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Baby J, Gull B, Ahmad W, Baki HA, Khader TA, Panicker NG, Akhlaq S, Rizvi TA, Mustafa F. The Host miR-17-92 Cluster Negatively Regulates Mouse Mammary Tumor Virus (MMTV) Replication Primarily Via Cluster Member miR-92a. J Mol Biol 2024; 436:168738. [PMID: 39117177 DOI: 10.1016/j.jmb.2024.168738] [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: 02/15/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024]
Abstract
The mouse mammary tumor virus (MMTV) is a well-known causative agent of breast cancer in mice. Previously, we have shown that MMTV dysregulates expression of the host miR-17-92 cluster in MMTV-infected mammary glands and MMTV-induced tumors. This cluster, better known as oncomiR-1, is frequently dysregulated in cancers, particularly breast cancer. In this study, our aim was to uncover a functional interaction between MMTV and the cluster. Our results reveal that MMTV expression led to dysregulation of the cluster in both mammary epithelial HC11 and HEK293T cells with the expression of miR-92a cluster member being affected the most. Conversely, overexpression of the whole or partial cluster significantly repressed MMTV expression. Notably, overexpression of cluster member miR-92a alone repressed MMTV expression to the same extent as overexpression of the complete/partial cluster. Inhibition of miR-92a led to nearly a complete restoration of MMTV expression, while deletion/substitution of the miR-92a seed sequence rescued MMTV expression. Dual luciferase assays identified MMTV genomic RNA as the potential target of miR-92a. These results show that the miR-17-92 cluster acts as part of the cell's well-known miRNA-based anti-viral response to thwart incoming MMTV infection. Thus, this study provides the first evidence highlighting the biological significance of host miRNAs in regulating MMTV replication and potentially influencing tumorigenesis.
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Affiliation(s)
- Jasmin Baby
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE.
| | - Bushra Gull
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE.
| | - Waqar Ahmad
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE.
| | - Hala Abdul Baki
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE.
| | - Thanumol Abdul Khader
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE; ASPIRE Research Institute in Precision Medicine, Abu Dhabi, UAE.
| | - Neena G Panicker
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE.
| | - Shaima Akhlaq
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE.
| | - Tahir A Rizvi
- Department of Microbiology and Immunology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE; Zayed Center for Health Sciences (ZCHS), UAE University, Al Ain, UAE; ASPIRE Research Institute in Precision Medicine, Abu Dhabi, UAE.
| | - Farah Mustafa
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE; Zayed Center for Health Sciences (ZCHS), UAE University, Al Ain, UAE; ASPIRE Research Institute in Precision Medicine, Abu Dhabi, UAE.
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Correia de Sousa M, Delangre E, Berthou F, El Harane S, Maeder C, Fournier M, Krause KH, Gjorgjieva M, Foti M. Hepatic miR-149-5p upregulation fosters steatosis, inflammation and fibrosis development in mice and in human liver organoids. JHEP Rep 2024; 6:101126. [PMID: 39263327 PMCID: PMC11388170 DOI: 10.1016/j.jhepr.2024.101126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 09/13/2024] Open
Abstract
Background & Aims The incidence of metabolic dysfunction-associated steatotic liver disease (MASLD) is increasing worldwide. Alterations of hepatic microRNA (miRNA) expression/activity significantly contribute to the development and progression of MASLD. Genetic polymorphisms of miR-149 are associated with an increased susceptibility to MASLD development in humans. Aberrant expression of miR-149 was also associated with metabolic alterations in several organs, but the impact of hepatic miR-149-5p deregulation in MASLD remains poorly characterized. Methods MiR-149-5p was downregulated in the livers of mice by in vivo transduction with hepatotropic adeno-associated virus 8 harboring short-hairpin RNAs (shRNAs) specific for miR-149-5p (shmiR149) or scrambled shRNAs (shCTL). MASLD was then induced with a methionine/choline-deficient (MCD, n = 7 per group) diet or a fructose/palmitate/cholesterol-enriched (FPC, n = 8-12 per group, per protocol) diet. The impact of miR-149-5p modulation on MASLD development was assessed in vivo and in vitro using multi-lineage 3D human liver organoids (HLOs) and Huh7 cells. Results MiR-149-5p expression was strongly upregulated in mouse livers from different models of MASLD (2-4-fold increase in ob/ob, db/db mice, high-fat and FPC-fed mice). In vivo downregulation of miR-149-5p led to an amelioration of diet-induced hepatic steatosis, inflammation/fibrosis, and to increased whole-body fatty acid consumption. In HLOs, miR-149-5p overexpression promoted lipid accumulation, inflammation and fibrosis. In vitro analyses of human Huh7 cells overexpressing miR-149-5p indicated that glycolysis and intracellular lipid accumulation was promoted, while mitochondrial respiration was impaired. Translatomic analyses highlighted deregulation of multiple potential miR-149-5p targets in hepatocytes involved in MASLD development. Conclusions MiR-149-5p upregulation contributes to MASLD development by affecting multiple metabolic/inflammatory/fibrotic pathways in hepatocytes. Our results further demonstrate that HLOs are a relevant 3D in vitro model to investigate hepatic steatosis and inflammation/fibrosis development. Impact and implications Our research shows compelling evidence that miR-149-5p plays a pivotal role in the development and progression of MASLD. By employing in vivo and innovative in vitro models using multi-lineage human liver organoids, we demonstrate that miR-149-5p upregulation significantly impacts hepatocyte energy metabolism, exacerbating hepatic steatosis and inflammation/fibrosis by modulating a wide network of target genes. These findings not only shed light on the intricate miR-149-5p-dependent molecular mechanisms underlying MASLD, but also underscore the importance of human liver organoids as valuable 3D in vitro models for studying the disease's pathogenesis.
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Affiliation(s)
- Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Etienne Delangre
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Flavien Berthou
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sanae El Harane
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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3
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Golmakani H, Azimian A, Golmakani E. Newly discovered functions of miRNAs in neuropathic pain: Transitioning from recent discoveries to innovative underlying mechanisms. Mol Pain 2024; 20:17448069231225845. [PMID: 38148597 PMCID: PMC10851769 DOI: 10.1177/17448069231225845] [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: 08/21/2023] [Revised: 09/12/2023] [Accepted: 10/11/2023] [Indexed: 12/28/2023] Open
Abstract
Neuropathic pain is a widespread clinical issue caused by somatosensory nervous system damage, affecting numerous individuals. It poses considerable economic and public health challenges, and managing it can be challenging due to unclear underlying mechanisms. Nevertheless, emerging evidence suggests that neurogenic inflammation and neuroinflammation play a role in developing pain patterns. Emerging evidence suggests that neurogenic inflammation and neuroinflammation play significant roles in developing neuropathic pain within the nervous system. Increased/decreased miRNA expression patterns could affect the progression of neuropathic and inflammatory pain by controlling nerve regeneration, neuroinflammation, and the expression of abnormal ion channels. However, our limited knowledge of miRNA targets hinders a complete grasp of miRNA's functions. Meanwhile, exploring exosomal miRNA, a recently uncovered role, has significantly advanced our comprehension of neuropathic pain's pathophysiology in recent times. In this review, we present a comprehensive overview of the latest miRNA studies and explore the possible ways miRNAs might play a role in the development of neuropathic pain.
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Affiliation(s)
- Hasan Golmakani
- Department of Pediatrics, Faculty of Medicine, Mashhad Azad University, Mashhad, Iran
| | - Amir Azimian
- Department of Pathobiology and Laboratory Sciences, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Ebrahim Golmakani
- Department of Anesthesiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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4
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The sheep miRNAome: Characterization and distribution of miRNAs in 21 tissues. Gene X 2023; 851:146998. [DOI: 10.1016/j.gene.2022.146998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
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Zhao YY, Wu ZJ, Zhu LJ, Niu TX, Liu B, Li J. Emerging roles of miRNAs in neuropathic pain: From new findings to novel mechanisms. Front Mol Neurosci 2023; 16:1110975. [PMID: 36873108 PMCID: PMC9981676 DOI: 10.3389/fnmol.2023.1110975] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/30/2023] [Indexed: 02/19/2023] Open
Abstract
Neuropathic pain, which results from damage to the somatosensory nervous system, is a global clinical condition that affects many people. Neuropathic pain imposes significant economic and public health burdens and is often difficult to manage because the underlying mechanisms remain unclear. However, mounting evidence indicates a role for neurogenic inflammation and neuroinflammation in pain pattern development. There is increasing evidence that the activation of neurogenic inflammation and neuroinflammation in the nervous system contribute to neuropathic pain. Altered miRNA expression profiles might be involved in the pathogenesis of both inflammatory and neuropathic pain by regulating neuroinflammation, nerve regeneration, and abnormal ion channel expression. However, the lack of knowledge about miRNA target genes prevents a full understanding of the biological functions of miRNAs. At the same time, an extensive study on exosomal miRNA, a newly discovered role, has advanced our understanding of the pathophysiology of neuropathic pain in recent years. This section provides a comprehensive overview of the current understanding of miRNA research and discusses the potential mechanisms of miRNAs in neuropathic pain.
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Affiliation(s)
- Yu-Ying Zhao
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Research Institute of Anesthesiology, Tianjin, China
| | - Zi-Jun Wu
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Research Institute of Anesthesiology, Tianjin, China
| | - Li-Juan Zhu
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Research Institute of Anesthesiology, Tianjin, China
| | - Tong-Xiang Niu
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Research Institute of Anesthesiology, Tianjin, China
| | - Bin Liu
- Department of Critical Care Medicine, General Hospital of Tianjin Medical University, Tianjin, China.,Center for Critical Care Medicine, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin, China
| | - Jing Li
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Research Institute of Anesthesiology, Tianjin, China
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Martinucci B, Cucielo MS, Minatel BC, Cury SS, Caxali GH, Aal MCE, Felisbino SL, Pinhal D, Carvalho RF, Delella FK. Fibronectin Modulates the Expression of miRNAs in Prostate Cancer Cell Lines. Front Vet Sci 2022; 9:879997. [PMID: 35898539 PMCID: PMC9310065 DOI: 10.3389/fvets.2022.879997] [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: 02/20/2022] [Accepted: 06/08/2022] [Indexed: 01/10/2023] Open
Abstract
Prostate cancer (PCa) is a significant cause of cancer-related deaths among men and companion animals, such as dogs. However, despite its high mortality and incidence rates, the molecular mechanisms underlying this disease remain to be fully elucidated. Among the many factors involved in prostate carcinogenesis, the extracellular matrix (ECM) plays a crucial role. This ECM in the prostate is composed mainly of collagen fibers, reticular fibers, elastic fibers, proteoglycans and glycoproteins, such as fibronectin. Fibronectin is a glycoprotein whose dysregulation has been implicated in the development of multiple types of cancer, and it has been associated with cell migration, invasion, and metastasis. Furthermore, our research group has previously shown that fibronectin induces transcriptional changes by modulating the expression of protein coding genes in LNCaP cells. However, potential changes at the post-transcriptional level are still not well understood. This study investigated the impact of exposure to fibronectin on the expression of a key class of regulatory RNAs, the microRNAs (miRNAs), in prostate cancer cell lines LNCaP and PC-3. Five mammalian miRNAs (miR-21, miR-29b, miR-125b, miR-221, and miR-222) were differentially expressed after fibronectin exposure in prostate cell lines. The expression profile of hundreds of mRNAs predicted to be targeted by these miRNAs was analyzed using publicly available RNA-Sequencing data (GSE64025, GSE68645, GSE29155). Also, protein-protein interaction networks and enrichment analysis were performed to gain insights into miRNA biological functions. Altogether, these functional analyzes revealed that fibronectin exposure impacts the expression of miRNAs potentially involved in PCa causing changes in critical signaling pathways such as PI3K-AKT, and response to cell division, death, proliferation, and migration. The relationship here demonstrated between fibronectin exposure and altered miRNA expression improves the comprehension of PCa in both men and other animals, such as dogs, which naturally develop prostate cancer.
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Affiliation(s)
- Bruno Martinucci
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Maira Smaniotto Cucielo
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Brenda Carvalho Minatel
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Sarah Santiloni Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Gabriel Henrique Caxali
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Mirian Carolini Esgoti Aal
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Sergio Luis Felisbino
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Danillo Pinhal
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Robson Francisco Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Flávia Karina Delella
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
- *Correspondence: Flávia Karina Delella
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Abdelbaky I, Tayara H, Chong KT. Identification of miRNA-Small Molecule Associations by Continuous Feature Representation Using Auto-Encoders. Pharmaceutics 2021; 14:pharmaceutics14010003. [PMID: 35056899 PMCID: PMC8780428 DOI: 10.3390/pharmaceutics14010003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that play important roles in the body and affect various diseases, including cancers. Controlling miRNAs with small molecules is studied herein to provide new drug repurposing perspectives for miRNA-related diseases. Experimental methods are time- and effort-consuming, so computational techniques have been applied, relying mostly on biological feature similarities and a network-based scheme to infer new miRNA–small molecule associations. Collecting such features is time-consuming and may be impractical. Here we suggest an alternative method of similarity calculation, representing miRNAs and small molecules through continuous feature representation. This representation is learned by the proposed deep learning auto-encoder architecture. Our suggested representation was compared to previous works and achieved comparable results using 5-fold cross validation (92% identified within top 25% predictions), and better predictions for most of the case studies (avg. of 31% vs. 25% identified within the top 25% of predictions). The results proved the effectiveness of our proposed method to replace previous time- and effort-consuming methods.
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Affiliation(s)
- Ibrahim Abdelbaky
- Artificial Intelligence Department, Faculty of Computers and Artificial Intelligence, Benha University, Banha 13518, Egypt;
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, Korea
- Correspondence: (H.T.); (K.T.C.); Tel.: +82-63-270-2478 (K.T.C.)
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea
- Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Korea
- Correspondence: (H.T.); (K.T.C.); Tel.: +82-63-270-2478 (K.T.C.)
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8
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Kazeminasab F, Marandi SM, Baharlooie M, Safaeinejad Z, Nasr-Esfahani MH, Ghaedi K. Aerobic exercise modulates noncoding RNA network upstream of FNDC5 in the Gastrocnemius muscle of high-fat-diet-induced obese mice. J Physiol Biochem 2021; 77:589-600. [PMID: 34405363 DOI: 10.1007/s13105-021-00825-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/01/2021] [Indexed: 11/26/2022]
Abstract
The purpose of the study was to determine the influence of aerobic exercise with a fat-rich diet on ncRNAs expression associated with FNDC5 in the Gastrocnemius muscle of the obese mice. Twenty-five male mice were grouped into two categories of normal diet (ND) and high-fat diet (HF) treatments for three months. For the subsequent treatment, HF-fed animals (obese) were proceeded in four groups: HF-Trained (n = 5), HF-Untrained (n = 5), ND-Trained (n = 5), and ND-Untrained (n = 5). Simultaneously, ND fed mice (n = 5) continued receiving normal diet and being untrained. In the training group, exercise was applied using a treadmill for 2 months. The Gastrocnemius muscle was excised for the assessment of FNDC5 mRNA, protein levels, and ncRNAs. Using bioinformatics tools, two potential miRNAs, miR-129-5p and miR-140-5p, and four lncRNAs constructing a network with FNDC5 were identified. Significant decrease was observed in both miR-129-5p and miR-140-5p in the HF-fed mice vs. ND-fed mice (p < 0.01). Significant increase of lncRNAs Meg3, Malat1, Neat1, and Kcnq1ot1 correlating in the network was also detected (p < 0.001 for all lncRNAs) in HF-fed mice and trained mice (p < 0.001 for Neat1, Meg3, and Kcnq1ot1). The present study suggests that an increase in the muscle FNDC5 of the high-fat diet mice is governed by an expression regulation of suggested ncRNAs, which were revealed by bioinformatics study to be involved in the insulin resistance and glucose homeostasis pathways.
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Affiliation(s)
- Fatemeh Kazeminasab
- Department of Physical Education and Sport Sciences, Faculty of Human Sciences, University of Kashan, Kashan, Iran , University of Kashan , Kashan , Iran.
| | - Sayed Mohammad Marandi
- Department of Exercise Physiology, Faculty of Sport Sciences, University of Isfahan, Isfahan, Iran , University of Isfahan , Isfahan , Iran.
| | - Maryam Baharlooie
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Zahra Safaeinejad
- Department of Animal Biotechnology, Cell Sciences Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Cell Sciences Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
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9
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Abstract
Hundreds of microRNAs (miRNAs) are expressed in distinct spatial and temporal patterns during embryonic and postnatal mouse development. The loss of all miRNAs through the deletion of critical miRNA biogenesis factors results in early lethality. The function of each miRNA stems from their cumulative negative regulation of multiple mRNA targets expressed in a particular cell type. During development, miRNAs often coordinate the timing and direction of cell fate transitions. In adults, miRNAs frequently contribute to organismal fitness through homeostatic roles in physiology. Here, we review how the recent dissection of miRNA-knockout phenotypes in mice as well as advances related to their targets, dosage, and interactions have collectively informed our understanding of the roles of miRNAs in mammalian development and adaptive responses.
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Abu-Izneid T, AlHajri N, Ibrahim AM, Javed MN, Salem KM, Pottoo FH, Kamal MA. Micro-RNAs in the regulation of immune response against SARS CoV-2 and other viral infections. J Adv Res 2021; 30:133-145. [PMID: 33282419 PMCID: PMC7708232 DOI: 10.1016/j.jare.2020.11.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023] Open
Abstract
Background Micro-RNAs (miRNAS) are non-coding, small RNAs that have essential roles in different biological processes through silencing genes, they consist of 18-24 nucleotide length RNA molecules. Recently, miRNAs have been viewed as important modulators of viral infections they can function as suppressors of gene expression by targeting cellular or viral RNAs during infection. Aim of review We describe the biological roles and effects of miRNAs on SARS-CoV-2 life-cycle and pathogenicity, and we discuss the modulation of the immune system with micro-RNAs which would serve as a new foundation for the treatment of SARS-CoV-2 and other viral infections. Key scientific concepts of review miRNAs are the key players that regulate the expression of the gene in the post-transcriptional phase and have important effects on viral infections, thus are potential targets in the development of novel therapeutics for the treatment of viral infections. Besides, micro-RNAs (miRNAs) modulation of immune-pathogenesis responses to viral infection is one of the most-known indirect effects, which leads to suppressing of the interferon (IFN-α/β) signalling cascade or upregulation of the IFN-α/β production another IFN-stimulated gene (ISGs) that inhibit replication of the virus. These virus-mediated alterations in miRNA levels lead to an environment that might either enhance or inhibit virus replication.
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Affiliation(s)
- Tareq Abu-Izneid
- Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Noora AlHajri
- Department of Epidemiology and Population Health, College of Medicine, Khalifa University, United Arab Emirates
| | - Abdallah Mohammad Ibrahim
- Fundamentals of Nursing Department, College of Nursing, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Md. Noushad Javed
- Department of Pharmaceutics, School of Pharmaceutical Education and Research (SPER), Jamia Hamdard, New-Delhi, India
| | - Khairi Mustafa Salem
- Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Faheem Hyder Pottoo
- Department of Pharmacology, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Mohammad Amjad Kamal
- West China School of Nursing/Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- King Fahd Medical Research Center, King Abdulaziz University, P. O. Box 80216, Jeddah 21589, Saudi Arabia
- Enzymoics, Novel Global Community Educational Foundation, 7 Peterlee Place, Hebersham, NSW 2770, Australia
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11
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Chang SH, Su YC, Chang M, Chen JA. MicroRNAs mediate precise control of spinal interneuron populations to exert delicate sensory-to-motor outputs. eLife 2021; 10:63768. [PMID: 33787491 PMCID: PMC8075582 DOI: 10.7554/elife.63768] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/19/2021] [Indexed: 12/17/2022] Open
Abstract
Although the function of microRNAs (miRNAs) during embryonic development has been intensively studied in recent years, their postnatal physiological functions remain largely unexplored due to inherent difficulties with the presence of redundant paralogs of the same seed. Thus, it is particularly challenging to uncover miRNA functions at neural circuit level since animal behaviors would need to be assessed upon complete loss of miRNA family functions. Here, we focused on the neural functions of MiR34/449 that manifests a dynamic expression pattern in the spinal cord from embryonic to postnatal stages. Our behavioral assays reveal that the loss of MiR34/449 miRNAs perturb thermally induced pain response thresholds and compromised delicate motor output in mice. Mechanistically, MiR34/449 directly target Satb1 and Satb2 to fine-tune the precise number of a sub-population of motor synergy encoder (MSE) neurons. Thus, MiR34/449 fine-tunes optimal development of Satb1/2on interneurons in the spinal cord, thereby refining explicit sensory-to-motor circuit outputs. The spinal cord is an information superhighway that connects the body with the brain. There, circuits of neurons process information from the brain before sending commands to muscles to generate movement. Each spinal cord circuit contains many types of neurons, whose identity is defined by the set of genes that are active or ‘expressed’ in each cell. When a gene is turned on, its DNA sequence is copied to produce a messenger RNA (mRNA), a type of molecule that the cell then uses as a template to produce a protein. MicroRNAs (or miRNAs), on the other hand, are tiny RNA molecules that help to regulate gene expression by binding to and ‘deactivating’ specific mRNAs, stopping them from being used to make proteins. Mammalian cells contain thousands of types of microRNAs, many of which have unknown roles: this includes MiR34/449, a group of six microRNAs found mainly within the nervous system. By using genetic technology to delete this family from the mouse genome, Chang et al. now show that MiR34/449 has a key role in regulating spinal cord circuits. The first clue came from discovering that mice without the MiR34/449 family had unusual posture and a tendency to walk on tiptoe. The animals were also more sensitive to heat, flicking their tails away from a heat source more readily than control mice. At a finer level, the spinal cords of the mutants contained greater numbers of cells in which two genes, Satb1 and Satb2, were turned on. Compared to their counterparts in control mice, the Satb1/2-positive neurons also showed differences in the rest of the genes they expressed. In essence, these neurons had a different genetic profile in MiR34/449 mutant mice, therefore disrupting the neural circuit they belong to. Based on these findings, Chang et al. propose that in wild-type mice, the MiR34/449 family fine-tunes the expression of Satb1/2 in the spinal cord during development. In doing so, it regulates the formation of the spinal cord circuits that help to control movement. More generally, these results provide clues about how miRNAs help to determine cell identities; further studies could then examine whether other miRNAs contribute to the development and maintenance of neuronal circuits.
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Affiliation(s)
- Shih-Hsin Chang
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang-Ming University and Academia Sinica, Taipei, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, Taiwan
| | - Yi-Ching Su
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Mien Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-An Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, Taiwan
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12
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miRNA as promising theragnostic biomarkers for predicting radioresistance in cancer: A systematic review and meta-analysis. Crit Rev Oncol Hematol 2020; 157:103183. [PMID: 33310279 DOI: 10.1016/j.critrevonc.2020.103183] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 02/08/2023] Open
Abstract
Radioresistance remains as an obstacle in cancer treatment. This systematic review and meta-analysis aimed to evaluate the association between the expression of miRNAs and responses to radiotherapy and the prognosis of different tumors. In total, 77 miRNAs in 19 cancer types were studied, in which 24 miRNAs were upregulated and 58 miRNAs were downregulated in cancer patients. Five miRNAs were differentially expressed. Moreover, 75 miRNAs were found to be related to radioresistance, while 5 were observed to be related to radiosensitivity. The pooled HR and 95 % confidence interval for the combined studies was 1.135 (0.819-1.574; P-value = 0.4). The HR values of the subgroup analysis for miR-21 (HR = 2.344; 95 % CI: 1.927-2.850; P-value = 0.000), nasopharyngeal carcinoma (HR = 0.448; 95 % CI: 0.265-0.760; P = 0.003) and breast cancer (HR = 1.131; 95 % CI: 0.311-4.109; P = .85) were obtained. Our results highlighted that across the published literature, miRNAs can modulate tumor radioresistance or sensitivity by affecting radiation-related signaling pathways. It seems that miRNAs could be considered as a theragnostic biomarker to predict and monitor clinical response to radiotherapy. Thus, the prediction of radioresistance in malignant patients will improve radiotherapy outcomes and radiotherapeutic resistance.
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13
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Hirano T, Yunoki T, Furusawa Y, Tabuchi Y, Hayashi A. Bioinformatics analysis of the microRNA-mRNA network in sebaceous gland carcinoma of the eyelid. Mol Med Rep 2020; 23:44. [PMID: 33179085 PMCID: PMC7684873 DOI: 10.3892/mmr.2020.11682] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Sebaceous gland carcinoma (SGC) of the eyelid is an uncommon aggressive tumor with a relatively high rate of local recurrence and a poor prognosis following metastasis. However, the molecular mechanisms underlying the pathogenesis of SGC remain unclear. The purpose of the present study was to clarify microRNA (miRNA) expression profiles in SGC and to explore novel miRNA-mRNA networks of SGC. A small RNA-sequencing analysis was performed to identify miRNAs differentially expressed between SGC and sebaceous adenoma control samples. Bioinformatics analyses were conducted to reveal biological functions, canonical pathways and molecular interaction networks using integrated miRNA-mRNA datasets, including mRNA expression profiles of SGC from our previous study. The present results demonstrated that 16 upregulated miRNAs and 516 downregulated mRNAs were associated with loss of lipid metabolism function and enriched in cholesterol biosynthesis pathways. By contrast, 29 downregulated miRNAs and 194 upregulated mRNAs were mainly associated with the promotion of cell survival and proliferation in addition to enrichment of DNA damage-induced cell cycle-regulation pathways. Furthermore, network analyses revealed that the upregulated miRNAs, miR-130a-3p and miR-939-5p, and the downregulated miRNAs, miR-146a-5p, miR-149-3p, miR-193a-3p, miR-195-5p and miR-4671-3p, could be upstream regulators related to these functional changes of SGC. These results improved the understanding of molecular mechanisms of SGC and may help to improve the diagnosis of SGC.
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Affiliation(s)
- Tetsushi Hirano
- Division of Molecular Genetics Research, Life Science Research Center, University of Toyama, Toyama 930-0194, Japan
| | - Tatsuya Yunoki
- Department of Ophthalmology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Yukihiro Furusawa
- Department of Liberal Arts and Sciences, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Yoshiaki Tabuchi
- Division of Molecular Genetics Research, Life Science Research Center, University of Toyama, Toyama 930-0194, Japan
| | - Atsushi Hayashi
- Department of Ophthalmology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
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14
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Ortho-silicic acid enhances osteogenesis of osteoblasts through the upregulation of miR-130b which directly targets PTEN. Life Sci 2020; 264:118680. [PMID: 33130075 DOI: 10.1016/j.lfs.2020.118680] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/15/2020] [Accepted: 10/25/2020] [Indexed: 12/22/2022]
Abstract
AIMS Osteoporosis is considered a common skeletal disease. Ortho-silicic acid has been found to enhance the osteogenic differentiation of osteoblasts. However, the molecular mechanism of osteogenesis induced by ortho-silicic acid is still undefined totally. MicroRNAs (miRs) play a key role in osteogenesis of osteoblasts. This study investigated the role of miR-130b in promoting osteogenesis induced by ortho-silicic acid. MAIN METHODS AND KEY FINDINGS In this study, we found ortho-silicic acid enhanced osteogenesis of osteoblasts in vitro and promoted preventing and treating osteoporosis in vivo. Furthermore, the expression of miR-130b increased under application of ortho-silicic acid. In vitro, experiments demonstrated miR-130b overexpression or inhibition significantly promoted or suppressed osteogenic differentiation of osteoblasts under application of ortho-silicic acid, respectively. Consistently, downregulation of miR-130b in ovariectomy (OVX) rats dropped off the beneficial effect of ortho-silicic acid against bone loss. Mechanistically, we identified phosphatase and tensin homologue deleted on human chromosome 10 (PTEN) as the direct target of miR-130b during osteogenesis induced by ortho-silicic acid. SIGNIFICANCE In conclusion, our findings reveal that ortho-silicic acid promotes the osteogenesis of osteoblasts mediated by the miR-130b/PTEN signaling axis, which identifies a new target to prevent and treat osteoporosis.
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15
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Niu YC, Tong J, Shi XF, Zhang T. MicroRNA-654-3p enhances cisplatin sensitivity by targeting QPRT and inhibiting the PI3K/AKT signaling pathway in ovarian cancer cells. Exp Ther Med 2020; 20:1467-1479. [PMID: 32742380 PMCID: PMC7388328 DOI: 10.3892/etm.2020.8878] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 10/28/2019] [Indexed: 12/17/2022] Open
Abstract
Dysregulation of microRNAs serves a crucial role in the chemosensitivity to cisplatin (DDP) in ovarian cancer (OVC). The abnormal expression of microRNA (miR)-654-3p has been reported in several types of human cancer. However, the association between miR-654-3p and cisplatin resistance in human OVC remains unclear. The present study aimed to investigate the role and mechanism of miR-654-3p in DDP resistance in OVC. The results demonstrated that miR-654-3p was significantly downregulated in ovarian cancer tissues and cells, as well as DDP-resistant IGROV-1/DDP cells, compared with adjacent non-tumoral tissue and IOSE386 cells. Overexpression of miR-654-3p significantly suppressed the proliferation and migration of ovarian cancer cells and increased the sensitivity of IGROV-1/DDP cells to DDP. Luciferase reporter assay demonstrated that quinolinate phosphoribosyl transferase (QPRT) was a target of miR-654-3p; overexpression of miR-654-3p inhibited QPRT expression by binding to the 3'-untranslated region of QPRT. In addition, inhibition of miR-654-3p reversed the suppressive effects of QPRT-targeting short interfering RNA on the proliferation and chemoresistance of ovarian cancer cells. Therefore, the results of the present study revealed a previously unrecognized regulatory mechanism that miR-654-3p enhances DDP sensitivity of OVC cells by downregulating QPRT expression; in addition, the present study highlighted the therapeutic implications of miR-654-3p upregulation in OVC.
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Affiliation(s)
- Yi-Chao Niu
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, P.R. China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, P.R. China
| | - Jing Tong
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, P.R. China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, P.R. China
| | - Xiao-Fei Shi
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 200126, P.R. China
| | - Ting Zhang
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, P.R. China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, P.R. China
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16
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Song Y, Li L, Yang W, Fu Q, Chen W, Fang Z, Li W, Gu N, Zhang R. Sense-antisense miRNA pairs constitute an elaborate reciprocal regulatory circuit. Genome Res 2020; 30:661-672. [PMID: 32424073 PMCID: PMC7263187 DOI: 10.1101/gr.257121.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 04/13/2020] [Indexed: 12/12/2022]
Abstract
Antisense transcription of protein-coding genes has been increasingly recognized as an important regulatory mechanism of gene expression. However, less is known about the extent and importance of antisense transcription of noncoding genes. Here, we investigate the breadth and dynamics of antisense transcription of miRNAs, a class of important noncoding RNAs. Because the antisense transcript of a miRNA is likely to form a hairpin suitable as the substrate of ADARs, which convert adenosine to inosine in double-stranded RNAs, we used A-to-I RNA editing as ultrasensitive readout for antisense transcription of the miRNAs. Through examining the unstranded targeted RNA-seq libraries covering all miRNA loci in 25 types of human tissues, we identified 7275 editing events located in 81% of the antisense strand of the miRNA loci, thus uncovering the previously unknown prevalent antisense transcription of the miRNAs. We found that antisense transcripts are tightly regulated, and a substantial fraction of miRNAs and their antisense transcripts are coexpressed. Sense miRNAs have been shown to down-regulate the coexpressed antisense transcripts, whereas the act of antisense transcription, rather than the transcripts themselves, regulates the expression of sense miRNAs. RNA editing tends to decrease the miRNA accessibility of the antisense transcripts, therefore protecting them from being degraded by the sense-mature miRNAs. Altogether, our study reveals the landscape of antisense transcription and editing of miRNAs, as well as a previously unknown reciprocal regulatory circuit of sense-antisense miRNA pairs.
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Affiliation(s)
- Yulong Song
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Lishi Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Wenbing Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Qiang Fu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Wanying Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Zeng Fang
- Laboratory of General Surgery, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Wen Li
- Laboratory of General Surgery, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Nannan Gu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Rui Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
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17
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Shen G, Ren H, Shang Q, Zhang Z, Zhao W, Yu X, Tang J, Yang Z, Liang D, Jiang X. miR-128 plays a critical role in murine osteoclastogenesis and estrogen deficiency-induced bone loss. Am J Cancer Res 2020; 10:4334-4348. [PMID: 32292498 PMCID: PMC7150474 DOI: 10.7150/thno.42982] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/17/2020] [Indexed: 12/26/2022] Open
Abstract
Postmenopausal osteoporosis (PMOP) is a severe health issue faced by postmenopausal women. microRNA-128 (miR-128) is associated with aging, inflammatory signaling, and inflammatory diseases, such as PMOP. It has also been reported to modulate in vitro osteogenic/adipogenic differentiation. However, its function in osteoclast formation is unknown. Methods: First, the expression of miR-128 and nuclear factor of activated T cells 1 (Nfatc1, bone resorption master marker) was investigated in bone tissues derived from PMOP patients, while their correlation to each other was also investigated. The levels of miR-128 and Nfatc1 in bone specimens and bone marrow-derived macrophages (BMMs) from mice subjected to ovariectomy (OVX) were also assayed. Next, we employed mice BMMs modified for overexpression and inhibition of miR-128 levels to determine its effect on osteoclast differentiation. Moreover, we generated osteoclastic miR-128 conditional knockout (miR-128Oc-/-) mice and isolated miR-128 deletion-BMMs to observe its biological function on bone phenotype and osteoclastogenesis in vivo, respectively. The miR-128Oc-/- BMMs were used to explore the downstream regulatory mechanisms using pull-down, luciferase reporter, and western-blotting assays. Finally, the impact of miR-128 deficiency on OVX-induced bone loss in mice was evaluated. Results: The miR-128 level was found to be positively correlated with the increase in Nfatc1 level in mouse/human bone specimens and mouse primary BMMs. In vitro experiments demonstrated miR-128 levels that were dependent on activity of osteoclast differentiation and miR-128 overexpression or inhibition in BMMs significantly increased or decreased osteoclastogenesis, respectively. In vivo, we revealed that osteoclastic miR-128 deletion remarkedly increased bone mass through the inhibition of osteoclastogenesis. Mechanistically, we identified sirtuin 1 (SIRT1) as the direct target of miR-128 at the post-transcriptional level during osteoclast differentiation. Increased levels of SIRT1 reduced nuclear factor κB (NF-κB) activity by decreasing the level of acetylation of Lysine 310, as well as inhibiting tumor necrosis factor-α (Tnf-α) and interleukin 1 (IL-1) expressions. Lastly, osteoclastic deletion of miR-128 significantly suppressed OVX-triggered osteoclastogenesis and exerted a protective effect against bone loss in mice. Conclusions: Our findings reveal a critical mechanism for osteoclastogenesis that is mediated by the miR-128/SIRT1/NF-κB signaling axis, highlighting a possible avenue for the further exploration of diagnostic and therapeutic target molecules in PMOP.
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18
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Inoue K, Hu X, Zhao B. Regulatory network mediated by RBP-J/NFATc1-miR182 controls inflammatory bone resorption. FASEB J 2020; 34:2392-2407. [PMID: 31908034 PMCID: PMC7018544 DOI: 10.1096/fj.201902227r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/21/2019] [Accepted: 11/29/2019] [Indexed: 12/13/2022]
Abstract
Bone resorption is a severe consequence of inflammatory diseases associated with osteolysis, such as rheumatoid arthritis (RA), often leading to disability in patients. In physiological conditions, the differentiation of bone-resorbing osteoclasts is delicately regulated by the balance between osteoclastogenic and anti-osteoclastogenic mechanisms. Inflammation has complex impact on osteoclastogenesis and bone destruction, and the underlying mechanisms of which, especially feedback inhibition, are underexplored. Here, we identify a novel regulatory network mediated by RBP-J/NFATc1-miR182 in TNF-induced osteoclastogenesis and inflammatory bone resorption. This network includes negative regulator RBP-J and positive regulators, NFATc1 and miR182, of osteoclast differentiation. In this network, miR182 is a direct target of both RBP-J and NFATc1. RBP-J represses, while NFATc1 activates miR182 expression through binding to specific open chromatin regions in the miR182 promoter. Inhibition of miR182 by RBP-J servers as a critical mechanism that limits TNF-induced osteoclast differentiation and inflammatory bone resorption. Inflammation, such as that which occurs in RA, shifts the expression levels of the components in this network mediated by RBP-J/NFATc1-miR182-FoxO3/PKR (previously identified miR182 targets) towards more osteoclastogenic, rather than healthy conditions. Treatment with TNF inhibitors in RA patients reverses the expression changes of the network components and osteoclastogenic potential. Thus, this network controls the balance between activating and repressive signals that determine the extent of osteoclastogenesis. These findings collectively highlight the biological significance and translational implication of this newly identified intrinsic regulatory network in inflammatory osteoclastogenesis and osteolysis.
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Affiliation(s)
- Kazuki Inoue
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Xiaoyu Hu
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Baohong Zhao
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
- Graduate Program in Cell and Development Biology, Weill Cornell Graduate School of Medical Sciences of Cornell University, New York, New York, USA
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19
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Wang S, Talukder A, Cha M, Li X, Hu H. Computational annotation of miRNA transcription start sites. Brief Bioinform 2020; 22:380-392. [PMID: 32003428 PMCID: PMC7820843 DOI: 10.1093/bib/bbz178] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/13/2019] [Accepted: 12/29/2019] [Indexed: 12/26/2022] Open
Abstract
Motivation MicroRNAs (miRNAs) are small noncoding RNAs that play important roles in gene regulation and phenotype development. The identification of miRNA transcription start sites (TSSs) is critical to understand the functional roles of miRNA genes and their transcriptional regulation. Unlike protein-coding genes, miRNA TSSs are not directly detectable from conventional RNA-Seq experiments due to miRNA-specific process of biogenesis. In the past decade, large-scale genome-wide TSS-Seq and transcription activation marker profiling data have become available, based on which, many computational methods have been developed. These methods have greatly advanced genome-wide miRNA TSS annotation. Results In this study, we summarized recent computational methods and their results on miRNA TSS annotation. We collected and performed a comparative analysis of miRNA TSS annotations from 14 representative studies. We further compiled a robust set of miRNA TSSs (RSmirT) that are supported by multiple studies. Integrative genomic and epigenomic data analysis on RSmirT revealed the genomic and epigenomic features of miRNA TSSs as well as their relations to protein-coding and long non-coding genes. Contact xiaoman@mail.ucf.edu, haihu@cs.ucf.edu
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Affiliation(s)
- Saidi Wang
- Computer Science, University of Central Florida, Orlando, FL-32816, US
| | - Amlan Talukder
- Computer Science, University of Central Florida, Orlando, FL-32816, US
| | - Mingyu Cha
- Computer Science, University of Central Florida, Orlando, FL-32816, US
| | - Xiaoman Li
- Burnett School of Biomedical Science, University of Central Florida, Orlando, FL-32816, US
| | - Haiyan Hu
- Computer Science, University of Central Florida, Orlando, FL-32816, US
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20
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Inoue K, Nakano S, Zhao B. Osteoclastic microRNAs and their translational potential in skeletal diseases. Semin Immunopathol 2019; 41:573-582. [PMID: 31591677 DOI: 10.1007/s00281-019-00761-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/09/2019] [Indexed: 12/16/2022]
Abstract
Skeleton undergoes constant remodeling process to maintain healthy bone mass. However, in pathological conditions, bone remodeling is deregulated, resulting in unbalanced bone resorption and formation. Abnormal osteoclast formation and activation play a key role in osteolysis, such as in rheumatoid arthritis and osteoporosis. As potential therapeutic targets or biomarkers, miRNAs have gained rapidly growing research and clinical attention. miRNA-based therapeutics is recently entering a new era for disease treatment. Such progress is emerging in treatment of skeletal diseases. In this review, we discuss miRNA biogenesis, advances in the strategies for miRNA target identification, important miRNAs involved in osteoclastogenesis and disease models, their regulated mechanisms, and translational potential and challenges in bone homeostasis and related diseases.
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Affiliation(s)
- Kazuki Inoue
- Arthritis and Tissue Degeneration Program and The David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA.,Department of Medicine, Weill Cornell Medical College, New York, USA
| | - Shinichi Nakano
- Arthritis and Tissue Degeneration Program and The David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Baohong Zhao
- Arthritis and Tissue Degeneration Program and The David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA. .,Department of Medicine, Weill Cornell Medical College, New York, USA. .,Graduate Program in Cell & Developmental Biology, Weill Cornell Graduate School of Medical Sciences,, New York, NY, USA.
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21
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Wermuth PJ, Piera-Velazquez S, Rosenbloom J, Jimenez SA. Existing and novel biomarkers for precision medicine in systemic sclerosis. Nat Rev Rheumatol 2019; 14:421-432. [PMID: 29789665 DOI: 10.1038/s41584-018-0021-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The discovery and validation of biomarkers resulting from technological advances in the analysis of genomic, transcriptomic, lipidomic and metabolomic pathways involved in the pathogenesis of complex human diseases have led to the development of personalized and rationally designed approaches for the clinical management of such disorders. Although some of these approaches have been applied to systemic sclerosis (SSc), an unmet need remains for validated, non-invasive biomarkers to aid in the diagnosis of SSc, as well as in the assessment of disease progression and response to therapeutic interventions. Advances in global transcriptomic technology over the past 15 years have enabled the assessment of microRNAs that circulate in the blood of patients and the analysis of the macromolecular content of a diverse group of lipid bilayer membrane-enclosed extracellular vesicles, such as exosomes and other microvesicles, which are released by all cells into the extracellular space and circulation. Such advances have provided new opportunities for the discovery of biomarkers in SSc that could potentially be used to improve the design and evaluation of clinical trials and that will undoubtedly enable the development of personalized and individualized medicine for patients with SSc.
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Affiliation(s)
- Peter J Wermuth
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA.,The Joan and Joel Rosenbloom Center for Fibrosis Research, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sonsoles Piera-Velazquez
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA.,The Joan and Joel Rosenbloom Center for Fibrosis Research, Thomas Jefferson University, Philadelphia, PA, USA
| | - Joel Rosenbloom
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA.,The Joan and Joel Rosenbloom Center for Fibrosis Research, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sergio A Jimenez
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA. .,The Joan and Joel Rosenbloom Center for Fibrosis Research, Thomas Jefferson University, Philadelphia, PA, USA. .,The Scleroderma Center, Thomas Jefferson University, Philadelphia, PA, USA.
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22
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Zhang F, Zhang Y, Lv X, Xu B, Zhang H, Yan J, Li H, Wu L. Evolution of an X-Linked miRNA Family Predominantly Expressed in Mammalian Male Germ Cells. Mol Biol Evol 2019; 36:663-678. [PMID: 30649414 PMCID: PMC6445303 DOI: 10.1093/molbev/msz001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are important posttranscriptional regulators of gene expression. However, comprehensive expression profiles of miRNAs during mammalian spermatogenesis are lacking. Herein, we sequenced small RNAs in highly purified mouse spermatogenic cells at different stages. We found that a family of X-linked miRNAs named spermatogenesis-related miRNAs (spermiRs) is predominantly expressed in the early meiotic phases and has a conserved testis-specific high expression pattern in different mammals. We identified one spermiR homolog in opossum; this homolog might originate from THER1, a retrotransposon that is active in marsupials but extinct in current placental mammals. SpermiRs have expanded rapidly with mammalian evolution and are diverged into two clades, spermiR-L and spermiR-R, which are likely to have been generated at least in part by tandem duplication mediated by flanking retrotransposable elements. Notably, despite having undergone highly frequent lineage-specific duplication events, the sequences encoding all spermiR family members are strictly located between two protein-coding genes, Slitrk2 and Fmr1. Moreover, spermiR-Ls and spermiR-Rs have evolved different expression patterns during spermatogenesis in different mammals. Intriguingly, the seed sequences of spermiRs, which are critical for the recognition of target genes, are highly divergent within and among mammals, whereas spermiR target genes largely overlap. When miR-741, the most highly expressed spermiR, is knocked out in cultured mouse spermatogonial stem cells (SSCs), another spermiR, miR-465a-5p, is dramatically upregulated and becomes the most abundant miRNA. Notably, miR-741−/− SSCs grow normally, and the genome-wide expression levels of mRNAs remain unchanged. All these observations indicate functional compensation between spermiR family members and strong coevolution between spermiRs and their targets.
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Affiliation(s)
- Fengjuan Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Ying Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaolong Lv
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Beiying Xu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Hongdao Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Haipeng Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ligang Wu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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Yin J, Chen X, Wang CC, Zhao Y, Sun YZ. Prediction of Small Molecule–MicroRNA Associations by Sparse Learning and Heterogeneous Graph Inference. Mol Pharm 2019; 16:3157-3166. [DOI: 10.1021/acs.molpharmaceut.9b00384] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jun Yin
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Chun-Chun Wang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Yan Zhao
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Ya-Zhou Sun
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
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24
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Guo WT, Wang Y. Dgcr8 knockout approaches to understand microRNA functions in vitro and in vivo. Cell Mol Life Sci 2019; 76:1697-1711. [PMID: 30694346 PMCID: PMC11105204 DOI: 10.1007/s00018-019-03020-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 01/07/2023]
Abstract
Biologic function of the majority of microRNAs (miRNAs) is still unknown. Uncovering the function of miRNAs is hurdled by redundancy among different miRNAs. The deletion of Dgcr8 leads to the deficiency in producing all canonical miRNAs, therefore, overcoming the redundancy issue. Dgcr8 knockout strategy has been instrumental in understanding the function of miRNAs in a variety of cells in vitro and in vivo. In this review, we will first give a brief introduction about miRNAs, miRNA biogenesis pathway and the role of Dgcr8 in miRNA biogenesis. We will then summarize studies performed with Dgcr8 knockout cell models with a focus on embryonic stem cells. After that, we will summarize results from various in vivo Dgcr8 knockout models. Given significant phenotypic differences in various tissues between Dgcr8 and Dicer knockout, we will also briefly review current progresses on understanding miRNA-independent functions of miRNA biogenesis factors. Finally, we will discuss the potential use of a new strategy to stably express miRNAs in Dgcr8 knockout cells. In future, Dgcr8 knockout approaches coupled with innovations in miRNA rescue strategy may provide further insights into miRNA functions in vitro and in vivo.
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Affiliation(s)
- Wen-Ting Guo
- Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, People's Republic of China
| | - Yangming Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, People's Republic of China.
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25
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Labi V, Schoeler K, Melamed D. miR-17∼92 in lymphocyte development and lymphomagenesis. Cancer Lett 2019; 446:73-80. [PMID: 30660648 DOI: 10.1016/j.canlet.2018.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/06/2018] [Accepted: 12/31/2018] [Indexed: 01/07/2023]
Abstract
microRNAs (miRNAs) down-modulate the levels of proteins by sequence-specific binding to their respective target mRNAs, causing translational repression or mRNA degradation. The miR-17∼92 cluster encodes for six miRNAs whose target recognition specificities are determined by their distinct sequence. In mice, the four miRNA families generated from the miR-17∼92 cluster coordinate to allow for proper lymphocyte development and effective adaptive immune responses following infection or immunization. Lymphocyte development and homeostasis rely on tight regulation of PI3K signaling to avoid autoimmunity or immunodeficiency, and the miR-17∼92 miRNAs appear as key mediators to appropriately tune PI3K activity. On the other hand, in lymphoid tumors overexpression of the miR-17∼92 miRNAs is a common oncogenic event. In this review, we touch on what we have learned so far about the miR-17∼92 miRNAs, particularly with respect to their role in lymphocyte development, homeostasis and pathology.
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Affiliation(s)
- Verena Labi
- Division of Developmental Immunology, Biocenter, Innsbruck Medical University, Innsbruck, 6020, Austria.
| | - Katia Schoeler
- Division of Developmental Immunology, Biocenter, Innsbruck Medical University, Innsbruck, 6020, Austria
| | - Doron Melamed
- Department of Immunology, Technion-Israel Institute of Technology, Haifa, 31096, Israel.
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Taylor SM, Giuffre E, Moseley P, Hitchcock PF. The MicroRNA, miR-18a, Regulates NeuroD and Photoreceptor Differentiation in the Retina of Zebrafish. Dev Neurobiol 2019; 79:202-219. [PMID: 30615274 PMCID: PMC6351175 DOI: 10.1002/dneu.22666] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 12/21/2022]
Abstract
During embryonic retinal development, six types of retinal neurons are generated from multipotent progenitors in a strict spatiotemporal pattern. This pattern requires cell cycle exit (i.e. neurogenesis) and differentiation to be precisely regulated in a lineage‐specific manner. In zebrafish, the bHLH transcription factor NeuroD governs photoreceptor genesis through Notch signaling but also governs photoreceptor differentiation though distinct mechanisms that are currently unknown. Also unknown are the mechanisms that regulate NeuroD and the spatiotemporal pattern of photoreceptor development. Members of the miR‐17‐92 microRNA cluster regulate CNS neurogenesis, and a member of this cluster, miR‐18a, is predicted to target neuroD mRNA. The purpose of this study was to determine if, in the developing zebrafish retina, miR‐18a regulates NeuroD and if it plays a role in photoreceptor development. Quantitative RT‐PCR showed that, of the three miR‐18 family members (miR‐18a, b, and c), miR‐18a expression most closely parallels neuroD expression. Morpholino oligonucleotides and CRISPR/Cas9 gene editing were used for miR‐18a loss‐of‐function (LOF) and both resulted in larvae with more mature photoreceptors at 70 hpf without affecting cell proliferation. Western blot showed that miR‐18a LOF increases NeuroD protein levels and in vitro dual luciferase assay showed that miR‐18a directly interacts with the 3′ UTR of neuroD. Finally, tgif1 mutants have increased miR‐18a expression, less NeuroD protein and fewer mature photoreceptors, and the photoreceptor deficiency is rescued by miR‐18a knockdown. Together, these results show that, independent of neurogenesis, miR‐18a regulates the timing of photoreceptor differentiation and indicate that this occurs through post‐transcriptional regulation of NeuroD.
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Affiliation(s)
- Scott M Taylor
- Department of Biology, University of West Florida, 11000 University Parkway, Pensacola, Florida, 32514
| | - Emily Giuffre
- Department of Biology, University of West Florida, 11000 University Parkway, Pensacola, Florida, 32514
| | - Patience Moseley
- Department of Biology, University of West Florida, 11000 University Parkway, Pensacola, Florida, 32514
| | - Peter F Hitchcock
- Ophthalmology and Visual Sciences, University of Michigan, W. K. Kellogg Eye Center, 1000 Wall Street, Ann Arbor, Michigan, 48105
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Ghodousi ES, Rahgozar S. Recovery of MicroRNA from Stored Bone Marrow Aspirate Slides. Avicenna J Med Biotechnol 2019; 11:24-27. [PMID: 30800239 PMCID: PMC6359693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Archived bone marrow aspirate slides are almost infinite, readily available resource of biospecimens that enable retrospective molecular investigations of diseases. RNAs obtained from slides has limitations in utility because of their low quality and highly fragmented nature. MicroRNAs are small (<22 nt) noncoding RNAs with various cellular regulatory roles. Due to their small size, microRNAs are less prone to degradation and modification, therefore, can be preserved well in archived tissues. METHODS The current study investigated the efficacy of archived bone marrow aspirate slides for miRNA expression analysis in pediatric leukemia. Total RNA was isolated from air-dried unstained archived slides using High pure miRNA isolation Kit with some modifications and from fresh samples using TRizol. After cDNA synthesis, RT-qPCR was then carried out using specific hsa-miR-326 LNA primers. Finally, statistical analyses were conducted using GraphPad Prism 6 software. RESULTS The difference observed in miRNA expression due to disease state was far greater than the differences between archived slides and their matching fresh bone marrow specimens. In fact, the expression of archival slide smears for the miR-326 closely mimicked that of fresh-frozen tissues (0.035±0.04 vs. 0.03±0.04) (Mean±SD, p>0.05). Differential expression of hsa-miR-326 was detected between leukemic and non-leukemic samples from archived slides or fresh frozen bone marrows. CONCLUSION The demonstration that archived bone marrow aspirate slides can be utilized for miRNA expression studies offers tremendous potential for future investigations into the role that miRNAs play in the development and long term outcome of hematologic, as well as non-hematologic diseases.
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Affiliation(s)
| | - Soheila Rahgozar
- Corresponding author: Soheila Rahgozar, Ph.D., Division of Cell and Molecular Biology, Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Iran, Tel: +98 31 37932455, Fax: +98 31 37932456, E-mail:
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28
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Gökbuget D, Pereira JA, Opitz L, Christe D, Kessler T, Marchais A, Suter U. The miRNA biogenesis pathway prevents inappropriate expression of injury response genes in developing and adult Schwann cells. Glia 2018; 66:2632-2644. [PMID: 30295958 PMCID: PMC6585637 DOI: 10.1002/glia.23516] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 12/24/2022]
Abstract
Proper function of the nervous system depends on myelination. In peripheral nerves, Schwann cells (SCs) myelinate axons and the miRNA biogenesis pathway is required for developmental myelination and myelin maintenance. However, regulatory roles of this pathway at different stages of myelination are only partially understood. We addressed the requirement of the core miRNA biogenesis pathway components Dgcr8, Drosha, and Dicer in developing and adult SCs using mouse mutants with a comparative genetics and transcriptomics approach. We found that the microprocessor components Dgcr8 and Drosha are crucial for axonal radial sorting and to establish correct SC numbers upon myelination. Transcriptome analyses revealed a requirement of the microprocessor to prevent aberrantly increased expression of injury-response genes. Those genes are predicted targets of abundant miRNAs in sciatic nerves (SNs) during developmental myelination. In agreement, Dgcr8 and Dicer are required for proper maintenance of the myelinated SC state, where abundant miRNAs in adult SNs are predicted to target injury-response genes. We conclude that the miRNA biogenesis pathway in SCs is crucial for preventing inappropriate activity of injury-response genes in developing and adult SCs.
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Affiliation(s)
- Deniz Gökbuget
- ETH Zurich, Department of BiologyInstitute of Molecular Health SciencesZurichSwitzerland
| | - Jorge A. Pereira
- ETH Zurich, Department of BiologyInstitute of Molecular Health SciencesZurichSwitzerland
| | - Lennart Opitz
- ETH Zurich/University of ZurichFunctional Genomics Center ZurichZurichSwitzerland
| | - Dominik Christe
- ETH Zurich, Department of BiologyInstitute of Molecular Health SciencesZurichSwitzerland
| | - Tobias Kessler
- ETH Zurich, Department of BiologyInstitute of Molecular Health SciencesZurichSwitzerland
| | - Antonin Marchais
- ETH Zurich, Department of BiologyInstitute of Agricultural SciencesZurichSwitzerland
| | - Ueli Suter
- ETH Zurich, Department of BiologyInstitute of Molecular Health SciencesZurichSwitzerland
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29
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Stappert L, Klaus F, Brüstle O. MicroRNAs Engage in Complex Circuits Regulating Adult Neurogenesis. Front Neurosci 2018; 12:707. [PMID: 30455620 PMCID: PMC6230569 DOI: 10.3389/fnins.2018.00707] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/18/2018] [Indexed: 12/27/2022] Open
Abstract
The finding that the adult mammalian brain is still capable of producing neurons has ignited a new field of research aiming to identify the molecular mechanisms regulating adult neurogenesis. An improved understanding of these mechanisms could lead to the development of novel approaches to delay cognitive decline and facilitate neuroregeneration in the adult human brain. Accumulating evidence suggest microRNAs (miRNAs), which represent a class of post-transcriptional gene expression regulators, as crucial part of the gene regulatory networks governing adult neurogenesis. This review attempts to illustrate how miRNAs modulate key processes in the adult neurogenic niche by interacting with each other and with transcriptional regulators. We discuss the function of miRNAs in adult neurogenesis following the life-journey of an adult-born neuron from the adult neural stem cell (NSCs) compartment to its final target site. We first survey how miRNAs control the initial step of adult neurogenesis, that is the transition of quiescent to activated proliferative adult NSCs, and then go on to discuss the role of miRNAs to regulate neuronal differentiation, survival, and functional integration of the newborn neurons. In this context, we highlight miRNAs that converge on functionally related targets or act within cross talking gene regulatory networks. The cooperative manner of miRNA action and the broad target repertoire of each individual miRNA could make the miRNA system a promising tool to gain control on adult NSCs in the context of therapeutic approaches.
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Affiliation(s)
- Laura Stappert
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Center, Bonn, Germany
| | - Frederike Klaus
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Center, Bonn, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Center, Bonn, Germany
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Abstract
Targeting microRNAs recently shows significant therapeutic promise; however, such progress is underdeveloped in treatment of skeletal diseases with osteolysis, such as osteoporosis and rheumatoid arthritis (RA). Here, we identified miR-182 as a key osteoclastogenic regulator in bone homeostasis and diseases. Myeloid-specific deletion of miR-182 protects mice against excessive osteoclastogenesis and bone resorption in disease models of ovariectomy-induced osteoporosis and inflammatory arthritis. Pharmacological treatment of these diseases with miR-182 inhibitors completely suppresses pathologic bone erosion. Mechanistically, we identify protein kinase double-stranded RNA-dependent (PKR) as a new and essential miR-182 target that is a novel inhibitor of osteoclastogenesis via regulation of the endogenous interferon (IFN)-β-mediated autocrine feedback loop. The expression levels of miR-182, PKR, and IFN-β are altered in RA and are significantly correlated with the osteoclastogenic capacity of RA monocytes. Our findings reveal a previously unrecognized regulatory network mediated by miR-182-PKR-IFN-β axis in osteoclastogenesis, and highlight the therapeutic implications of miR-182 inhibition in osteoprotection. Osteoclasts mediate bone disruption in a number of degenerative bone diseases. Here, the authors show that miR-182 regulates osteoclastogenesis via PKR and IFN-beta signaling, is correlated with rheumatoid arthritis, and that its ablation or inhibition is protective against bone erosion in mouse models of osteoporosis or inflammatory arthritis.
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31
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Wang H, Li K, Mei Y, Huang X, Li Z, Yang Q, Yang H. Sp1 Suppresses miR-3178 to Promote the Metastasis Invasion Cascade via Upregulation of TRIOBP. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 12:1-11. [PMID: 30195749 PMCID: PMC6023786 DOI: 10.1016/j.omtn.2018.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/27/2018] [Accepted: 04/20/2018] [Indexed: 02/06/2023]
Abstract
Specificity protein (Sp1) plays an important role in invasion-metastasis cascade. Sp1 regulation on protein coding genes has been extensively investigated; however, little is known about its regulation on protein non-coding genes. In this study, miR-3178 is reported as a novel target of Sp1 in multiple cancer cell models. Sp1 functions as its transcriptional suppressor as evidenced by luciferase reporter and chromatin immunoprecipitation (ChIP) assays. In line with the pro-metastatic role of Sp1, miR-3178 exerts anti-metastasis function. Overexpression of miR-3178 inhibits both migration and invasion of highly metastatic prostate, lung, and breast cancer cells whereas antagonizing miR-3178 promotes those events in their lowly metastatic counterparts. The in vivo study demonstrates that miR-3178 suppresses the tail vein inoculated prostate cancer cells to form colonies in lung, lymph node, and liver of BALB/c nude mice. miR-3178 directly targets the 3′ UTR of TRIOBP-1 and TRIOBP-5, two isoforms of TRIOBP expressed in prostate, lung, and breast cancer cells. Overexpression of TRIOBP-1 could rescue miR-3178 inhibition on cell migration and invasion. Collectively, our findings reveal the regulatory axis of Sp1/miR-3178/TRIOBP in metastasis cascade. Our results suggest miR-3178 as a promising application to suppress metastasis in Sp1-overexpressed cancers.
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Affiliation(s)
- Hui Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Kai Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Yu Mei
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Xuemei Huang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Zhenglin Li
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Qingzhu Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Huanjie Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
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Ghodousi ES, Rahgozar S. MicroRNA-326 and microRNA-200c: Two novel biomarkers for diagnosis and prognosis of pediatric acute lymphoblastic leukemia. J Cell Biochem 2018; 119:6024-6032. [PMID: 29630744 DOI: 10.1002/jcb.26800] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/21/2018] [Indexed: 12/12/2022]
Abstract
Multidrug resistance (MDR) is considered as the major obstacle for treating pediatric acute lymphoblastic leukemia (ALL). MicroRNAs (miRNAs) are small non coding RNAs which may potentially regulate response to chemotherapy. In this study, total RNA was isolated from bone marrow samples of 46 children with de novo ALL and 16 controls. Quantitative reverse transcriptase polymerase chain reaction was used to investigate the expression profile of the predicted miRNAs; miR-326 and miR-200c, and their predicted targets ABCA2, and ABCA3 transporters. The presence of minimal residual disease was studied using PCR-SSCP (single-strand conformation polymorphism) 1 year after treatment. The association between the miRNA expression and drug resistance was analyzed statistically. Results showed a significant down-regulation of both miR-326 and miR-200c expressions in ALL patients compared with non-cancer controls (P = 0.0002, AUC = 0.813 and P = 0.035, AUC = 0.79, respectively). A considerable negative association between miR-326 expression and MDR was identified which could raise the risk of chemoresistance by 4.8- fold. The expression profiles of miR-326 and ABCA2 transporter were inversely correlated. Data revealed, a novel diagnostic role for miR-326 and miR-200c as potential biomarkers of pediatric ALL. Down-regulation of miR-326 was introduced, for the first time, as a prognostic factor for drug resistance in childhood ALL. To the best of our knowledge, this is the first time that ABCA2 transporter is proposed as a target gene for miR-326, through which it can exert its impact on drug resistance. These data may provide novel approaches to new therapeutics and diagnostics.
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Affiliation(s)
- Elaheh S Ghodousi
- Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Iran
| | - Soheila Rahgozar
- Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Iran
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33
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Miller WB. Biological information systems: Evolution as cognition-based information management. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 134:1-26. [PMID: 29175233 DOI: 10.1016/j.pbiomolbio.2017.11.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 01/08/2023]
Abstract
An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction. That deployment of information and its subsequent selection enacted the dominant stable unicellular informational architectures whose biological expressions are the prokaryotic, archaeal, and eukaryotic unicellular forms. Multicellularity represents the collective appraisal of equivocal environmental information through a shared information space. This concerted action can be viewed as systematized information management to improve information quality for the maintenance of preferred homeostatic boundaries among the varied participants. When reiterated in successive scales, this same collaborative exchange of information yields macroscopic organisms as obligatory multicellular holobionts. Cognition-Based Evolution (CBE) upholds that assessment of information precedes biological action, and the deployment of information through integrative self-referential niche construction and natural cellular engineering antecedes selection. Therefore, evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses.
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Wang XW, Hao J, Guo WT, Liao LQ, Huang SY, Guo X, Bao X, Esteban MA, Wang Y. A DGCR8-Independent Stable MicroRNA Expression Strategy Reveals Important Functions of miR-290 and miR-183-182 Families in Mouse Embryonic Stem Cells. Stem Cell Reports 2017; 9:1618-1629. [PMID: 28988987 PMCID: PMC5830984 DOI: 10.1016/j.stemcr.2017.08.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 12/21/2022] Open
Abstract
Dgcr8 knockout cells provide a great means to understand the function of microRNAs (miRNAs) in vitro and in vivo. Current strategies to study miRNA function in Dgcr8 knockout cells depend on transient transfection of chemically synthesized miRNA mimics, which is costly and not suitable for long-term study and genetic selection of miRNA function. Here, we developed a cost-effective DGCR8-independent stable miRNA expression (DISME) strategy based on a short hairpin RNA vector that can be precisely processed by DICER. Using DISME, we found that miR-294 promoted the formation of meso-endoderm lineages during embryonic stem cell differentiation. Furthermore, DISME allowed for a pooled screen of miRNA function and identified an miR-183-182 cluster of miRNAs promoting self-renewal and pluripotency in mouse embryonic stem cells. Altogether, our study demonstrates that DISME is a robust and cost-effective strategy that allows for long-term study and genetic selection of miRNA function in a Dgcr8 knockout background.
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Affiliation(s)
- Xi-Wen Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Jing Hao
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Wen-Ting Guo
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Le-Qi Liao
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Si-Yue Huang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Xiangpeng Guo
- Laboratory of RNA, Chromatin, and Human Disease, Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xichen Bao
- Laboratory of RNA, Chromatin, and Human Disease, Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Miguel A Esteban
- Laboratory of RNA, Chromatin, and Human Disease, Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yangming Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China.
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Wermuth PJ, Piera-Velazquez S, Jimenez SA. Exosomes isolated from serum of systemic sclerosis patients display alterations in their content of profibrotic and antifibrotic microRNA and induce a profibrotic phenotype in cultured normal dermal fibroblasts. Clin Exp Rheumatol 2017; 35 Suppl 106:21-30. [PMID: 28094758 PMCID: PMC6530475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/06/2016] [Indexed: 06/06/2023]
Abstract
OBJECTIVES Exosomes are lipid bilayer-bound microvesicles containing various macromolecules including numerous microRNA (miRNA). Exosomes mediate intercellular communication by fusing and releasing their macromolecular content into target cells. Here, we analysed the content of profibrotic and antifibrotic miRNAs in exosomes isolated from the serum of systemic sclerosis (SSc) patients and tested their ability to induce a profibrotic phenotype in normal human dermal fibroblasts in vitro. METHODS Exosomes were isolated from serum from patients with limited cutaneous or diffuse cutaneous SSc and were characterised by Nanosight Particle Tracking Analysis, exosome antibody arrays, and transmission electron microscopy. The content of nine profibrotic and eighteen antifibrotic miRNA was assessed in the isolated exosomes by semiquantitative real time PCR. The effects of the isolated exosomes on cultured normal human dermal fibroblasts were assessed by real time PCR and Western blotting. RESULTS The isolated serum exosomes displayed the expected exosome size and morphology and contained characteristic exosome proteins. Six profibrotic miRNAs were increased and ten antifibrotic miRNAs were decreased in SSc serum exosomes compared to normal serum exosomes. The levels of eight miRNA were significantly different between exosomes from limited and diffuse SSc. Exosomes isolated from both limited or diffuse SSc patients caused dose-dependent stimulation of profibrotic gene expression and type I collagen and fibronectin production and secretion in normal human dermal fibroblasts in vitro. CONCLUSIONS Serum exosomes from SSc patients contain miRNA displaying a markedly profibrotic profile and induce a profibrotic phenotype in target normal fibroblasts in vitro suggesting a plausible mechanism for the extension of the fibrotic SSc process to non-affected tissues.
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Affiliation(s)
- Peter J Wermuth
- The Scleroderma Center and The Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sonsoles Piera-Velazquez
- The Scleroderma Center and The Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sergio A Jimenez
- The Scleroderma Center and The Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA.
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36
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Spolverini A, Fuchs G, Bublik DR, Oren M. let-7b and let-7c microRNAs promote histone H2B ubiquitylation and inhibit cell migration by targeting multiple components of the H2B deubiquitylation machinery. Oncogene 2017; 36:5819-5828. [PMID: 28604753 PMCID: PMC5600258 DOI: 10.1038/onc.2017.187] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/18/2017] [Accepted: 05/10/2017] [Indexed: 02/07/2023]
Abstract
Monoubiquitylation of histone H2B (H2Bub1) is catalyzed mainly by the RNF20/RNF40 complex and erased by multiple deubiquitylating enzymes (DUBs). H2Bub1 influences many aspects of chromatin function, including transcription regulation and DNA repair. Cancer cells often display reduced levels of H2Bub1, and this reduction may contribute to cancer progression. The let-7 family of microRNAs comprises multiple members with reported tumor suppressive features, whose expression is frequently downregulated in cancer. We now report that let-7b and let-7c can positively regulate cellular H2Bub1 levels. Overexpression of let-7b and let-7c in a variety of non-transformed and cancer-derived cell lines results in H2Bub1 elevation. The positive effect of let-7b and let-7c on H2Bub1 levels is achieved through targeting of multiple mRNAs, coding for distinct components of the H2B deubiquitylation machinery. Specifically, let-7b and let-7c bind directly and inhibit the mRNAs encoding the DUBs USP42 and USP44, and also the mRNA encoding the adapter protein ATXN7L3, which is part of the DUB module of the SAGA complex. RNF20 knockdown strongly reduces H2Bub1 levels and increases the migration of non-transformed mammary epithelial cells and breast cancer-derived cells. Remarkably, overexpression of let-7b, which partly counteracts the effect of RNF20 knockdown on H2Bub1 levels, also reverses the pro-migratory effect of RNF20 knockdown. Likewise, ATXN7L3 knockdown also increases H2Bub1 levels and reduces cell migration, and this anti-migratory effect is abolished by simultaneous knockdown of RNF20. Together, our findings uncover a novel function of let-7 microRNAs as regulators of H2B ubiquitylation, suggesting an additional mechanism whereby these microRNAs can exert their tumor suppressive effects.
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Affiliation(s)
- A Spolverini
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - G Fuchs
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - D R Bublik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - M Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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37
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Jin HY, Oda H, Chen P, Yang C, Zhou X, Kang SG, Valentine E, Kefauver JM, Liao L, Zhang Y, Gonzalez-Martin A, Shepherd J, Morgan GJ, Mondala TS, Head SR, Kim PH, Xiao N, Fu G, Liu WH, Han J, Williamson JR, Xiao C. Differential Sensitivity of Target Genes to Translational Repression by miR-17~92. PLoS Genet 2017; 13:e1006623. [PMID: 28241004 PMCID: PMC5348049 DOI: 10.1371/journal.pgen.1006623] [Citation(s) in RCA: 28] [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: 08/26/2016] [Revised: 03/13/2017] [Accepted: 02/08/2017] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are thought to exert their functions by modulating the expression of hundreds of target genes and each to a small degree, but it remains unclear how small changes in hundreds of target genes are translated into the specific function of a miRNA. Here, we conducted an integrated analysis of transcriptome and translatome of primary B cells from mutant mice expressing miR-17~92 at three different levels to address this issue. We found that target genes exhibit differential sensitivity to miRNA suppression and that only a small fraction of target genes are actually suppressed by a given concentration of miRNA under physiological conditions. Transgenic expression and deletion of the same miRNA gene regulate largely distinct sets of target genes. miR-17~92 controls target gene expression mainly through translational repression and 5’UTR plays an important role in regulating target gene sensitivity to miRNA suppression. These findings provide molecular insights into a model in which miRNAs exert their specific functions through a small number of key target genes. MicroRNAs (miRNAs) are small RNAs encoded by our genome. Each miRNA binds hundreds of target mRNAs and performs specific functions. It is thought that miRNAs exert their function by reducing the expression of all these target genes and each to a small degree. However, these target genes often have very diverse functions. It has been unclear how small changes in hundreds of target genes with diverse functions are translated into the specific function of a miRNA. Here we take advantage of recent technical advances to globally examine the mRNA and protein levels of 868 target genes regulated by miR-17~92, the first oncogenic miRNA, in mutant mice with transgenic overexpression or deletion of this miRNA gene. We show that miR-17~92 regulates target gene expression mainly at the protein level, with little effect on mRNA. Surprisingly, only a small fraction of target genes respond to miR-17~92 expression changes. Further studies show that the sensitivity of target genes to miR-17~92 is determined by a non-coding region of target mRNA. Our findings demonstrate that not every target gene is equal, and suggest that the function of a miRNA is mediated by a small number of key target genes.
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Affiliation(s)
- Hyun Yong Jin
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
- Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Hiroyo Oda
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Pengda Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Chao Yang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiaojuan Zhou
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Seung Goo Kang
- Division of Biomedical Convergence/Institute of Bioscience & Biotechnology, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Elizabeth Valentine
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jennifer M. Kefauver
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
- Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Key Laboratory of Brain Functional Genomics (Ministry of Education), School of Life Sciences, East China Normal University, Shanghai, China
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Alicia Gonzalez-Martin
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jovan Shepherd
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Gareth J. Morgan
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tony S. Mondala
- Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, California, United States of America
| | - Steven R. Head
- Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, California, United States of America
| | - Pyeung-Hyeun Kim
- Department of Molecular Bioscience/Institute of Bioscience & Biotechnology, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Nengming Xiao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Guo Fu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Wen-Hsien Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - James R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Changchun Xiao
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
- * E-mail:
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Ortiz-Quintero B. Cell-free microRNAs in blood and other body fluids, as cancer biomarkers. Cell Prolif 2017; 49:281-303. [PMID: 27218664 DOI: 10.1111/cpr.12262] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 04/07/2016] [Indexed: 12/17/2022] Open
Abstract
The discovery of cell-free microRNAs (miRNAs) in serum, plasma and other body fluids has yielded an invaluable potential source of non-invasive biomarkers for cancer and other non-malignant diseases. miRNAs in the blood and other body fluids are highly stable in biological samples and are resistant to environmental conditions, such as freezing, thawing or enzymatic degradation, which makes them convenient as potential biomarkers. In addition, they are more easily sampled than tissue miRNAs. Altered levels of cell-free miRNAs have been found in every type of cancer analysed, and increasing evidence indicates that they may participate in carcinogenesis by acting as cell-to-cell signalling molecules. This review summarizes the biological characteristics and mechanisms of release of cell-free miRNAs that make them promising candidates as non-invasive biomarkers of cancer.
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Affiliation(s)
- Blanca Ortiz-Quintero
- Research Unit, Instituto Nacional de Enfermedades Respiratorias, Ismael Cosio Villegas, 14080, Mexico City, Mexico
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39
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Lee HM, Kim TS, Jo EK. MiR-146 and miR-125 in the regulation of innate immunity and inflammation. BMB Rep 2017; 49:311-8. [PMID: 26996343 PMCID: PMC5070718 DOI: 10.5483/bmbrep.2016.49.6.056] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Indexed: 12/11/2022] Open
Abstract
Innate immune responses are primary, relatively limited, and specific responses
to numerous pathogens and toxic molecules. Protein expression involved in these
innate responses must be tightly regulated at both transcriptional level and
post-transcriptional level to avoid the development of excessive inflammation
that can be potentially harmful to the host. MicroRNAs are small noncoding RNAs
(∼22 nucleotides [nts]) that participate in the regulation of numerous
physiological responses by targeting specific messenger RNAs to suppress their
translation. Recent work has shown that several negative regulators of
transcription including microRNAs play important roles in inhibiting the
exacerbation of inflammatory responses and in the maintenance of immunological
homeostasis. This emerging research area will provide new insights on how
microRNAs regulate innate immune signaling. It might show that dysregulation of
microRNA synthesis is associated with the pathogenesis of inflammatory and
infectious diseases. In this review, we focused on miR-146 and miR-125 and
described the roles these miRNAs in modulating innate immune signaling. These
microRNAs can control inflammatory responses and the outcomes of pathogenic
infections. [BMB Reports 2016; 49(6): 311-318]
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Affiliation(s)
- Hye-Mi Lee
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon 35015, Korea
| | - Tae Sung Kim
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Korea
| | - Eun-Kyeong Jo
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Korea
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40
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Iguchi E, Safgren SL, Marks DL, Olson RL, Fernandez-Zapico ME. Pancreatic Cancer, A Mis-interpreter of the Epigenetic Language. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:575-590. [PMID: 28018146 PMCID: PMC5168833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Pancreatic cancer is the third leading cause of cancer mortality in the U.S. with close to 40,000 deaths per year. Pancreatic ductal adenocarcinoma (PDAC) represents approximately 90 percent of all pancreatic cancer cases and is the most lethal form of the disease. Current therapies for PDAC are ineffective and most patients cannot be treated by surgical resection. Most research efforts have primarily focused on how genetic alterations cause, alter progression, contribute to diagnosis, and influence PDAC management. Over the past two decades, a model has been advanced of PDAC initiation and progression as a multi-step process driven by the acquisition of mutations leading to loss of tumor suppressors and activation of oncogenes. The recognition of the essential roles of these genetic alterations in the development of PDAC has revolutionized our knowledge of this disease. However, none of these findings have turned into effective treatment for this dismal malignancy. In recent years, studies in the areas of chromatin modifications, and non-coding RNAs have uncovered mechanisms for regulating gene expression which occur independently of genetic alterations. Chromatin-based mechanisms are interwoven with microRNA-driven regulation of protein translation to create an integrated epigenetic language, which is grossly dysregulated in PDAC. Thus in PDAC, key tumor suppressors that are well established to play a role in PDAC may be repressed, and oncogenes can be upregulated secondary to epigenetic alterations. Unlike mutations, epigenetic changes are potentially reversible. Given this feature of epigenetic mechanisms, it is conceivable that targeting epigenetic-based events promoting and maintaining PDAC could serve as foundation for the development of new therapeutic and diagnostic approaches for this disease.
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Affiliation(s)
- Eriko Iguchi
- Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
| | | | - David L. Marks
- Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Rachel L. Olson
- Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
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41
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The emerging roles of MicroRNAs in autism spectrum disorders. Neurosci Biobehav Rev 2016; 71:729-738. [DOI: 10.1016/j.neubiorev.2016.10.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/27/2016] [Accepted: 10/22/2016] [Indexed: 12/21/2022]
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Schuster A, Tang C, Xie Y, Ortogero N, Yuan S, Yan W. SpermBase: A Database for Sperm-Borne RNA Contents. Biol Reprod 2016; 95:99. [PMID: 27628216 PMCID: PMC5178153 DOI: 10.1095/biolreprod.116.142190] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/07/2016] [Indexed: 12/31/2022] Open
Abstract
Since their discovery approximately three decades ago, sperm-borne RNAs, both large/small and coding/noncoding, have been reported in multiple organisms, and some have been implicated in spermatogenesis, early development, and epigenetic inheritance. Despite these advances, isolation, quantification, and annotation of sperm-borne RNAs remain nontrivial. The yields and subspecies of sperm-borne RNAs isolated from sperm can vary drastically depending on the methods used, and no cross-species analyses of sperm RNA contents have ever been conducted using a standardized sperm RNA isolation protocol. To address these issues, we developed a simple RNA isolation method that is applicable to sperm of various species, thus allowing for reliable interspecies comparisons. Based on RNA-Seq analyses, we established SpermBase (
www.spermbase.org), a database dedicated to sperm-borne RNA profiling of multiple species. Currently, SpermBase contains large and small RNA expression data for mouse, rat, rabbit, and human total sperm and sperm heads. By analyzing large and small RNAs for conserved features, we found that many sperm-borne RNA species were conserved across all four species analyzed, and among the conserved small RNAs, sperm-borne tRNA-derived small noncoding RNAs and miRNAs can target a large number of genes known to be critical for early development.
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Affiliation(s)
- Andrew Schuster
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada
| | - Chong Tang
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada
| | - Nicole Ortogero
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada
| | - Shuiqiao Yuan
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada
- Department of Biology, University of Nevada, Reno, Reno, Nevada
- Correspondence: Wei Yan, University of Nevada, Reno School of Medicine, Center for Molecular Medicine, Room 207B, 1664 North Virginia Street, MS/0575, Reno, NV 89557. E-mail:
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43
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Chang TC, Pertea M, Lee S, Salzberg SL, Mendell JT. Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms. Genome Res 2016; 25:1401-9. [PMID: 26290535 PMCID: PMC4561498 DOI: 10.1101/gr.193607.115] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Precise regulation of microRNA (miRNA) expression is critical for diverse physiologic and pathophysiologic processes. Nevertheless, elucidation of the mechanisms through which miRNA expression is regulated has been greatly hindered by the incomplete annotation of primary miRNA (pri-miRNA) transcripts. While a subset of miRNAs are hosted in protein-coding genes, the majority of pri-miRNAs are transcribed as poorly characterized noncoding RNAs that are 10's to 100's of kilobases in length and low in abundance due to efficient processing by the endoribonuclease DROSHA, which initiates miRNA biogenesis. Accordingly, these transcripts are poorly represented in existing RNA-seq data sets and exhibit limited and inaccurate annotation in current transcriptome assemblies. To overcome these challenges, we developed an experimental and computational approach that allows genome-wide detection and mapping of pri-miRNA structures. Deep RNA-seq in cells expressing dominant-negative DROSHA resulted in much greater coverage of pri-miRNA transcripts compared with standard RNA-seq. A computational pipeline was developed that produces highly accurate pri-miRNA assemblies, as confirmed by extensive validation. This approach was applied to a panel of human and mouse cell lines, providing pri-miRNA transcript structures for 1291/1871 human and 888/1181 mouse miRNAs, including 594 human and 425 mouse miRNAs that fall outside protein-coding genes. These new assemblies uncovered unanticipated features and new potential regulatory mechanisms, including links between pri-miRNAs and distant protein-coding genes, alternative pri-miRNA splicing, and transcripts carrying subsets of miRNAs encoded by polycistronic clusters. These results dramatically expand our understanding of the organization of miRNA-encoding genes and provide a valuable resource for the study of mammalian miRNA regulation.
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Affiliation(s)
- Tsung-Cheng Chang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Mihaela Pertea
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Sungyul Lee
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA; Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Schober A, Weber C. Mechanisms of MicroRNAs in Atherosclerosis. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2016; 11:583-616. [DOI: 10.1146/annurev-pathol-012615-044135] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andreas Schober
- Institute for Cardiovascular Prevention, Ludwig Maximilians University Munich, Munich 80336, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich 80336, Germany;
| | - Christian Weber
- Institute for Cardiovascular Prevention, Ludwig Maximilians University Munich, Munich 80336, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich 80336, Germany;
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Miller CH, Smith SM, Elguindy M, Zhang T, Xiang JZ, Hu X, Ivashkiv LB, Zhao B. RBP-J-Regulated miR-182 Promotes TNF-α-Induced Osteoclastogenesis. THE JOURNAL OF IMMUNOLOGY 2016; 196:4977-86. [PMID: 27183593 DOI: 10.4049/jimmunol.1502044] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 04/21/2016] [Indexed: 01/06/2023]
Abstract
Increased osteoclastogenesis is responsible for osteolysis, which is a severe consequence of inflammatory diseases associated with bone destruction, such as rheumatoid arthritis and periodontitis. The mechanisms that limit osteoclastogenesis under inflammatory conditions are largely unknown. We previously identified transcription factor RBP-J as a key negative regulator that restrains TNF-α-induced osteoclastogenesis and inflammatory bone resorption. In this study, we tested whether RBP-J suppresses inflammatory osteoclastogenesis by regulating the expression of microRNAs (miRNAs) important for this process. Using high-throughput sequencing of miRNAs, we obtained the first, to our knowledge, genome-wide profile of miRNA expression induced by TNF-α in mouse bone marrow-derived macrophages/osteoclast precursors during inflammatory osteoclastogenesis. Furthermore, we identified miR-182 as a novel miRNA that promotes inflammatory osteoclastogenesis driven by TNF-α and whose expression is suppressed by RBP-J. Downregulation of miR-182 dramatically suppressed the enhanced osteoclastogenesis program induced by TNF-α in RBP-J-deficient cells. Complementary loss- and gain-of-function approaches showed that miR-182 is a positive regulator of osteoclastogenic transcription factors NFATc1 and B lymphocyte-induced maturation protein-1. Moreover, we identified that direct miR-182 targets, Foxo3 and Maml1, play important inhibitory roles in TNF-α-mediated osteoclastogenesis. Thus, RBP-J-regulated miR-182 promotes TNF-α-induced osteoclastogenesis via inhibition of Foxo3 and Maml1. Suppression of miR-182 by RBP-J serves as an important mechanism that restrains TNF-α-induced osteoclastogenesis. Our results provide a novel miRNA-mediated mechanism by which RBP-J inhibits osteoclastogenesis and suggest that targeting of the newly described RBP-J-miR-182-Foxo3/Maml1 axis may represent an effective therapeutic approach to suppress inflammatory osteoclastogenesis and bone resorption.
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Affiliation(s)
- Christine H Miller
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021
| | - Sinead M Smith
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021
| | - Mahmoud Elguindy
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medical College, New York, NY 10065
| | - Jenny Z Xiang
- Genomics Resources Core Facility, Weill Cornell Medical College, New York, NY 10065
| | - Xiaoyu Hu
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China; Collaborative Innovation Center for Biotherapy, Tsinghua University, Beijing 100084, China
| | - Lionel B Ivashkiv
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021; Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065; and
| | - Baohong Zhao
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021; Department of Medicine, Weill Cornell Medical College, New York, NY 10065
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Köberle V, Kakoschky B, Ibrahim AA, Schmithals C, Peveling-Oberhag J, Zeuzem S, Kronenberger B, Waidmann O, Pleli T, Piiper A. Vesicle-associated microRNAs are released from blood cells on incubation of blood samples. Transl Res 2016; 169:40-6. [PMID: 26608461 DOI: 10.1016/j.trsl.2015.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 10/26/2015] [Accepted: 10/29/2015] [Indexed: 01/09/2023]
Abstract
MicroRNAs (miRNAs) circulating extracellularly in the blood are currently intensively studied as novel disease markers. However, the preanalytical factors influencing the levels of the extracellular miRNAs are still incompletely explored. In particular, it is unknown, whether the incubation of blood samples as occurring in clinical routine can lead to a release of miRNAs from blood cells and thus alter the extracellular miRNA levels before the preparation of serum or plasma from the blood cells. Using a set of marker miRNAs and quantitative RT-PCR, we found that the levels of extracellular miRNA-1, miRNA-16, and miRNA-21 were increased in EDTA and serum collection tubes incubated for 1-3 hours at room temperature and declined thereafter; the levels of the liver-specific miRNA-122 declined monophasically. These events occurred in the absence of significant hemolysis. When the blood was supplemented with Ribonuclease A inhibitor, the levels of miRNA-1, miRNA-16, and miRNA-21 increased substantially during the initial 3 hours of incubation and those of miRNA-122 remained unchanged, indicating that the release of blood cell-derived miRNAs occurred during the initial 3 hours of incubation of the blood tubes, but not at later time points. Separation of 5-hour preincubated blood into vesicle and nonvesicle fractions revealed a selective increase in the portion of vesicle-associated miRNAs. Together, these data indicate that the release of vesicle-associated miRNAs from blood cells can occur in blood samples within the time elapsing in normal clinical practice until their processing without significant hemolysis. This becomes particularly visible on the inhibition of miRNA degradation by Ribonuclease A inhibitor.
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Affiliation(s)
- Verena Köberle
- Department of Medicine I, University Hospital Frankfurt, Frankfurt, Germany
| | - Bianca Kakoschky
- Department of Medicine I, University Hospital Frankfurt, Frankfurt, Germany
| | - Ahmed Atef Ibrahim
- Department of Medicine I, University Hospital Frankfurt, Frankfurt, Germany
| | | | | | - Stefan Zeuzem
- Department of Medicine I, University Hospital Frankfurt, Frankfurt, Germany
| | - Bernd Kronenberger
- Department of Medicine I, University Hospital Frankfurt, Frankfurt, Germany
| | - Oliver Waidmann
- Department of Medicine I, University Hospital Frankfurt, Frankfurt, Germany
| | - Thomas Pleli
- Department of Medicine I, University Hospital Frankfurt, Frankfurt, Germany
| | - Albrecht Piiper
- Department of Medicine I, University Hospital Frankfurt, Frankfurt, Germany.
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Abstract
He studies how the noncoding genome shapes development and cancer.
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48
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Heterochronic microRNAs in temporal specification of neural stem cells: application toward rejuvenation. NPJ Aging Mech Dis 2016; 2:15014. [PMID: 28721261 PMCID: PMC5514991 DOI: 10.1038/npjamd.2015.14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/29/2015] [Accepted: 11/01/2015] [Indexed: 12/27/2022] Open
Abstract
Plasticity is a critical factor enabling stem cells to contribute to the development and regeneration of tissues. In the mammalian central nervous system (CNS), neural stem cells (NSCs) that are defined by their capability for self-renewal and differentiation into neurons and glia, are present in the ventricular neuroaxis throughout life. However, the differentiation potential of NSCs changes in a spatiotemporally regulated manner and these cells progressively lose plasticity during development. One of the major alterations in this process is the switch from neurogenesis to gliogenesis. NSCs initiate neurogenesis immediately after neural tube closure and then turn to gliogenesis from midgestation, which requires an irreversible competence transition that enforces a progressive reduction of neuropotency. A growing body of evidence indicates that the neurogenesis-to-gliogenesis transition is governed by multiple layers of regulatory networks consisting of multiple factors, including epigenetic regulators, transcription factors, and non-coding RNA (ncRNA). In this review, we focus on critical roles of microRNAs (miRNAs), a class of small ncRNA that regulate gene expression at the post-transcriptional level, in the regulation of the switch from neurogenesis to gliogenesis in NSCs in the developing CNS. Unraveling the regulatory interactions of miRNAs and target genes will provide insights into the regulation of plasticity of NSCs, and the development of new strategies for the regeneration of damaged CNS.
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Jin HY, Gonzalez-Martin A, Miletic AV, Lai M, Knight S, Sabouri-Ghomi M, Head SR, Macauley MS, Rickert RC, Xiao C. Transfection of microRNA Mimics Should Be Used with Caution. Front Genet 2015; 6:340. [PMID: 26697058 PMCID: PMC4667072 DOI: 10.3389/fgene.2015.00340] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 11/12/2015] [Indexed: 12/19/2022] Open
Abstract
Transient transfection of chemically synthesized microRNA (miRNA) mimics is being used extensively to study the functions and mechanisms of endogenous miRNAs. However, it remains unclear whether transfected miRNAs behave similarly to endogenous miRNAs. Here we show that transient transfection of miRNA mimics into HeLa cells by a commonly used method led to the accumulation of high molecular weight RNA species and a few hundred fold increase in mature miRNA levels. In contrast, expression of the same miRNAs through lentiviral infection or plasmid transfection of HeLa cells, transgenic expression in primary lymphocytes, and endogenous overexpression in lymphoma and leukemia cell lines did not lead to the appearance of high molecular weight RNA species. The increase of mature miRNA levels in these cells was below 10-fold, which was sufficient to suppress target gene expression and to drive lymphoma development in mice. Moreover, transient transfection of miRNA mimics at high concentrations caused non-specific alterations in gene expression, while at low concentrations achieved expression levels comparable to other methods but failed to efficiently suppress target gene expression. Small RNA deep sequencing analysis revealed that the guide strands of miRNA mimics were frequently mutated, while unnatural passenger strands of some miRNA mimics accumulated to high levels. The high molecular weight RNA species were a heterogeneous mixture of several classes of RNA species generated by concatemerization, 5'- and 3'-end tailing of miRNA mimics. We speculate that the supraphysiological levels of mature miRNAs and these artifactual RNA species led to non-specific changes in gene expression. Our results have important implications for the design and interpretation of experiments primarily employing transient transfection of miRNA mimics.
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Affiliation(s)
- Hyun Yong Jin
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA ; Kellogg School of Science and Technology, The Scripps Research Institute La Jolla, CA, USA
| | - Alicia Gonzalez-Martin
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA
| | - Ana V Miletic
- Program on Immunity and Pathogenesis, Sanford-Burnham Medical Research Institute La Jolla, CA, USA
| | - Maoyi Lai
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA
| | - Sarah Knight
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA ; Department of Cell and Molecular Biology, The Scripps Research Institute La Jolla, CA, USA ; Department of Chemical Physiology, The Scripps Research Institute La Jolla, CA, USA
| | - Mohsen Sabouri-Ghomi
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA
| | - Steven R Head
- Next Generation Sequencing Core, The Scripps Research Institute La Jolla, CA, USA
| | - Matthew S Macauley
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA ; Department of Cell and Molecular Biology, The Scripps Research Institute La Jolla, CA, USA ; Department of Chemical Physiology, The Scripps Research Institute La Jolla, CA, USA
| | - Robert C Rickert
- Program on Immunity and Pathogenesis, Sanford-Burnham Medical Research Institute La Jolla, CA, USA
| | - Changchun Xiao
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA
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Jin HY, Xiao C. MicroRNA Mechanisms of Action: What have We Learned from Mice? Front Genet 2015; 6:328. [PMID: 26635864 PMCID: PMC4644800 DOI: 10.3389/fgene.2015.00328] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/22/2015] [Indexed: 12/12/2022] Open
Affiliation(s)
- Hyun Yong Jin
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA ; Kellogg School of Science and Technology, The Scripps Research Institute La Jolla, CA, USA
| | - Changchun Xiao
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA
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