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Arnaldo L, Mena J, Serradell M, Gaig C, Adamuz D, Vilas D, Samaniego D, Ispierto L, Montini A, Mayà G, Álvarez R, Pastor P, Iranzo A, Beyer K. Platelet miRNAs as early biomarkers for progression of idiopathic REM sleep behavior disorder to a synucleinopathy. Sci Rep 2025; 15:12136. [PMID: 40204936 PMCID: PMC11982324 DOI: 10.1038/s41598-025-96926-3] [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] [Received: 01/10/2025] [Accepted: 04/01/2025] [Indexed: 04/11/2025] Open
Abstract
Individuals diagnosed with isolated REM sleep behavior disorder (IRBD) have a high risk of developing Lewy body disorders (LBD), mainly Parkinson's disease (PD) or dementia with Lewy bodies (DLB). As we have previously identified seven platelet-derived miRNAs as potential biomarkers for DLB, in this pilot study we aimed to investigate whether specific expression changes of these miRNAs are also present in IRBD. RNA was obtained from platelets of individuals with IRBD (n = 29) and controls (n = 34), and miRNA levels were determined with a miRCURY LNA miRNA Custom PCR Panel. miRNA interactomes of deregulated miRNAs were determined, and mRNA quantification of miRNA target genes was carried out using real-time PCR and the ΔΔCt method. We found that the expression of hsa-miR- 139 - 5p (p = 0.010) and hsa-miR- 142 - 3p (p = 0.017) was diminished, while hsa-miR- 191 - 5p (p = 0.023) was increased in platelets of IRBD patients compared with controls. Interactome analysis of these miRNAs showed that hsa-miR- 142 - 3p regulates genes related to the structure and maintenance of the cytoskeleton. Of the 15 genes expressed in platelets, the expression of WASL, a gene involved in actin filament organization, was increased in platelets of IRBD patients. Additionally, WASL expression correlated inversely with hsa-miR- 142 - 3p expression. Since the interactomes of hsa-miR- 139 - 5p and hsa-miR- 191 - 5p play a role in several cancer types, their expression was not addressed. Changes in hsa-miR- 142 - 3p, hsa-miR- 139 - 5p, and hsa-miR- 191 - 5p expression were found in IRBD platelets and might represent early biomarkers for LBD involving cytoskeleton dysfunction. Increased expression of WASL could indicate that altered platelet activation occurs early during the development of LBD.
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Affiliation(s)
- Laura Arnaldo
- Department of Neuroscience, Research Institute Germans Trias i Pujol, Badalona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jorge Mena
- Department of Neuroscience, Research Institute Germans Trias i Pujol, Badalona, Spain
| | - Mònica Serradell
- Department of Neurology, Sleep Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERNED, Barcelona, Spain
| | - Carles Gaig
- Department of Neurology, Sleep Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERNED, Barcelona, Spain
| | - David Adamuz
- Department of Neuroscience, Research Institute Germans Trias i Pujol, Badalona, Spain
| | - Dolores Vilas
- Unit of Neurodegenerative diseases, Department of Neurology, University Hospital Germans Trias I Pujol and the Germans Trias I Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
| | - Daniela Samaniego
- Unit of Neurodegenerative diseases, Department of Neurology, University Hospital Germans Trias I Pujol and the Germans Trias I Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
| | - Lourdes Ispierto
- Unit of Neurodegenerative diseases, Department of Neurology, University Hospital Germans Trias I Pujol and the Germans Trias I Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
| | - Angelica Montini
- Department of Neurology, Sleep Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERNED, Barcelona, Spain
| | - Gerard Mayà
- Department of Neurology, Sleep Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERNED, Barcelona, Spain
| | - Ramiro Álvarez
- Unit of Neurodegenerative diseases, Department of Neurology, University Hospital Germans Trias I Pujol and the Germans Trias I Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
| | - Pau Pastor
- Department of Neuroscience, Research Institute Germans Trias i Pujol, Badalona, Spain.
- Department of Neurology, Sleep Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERNED, Barcelona, Spain.
- Unit of Neurodegenerative diseases, Department of Neurology, University Hospital Germans Trias I Pujol and the Germans Trias I Pujol Research Institute (IGTP) Badalona, Barcelona, Spain.
| | - Alex Iranzo
- Department of Neurology, Sleep Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERNED, Barcelona, Spain.
- Neurology Service, Sleep Unit, Hospital Clínic de Barcelona, Barcelona, Spain.
| | - Katrin Beyer
- Department of Neuroscience, Research Institute Germans Trias i Pujol, Badalona, Spain.
- Universitat Autònoma de Barcelona, Barcelona, Spain.
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Bayraktar R, Tang Y, Dragomir MP, Ivan C, Peng X, Fabris L, Zhang J, Carugo A, Aneli S, Liu J, Chen MJM, Srinivasan S, Sahnoune I, Bayraktar E, Akdemir KC, Chen M, Narayanan P, Huang W, Ott LF, Eterovic AK, Villarreal OE, Mohammad MM, Peoples MD, Walsh DM, Hernandez JA, Morgan MB, Shaw KR, Davis JS, Menter D, Tam CS, Yeh P, Dawson SJ, Rassenti LZ, Kipps TJ, Kunej T, Estrov Z, Joosse SA, Pagani L, Alix-Panabières C, Pantel K, Ferajoli A, Futreal A, Wistuba II, Radovich M, Kopetz S, Keating MJ, Draetta GF, Mattick JS, Liang H, Calin GA. The mutational landscape and functional effects of noncoding ultraconserved elements in human cancers. SCIENCE ADVANCES 2025; 11:eado2830. [PMID: 39970212 PMCID: PMC11837999 DOI: 10.1126/sciadv.ado2830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 01/15/2025] [Indexed: 02/21/2025]
Abstract
The mutational landscape of phylogenetically ultraconserved elements (UCEs), especially those in noncoding DNAs (ncUCEs), and their functional relevance in cancers remain poorly characterized. Here, we perform a systematic analysis of whole-genome and in-house targeted UCE sequencing datasets from more than 3000 patients with cancer of 13,736 UCEs and demonstrate that ncUCE somatic alterations are common. Using a multiplexed CRISPR knockout screen in colorectal cancer cells, we show that the loss of several altered ncUCEs significantly affects cell proliferation. In-depth functional studies in vitro and in vivo further reveal that specific ncUCEs can be enhancers of tumor suppressors (such as ARID1B) and silencers of oncogenic proteins (such as RPS13). Moreover, several miRNAs located in ncUCEs are recurrently mutated. Mutations in miR-142 locus can affect the Drosha-mediated processing of precursor miRNAs, resulting in the down-regulation of the mature transcript. These results provide systematic evidence that specific ncUCEs play diverse regulatory roles in cancer.
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Affiliation(s)
- Recep Bayraktar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX 77030, USA
| | - Yitao Tang
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX 77030, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mihnea P. Dragomir
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Institute of Pathology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, CCM, Charitéplatz 1, 10117 Berlin, Germany
- Berlin Institute of Health at Charité, Charitéplatz 1, 10117 Berlin, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Berlin, 69210 Heidelberg, Germany
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Caris Life Science, Irving, TX 75039, USA
| | - Xinxin Peng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Linda Fabris
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alessandro Carugo
- TRACTION Platform, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Serena Aneli
- Department of Biology, University of Padova, Padova, Italy
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126, Turin, Italy
| | - Jintan Liu
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mei-Ju M. Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sanjana Srinivasan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Iman Sahnoune
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Emine Bayraktar
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX 77030, USA
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kadir C. Akdemir
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Meng Chen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pranav Narayanan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Wilson Huang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Johns Hopkins Physical Science– Oncology Center and Institute for NanoBioTechnology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Leonie Florence Ott
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Agda Karina Eterovic
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Viracor Eurofins, Oncology Diagnostics, Lee's Summit, MO 64086, USA
| | - Oscar Eduardo Villarreal
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mohammad Moustaf Mohammad
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael D. Peoples
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- TRACTION Platform, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Danielle M. Walsh
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jon Andrew Hernandez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Margaret B. Morgan
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenna R. Shaw
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer S. Davis
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Constantine S. Tam
- Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Victoria, Australia
| | - Paul Yeh
- Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Victoria, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Victoria, Australia
| | - Laura Z. Rassenti
- Center for Novel Therapeutics, Moores Cancer Center, University of California San Diego, La Jolla, CA 92037, USA
| | - Thomas J. Kipps
- Center for Novel Therapeutics, Moores Cancer Center, University of California San Diego, La Jolla, CA 92037, USA
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, SI-1230 Domzale, Slovenia
| | - Zeev Estrov
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Simon A. Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Luca Pagani
- Department of Biology, University of Padova, Padova, Italy
| | - Catherine Alix-Panabières
- The Laboratory Rare Human Circulating Cells and Liquid Biopsy, The University Medical Center of Montpellier, Montpellier, France
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alessandra Ferajoli
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Milan Radovich
- Caris Life Science, Irving, TX 75039, USA
- Department of Surgery, Division of General Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael J. Keating
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Giulio F. Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John S. Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales 2052, Australia
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Ranjbarnejad T, Gholaminejad A, Abolhassani H, Sherkat R, Salehi M, Sharifi M. Decreased expression of hsa-miR-142-3p and hsa-miR-155-5p in common variable immunodeficiency and involvement of their target genes and biological pathways. Allergol Immunopathol (Madr) 2025; 53:153-169. [PMID: 39786889 DOI: 10.15586/aei.v53i1.1234] [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: 10/08/2024] [Accepted: 12/10/2024] [Indexed: 01/12/2025]
Abstract
Common variable immunodeficiency (CVID) is the most common symptomatic and heterogeneous type of inborn errors of immunity (IEI). However, the pathogenesis process of this disease is often unknown. Epigenetic modifications may be involved in unresolved patients. MiR-142 and miR-155 were identified as immune system modulators and dysregulated in autoimmune and inflammatory diseases. We assessed hsa-miR-142-3p and hsa-miR-155-5p expression in a selected cohort of unresolved CVID cases and identified experimentally validated targets of these miRNAs. We constructed a protein-protein interaction (PPI) network from the common targets of two miRNAs and determined the hub genes. The hub genes' expression was investigated in GEO datasets. Gene ontology (GO) and pathway enrichment analysis were done for target genes. Hsa-miR-142-3p and hsa-miR-155-5p expression were significantly reduced in CVID patients. Evaluation of the PPI network demonstrated some hub genes in which pathogenic mutations have been reported in IEI, and other hub genes directly contribute to immune responses and the pathophysiology of IEI. Expression analysis of hub genes showed that they were significantly dysregulated in validating the CVID cohort. The pathway enrichment analysis indicated the involvement of the FOXO-mediated signaling pathway, TGFβ receptor complex, and VEGFR2-mediated vascular permeability. Considering the dysregulation of hsa-miR-142-3p and hsa-miR-155-5p in CVID and the known role of their target genes in the immune system, their involvement in the pathogenesis of CVID can be suggested.
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Affiliation(s)
- Tayebeh Ranjbarnejad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Alieh Gholaminejad
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hassan Abolhassani
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Roya Sherkat
- Immunodeficiency Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansoor Salehi
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammadreza Sharifi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran;
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Janosevic D, De Luca T, Melo Ferreira R, Gisch DL, Cheng YH, Hato T, Luo J, Yang Y, Hodgin JB, Phillips CL, Dagher PC, Eadon MT. miRNA and mRNA Signatures in Human Acute Kidney Injury Tissue. THE AMERICAN JOURNAL OF PATHOLOGY 2025; 195:102-114. [PMID: 39332675 PMCID: PMC11686445 DOI: 10.1016/j.ajpath.2024.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/23/2024] [Accepted: 08/21/2024] [Indexed: 09/29/2024]
Abstract
Acute kidney injury (AKI) is an important contributor to the development of chronic kidney disease (CKD). There is a need to understand molecular mediators that drive recovery and progression to CKD. In particular, the regulatory role of miRNAs in AKI is poorly understood. Herein, miRNA and mRNA sequencing were performed on biobanked human kidney tissues obtained during the routine care of subjects with a diagnosis of AKI, minimal change disease, or on nephrectomy tissue with no known kidney disease. mRNA analysis revealed that nephrectomy tissues exhibited an injury signature similar to that of AKI which was not identified in minimal change disease samples. The transcriptomic signature of human AKI was enriched in pathways involved in cell adhesion, epithelial-to-mesenchymal transition, and cell cycle arrest (eg, CDH6, ITGB6, CDKN1A). In AKI, up-regulation of miR-146a, miR-155, miR-142, and miR-122 was associated with pathways involved in immune cell recruitment, inflammation, and epithelial-to-mesenchymal transition. miR-122 and miR-146 were associated with down-regulation of DDR2 and IGFBP6, which are genes involved in the recovery and progression of kidney disease. These data provide integrated miRNA signatures that complement mRNA and other epigenetic data available in kidney atlases.
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Affiliation(s)
- Danielle Janosevic
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Thomas De Luca
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ricardo Melo Ferreira
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Debora L Gisch
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ying-Hua Cheng
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Takashi Hato
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jinghui Luo
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Yingbao Yang
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Carrie L Phillips
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Pierre C Dagher
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Michael T Eadon
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana; Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana
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Toropko M, Chuvpilo S, Karabelsky A. miRNA-Mediated Mechanisms in the Generation of Effective and Safe Oncolytic Viruses. Pharmaceutics 2024; 16:986. [PMID: 39204331 PMCID: PMC11360794 DOI: 10.3390/pharmaceutics16080986] [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: 06/30/2024] [Revised: 07/19/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression by inhibiting the translation of target transcripts. The expression profiles of miRNAs vary in different tissues and change with the development of diseases, including cancer. This feature has begun to be used for the modification of oncolytic viruses (OVs) in order to increase their selectivity and efficacy. OVs represent a relatively new class of anticancer drugs; they are designed to replicate in cancer tumors and destroy them. These can be natural viruses that can replicate within cancer tumor cells, or recombinant viruses created in laboratories. There are some concerns regarding OVs' toxicity, due to their ability to partially replicate in healthy tissues. In addition, lytic and immunological responses upon OV therapy are not always sufficient, so various OV editing methods are used. This review discusses the latest results of preclinical and clinical studies of OVs, modifications of which are associated with the miRNA-mediated mechanism of gene silencing.
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Affiliation(s)
- Mariia Toropko
- Gene Therapy Department, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia; (S.C.); (A.K.)
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Masoudikabir P, Shirazy M, Taghizadeh FS, Gheydari ME, Hamidpour M. Platelet-enriched microRNAs as novel biomarkers in atherosclerotic and cardiovascular disease patients. ARYA ATHEROSCLEROSIS 2024; 20:47-67. [PMID: 39717424 PMCID: PMC11663285 DOI: 10.48305/arya.2024.41664.2898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/26/2023] [Indexed: 12/25/2024]
Abstract
BACKGROUND Cardiovascular disease (CVD) is a global health challenge. Various studies have shown that genetic and environmental factors play roles in the development and progression of CVD. Small non-coding RNAs, namely microRNAs (miRs), regulate gene expression and have key roles in essential cellular processes such as apoptosis, cell cycle, differentiation, and proliferation. Currently, clinical studies highlight the critical role of platelets and miRs in coronary thrombosis, atherosclerosis, and CVD. METHODS Using search engines such as PubMed and Scopus, articles studying platelet miRs and their effects on atherosclerosis and cardiovascular disease were reviewed. RESULTS This article presents a comprehensive analysis of the association of platelet-related miRs as prognostic, diagnostic, and therapeutic biomarkers with the pathogenesis of atherosclerosis and cardiovascular disease. CONCLUSION Taken together, data show that platelet-related miRs not only play important roles in the initial development of atherosclerosis and cardiovascular disease (CVD), but they are also considered prognostic and diagnostic biomarkers in CVD.
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Affiliation(s)
- Parisa Masoudikabir
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Shirazy
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Mohamad Esmail Gheydari
- Department of Cardiology, Taleghani General Hospital. School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Hamidpour
- Hematopoietic stem cell Research Centre- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Nassiri SM, Ahmadi Afshar N, Almasi P. Insight into microRNAs' involvement in hematopoiesis: current standing point of findings. Stem Cell Res Ther 2023; 14:282. [PMID: 37794439 PMCID: PMC10552299 DOI: 10.1186/s13287-023-03504-3] [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: 12/28/2022] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
Hematopoiesis is a complex process in which hematopoietic stem cells are differentiated into all mature blood cells (red blood cells, white blood cells, and platelets). Different microRNAs (miRNAs) involve in several steps of this process. Indeed, miRNAs are small single-stranded non-coding RNA molecules, which control gene expression by translational inhibition and mRNA destabilization. Previous studies have revealed that increased or decreased expression of some of these miRNAs by targeting several proto-oncogenes could inhibit or stimulate the myeloid and erythroid lineage commitment, proliferation, and differentiation. During the last decades, the development of molecular and bioinformatics techniques has led to a comprehensive understanding of the role of various miRNAs in hematopoiesis. The critical roles of miRNAs in cell processes such as the cell cycle, apoptosis, and differentiation have been confirmed as well. However, the main contribution of some miRNAs is still unclear. Therefore, it seems undeniable that future studies are required to focus on miRNA activities during various hematopoietic stages and hematological malignancy.
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Affiliation(s)
- Seyed Mahdi Nassiri
- Department of Clinical Pathology, Faculty of Veterinary Medicine, University of Tehran, Qarib St., Azadi Ave, Tehran, Iran.
| | - Neda Ahmadi Afshar
- Department of Clinical Pathology, Faculty of Veterinary Medicine, University of Tehran, Qarib St., Azadi Ave, Tehran, Iran
| | - Parsa Almasi
- Department of Clinical Pathology, Faculty of Veterinary Medicine, University of Tehran, Qarib St., Azadi Ave, Tehran, Iran
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Janosevic D, De Luca T, Ferreira RM, Gisch DL, Hato T, Luo J, Yang Y, Hodgin JB, Dagher PC, Eadon MT. miRNA and mRNA Signatures in Human Acute Kidney Injury Tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557054. [PMID: 37745313 PMCID: PMC10515816 DOI: 10.1101/2023.09.11.557054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Acute kidney injury (AKI) is an important contributor to the development of chronic kidney disease (CKD). There is a need to understand molecular mediators that drive either recovery or progression to CKD. In particular, the role of miRNA and its regulatory role in AKI is poorly understood. We performed miRNA and mRNA sequencing on biobanked human kidney tissues obtained in the routine clinical care of patients with the diagnoses of AKI and minimal change disease (MCD), in addition to nephrectomized (Ref) tissue from individuals without known kidney disease. Transcriptomic analysis of mRNA revealed that Ref tissues exhibited a similar injury signature to AKI, not identified in MCD samples. The transcriptomic signature of human AKI was enriched with genes in pathways involved in cell adhesion and epithelial-to-mesenchymal transition (e.g., CDH6, ITGB6, CDKN1A ). miRNA DE analysis revealed upregulation of miRNA associated with immune cell recruitment and inflammation (e.g., miR-146a, miR-155, miR-142, miR-122). These miRNA (i.e., miR-122, miR-146) are also associated with downregulation of mRNA such as DDR2 and IGFBP6 , respectively. These findings suggest integrated interactions between miRNAs and target mRNAs in AKI-related processes such as inflammation, immune cell activation and epithelial-to-mesenchymal transition. These data contribute several novel findings when describing the epigenetic regulation of AKI by miRNA, and also underscores the importance of utilizing an appropriate reference control tissue to understand canonical pathway alterations in AKI.
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Olson WJ, Derudder E. The miR-142 miRNAs: Shaping the naïve immune system. Immunol Lett 2023; 261:37-46. [PMID: 37459958 DOI: 10.1016/j.imlet.2023.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 06/21/2023] [Accepted: 07/10/2023] [Indexed: 08/01/2023]
Abstract
Immunity in a naïve organism is tightly controlled. Adequate proportions of the many immune cell subsets must be produced to mount efficient responses to eventual challenges. In addition, a functioning immune system is highly dynamic at steady state. Mature immune cells must be positioned properly and/or circulate to facilitate the detection of dangers. They must also be poised to promptly react to unusual encounters, while ignoring innocuous germs and self. Numerous regulatory mechanisms act at the molecular level to generate such an exquisite structure, including miRNA-mediated repression of protein synthesis. Notably, the miRNAs from the miR-142 locus are preferentially expressed in hematopoietic cells. Their importance is underscored by the deeply disturbed immune system seen upon inactivation of the locus in mice. In this review, we explore reported roles for the miR-142 miRNAs in the shaping of immunity in vertebrates, discussing in particular their contributions to the generation, migration and survival of hematopoietic cells.
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Affiliation(s)
- William J Olson
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Emmanuel Derudder
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria.
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10
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Morris JA, Caragine C, Daniloski Z, Domingo J, Barry T, Lu L, Davis K, Ziosi M, Glinos DA, Hao S, Mimitou EP, Smibert P, Roeder K, Katsevich E, Lappalainen T, Sanjana NE. Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens. Science 2023; 380:eadh7699. [PMID: 37141313 PMCID: PMC10518238 DOI: 10.1126/science.adh7699] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
Most variants associated with complex traits and diseases identified by genome-wide association studies (GWAS) map to noncoding regions of the genome with unknown effects. Using ancestrally diverse, biobank-scale GWAS data, massively parallel CRISPR screens, and single-cell transcriptomic and proteomic sequencing, we discovered 124 cis-target genes of 91 noncoding blood trait GWAS loci. Using precise variant insertion through base editing, we connected specific variants with gene expression changes. We also identified trans-effect networks of noncoding loci when cis target genes encoded transcription factors or microRNAs. Networks were themselves enriched for GWAS variants and demonstrated polygenic contributions to complex traits. This platform enables massively parallel characterization of the target genes and mechanisms of human noncoding variants in both cis and trans.
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Affiliation(s)
- John A. Morris
- New York Genome Center, New York, NY, 10013, USA
- Department of Biology, New York University, New York, NY, 10003, USA
| | | | - Zharko Daniloski
- New York Genome Center, New York, NY, 10013, USA
- Department of Biology, New York University, New York, NY, 10003, USA
| | | | - Timothy Barry
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Lu Lu
- New York Genome Center, New York, NY, 10013, USA
| | - Kyrie Davis
- New York Genome Center, New York, NY, 10013, USA
| | | | | | - Stephanie Hao
- Technology Innovation Lab, New York Genome Center, New York, NY, 10013, USA
| | - Eleni P. Mimitou
- Technology Innovation Lab, New York Genome Center, New York, NY, 10013, USA
| | - Peter Smibert
- Technology Innovation Lab, New York Genome Center, New York, NY, 10013, USA
| | - Kathryn Roeder
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Eugene Katsevich
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, 10013, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 171 65 Solna, Stockholm, Sweden
| | - Neville E. Sanjana
- New York Genome Center, New York, NY, 10013, USA
- Department of Biology, New York University, New York, NY, 10003, USA
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11
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Menegatti J, Nakel J, Stepanov YK, Caban KM, Ludwig N, Nord R, Pfitzner T, Yazdani M, Vilimova M, Kehl T, Lenhof HP, Philipp SE, Meese E, Fröhlich T, Grässer FA, Hart M. Changes of Protein Expression after CRISPR/Cas9 Knockout of miRNA-142 in Cell Lines Derived from Diffuse Large B-Cell Lymphoma. Cancers (Basel) 2022; 14:cancers14205031. [PMID: 36291816 PMCID: PMC9600116 DOI: 10.3390/cancers14205031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/22/2022] Open
Abstract
Simple Summary The gene of the human tumor suppressive microRNA-142 (miR-142) carries mutations in about 20% of cases of diffuse large B-cell lymphoma (DLBCL). Because microRNAs post-transcriptionally regulate the protein expression of their cognate messenger RNA (mRNAs) targets, we determined the effect of miR-142 knockout on protein expression in two cell lines derived from DLBCL. We found a significant up-regulation of 52 proteins but also a down-regulation of 41 proteins upon miR-142 deletion. Knockout of a miRNA may be used to identify novel targets, and seed-sequence mutants of a miRNA unable to bind to their targets can be used to confirm potential novel targets. With this approach, we identify AKT1S1, CCNB1, LIMA1 and TFRC as novel targets of miR-142. As miR-142 is highly present in the miRNA processing RISC complexes, the deletion of this miRNA might result in its replacement by other miRNAs, thus introducing an additional layer of complexity regarding gene regulation. Abstract Background: As microRNA-142 (miR-142) is the only human microRNA gene where mutations have consistently been found in about 20% of all cases of diffuse large B-cell lymphoma (DLBCL), we wanted to determine the impact of miR-142 inactivation on protein expression of DLBCL cell lines. Methods: miR-142 was deleted by CRISPR/Cas9 knockout in cell lines from DLBCL. Results: By proteome analyses, miR-142 knockout resulted in a consistent up-regulation of 52 but also down-regulation of 41 proteins in GC-DLBCL lines BJAB and SUDHL4. Various mitochondrial ribosomal proteins were up-regulated in line with their pro-tumorigenic properties, while proteins necessary for MHC-I presentation were down-regulated in accordance with the finding that miR-142 knockout mice have a defective immune response. CFL2, CLIC4, STAU1, and TWF1 are known targets of miR-142, and we could additionally confirm AKT1S1, CCNB1, LIMA1, and TFRC as new targets of miR-142-3p or -5p. Conclusions: Seed-sequence mutants of miR-142 confirmed potential targets and novel targets of miRNAs can be identified in miRNA knockout cell lines. Due to the complex contribution of miRNAs within cellular regulatory networks, in particular when miRNAs highly present in RISC complexes are replaced by other miRNAs, primary effects on gene expression may be covered by secondary layers of regulation.
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Affiliation(s)
- Jennifer Menegatti
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Jacqueline Nakel
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Youli K. Stepanov
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Karolina M. Caban
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Nicole Ludwig
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Ruth Nord
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Thomas Pfitzner
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Maryam Yazdani
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Monika Vilimova
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Germany
| | - Stephan E. Philipp
- Experimental and Clinical Pharmacology and Toxicology, Saarland University Medical School, 66421 Homburg, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Friedrich A. Grässer
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
- Correspondence: (F.A.G.); (M.H.)
| | - Martin Hart
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
- Correspondence: (F.A.G.); (M.H.)
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12
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Actin dynamics in protein homeostasis. Biosci Rep 2022; 42:231720. [PMID: 36043949 PMCID: PMC9469105 DOI: 10.1042/bsr20210848] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Cell homeostasis is maintained in all organisms by the constant adjustment of cell constituents and organisation to account for environmental context. Fine-tuning of the optimal balance of proteins for the conditions, or protein homeostasis, is critical to maintaining cell homeostasis. Actin, a major constituent of the cytoskeleton, forms many different structures which are acutely sensitive to the cell environment. Furthermore, actin structures interact with and are critically important for the function and regulation of multiple factors involved with mRNA and protein production and degradation, and protein regulation. Altogether, actin is a key, if often overlooked, regulator of protein homeostasis across eukaryotes. In this review, we highlight these roles and how they are altered following cell stress, from mRNA transcription to protein degradation.
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13
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Leng Q, Ding J, Dai M, Liu L, Fang Q, Wang DW, Wu L, Wang Y. Insights Into Platelet-Derived MicroRNAs in Cardiovascular and Oncologic Diseases: Potential Predictor and Therapeutic Target. Front Cardiovasc Med 2022; 9:879351. [PMID: 35757325 PMCID: PMC9218259 DOI: 10.3389/fcvm.2022.879351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/24/2022] [Indexed: 11/28/2022] Open
Abstract
Non-communicable diseases (NCDs), represented by cardiovascular diseases and cancer, have been the leading cause of death globally. Improvements in mortality from cardiovascular (CV) diseases (decrease of 14%/100,000, United States) or cancers (increase 7.5%/100,000, United States) seem unsatisfactory during the past two decades, and so the search for innovative and accurate biomarkers of early diagnosis and prevention, and novel treatment strategies is a valuable clinical and economic endeavor. Both tumors and cardiovascular system are rich in angiological systems that maintain material exchange, signal transduction and distant regulation. This pattern determines that they are strongly influenced by circulating substances, such as glycolipid metabolism, inflammatory homeostasis and cyclic non-coding RNA and so forth. Platelets, a group of small anucleated cells, inherit many mature proteins, mRNAs, and non-coding RNAs from their parent megakaryocytes during gradual formation and manifest important roles in inflammation, angiogenesis, atherosclerosis, stroke, myocardial infarction, diabetes, cancer, and many other diseases apart from its classical function in hemostasis. MicroRNAs (miRNAs) are a class of non-coding RNAs containing ∼22 nucleotides that participate in many key cellular processes by pairing with mRNAs at partially complementary binding sites for post-transcriptional regulation of gene expression. Platelets contain fully functional miRNA processors in their microvesicles and are able to transport their miRNAs to neighboring cells and regulate their gene expression. Therefore, the importance of platelet-derived miRNAs for the human health is of increasing interest. Here, we will elaborate systematically the roles of platelet-derived miRNAs in cardiovascular disease and cancer in the hope of providing clinicians with new ideas for early diagnosis and therapeutic strategies.
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14
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Wunderlich F, Delic D, Gerovska D, Araúzo-Bravo MJ. Vaccination Accelerates Liver-Intrinsic Expression of Megakaryocyte-Related Genes in Response to Blood-Stage Malaria. Vaccines (Basel) 2022; 10:vaccines10020287. [PMID: 35214745 PMCID: PMC8880532 DOI: 10.3390/vaccines10020287] [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: 11/29/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023] Open
Abstract
Erythropoiesis and megakaryo-/thrombopoiesis occur in the bone marrow proceeding from common, even bipotent, progenitor cells. Recently, we have shown that protective vaccination accelerates extramedullary hepatic erythroblastosis in response to blood-stage malaria of Plasmodium chabaudi. Here, we investigated whether protective vaccination also accelerates extramedullary hepatic megakaryo-/thrombopoiesis. Female Balb/c mice were twice vaccinated with a non-infectious vaccine before infecting with 106 P. chabaudi-parasitized erythrocytes. Using gene expression microarrays and quantitative real-time PCR, transcripts of genes known to be expressed in the bone marrow by cells of the megakaryo-/thrombocytic lineage were compared in livers of vaccination-protected and unprotected mice on days 0, 1, 4, 8, and 11 p.i. Livers of vaccination-protected mice responded with expression of megakaryo-/thrombocytic genes faster to P. chabaudi than those of unvaccinated mice, evidenced at early patency on day 4 p.i., when livers exhibited significantly higher levels of malaria-induced transcripts of the genes Selp and Pdgfb (p-values < 0.0001), Gp5 (p-value < 0.001), and Fli1, Runx1, Myb, Mpl, Gp1ba, Gp1bb, Gp6, Gp9, Pf4, and Clec1b (p-values < 0.01). Together with additionally analyzed genes known to be related to megakaryopoiesis, our data suggest that protective vaccination accelerates liver-intrinsic megakaryo-/thrombopoiesis in response to blood-stage malaria that presumably contributes to vaccination-induced survival of otherwise lethal blood-stage malaria.
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Affiliation(s)
- Frank Wunderlich
- Department of Biology, Heinrich-Heine-University, 40225 Düsseldorf, Germany;
| | - Denis Delic
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach, Germany
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, 68167 Heidelberg, Germany
- Correspondence: (D.D.); (M.J.A.-B.)
| | - Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastian, Spain;
| | - Marcos J. Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastian, Spain;
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
- TransBioNet Thematic Network of Excellence for Transitional Bioinformatics, Barcelona Supercomputing Center, 08034 Barcelona, Spain
- Correspondence: (D.D.); (M.J.A.-B.)
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15
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Wang WL, Ouyang C, Graham NM, Zhang Y, Cassady K, Reyes EY, Xiong M, Davis AM, Tang K, Zeng D, Boldin MP. microRNA-142 guards against autoimmunity by controlling Treg cell homeostasis and function. PLoS Biol 2022; 20:e3001552. [PMID: 35180231 PMCID: PMC8893712 DOI: 10.1371/journal.pbio.3001552] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/03/2022] [Accepted: 01/21/2022] [Indexed: 01/10/2023] Open
Abstract
Regulatory T (Treg) cells are critical in preventing aberrant immune responses. Posttranscriptional control of gene expression by microRNA (miRNA) has recently emerged as an essential genetic element for Treg cell function. Here, we report that mice with Treg cell-specific ablation of miR-142 (hereafter Foxp3CremiR-142fl/fl mice) developed a fatal systemic autoimmune disorder due to a breakdown in peripheral T-cell tolerance. Foxp3CremiR-142fl/fl mice displayed a significant decrease in the abundance and suppressive capacity of Treg cells. Expression profiling of miR-142-deficient Treg cells revealed an up-regulation of multiple genes in the interferon gamma (IFNγ) signaling network. We identified several of these IFNγ-associated genes as direct miR-142-3p targets and observed excessive IFNγ production and signaling in miR-142-deficient Treg cells. Ifng ablation rescued the Treg cell homeostatic defect and alleviated development of autoimmunity in Foxp3CremiR-142fl/fl mice. Thus, our findings implicate miR-142 as an indispensable regulator of Treg cell homeostasis that exerts its function by attenuating IFNγ responses.
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Affiliation(s)
- Wei-Le Wang
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States of America
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Ching Ouyang
- Center for Informatics, Beckman Research Institute, City of Hope, Duarte, California, United States of America
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Natalie M. Graham
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States of America
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Yuankun Zhang
- Department of Diabetes Research, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Kaniel Cassady
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States of America
- Department of Diabetes Research, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Estefany Y. Reyes
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Min Xiong
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States of America
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Alicia M. Davis
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Kathie Tang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Defu Zeng
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States of America
- Department of Diabetes Research, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Mark P. Boldin
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States of America
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, California, United States of America
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16
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Screening Analysis of Platelet miRNA Profile Revealed miR-142-3p as a Potential Biomarker in Modeling the Risk of Acute Coronary Syndrome. Cells 2021; 10:cells10123526. [PMID: 34944034 PMCID: PMC8700136 DOI: 10.3390/cells10123526] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/04/2021] [Accepted: 12/11/2021] [Indexed: 12/18/2022] Open
Abstract
Transcriptome analysis constitutes one of the major methods of elucidation of the genetic basis underlying the pathogenesis of various diseases. The post-transcriptional regulation of gene expression is mainly provided by microRNAs. Their remarkable stability in biological fluids and their high sensitivity to disease alteration indicates their potential role as biomarkers. Given the high mortality and morbidity of cardiovascular diseases, novel predictive biomarkers are sorely needed. Our study focuses for the first time on assessing potential biomarkers of acute coronary syndrome (ACS) based on the microRNA profiles of platelets. The study showed the overexpression of eight platelet microRNAs in ACS (miR-142-3p; miR-107; miR-338-3p, miR-223-3p, miR-21-5p, miR-130b-3p, miR-301a-3p, miR-221-3p) associated with platelet reactivity and functionality. Our results show that the combined model based on miR-142-3p and aspartate transaminase reached 82% sensitivity and 88% specificity in the differentiation of the studied groups. Furthermore, the analyzed miRNAs were shown to cluster into two orthogonal groups, regulated by two different biological factors. Bioinformatic analysis demonstrated that one group of microRNAs may be associated with the physiological processes of platelets, whereas the other group may be linked to platelet-vascular environment interactions. This analysis paves the way towards a better understanding of the role of platelet microRNAs in ACS pathophysiology and better modeling of the risk of ACS.
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17
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Bhatlekar S, Jacob S, Manne BK, Guo L, Denorme F, Tugolukova EA, Cody MJ, Kosaka Y, Rigoutsos I, Campbell RA, Rowley JW, O'Connell RM, Bray PF. Megakaryocyte-specific knockout of the Mir-99b/let7e/125a cluster lowers platelet count without altering platelet function. Blood Cells Mol Dis 2021; 92:102624. [PMID: 34775219 PMCID: PMC8682963 DOI: 10.1016/j.bcmd.2021.102624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 12/11/2022]
Abstract
The purpose of this research was to assess the effects of a microRNA (miRNA) cluster on platelet production. Human chromosome 19q13.41 harbors an evolutionarily conserved cluster of three miRNA genes (MIR99B, MIRLET7E, MIR125A) within 727 base-pairs. We now report that levels of miR-99b-5p, miR-let7e-5p and miR-125a-5p are strongly correlated in human platelets, and all are positively associated with platelet count, but not white blood count or hemoglobin level. Although the cluster regulates hematopoietic stem cell proliferation, the function of this genomic locus in megakaryocyte (MK) differentiation and platelet production is unknown. Furthermore, studies of individual miRNAs do not represent broader effects in the context of a cluster. To address this possibility, MK/platelet lineage-specific Mir-99b/let7e/125a knockout mice were generated. Compared to wild type littermates, cluster knockout mice had significantly lower platelet counts and reduced MK proplatelet formation, but no differences in MK numbers, ploidy, maturation or ultra-structural morphology, and no differences in platelet function. Compared to wild type littermates, knockout mice showed similar survival after pulmonary embolism. The major conclusions are that the effect of the Mir-99b/let7e/125a cluster is confined to a late stage of thrombopoiesis, and this effect on platelet number is uncoupled from platelet function.
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Affiliation(s)
- Seema Bhatlekar
- Program in Molecular Medicine and Department of Internal Medicine, 15 North 2030 East, Bldg 533, University of Utah, Salt Lake City, UT 84112, United States of America
| | - Shancy Jacob
- Program in Molecular Medicine and Department of Internal Medicine, 15 North 2030 East, Bldg 533, University of Utah, Salt Lake City, UT 84112, United States of America
| | - Bhanu K Manne
- Program in Molecular Medicine and Department of Internal Medicine, 15 North 2030 East, Bldg 533, University of Utah, Salt Lake City, UT 84112, United States of America
| | - Li Guo
- Program in Molecular Medicine and Department of Internal Medicine, 15 North 2030 East, Bldg 533, University of Utah, Salt Lake City, UT 84112, United States of America
| | - Frederik Denorme
- Program in Molecular Medicine and Department of Internal Medicine, 15 North 2030 East, Bldg 533, University of Utah, Salt Lake City, UT 84112, United States of America
| | - Emilia A Tugolukova
- Program in Molecular Medicine and Department of Internal Medicine, 15 North 2030 East, Bldg 533, University of Utah, Salt Lake City, UT 84112, United States of America
| | - Mark J Cody
- Program in Molecular Medicine and Department of Internal Medicine, 15 North 2030 East, Bldg 533, University of Utah, Salt Lake City, UT 84112, United States of America
| | - Yasuhiro Kosaka
- Program in Molecular Medicine and Department of Internal Medicine, 15 North 2030 East, Bldg 533, University of Utah, Salt Lake City, UT 84112, United States of America
| | - Isidore Rigoutsos
- Computational Medicine Center, Thomas Jefferson University, 1020 Locust, Philadelphia, PA 19107, United States of America
| | - Robert A Campbell
- Program in Molecular Medicine and Department of Internal Medicine, 15 North 2030 East, Bldg 533, University of Utah, Salt Lake City, UT 84112, United States of America
| | - Jesse W Rowley
- Program in Molecular Medicine and Department of Internal Medicine, 15 North 2030 East, Bldg 533, University of Utah, Salt Lake City, UT 84112, United States of America
| | - Ryan M O'Connell
- Division of Microbiology and Immunology, Department of Pathology, Huntsman Cancer Institute, University of Utah, 2000 Cir of Hope Dr, Salt Lake City, UT 84112, United States of America
| | - Paul F Bray
- Program in Molecular Medicine and Department of Internal Medicine, 15 North 2030 East, Bldg 533, University of Utah, Salt Lake City, UT 84112, United States of America; Division of Hematology and Hematologic Malignancies, Department of Internal Medicine, University of Utah, 2000 Cir of Hope Dr, Salt Lake City, UT 84112, United States of America.
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18
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Roberts LB, Kapoor P, Howard JK, Shah AM, Lord GM. An update on the roles of immune system-derived microRNAs in cardiovascular diseases. Cardiovasc Res 2021; 117:2434-2449. [PMID: 33483751 PMCID: PMC8562329 DOI: 10.1093/cvr/cvab007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/08/2021] [Indexed: 12/12/2022] Open
Abstract
Cardiovascular diseases (CVD) are a leading cause of human death worldwide. Over the past two decades, the emerging field of cardioimmunology has demonstrated how cells of the immune system play vital roles in the pathogenesis of CVD. MicroRNAs (miRNAs) are critical regulators of cellular identity and function. Cell-intrinsic, as well as cell-extrinsic, roles of immune and inflammatory cell-derived miRNAs have been, and continue to be, extensively studied. Several 'immuno-miRNAs' appear to be specifically expressed or demonstrate greatly enriched expression within leucocytes. Identification of miRNAs as critical regulators of immune system signalling pathways has posed the question of whether and how targeting these molecules therapeutically, may afford opportunities for disease treatment and/or management. As the field of cardioimmunology rapidly continues to advance, this review discusses findings from recent human and murine studies which contribute to our understanding of how leucocytes of innate and adaptive immunity are regulated-and may also regulate other cell types, via the actions of the miRNAs they express, in the context of CVD. Finally, we focus on available information regarding miRNA regulation of regulatory T cells and argue that targeted manipulation of miRNA regulated pathways in these cells may hold therapeutic promise for the treatment of CVD and associated risk factors.
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Affiliation(s)
- Luke B Roberts
- School of Immunology and Microbial Sciences, King’s College London, Great Maze Pond, London SE1 9RT, UK
| | - Puja Kapoor
- School of Immunology and Microbial Sciences, King’s College London, Great Maze Pond, London SE1 9RT, UK
- School of Cardiovascular Medicine and Sciences, King’s British Heart Foundation Centre, King’s College London, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Jane K Howard
- School of Life Course Sciences, King’s College London, Great Maze Pond, London SE1 9RT, UK
| | - Ajay M Shah
- School of Cardiovascular Medicine and Sciences, King’s British Heart Foundation Centre, King’s College London, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Graham M Lord
- School of Immunology and Microbial Sciences, King’s College London, Great Maze Pond, London SE1 9RT, UK
- Faculty of Biology, Medicine and Health, University of Manchester, 46 Grafton Street, Manchester M13 9NT, UK
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19
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Receptor tyrosine kinase ROR1 ameliorates Aβ 1-42 induced cytoskeletal instability and is regulated by the miR146a-NEAT1 nexus in Alzheimer's disease. Sci Rep 2021; 11:19254. [PMID: 34584188 PMCID: PMC8479066 DOI: 10.1038/s41598-021-98882-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/19/2021] [Indexed: 11/25/2022] Open
Abstract
Alzheimer’s disease (AD) involves severe cytoskeletal degradation and microtubule disruption. Here, we studied the altered dynamics of ROR1, a Receptor Tyrosine Kinase (RTK), and how it could counter these abnormalities. We found that in an Aβ1–42 treated cell model of AD, ROR1 was significantly decreased. Over expressed ROR1 led to the abrogation of cytoskeletal protein degradation, even in the presence of Aβ1–42, preserved the actin network, altered actin dynamics and promoted neuritogenesis. Bioinformatically predicted miRNAs hsa-miR-146a and 34a were strongly up regulated in the cell model and their over expression repressed ROR1. LncRNA NEAT1, an interactor of these miRNAs, was elevated in mice AD brain and cell model concordantly. RNA Immunoprecipitation confirmed a physical interaction between the miRNAs and NEAT1. Intuitively, a transient knock down of NEAT1 increased their levels. To our knowledge, this is the first instance which implicates ROR1 in AD and proposes its role in preserving the cytoskeleton. The signalling modalities are uniquely analyzed from the regulatory perspectives with miR-146a and miR-34a repressing ROR1 and in turn getting regulated by NEAT1.
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20
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Roberts LB, Jowett GM, Read E, Zabinski T, Berkachy R, Selkirk ME, Jackson I, Niazi U, Anandagoda N, Araki M, Araki K, Kasturiarachchi J, James C, Enver T, Nimmo R, Reis R, Howard JK, Neves JF, Lord GM. MicroRNA-142 Critically Regulates Group 2 Innate Lymphoid Cell Homeostasis and Function. THE JOURNAL OF IMMUNOLOGY 2021; 206:2725-2739. [PMID: 34021046 PMCID: PMC7610861 DOI: 10.4049/jimmunol.2000647] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 03/19/2021] [Indexed: 02/06/2023]
Abstract
MicroRNA-142 isoforms critically regulate ILC2 homeostasis and effector functions. MicroRNA-142 isoforms regulate the ILC2 lineage cell intrinsically. Socs1 and Gfi1 are miR-142 isoform regulated targets in ILC2s.
Innate lymphoid cells are central to the regulation of immunity at mucosal barrier sites, with group 2 innate lymphoid cells (ILC2s) being particularly important in type 2 immunity. In this study, we demonstrate that microRNA(miR)-142 plays a critical, cell-intrinsic role in the homeostasis and function of ILC2s. Mice deficient for miR-142 expression demonstrate an ILC2 progenitor–biased development in the bone marrow, and along with peripheral ILC2s at mucosal sites, these cells display a greatly altered phenotype based on surface marker expression. ILC2 proliferative and effector functions are severely dysfunctional following Nippostrongylus brasiliensis infection, revealing a critical role for miR-142 isoforms in ILC2-mediated immune responses. Mechanistically, Socs1 and Gfi1 expression are regulated by miR-142 isoforms in ILC2s, impacting ILC2 phenotypes as well as the proliferative and effector capacity of these cells. The identification of these novel pathways opens potential new avenues to modulate ILC2-dependent immune functions.
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Affiliation(s)
- Luke B Roberts
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Geraldine M Jowett
- Centre for Host-Microbiome Interactions, King's College London, London, United Kingdom.,Centre for Craniofacial and Regenerative Biology, King's College London, London, United Kingdom.,Wellcome Trust Cell Therapies and Regenerative Medicine PhD program, London, United Kingdom
| | - Emily Read
- Centre for Host-Microbiome Interactions, King's College London, London, United Kingdom.,Wellcome Trust Cell Therapies and Regenerative Medicine PhD program, London, United Kingdom
| | - Tomas Zabinski
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Rita Berkachy
- Department of Life Sciences, Imperial College London, United Kingdom
| | - Murray E Selkirk
- Department of Life Sciences, Imperial College London, United Kingdom
| | - Ian Jackson
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Umar Niazi
- Guy's and St Thomas' National Health Service Foundation Trust and King's College London National Institute for Health Research Biomedical Research Centre Translational Bioinformatics Platform, Guy's Hospital, London, United Kingdom
| | - Nelomi Anandagoda
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Masatake Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Jagath Kasturiarachchi
- University College London Cancer Institute, University College London, London, United Kingdom
| | - Chela James
- University College London Cancer Institute, University College London, London, United Kingdom
| | - Tariq Enver
- University College London Cancer Institute, University College London, London, United Kingdom
| | - Rachael Nimmo
- University College London Cancer Institute, University College London, London, United Kingdom
| | - Rita Reis
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Jane K Howard
- School of Life Course Sciences, King's College London, London, United Kingdom; and
| | - Joana F Neves
- Centre for Host-Microbiome Interactions, King's College London, London, United Kingdom
| | - Graham M Lord
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom; .,Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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21
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MicroRNAs in shaping the resolution phase of inflammation. Semin Cell Dev Biol 2021; 124:48-62. [PMID: 33934990 DOI: 10.1016/j.semcdb.2021.03.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022]
Abstract
Inflammation is a host defense mechanism orchestrated through imperative factors - acute inflammatory responses mediated by cellular and molecular events leading to activation of defensive immune subsets - to marginalize detrimental injury, pathogenic agents and infected cells. These potent inflammatory events, if uncontrolled, may cause tissue damage by perturbing homeostasis towards immune dysregulation. A parallel host mechanism operates to contain inflammatory pathways and facilitate tissue regeneration. Thus, resolution of inflammation is an effective moratorium on the pro-inflammatory pathway to avoid the tissue damage inside the host and leads to reestablishment of tissue homeostasis. Dysregulation of the resolution pathway can have a detrimental impact on tissue functionality and contribute to the diseased state. Multiple reports have suggested peculiar dynamics of miRNA expression during various pro- and anti-inflammatory events. The roles of miRNAs in the regulation of immune responses are well-established. However, understanding of miRNA regulation of the resolution phase of events in infection or wound healing models, which is sometimes misconstrued as anti-inflammatory signaling, remains limited. Due to the deterministic role of miRNAs in pro-inflammatory and anti-inflammatory pathways, in this review we have provided a broad perspective on the putative role of miRNAs in the resolution of inflammation and explored their imminent role in therapeutics.
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22
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Mir142 loss unlocks IDH2 R140-dependent leukemogenesis through antagonistic regulation of HOX genes. Sci Rep 2020; 10:19390. [PMID: 33173219 PMCID: PMC7656267 DOI: 10.1038/s41598-020-76218-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 10/22/2020] [Indexed: 12/30/2022] Open
Abstract
AML is a genetically heterogeneous disease and understanding how different co-occurring mutations cooperate to drive leukemogenesis will be crucial for improving diagnostic and therapeutic options for patients. MIR142 mutations have been recurrently detected in IDH-mutated AML samples. Here, we have used a mouse model to investigate the interaction between these two mutations and demonstrate a striking synergy between Mir142 loss-of-function and IDH2R140Q, with only recipients of double mutant cells succumbing to leukemia. Transcriptomic analysis of the non-leukemic single and leukemic double mutant progenitors, isolated from these mice, suggested a novel mechanism of cooperation whereby Mir142 loss-of-function counteracts aberrant silencing of Hoxa cluster genes by IDH2R140Q. Our analysis suggests that IDH2R140Q is an incoherent oncogene, with both positive and negative impacts on leukemogenesis, which requires the action of cooperating mutations to alleviate repression of Hoxa genes in order to advance to leukemia. This model, therefore, provides a compelling rationale for understanding how different mutations cooperate to drive leukemogenesis and the context-dependent effects of oncogenic mutations.
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23
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Bhatlekar S, Manne BK, Basak I, Edelstein LC, Tugolukova E, Stoller ML, Cody MJ, Morley SC, Nagalla S, Weyrich AS, Rowley JW, O'Connell RM, Rondina MT, Campbell RA, Bray PF. miR-125a-5p regulates megakaryocyte proplatelet formation via the actin-bundling protein L-plastin. Blood 2020; 136:1760-1772. [PMID: 32844999 PMCID: PMC7544541 DOI: 10.1182/blood.2020005230] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/24/2020] [Indexed: 12/17/2022] Open
Abstract
There is heritability to interindividual variation in platelet count, and better understanding of the regulating genetic factors may provide insights for thrombopoiesis. MicroRNAs (miRs) regulate gene expression in health and disease, and megakaryocytes (MKs) deficient in miRs have lower platelet counts, but information about the role of miRs in normal human MK and platelet production is limited. Using genome-wide miR profiling, we observed strong correlations among human bone marrow MKs, platelets, and differentiating cord blood-derived MK cultures, and identified MK miR-125a-5p as associated with human platelet number but not leukocyte or hemoglobin levels. Overexpression and knockdown studies showed that miR-125a-5p positively regulated human MK proplatelet (PP) formation in vitro. Inhibition of miR-125a-5p in vivo lowered murine platelet counts. Analyses of MK and platelet transcriptomes identified LCP1 as a miR-125a-5p target. LCP1 encodes the actin-bundling protein, L-plastin, not previously studied in MKs. We show that miR-125a-5p directly targets and reduces expression of MK L-plastin. Overexpression and knockdown studies show that L-plastin promotes MK progenitor migration, but negatively correlates with human platelet count and inhibits MK PP formation (PPF). This work provides the first evidence for the actin-bundling protein, L-plastin, as a regulator of human MK PPF via inhibition of the late-stage MK invagination system, podosome and PPF, and PP branching. We also provide resources of primary and differentiating MK transcriptomes and miRs associated with platelet counts. miR-125a-5p and L-plastin may be relevant targets for increasing in vitro platelet manufacturing and for managing quantitative platelet disorders.
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Affiliation(s)
- Seema Bhatlekar
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT
| | - Bhanu K Manne
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT
| | - Indranil Basak
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT
| | - Leonard C Edelstein
- Cardeza Foundation for Hematologic Research, Thomas Jefferson University, Philadelphia, PA
| | - Emilia Tugolukova
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT
| | | | - Mark J Cody
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT
| | - Sharon C Morley
- Division of Infectious Diseases, Department of Pediatrics and
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Srikanth Nagalla
- Division of Hematology and Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Andrew S Weyrich
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT
- Division of Pulmonary, Department of Internal Medicine
| | - Jesse W Rowley
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT
- Division of Pulmonary, Department of Internal Medicine
| | - Ryan M O'Connell
- Division of Microbiology and Immunology, Department of Pathology, and
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Matthew T Rondina
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT
- Geriatric Research, Education and Clinical Center, George E. Wahlen VAMC GRECC, Salt Lake City, UT; and
- Division of General Internal Medicine and
| | - Robert A Campbell
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT
- Division of General Internal Medicine and
| | - Paul F Bray
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT
- Division of Hematology and Hematologic Malignancies, Department of Internal Medicine, University of Utah, Salt Lake City, UT
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24
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Valverde A, Nares S, Naqvi AR. Impaired cell migration and structural defects in myeloid cells overexpressing miR-30b and miR-142-3p. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194628. [PMID: 32979559 DOI: 10.1016/j.bbagrm.2020.194628] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 12/27/2022]
Abstract
Macrophages (MΦ) and dendritic cells (DC) play a fundamental role in shaping immune responses by sensing a plethora of Pathogen Associated Molecular Patterns (PAMPs), phagocytosis and antigen presentation to T lymphocytes. These important biological processes require efficient cell movement and an intact cellular morphology for dynamic interaction. The role of microRNAs (miRs) in this regard, however, is not well understood. In the present study, we show that miR-30b and miR-142-3p regulate migration and morphology of MΦ and DC. Transient overexpression of miR-30b and miR-142-3p attenuates migration and these cells display unique morphological deformities observed under electron microscopy. In addition, miR-142-3p overexpression in MΦ impaired phagocytosis of FITC-conjugated latex beads using live microscopy imaging. Interestingly, live cell imaging and F-actin staining revealed marked changes in the cell polarity and actin polymerization status, respectively. To identify miR-142-3p regulated pathways, we profiled global transcriptome changes in miR-142-3p or control mimic transfected DC. Expression of several genes were differentially altered by miR-142-3p and were associated with pathways related to cell movement, cell adhesion, and cytoskeletal rearrangement. Bioinformatics analysis identified a significant subset of downregulated genes with one or more predicted miR-142-3p binding sites in their 3'UTR strongly suggesting direct post-transcriptional impact of these miRNAs on multiple transcripts. Using dual luciferase assays, novel miR-142-3p binding sites were validated for three genes (Vinculin, Dab2 and Skap2) directly associated with cytoskeletal rearrangement and cell movement. In summary, our results show that miR-30b and miR-142-3p are regulators of myeloid cell cytoskeletal homeostasis and morphology.
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Affiliation(s)
- Araceli Valverde
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, United States of America
| | - Salvador Nares
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, United States of America
| | - Afsar Raza Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, United States of America.
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25
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Uray K, Major E, Lontay B. MicroRNA Regulatory Pathways in the Control of the Actin-Myosin Cytoskeleton. Cells 2020; 9:E1649. [PMID: 32660059 PMCID: PMC7408560 DOI: 10.3390/cells9071649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are key modulators of post-transcriptional gene regulation in a plethora of processes, including actin-myosin cytoskeleton dynamics. Recent evidence points to the widespread effects of miRNAs on actin-myosin cytoskeleton dynamics, either directly on the expression of actin and myosin genes or indirectly on the diverse signaling cascades modulating cytoskeletal arrangement. Furthermore, studies from various human models indicate that miRNAs contribute to the development of various human disorders. The potentially huge impact of miRNA-based mechanisms on cytoskeletal elements is just starting to be recognized. In this review, we summarize recent knowledge about the importance of microRNA modulation of the actin-myosin cytoskeleton affecting physiological processes, including cardiovascular function, hematopoiesis, podocyte physiology, and osteogenesis.
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Affiliation(s)
- Karen Uray
- Correspondence: (K.U.); (B.L.); Tel.: +36-52-412345 (K.U. & B.L.)
| | | | - Beata Lontay
- Correspondence: (K.U.); (B.L.); Tel.: +36-52-412345 (K.U. & B.L.)
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26
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Pua HH, Happ HC, Gray CJ, Mar DJ, Chiou NT, Hesse LE, Ansel KM. Increased Hematopoietic Extracellular RNAs and Vesicles in the Lung during Allergic Airway Responses. Cell Rep 2020; 26:933-944.e4. [PMID: 30673615 PMCID: PMC6365014 DOI: 10.1016/j.celrep.2019.01.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/28/2018] [Accepted: 12/27/2018] [Indexed: 12/30/2022] Open
Abstract
Extracellular RNAs (exRNAs) can be released by numerous cell types in vitro, are often protected within vesicles, and can modify recipient cell function. To determine how the composition and cellular sources of exRNAs and the extracellular vesicles (EVs) that carry them change in vivo during tissue inflammation, we analyzed bronchoalveolar lavage fluid (BALF) from mice before and after lung allergen challenge. In the lung, extracellular microRNAs (ex-miRNAs) had a composition that was highly correlated with airway-lining epithelium. Using cell type-specific membrane tagging and single vesicle flow, we also found that 80% of detected vesicles were of epithelial origin. After the induction of allergic airway inflammation, miRNAs selectively expressed by immune cells, including miR-223 and miR-142a, increased and hematopoietic-cell-derived EVs also increased >2-fold. These data demonstrate that infiltrating immune cells release ex-miRNAs and EVs in inflamed tissues to alter the local extracellular environment.
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Affiliation(s)
- Heather H Pua
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| | - Hannah C Happ
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Carleigh J Gray
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Darryl J Mar
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ni-Ting Chiou
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura E Hesse
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - K Mark Ansel
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
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27
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Houri K, Mori T, Onodera Y, Tsujimoto T, Takehara T, Nakao S, Teramura T, Fukuda K. miR-142 induces accumulation of reactive oxygen species (ROS) by inhibiting pexophagy in aged bone marrow mesenchymal stem cells. Sci Rep 2020; 10:3735. [PMID: 32111926 PMCID: PMC7048811 DOI: 10.1038/s41598-020-60346-2] [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: 05/07/2019] [Accepted: 02/06/2020] [Indexed: 12/26/2022] Open
Abstract
Elevation of the levels of reactive oxygen species (ROS) is a major tissue-degenerative phenomenon involved in aging and aging-related diseases. The detailed mechanisms underlying aging-related ROS generation remain unclear. Presently, the expression of microRNA (miR)-142-5p was significantly upregulated in bone marrow mesenchymal stem cells (BMMSCs) of aged mice. Overexpression of miR-142 and subsequent observation revealed that miR-142 involved ROS accumulation through the disruption of selective autophagy for peroxisomes (pexophagy). Mechanistically, attenuation of acetyltransferase Ep300 triggered the upregulation of miR-142 in aged BMMSCs, and miR-142 targeted endothelial PAS domain protein 1 (Epas1) was identified as a regulatory protein of pexophagy. These findings support a novel molecular mechanism relating aging-associated ROS generation and organelle degradation in BMMSCs, and suggest a potential therapeutic target for aging-associated disorders that are accompanied by stem cell degeneration.
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Affiliation(s)
- Kei Houri
- Department of Anesthesiology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Tatsufumi Mori
- Kindai University Life Science Research Institute, Kindai University, Osaka, Japan
| | - Yuta Onodera
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University Faculty of Medicine, Osaka, Japan
| | - Takatoshi Tsujimoto
- Department of Anesthesiology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Toshiyuki Takehara
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University Faculty of Medicine, Osaka, Japan
| | - Shinichi Nakao
- Department of Anesthesiology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Takeshi Teramura
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University Faculty of Medicine, Osaka, Japan.
| | - Kanji Fukuda
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University Faculty of Medicine, Osaka, Japan
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28
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Nasr MA, Salah RA, Abd Elkodous M, Elshenawy SE, El-Badri N. Dysregulated MicroRNA Fingerprints and Methylation Patterns in Hepatocellular Carcinoma, Cancer Stem Cells, and Mesenchymal Stem Cells. Front Cell Dev Biol 2019; 7:229. [PMID: 31681762 PMCID: PMC6811506 DOI: 10.3389/fcell.2019.00229] [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: 07/25/2019] [Accepted: 09/26/2019] [Indexed: 12/14/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the top causes of cancer mortality worldwide. Although HCC has been researched extensively, there is still a need for novel and effective therapeutic interventions. There is substantial evidence that initiation of carcinogenesis in liver cirrhosis, a leading cause of HCC, is mediated by cancer stem cells (CSCs). CSCs were also shown to be responsible for relapse and chemoresistance in several cancers, including HCC. MicroRNAs (miRNAs) constitute important epigenetic markers that regulate carcinogenesis by acting post-transcriptionally on mRNAs, contributing to the progression of HCC. We have previously shown that co-culture of cancer cells with mesenchymal stem cells (MSCs) could induce the reprogramming of MSCs into CSC-like cells. In this review, we evaluate the available data concerning the epigenetic regulation of miRNAs through methylation and the possible role of this regulation in stem cell and somatic reprogramming in HCC.
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Affiliation(s)
- Mohamed A Nasr
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 6th of October City, Egypt
| | - Radwa Ayman Salah
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 6th of October City, Egypt
| | - M Abd Elkodous
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 6th of October City, Egypt
| | - Shimaa E Elshenawy
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 6th of October City, Egypt
| | - Nagwa El-Badri
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 6th of October City, Egypt
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29
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Berrien-Elliott MM, Sun Y, Neal C, Ireland A, Trissal MC, Sullivan RP, Wagner JA, Leong JW, Wong P, Mah-Som AY, Wong TN, Schappe T, Keppel CR, Cortez VS, Stamatiades EG, Li MO, Colonna M, Link DC, French AR, Cooper MA, Wang WL, Boldin MP, Reddy P, Fehniger TA. MicroRNA-142 Is Critical for the Homeostasis and Function of Type 1 Innate Lymphoid Cells. Immunity 2019; 51:479-490.e6. [PMID: 31402259 PMCID: PMC6750984 DOI: 10.1016/j.immuni.2019.06.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/16/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023]
Abstract
Natural killer (NK) cells are cytotoxic type 1 innate lymphoid cells (ILCs) that defend against viruses and mediate anti-tumor responses, yet mechanisms controlling their development and function remain incompletely understood. We hypothesized that the abundantly expressed microRNA-142 (miR-142) is a critical regulator of type 1 ILC biology. Interleukin-15 (IL-15) signaling induced miR-142 expression, whereas global and ILC-specific miR-142-deficient mice exhibited a cell-intrinsic loss of NK cells. Death of NK cells resulted from diminished IL-15 receptor signaling within miR-142-deficient mice, likely via reduced suppressor of cytokine signaling-1 (Socs1) regulation by miR-142-5p. ILCs persisting in Mir142-/- mice demonstrated increased expression of the miR-142-3p target αV integrin, which supported their survival. Global miR-142-deficient mice exhibited an expansion of ILC1-like cells concurrent with increased transforming growth factor-β (TGF-β) signaling. Further, miR-142-deficient mice had reduced NK-cell-dependent function and increased susceptibility to murine cytomegalovirus (MCMV) infection. Thus, miR-142 critically integrates environmental cues for proper type 1 ILC homeostasis and defense against viral infection.
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Affiliation(s)
- Melissa M Berrien-Elliott
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Yaping Sun
- Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Carly Neal
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Aaron Ireland
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Maria C Trissal
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ryan P Sullivan
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Julia A Wagner
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jeffrey W Leong
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Pamela Wong
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Annelise Y Mah-Som
- Department of Pediatrics, Division of Rheumatology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Terrence N Wong
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Timothy Schappe
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Catherine R Keppel
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Victor S Cortez
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | | | - Ming O Li
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Daniel C Link
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Anthony R French
- Department of Pediatrics, Division of Rheumatology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Wei-Le Wang
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Mark P Boldin
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Pavan Reddy
- Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Todd A Fehniger
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA.
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30
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Kang H, Liang QJ, Hu R, Li ZH, Liu Y, Wang WN. Integrative mRNA-miRNA interaction analysis associated with the immune response of Epinephelus coioddes to Vibrio alginolyticus infection. FISH & SHELLFISH IMMUNOLOGY 2019; 90:404-412. [PMID: 31077847 DOI: 10.1016/j.fsi.2019.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/29/2019] [Accepted: 05/04/2019] [Indexed: 06/09/2023]
Abstract
MicroRNAs (miRNAs) are a kind of small non-coding RNAs that have been reported to play a vital role in mediating host-pathogen interactions. High-throughput sequencing technology was applied to identify and illuminate mRNAs and miRNAs from grouper infected with Vibrio alginolyticus. The KEGG pathway enrichment analysis showed that the most significate DEGs are associated with Toll-like receptor signaling pathway and NOD-like receptor signaling pathway. We obtained 374 known miRNAs and 116 novel miRNAs. During them, there are 31 up-regulated miRNAs and 93 down-regulated miRNAs. miRNA-mRNA GO and KEGG analysis show that there are 90 miRNAs associated with the immune system. The target genes of immune-related miRNAs (miR-142, miR-146, miR-150, miR-155, miR-203, miR-205, miR-24, miR-31) and genes (CD80, IL-2, AMPK, PI3K) in Epinephelus coioddes were predicted and validated. This study provides an opportunity to further understanding the molecular mechanisms especially the immune system of miRNA regulation in Epinephelus coioddes host-pathogen interactions.
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Affiliation(s)
- Huan Kang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Qing-Jian Liang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Rui Hu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Zhong-Hua Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Yuan Liu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Wei-Na Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China.
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31
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de Kerckhove M, Tanaka K, Umehara T, Okamoto M, Kanematsu S, Hayashi H, Yano H, Nishiura S, Tooyama S, Matsubayashi Y, Komatsu T, Park S, Okada Y, Takahashi R, Kawano Y, Hanawa T, Iwasaki K, Nozaki T, Torigoe H, Ikematsu K, Suzuki Y, Tanaka K, Martin P, Shimokawa I, Mori R. Targeting miR-223 in neutrophils enhances the clearance of Staphylococcus aureus in infected wounds. EMBO Mol Med 2019; 10:emmm.201809024. [PMID: 30171089 PMCID: PMC6180296 DOI: 10.15252/emmm.201809024] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Argonaute 2 bound mature microRNA (Ago2-miRNA) complexes are key regulators of the wound inflammatory response and function in the translational processing of target mRNAs. In this study, we identified four wound inflammation-related Ago2-miRNAs (miR-139-5p, miR-142-3p, miR-142-5p, and miR-223) and show that miR-223 is critical for infection control. miR-223 Y/- mice exhibited delayed sterile healing with prolonged neutrophil activation and interleukin-6 expression, and markedly improved repair of Staphylococcus aureus-infected wounds. We also showed that the expression of miR-223 was regulated by CCAAT/enhancer binding protein alpha in human neutrophils after exposure to S. aureus peptides. Treatment with miR-223 Y/--derived neutrophils, or miR-223 antisense oligodeoxynucleotides in S. aureus-infected wild-type wounds markedly improved the healing of these otherwise chronic, slow healing wounds. This study reveals how miR-223 regulates the bactericidal capacity of neutrophils at wound sites and indicates that targeting miR-223 might be of therapeutic benefit for infected wounds in the clinic.
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Affiliation(s)
- Maiko de Kerckhove
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsuya Tanaka
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Plastic and Reconstructive Surgery, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Plastic and Reconstructive Surgery, Ehime Prefectural Center Hospital, Ehime, Japan
| | - Takahiro Umehara
- Department of Forensic Pathology and Science, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Momoko Okamoto
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Immunology and Rheumatology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Sotaro Kanematsu
- Laboratory of Functional Genomics, Department of Medical Genome Science, Graduate of Frontier Science, The University of Tokyo, Tokyo, Japan
| | - Hiroko Hayashi
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroki Yano
- Department of Plastic and Reconstructive Surgery, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Soushi Nishiura
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shiho Tooyama
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yutaka Matsubayashi
- Schools of Biochemistry and Physiology, Pharmacology & Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol, UK.,Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Toshimitsu Komatsu
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Seongjoon Park
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yuka Okada
- Department of Ophthalmology, Wakayama Medical University, Wakayama, Japan
| | - Rina Takahashi
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Yayoi Kawano
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Takehisa Hanawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Keisuke Iwasaki
- Department of Pathology, Sasebo City General Hospital, Sasebo Nagasaki, Japan
| | - Tadashige Nozaki
- Department of Pharmacology, Faculty of Dentistry, Osaka Dental University, Hirakata Osaka, Japan
| | - Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | - Kazuya Ikematsu
- Department of Forensic Pathology and Science, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yutaka Suzuki
- Laboratory of Functional Genomics, Department of Medical Genome Science, Graduate of Frontier Science, The University of Tokyo, Tokyo, Japan
| | - Katsumi Tanaka
- Department of Plastic and Reconstructive Surgery, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Paul Martin
- Schools of Biochemistry and Physiology, Pharmacology & Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol, UK
| | - Isao Shimokawa
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Ryoichi Mori
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
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32
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Raghuwanshi S, Dahariya S, Musvi SS, Gutti U, Kandi R, Undi RB, Sahu I, Gautam DK, Paddibhatla I, Gutti RK. MicroRNA function in megakaryocytes. Platelets 2018; 30:809-816. [DOI: 10.1080/09537104.2018.1528343] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sanjeev Raghuwanshi
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Swati Dahariya
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Syed Shahid Musvi
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Usha Gutti
- Department of Biotechnology, GITAM Institute of Science, GITAM University, Visakhapatnam, AP, India
| | - Ravinder Kandi
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Ram Babu Undi
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Itishri Sahu
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Dushyant Kumar Gautam
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Indira Paddibhatla
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
| | - Ravi Kumar Gutti
- Stem Cells and Haematological Disorders Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, TS, India
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33
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Trissal MC, Wong TN, Yao JC, Ramaswamy R, Kuo I, Baty J, Sun Y, Jih G, Parikh N, Berrien-Elliott MM, Fehniger TA, Ley TJ, Maillard I, Reddy PR, Link DC. MIR142 Loss-of-Function Mutations Derepress ASH1L to Increase HOXA Gene Expression and Promote Leukemogenesis. Cancer Res 2018; 78:3510-3521. [PMID: 29724719 PMCID: PMC6030481 DOI: 10.1158/0008-5472.can-17-3592] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/12/2018] [Accepted: 04/23/2018] [Indexed: 12/22/2022]
Abstract
Point mutations in the seed sequence of miR-142-3p are present in a subset of acute myelogenous leukemia (AML) and in several subtypes of B-cell lymphoma. Here, we show that mutations associated with AML result both in loss of miR-142-3p function and in decreased miR-142-5p expression. Mir142 loss altered the hematopoietic differentiation of multipotent hematopoietic progenitors, enhancing their myeloid potential while suppressing their lymphoid potential. During hematopoietic maturation, loss of Mir142 increased ASH1L protein expression and consequently resulted in the aberrant maintenance of Hoxa gene expression in myeloid-committed hematopoietic progenitors. Mir142 loss also enhanced the disease-initiating activity of IDH2-mutant hematopoietic cells in mice. Together these data suggest a novel model in which miR-142, through repression of ASH1L activity, plays a key role in suppressing HOXA9/A10 expression during normal myeloid differentiation. AML-associated loss-of-function mutations of MIR142 disrupt this negative signaling pathway, resulting in sustained HOXA9/A10 expression in myeloid progenitors/myeloblasts and ultimately contributing to leukemic transformation.Significance: These findings provide mechanistic insights into the role of miRNAs in leukemogenesis and hematopoietic stem cell function. Cancer Res; 78(13); 3510-21. ©2018 AACR.
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Affiliation(s)
- Maria C Trissal
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Terrence N Wong
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Juo-Chin Yao
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Rahul Ramaswamy
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Iris Kuo
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Jack Baty
- Division of Biostatistics, Washington University, St. Louis, Missouri
| | - Yaping Sun
- Division of Hematology-Oncology, University of Michigan, Ann Arbor, Michigan
| | - Gloria Jih
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Nishi Parikh
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | | | - Todd A Fehniger
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Timothy J Ley
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Ivan Maillard
- Division of Hematology-Oncology, University of Michigan, Ann Arbor, Michigan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Pavan R Reddy
- Division of Hematology-Oncology, University of Michigan, Ann Arbor, Michigan
| | - Daniel C Link
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri.
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34
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Mori R, Tanaka K, Shimokawa I. Identification and functional analysis of inflammation-related miRNAs in skin wound repair. Dev Growth Differ 2018; 60:306-315. [PMID: 29873073 DOI: 10.1111/dgd.12542] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 12/11/2022]
Abstract
Inflammation at a wound site is essential for preventing infection. However, misregulated inflammation leads to pathologies of the healing process, including chronic non-healing wounds and scarring. MicroRNAs (miRNAs) are key regulators of the inflammatory response and tissue repair, acting by translational processing of target mRNAs. In the final step of miRNA processing, Argonaute 2 (Ago2)-bound mature miRNA complexes bind to target mRNAs and inhibit their translation. A variety of wound healing-related miRNAs have been identified and their misregulation likely contributes to wound pathologies, including scarring and chronic healing. Recently, we have developed an Ago2-bound mature miRNA purification system that uses Ago2 antibody to analyze the expression of miRNAs from wound tissues by microarray and next generation sequencing. We have identified several wound inflammation-related miRNAs via Ago2-target immunoprecipitation assays and next generation sequencing of wound tissues from wild-type and PU.1 knockout mice, which exhibit no inflammatory response because of a lack of immune cell lineages. We demonstrated that miR-142, an identified inflammation-related miRNA, is essential role for neutrophilic chemotaxis via inhibition of small GTPase translation; its misregulation leads to susceptibility to infection against Staphylococcus aureus at skin wound sites. In this review, we summarize recent advances of miRNA studies in skin wound healing, introduce our miRNA purification system using an immunoprecipitation assay method, and discuss the function of miR-142 in skin wound healing.
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Affiliation(s)
- Ryoichi Mori
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsuya Tanaka
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Plastic and Reconstructive Surgery, Ehime Prefectural Center Hospital, Matsuyama, Japan
| | - Isao Shimokawa
- Department of Pathology, Nagasaki University School of Medicine and Graduate School of Biomedical Sciences, Nagasaki, Japan
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35
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Abstract
MicroRNAs (miRNAs) are ∼22 nt RNAs that direct posttranscriptional repression of mRNA targets in diverse eukaryotic lineages. In humans and other mammals, these small RNAs help sculpt the expression of most mRNAs. This article reviews advances in our understanding of the defining features of metazoan miRNAs and their biogenesis, genomics, and evolution. It then reviews how metazoan miRNAs are regulated, how they recognize and cause repression of their targets, and the biological functions of this repression, with a compilation of knockout phenotypes that shows that important biological functions have been identified for most of the broadly conserved miRNAs of mammals.
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Affiliation(s)
- David P Bartel
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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36
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Islam F, Gopalan V, Vider J, Lu CT, Lam AKY. MiR-142-5p act as an oncogenic microRNA in colorectal cancer: Clinicopathological and functional insights. Exp Mol Pathol 2018; 104:98-107. [PMID: 29337244 DOI: 10.1016/j.yexmp.2018.01.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/10/2018] [Indexed: 12/31/2022]
Abstract
OBJECTIVES miR-142-5p was noted aberrantly expressed and plays important roles in different pathophysiological conditions in human. The present study aims to examine the expression of miR-142-5p and its association with clinicopathological factors in a large cohort of patients with colorectal cancer. In addition, the cellular effects of miR-142-5p and its interacting targets in colon cancer cells were investigated. METHODS Expression of miR-142-5p in colorectal cancer tissues (n=125) and colon cancer cell lines were analysed using real-time polymerase chain reaction. In vitro assays (cell proliferation, wound healing and colony formation) were used to study the miR-142-5p induced cellular effects. Western blots were used to examine the modulation of FAM134B, KRAS, EPAS1 and KLF6 proteins expression followed by miR-142-5p expression-manipulation. RESULTS Significant high expression of miR-142-5p was noted in cancer tissues and cells when compared to the controls (p<0.001). Overexpression of miR-142-5p in patients with colorectal cancer was common (72%; 90/125). miR-142-5p overexpression was associated with cancer in the proximal colorectum and with B-raf positive patients (p=0.05). Exogenous overexpression of miR-142-5p resulted in significantly increased cell proliferation, colony formation, and wound healing capacities, whereas inhibition of endogenous miR-142-5p led reduced cancer growth properties. The cellular effects of miR-142-5p were mediated by the modulation of tumour suppressor KLF6 expression, as the expression of miR-142-5p and KLF6 protein are inversely correlated in colon cancer cells. CONCLUSION High miR-142-5p expression was associated with the biological aggressiveness of cancer. Thus, suppression of miR-142-5p could be a therapeutic strategy for patients with colorectal cancers.
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Affiliation(s)
- Farhadul Islam
- Cancer Molecular Pathology, School of Medicine and Griffith Health Institute, Griffith University, Gold Coast, Queensland, 4222, Australia; Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Vinod Gopalan
- Cancer Molecular Pathology, School of Medicine and Griffith Health Institute, Griffith University, Gold Coast, Queensland, 4222, Australia; School of Medical Science and Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Jelena Vider
- School of Medical Science and Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Cu-Tai Lu
- Department of Surgery, Gold Coast University Hospital, Gold Coast, Queensland, Australia
| | - Alfred K-Y Lam
- Cancer Molecular Pathology, School of Medicine and Griffith Health Institute, Griffith University, Gold Coast, Queensland, 4222, Australia.
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37
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Pan D, Du Y, Ren Z, Chen Y, Li X, Wang J, Hu B. Radiation induces premature chromatid separation via the miR-142-3p/Bod1 pathway in carcinoma cells. Oncotarget 2018; 7:60432-60445. [PMID: 27527863 PMCID: PMC5312394 DOI: 10.18632/oncotarget.11080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 07/26/2016] [Indexed: 12/24/2022] Open
Abstract
Radiation-induced genomic instability plays a vital role in carcinogenesis. Bod1 is required for proper chromosome biorientation, and Bod1 depletion increases premature chromatid separation. MiR-142-3p influences cell cycle progression and inhibits proliferation and invasion in cervical carcinoma cells. We found that radiation induced premature chromatid separation and altered miR-142-3p and Bod1 expression in 786-O and A549 cells. Overexpression of miR-142-3p increased premature chromatid separation and G2/M cell cycle arrest in 786-O cells by suppressing Bod1 expression. We also found that either overexpression of miR-142-3p or knockdown of Bod1 sensitized 786-O and A549 cells to X-ray radiation. Overexpression of Bod1 inhibited radiation- and miR-142-3p-induced premature chromatid separation and increased resistance to radiation in 786-O and A549 cells. Taken together, these results suggest that radiation alters miR-142-3p and Bod1 expression in carcinoma cells, and thus contributes to early stages of radiation-induced genomic instability. Combining ionizing radiation with epigenetic regulation may help improve cancer therapies.
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Affiliation(s)
- Dong Pan
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences & Key Laboratory of Space Radiobiology of Gansu Province, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yarong Du
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences & Key Laboratory of Space Radiobiology of Gansu Province, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Zhenxin Ren
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences & Key Laboratory of Space Radiobiology of Gansu Province, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Yaxiong Chen
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences & Key Laboratory of Space Radiobiology of Gansu Province, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Xiaoman Li
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences & Key Laboratory of Space Radiobiology of Gansu Province, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jufang Wang
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences & Key Laboratory of Space Radiobiology of Gansu Province, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Burong Hu
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences & Key Laboratory of Space Radiobiology of Gansu Province, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions and School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou, Jiangsu, China
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38
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High content image analysis reveals function of miR-124 upstream of Vimentin in regulating motor neuron mitochondria. Sci Rep 2018; 8:59. [PMID: 29311649 PMCID: PMC5758812 DOI: 10.1038/s41598-017-17878-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 12/02/2017] [Indexed: 01/24/2023] Open
Abstract
microRNAs (miRNAs) are critical for neuronal function and their dysregulation is repeatedly observed in neurodegenerative diseases. Here, we implemented high content image analysis for investigating the impact of several miRNAs in mouse primary motor neurons. This survey directed our attention to the neuron-specific miR-124, which controls axonal morphology. By performing next generation sequencing analysis and molecular studies, we characterized novel roles for miR-124 in control of mitochondria localization and function. We further demonstrated that the intermediate filament Vimentin is a key target of miR-124 in this system. Our data establishes a new pathway for control of mitochondria function in motor neurons, revealing the value of a neuron-specific miRNA gene as a mechanism for the re-shaping of otherwise ubiquitously-expressed intermediate filament network, upstream of mitochondria activity and cellular metabolism.
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39
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Megakaryocyte and polyploidization. Exp Hematol 2018; 57:1-13. [DOI: 10.1016/j.exphem.2017.10.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/10/2017] [Accepted: 10/12/2017] [Indexed: 12/12/2022]
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40
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A viral Sm-class RNA base-pairs with mRNAs and recruits microRNAs to inhibit apoptosis. Nature 2017; 550:275-279. [PMID: 28976967 DOI: 10.1038/nature24034] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/22/2017] [Indexed: 01/17/2023]
Abstract
Viruses express several classes of non-coding RNAs; the functions and mechanisms by which most of these act are unknown. Herpesvirus saimiri, a γ-herpesvirus that establishes latency in the T cells of New World primates and has the ability to cause aggressive leukaemias and lymphomas in non-natural hosts, expresses seven small nuclear uracil-rich non-coding RNAs (called HSURs) in latently infected cells. These HSURs associate with Sm proteins, and share biogenesis and structural features with cellular Sm-class small nuclear RNAs. One of these HSURs (HSUR2) base-pairs with two host cellular microRNAs (miR-142-3p and miR-16) but does not affect their abundance or activity, which suggests that its interactions with them perform alternative functions. Here we show that HSUR2 also base-pairs with mRNAs in infected cells. We combined in vivo psoralen-mediated RNA-RNA crosslinking and high-throughput sequencing to identify the mRNAs targeted by HSUR2, which include mRNAs that encode retinoblastoma and factors involved in p53 signalling and apoptosis. We show that HSUR2 represses the expression of target mRNAs and that base-pairing between HSUR2 and miR-142-3p and miR-16 is essential for this repression, suggesting that HSUR2 recruits these two cellular microRNAs to its target mRNAs. Furthermore, we show that HSUR2 uses this mechanism to inhibit apoptosis. Our results uncover a role for this viral Sm-class RNA as a microRNA adaptor in the regulation of gene expression that follows precursor mRNA processing.
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41
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Rivkin N, Chapnik E, Birger Y, Yanowski E, Curato C, Mildner A, Porat Z, Amir G, Izraeli S, Jung S, Hornstein E. Rac1 functions downstream of miR-142 in regulation of erythropoiesis. Haematologica 2017; 102:e476-e480. [PMID: 28912177 DOI: 10.3324/haematol.2017.171736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Natalia Rivkin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot
| | - Elik Chapnik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot
| | - Yehudit Birger
- Functional Genomics and Leukemic Research, Cancer Research Center, Sheba Medical Center, Ramat Gan
| | - Eran Yanowski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot
| | - Caterina Curato
- Department of Immunology Weizmann Institute of Science, Rehovot
| | | | - Ziv Porat
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot
| | - Gail Amir
- Department of Pathology, Hadassah Medical Center, Jerusalem
| | - Shai Izraeli
- Functional Genomics and Leukemic Research, Cancer Research Center, Sheba Medical Center, Ramat Gan.,Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Israel
| | - Steffen Jung
- Department of Immunology Weizmann Institute of Science, Rehovot
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot
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Self-Fordham JB, Naqvi AR, Uttamani JR, Kulkarni V, Nares S. MicroRNA: Dynamic Regulators of Macrophage Polarization and Plasticity. Front Immunol 2017; 8:1062. [PMID: 28912781 PMCID: PMC5583156 DOI: 10.3389/fimmu.2017.01062] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/15/2017] [Indexed: 12/11/2022] Open
Abstract
The ability of a healthy immune system to clear the plethora of antigens it encounters incessantly relies on the enormous plasticity displayed by the comprising cell types. Macrophages (MΦs) are crucial member of the mononuclear phagocyte system (MPS) that constantly patrol the peripheral tissues and are actively recruited to the sites of injury and infection. In tissues, infiltrating monocytes replenish MΦ. Under the guidance of the local micro-milieu, MΦ can be activated to acquire specialized functional phenotypes. Similar to T cells, functional polarization of macrophage phenotype viz., inflammatory (M1) and reparative (M2) is proposed. Equipped with diverse toll-like receptors (TLRs), these cells of the innate arm of immunity recognize and phagocytize antigens and secrete cytokines that activate the adaptive arm of the immune system and perform key roles in wound repair. Dysregulation of MΦ plasticity has been associated with various diseases and infection. MicroRNAs (miRNAs) have emerged as critical regulators of transcriptome output. Their importance in maintaining health, and their contribution toward disease, encompasses virtually all aspects of human biology. Our understanding of miRNA-mediated regulation of MΦ plasticity and polarization can be utilized to modulate functional phenotypes to counter their role in the pathogenesis of numerous disease, including cancer, autoimmunity, periodontitis, etc. Here, we provide an overview of current knowledge regarding the role of miRNA in shaping MΦ polarization and plasticity through targeting of various pathways and genes. Identification of miRNA biomarkers of diagnostic/prognostic value and their therapeutic potential by delivery of miRNA mimics or inhibitors to dynamically alter gene expression profiles in vivo is highlighted.
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Affiliation(s)
| | - Afsar Raza Naqvi
- Department of Periodontics, University of Illinois at Chicago, Chicago, IL, United States
| | - Juhi Raju Uttamani
- Department of Periodontics, University of Illinois at Chicago, Chicago, IL, United States
| | - Varun Kulkarni
- Department of Periodontics, University of Illinois at Chicago, Chicago, IL, United States
| | - Salvador Nares
- Department of Periodontics, University of Illinois at Chicago, Chicago, IL, United States
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miR-142-3p Is a Key Regulator of IL-1β-Dependent Synaptopathy in Neuroinflammation. J Neurosci 2017; 37:546-561. [PMID: 28100738 DOI: 10.1523/jneurosci.0851-16.2016] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNA) play an important role in post-transcriptional gene regulation of several physiological and pathological processes. In multiple sclerosis (MS), a chronic inflammatory and degenerative disease of the CNS, and in its mouse model, the experimental autoimmune encephalomyelitis (EAE), miRNA dysregulation has been mainly related to immune system dysfunction and white matter (WM) pathology. However, little is known about their role in gray matter pathology. Here, we explored miRNA involvement in the inflammation-driven alterations of synaptic structure and function, collectively known as synaptopathy, a neuropathological process contributing to excitotoxic neurodegeneration in MS/EAE. Particularly, we observed that miR-142-3p is increased in the CSF of patients with active MS and in EAE brains. We propose miR-142-3p as a molecular mediator of the IL-1β-dependent downregulation of the glial glutamate-aspartate transporter (GLAST), which causes an enhancement of the glutamatergic transmission in the EAE cerebellum. The synaptic abnormalities mediated by IL-1β and the clinical and neuropathological manifestations of EAE disappeared in miR-142 knock-out mice. Furthermore, we observed that in vivo miR-142-3p inhibition, either by a preventive and local treatment or by a therapeutic and systemic strategy, abolished IL-1β- and GLAST-dependent synaptopathy in EAE wild-type mice. Consistently, miR-142-3p was responsible for the glutamatergic synaptic alterations caused by CSF of patients with MS, and CSF levels of miR-142-3p correlated with prospective MS disease progression. Our findings highlight miR-142-3p as key molecular player in IL-1β-mediated synaptic dysfunction, possibly leading to excitotoxic damage in both EAE and MS diseases. Inhibition of miR-142-3p could be neuroprotective in MS. SIGNIFICANCE STATEMENT Current studies suggest the role of glutamate excitotoxicity in the development and progression of multiple sclerosis (MS) and of its mouse model experimental autoimmune encephalomyelitis (EAE). The molecular mechanisms linking inflammation and synaptic alterations in MS/EAE are still unknown. Here, we identified miR-142-3p as a determinant molecular actor in inflammation-dependent synaptopathy typical of both MS and EAE. miR-142-3p was upregulated in the CSF of MS patients and in EAE cerebellum. Inhibition of miR-142-3p, locally in EAE brain and in a MS chimeric ex vivo model, recovered glutamatergic synaptic enhancement typical of EAE/MS. We proved that miR-142-3p promoted the IL-1β-dependent glutamate dysfunction by targeting glutamate-aspartate transporter (GLAST), a crucial glial transporter involved in glutamate homeostasis. Finally, we suggest miR-142-3p as a negative prognostic factor in patients with relapsing-remitting multiple sclerosis.
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Kulkarni V, Uttamani JR, Naqvi AR, Nares S. microRNAs: Emerging players in oral cancers and inflammatory disorders. Tumour Biol 2017; 39:1010428317698379. [PMID: 28459366 DOI: 10.1177/1010428317698379] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Association of oral diseases and disorders with altered microRNA profiles is firmly recognized. These evidences support the potential use of microRNAs as therapeutic tools for diagnosis, prognosis, and treatment of various diseases. In this review, we highlight the association of altered microRNA signatures in oral cancers and oral inflammatory diseases. Advances in our ability to detect microRNAs in human sera and saliva further highlight their clinical value as potential biomarkers. We have discussed key mechanisms underlying microRNA dysregulation in pathological conditions. The use of microRNAs in diagnostics and their potential therapeutic value in the treatment of oral diseases are reviewed.
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Affiliation(s)
- Varun Kulkarni
- 1 Department of Periodontics, College of Dentistry, The University of Illinois at Chicago, Chicago, IL, USA
| | - Juhi Raju Uttamani
- 1 Department of Periodontics, College of Dentistry, The University of Illinois at Chicago, Chicago, IL, USA
| | - Afsar Raza Naqvi
- 1 Department of Periodontics, College of Dentistry, The University of Illinois at Chicago, Chicago, IL, USA
| | - Salvador Nares
- 1 Department of Periodontics, College of Dentistry, The University of Illinois at Chicago, Chicago, IL, USA
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45
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Mildner A, Chapnik E, Varol D, Aychek T, Lampl N, Rivkin N, Bringmann A, Paul F, Boura-Halfon S, Hayoun YS, Barnett-Itzhaki Z, Amit I, Hornstein E, Jung S. MicroRNA-142 controls thymocyte proliferation. Eur J Immunol 2017; 47:1142-1152. [PMID: 28471480 DOI: 10.1002/eji.201746987] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/03/2017] [Accepted: 04/28/2017] [Indexed: 01/25/2023]
Abstract
T-cell development is a spatially and temporally regulated process, orchestrated by well-defined contributions of transcription factors and cytokines. Here, we identify the noncoding RNA miR-142 as an additional regulatory layer within murine thymocyte development and proliferation. MiR-142 deficiency impairs the expression of cell cycle-promoting genes in mature mouse thymocytes and early progenitors, accompanied with increased levels of cyclin-dependent kinase inhibitor 1B (Cdkn1b, also known as p27Kip1 ). By using CRISPR/Cas9 technology to delete the miR-142-3p recognition element in the 3'UTR of cdkn1b, we confirm that this gene is a novel target of miR-142-3p in vivo. Increased Cdkn1b protein expression alone however was insufficient to cause proliferation defects in thymocytes, indicating the existence of additional critical miR-142 targets. Collectively, we establish a key role for miR-142 in the control of early and mature thymocyte proliferation, demonstrating the multifaceted role of a single miRNA on several target genes.
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Affiliation(s)
- Alexander Mildner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Elik Chapnik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Diana Varol
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Tegest Aychek
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Nardi Lampl
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Natalia Rivkin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Anita Bringmann
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Franziska Paul
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Yifat Segal Hayoun
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Steffen Jung
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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46
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Tanaka K, Kim SE, Yano H, Matsumoto G, Ohuchida R, Ishikura Y, Araki M, Araki K, Park S, Komatsu T, Hayashi H, Ikematsu K, Tanaka K, Hirano A, Martin P, Shimokawa I, Mori R. MiR-142 Is Required for Staphylococcus aureus Clearance at Skin Wound Sites via Small GTPase-Mediated Regulation of the Neutrophil Actin Cytoskeleton. J Invest Dermatol 2017; 137:931-940. [DOI: 10.1016/j.jid.2016.11.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 11/26/2022]
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Shrestha A, Mukhametshina RT, Taghizadeh S, Vásquez-Pacheco E, Cabrera-Fuentes H, Rizvanov A, Mari B, Carraro G, Bellusci S. MicroRNA-142 is a multifaceted regulator in organogenesis, homeostasis, and disease. Dev Dyn 2017; 246:285-290. [PMID: 27884048 DOI: 10.1002/dvdy.24477] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/18/2016] [Accepted: 11/18/2016] [Indexed: 12/27/2022] Open
Abstract
Over the past decade, microRNA-142 (miR-142) is emerging as a major regulator of cell fate decision in the hematopoietic system. However, miR-142 is expressed in many other tissues, and recent evidence suggests that it may play a more pleiotropic role during embryonic development. In addition, miR-142 has been shown to play important functions in disease. miR-142 displays a functional role in cancer, virus infection, inflammation, and immune tolerance. Both a guide strand (miR-142-3p) and passenger strand (miR-142-5p) are generated from the miR-142 hairpin. miR-142-3p and -5p display overlapping but also independent target genes. Loss of function mouse models (genetrap, global knock out [KO], and conditional KO) have been reported and support the important role of miR-142 in different biological processes. This review will summarize the abundant literature already available for miR-142 and will lay the foundation for future works on this important microRNA. Developmental Dynamics 246:285-290, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Amit Shrestha
- German Center for Lung Research, Excellence Cluster Cardio-Pulmonary System, Universities of Giessen and Marburg Lung Center, Giessen, Hessen, Germany
| | - Regina T Mukhametshina
- Institute of Fundamental Medicine and Biology. Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Sara Taghizadeh
- German Center for Lung Research, Excellence Cluster Cardio-Pulmonary System, Universities of Giessen and Marburg Lung Center, Giessen, Hessen, Germany
| | | | - Hector Cabrera-Fuentes
- Cardiovascular & Metabolic Diseases Program, Duke-NUS Graduate Medical School Singapore, Singapore.,Institute of Biochemistry, Justus-Liebig-University Giessen, Germany
| | - Albert Rizvanov
- Institute of Fundamental Medicine and Biology. Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Bernard Mari
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Centre National de la Recherche Scientifique, CNRS, UMR 7275, Sophia Antipolis, France.,Université Côte d'Azur, France
| | - Gianni Carraro
- Lung and Regenerative Medicine Institutes, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Saverio Bellusci
- German Center for Lung Research, Excellence Cluster Cardio-Pulmonary System, Universities of Giessen and Marburg Lung Center, Giessen, Hessen, Germany.,Institute of Fundamental Medicine and Biology. Kazan (Volga Region) Federal University, Kazan, Russian Federation
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Dkhil MA, Al-Quraishy SA, Abdel-Baki AAS, Delic D, Wunderlich F. Differential miRNA Expression in the Liver of Balb/c Mice Protected by Vaccination during Crisis of Plasmodium chabaudi Blood-Stage Malaria. Front Microbiol 2017; 7:2155. [PMID: 28123381 PMCID: PMC5225092 DOI: 10.3389/fmicb.2016.02155] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/21/2016] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs are increasingly recognized as epigenetic regulators for outcome of diverse infectious diseases and vaccination efficacy, but little information referring to this exists for malaria. This study investigates possible effects of both protective vaccination and P. chabaudi malaria on the miRNome of the liver as an effector against blood-stage malaria using miRNA microarrays and quantitative PCR. Plasmodium chabaudi blood-stage malaria takes a lethal outcome in female Balb/c mice, but a self-healing course after immunization with a non-infectious blood-stage vaccine. The liver robustly expresses 71 miRNA species at varying levels, among which 65 miRNA species respond to malaria evidenced as steadily increasing or decreasing expressions reaching highest or lowest levels toward the end of the crisis phase on day 11 p.i. in lethal malaria. Protective vaccination does not affect constitutive miRNA expression, but leads to significant (p < 0.05) changes in the expression of 41 miRNA species, however evidenced only during crisis. In vaccination-induced self-healing infections, 18 miRNA-species are up- and 14 miRNA-species are down-regulated by more than 50% during crisis in relation to non-vaccinated mice. Vaccination-induced self-healing and survival of otherwise lethal infections of P. chabaudi activate epigenetic miRNA-regulated remodeling processes in the liver manifesting themselves during crisis. Especially, liver regeneration is accelerated as suggested by upregulation of let-7a-5p, let-7b-5p, let-7c-5p, let-7d-5p, let-7f-5p, let-7g-5p, let-7i-5p, miR-26a, miR-122-5p, miR30a, miR27a, and mir-29a, whereas the up-regulated expression of miR-142-3p by more than 100% is compatible with the view of enhanced hepatic erythropoiesis, possibly at expense of megakaryopoiesis, during crisis of P. chabaudi blood-stage malaria.
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Affiliation(s)
- Mohamed A Dkhil
- Department of Zoology, College of Science, King Saud UniversityRiyadh, Saudi Arabia; Department of Zoology and Entomology, Faculty of Science, Helwan UniversityCairo, Egypt
| | - Saleh A Al-Quraishy
- Department of Zoology, College of Science, King Saud University Riyadh, Saudi Arabia
| | - Abdel-Azeem S Abdel-Baki
- Department of Zoology, College of Science, King Saud UniversityRiyadh, Saudi Arabia; Department of Zoology, Faculty of Science, Beni-Suef UniversityBeni-Suef, Egypt
| | - Denis Delic
- Boehringer-Ingelheim Pharma Biberach, Germany
| | - Frank Wunderlich
- Department of Biology, Heinrich-Heine-University Duesseldorf, Germany
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49
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Deng L, Wang X, Jiang L, Yang J, Zhou X, Lu Z, Hu H. Modulation of miR-185-5p expression by EBV-miR-BART6 contributes to developmental differences in ABCG4 gene expression in human megakaryocytes. Int J Biochem Cell Biol 2016; 81:105-111. [DOI: 10.1016/j.biocel.2016.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/29/2016] [Accepted: 11/01/2016] [Indexed: 11/16/2022]
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50
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Rivkin N, Chapnik E, Mildner A, Barshtein G, Porat Z, Kartvelishvily E, Dadosh T, Birger Y, Amir G, Yedgar S, Izraeli S, Jung S, Hornstein E. Erythrocyte survival is controlled by microRNA-142. Haematologica 2016; 102:676-685. [PMID: 27909218 PMCID: PMC5395108 DOI: 10.3324/haematol.2016.156109] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/22/2016] [Indexed: 01/23/2023] Open
Abstract
Hematopoietic–specific microRNA-142 is a critical regulator of various blood cell lineages, but its role in erythrocytes is unexplored. Herein, we characterize the impact of microRNA-142 on erythrocyte physiology and molecular cell biology, using a mouse loss-of-function allele. We report that microRNA-142 is required for maintaining the typical erythrocyte biconcave shape and structural resilience, for the normal metabolism of reactive oxygen species, and for overall lifespan. microRNA-142 further controls ACTIN filament homeostasis and membrane skeleton organization. The analyses presented reveal previously unappreciated functions of microRNA-142 and contribute to an emerging view of small RNAs as key players in erythropoiesis. Finally, the work herein demonstrates how a housekeeping network of cytoskeletal regulators can be reshaped by a single micro-RNA denominator in a cell type specific manner.
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Affiliation(s)
- Natalia Rivkin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Elik Chapnik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Mildner
- Department of Immunology Weizmann Institute of Science, Rehovot, Israel
| | - Gregory Barshtein
- Department of Biochemistry and Molecular Biology, Hebrew university, Hadassah Medical School, Jerusalem, Israel
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Elena Kartvelishvily
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Dadosh
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Yehudit Birger
- Functional Genomics and Leukemic Research, Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Gail Amir
- Department of Pathology, Hadassah Medical Center, Jerusalem, Israel
| | - Saul Yedgar
- Department of Biochemistry and Molecular Biology, Hebrew university, Hadassah Medical School, Jerusalem, Israel
| | - Shai Izraeli
- Functional Genomics and Leukemic Research, Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel.,Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Jerusalem, Israel
| | - Steffen Jung
- Department of Immunology Weizmann Institute of Science, Rehovot, Israel
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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