followed by the conclusion that a meaningful and comprehensive understanding of evolution depends including codes into the equation of life.
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9
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What Do We Know about Barley miRNAs? Int J Mol Sci 2022; 23:ijms232314755. [PMID: 36499082 PMCID: PMC9740008 DOI: 10.3390/ijms232314755] [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: 09/30/2022] [Revised: 11/09/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Plant miRNAs are powerful regulators of gene expression at the post-transcriptional level, which was repeatedly proved in several model plant species. miRNAs are considered to be key regulators of many developmental, homeostatic, and immune processes in plants. However, our understanding of plant miRNAs is still limited, despite the fact that an increasing number of studies have appeared. This systematic review aims to summarize our current knowledge about miRNAs in spring barley (Hordeum vulgare), which is an important agronomical crop worldwide and serves as a common monocot model for studying abiotic stress responses as well. This can help us to understand the connection between plant miRNAs and (not only) abiotic stresses in general. In the end, some future perspectives and open questions are summarized.
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MicroRNAs’ Crucial Role in Salivary Gland Cancers’ Onset and Prognosis. Cancers (Basel) 2022; 14:cancers14215304. [PMID: 36358723 PMCID: PMC9657964 DOI: 10.3390/cancers14215304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Salivary gland cancers are incredibly heterogeneous, both in the physical onset and in the aggressiveness. Setting up a novel diagnostic and prognostic detection method based on the noninvasive microRNAs’ profiling might represent a goal for the clinical management of those particular malignancies, saving precious time for the patients. Abstract Salivary gland cancer (SGC) is an uncommon and heterogeneous disease that accounts for around 8.5% of all head and neck cancers. MicroRNAs (miRNAs) consist of a class of highly conserved, short, single-stranded segments (18–25 nucleotides) of noncoding RNA that represent key gene-transcription regulators in physiological and pathological human conditions. However, their role in SGC development and progression is not completely clear. This review aims to compile and summarize the recent findings on the topic, focusing on the prognostic and diagnostic value of the major modulated and validated microRNAs in SGC. Their differential expression could possibly aid the clinician in delivering an early diagnosis, therapeutic strategy and precision medicine.
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11
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Nersisyan S, Gorbonos A, Makhonin A, Zhiyanov A, Shkurnikov M, Tonevitsky A. isomiRTar: a comprehensive portal of pan-cancer 5'-isomiR targeting. PeerJ 2022; 10:e14205. [PMID: 36275459 PMCID: PMC9583861 DOI: 10.7717/peerj.14205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/19/2022] [Indexed: 01/24/2023] Open
Abstract
Inaccurate cleavage of pri- and pre-miRNA hairpins by Drosha and Dicer results in the generation of miRNA isoforms known as isomiRs. isomiRs with 5'-end variations (5'-isomiRs) create a new dimension in miRNA research since they have different seed regions and distinct targetomes. We developed isomiRTar (https://isomirtar.hse.ru)-a comprehensive portal that allows one to analyze expression profiles and targeting activity of 5'-isomiRs in cancer. Using the Cancer Genome Atlas sequencing data, we compiled the list of 1022 5'-isomiRs expressed in 9282 tumor samples across 31 cancer types. Sequences of these isomiRs were used to predict target genes with miRDB and TargetScan. The putative interactions were then subjected to the co-expression analysis in each cancer type to identify isomiR-target pairs supported by significant negative correlations. Downstream analysis of the data deposited in isomiRTar revealed both cancer-specific and cancer-conserved 5'-isomiR expression landscapes. Pairs of isomiRs differing in one nucleotide shift from 5'-end had poorly overlapping targetomes with the median Jaccard index of 0.06. The analysis of colorectal cancer 5'-isomiR-mediated regulatory networks revealed promising candidate tumor suppressor isomiRs: hsa-miR-203a-3p-+1, hsa-miR-192-5p-+1 and hsa-miR-148a-3p-0. In summary, we believe that isomiRTar will help researchers find novel mechanisms of isomiR-mediated gene silencing in different types of cancer.
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Affiliation(s)
- Stepan Nersisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia,Armenian Bioinformatics Institute (ABI), Yerevan, Armenia,Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | | | - Alexey Makhonin
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Anton Zhiyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Art Photonics GmbH, Berlin, Germany
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12
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When a Synonymous Variant Is Nonsynonymous. Genes (Basel) 2022; 13:genes13081485. [PMID: 36011397 PMCID: PMC9408308 DOI: 10.3390/genes13081485] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 12/27/2022] Open
Abstract
Term synonymous variation is widely used, but frequently in a wrong or misleading meaning and context. Twenty three point eight % of possible nucleotide substitution types in the universal genetic code are for synonymous amino acid changes, but when these variants have a phenotype and functional effect, they are very seldom synonymous. Such variants may manifest changes at DNA, RNA and/or protein levels. Large numbers of variations are erroneously annotated as synonymous, which causes problems e.g., in clinical genetics and diagnosis of diseases. To facilitate precise communication, novel systematics and nomenclature are introduced for variants that when looking only at the genetic code seem like synonymous, but which have phenotypes. A new term, unsense variant is defined as a substitution in the mRNA coding region that affects gene expression and protein production without introducing a stop codon in the variation site. Such variants are common and need to be correctly annotated. Proper naming and annotation are important also to increase awareness of these variants and their consequences.
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13
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Kim WR, Park EG, Lee HE, Park SJ, Huh JW, Kim JN, Kim HS. Hsa-miR-422a Originated from Short Interspersed Nuclear Element Increases ARID5B Expression by Collaborating with NF-E2. Mol Cells 2022; 45:465-478. [PMID: 35444070 PMCID: PMC9260135 DOI: 10.14348/molcells.2022.2158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 12/13/2021] [Accepted: 12/27/2021] [Indexed: 12/03/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate the expression of target messenger RNA (mRNA) complementary to the 3' untranslated region (UTR) at the post-transcriptional level. Hsa-miR-422a, which is commonly known as miRNA derived from transposable element (MDTE), was derived from short interspersed nuclear element (SINE). Through expression analysis, hsa-miR-422a was found to be highly expressed in both the small intestine and liver of crab-eating monkey. AT-Rich Interaction Domain 5 B (ARID5B) was selected as the target gene of hsa-miR-422a, which has two binding sites in both the exon and 3'UTR of ARID5B. To identify the interaction between hsa-miR-422a and ARID5B, a dual luciferase assay was conducted in HepG2 cell line. The luciferase activity of cells treated with the hsa-miR-422a mimic was upregulated and inversely downregulated when both the hsa-miR-422a mimic and inhibitor were administered. Nuclear factor erythroid-2 (NF-E2) was selected as the core transcription factor (TF) via feed forward loop analysis. The luciferase expression was downregulated when both the hsa-miR-422a mimic and siRNA of NF-E2 were treated, compared to the treatment of the hsa-miR-422a mimic alone. The present study suggests that hsa-miR-422a derived from SINE could bind to the exon region as well as the 3'UTR of ARID5B. Additionally, hsa-miR-422a was found to share binding sites in ARID5Bwith several TFs, including NF-E2. The hsa-miR-422a might thus interact with TF to regulate the expression of ARID5B, as demonstrated experimentally. Altogether, hsa-miR-422a acts as a super enhancer miRNA of ARID5Bby collaborating with TF and NF-E2.
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Affiliation(s)
- Woo Ryung Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Eun Gyung Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Hee-Eun Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28199, Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28199, Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28199, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jeong Nam Kim
- Department of Microbiology, College of Natural Sciences, Pusan National University, Busan 46241, Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea
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14
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Lin LR, Hu XQ, Lu LH, Dai JZ, Lin NN, Wang RH, Xie ZX, Chen XM. MicroRNA expression profiles in familial hypertrophic cardiomyopathy with myosin-binding protein C3 (MYBPC3) gene mutations. BMC Cardiovasc Disord 2022; 22:278. [PMID: 35717150 PMCID: PMC9206743 DOI: 10.1186/s12872-022-02714-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/08/2022] [Indexed: 11/30/2022] Open
Abstract
Familial hypertrophic cardiomyopathy (FHCM) is an autosomal dominant inherited disease caused by mutations in genes encoding cardiac sarcomere proteins. MicroRNAs (miRNAs) play an important role in the pathogenesis of FHCM. In the present study, we aimed to determine the miRNA profile in FHCM patients with myosin-binding protein C3 (MYBPC3) gene mutations. We recruited three FHCM patients and age- and sex-matched controls. The three probands all had hypertrophic obstructive cardiomyopathy with severe myocardial hypertrophy, and two of the three had a history of sudden cardiac death, representing a “malignant” phenotype. We then compared the miRNA expression profiles of three FHCM patients carrying MYBPC3 gene mutations with those of the normal control group using miRNA sequencing technology. Differentially expressed miRNAs were verified using real-time polymerase chain reaction (qPCR). Target genes and signaling pathways of the identified differentially expressed miRNAs were predicted using bioinformatics analysis. A total of 33 significantly differentially expressed miRNAs were detected in the peripheral blood of the three probands, of which 28 were upregulated, including miR-208b-3p, and 5 were downregulated. Real-time PCR confirmed the upregulated expression of miR-208b-3p in FHCM patients (P < 0.05). Bioinformatics analysis showed that miR-208b-3p was mainly enriched in 79 target genes including UBE2V2, MED13, YBX1, CNKSR2, GATA4, andSOX5/6, et al. Gene ontology (GO) analysis of target genes showed that miR-208b was mainly involved in the processes of negative regulation of transcription from RNA polymerase II promoter, and regulation of transcription, DNA templated. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the target genes regulated by miR-208b-3p were mainly involved in the Wnt signaling pathway. These findings suggest that FHCM patients with MYBPC3 gene mutations have a specific miRNA expression profile, and that miR-208b-3p is significantly upregulated in cardiac hypertrophy. Our results also indicate that miRNA-208b-3p activates the Wnt signaling pathway through its target gene to promote cardiac hypertrophy.
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Affiliation(s)
- Li-Rong Lin
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China.,Department of Cardiology, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Xue-Qun Hu
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China.,Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Li-Hong Lu
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China. .,Department of Cardiology, Fujian Provincial Hospital, Fuzhou, 350001, China.
| | - Jia-Zhen Dai
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Ning-Ning Lin
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Re-Hua Wang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China.,Department of Cardiology, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Zhang-Xin Xie
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China.,Department of Emergency, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Xue-Mei Chen
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China.,Department of Cardiology, Fujian Provincial Hospital, Fuzhou, 350001, China
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Kaissarian NM, Meyer D, Kimchi-Sarfaty C. Synonymous Variants: Necessary Nuance in our Understanding of Cancer Drivers and Treatment Outcomes. J Natl Cancer Inst 2022; 114:1072-1094. [PMID: 35477782 PMCID: PMC9360466 DOI: 10.1093/jnci/djac090] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/24/2022] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Abstract
Once called "silent mutations" and assumed to have no effect on protein structure and function, synonymous variants are now recognized to be drivers for some cancers. There have been significant advances in our understanding of the numerous mechanisms by which synonymous single nucleotide variants (sSNVs) can affect protein structure and function by affecting pre-mRNA splicing, mRNA expression, stability, folding, miRNA binding, translation kinetics, and co-translational folding. This review highlights the need for considering sSNVs in cancer biology to gain a better understanding of the genetic determinants of human cancers and to improve their diagnosis and treatment. We surveyed the literature for reports of sSNVs in cancer and found numerous studies on the consequences of sSNVs on gene function with supporting in vitro evidence. We also found reports of sSNVs that have statistically significant associations with specific cancer types but for which in vitro studies are lacking to support the reported associations. Additionally, we found reports of germline and somatic sSNVs that were observed in numerous clinical studies and for which in silico analysis predicts possible effects on gene function. We provide a review of these investigations and discuss necessary future studies to elucidate the mechanisms by which sSNVs disrupt protein function and are play a role in tumorigeneses, cancer progression, and treatment efficacy. As splicing dysregulation is one of the most well recognized mechanisms by which sSNVs impact protein function, we also include our own in silico analysis for predicting which sSNVs may disrupt pre-mRNA splicing.
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Affiliation(s)
- Nayiri M Kaissarian
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Douglas Meyer
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
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16
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Dweep H, Showe LC, Kossenkov AV. Functional Annotation of MicroRNAs Using Existing Resources. Methods Mol Biol 2022; 2257:57-77. [PMID: 34432273 DOI: 10.1007/978-1-0716-1170-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are endogenous small noncoding RNAs that are involved in most biological signaling pathways, including the cell cycle, apoptosis, proliferation, immune response, metabolism as well as in biological processes including organ development and in human diseases like cancers. During the past two decades, high-throughput transcriptomic profiling using next generation sequencing and microarrays have been extensively utilized to identify differentially expressed miRNAs across different conditions and diseases. A natural extension of miRNA identification is to the process of functionally annotating known or predicted gene targets of those miRNAs and, by inference, revealing their potential influences on diverse biological pathways and functions. In this chapter, we provide a stepwise guideline on how to perform functional enrichment analyses on miRNAs of interest using publicly available resources such as miRWalk2.0.
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Affiliation(s)
- Harsh Dweep
- The Wistar Institute, Philadelphia, PA, USA.
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Li W, Zhang Y, Xu J, Chen J, Gao X. Fasudil prevents neomycin-induced hair cell damage by inhibiting autophagy through the miR-489/NDP52 signaling pathway in HEI-OC1 cells. Exp Ther Med 2021; 23:43. [PMID: 34849158 DOI: 10.3892/etm.2021.10965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 08/11/2021] [Indexed: 11/05/2022] Open
Abstract
Hearing loss is a common sensory disorder that is mainly caused by the loss of hair cells (HCs). Drug-induced deafness, for which there is currently no effective treatment, is mainly caused by the inappropriate use of aminoglycoside antibiotics. Fasudil (Fas), a novel isoquinoline sulfonamide derivative, has exhibited antioxidant abilities in a number of previous studies. The aim of the present study was to investigate the potential effects of Fas against neomycin (Neo)-induced hair cell damage and elucidate the underlying mechanism. Flow cytometry and western blot analysis were used to detect the effects of Fas on cell apoptosis and to determine the expression levels of autophagy-related proteins, LC3B and Beclin 1, induced by Neo. Mitochondrial membrane potential and reactive oxygen species (ROS) levels were detected using fluorescent probes. The effect of Fas on Neo-induced hair cell injury marker, GFP-LC3B, was also examined using the immunofluorescence technique. Fas was found to inhibit Neo-induced mitochondrial autophagy and mitochondrial membrane potential decline, in addition to reducing ROS levels and cell apoptosis caused by Neo treatment. However, Fas failed to inhibit the Neo-induced these above changes in cells with NDP52 overexpression. The putative binding sites of microRNA (miR)-489 on the 3'-untranslated region of nuclear dot protein 52 (NDP52) were predicted using the TargetScan 7.0 online tool, and this association was further verified using a dual-luciferase reporter assay. Moreover, the expression of miR-489 negatively regulated the expression of NDP52. Fas and miR-489 mimic inhibited the Neo-induced mitochondrial autophagy and mitochondrial membrane potential decline, in addition to reducing ROS levels and cell apoptosis. Knockdown of miR-489 expression using a miR-489 inhibitor blocked the inhibitory effects of Fas on the mitochondrial membrane potential, cell apoptosis and ROS production. Therefore, Fas may upregulate the expression of miR-489 to negatively regulate the expression of NDP52 at the post-transcriptional level, which in turn inhibits the activation of mitophagy and cell injury induced by Neo. Thus, Fas may act as a novel therapeutic option in the clinical treatment of hearing loss in the future.
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Affiliation(s)
- Wei Li
- Department of Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221006, P.R. China
| | - Yanqiu Zhang
- Department of Otolaryngology Head and Neck Surgery, Xuzhou Cancer Hospital, Xuzhou, Jiangsu 221005, P.R. China
| | - Jifeng Xu
- Department of Otolaryngology Head and Neck Surgery, The First Clinical Medical College of Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Jincan Chen
- Department of Otolaryngology Head and Neck Surgery, The First Clinical Medical College of Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Xia Gao
- Research Institute of Otolaryngology, Gulou Hospital Affiliated to Medical College of Nanjing University, Nanjing, Jiangsu 210008, P.R. China.,Department of Otolaryngology Head and Neck Surgery, Gulou Hospital Affiliated to Medical College of Nanjing University, Nanjing, Jiangsu 210008, P.R. China
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18
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Sunny JS, Saleena LM. In-Silico Analysis of rSNPsin miRNA:mRNA Duplex Involved in Insulin Signaling Genes Shows a Possible Pathogenesis of Insulin Resistance. Microrna 2021; 10:200-205. [PMID: 34503438 DOI: 10.2174/2211536610666210909164348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/23/2021] [Accepted: 07/07/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Insulin resistance is a condition in which the body produces insulin but is unable to use it effectively. Aberrations in insulin signaling are known to play a crucial role in pathogenesis of this disease state. Eventually patients will have glucose build up in their blood instead of being absorbed by the cells, leading to type 2 diabetes. OBJECTIVE In the current study we focus on understanding the role of rSNP mediated miRNA:mRNA dysregulation and its impact on the above metabolic condition. METHODS More than 30 genes involved in insulin signaling pathway were found using KEGG database. The 3'UTR end of genes was studied by using RegRNA and Ensembl, whereas TargetScan along with miRbase were used to identify their target miRNAs.Binding free energy was used as a parameter to analyze the affect of polymorphism on the miRNA:mRNA duplex formation.Further, UNA fold was used to determine the heat capacity changes. RESULTS The following genes INSR, INS, GLUT4, FOXO1, IL6, TRIB3 and SREBF1 were selected for analysis. Multiple miRNAs, hsa-miR-16-5p, hsa-miR-15a-15p were identified in the SNP occurring region for INSR. INS too showed similar results.INSR, INS and TRIB3 were found to have the maximum change in their binding free energy due to rSNP variation. A destabilisation in the heat capacity values was observed too, contributed due to rSNP induction. CONCLUSION A direct relationship between miRNA target polymorphism and the stability of the miRNA:mRNA duplex was observed. The current methodology used to study insulin resistance pathogenesis could elaborate on our existing knowledge of miRNA mediated disease states.
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Affiliation(s)
- Jithin S Sunny
- Department of Biotechnology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai TN. India
| | - Lilly M Saleena
- Department of Biotechnology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai TN. India
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19
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Paul S, Bravo Vázquez LA, Márquez Nafarrate M, Gutiérrez Reséndiz AI, Srivastava A, Sharma A. The regulatory activities of microRNAs in non-vascular plants: a mini review. PLANTA 2021; 254:57. [PMID: 34424349 DOI: 10.1007/s00425-021-03707-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/14/2021] [Indexed: 05/21/2023]
Abstract
MicroRNA-mediated gene regulation in non-vascular plants is potentially involved in several unique biological functions, including biosynthesis of several highly valuable exclusive bioactive compounds, and those small RNAs could be manipulated for the overproduction of essential bioactive compounds in the future. MicroRNAs (miRNAs) are a class of endogenous, small (20-24 nucleotides), non-coding RNA molecules that regulate gene expression through the miRNA-mediated mechanisms of either translational inhibition or messenger RNA (mRNA) cleavage. In the past years, studies have mainly focused on elucidating the roles of miRNAs in vascular plants as compared to non-vascular plants. However, non-vascular plant miRNAs have been predicted to be involved in a wide variety of specific biological mechanisms; nevertheless, some of them have been demonstrated explicitly, thus showing that the research field of this plant group owns a noteworthy potential to develop novel investigations oriented towards the functional characterization of these miRNAs. Furthermore, the insights into the roles of miRNAs in non-vascular plants might be of great importance for designing the miRNA-based genetically modified plants for valuable secondary metabolites, active compounds, and biofuels in the future. Therefore, in this current review, we provide an overview of the potential roles of miRNAs in different groups of non-vascular plants such as algae and bryophytes.
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Affiliation(s)
- Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico.
| | - Luis Alberto Bravo Vázquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico
| | - Marilyn Márquez Nafarrate
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Av. Eugenio Garza Sada, No. 2501 Tecnologico, CP 64849, Monterrey, Mexico
| | - Ana Isabel Gutiérrez Reséndiz
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico
| | - Aashish Srivastava
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico.
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20
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MicroRNA: Could It Play a Role in Bovine Endometritis? Inflammation 2021; 44:1683-1695. [PMID: 33907916 DOI: 10.1007/s10753-021-01458-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/15/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023]
Abstract
Endometritis in dairy cows is a major economic problem worldwide; without advances in lifestyle management and drug treatment, it causes high morbidity and death. Micro ribonucleic acid (miRNAs) these days is seen as an important part of gene control networks. It is a class of small nucleotides 20-25, single-stranded RNA molecules. In endometritis, the inflammatory response caused by the gram-negative bacteria Escherichia coli (E. coli) alters the expression of miRNA which can regulate the innate immune system. This manuscript reviews (1) the interaction of miRNAs with the signaling of NF-κB and dysregulation of miRNAs and NF-κB activity in endometritis and (2) the activity of miR-let-7c, miR-148a, and miR-488 in NF-κB activation and their effect on endometritis. Cows with reduced immunity are more vulnerable to transition diseases, such as endometritis. During post-partum, cows undergo stress, metabolic disorders, hormonal imbalance, negative energy balance, and changes in diet. One of the many categories of regulatory molecules, which explain its natural function and pathological impact on NF-κB dysregulation, is important to inform the complexity of the immune system and to develop treatments for endometritis. It shows that miRNAs could have multiple applications in veterinary medicine. Nevertheless, a comprehensive study of is essential which should be aimed at exploring the role of microRNA at physiological level and its effect due to dysfunction and dysregulation.
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Panebianco C, Trivieri N, Villani A, Terracciano F, Latiano TP, Potenza A, Perri F, Binda E, Pazienza V. Improving Gemcitabine Sensitivity in Pancreatic Cancer Cells by Restoring miRNA-217 Levels. Biomolecules 2021; 11:639. [PMID: 33925948 PMCID: PMC8146031 DOI: 10.3390/biom11050639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/02/2021] [Accepted: 04/23/2021] [Indexed: 12/21/2022] Open
Abstract
Chemoresistance is a major problem in the therapeutic management of pancreatic cancer, concurring to poor clinical outcome. A number of mechanisms have been proposed to explain resistance to gemcitabine, a standard of care for this malignancy, among which is included aberrant miRNA expression. In the current study, we investigated the role of miR-217, which is strongly down-regulated in cancerous, compared to normal, pancreatic tissues or cells, in sensitizing human pancreatic cancer cell lines to this drug. The low expression of miR-217 in pancreatic cancer patients was confirmed in two gene expression datasets (GSE41372 and GSE60980), and the prognostic value of two target genes (ANLN and TRPS1), was estimated on clinical data from the Tumor Cancer Genome Atlas (TCGA). Transfecting miR-217 mimic in pancreatic cancer cells reduced viability, enhanced apoptosis, and affected cell cycle by promoting a S phase arrest in gemcitabine-treated cells. Moreover, in drug-exposed cells subjected to miR-217 forced expression, a down-regulation for several genes involved in cancer drug resistance was observed, many of which are cell cycle regulators, such as CCND1, CCNE1, CDK2, CDKN1A, CDKN1B, while others, such as ARNT, BRCA1, BRCA2, ELK1, EGFR, ERBB4, and RARA are involved in proliferation and cell cycle progression. Our results support the notion that miR-217 enhances pancreatic cancer sensitivity to gemcitabine, mainly impairing cell cycle progression.
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Affiliation(s)
- Concetta Panebianco
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (C.P.); (A.V.); (F.T.); (F.P.)
| | - Nadia Trivieri
- Cancer Stem Cell Unit, Institute for Stem-Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy;
| | - Annacandida Villani
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (C.P.); (A.V.); (F.T.); (F.P.)
| | - Fulvia Terracciano
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (C.P.); (A.V.); (F.T.); (F.P.)
| | - Tiziana Pia Latiano
- Oncology Unit Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy;
| | - Adele Potenza
- Dietetic and Clinical Nutrition Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy;
| | - Francesco Perri
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (C.P.); (A.V.); (F.T.); (F.P.)
| | - Elena Binda
- Cancer Stem Cell Unit, Institute for Stem-Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy;
| | - Valerio Pazienza
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (C.P.); (A.V.); (F.T.); (F.P.)
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Wang X, Miao X, Chen G, Cui Y, Sun F, Fan J, Gao Z, Meng C. Identification of microRNAs involved in astaxanthin accumulation responding to high light and high sodium acetate (NaAC) stresses in Haematococcus pluvialis. ALGAL RES 2021. [DOI: 10.1016/j.algal.2020.102179] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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23
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The Importance of Epigenetics in Diagnostics and Treatment of Major Depressive Disorder. J Pers Med 2021; 11:jpm11030167. [PMID: 33804455 PMCID: PMC7999864 DOI: 10.3390/jpm11030167] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/09/2021] [Accepted: 02/17/2021] [Indexed: 12/15/2022] Open
Abstract
Recent studies imply that there is a tight association between epigenetics and a molecular mechanism of major depressive disorder (MDD). Epigenetic modifications, i.e., DNA methylation, post-translational histone modification and interference of microRNA (miRNA) or long non-coding RNA (lncRNA), are able to influence the severity of the disease and the outcome of the therapy. This article summarizes the most recent literature data on this topic, i.e., usage of histone deacetylases as therapeutic agents with an antidepressant effect and miRNAs or lncRNAs as markers of depression. Due to the noteworthy potential of the role of epigenetics in MDD diagnostics and therapy, we have gathered the most relevant data in this area.
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Luo J, Hou Y, Ma W, Xie M, Jin Y, Xu L, Li C, Wang Y, Chen J, Chen W, Zheng Y, Yu D. A novel mechanism underlying alcohol dehydrogenase expression: hsa-miR-148a-3p promotes ADH4 expression via an AGO1-dependent manner in control and ethanol-exposed hepatic cells. Biochem Pharmacol 2021; 189:114458. [PMID: 33556337 DOI: 10.1016/j.bcp.2021.114458] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 02/06/2023]
Abstract
The alcohol dehydrogenases (ADHs) and aldehyde dehydrogenases (ALDHs) play critical roles in alcoholism development and alcohol toxicology; however, few studies have focused on the miRNA-mediated mechanisms underlying the expressions of alcohol-metabolizing enzymes. In the present study, we showed the expression changes of each alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) in the liver samples of alcoholic hepatitis (AH) patients, and predicted the miRNAs targeting the dysregulated alcohol-metabolizing genes by a systematic in silico analysis. 13 miRNAs were predicted to regulate the expressions of ADH1A, ADH4, and ALDH2, respectively, with hsa-miR-148a-3p (miR-148a) showing the most significant down-regulation in AH patients. Following experimental evidence using HepG2 cells proved that miR-148a promoted ADH4 expression by directly binding to the coding sequence of ADH4 and increasing the mRNA stability via an AGO1-dependent manner. Additional assays showed that secondary structure of ADH4 transcript affected the target accessibility and binding of miR-148a-3p. In sum, our results suggest that the expressions of key alcohol-metabolizing enzymes are repressed in AH patients, and the non-canonical positive regulation of miR-148a on ADH4 reveals a new regulationary mechanism for ADH genes.
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Affiliation(s)
- Jiao Luo
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Yufei Hou
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Wanli Ma
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Mengyue Xie
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Yuan Jin
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Lin Xu
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Chuanhai Li
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Ying Wang
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Jing Chen
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Wendi Chen
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Yuxin Zheng
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Dianke Yu
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China.
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25
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Mukushkina D, Aisina D, Pyrkova A, Ryskulova A, Labeit S, Ivashchenko A. In silico Prediction of miRNA Interactions With Candidate Atherosclerosis Gene mRNAs. Front Genet 2020; 11:605054. [PMID: 33329752 PMCID: PMC7672156 DOI: 10.3389/fgene.2020.605054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022] Open
Abstract
The involvement of genes and miRNAs in the development of atherosclerosis is a challenging problem discussed in recent publications. It is necessary to establish which miRNAs affect the expression of candidate genes. We used known candidate atherosclerosis genes to predict associations. The quantitative characteristics of interactions of miRNAs with mRNA candidate genes were determined using the program, which identifies the localization of miRNA binding sites in mRNA, the free energy interaction of miRNA with mRNA. In mRNAs of GAS6 and NFE2L2 candidate genes, binding sites of 21 miRNAs and of 15 miRNAs, respectively, were identified. In IRS2 mRNA binding sites of 25 miRNAs were located in a cluster of 41 nt. In ADRB3, CD36, FASLG, FLT1, PLA2G7, and PPARGC1A mRNAs, clusters of miR-466, ID00436.3p-miR, and ID01030.3p-miR BS were identified. The organization of overlapping miRNA binding sites in clusters led to their compaction and caused competition among the miRNAs. The binding of 53 miRNAs to the mRNAs of 14 candidate genes with free energy interactions greater than -130 kJ/mole was determined. The miR-619-5p was fully complementary to ADAM17 and CD36 mRNAs, ID01593.5p-miR to ANGPTL4 mRNA, ID01935.5p-miR to NFE2L2, and miR-5096 to IL18 mRNA. Associations of miRNAs and candidate atherosclerosis genes are proposed for the early diagnosis of this disease.
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Affiliation(s)
- Dina Mukushkina
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Dana Aisina
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anna Pyrkova
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Alma Ryskulova
- Department of microbiology, Kazakh Medical University of Continuing Education, Almaty, Kazakhstan
| | - Siegfried Labeit
- Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Anatoliy Ivashchenko
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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26
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Ortega MA, Fraile-Martínez O, Guijarro LG, Casanova C, Coca S, Álvarez-Mon M, Buján J, García-Honduvilla N, Asúnsolo Á. The Regulatory Role of Mitochondrial MicroRNAs (MitomiRs) in Breast Cancer: Translational Implications Present and Future. Cancers (Basel) 2020; 12:cancers12092443. [PMID: 32872155 PMCID: PMC7564393 DOI: 10.3390/cancers12092443] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Mitochondrial microRNAs (mitomiRs) are an emerging field of study in a wide range of tumours including breast cancer. By targeting mitochondrial, or non-mitochondrial products, mitomiRs are able to regulate the functions of this organelle, thus controlling multiple carcinogenic processes. The knowledge of this system may provide a novel approach for targeted therapies, as potential biomarkers or helping in the diagnosis of such a complex malignancy. Abstract Breast cancer is the most prevalent and incident female neoplasm worldwide. Although survival rates have considerably improved, it is still the leading cause of cancer-related mortality in women. MicroRNAs are small non-coding RNA molecules that regulate the posttranscriptional expression of a wide variety of genes. Although it is usually located in the cytoplasm, several studies have detected a regulatory role of microRNAs in other cell compartments such as the nucleus or mitochondrion, known as “mitomiRs”. MitomiRs are essential modulators of mitochondrion tasks and their abnormal expression has been linked to the aetiology of several human diseases related to mitochondrial dysfunction, including breast cancer. This review aims to examine basic knowledge of the role of mitomiRs in breast cancer and discusses their prospects as biomarkers or therapeutic targets.
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Affiliation(s)
- Miguel A. Ortega
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
- Cancer Registry and Pathology Department, Hospital Universitario Principe de Asturias, 28806 Alcalá de Henares, Madrid, Spain
- Correspondence: ; Tel.: +34-91-885-4540; Fax: +34-91-885-4885
| | - Oscar Fraile-Martínez
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
| | - Luis G. Guijarro
- Department of System Biology, Unit of Biochemistry and Molecular Biology (CIBEREHD), University of Alcalá, 28801 Alcalá de Henares, Spain;
| | - Carlos Casanova
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
| | - Santiago Coca
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
| | - Melchor Álvarez-Mon
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
- Immune System Diseases-Rheumatology, Oncology Service an Internal Medicine, University Hospital Príncipe de Asturias, (CIBEREHD), 28806 Alcalá de Henares, Madrid, Spain
| | - Julia Buján
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
| | - Natalio García-Honduvilla
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
| | - Ángel Asúnsolo
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Madrid, Spain
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Artificial miRNAs targeting CAG repeat expansion in ORFs cause rapid deadenylation and translation inhibition of mutant transcripts. Cell Mol Life Sci 2020; 78:1577-1596. [PMID: 32696070 PMCID: PMC7904544 DOI: 10.1007/s00018-020-03596-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
Abstract
Polyglutamine (polyQ) diseases are incurable neurological disorders caused by CAG repeat expansion in the open reading frames (ORFs) of specific genes. This type of mutation in the HTT gene is responsible for Huntington’s disease (HD). CAG repeat-targeting artificial miRNAs (art-miRNAs) were shown as attractive therapeutic approach for polyQ disorders as they caused allele-selective decrease in the level of mutant proteins. Here, using polyQ disease models, we aimed to demonstrate how miRNA-based gene expression regulation is dependent on target sequence features. We show that the silencing efficiency and selectivity of art-miRNAs is influenced by the localization of the CAG repeat tract within transcript and the specific sequence context. Furthermore, we aimed to reveal the events leading to downregulation of mutant polyQ proteins and found very rapid activation of translational repression and HTT transcript deadenylation. Slicer-activity of AGO2 was dispensable in this process, as determined in AGO2 knockout cells generated with CRISPR-Cas9 technology. We also showed highly allele-selective downregulation of huntingtin in human HD neural progenitors (NPs). Taken together, art-miRNA activity may serve as a model of the cooperative activity and targeting of ORF regions by endogenous miRNAs.
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28
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Dexheimer PJ, Cochella L. MicroRNAs: From Mechanism to Organism. Front Cell Dev Biol 2020; 8:409. [PMID: 32582699 PMCID: PMC7283388 DOI: 10.3389/fcell.2020.00409] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are short, regulatory RNAs that act as post-transcriptional repressors of gene expression in diverse biological contexts. The emergence of small RNA-mediated gene silencing preceded the onset of multicellularity and was followed by a drastic expansion of the miRNA repertoire in conjunction with the evolution of complexity in the plant and animal kingdoms. Along this process, miRNAs became an essential feature of animal development, as no higher metazoan lineage tolerated loss of miRNAs or their associated protein machinery. In fact, ablation of the miRNA biogenesis machinery or the effector silencing factors results in severe embryogenesis defects in every animal studied. In this review, we summarize recent mechanistic insight into miRNA biogenesis and function, while emphasizing features that have enabled multicellular organisms to harness the potential of this broad class of repressors. We first discuss how different mechanisms of regulation of miRNA biogenesis are used, not only to generate spatio-temporal specificity of miRNA production within an animal, but also to achieve the necessary levels and dynamics of expression. We then explore how evolution of the mechanism for small RNA-mediated repression resulted in a diversity of silencing complexes that cause different molecular effects on their targets. Multicellular organisms have taken advantage of this variability in the outcome of miRNA-mediated repression, with differential use in particular cell types or even distinct subcellular compartments. Finally, we present an overview of how the animal miRNA repertoire has evolved and diversified, emphasizing the emergence of miRNA families and the biological implications of miRNA sequence diversification. Overall, focusing on selected animal models and through the lens of evolution, we highlight canonical mechanisms in miRNA biology and their variations, providing updated insight that will ultimately help us understand the contribution of miRNAs to the development and physiology of multicellular organisms.
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Affiliation(s)
- Philipp J Dexheimer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
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29
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Phenolic Compounds Exerting Lipid-Regulatory, Anti-Inflammatory and Epigenetic Effects as Complementary Treatments in Cardiovascular Diseases. Biomolecules 2020; 10:biom10040641. [PMID: 32326376 PMCID: PMC7226566 DOI: 10.3390/biom10040641] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022] Open
Abstract
Atherosclerosis is the main process behind cardiovascular diseases (CVD), maladies which continue to be responsible for up to 70% of death worldwide. Despite the ongoing development of new and potent drugs, their incomplete efficacy, partial intolerance and numerous side effects make the search for new alternatives worthwhile. The focus of the scientific world turned to the potential of natural active compounds to prevent and treat CVD. Essential for effective prevention or treatment based on phytochemicals is to know their mechanisms of action according to their bioavailability and dosage. The present review is focused on the latest data about phenolic compounds and aims to collect and correlate the reliable existing knowledge concerning their molecular mechanisms of action to counteract important risk factors that contribute to the initiation and development of atherosclerosis: dyslipidemia, and oxidative and inflammatory-stress. The selection of phenolic compounds was made to prove their multiple benefic effects and endorse them as CVD remedies, complementary to allopathic drugs. The review also highlights some aspects that still need clear scientific explanations and draws up some new molecular approaches to validate phenolic compounds for CVD complementary therapy in the near future.
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30
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Leptin Modulates the Expression of miRNAs-Targeting POMC mRNA by the JAK2-STAT3 and PI3K-Akt Pathways. J Clin Med 2019; 8:jcm8122213. [PMID: 31847355 PMCID: PMC6947463 DOI: 10.3390/jcm8122213] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/05/2019] [Accepted: 12/12/2019] [Indexed: 12/17/2022] Open
Abstract
The central control of energy balance involves a strongly regulated neuronal network within the hypothalamus and the brainstem. In these structures, pro-opiomelanocortin (POMC) neurons are known to decrease food intake and to increase energy expenditure. Thus, leptin, a peripheral signal that relays information regarding body fat content, modulates the activity of POMC neurons. MicroRNAs (miRNAs) are short non-coding RNAs of 22–26 nucleotides that post-transcriptionally interfere with target gene expression by binding to their mRNAs. It has been demonstrated that leptin is able to modulate the expression of miRNAs (miR-383, miR-384-3p, and miR-488) that potentially target POMC mRNA. However, no study has identified the transduction pathways involved in this effect of leptin on miRNA expression. In addition, miRNAs targeting POMC mRNAs are not clearly identified. In this work, using in vitro models, we have identified and confirmed that miR-383, miR-384-3p, and miR-488 physically binds to the 3′ untranslated (3′UTR) regions of POMC mRNA. Importantly, we show that leptin inhibits these miRNAs expression by different transduction pathways. Taken together, these results allowed us to highlight the miRNA involvement in the regulation of POMC expression downstream of the leptin signaling and satiety signal integration.
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31
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MicroRNAs in Cardiac Hypertrophy. Int J Mol Sci 2019; 20:ijms20194714. [PMID: 31547607 PMCID: PMC6801828 DOI: 10.3390/ijms20194714] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/02/2019] [Accepted: 09/06/2019] [Indexed: 12/17/2022] Open
Abstract
Like other organs, the heart undergoes normal adaptive remodeling, such as cardiac hypertrophy, with age. This remodeling, however, is intensified under stress and pathological conditions. Cardiac remodeling could be beneficial for a short period of time, to maintain a normal cardiac output in times of need; however, chronic cardiac hypertrophy may lead to heart failure and death. MicroRNAs (miRNAs) are known to have a role in the regulation of cardiac hypertrophy. This paper reviews recent advances in the field of miRNAs and cardiac hypertrophy, highlighting the latest findings for targeted genes and involved signaling pathways. By targeting pro-hypertrophic genes and signaling pathways, some of these miRNAs alleviate cardiac hypertrophy, while others enhance it. Therefore, miRNAs represent very promising potential pharmacotherapeutic targets for the management and treatment of cardiac hypertrophy.
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32
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Sethuraman S, Thomas M, Gay LA, Renne R. Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs. Nucleic Acids Res 2019; 46:8574-8589. [PMID: 29846699 PMCID: PMC6144796 DOI: 10.1093/nar/gky459] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/14/2018] [Indexed: 12/16/2022] Open
Abstract
Ribonomics experiments involving crosslinking and immuno-precipitation (CLIP) of Ago proteins have expanded the understanding of the miRNA targetome of several organisms. These techniques, collectively referred to as CLIP-seq, have been applied to identifying the mRNA targets of miRNAs expressed by Kaposi’s Sarcoma-associated herpes virus (KSHV) and Epstein–Barr virus (EBV). However, these studies focused on identifying only those RNA targets of KSHV and EBV miRNAs that are known to encode proteins. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are also targeted by miRNAs. In this study, we performed a systematic re-analysis of published datasets from KSHV- and EBV-driven cancers. We used CLIP-seq data from lymphoma cells or EBV-transformed B cells, and a crosslinking, ligation and sequencing of hybrids dataset from KSHV-infected endothelial cells, to identify novel lncRNA targets of viral miRNAs. Here, we catalog the lncRNA targetome of KSHV and EBV miRNAs, and provide a detailed in silico analysis of lncRNA–miRNA binding interactions. Viral miRNAs target several hundred lncRNAs, including a subset previously shown to be aberrantly expressed in human malignancies. In addition, we identified thousands of lncRNAs to be putative targets of human miRNAs, suggesting that miRNA–lncRNA interactions broadly contribute to the regulation of gene expression.
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Affiliation(s)
- Sunantha Sethuraman
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Merin Thomas
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Lauren A Gay
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA.,UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.,UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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33
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Landrier JF, Derghal A, Mounien L. MicroRNAs in Obesity and Related Metabolic Disorders. Cells 2019; 8:cells8080859. [PMID: 31404962 PMCID: PMC6721826 DOI: 10.3390/cells8080859] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/01/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022] Open
Abstract
Metabolic disorders are characterized by the inability to properly use and/or store energy. The burdens of metabolic disease, such as obesity or diabetes, are believed to arise through a complex interplay between genetics and epigenetics predisposition, environment and nutrition. Therefore, understanding the molecular mechanisms for the onset of metabolic disease will provide new insights for prevention and treatment. There is growing concern about the dysregulation of micro-RNAs (miRNAs) in metabolic diseases. MiRNAs are short non-coding RNA molecules that post-transcriptionally repress the expression of genes by binding to untranslated regions and coding sequences of the target mRNAs. This review aims to provide recent data about the potential involvement of miRNAs in metabolic diseases, particularly obesity and type 2 diabetes.
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Affiliation(s)
| | - Adel Derghal
- Aix Marseille Univ, INSERM, INRA, C2VN, 13005 Marseille, France
| | - Lourdes Mounien
- Aix Marseille Univ, INSERM, INRA, C2VN, 13005 Marseille, France.
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34
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Rigoutsos I, Londin E, Kirino Y. Short RNA regulators: the past, the present, the future, and implications for precision medicine and health disparities. Curr Opin Biotechnol 2019; 58:202-210. [PMID: 31323485 DOI: 10.1016/j.copbio.2019.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/09/2019] [Accepted: 05/27/2019] [Indexed: 01/03/2023]
Abstract
We herein provide a brief review of the trajectory that the field of short RNA research followed in the last 25 years. We place emphasis on the unexpected discoveries and the ramifications of these discoveries for the field, as well as offer some thoughts about what the next 25 years may bring. Arguably, the uncovered dependence of different types of short RNAs on individual attributes such as a person's sex, population origin, race, and on tissue type, tissue state, and disease was most unexpected. This dependence has important ramifications in that it will provide a boost to our understanding of the molecular mechanisms of health disparities as well as pave the way for novel approaches to designing improved and personalized diagnostics and therapeutics.
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Affiliation(s)
- Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
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35
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Goeppert B, Truckenmueller F, Ori A, Fritz V, Albrecht T, Fraas A, Scherer D, Silos RG, Sticht C, Gretz N, Mehrabi A, Bewerunge-Hudler M, Pusch S, Bermejo JL, Dietrich P, Schirmacher P, Renner M, Roessler S. Profiling of gallbladder carcinoma reveals distinct miRNA profiles and activation of STAT1 by the tumor suppressive miRNA-145-5p. Sci Rep 2019; 9:4796. [PMID: 30886199 PMCID: PMC6423323 DOI: 10.1038/s41598-019-40857-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 02/25/2019] [Indexed: 12/13/2022] Open
Abstract
Gallbladder carcinoma (GBC) is a biliary tract cancer with few treatment options and poor prognosis. Radical surgery is the only potentially curative treatment option but most patients diagnosed with GBC are unresectable. Thus, there is a great need for the development of new treatment options including targeted therapy. Here, we aimed at identifying deregulated miRNAs and affected pathways involved in GBC development and progression. We performed global miRNA profiling of 40 GBC and 8 normal gallbladder tissues and identified large differences with 30% of miRNAs being differentially expressed (false discovery rate: FDR < 0.001). We found 24 miRNAs to be differentially regulated in GBC with poor outcome (p < 0.05) of which miR-145-5p was the most downregulated miRNA. Overexpression of miR-145-5p significantly reduced cell proliferation and colony formation. Gene expression analysis of cells expressing miR-145-5p mimics revealed activation of the Signal transducer and activator of transcription 1 (STAT1) signaling pathway which is mainly tumor suppressive. Furthermore, the activation of STAT1 by miR-145-5p was specifically observed in gallbladder carcinoma and cholangiocarcinoma but not in hepatocellular carcinoma cells. The Protein Tyrosine Phosphatase Receptor Type F (PTPRF) is downregulated upon miR-145 expression and may be involved in STAT1 regulation. In addition, we found that the STAT1-regulated protein IRF7 is downregulated in GBC compared to normal gallbladder tissue and low IRF7 expression is associated with significantly lower overall survival of GBC patients. Thus, this study identified GBC patient subgroups and provides new mechanistic insights in the tumor suppressive function of miR-145-5p leading to activation of STAT1 signaling.
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Affiliation(s)
- Benjamin Goeppert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Valerie Fritz
- Institute of Biochemistry, Emil-Fischer Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Albrecht
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Angelika Fraas
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Dominique Scherer
- Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Heidelberg, Germany
| | - Rosa González Silos
- Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Heidelberg, Germany
| | - Carsten Sticht
- Center of Medical Research, University Hospital Mannheim, Mannheim, Germany
| | - Norbert Gretz
- Center of Medical Research, University Hospital Mannheim, Mannheim, Germany
| | - Arianeb Mehrabi
- Department of General Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Melanie Bewerunge-Hudler
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Pusch
- Heidelberg University Hospital, Institute of Pathology, Department of Neuropathology, Heidelberg, Germany and Clinical Cooperation Unit Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - Justo Lorenzo Bermejo
- Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Heidelberg, Germany
| | - Peter Dietrich
- Institute of Biochemistry, Emil-Fischer Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany.,Department of Medicine, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcus Renner
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
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36
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Jaree P, Wongdontri C, Somboonwiwat K. White Spot Syndrome Virus-Induced Shrimp miR-315 Attenuates Prophenoloxidase Activation via PPAE3 Gene Suppression. Front Immunol 2018; 9:2184. [PMID: 30337920 PMCID: PMC6178132 DOI: 10.3389/fimmu.2018.02184] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/04/2018] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs), the small non-coding RNAs, play a pivotal role in post-transcriptional gene regulation in various cellular processes. However, the miRNA function in shrimp antiviral response is not clearly understood. This research aims to uncover the function of pmo-miR-315, a white spot syndrome virus (WSSV)-responsive miRNAs identified from Penaeus monodon hemocytes during WSSV infection. The expression of the predicted pmo-miR-315 target mRNA, a novel PmPPAE gene called PmPPAE3, was negatively correlated with that of the pmo-miR-315. Furthermore, the luciferase assay indicated that the pmo-miR-315 directly interacted with the target site in PmPPAE3 suggesting the regulatory role of pmo-miR-315 on PmPPAE3 gene expression. Introducing the pmo-miR-315 into the WSSV-infected shrimp caused the reduction of the PmPPAE3 transcript level and, hence, the PO activity activated by the PmPPAE3 whereas the WSSV copy number in the shrimp hemocytes was increased. Taken together, our findings state a crucial role of pmo-miR-315 in attenuating proPO activation via PPAE3 gene suppression and facilitating the WSSV propagation in shrimp WSSV infection.
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Affiliation(s)
- Phattarunda Jaree
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chantaka Wongdontri
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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37
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Dhungel B, Ramlogan-Steel CA, Steel JC. MicroRNA-Regulated Gene Delivery Systems for Research and Therapeutic Purposes. Molecules 2018; 23:E1500. [PMID: 29933586 PMCID: PMC6099389 DOI: 10.3390/molecules23071500] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 12/18/2022] Open
Abstract
Targeted gene delivery relies on the ability to limit the expression of a transgene within a defined cell/tissue population. MicroRNAs represent a class of highly powerful and effective regulators of gene expression that act by binding to a specific sequence present in the corresponding messenger RNA. Involved in almost every aspect of cellular function, many miRNAs have been discovered with expression patterns specific to developmental stage, lineage, cell-type, or disease stage. Exploiting the binding sites of these miRNAs allows for construction of targeted gene delivery platforms with a diverse range of applications. Here, we summarize studies that have utilized miRNA-regulated systems to achieve targeted gene delivery for both research and therapeutic purposes. Additionally, we identify criteria that are important for the effectiveness of a particular miRNA for such applications and we also discuss factors that have to be taken into consideration when designing miRNA-regulated expression cassettes.
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Affiliation(s)
- Bijay Dhungel
- Gallipoli Medical Research Institute, Greenslopes Private Hospital, 102 Newdegate Street, Brisbane, QLD 4120, Australia.
- Faculty of Medicine, University of Queensland, 288 Herston Road, Herston, Brisbane, QLD 4006, Australia.
- University of Queensland Diamantina Institute, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD 4102, Australia.
| | - Charmaine A Ramlogan-Steel
- Faculty of Medicine, University of Queensland, 288 Herston Road, Herston, Brisbane, QLD 4006, Australia.
- Layton Vision Foundation, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD 4102, Australia.
| | - Jason C Steel
- Faculty of Medicine, University of Queensland, 288 Herston Road, Herston, Brisbane, QLD 4006, Australia.
- OcuGene, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD 4102, Australia.
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Parveen A, Gretz N, Dweep H. Obtaining miRNA‐Target Interaction Information from miRWalk2.0. ACTA ACUST UNITED AC 2018; 55:12.15.1-12.15.27. [DOI: 10.1002/cpbi.14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Alisha Parveen
- Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg Mannheim Germany
| | - Norbert Gretz
- Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg Mannheim Germany
| | - Harsh Dweep
- Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg Mannheim Germany
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Hu C, Huang S, Wu F, Ding H. miR-98 inhibits cell proliferation and induces cell apoptosis by targeting MAPK6 in HUVECs. Exp Ther Med 2018; 15:2755-2760. [PMID: 29456679 PMCID: PMC5795499 DOI: 10.3892/etm.2018.5735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 11/28/2017] [Indexed: 12/14/2022] Open
Abstract
The aim of current study was to explore the role of microRNA (miR)-98 in atherosclerosis. Human vascular endothelial cells (HVECs) were isolated from the peripheral blood of healthy volunteers and patients with atherosclerosis. Compared with endothelial cells from the healthy control group, the expression level of mitogen activated protein kinase (MAPK)6 was significantly upregulated and miR-98 was downregulated in the endothelial cells of patients with atherosclerosis. The human umbilical vein endothelial cell line (HUVEC) was adopted to perform in vitro studies. Overexpression of miR-98 reduced the proliferation and induced the apoptosis of HUVECs, which were revealed using an MTT assay, and flow cytometry assay, respectively. The aforementioned influences of miR-98 on HUVECs were mediated by targeting MAPK6, which was verified using luciferase assays. Additionally, the overexpression of miR-98 reduced the protein level of apoptosis regulator Bcl-2 and MAPK6; however, it induced the protein expression of caspase-3 and apoptosis regulator Bax. In conclusion, these findings demonstrate that miR-98 is an important regulator of atherosclerosis, suggesting that miR-98 may be a potential therapeutic target for the treatment of atherosclerosis.
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Affiliation(s)
- Chuanxian Hu
- Cardiopulmonary Surgery, Huai'an First People's Hospital, Jiangsu, Huai'an 223300, P.R. China
| | - Su Huang
- Cardiopulmonary Surgery, Huai'an First People's Hospital, Jiangsu, Huai'an 223300, P.R. China
| | - Fafu Wu
- Cardiopulmonary Surgery, Huai'an First People's Hospital, Jiangsu, Huai'an 223300, P.R. China
| | - Hui Ding
- Cardiopulmonary Surgery, Huai'an First People's Hospital, Jiangsu, Huai'an 223300, P.R. China
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40
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Koroleva IA, Nazarenko MS, Kucher AN. Role of microRNA in Development of Instability of Atherosclerotic Plaques. BIOCHEMISTRY (MOSCOW) 2018; 82:1380-1390. [PMID: 29223165 DOI: 10.1134/s0006297917110165] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNAs are small noncoding single-stranded RNAs that regulate gene expression. Today, we see an increasing number of studies highlighting the important role of microRNAs in the development and progression of cardiovascular diseases caused by atherosclerotic lesions of arteries. We review the available scientific data on association of the expression of these biomolecules with instability of atherosclerotic plaques in animal models and humans. We made special emphasis on miR-21, -100, -127, -133, -143/145, -221/222, and -494 because they were analyzed in more than one study. We discuss the possibility of microRNAs using in the diagnosis and therapy of atherosclerosis and its complications.
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Affiliation(s)
- I A Koroleva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050, Russia.
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41
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Romano G, Kwong LN. miRNAs, Melanoma and Microenvironment: An Intricate Network. Int J Mol Sci 2017; 18:ijms18112354. [PMID: 29112174 PMCID: PMC5713323 DOI: 10.3390/ijms18112354] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 11/02/2017] [Accepted: 11/05/2017] [Indexed: 12/14/2022] Open
Abstract
miRNAs are central players in cancer biology and they play a pivotal role in mediating the network communication between tumor cells and their microenvironment. In melanoma, miRNAs can impair or facilitate a wide array of processes, and here we will focus on: the epithelial to mesenchymal transition (EMT), the immune milieu, and metabolism. Multiple miRNAs can affect the EMT process, even at a distance, for example through exosome-mediated mechanisms. miRNAs also strongly act on some components of the immune system, regulating the activity of key elements such as antigen presenting cells, and can facilitate an immune evasive/suppressive phenotype. miRNAs are also involved in the regulation of metabolic processes, specifically in response to hypoxic stimuli where they can mediate the metabolic switch from an oxidative to a glycolytic metabolism. Overall, this review discusses and summarizes recent findings on miRNA regulation in the melanoma tumor microenvironment, analyzing their potential diagnostic and therapeutic applications.
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Affiliation(s)
- Gabriele Romano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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42
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microRNAs as cancer therapeutics: A step closer to clinical application. Cancer Lett 2017; 407:113-122. [DOI: 10.1016/j.canlet.2017.04.007] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 03/31/2017] [Accepted: 04/05/2017] [Indexed: 12/12/2022]
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43
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Gill P, Bhattacharyya S, McCullough S, Letzig L, Mishra PJ, Luo C, Dweep H, James L. MicroRNA regulation of CYP 1A2, CYP3A4 and CYP2E1 expression in acetaminophen toxicity. Sci Rep 2017; 7:12331. [PMID: 28951593 PMCID: PMC5614957 DOI: 10.1038/s41598-017-11811-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/30/2017] [Indexed: 01/29/2023] Open
Abstract
MicroRNAs (miRNAs) that regulate the cytochrome P-450 isoforms involved in acetaminophen (APAP) toxicity were examined in HepaRG cells treated with APAP (20 mM). In-vitro studies found that APAP protein adducts were increased at 1 h, followed by ALT increases at 12 and 24 h. CYP1A2, CYP3A4 and CYP2E1 mRNA levels were decreased, while miRNAs were increased for miR-122-5p, miR-378a-5p, miR-27b-3p at 6 h and miR-125b-5p at 12 h and miR-27b-3p at 24 h. Putative miRNA binding sites on the 3′UTRs of the CYPs were identified in-silico. Overexpression of miR-122-5p and miR-378a-5p in cells suppressed protein expression of CYP1A2, CYP3A4 and CYP2E1. Luciferase reporter assays confirmed the interaction between miR-122 and the 3′UTR of the CYP1A2 and CYP3A4. Thus, the in-vitro experiments showed that miR-122-5p and miR-378a-5p upregulation were associated with translational repression of CYPs. Serum samples of children with APAP overdose had significant elevation of miR-122-5p, miR-378a-5p, miR-125b-5p and miR-27b-3p, compared to healthy controls and receiver operator curves of the miRNAs had AUCs of 91 to 100%. Collectively, the data suggest that miRNA elevations in APAP toxicity represent a regulatory response to modify CYP1A2, CYP3A4 and CYP2E1 translation due to cellular stress and injury.
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Affiliation(s)
- Pritmohinder Gill
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA. .,Arkansas Children's Research Institute, Little Rock, AR, 72202, USA.
| | - Sudeepa Bhattacharyya
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA.,Arkansas Children's Research Institute, Little Rock, AR, 72202, USA
| | - Sandra McCullough
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA.,Arkansas Children's Research Institute, Little Rock, AR, 72202, USA
| | - Lynda Letzig
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA.,Arkansas Children's Research Institute, Little Rock, AR, 72202, USA
| | - Prasun J Mishra
- Department of Biochemical and Cellular Pharmacology, Genentech, 1, DNA Way, South San Francisco, California, 94080, USA
| | - Chunqiao Luo
- Arkansas Children's Research Institute, Little Rock, AR, 72202, USA
| | - Harsh Dweep
- The Wistar Institute, 3601 Spruce St, Philadelphia, Pennsylvania, 19104, USA
| | - Laura James
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA.,Arkansas Children's Research Institute, Little Rock, AR, 72202, USA
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44
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Jin P, Li S, Sun L, Lv C, Ma F. Transcriptome-wide analysis of microRNAs in Branchiostoma belcheri upon Vibrio parahemolyticus infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 74:243-252. [PMID: 28487235 DOI: 10.1016/j.dci.2017.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/03/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that participate in diverse biological processes via regulating expressions of target genes at post-transcriptional level. Amphioxus, as modern survivor of an ancient chordate lineage, is a model organism for comparative genomics study. However, miRNAs involved in regulating immune responses in Branchiostoma belcheri are largely unclear. Here, we systematically investigated the microRNAs (miRNAs) involved in regulating immune responses in the cephalochordate amphioxus (Branchiostoma belcheri) through next-generation deep sequencing of amphioxus samples infected with Vibrio parahemolyticus. We identified 198 novel amphioxus miRNAs, consisting of 12 conserved miRNAs, 33 candidate star miRNAs and 153 potential amphioxus-specific-miRNAs. Using microarray profiling, 14 miRNAs were differentially expressed post infection, suggesting they are immune-related miRNAs. Eight miRNAs (bbe-miR-92a-3p, bbe-miR-92c-3p, bbe-miR-210-5p, bbe-miR-22-3p, bbe-miR-1∼bbe-miR-133 and bbe-miR-217∼bbe-miR-216 clusters) were significantly increased at 12 h post-infection, while bbe-miR-2072-5p was downregulated at 6 h and 12 h. Three miRNAs, bbe-miR-1-3p, bbe-miR-22-3p and bbe-miR-92a-3p, were confirmed to be involved in immune responses to infection by qRT-PCR. Our findings further clarify important regulatory roles of miRNAs in the innate immune response to bacterial infection in amphioxus.
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Affiliation(s)
- Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Shengjie Li
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Lianjie Sun
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Caiyun Lv
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
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45
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Durban J, Sanz L, Trevisan-Silva D, Neri-Castro E, Alagón A, Calvete JJ. Integrated Venomics and Venom Gland Transcriptome Analysis of Juvenile and Adult Mexican Rattlesnakes Crotalus simus, C. tzabcan, and C. culminatus Revealed miRNA-modulated Ontogenetic Shifts. J Proteome Res 2017; 16:3370-3390. [PMID: 28731347 DOI: 10.1021/acs.jproteome.7b00414] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Adult rattlesnakes within genus Crotalus express one of two distinct venom phenotypes, type I (hemorrhagic) and type II (neurotoxic). In Costa Rican Central American rattlesnake, ontogenetic changes in the concentration of miRNAs modulate venom type II to type I transition. Venomics and venom gland transcriptome analyses showed that adult C. simus and C. tzabcan expressed intermediate patterns between type II and type I venoms, whereas C. culminatus had a canonical type I venom. Neonate/juvenile and adult Mexican rattlesnakes showed notable inter- and intraspecific variability in the number, type, abundance and ontogenetic shifts of the transcriptional and translational venom gland activities. These results support a role for miRNAs in the ontogenetic venom compositional changes in the three congeneric Mexican rattlesnakes. It is worth noting the finding of dual-action miRNAs, which silence the translation of neurotoxic heterodimeric PLA2 crotoxin and acidic PLA2 mRNAs while simultaneously up-regulating SVMP-targeting mRNAs. Dual transcriptional regulation potentially explains the existence of mutually exclusive crotoxin-rich (type-II) and SVMP-rich (type-I) venom phenotypic dichotomy among rattlesnakes. Our results support the hypothesis that alterations of the distribution of miRNAs, modulating the translational activity of venom gland toxin-encoding mRNAs in response to an external cue, may contribute to the mechanism generating adaptive venom variability.
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Affiliation(s)
- Jordi Durban
- Instituto de Biomedicina de Valencia , Consejo Superior de Investigaciones Científicas, Jaime Roig 11, 46010 Valencia, Spain
| | - Libia Sanz
- Instituto de Biomedicina de Valencia , Consejo Superior de Investigaciones Científicas, Jaime Roig 11, 46010 Valencia, Spain
| | - Dilza Trevisan-Silva
- Instituto de Biomedicina de Valencia , Consejo Superior de Investigaciones Científicas, Jaime Roig 11, 46010 Valencia, Spain.,Department of Cell Biology, Federal University of Paraná , Jardim das Américas, Curitiba, Paraná, Brazil
| | - Edgar Neri-Castro
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México , Cuernavaca, Morelos, México
| | - Alejandro Alagón
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México , Cuernavaca, Morelos, México
| | - Juan J Calvete
- Instituto de Biomedicina de Valencia , Consejo Superior de Investigaciones Científicas, Jaime Roig 11, 46010 Valencia, Spain
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46
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Tu J, Tian C, Zhao P, Sun J, Wang M, Fan Q, Yuan Y. Identification and profiling of growth-related microRNAs in Chinese perch (Siniperca chuatsi). BMC Genomics 2017; 18:489. [PMID: 28659132 PMCID: PMC5490230 DOI: 10.1186/s12864-017-3851-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 06/07/2017] [Indexed: 12/17/2022] Open
Abstract
Background MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play important roles in the regulation of diverse biological processes in eukaryotes. Chinese perch (Siniperca chuatsi) is one of the most economically important fish species widely cultured in China. Growth is an extremely important characteristic in fish. Individual differences in body size are common in Siniperca chuatsi, which significantly influence the aquaculture production of Siniperca chuatsi. However, the underline growth-related regulatory factors, such as miRNAs, are still unknown. Results To investigate the growth-related miRNAs in Siniperca chuatsi, two RNA libraries from four growth-related tissues (brain, pituitary, liver, and muscle) of Siniperca chuatsi at 6-month stage with relatively high or low growth rates (big-size group or small-size group) were obtained and sequenced using Solexa sequencing. A total of 252 known miRNAs and 12 novel miRNAs were identified. The expression patterns of these miRNAs in big-size group and small-size group were compared, and the results showed that 31 known and 5 novel miRNAs were differently expressed (DE). Furthermore, to verify the Solexa sequencing, five DE miRNAs were randomly selected and quantified by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The results showed that their expression patterns were consistent with those of Solexa sequencing. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of target genes of DE miRNAs was performed. It showed that the target genes were involved in multiple biological processes including metabolic process, suggesting that metabolic process played an important role in growth of fish. Conclusions Siniperca chuatsi is a popular and economically important species in aquaculture. In this study, miRNAs in Siniperca chuatsi with different growth rates were identified, and their expression profiles were compared. The data provides the first large-scale miRNA profiles related to growth of Siniperca chuatsi, which is expected to contribute to a better understanding of the role of miRNAs in regulating the biological processes of growth and possibly useful for Siniperca chuatsi breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3851-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiagang Tu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Changxu Tian
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Peiqi Zhao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junxiao Sun
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Min Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qixue Fan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yongchao Yuan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. .,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, Hubei, 430070, China.
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47
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Bianchi M, Renzini A, Adamo S, Moresi V. Coordinated Actions of MicroRNAs with other Epigenetic Factors Regulate Skeletal Muscle Development and Adaptation. Int J Mol Sci 2017; 18:E840. [PMID: 28420141 PMCID: PMC5412424 DOI: 10.3390/ijms18040840] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/04/2017] [Accepted: 04/13/2017] [Indexed: 01/01/2023] Open
Abstract
Epigenetics plays a pivotal role in regulating gene expression in development, in response to cellular stress or in disease states, in virtually all cell types. MicroRNAs (miRNAs) are short, non-coding RNA molecules that mediate RNA silencing and regulate gene expression. miRNAs were discovered in 1993 and have been extensively studied ever since. They can be expressed in a tissue-specific manner and play a crucial role in tissue development and many biological processes. miRNAs are responsible for changes in the cell epigenome because of their ability to modulate gene expression post-transcriptionally. Recently, numerous studies have shown that miRNAs and other epigenetic factors can regulate each other or cooperate in regulating several biological processes. On the one hand, the expression of some miRNAs is silenced by DNA methylation, and histone modifications have been demonstrated to modulate miRNA expression in many cell types or disease states. On the other hand, miRNAs can directly target epigenetic factors, such as DNA methyltransferases or histone deacetylases, thus regulating chromatin structure. Moreover, several studies have reported coordinated actions between miRNAs and other epigenetic mechanisms to reinforce the regulation of gene expression. This paper reviews multiple interactions between miRNAs and epigenetic factors in skeletal muscle development and in response to stimuli or disease.
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Affiliation(s)
- Marzia Bianchi
- DAHFMO Unit of Histology and Medical Embryology, Interuniversity Institute of Myology, Sapienza University of Rome, Via Antonio Scarpa 14, 00161 Rome, Italy.
| | - Alessandra Renzini
- DAHFMO Unit of Histology and Medical Embryology, Interuniversity Institute of Myology, Sapienza University of Rome, Via Antonio Scarpa 14, 00161 Rome, Italy.
| | - Sergio Adamo
- DAHFMO Unit of Histology and Medical Embryology, Interuniversity Institute of Myology, Sapienza University of Rome, Via Antonio Scarpa 14, 00161 Rome, Italy.
| | - Viviana Moresi
- DAHFMO Unit of Histology and Medical Embryology, Interuniversity Institute of Myology, Sapienza University of Rome, Via Antonio Scarpa 14, 00161 Rome, Italy.
- Laboratory of Cardiovascular Endocrinology, IRCCS San Raffaele Pisana, 00166 Rome, Italy.
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48
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Identification and characterization of two putative microRNAs encoded by Bombyx mori cypovirus. Virus Res 2017; 233:86-94. [DOI: 10.1016/j.virusres.2017.03.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/03/2017] [Accepted: 03/04/2017] [Indexed: 01/23/2023]
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49
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Zafrir Z, Tuller T. Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking. BMC Bioinformatics 2017; 18:77. [PMID: 28143396 PMCID: PMC5286865 DOI: 10.1186/s12859-017-1497-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/27/2017] [Indexed: 12/30/2022] Open
Abstract
Background The regulation of all gene expression steps (e.g., Transcription, RNA processing, Translation, and mRNA Degradation) is known to be primarily encoded in different parts of genes and in genomic regions in proximity to genes (e.g., promoters, untranslated regions, coding regions, introns, etc.). However, the entire gene expression codes and the genomic regions where they are encoded are still unknown. Results Here, we employ an unsupervised approach to estimate the concentration of gene expression codes in different non-coding parts of genes and transcripts, such as introns and untranslated regions, focusing on three model organisms (Escherichia coli, Saccharomyces cerevisiae, and Schizosaccharomyces pombe). Our analyses support the conjecture that regions adjacent to the beginning and end of ORFs and the beginning and end of introns tend to include higher concentration of gene expression information relatively to regions further away. In addition, we report the exact regions with elevated concentration of gene expression codes. Furthermore, we demonstrate that the concentration of these codes in different genetic regions is correlated with the expression levels of the corresponding genes, and with splicing efficiency measurements and meiotic stage gene expression measurements in S. cerevisiae. Conclusion We suggest that these discoveries improve our understanding of gene expression regulation and evolution; they can also be used for developing improved models of genome/gene evolution and for engineering gene expression in various biotechnological and synthetic biology applications. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1497-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zohar Zafrir
- Department of Biomedical Engineering, Tel Aviv University, P.O. Box 39040, Tel Aviv, 6997801, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, P.O. Box 39040, Tel Aviv, 6997801, Israel. .,Sagol School of Neuroscience, Tel Aviv University, P.O. Box 39040, Tel Aviv, 6997801, Israel.
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Catalanotto C, Cogoni C, Zardo G. MicroRNA in Control of Gene Expression: An Overview of Nuclear Functions. Int J Mol Sci 2016; 17:ijms17101712. [PMID: 27754357 PMCID: PMC5085744 DOI: 10.3390/ijms17101712] [Citation(s) in RCA: 757] [Impact Index Per Article: 94.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/04/2016] [Accepted: 10/07/2016] [Indexed: 12/14/2022] Open
Abstract
The finding that small non-coding RNAs (ncRNAs) are able to control gene expression in a sequence specific manner has had a massive impact on biology. Recent improvements in high throughput sequencing and computational prediction methods have allowed the discovery and classification of several types of ncRNAs. Based on their precursor structures, biogenesis pathways and modes of action, ncRNAs are classified as small interfering RNAs (siRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs), promoter associate RNAs (pRNAs), small nucleolar RNAs (snoRNAs) and sno-derived RNAs. Among these, miRNAs appear as important cytoplasmic regulators of gene expression. miRNAs act as post-transcriptional regulators of their messenger RNA (mRNA) targets via mRNA degradation and/or translational repression. However, it is becoming evident that miRNAs also have specific nuclear functions. Among these, the most studied and debated activity is the miRNA-guided transcriptional control of gene expression. Although available data detail quite precisely the effectors of this activity, the mechanisms by which miRNAs identify their gene targets to control transcription are still a matter of debate. Here, we focus on nuclear functions of miRNAs and on alternative mechanisms of target recognition, at the promoter lavel, by miRNAs in carrying out transcriptional gene silencing.
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Affiliation(s)
- Caterina Catalanotto
- Department of Cellular Biotechnologies and Hematology, University of Rome Sapienza, Rome 00179, Italy.
| | - Carlo Cogoni
- Department of Cellular Biotechnologies and Hematology, University of Rome Sapienza, Rome 00179, Italy.
| | - Giuseppe Zardo
- Department of Cellular Biotechnologies and Hematology, University of Rome Sapienza, Rome 00179, Italy.
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