101
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Hudson M, Mead ATP, Chagné D, Roskruge N, Morrison S, Wilcox PL, Allan AC. Indigenous Perspectives and Gene Editing in Aotearoa New Zealand. Front Bioeng Biotechnol 2019; 7:70. [PMID: 31032252 PMCID: PMC6470265 DOI: 10.3389/fbioe.2019.00070] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 03/12/2019] [Indexed: 11/13/2022] Open
Abstract
Gene editing is arguably the most significant recent addition to the modern biotechnology toolbox, bringing both profoundly challenging and enabling opportunities. From a technical point of view the specificity and relative simplicity of these new tools has broadened the potential applications. However, from an ethical point of view it has re-ignited the debates generated by earlier forms of genetic modification. In New Zealand gene editing is currently considered genetic modification and is subject to approval processes under the Environmental Protection Authority (EPA). This process requires decision makers to take into account Māori perspectives. This article outlines previously articulated Māori perspectives on genetic modification and considers the continuing influence of those cultural and ethical arguments within the new context of gene editing. It also explores the range of ways cultural values might be used to analyse the risks and benefits of gene editing in the Aotearoa New Zealand context. Methods used to obtain these perspectives consisted of (a) review of relevant literature regarding lessons learned from the responses of Maori to genetic modification, (b) interviews of selected 'key Maori informants' and (c) surveys of self-selected individuals from groups with interests in either genetics or environmental management. The outcomes of this pilot study identified that while Māori informants were not categorically opposed to new and emerging gene editing technologies a priori, they suggest a dynamic approach to regulation is required where specific uses or types of uses are approved on a case by case basis. This study demonstrates how the cultural cues that Māori referenced in the genetic modification debate continue to be relevant in the context of gene editing but that further work is required to characterize the strength of various positions across the broader community.
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Affiliation(s)
- Maui Hudson
- Faculty of Māori and Indigenous Studies, University of Waikato, Hamilton, New Zealand
| | | | - David Chagné
- Plant and Food Research, Palmerston North, New Zealand
| | - Nick Roskruge
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Sandy Morrison
- Faculty of Māori and Indigenous Studies, University of Waikato, Hamilton, New Zealand
| | - Phillip L Wilcox
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
| | - Andrew C Allan
- Plant and Food Research, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
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102
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Metzinger-Le Meuth V, Metzinger L. miR-223 and other miRNA's evaluation in chronic kidney disease: Innovative biomarkers and therapeutic tools. Noncoding RNA Res 2019; 4:30-35. [PMID: 30891535 PMCID: PMC6404357 DOI: 10.1016/j.ncrna.2019.01.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/04/2018] [Accepted: 01/18/2019] [Indexed: 02/06/2023] Open
Abstract
microRNAs (miRNAs) represent a recent breakthrough regarding gene expression regulation. They are instrumental players known to regulate post-transcriptional expression. miRNAs are short single stranded RNAs that base-pair with target mRNAs in specific regions mainly within their 3' untranslated region. We know now that miRNAs are involved in kidney physiopathology. We outline in this review the recent discoveries made on the roles of miRNAs in cellular and animal models of kidney disease but also in patients suffering from chronic kidney disease, acute kidney injury and so forth. miRNAs are potential innovative biomarkers in nephrology, but before being used in daily clinical routine, their expression in large cohorts will have to be assessed, and an effort will have to be made to standardize measurement methods and to select the most suitable tissues and biofluids. In addition to a putative role as biomarkers, up- or down-regulating miRNAs is a novel therapeutic approach to cure kidney disorders. We discuss in this review recent methods that could be used to deliver miRNAs in a specific and suitable way in kidney and other organs damaged by kidney failure such as the cardiovascular system.
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Affiliation(s)
- Valérie Metzinger-Le Meuth
- INSERM U1148, Laboratory for Vascular Translational Science (LVTS), UFR SMBH, Université Paris 13-Sorbonne Paris Cité, 93017 Bobigny Cedex, France
| | - Laurent Metzinger
- HEMATIM EA4666, C.U.R.S, Université de Picardie Jules Verne, 80025 Amiens Cedex 1, France
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103
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MiR-33a is a therapeutic target in SPG4-related hereditary spastic paraplegia human neurons. Clin Sci (Lond) 2019; 133:583-595. [PMID: 30777884 DOI: 10.1042/cs20180980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/13/2019] [Accepted: 02/18/2019] [Indexed: 02/06/2023]
Abstract
Recent reports, including ours, have indicated that microRNA (miR)-33 located within the intron of sterol regulatory element binding protein (SREBP) 2 controls cholesterol homeostasis and can be a potential therapeutic target for the treatment of atherosclerosis. Here, we show that SPAST, which encodes a microtubule-severing protein called SPASTIN, was a novel target gene of miR-33 in human. Actually, the miR-33 binding site in the SPAST 3'-UTR is conserved not in mice but in mid to large mammals, and it is impossible to clarify the role of miR-33 on SPAST in mice. We demonstrated that inhibition of miR-33a, a major form of miR-33 in human neurons, via locked nucleic acid (LNA)-anti-miR ameliorated the pathological phenotype in hereditary spastic paraplegia (HSP)-SPG4 patient induced pluripotent stem cell (iPSC)-derived cortical neurons. Thus, miR-33a can be a potential therapeutic target for the treatment of HSP-SPG4.
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104
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Yuan L, Li JY. Exosomes in Parkinson's Disease: Current Perspectives and Future Challenges. ACS Chem Neurosci 2019; 10:964-972. [PMID: 30664350 DOI: 10.1021/acschemneuro.8b00469] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Exosomes, which are lipid bilayer membrane vesicles, have been implicated as carriers of biological macromolecules. In recent years, the functions of exosomes in the spreading of pathological conversion of proteins among neurons have drawn particular attention in Parkinson's disease research. Extracellular α-synuclein is proven to be associated with exosomes in vivo and in vitro. The contents of these exosomes may be altered during the pathological and clinical processes, serving as a potential target for biomarker development in Parkinson's disease. This Review highlights the current understanding of biogenesis and pathophysiological roles of exosomes. Meanwhile, exosomes are promising delivery vehicles. Artificial exosomes can be loaded with defined therapeutically active molecules, such as drugs, small interfering RNAs, long noncoding RNAs, and proteins to the brain, ensuring the site-specific targeting strategy to the recipient cells. Therefore, we will also discuss the potential applications of exosomes in developing modified exosome-based drug carrier systems to halt the pathologic propagation of Parkinson's disease.
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Affiliation(s)
- Lin Yuan
- Institute of Health Science, China Medical University, Shenyang 110122, China
| | - Jia-Yi Li
- Institute of Health Science, China Medical University, Shenyang 110122, China
- Neural Plasticity and Repair Unit, Wallenberg Neuroscience Center, Department of Experimental Medical Science, Lund University, BMC A10, 22184 Lund, Sweden
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105
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Label-free Quantitative Analysis of Protein Expression Alterations in miR-26a-Knockout HeLa Cells using SWATH-MS Technology. Sci Rep 2019; 9:1399. [PMID: 30718521 PMCID: PMC6362012 DOI: 10.1038/s41598-018-34904-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 10/24/2018] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) bind to the 3ʹ-untranslated region of target mRNAs in a sequence-specific manner and subsequently repress gene translation. Human miR-26a has been studied extensively, but the target transcripts are far from complete. We first employed the CRISPR-Cas9 system to generate an miR-26a-knockout line in human cervical cancer HeLa cells. The miR26a-knockout line showed increased cell growth and altered proliferation. Proteomics technology of sequential window acquisition of all theoretical mass spectra (SWATH-MS) was utilized to compare the protein abundance between the wild-type and the knockout lines, with an attempt to identify transcripts whose translation was influenced by miR-26a. Functional classification of the proteins with significant changes revealed their function in stress response, proliferation, localization, development, signaling, etc. Several proteins in the cell cycle/proliferation signaling pathway were chosen to be validated by western blot and parallel reaction monitoring (PRM). The satisfactory consistency among the three approaches indicated the reliability of the SWATH-MS quantification. Among the computationally predicted targets, a subset of the targets was directly regulated by miR-26a, as demonstrated by luciferase assays and Western blotting. This study creates an inventory of miR-26a-targeted transcripts in HeLa cells and provides fundamental knowledge to further explore the functions of miR-26a in human cancer.
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106
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Yang X, Zhao C, Bamunuarachchi G, Wang Y, Liang Y, Huang C, Zhu Z, Xu D, Lin K, Senavirathna LK, Xu L, Liu L. miR-193b represses influenza A virus infection by inhibiting Wnt/β-catenin signalling. Cell Microbiol 2019; 21:e13001. [PMID: 30650225 PMCID: PMC6459727 DOI: 10.1111/cmi.13001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 12/12/2018] [Accepted: 12/19/2018] [Indexed: 12/29/2022]
Abstract
Due to an increasing emergence of new and drug‐resistant strains of the influenza A virus (IAV), developing novel measures to combat influenza is necessary. We have previously shown that inhibiting Wnt/β‐catenin pathway reduces IAV infection. In this study, we aimed to identify antiviral human microRNAs (miRNAs) that target the Wnt/β‐catenin signalling pathway. Using a miRNA expression library, we identified 85 miRNAs that up‐regulated and 20 miRNAs that down‐regulated the Wnt/β‐catenin signalling pathway. Fifteen miRNAs were validated to up‐regulate and five miRNAs to down‐regulate the pathway. Overexpression of four selected miRNAs (miR‐193b, miR‐548f‐1, miR‐1‐1, and miR‐509‐1) that down‐regulated the Wnt/β‐catenin signalling pathway reduced viral mRNA, protein levels in A/PR/8/34‐infected HEK293 cells, and progeny virus production. Overexpression of miR‐193b in lung epithelial A549 cells also resulted in decreases of A/PR/8/34 infection. Furthermore, miR‐193b inhibited the replication of various strains, including H1N1 (A/PR/8/34, A/WSN/33, A/Oklahoma/3052/09) and H3N2 (A/Oklahoma/309/2006), as determined by a viral reporter luciferase assay. Further studies revealed that β‐catenin was a target of miR‐193b, and β‐catenin rescued miR‐193b‐mediated suppression of IAV infection. miR‐193b induced G0/G1 cell cycle arrest and delayed vRNP nuclear import. Finally, adenovirus‐mediated gene transfer of miR‐193b to the lung reduced viral load in mice challenged by a sublethal dose of A/PR/8/34. Collectively, our findings suggest that miR‐193b represses IAV infection by inhibiting Wnt/β‐catenin signalling.
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Affiliation(s)
- Xiaoyun Yang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Chunling Zhao
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Gayan Bamunuarachchi
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Yang Wang
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Yurong Liang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Chaoqun Huang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Zhengyu Zhu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Dao Xu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Kong Lin
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lakmini Kumari Senavirathna
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lan Xu
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lin Liu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
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107
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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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108
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Wang T, Zhang H, Zhu H. CRISPR technology is revolutionizing the improvement of tomato and other fruit crops. HORTICULTURE RESEARCH 2019; 6:77. [PMID: 31240102 PMCID: PMC6570646 DOI: 10.1038/s41438-019-0159-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/25/2019] [Accepted: 04/26/2019] [Indexed: 05/06/2023]
Abstract
Fruits are major sources of essential nutrients and serve as staple foods in some areas of the world. The increasing human population and changes in climate experienced worldwide make it urgent to the production of fruit crops with high yield and enhanced adaptation to the environment, for which conventional breeding is unlikely to meet the demand. Fortunately, clustered regularly interspaced short palindromic repeat (CRISPR) technology paves the way toward a new horizon for fruit crop improvement and consequently revolutionizes plant breeding. In this review, the mechanism and optimization of the CRISPR system and its application to fruit crops, including resistance to biotic and abiotic stresses, fruit quality improvement, and domestication are highlighted. Controversies and future perspectives are discussed as well.
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Affiliation(s)
- Tian Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
| | - Hongyan Zhang
- Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Science, Shandong Normal University, 250014 Jinan, China
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
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109
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Wadley GD, Lamon S, Alexander SE, McMullen JR, Bernardo BC. Noncoding RNAs regulating cardiac muscle mass. J Appl Physiol (1985) 2018; 127:633-644. [PMID: 30571279 DOI: 10.1152/japplphysiol.00904.2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Noncoding RNAs, including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs) play roles in the development and homeostasis of nearly every tissue of the body, including the regulation of processes underlying heart growth. Cardiac hypertrophy can be classified as either physiological (beneficial heart growth) or pathological (detrimental heart growth), the latter of which results in impaired cardiac function and heart failure and is predictive of a higher incidence of death due to cardiovascular disease. Several miRNAs have a functional role in exercise-induced cardiac hypertrophy, while both miRNAs and lncRNAs are heavily involved in pathological heart growth and heart failure. The latter have the potential to act as an endogenous sponge RNA and interact with specific miRNAs to control cardiac hypertrophy, adding another level of complexity to our understanding of the regulation of cardiac muscle mass. In addition to tissue-specific effects, ncRNA-mediated tissue cross talk occurs via exosomes. In particular, miRNAs can be internalized in exosomes and secreted from various cardiac and vascular cell types to promote angiogenesis, as well as protection and repair of ischemic tissues. ncRNAs hold promising therapeutic potential to protect the heart against ischemic injury and aid in regeneration. Numerous preclinical studies have demonstrated the therapeutic potential of ncRNAs, specifically miRNAs, for the treatment of cardiovascular disease. Most of these studies employ antisense oligonucleotides to inhibit miRNAs of interest; however, off-target effects often limit their potential to be translated to the clinic. In this context, approaches using viral and nonviral delivery tools are promising means to provide targeted delivery in vivo.
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Affiliation(s)
- Glenn D Wadley
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Burwood, Australia
| | - Séverine Lamon
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Burwood, Australia
| | - Sarah E Alexander
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Burwood, Australia
| | - Julie R McMullen
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Department of Diabetes, Central Clinical School, Monash University, Clayton, Victoria, Australia.,Department of Medicine, Monash University, Clayton, Victoria, Australia.,Department of Physiology, Monash University, Clayton, Victoria, Australia.,Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Bianca C Bernardo
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Department of Diabetes, Central Clinical School, Monash University, Clayton, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Victoria, Australia
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110
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Jung M, Dodsworth M, Thum T. Inflammatory cells and their non-coding RNAs as targets for treating myocardial infarction. Basic Res Cardiol 2018; 114:4. [PMID: 30523422 PMCID: PMC6290728 DOI: 10.1007/s00395-018-0712-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 11/29/2018] [Indexed: 12/22/2022]
Abstract
Myocardial infarction triggers infiltration of several types of immune cells that coordinate both innate and adaptive immune responses. These play a dual role in post-infarction cardiac remodeling by initiating and resolving inflammatory processes, which needs to occur in a timely and well-orchestrated way to ensure a reestablishment of normalized cardiac functions. Thus, therapeutic modulation of immune responses might have benefits for infarct patients. While such strategies have shown great potential in treating cancer, applications in the post-infarction context have been disappointing. One challenge has been the complexity and plasticity of immune cells and their functions in cardiac regulation and healing. The types appear in patterns that are temporally and spatially distinct, while influencing each other and the surrounding tissue. A comprehensive understanding of the immune cell repertoire and their regulatory functions following infarction is sorely needed. Processes of cardiac remodeling trigger additional genetic changes that may also play critical roles in the aftermath of cardiovascular disease. Some of these changes involve non-coding RNAs that play crucial roles in the regulation of immune cells and may, therefore, be of therapeutic interest. This review summarizes what is currently known about the functions of immune cells and non-coding RNAs during post-infarction wound healing. We address some of the challenges that remain and describe novel therapeutic approaches under development that are based on regulating immune responses through non-coding RNAs in the aftermath of the disease.
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Affiliation(s)
- Mira Jung
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Michael Dodsworth
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
- National Heart and Lung Institute, Imperial College London, London, UK.
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111
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Hung J, Miscianinov V, Sluimer JC, Newby DE, Baker AH. Targeting Non-coding RNA in Vascular Biology and Disease. Front Physiol 2018; 9:1655. [PMID: 30524312 PMCID: PMC6262071 DOI: 10.3389/fphys.2018.01655] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/02/2018] [Indexed: 12/16/2022] Open
Abstract
Only recently have we begun to appreciate the importance and complexity of the non-coding genome, owing in some part to truly significant advances in genomic technology such as RNA sequencing and genome-wide profiling studies. Previously thought to be non-functional transcriptional “noise,” non-coding RNAs (ncRNAs) are now known to play important roles in many diverse biological pathways, not least in vascular disease. While microRNAs (miRNA) are known to regulate protein-coding gene expression principally through mRNA degradation, long non-coding RNAs (lncRNAs) can activate and repress genes by a variety of mechanisms at both transcriptional and translational levels. These versatile molecules, with complex secondary structures, may interact with chromatin, proteins, and other RNA to form complexes with an array of functional consequences. A body of emerging evidence indicates that both classes of ncRNAs regulate multiple physiological and pathological processes in vascular physiology and disease. While dozens of miRNAs are now implicated and described in relative mechanistic depth, relatively fewer lncRNAs are well described. However, notable examples include ANRIL, SMILR, and SENCR in vascular smooth muscle cells; MALAT1 and GATA-6S in endothelial cells; and mitochondrial lncRNA LIPCAR as a powerful biomarker. Due to such ubiquitous involvement in pathology and well-known biogenesis and functional genetics, novel miRNA-based therapies and delivery methods are now in development, including some early stage clinical trials. Although lncRNAs may hold similar potential, much more needs to be understood about their relatively complex molecular behaviours before realistic translation into novel therapies. Here, we review the current understanding of the mechanism and function of ncRNA, focusing on miRNAs and lncRNAs in vascular disease and atherosclerosis. We discuss existing therapies and current delivery methods, emphasising the importance of miRNAs and lncRNAs as effectors and biomarkers in vascular pathology.
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Affiliation(s)
- John Hung
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom.,Deanery of Clinical Sciences, Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Vladislav Miscianinov
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | | | - David E Newby
- Deanery of Clinical Sciences, Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew H Baker
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
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112
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Targeting ncRNAs by plant secondary metabolites: The ncRNAs game in the balance towards malignancy inhibition. Biotechnol Adv 2018; 36:1779-1799. [DOI: 10.1016/j.biotechadv.2017.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/31/2017] [Accepted: 11/06/2017] [Indexed: 02/06/2023]
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113
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Schrank Z, Khan N, Osude C, Singh S, Miller RJ, Merrick C, Mabel A, Kuckovic A, Puri N. Oligonucleotides Targeting Telomeres and Telomerase in Cancer. Molecules 2018; 23:molecules23092267. [PMID: 30189661 PMCID: PMC6225148 DOI: 10.3390/molecules23092267] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/27/2018] [Accepted: 09/04/2018] [Indexed: 02/07/2023] Open
Abstract
Telomeres and telomerase have become attractive targets for the development of anticancer therapeutics due to their involvement in cancer cell immortality. Currently, several therapeutics have been developed that directly target telomerase and telomeres, such as telomerase inhibitors and G-quadruplex stabilizing ligands. Telomere-specific oligonucleotides that reduce telomerase activity and disrupt telomere architecture are also in development as novel anticancer therapeutics. Specifically, GRN163L and T-oligos have demonstrated promising anticancer activity in multiple cancers types via induction of potent DNA damage responses. Currently, several miRNAs have been implicated in the regulation of telomerase activity and may prove to be valuable targets in the development of novel therapies by reducing expression of telomerase subunits. Targeting miRNAs that are known to increase expression of telomerase subunits may be another strategy to reduce carcinogenesis. This review aims to provide a comprehensive understanding of current oligonucleotide-based anticancer therapies that target telomeres and telomerase. These studies may help design novel therapeutic approaches to overcome the challenges of oligonucleotide therapy in a clinical setting.
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Affiliation(s)
- Zachary Schrank
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Nabiha Khan
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Chike Osude
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Sanjana Singh
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Rachel J Miller
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Collin Merrick
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Alexander Mabel
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Adijan Kuckovic
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
| | - Neelu Puri
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA.
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114
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Vesikansa A. Unraveling of Central Nervous System Disease Mechanisms Using CRISPR Genome Manipulation. J Cent Nerv Syst Dis 2018; 10:1179573518787469. [PMID: 30013417 PMCID: PMC6043941 DOI: 10.1177/1179573518787469] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 06/09/2018] [Indexed: 12/26/2022] Open
Abstract
The complex structure and highly variable gene expression profile of the brain makes it among the most challenging fields to study in both basic and translational biological research. Most of the brain diseases are multifactorial and despite the rapidly increasing genomic data, molecular pathways and causal links between genes and central nervous system (CNS) diseases are largely unknown. The advent of an easy and flexible CRISPR-Cas genome editing technology has rapidly revolutionized the field of functional genomics and opened unprecedented possibilities to dissect the mechanisms of CNS disease. CRISPR-Cas allows a plenitude of applications for both gene-focused and genome-wide approaches, ranging from original “gene scissors” making permanent modifications in the genome to the regulation of gene expression and epigenetics. CRISPR technology provides a unique opportunity to establish new cellular and animal models of CNS diseases and holds potential for breakthroughs in the CNS research and drug development.
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Affiliation(s)
- Aino Vesikansa
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.,Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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115
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Novel Epigenetic Techniques Provided by the CRISPR/Cas9 System. Stem Cells Int 2018; 2018:7834175. [PMID: 30123293 PMCID: PMC6079388 DOI: 10.1155/2018/7834175] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 02/04/2018] [Accepted: 03/27/2018] [Indexed: 12/26/2022] Open
Abstract
Epigenetics classically refers to the inheritable changes of hereditary information without perturbing DNA sequences. Understanding mechanisms of how epigenetic factors contribute to inheritable phenotype changes and cell identity will pave the way for us to understand diverse biological processes. In recent years, the emergence of CRISPR/Cas9 technology has provided us with new routes to the epigenetic field. In this review, novel epigenetic techniques utilizing the CRISPR/Cas9 system are the main contents to be discussed, including epigenome editing, temporal and spatial control of epigenetic effectors, noncoding RNA manipulation, chromatin in vivo imaging, and epigenetic element screening.
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116
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Roy B, Zhao J, Yang C, Luo W, Xiong T, Li Y, Fang X, Gao G, Singh CO, Madsen L, Zhou Y, Kristiansen K. CRISPR/Cascade 9-Mediated Genome Editing-Challenges and Opportunities. Front Genet 2018; 9:240. [PMID: 30026755 PMCID: PMC6042012 DOI: 10.3389/fgene.2018.00240] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/18/2018] [Indexed: 12/26/2022] Open
Abstract
Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and Cascade 9 (also known as Cas9, CRISPR associated protein 9) confer protection against invading viruses or plasmids. The CRISPR/Cascade 9 system constitutes one of the most powerful genome technologies available to researchers today. So far, this technology has enabled efficient genome editing and modification in several model organisms and has successfully been used in biomedicine and biomedical engineering. However, challenges for efficient and safe genetic manipulation in several organisms persist. Here, we review functional approaches and future challenges associated with the use of the CRISPR/Cascade 9 genome editing system and discuss opportunities, ethical issues and future directions within this field.
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Affiliation(s)
| | - Jing Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Chao Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Wen Luo
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Teng Xiong
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yong Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Guanjun Gao
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Chabungbam O Singh
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Lise Madsen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Institute of Marine Research, Bergen, Norway
| | - Yong Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Karsten Kristiansen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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117
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Das A, Samidurai A, Salloum FN. Deciphering Non-coding RNAs in Cardiovascular Health and Disease. Front Cardiovasc Med 2018; 5:73. [PMID: 30013975 PMCID: PMC6036139 DOI: 10.3389/fcvm.2018.00073] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/29/2018] [Indexed: 12/16/2022] Open
Abstract
After being long considered as “junk” in the human genome, non-coding RNAs (ncRNAs) currently represent one of the newest frontiers in cardiovascular disease (CVD) since they have emerged in recent years as potential therapeutic targets. Different types of ncRNAs exist, including small ncRNAs that have fewer than 200 nucleotides, which are mostly known as microRNAs (miRNAs), and long ncRNAs that have more than 200 nucleotides. Recent discoveries on the role of ncRNAs in epigenetic and transcriptional regulation, atherosclerosis, myocardial ischemia/reperfusion (I/R) injury and infarction (MI), adverse cardiac remodeling and hypertrophy, insulin resistance, and diabetic cardiomyopathy prompted vast interest in exploring candidate ncRNAs for utilization as potential therapeutic targets and/or diagnostic/prognostic biomarkers in CVDs. This review will discuss our current knowledge concerning the roles of different types of ncRNAs in cardiovascular health and disease and provide some insight on the cardioprotective signaling pathways elicited by the non-coding genome. We will highlight important basic and clinical breakthroughs that support employing ncRNAs for treatment or early diagnosis of a variety of CVDs, and also depict the most relevant limitations that challenge this novel therapeutic approach.
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Affiliation(s)
- Anindita Das
- Pauley Heart Center, Division of Cardiology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Arun Samidurai
- Pauley Heart Center, Division of Cardiology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Fadi N Salloum
- Pauley Heart Center, Division of Cardiology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States
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118
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Kurata JS, Lin RJ. MicroRNA-focused CRISPR-Cas9 library screen reveals fitness-associated miRNAs. RNA (NEW YORK, N.Y.) 2018; 24:966-981. [PMID: 29720387 PMCID: PMC6004052 DOI: 10.1261/rna.066282.118] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional gene regulators that play important roles in the control of cell fitness, differentiation, and development. The CRISPR-Cas9 gene-editing system is composed of the Cas9 nuclease in complex with a single guide RNA (sgRNA) and directs DNA cleavage at a predetermined site. Several CRISPR-Cas9 libraries have been constructed for genome-scale knockout screens of protein function; however, few libraries have included miRNA genes. Here we constructed a miRNA-focused CRISPR-Cas9 library that targets 1594 (85%) annotated human miRNA stem-loops. The sgRNAs in our LX-miR library are designed to have high on-target and low off-target activity, and each miRNA is targeted by four to five sgRNAs. We used this sgRNA library to screen for miRNAs that affect cell fitness of HeLa or NCI-N87 cells by monitoring the change in frequency of each sgRNA over time. By considering the expression in the tested cells and the dysregulation of the miRNAs in cancer specimens, we identified five HeLa pro-fitness and cervical cancer up-regulated miRNAs (miR-31-5p, miR-92b-3p, miR-146b-5p, miR-151a-3p, and miR-194-5p). Similarly, we identified six NCI-N87 pro-fitness and gastric cancer up-regulated miRNAs (miR-95-3p, miR-181a-5p, miR-188-5p, miR-196b-5p, miR-584-5p, and miR-1304-3p), as well as three anti-fitness and down-regulated miRNAs (let-7a-3p, miR-100-5p, and miR-149-5p). Some of those miRNAs are known to be oncogenic or tumor-suppressive, but others are novel. Taken together, the LX-miR library is useful for genome-wide unbiased screening to identify miRNAs important for cellular fitness and likely to be useful for other functional screens.
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Affiliation(s)
- Jessica S Kurata
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences of the City of Hope, Duarte, California 91010, USA
| | - Ren-Jang Lin
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences of the City of Hope, Duarte, California 91010, USA
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119
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Li B, Meng X, Zhang L. microRNAs and cardiac stem cells in heart development and disease. Drug Discov Today 2018; 24:233-240. [PMID: 29852125 DOI: 10.1016/j.drudis.2018.05.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/24/2018] [Accepted: 05/22/2018] [Indexed: 12/20/2022]
Abstract
Cumulative evidence has proven that proliferation, differentiation and migration of cardiac stem cells (CSCs) dominate early heart development and contribute to the later occurrence of heart disease. Among other mechanisms, microRNAs work as the 'fine-tuning' to modulate the levels of target genes in a specific cell type. The distinct microRNA signatures in CSCs reveal the stages and functions of CSCs. The focus of this review is to summarize recent knowledge advances in CSC proliferation, differentiation and migration and to discuss how microRNAs regulate these processes during heart development and in heart disease. Better understanding of microRNA regulation on CSCs under different situations will enable the unveiling of the mechanisms of heart disease and open new avenues in the therapeutic potentials of microRNA modulation to treat heart disease.
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Affiliation(s)
- Bo Li
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA.
| | - Xianmei Meng
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Lubo Zhang
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
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120
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Shah SZA, Zhao D, Hussain T, Sabir N, Yang L. Regulation of MicroRNAs-Mediated Autophagic Flux: A New Regulatory Avenue for Neurodegenerative Diseases With Focus on Prion Diseases. Front Aging Neurosci 2018; 10:139. [PMID: 29867448 PMCID: PMC5962651 DOI: 10.3389/fnagi.2018.00139] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/25/2018] [Indexed: 02/06/2023] Open
Abstract
Prion diseases are fatal neurological disorders affecting various mammalian species including humans. Lack of proper diagnostic tools and non-availability of therapeutic remedies are hindering the control strategies for prion diseases. MicroRNAs (miRNAs) are abundant endogenous short non-coding essential RNA molecules that negatively regulate the target genes after transcription. Several biological processes depend on miRNAs, and altered profiles of these miRNAs are potential biomarkers for various neurodegenerative diseases, including prion diseases. Autophagic flux degrades the misfolded prion proteins to reduce chronic endoplasmic reticulum stress and enhance cell survival. Recent evidence suggests that specific miRNAs target and regulate the autophagic mechanism, which is critical for alleviating cellular stress. miRNAs-mediated regulation of these specific proteins involved in the autophagy represents a new target with highly significant therapeutic prospects. Here, we will briefly describe the biology of miRNAs, the use of miRNAs as potential biomarkers with their credibility, the regulatory mechanism of miRNAs in major neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and prion diseases, degradation pathways for aggregated prion proteins, the role of autophagy in prion diseases. Finally, we will discuss the miRNAs-modulated autophagic flux in neurodegenerative diseases and employ them as potential therapeutic intervention strategy in prion diseases.
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Affiliation(s)
- Syed Zahid Ali Shah
- National Animal Transmissible Spongiform Encephalopathy Laboratory and Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Deming Zhao
- National Animal Transmissible Spongiform Encephalopathy Laboratory and Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Tariq Hussain
- National Animal Transmissible Spongiform Encephalopathy Laboratory and Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Naveed Sabir
- National Animal Transmissible Spongiform Encephalopathy Laboratory and Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Lifeng Yang
- National Animal Transmissible Spongiform Encephalopathy Laboratory and Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
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121
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Zhang S, Li J, Li J, Yang Y, Kang X, Li Y, Wu X, Zhu Q, Zhou Y, Hu Y. Up-regulation of microRNA-203 in influenza A virus infection inhibits viral replication by targeting DR1. Sci Rep 2018; 8:6797. [PMID: 29717211 PMCID: PMC5931597 DOI: 10.1038/s41598-018-25073-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/13/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules that play important roles in various biological processes. Much evidence shows that miRNAs are closely associated with numerous virus infections; however, involvement of cellular miRNAs in influenza A virus (IAV) infection is unclear. Here, we found that expression of miR-203 was up-regulated markedly via two different mechanisms during IAV infection. First, we examined the effects of type I interferon induced by IAV on direct activation of miR-203 expression. Next, we showed that DNA demethylation within the miR-203 promoter region in A549 cells induced its up-regulation, and that expression of DNA methyltransferase 1 was down-regulated following H5N1 virus infection. Ectopic expression of miR-203 in turn inhibited H5N1 virus replication by targeting down-regulator of transcription 1 (DR1), which was identified as a novel target of miR-203. Silencing DR1 in miR-203 knockout cells using a specific siRNA inhibited replication of the H5N1 virus, an effect similar to that of miR-203. In summary, the data show that host cell expression of miR-203 is up-regulated upon IAV infection, which increases antiviral responses by suppressing a novel target gene, DR1. Thus, we have identified a novel mechanism underlying the relationship between miR-203 and IAV infection.
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Affiliation(s)
- Sen Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Jing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Junfeng Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Yinhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Xiaoping Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Yuchang Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Xiaoyan Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Qingyu Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Yusen Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
| | - Yi Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
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122
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Mollanoori H, Teimourian S. Therapeutic applications of CRISPR/Cas9 system in gene therapy. Biotechnol Lett 2018; 40:907-914. [PMID: 29704220 DOI: 10.1007/s10529-018-2555-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/16/2018] [Indexed: 12/11/2022]
Abstract
Gene therapy is based on the principle of the genetic manipulation of DNA or RNA for treating and preventing human diseases. The clustered regularly interspaced short palindromic repeats/CRISPR associated nuclease9 (CRISPR/Cas9) system, derived from the acquired immune system in bacteria and archaea, has provided a new tool for accurate manipulation of genomic sequence to attain a therapeutic result. The advantage of CRISPR which made it an easy and flexible tool for diverse genome editing purposes is that a single protein (Cas9) complex with 2 short RNA sequences, function as a site-specific endonuclease. Recently, application of CRISPR/Cas9 system has become popular for therapeutic aims such as gene therapy. In this article, we review the fundamental mechanisms of CRISPR-Cas9 function and summarize preclinical CRISPR-mediated gene therapy reports on a wide variety of disorders.
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Affiliation(s)
- Hasan Mollanoori
- Department of Medical Genetics, Iran University of Medical Sciences (IUMS), Crossroads of Shahid Hemmat & Shahid Chamran Highways, P.O. Box: 15875-6171, 1449614535, Tehran, Iran
| | - Shahram Teimourian
- Department of Medical Genetics, Iran University of Medical Sciences (IUMS), Crossroads of Shahid Hemmat & Shahid Chamran Highways, P.O. Box: 15875-6171, 1449614535, Tehran, Iran. .,Department of Infectious Diseases, School of Medicine, Pediatric Infectious Diseases Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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123
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Herzog S. Generation of microRNA Sponge Library. Bio Protoc 2018; 8:e2820. [PMID: 34286030 DOI: 10.21769/bioprotoc.2820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/09/2018] [Accepted: 04/21/2018] [Indexed: 11/02/2022] Open
Abstract
This protocol describes the generation and functional validation of microRNA (miRNA) sponge or decoy constructs. When expressed from a strong promoter, these transcripts can sequester specific miRNA:RISC complexes, thereby resulting in a derepression of endogenous target mRNA. Hence, cells expressing such sponges display a partial or full miRNA loss-of-function phenotype. Depending on the sponge sequence, the activity of any miRNA of choice can be inhibited by sponge sequestration, but it should be noted that these constructs do not seem to be specific for one particular miRNA. Rather, all miRNAs of the same family as defined by the seed sequence will be affected, albeit to a different degree.
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Affiliation(s)
- Sebastian Herzog
- Department of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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124
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Sherstyuk VV, Medvedev SP, Ri MT, Vyatkin YV, Saik OV, Shtokalo DN, Zakian SM. The search for microRNAs potentially involved in the selfrenewal maintaining of laboratory rat pluripotent stem cells. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Self-renewal of cultured pluripotent stem cells is a complex process, which includes multiple functional and regulatory levels. Transcription factors, their target genes, chromatin modifiers, signaling pathways, and regulatory noncoding RNAs are involved in the maintaining of self-renewal. Studies of molecular and genetic bases of maintaining self-renewal and pluripotency in cultured mammalian cells are important to understand processes in preimplantation embryogenesis and to develop efficient techniques to obtain pluripotent stem cell lines for experimental biology and medicine. MicroRNAs (miRNAs) play an important role in pluripotency maintaining and reprogramming. However, involvement of this class of noncoding RNAs and functions of individual molecules are poorly studied. The goal of this study was the search for the miRNAs potentially involved in the pluripotency maintaining and reprogramming of Rattus norvegicus cells. We analyzed the expression of miRNAs in rat embryonic stem cells, induced pluripotent stem cells and embryonic fibroblasts using bioinformatic methods and data obtained with next generation sequencing. The analysis of differential expression between groups of rat pluripotent cells and fibroblasts, and the analysis of experimentally confirmed target genes of differentially expressed known rat miRNAs revealed novel potential players of pluripotency maintaining and reprogramming processes. In addition, novel members of these processes were revealed among novel rat miRNAs. The use of bioinformatic and systems biology approaches is the first step, which is necessary for choosing candidates for the subsequent experimental studies. The results obtained substantially improve our understanding of the self-renewal regulation system of the laboratory rat, a popular biomedical object, and our knowledge about the system in mammals.
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Affiliation(s)
- V. V. Sherstyuk
- Institute of Cytology and Genetics SB RAS; E.N. Meshalkin National Medical Research Center, Ministry of Health of Russian Federation; Institute of Chemical Biology and Fundamental Medicine SB RAS; Novosibirsk State University
| | - S. P. Medvedev
- Institute of Cytology and Genetics SB RAS; E.N. Meshalkin National Medical Research Center, Ministry of Health of Russian Federation; Institute of Chemical Biology and Fundamental Medicine SB RAS; Novosibirsk State University
| | - M. T. Ri
- AcademGene LLC; St. Laurent Institute
| | - Y. V. Vyatkin
- Institute of Cytology and Genetics SB RAS; Novosibirsk State University; AcademGene LLC; St. Laurent Institute
| | - O. V. Saik
- Institute of Cytology and Genetics SB RAS
| | - D. N. Shtokalo
- Institute of Cytology and Genetics SB RAS; AcademGene LLC; St. Laurent Institute; A.P. Ershov Institute of Informatics Systems SB RAS
| | - S. M. Zakian
- Institute of Cytology and Genetics SB RAS; E.N. Meshalkin National Medical Research Center, Ministry of Health of Russian Federation; Institute of Chemical Biology and Fundamental Medicine SB RAS; Novosibirsk State University
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125
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Affiliation(s)
- Andrea Ventura
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lukas E. Dow
- Department of Medicine, Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10021, USA
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126
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MicroRNA-Based Drugs for Brain Tumors. Trends Cancer 2018; 4:222-238. [PMID: 29506672 DOI: 10.1016/j.trecan.2017.12.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/18/2017] [Accepted: 12/24/2017] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are key regulatory elements encoded by the genome. A single miRNA can downregulate the expression of multiple genes involved in diverse functions. Because cancer is a disease with multiple gene aberrations, developing novel approaches to identify and modulate miRNA pathways may result in a breakthrough for cancer treatment. With a special focus on glioblastoma (GBM), this review provides an up-to-date summary of miRNA biogenesis, the role of miRNA in cancer resistance, and essential tools for modulating miRNA expression, as well as of clinically promising RNAi delivery systems and how they can be adapted for therapy.
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127
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Kellner K, Solanki A, Amann T, Lao N, Barron N. Targeting miRNAs with CRISPR/Cas9 to Improve Recombinant Protein Production of CHO Cells. Methods Mol Biol 2018; 1850:221-235. [PMID: 30242690 DOI: 10.1007/978-1-4939-8730-6_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNAs with their unique ability to target hundreds of genes have been highlighted as powerful tools to improve bioprocess behavior of cells. The common approaches to stably deplete miRNAs are the use of sponge decoy transcripts or shRNA inhibitors, which requires the introduction and expression of extra genetic material. As an alternative, we implemented the CRISPR/Cas9 system in our laboratory to generate Chinese hamster ovary (CHO) cells which lack the expression of a specific miRNA for the purpose of functional studies. To implement the system, miR-27a/b was chosen as it has been shown to be upregulated during hypothermic conditions and therefore may be involved in controlling CHO cell growth and recombinant protein productivity. In this chapter, we present a protocol for targeting miRNAs in CHO cells using CRISPR/Cas9 and the analysis of the resulting phenotype, using miR-27 as an example. We showed that it is possible to target miRNAs in CHO cells and achieved ≥80% targeting efficiency. Indel analysis and TOPO-TA cloning combined with Sanger sequencing showed a range of different indels. Furthermore, it was possible to identify clones with no detectable expression of mature miR-27b. Depletion of miR-27b led to improved viability in late stages of batch and fed-batch cultures making it a potentially interesting target to improve bioprocess performance of CHO cells.
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Affiliation(s)
- Kevin Kellner
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland.
| | - Ankur Solanki
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland
| | - Thomas Amann
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nga Lao
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland
| | - Niall Barron
- National Institute for Bioprocessing Research and Training, Dublin, Ireland.,School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
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128
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Kilic T, Erdem A, Ozsoz M, Carrara S. microRNA biosensors: Opportunities and challenges among conventional and commercially available techniques. Biosens Bioelectron 2018; 99:525-546. [DOI: 10.1016/j.bios.2017.08.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 12/19/2022]
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129
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130
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Nguyen DD, Chang S. Development of Novel Therapeutic Agents by Inhibition of Oncogenic MicroRNAs. Int J Mol Sci 2017; 19:E65. [PMID: 29280958 PMCID: PMC5796015 DOI: 10.3390/ijms19010065] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/14/2017] [Accepted: 12/22/2017] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRs, miRNAs) are regulatory small noncoding RNAs, with their roles already confirmed to be important for post-transcriptional regulation of gene expression affecting cell physiology and disease development. Upregulation of a cancer-causing miRNA, known as oncogenic miRNA, has been found in many types of cancers and, therefore, represents a potential new class of targets for therapeutic inhibition. Several strategies have been developed in recent years to inhibit oncogenic miRNAs. Among them is a direct approach that targets mature oncogenic miRNA with an antisense sequence known as antimiR, which could be an oligonucleotide or miRNA sponge. In contrast, an indirect approach is to block the biogenesis of miRNA by genome editing using the CRISPR/Cas9 system or a small molecule inhibitor. The development of these inhibitors is straightforward but involves significant scientific and therapeutic challenges that need to be resolved. In this review, we summarize recent relevant studies on the development of miRNA inhibitors against cancer.
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Affiliation(s)
- Dinh-Duc Nguyen
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea.
| | - Suhwan Chang
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea.
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Aquino-Jarquin G. Emerging Role of CRISPR/Cas9 Technology for MicroRNAs Editing in Cancer Research. Cancer Res 2017; 77:6812-6817. [PMID: 29208606 DOI: 10.1158/0008-5472.can-17-2142] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/05/2017] [Accepted: 09/21/2017] [Indexed: 11/16/2022]
Abstract
MicroRNAs (miRNA) are small, noncoding RNA molecules with a master role in the regulation of important tasks in different critical processes of cancer pathogenesis. Because there are different miRNAs implicated in all the stages of cancer, for example, functioning as oncogenes, this makes these small molecules suitable targets for cancer diagnosis and therapy. RNA-mediated interference has been one major approach for sequence-specific regulation of gene expression in eukaryotic organisms. Recently, the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system, first identified in bacteria and archaea as an adaptive immune response to invading genetic material, has been explored as a sequence-specific molecular tool for editing genomic sequences for basic research in life sciences and for therapeutic purposes. There is growing evidence that small noncoding RNAs, including miRNAs, can be targeted by the CRISPR/Cas9 system despite their lacking an open reading frame to evaluate functional loss. Thus, CRISPR/Cas9 technology represents a novel gene-editing strategy with compelling robustness, specificity, and stability for the modification of miRNA expression. Here, I summarize key features of current knowledge of genomic editing by CRISPR/Cas9 technology as a feasible strategy for globally interrogating miRNA gene function and miRNA-based therapeutic intervention. Alternative emerging strategies for nonviral delivery of CRISPR/Cas9 core components into human cells in a clinical context are also analyzed critically. Cancer Res; 77(24); 6812-7. ©2017 AACR.
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Affiliation(s)
- Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, 4to. Piso, Sección II, Hospital Infantil de México, Federico Gómez, Mexico.
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133
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Yang J, Meng X, Pan J, Jiang N, Zhou C, Wu Z, Gong Z. CRISPR/Cas9-mediated noncoding RNA editing in human cancers. RNA Biol 2017; 15:35-43. [PMID: 29028415 DOI: 10.1080/15476286.2017.1391443] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cancer is characterized by multiple genetic and epigenetic alterations, including a higher prevalence of mutations of oncogenes and/or tumor suppressors. Mounting evidences have shown that noncoding RNAs (ncRNAs) are involved in the epigenetic regulation of cancer genes and their associated pathways. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (CRISPR/Cas9) system, a revolutionary genome-editing technology, has shed light on ncRNA-based cancer therapy. Here, we briefly introduce the classifications and mechanisms of CRISPR/Cas9 system. Importantly, we mainly focused on the applications of CRISPR/Cas9 system as a molecular tool for ncRNA (microRNA, long noncoding RNA and circular RNA, etc.) editing in human cancers, and the novel techniques that are based on CRISPR/Cas9 system. Additionally, the off-target effects and the corresponding solutions as well as the challenges toward CRISPR/Cas9 were also evaluated and discussed. Long- and short-ncRNAs have been employed as targets in precision oncology, and CRISPR/Cas9-mediated ncRNA editing may provide an excellent way to cure cancer.
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Affiliation(s)
- Jie Yang
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Xiaodan Meng
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Jinchang Pan
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Nan Jiang
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Chengwei Zhou
- c Department of Thoracic Surgery , The Affiliated Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Zhenhua Wu
- d Department of Otolaryngology Head and Neck Surgery , The Affiliated Ningbo Medical Center Lihuili Eastern Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Zhaohui Gong
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
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134
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Liu Q, Yan S, Yang T, Zhang S, Chen YQ, Liu B. Small RNAs in regulating temperature stress response in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:774-791. [PMID: 28731217 DOI: 10.1111/jipb.12571] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/12/2017] [Indexed: 05/21/2023]
Abstract
Due to global climate change, temperature stress has become one of the primary causes of crop losses worldwide. Much progress has been made in unraveling the complex stress response mechanisms in plants, particularly in the identification of temperature stress responsive protein-coding genes. Recently discovered microRNAs (miRNAs) and endogenous small-interfering RNAs (siRN As) have also been demonstrated as important players in plant temperature stress response. Using high-throughput sequencing, many small RNAs, especially miRNAs, have been identified to be triggered by cold or heat. Subsequently, several studies have shown an important functional role for these small RNAs in cold or heat tolerance. These findings greatly broaden our understanding of endogenous small RNAs in plant stress response control. Here, we highlight new findings regarding the roles of miRNAs and siRNAs in plant temperature stress response and acclimation. We also review the current understanding of the regulatory mechanisms of small RNAs in temperature stress response, and explore the outlook for the use of these small RNAs in molecular breeding for improvement of temperature stress tolerance in plants.
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Affiliation(s)
- Qing Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shijuan Yan
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Tifeng Yang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shaohong Zhang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yue-Qin Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Bin Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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135
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Yoshino H, Yonemori M, Miyamoto K, Tatarano S, Kofuji S, Nohata N, Nakagawa M, Enokida H. microRNA-210-3p depletion by CRISPR/Cas9 promoted tumorigenesis through revival of TWIST1 in renal cell carcinoma. Oncotarget 2017; 8:20881-20894. [PMID: 28152509 PMCID: PMC5400553 DOI: 10.18632/oncotarget.14930] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/05/2016] [Indexed: 12/11/2022] Open
Abstract
Previous studies showed that five miRNAs (miR-885-5p, miR-1274, miR-210-3p, miR-224 and miR-1290) were upregulated the most in clear cell renal cell carcinoma (ccRCC). Our focus was to understand from a clinical standpoint the functional consequences of upregulating miR-210-3p. Towards this, we utilized the CRISPR/Cas9 gene editing system to deplete miR-210-3p in RCC cell lines (786-o, A498 and Caki2) and characterized the outcomes. We observed that miR-210-3p depletion dramatically increased tumorigenesis, including altering the morphology of A498 and Caki2 cells in a manner characteristic of epithelial-mesenchymal transition (EMT). These results were corroborated by in vivo xenograft studies, which showed enhanced growth of tumors from miR-210-3p-depleted A498 cells. We identified Twist-related protein 1 (TWIST1) as a key target of miR-210-3p. Analysis of the ccRCC patient data in The Cancer Genome Atlas database showed a negative correlation between miR-210-3p and TWIST1 expression. High TWIST1 and low miR-210-3p expression associated with poorer overall and disease-free survival as compared to low TWIST1 and high miR-210-3p expression. These findings suggest that renal cell carcinoma progression is promoted by TWIST1 suppression mediated by miR-210-3p.
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Affiliation(s)
- Hirofumi Yoshino
- Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
| | - Masaya Yonemori
- Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
| | - Kazutaka Miyamoto
- Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
| | - Syuichi Tatarano
- Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
| | - Satoshi Kofuji
- Department of Internal Medicine, Vontz Center, University of Cincinnati, College of Medicine, Ohio 45267-0508, USA
| | - Nijiro Nohata
- Moores UCSD Cancer Center, La Jolla, CA 92093-0803, USA
| | - Masayuki Nakagawa
- Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
| | - Hideki Enokida
- Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
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136
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CRISPR/Cas9 editing reveals novel mechanisms of clustered microRNA regulation and function. Sci Rep 2017; 7:8585. [PMID: 28819307 PMCID: PMC5561095 DOI: 10.1038/s41598-017-09268-0] [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: 03/16/2017] [Accepted: 07/18/2017] [Indexed: 12/27/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of diverse physiological and pathophysiological processes. MiRNA families and clusters are two key features in miRNA biology. Here we explore the use of CRISPR/Cas9 as a powerful tool to delineate the function and regulation of miRNA families and clusters. We focused on four miRNA clusters composed of miRNA members of the same family, homo-clusters or different families, hetero-clusters. Our results highlight different regulatory mechanisms in miRNA cluster expression. In the case of the miR-497~195 cluster, editing of miR-195 led to a significant decrease in the expression of the other miRNA in the cluster, miR-497a. Although no gene editing was detected in the miR-497a genomic locus, computational simulation revealed alteration in the three dimensional structure of the pri-miR-497~195 that may affect its processing. In cluster miR-143~145 our results imply a feed-forward regulation, although structural changes cannot be ruled out. Furthermore, in the miR-17~92 and miR-106~25 clusters no interdependency in miRNA expression was observed. Our findings suggest that CRISPR/Cas9 is a powerful gene editing tool that can uncover novel mechanisms of clustered miRNA regulation and function.
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Mandilaras V, Vernon M, Meryet-Figuière M, Karakasis K, Lambert B, Poulain L, Oza A, Denoyelle C, Lheureux S. Updates and current challenges in microRNA research for personalized medicine in ovarian cancer. Expert Opin Biol Ther 2017. [DOI: 10.1080/14712598.2017.1340935] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Victoria Mandilaras
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Mégane Vernon
- INSERM U1086 “ANTICIPE” (Interdisciplinary Research Unit for Cancers Prevention and Treatment, Axis BioTICLA “Biology and Innovative Therapeutics for Ovarian Cancers”), Normandie Univ, UNICAEN, Caen, France
- Comprehensive Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Matthieu Meryet-Figuière
- INSERM U1086 “ANTICIPE” (Interdisciplinary Research Unit for Cancers Prevention and Treatment, Axis BioTICLA “Biology and Innovative Therapeutics for Ovarian Cancers”), Normandie Univ, UNICAEN, Caen, France
- Comprehensive Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Katherine Karakasis
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Bernard Lambert
- INSERM U1086 “ANTICIPE” (Interdisciplinary Research Unit for Cancers Prevention and Treatment, Axis BioTICLA “Biology and Innovative Therapeutics for Ovarian Cancers”), Normandie Univ, UNICAEN, Caen, France
- Comprehensive Cancer Centre François Baclesse, UNICANCER, Caen, France
- Délégation régionale de Normandie, CNRS, Caen, France
| | - Laurent Poulain
- INSERM U1086 “ANTICIPE” (Interdisciplinary Research Unit for Cancers Prevention and Treatment, Axis BioTICLA “Biology and Innovative Therapeutics for Ovarian Cancers”), Normandie Univ, UNICAEN, Caen, France
- Comprehensive Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Amit Oza
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Christophe Denoyelle
- INSERM U1086 “ANTICIPE” (Interdisciplinary Research Unit for Cancers Prevention and Treatment, Axis BioTICLA “Biology and Innovative Therapeutics for Ovarian Cancers”), Normandie Univ, UNICAEN, Caen, France
- Comprehensive Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Stephanie Lheureux
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
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138
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Type II CRISPR/Cas9 approach in the oncological therapy. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:80. [PMID: 28619109 PMCID: PMC5472952 DOI: 10.1186/s13046-017-0550-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/09/2017] [Indexed: 12/19/2022]
Abstract
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a prokaryotic adaptable immune mechanism used by many bacteria and archaea to protect themselves from foreign nucleic acids. This complex system can recognize and cut non-self DNA in order to provide the prokaryotic organisms a strong defense against foreign viral or plasmid attacks and make the cell immune from further assaults. Today, it has been adapted to be used in vitro and in vivo in eukaryotic cells to perform a complete and highly selective gene knockout or a specific gene editing. The ease of use and the low cost are only two features that have made it very popular among the scientific community and the possibility to be used as a clinical treatment in several genetic derived pathologies has rapidly spread its fame worldwide. However, CRISPR is still not fully understood and many efforts need to be done in order to make it a real power tool for the human clinical treatment especially for oncological patients. Indeed, since cancer originates from non-lethal genetic disorders, CRISPR discovery fuels the hope to strike tumors on their roots. More than 4000 papers regarding CRISPR were published in the last ten years and only few of them take in count the possible applications in oncology. The purpose of this review is to clarify many problematics on the CRISPR usage and highlight its potential in oncological therapy.
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139
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Zhou SJ, Deng YL, Liang HF, Jaoude JC, Liu FY. Hepatitis B virus X protein promotes CREB-mediated activation of miR-3188 and Notch signaling in hepatocellular carcinoma. Cell Death Differ 2017; 24:1577-1587. [PMID: 28574502 PMCID: PMC5563993 DOI: 10.1038/cdd.2017.87] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 02/07/2023] Open
Abstract
Familiar clustering of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) has been frequently reported. However, limited information is available about the underlying molecular mechanisms in HBV-related HCC patients with family history of HCC. In our previous study, Agilent miRNA Base 16.0 microarray showed miRNA profiles of the plasma of HBV-related HCC patients who had a family history of HCC. This study aims to explore the expression, function, and mechanisms of miR-3188 in HCC that might provide novel insights into the role of family history on the risk of HCC. The expression levels of miR-3188 were markedly overexpressed in HCC tissues, HBV transgenic mice, and HepG2.215 cells. We knocked out miR-3188 in HCC cell lines using the CRISPR/Cas9 system, and demonstrated that miR-3188 knockout (KO) suppressed cell growth, migration, and invasion, and inhibited xenografts tumor growth in nude mice. Next, we determined that miR-3188 KO exerts antitumor functions by directly repressing ZHX2. It has been reported that HBV X protein (HBx) plays a critical role in HBV-related HCC, promoting CREB-mediated activation of miR-3188 and activation of Notch signaling through repressing ZHX2. Finally, we verified that ZHX2 functions as a transcriptional repressor to Notch1 via interaction with NF-YA. Our data demonstrate that the HBx–miR-3188–ZHX2-Notch1 signaling pathway plays an important role in the pathogenesis and progression of HBV-related HCC with family history of HCC. These findings have important implications for identifying new therapeutic targets in HBV-related HCC.
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Affiliation(s)
- Shao-Jun Zhou
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Yue-Ling Deng
- Department of Gastroenterology, Wuhan Central Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui-Fang Liang
- Department of Hepatology Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jonathan C Jaoude
- Department of GI Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Fu-Yao Liu
- Department of GI Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
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140
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Munk R, Panda AC, Grammatikakis I, Gorospe M, Abdelmohsen K. Senescence-Associated MicroRNAs. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 334:177-205. [PMID: 28838538 PMCID: PMC8436595 DOI: 10.1016/bs.ircmb.2017.03.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Senescent cells arise as a consequence of cellular damage and can have either a detrimental or advantageous impact on tissues and organs depending on the specific cell type and metabolic state. As senescent cells accumulate in tissues with advancing age, they have been implicated in many age-related declines and diseases. The major facets of senescence include two pathways responsible for establishing and maintaining a senescence program, p53/CDKN1A(p21) and CDKN2A(p16)/RB, as well as the senescence-associated secretory phenotype. Numerous MicroRNAs influence senescence by modulating the abundance of key senescence regulatory proteins, generally by lowering the stability and/or translation of mRNAs that encode such factors. Accordingly, understanding the molecular mechanisms by which MicroRNAs influence senescence will enable diagnostic and therapeutic opportunities directed at senescent cells. Here, we review senescence-associated (SA)-MicroRNAs and discuss their implications in senescence-relevant pathologies.
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Affiliation(s)
- Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Amaresh C Panda
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Ioannis Grammatikakis
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States.
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141
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Ramlee MK, Wang J, Cheung AMS, Li S. Using a Fluorescent PCR-capillary Gel Electrophoresis Technique to Genotype CRISPR/Cas9-mediated Knockout Mutants in a High-throughput Format. J Vis Exp 2017:55586. [PMID: 28448034 PMCID: PMC5564488 DOI: 10.3791/55586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The development of programmable genome-editing tools has facilitated the use of reverse genetics to understand the roles specific genomic sequences play in the functioning of cells and whole organisms. This cause has been tremendously aided by the recent introduction of the CRISPR/Cas9 system-a versatile tool that allows researchers to manipulate the genome and transcriptome in order to, among other things, knock out, knock down, or knock in genes in a targeted manner. For the purpose of knocking out a gene, CRISPR/Cas9-mediated double-strand breaks recruit the non-homologous end-joining DNA repair pathway to introduce the frameshift-causing insertion or deletion of nucleotides at the break site. However, an individual guide RNA may cause undesirable off-target effects, and to rule these out, the use of multiple guide RNAs is necessary. This multiplicity of targets also means that a high-volume screening of clones is required, which in turn begs the use of an efficient high-throughput technique to genotype the knockout clones. Current genotyping techniques either suffer from inherent limitations or incur high cost, hence rendering them unsuitable for high-throughput purposes. Here, we detail the protocol for using fluorescent PCR, which uses genomic DNA from crude cell lysate as a template, and then resolving the PCR fragments via capillary gel electrophoresis. This technique is accurate enough to differentiate one base-pair difference between fragments and hence is adequate in indicating the presence or absence of a frameshift in the coding sequence of the targeted gene. This precise knowledge effectively precludes the need for a confirmatory sequencing step and allows users to save time and cost in the process. Moreover, this technique has proven to be versatile in genotyping various mammalian cells of various tissue origins targeted by guide RNAs against numerous genes, as shown here and elsewhere.
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Affiliation(s)
| | - Jing Wang
- Cancer & Stem Cell Biology Programme, Duke-NUS Medical School
| | | | - Shang Li
- Cancer & Stem Cell Biology Programme, Duke-NUS Medical School;
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142
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Abstract
MicroRNAs are small, noncoding, RNAs known for their powerful modulation of molecular processes, making them a major focus for studying pathological mechanisms. The human miR-146 family of microRNAs consists of two member genes, MIR146A and MIR146B These two microRNAs are located on different chromosomes and exhibit differential regulation in many cases. However, they are nearly identical in sequence, sharing a seed region, and are thus predicted to target the same set of genes. A large proportion of the microRNA (miR)-146 literature focuses on its role in regulating the innate immune response in the context of various pathologies by modulating two widely studied target genes in the toll-like receptor signaling cascade. A growing subset of the literature reports a role of miR-146 in cardiovascular and renal disease, and data suggest there is exciting potential for miR-146 as a diagnostic and therapeutic target. Nevertheless, the published literature is confounded by unclear and imprecise language concerning the specific effects of the two miR-146 family members. The present review will compare the genomic origin and regulation of miR-146a and miR-146b, discuss some approaches to overcome analytical and experimental challenges, and summarize findings in major areas of miR-146 research. Moving forward, careful evaluation of miR-146a/b specificity in analytical and experimental approaches will aid researchers in elucidating the functional relevance of differential regulation of the miR-146 family members in health and disease.
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Affiliation(s)
- Mark R Paterson
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin; and
| | - Alison J Kriegel
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin; and
- Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
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143
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Djami-Tchatchou AT, Sanan-Mishra N, Ntushelo K, Dubery IA. Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection. FRONTIERS IN PLANT SCIENCE 2017; 8:378. [PMID: 28382044 PMCID: PMC5360763 DOI: 10.3389/fpls.2017.00378] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic-or abiotic origin.
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Affiliation(s)
- Arnaud T. Djami-Tchatchou
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg (Auckland Park Kingsway Campus)Johannesburg, South Africa
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144
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Zhuo C, Hou W, Hu L, Lin C, Chen C, Lin X. Genomic Editing of Non-Coding RNA Genes with CRISPR/Cas9 Ushers in a Potential Novel Approach to Study and Treat Schizophrenia. Front Mol Neurosci 2017; 10:28. [PMID: 28217082 PMCID: PMC5289958 DOI: 10.3389/fnmol.2017.00028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/23/2017] [Indexed: 12/13/2022] Open
Abstract
Schizophrenia is a genetically related mental illness, in which the majority of genetic alterations occur in the non-coding regions of the human genome. In the past decade, a growing number of regulatory non-coding RNAs (ncRNAs) including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been identified to be strongly associated with schizophrenia. However, the studies of these ncRNAs in the pathophysiology of schizophrenia and the reverting of their genetic defects in restoration of the normal phenotype have been hampered by insufficient technology to manipulate these ncRNA genes effectively as well as a lack of appropriate animal models. Most recently, a revolutionary gene editing technology known as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9; CRISPR/Cas9) has been developed that enable researchers to overcome these challenges. In this review article, we mainly focus on the schizophrenia-related ncRNAs and the use of CRISPR/Cas9-mediated editing on the non-coding regions of the genomic DNA in proving causal relationship between the genetic defects and the pathophysiology of schizophrenia. We subsequently discuss the potential of translating this advanced technology into a clinical therapy for schizophrenia, although the CRISPR/Cas9 technology is currently still in its infancy and immature to put into use in the treatment of diseases. Furthermore, we suggest strategies to accelerate the pace from the bench to the bedside. This review describes the application of the powerful and feasible CRISPR/Cas9 technology to manipulate schizophrenia-associated ncRNA genes. This technology could help researchers tackle this complex health problem and perhaps other genetically related mental disorders due to the overlapping genetic alterations of schizophrenia with other mental illnesses.
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Affiliation(s)
- Chuanjun Zhuo
- Department of Psychiatry, Wenzhou Seventh People's HospitalWenzhou, China; Department of Psychiatry, Tianjin Mental Health Center, Tianjin Anding HospitalTianjin, China; Department of Psychiatry, Tianjin Anning HospitalTianjin, China
| | - Weihong Hou
- Department of Biology, University of North Carolina at Charlotte Charlotte, NC, USA
| | - Lirong Hu
- Department of Psychiatry, Wenzhou Seventh People's Hospital Wenzhou, China
| | - Chongguang Lin
- Department of Psychiatry, Wenzhou Seventh People's Hospital Wenzhou, China
| | - Ce Chen
- Department of Psychiatry, Wenzhou Seventh People's Hospital Wenzhou, China
| | - Xiaodong Lin
- Department of Psychiatry, Wenzhou Seventh People's Hospital Wenzhou, China
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145
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Huo W, Zhao G, Yin J, Ouyang X, Wang Y, Yang C, Wang B, Dong P, Wang Z, Watari H, Chaum E, Pfeffer LM, Yue J. Lentiviral CRISPR/Cas9 vector mediated miR-21 gene editing inhibits the epithelial to mesenchymal transition in ovarian cancer cells. J Cancer 2017; 8:57-64. [PMID: 28123598 PMCID: PMC5264040 DOI: 10.7150/jca.16723] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/29/2016] [Indexed: 12/15/2022] Open
Abstract
CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats) mediated genome editing is a powerful approach for loss of function studies. Here we report that lentiviral CRISPR/Cas9 vectors are highly efficient in introducing mutations in the precursor miRNA sequence, thus leading to the loss of miRNA expression and function. We constructed four different lentiviral CRISPR/Cas9 vectors that target different regions of the precursor miR-21 sequence and found that these lentiviral CRISPR/Cas9 miR-21 gRNA vectors induced mutations in the precursor sequences as shown by DNA surveyor mutation assay and Sanger sequencing. Two miR-21 lentiviral CRISPR/Cas9 gRNA vectors were selected to probe miR-21 function in ovarian cancer SKOV3 and OVCAR3 cell lines. Our data demonstrate that disruption of pre-miR-21 sequences leads to reduced cell proliferation, migration and invasion. Moreover, CRISPR/Cas9-mediated miR-21 gene editing sensitizes both SKOV3 and OVCAR3 cells to chemotherapeutic drug treatment. Disruption of miR-21 leads to the inhibition of epithelial to mesenchymal transition (EMT) in both SKOV3 and OVCAR3 cells as evidenced by the upregulation of epithelial cell marker E-cadherin and downregulation of mesenchymal marker genes, vimentin and Snai2. The miR-21 target genes PDCD4 and SPRY2 were upregulated in cells transduced with miR-21gRNAs compared to controls. Our study indicates that lentiviral CRISPR/Cas9-mediated miRNA gene editing is an effective approach to address miRNA function, and disruption of miR-21 inhibits EMT in ovarian cancer cells.
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Affiliation(s)
- Wenying Huo
- Department of Pathology and Laboratory Medicine
- Center for Cancer Research
- Department of Physiology
- Henan Agricultural University
- Henan University of Animal Husbandry and Economy, P.R. China
| | - Guannan Zhao
- Department of Pathology and Laboratory Medicine
- Center for Cancer Research
| | - Jinggang Yin
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Xuan Ouyang
- Department of Pathology and Laboratory Medicine
- Center for Cancer Research
| | - Yinan Wang
- Department of Pathology and Laboratory Medicine
- Center for Cancer Research
| | - Chuanhe Yang
- Department of Pathology and Laboratory Medicine
- Center for Cancer Research
| | - Baojing Wang
- Department of Pathology and Laboratory Medicine
- Center for Cancer Research
| | - Peixin Dong
- Department of Women's Health Educational System
- ✉ Corresponding authors: Dr. Junming Yue, University of Tennessee Health Science Center, 19 S. Manassas St., Rm. 266, Memphis, TN 38163; Fax: 901-448-3910; Phone: 901-448-2091; . Or Dr. Peixin Dong, Department of Women's Health Educational System, Hokkaido University School of Medicine, Hokkaido University, Sapporo, Japan.
| | | | - Hidemichi Watari
- Department of Gynecology, Hokkaido University School of Medicine, Hokkaido University, Sapporo, Japan
| | - Edward Chaum
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Junming Yue
- Department of Pathology and Laboratory Medicine
- Center for Cancer Research
- ✉ Corresponding authors: Dr. Junming Yue, University of Tennessee Health Science Center, 19 S. Manassas St., Rm. 266, Memphis, TN 38163; Fax: 901-448-3910; Phone: 901-448-2091; . Or Dr. Peixin Dong, Department of Women's Health Educational System, Hokkaido University School of Medicine, Hokkaido University, Sapporo, Japan.
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146
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MicroRNAs in epilepsy: pathophysiology and clinical utility. Lancet Neurol 2016; 15:1368-1376. [DOI: 10.1016/s1474-4422(16)30246-0] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/14/2016] [Accepted: 09/16/2016] [Indexed: 12/18/2022]
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147
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Targeted Inhibition of the miR-199a/214 Cluster by CRISPR Interference Augments the Tumor Tropism of Human Induced Pluripotent Stem Cell-Derived Neural Stem Cells under Hypoxic Condition. Stem Cells Int 2016; 2016:3598542. [PMID: 27965712 PMCID: PMC5124688 DOI: 10.1155/2016/3598542] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/15/2016] [Accepted: 10/25/2016] [Indexed: 12/30/2022] Open
Abstract
The human induced pluripotent stem cell (hiPSC) provides a breakthrough approach that helps overcoming ethical and allergenic challenges posed in application of neural stem cells (NSCs) in targeted cancer gene therapy. However, the tumor-tropic capacity of hiPSC-derived NSCs (hiPS-NSCs) still has much room to improve. Here we attempted to promote the tumor tropism of hiPS-NSCs by manipulating the activity of endogenous miR-199a/214 cluster that is involved in regulation of hypoxia-stimulated cell migration. We first developed a baculovirus-delivered CRISPR interference (CRISPRi) system that sterically blocked the E-box element in the promoter of the miR-199a/214 cluster with an RNA-guided catalytically dead Cas9 (dCas9). We then applied this CRISPRi system to hiPS-NSCs and successfully suppressed the expression of miR-199a-5p, miR-199a-3p, and miR-214 in the microRNA gene cluster. Meanwhile, the expression levels of their targets related to regulation of hypoxia-stimulated cell migration, such as HIF1A, MET, and MAPK1, were upregulated. Further migration assays demonstrated that the targeted inhibition of the miR-199a/214 cluster significantly enhanced the tumor tropism of hiPS-NSCs both in vitro and in vivo. These findings suggest a novel application of CRISPRi in NSC-based tumor-targeted gene therapy.
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148
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Onyido EK, Sweeney E, Nateri AS. Wnt-signalling pathways and microRNAs network in carcinogenesis: experimental and bioinformatics approaches. Mol Cancer 2016; 15:56. [PMID: 27590724 PMCID: PMC5010773 DOI: 10.1186/s12943-016-0541-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/26/2016] [Indexed: 02/02/2023] Open
Abstract
Over the past few years, microRNAs (miRNAs) have not only emerged as integral regulators of gene expression at the post-transcriptional level but also respond to signalling molecules to affect cell function(s). miRNAs crosstalk with a variety of the key cellular signalling networks such as Wnt, transforming growth factor-β and Notch, control stem cell activity in maintaining tissue homeostasis, while if dysregulated contributes to the initiation and progression of cancer. Herein, we overview the molecular mechanism(s) underlying the crosstalk between Wnt-signalling components (canonical and non-canonical) and miRNAs, as well as changes in the miRNA/Wnt-signalling components observed in the different forms of cancer. Furthermore, the fundamental understanding of miRNA-mediated regulation of Wnt-signalling pathway and vice versa has been significantly improved by high-throughput genomics and bioinformatics technologies. Whilst, these approaches have identified a number of specific miRNA(s) that function as oncogenes or tumour suppressors, additional analyses will be necessary to fully unravel the links among conserved cellular signalling pathways and miRNAs and their potential associated components in cancer, thereby creating therapeutic avenues against tumours. Hence, we also discuss the current challenges associated with Wnt-signalling/miRNAs complex and the analysis using the biomedical experimental and bioinformatics approaches.
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Affiliation(s)
- Emenike K Onyido
- Cancer Genetics & Stem Cell Group, Cancer Biology Unit, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Eloise Sweeney
- Cancer Genetics & Stem Cell Group, Cancer Biology Unit, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Abdolrahman Shams Nateri
- Cancer Genetics & Stem Cell Group, Cancer Biology Unit, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK.
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149
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Narayanan A, Hill-Teran G, Moro A, Ristori E, Kasper DM, A. Roden C, Lu J, Nicoli S. In vivo mutagenesis of miRNA gene families using a scalable multiplexed CRISPR/Cas9 nuclease system. Sci Rep 2016; 6:32386. [PMID: 27572667 PMCID: PMC5004112 DOI: 10.1038/srep32386] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/08/2016] [Indexed: 01/06/2023] Open
Abstract
A large number of microRNAs (miRNAs) are grouped into families derived from the same phylogenetic ancestors. miRNAs within a family often share the same physiological functions despite differences in their primary sequences, secondary structures, or chromosomal locations. Consequently, the generation of animal models to analyze the activity of miRNA families is extremely challenging. Using zebrafish as a model system, we successfully provide experimental evidence that a large number of miRNAs can be simultaneously mutated to abrogate the activity of an entire miRNA family. We show that injection of the Cas9 nuclease and two, four, ten, and up to twenty-four multiplexed single guide RNAs (sgRNAs) can induce mutations in 90% of the miRNA genomic sequences analyzed. We performed a survey of these 45 mutations in 10 miRNA genes, analyzing the impact of our mutagenesis strategy on the processing of each miRNA both computationally and in vivo. Our results offer an effective approach to mutate and study the activity of miRNA families and pave the way for further analysis on the function of complex miRNA families in higher multicellular organisms.
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Affiliation(s)
- Anand Narayanan
- Yale Cardiovascular Research Center, Section of Cardiology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Guillermina Hill-Teran
- Yale Cardiovascular Research Center, Section of Cardiology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Albertomaria Moro
- Yale Cardiovascular Research Center, Section of Cardiology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Emma Ristori
- Yale Cardiovascular Research Center, Section of Cardiology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Dionna M. Kasper
- Yale Cardiovascular Research Center, Section of Cardiology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Christine A. Roden
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, CT, 06520, USA
| | - Jun Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, CT, 06520, USA
| | - Stefania Nicoli
- Yale Cardiovascular Research Center, Section of Cardiology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
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150
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Luoni A, Riva MA. MicroRNAs and psychiatric disorders: From aetiology to treatment. Pharmacol Ther 2016; 167:13-27. [PMID: 27452338 DOI: 10.1016/j.pharmthera.2016.07.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/14/2016] [Indexed: 01/09/2023]
Abstract
The emergence of psychiatric disorders relies on the interaction between genetic vulnerability and environmental adversities. Several studies have demonstrated a crucial role for epigenetics (e.g. DNA methylation, post-translational histone modifications and microRNA-mediated post-transcriptional regulation) in the translation of environmental cues into adult behavioural outcome, which can prove to be harmful thus increasing the risk to develop psychopathology. Within this frame, non-coding RNAs, especially microRNAs, came to light as pivotal regulators of many biological processes occurring in the Central Nervous System, both during the neuronal development as well as in the regulation of adult function, including learning, memory and neuronal plasticity. On these basis, in recent years it has been hypothesised a central role for microRNA modulation and expression regulation in many brain disorders, including neurodegenerative disorders and mental illnesses. Indeed, the aim of the present review is to present the most recent state of the art regarding microRNA involvement in psychiatric disorders. We will first describe the mechanisms that regulate microRNA biogenesis and we will report evidences of microRNA dysregulation in peripheral body fluids, in postmortem brain tissues from patients suffering from psychopathology as well as in animal models. Last, we will discuss the potential to consider microRNAs as putative target for pharmacological intervention, using common psychotropic drugs or more specific tools, with the aim to normalize functions that are disrupted in different psychiatric conditions.
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Affiliation(s)
- Alessia Luoni
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
| | - Marco Andrea Riva
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy.
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