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Yelick J, Men Y, Jin S, Seo S, Espejo-Porras F, Yang Y. Elevated exosomal secretion of miR-124-3p from spinal neurons positively associates with disease severity in ALS. Exp Neurol 2020; 333:113414. [PMID: 32712030 DOI: 10.1016/j.expneurol.2020.113414] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/24/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRs) are powerful regulators of CNS development and diseases. Plasma and cerebrospinal fluid (CSF) miRs have recently been implicated as potential new sources for biomarker development. Previously we showed that miR-124-3p, an essential miR for neuronal identity, is highly abundant in neuronal exosomes and its expression decreases in spinal cord of ALS model SOD1G93A mice. In the current study, we found a disease associated reduction of miR-124-3p levels specifically in spinal neurons using in situ hybridization. By employing our recently developed exosome reporter mice in combination with sciatic nerve injections, we observed an increased association of miR-124-3p with spinal motor neuron-derived exosomes in SOD1G93A mice, even at the pre-symptomatic stage. Sciatic nerve injection delivered miR-124-3p is also more frequently localized outside of spinal motor neurons in SOD1G93A mice. Subsequent quantitative analysis of miR-124-3p levels in CSF exosomes from ALS patients found a significant correlation between CSF exosomal miR-124-3p levels and disease stage (indicated by the ALSFRS-R score) of (male) ALS patients. These results provide preliminary evidence to support the potential use of CSF exosomal miR-124-3p as a disease stage indicator in ALS.
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Affiliation(s)
- Julia Yelick
- Tufts University School of Medicine, Department of Neuroscience, 136 Harrison Ave, Boston, MA 02111, United States of America; Tufts University, Graudate School of Biomedical Sciences, 145 Harrison Ave, Boston, MA 02111, United States of America
| | - Yuqin Men
- Tufts University School of Medicine, Department of Neuroscience, 136 Harrison Ave, Boston, MA 02111, United States of America
| | - Shijie Jin
- Tufts University School of Medicine, Department of Neuroscience, 136 Harrison Ave, Boston, MA 02111, United States of America
| | - Sabrina Seo
- Tufts University School of Medicine, Department of Neuroscience, 136 Harrison Ave, Boston, MA 02111, United States of America
| | - Francisco Espejo-Porras
- Tufts University School of Medicine, Department of Neuroscience, 136 Harrison Ave, Boston, MA 02111, United States of America
| | - Yongjie Yang
- Tufts University School of Medicine, Department of Neuroscience, 136 Harrison Ave, Boston, MA 02111, United States of America; Tufts University, Graudate School of Biomedical Sciences, 145 Harrison Ave, Boston, MA 02111, United States of America.
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52
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Coordinated AR and microRNA regulation in prostate cancer. Asian J Urol 2020; 7:233-250. [PMID: 32742925 PMCID: PMC7385519 DOI: 10.1016/j.ajur.2020.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 03/22/2020] [Accepted: 04/17/2020] [Indexed: 12/26/2022] Open
Abstract
The androgen receptor (AR) remains a key driver of prostate cancer (PCa) progression, even in the advanced castrate-resistant stage, where testicular androgens are absent. It is therefore of critical importance to understand the molecular mechanisms governing its activity and regulation during prostate tumourigenesis. MicroRNAs (miRs) are small ∼22 nt non-coding RNAs that regulate target gene, often through association with 3′ untranslated regions (3′UTRs) of transcripts. They display dysregulation during cancer progression, can function as oncogenes or tumour suppressors, and are increasingly recognised as targets or regulators of hormonal action. Thus, understanding factors which modulate miRs synthesis is essential. There is increasing evidence for complex and dynamic bi-directional cross-talk between the multi-step miR biogenesis cascade and the AR signalling axis in PCa. This review summarises the wealth of mechanisms by which miRs are regulated by AR, and conversely, how miRs impact AR's transcriptional activity, including that of AR splice variants. In addition, we assess the implications of the convergence of these pathways on the clinical employment of miRs as PCa biomarkers and therapeutic targets.
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53
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Pham J, Keon M, Brennan S, Saksena N. Connecting RNA-Modifying Similarities of TDP-43, FUS, and SOD1 with MicroRNA Dysregulation Amidst A Renewed Network Perspective of Amyotrophic Lateral Sclerosis Proteinopathy. Int J Mol Sci 2020; 21:ijms21103464. [PMID: 32422969 PMCID: PMC7278980 DOI: 10.3390/ijms21103464] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022] Open
Abstract
Beyond traditional approaches in understanding amyotrophic lateral sclerosis (ALS), multiple recent studies in RNA-binding proteins (RBPs)-including transactive response DNA-binding protein (TDP-43) and fused in sarcoma (FUS)-have instigated an interest in their function and prion-like properties. Given their prominence as hallmarks of a highly heterogeneous disease, this prompts a re-examination of the specific functional interrelationships between these proteins, especially as pathological SOD1-a non-RBP commonly associated with familial ALS (fALS)-exhibits similar properties to these RBPs including potential RNA-regulatory capabilities. Moreover, the cytoplasmic mislocalization, aggregation, and co-aggregation of TDP-43, FUS, and SOD1 can be identified as proteinopathies akin to other neurodegenerative diseases (NDs), eliciting strong ties to disrupted RNA splicing, transport, and stability. In recent years, microRNAs (miRNAs) have also been increasingly implicated in the disease, and are of greater significance as they are the master regulators of RNA metabolism in disease pathology. However, little is known about the role of these proteins and how they are regulated by miRNA, which would provide mechanistic insights into ALS pathogenesis. This review seeks to discuss current developments across TDP-43, FUS, and SOD1 to build a detailed snapshot of the network pathophysiology underlying ALS while aiming to highlight possible novel therapeutic targets to guide future research.
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Affiliation(s)
- Jade Pham
- Faculty of Medicine, The University of New South Wales, Kensington, Sydney, NSW 2033, Australia;
| | - Matt Keon
- Iggy Get Out, Neurodegenerative Disease Section, Darlinghurst, Sydney, NSW 2010, Australia; (M.K.); (S.B.)
| | - Samuel Brennan
- Iggy Get Out, Neurodegenerative Disease Section, Darlinghurst, Sydney, NSW 2010, Australia; (M.K.); (S.B.)
| | - Nitin Saksena
- Iggy Get Out, Neurodegenerative Disease Section, Darlinghurst, Sydney, NSW 2010, Australia; (M.K.); (S.B.)
- Correspondence:
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54
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Christoforidou E, Joilin G, Hafezparast M. Potential of activated microglia as a source of dysregulated extracellular microRNAs contributing to neurodegeneration in amyotrophic lateral sclerosis. J Neuroinflammation 2020; 17:135. [PMID: 32345319 PMCID: PMC7187511 DOI: 10.1186/s12974-020-01822-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common form of motor neuron degeneration in adults, and several mechanisms underlying the disease pathology have been proposed. It has been shown that glia communicate with other cells by releasing extracellular vesicles containing proteins and nucleic acids, including microRNAs (miRNAs), which play a role in the post-transcriptional regulation of gene expression. Dysregulation of miRNAs is commonly observed in ALS patients, together with inflammation and an altered microglial phenotype. However, the role of miRNA-containing vesicles in microglia-to-neuron communication in the context of ALS has not been explored in depth. This review summarises the evidence for the presence of inflammation, pro-inflammatory microglia and dysregulated miRNAs in ALS, then explores how microglia may potentially be responsible for this miRNA dysregulation. The possibility of pro-inflammatory ALS microglia releasing miRNAs which may then enter neuronal cells to contribute to degeneration is also explored. Based on the literature reviewed here, microglia are a likely source of dysregulated miRNAs and potential mediators of neurodegenerative processes. Therefore, dysregulated miRNAs may be promising candidates for the development of therapeutic strategies.
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Affiliation(s)
| | - Greig Joilin
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Majid Hafezparast
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK.
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55
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Loffreda A, Nizzardo M, Arosio A, Ruepp MD, Calogero RA, Volinia S, Galasso M, Bendotti C, Ferrarese C, Lunetta C, Rizzuti M, Ronchi AE, Mühlemann O, Tremolizzo L, Corti S, Barabino SML. miR-129-5p: A key factor and therapeutic target in amyotrophic lateral sclerosis. Prog Neurobiol 2020; 190:101803. [PMID: 32335272 DOI: 10.1016/j.pneurobio.2020.101803] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 04/02/2020] [Accepted: 04/09/2020] [Indexed: 12/30/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a relentless and fatal neurological disease characterized by the selective degeneration of motor neurons. No effective therapy is available for this disease. Several lines of evidence indicate that alteration of RNA metabolism, including microRNA (miRNA) processing, is a relevant pathogenetic factor and a possible therapeutic target for ALS. Here, we showed that the abundance of components in the miRNA processing machinery is altered in a SOD1-linked cellular model, suggesting consequent dysregulation of miRNA biogenesis. Indeed, high-throughput sequencing of the small RNA fraction showed that among the altered miRNAs, miR-129-5p was increased in different models of SOD1-linked ALS and in peripheral blood cells of sporadic ALS patients. We demonstrated that miR-129-5p upregulation causes the downregulation of one of its targets: the RNA-binding protein ELAVL4/HuD. ELAVL4/HuD is predominantly expressed in neurons, where it controls several key neuronal mRNAs. Overexpression of pre-miR-129-1 inhibited neurite outgrowth and differentiation via HuD silencing in vitro, while its inhibition with an antagomir rescued the phenotype. Remarkably, we showed that administration of an antisense oligonucleotide (ASO) inhibitor of miR-129-5p to an ALS animal model, SOD1 (G93A) mice, result in a significant increase in survival and improved the neuromuscular phenotype in treated mice. These results identify miR-129-5p as a therapeutic target that is amenable to ASO modulation for the treatment of ALS patients.
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Affiliation(s)
- Alessia Loffreda
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Monica Nizzardo
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Alessandro Arosio
- School of Medicine and Surgery and Milan Center for Neuroscience (NeuroMI), University of Milano-Bicocca, 20052 Monza, MB, Italy
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Turin, Italy
| | - Stefano Volinia
- Department of Morphology, Surgery and Experimental Medicine, Università degli Studi, 44121 Ferrara, Italy
| | - Marco Galasso
- Department of Morphology, Surgery and Experimental Medicine, Università degli Studi, 44121 Ferrara, Italy
| | - Caterina Bendotti
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", 20156 Milan, Italy
| | - Carlo Ferrarese
- School of Medicine and Surgery and Milan Center for Neuroscience (NeuroMI), University of Milano-Bicocca, 20052 Monza, MB, Italy; Neurology Unit, San Gerardo Hospital, Monza, MB, Italy
| | - Christian Lunetta
- NEuroMuscular Omnicentre (NEMO), Fondazione Serena Onlus, 20162 Milan, Italy
| | - Mafalda Rizzuti
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Antonella E Ronchi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Lucio Tremolizzo
- School of Medicine and Surgery and Milan Center for Neuroscience (NeuroMI), University of Milano-Bicocca, 20052 Monza, MB, Italy; Neurology Unit, San Gerardo Hospital, Monza, MB, Italy
| | - Stefania Corti
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Italy; Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Silvia M L Barabino
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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56
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Picchiarelli G, Dupuis L. Role of RNA Binding Proteins with prion-like domains in muscle and neuromuscular diseases. Cell Stress 2020; 4:76-91. [PMID: 32292882 PMCID: PMC7146060 DOI: 10.15698/cst2020.04.217] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A number of neuromuscular and muscular diseases, including amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA) and several myopathies, are associated to mutations in related RNA-binding proteins (RBPs), including TDP-43, FUS, MATR3 or hnRNPA1/B2. These proteins harbor similar modular primary sequence with RNA binding motifs and low complexity domains, that enables them to phase separate and create liquid microdomains. These RBPs have been shown to critically regulate multiple events of RNA lifecycle, including transcriptional events, splicing and RNA trafficking and sequestration. Here, we review the roles of these disease-related RBPs in muscle and motor neurons, and how their dysfunction in these cell types might contribute to disease.
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Affiliation(s)
- Gina Picchiarelli
- Université de Strasbourg, INSERM, Mécanismes Centraux et Périphériques de la Neurodégénérescence, UMR_S 1118, Strasbourg, France
| | - Luc Dupuis
- Université de Strasbourg, INSERM, Mécanismes Centraux et Périphériques de la Neurodégénérescence, UMR_S 1118, Strasbourg, France
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57
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Hamad N, Mashima T, Yamaoki Y, Kondo K, Yoneda R, Oyoshi T, Kurokawa R, Nagata T, Katahira M. RNA sequence and length contribute to RNA-induced conformational change of TLS/FUS. Sci Rep 2020; 10:2629. [PMID: 32060318 PMCID: PMC7021683 DOI: 10.1038/s41598-020-59496-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/29/2020] [Indexed: 12/03/2022] Open
Abstract
Translocated in liposarcoma (TLS)/fused in sarcoma (FUS) is a multitasking DNA/RNA binding protein implicated in cancer and neurodegenerative diseases. Upon DNA damage, TLS is recruited to the upstream region of the cyclin D1 gene (CCND1) through binding to the promotor associated non-coding RNA (pncRNA) that is transcribed from and tethered at the upstream region. Binding to pncRNA is hypothesized to cause the conformational change of TLS that enables its inhibitive interaction with histone acetyltransferases and resultant repression of CCND1 expression, although no experimental proof has been obtained. Here, the closed-to-open conformational change of TLS on binding pncRNA was implied by fluorescence resonance energy transfer. A small fragment (31 nucleotides) of the full-length pncRNA (602 nucleotides) was shown to be sufficient for the conformational change of TLS. Dissection of pncRNA identified the G-rich RNA sequence that is critical for the conformational change. The length of RNA was also revealed to be critical for the conformational change. Furthermore, it was demonstrated that the conformational change of TLS is caused by another target DNA and RNA, telomeric DNA and telomeric repeat-containing RNA. The conformational change of TLS on binding target RNA/DNA is suggested to be essential for biological functions.
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Affiliation(s)
- Nesreen Hamad
- Institute of Advanced Energy, Kyoto University, Kyoto, 611-0011, Japan.,Graduate School of Energy Science, Kyoto University, Kyoto, 606-8501, Japan
| | - Tsukasa Mashima
- Institute of Advanced Energy, Kyoto University, Kyoto, 611-0011, Japan.,Graduate School of Energy Science, Kyoto University, Kyoto, 606-8501, Japan
| | - Yudai Yamaoki
- Institute of Advanced Energy, Kyoto University, Kyoto, 611-0011, Japan
| | - Keiko Kondo
- Institute of Advanced Energy, Kyoto University, Kyoto, 611-0011, Japan
| | - Ryoma Yoneda
- Research Center of Genomic Medicine, Saitama Medical University, Saitama, 350-0495, Japan
| | - Takanori Oyoshi
- Department of Chemistry, Graduate School of Science, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Riki Kurokawa
- Research Center of Genomic Medicine, Saitama Medical University, Saitama, 350-0495, Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Kyoto, 611-0011, Japan.,Graduate School of Energy Science, Kyoto University, Kyoto, 606-8501, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Kyoto, 611-0011, Japan. .,Graduate School of Energy Science, Kyoto University, Kyoto, 606-8501, Japan.
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58
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Chen TH, Chen JA. Multifaceted roles of microRNAs: From motor neuron generation in embryos to degeneration in spinal muscular atrophy. eLife 2019; 8:50848. [PMID: 31738166 PMCID: PMC6861003 DOI: 10.7554/elife.50848] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/05/2019] [Indexed: 12/12/2022] Open
Abstract
Two crucial questions in neuroscience are how neurons establish individual identity in the developing nervous system and why only specific neuron subtypes are vulnerable to neurodegenerative diseases. In the central nervous system, spinal motor neurons serve as one of the best-characterized cell types for addressing these two questions. In this review, we dissect these questions by evaluating the emerging role of regulatory microRNAs in motor neuron generation in developing embryos and their potential contributions to neurodegenerative diseases such as spinal muscular atrophy (SMA). Given recent promising results from novel microRNA-based medicines, we discuss the potential applications of microRNAs for clinical assessments of SMA disease progression and treatment.
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Affiliation(s)
- Tai-Heng Chen
- PhD Program in Translational Medicine, Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Academia Sinica, Kaohsiung, Taiwan.,Department of Pediatrics, Division of Pediatric Emergency, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jun-An Chen
- PhD Program in Translational Medicine, Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Academia Sinica, Kaohsiung, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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59
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Niaki AG, Sarkar J, Cai X, Rhine K, Vidaurre V, Guy B, Hurst M, Lee JC, Koh HR, Guo L, Fare CM, Shorter J, Myong S. Loss of Dynamic RNA Interaction and Aberrant Phase Separation Induced by Two Distinct Types of ALS/FTD-Linked FUS Mutations. Mol Cell 2019; 77:82-94.e4. [PMID: 31630970 DOI: 10.1016/j.molcel.2019.09.022] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/19/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022]
Abstract
FUS is a nuclear RNA-binding protein, and its cytoplasmic aggregation is a pathogenic signature of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). It remains unknown how the FUS-RNA interactions contribute to phase separation and whether its phase behavior is affected by ALS-linked mutations. Here we demonstrate that wild-type FUS binds single-stranded RNA stoichiometrically in a length-dependent manner and that multimers induce highly dynamic interactions with RNA, giving rise to small and fluid condensates. In contrast, mutations in arginine display a severely altered conformation, static binding to RNA, and formation of large condensates, signifying the role of arginine in driving proper RNA interaction. Glycine mutations undergo rapid loss of fluidity, emphasizing the role of glycine in promoting fluidity. Strikingly, the nuclear import receptor Karyopherin-β2 reverses the mutant defects and recovers the wild-type FUS behavior. We reveal two distinct mechanisms underpinning potentially disparate pathogenic pathways of ALS-linked FUS mutants.
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Affiliation(s)
- Amirhossein Ghanbari Niaki
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Jaya Sarkar
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Xinyi Cai
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Kevin Rhine
- Cellular Molecular Developmental Biology and Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Velinda Vidaurre
- Cellular Molecular Developmental Biology and Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Brian Guy
- Cellular Molecular Developmental Biology and Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Miranda Hurst
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Jong Chan Lee
- Department of Biophysics and Biophysical Chemistry and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Hye Ran Koh
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA; Department of Chemistry, Chung-Ang University, Seoul 054974, Korea
| | - Lin Guo
- Department of Biochemistry and Molecular Biology, Jefferson University, Philadelphia, PA 19107, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sua Myong
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA; Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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60
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Klatt CL, Theis V, Hahn S, Theiss C, Matschke V. Deregulated miR-29b-3p Correlates with Tissue-Specific Activation of Intrinsic Apoptosis in An Animal Model of Amyotrophic Lateral Sclerosis. Cells 2019; 8:cells8091077. [PMID: 31547454 PMCID: PMC6770833 DOI: 10.3390/cells8091077] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/06/2019] [Accepted: 09/11/2019] [Indexed: 12/18/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is one of the most common incurable motor neuron disorders in adults. The majority of all ALS cases occur sporadically (sALS). Symptoms of ALS are caused by a progressive degeneration of motor neurons located in the motor cortex and spinal cord. The question arises why motor neurons selectively degenerate in ALS, while other cells and systems appear to be spared the disease. Members of the intrinsic apoptotic pathway are frequent targets of altered microRNA expression. Therefore, microRNAs and their effects on cell survival are subject of controversial debates. In this study, we investigated the expression of numerous members of the intrinsic apoptotic cascade by qPCR, western blot, and immunostaining in two different regions of the CNS of wobbler mice. Further we addressed the expression of miR-29b-3p targeting BMF, Bax, and, Bak, members of the apoptotic pathway. We show a tissue-specific differential expression of BMF, Bax, and cleaved-Caspase 3 in wobbler mice. An opposing regulation of miR-29b-3p expression in the cerebellum and cervical spinal cord of wobbler mice suggests different mechanisms regulating the intrinsic apoptotic pathway. Based on our findings, it could be speculated that miR-29b-3p might regulate antiapoptotic survival mechanisms in CNS areas that are not affected by neurodegeneration in the wobbler mouse ALS model.
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Affiliation(s)
- Christina L Klatt
- Ruhr University Bochum, Medical Faculty, Institute of Anatomy, Department of Cytology, 44801 Bochum, Germany.
| | - Verena Theis
- Ruhr University Bochum, Medical Faculty, Institute of Anatomy, Department of Cytology, 44801 Bochum, Germany.
| | - Stephan Hahn
- Ruhr University Bochum, Clinical Research Center, Department of Molecular Gastrointestinal Oncology, 44801 Bochum, Germany.
| | - Carsten Theiss
- Ruhr University Bochum, Medical Faculty, Institute of Anatomy, Department of Cytology, 44801 Bochum, Germany.
| | - Veronika Matschke
- Ruhr University Bochum, Medical Faculty, Institute of Anatomy, Department of Cytology, 44801 Bochum, Germany.
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61
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De Santis R, Alfano V, de Turris V, Colantoni A, Santini L, Garone MG, Antonacci G, Peruzzi G, Sudria-Lopez E, Wyler E, Anink JJ, Aronica E, Landthaler M, Pasterkamp RJ, Bozzoni I, Rosa A. Mutant FUS and ELAVL4 (HuD) Aberrant Crosstalk in Amyotrophic Lateral Sclerosis. Cell Rep 2019; 27:3818-3831.e5. [PMID: 31242416 PMCID: PMC6613039 DOI: 10.1016/j.celrep.2019.05.085] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 04/04/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) has been genetically linked to mutations in RNA-binding proteins (RBPs), including FUS. Here, we report the RNA interactome of wild-type and mutant FUS in human motor neurons (MNs). This analysis identified a number of RNA targets. Whereas the wild-type protein preferentially binds introns, the ALS mutation causes a shift toward 3' UTRs. Neural ELAV-like RBPs are among mutant FUS targets. As a result, ELAVL4 protein levels are increased in mutant MNs. ELAVL4 and mutant FUS interact and co-localize in cytoplasmic speckles with altered biomechanical properties. Upon oxidative stress, ELAVL4 and mutant FUS are engaged in stress granules. In the spinal cord of FUS ALS patients, ELAVL4 represents a neural-specific component of FUS-positive cytoplasmic aggregates, whereas in sporadic patients it co-localizes with phosphorylated TDP-43-positive inclusions. We propose that pathological mutations in FUS trigger an aberrant crosstalk with ELAVL4 with implications for ALS.
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Affiliation(s)
- Riccardo De Santis
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Vincenzo Alfano
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Valeria de Turris
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Alessio Colantoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Laura Santini
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Maria Giovanna Garone
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Giuseppe Antonacci
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Emma Sudria-Lopez
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Jasper J Anink
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Eleonora Aronica
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany; IRI Life Sciences, Institute für Biologie, Humboldt Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Irene Bozzoni
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessandro Rosa
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
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62
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Ouyang H, Zhang K, Fox-Walsh K, Yang Y, Zhang C, Huang J, Li H, Zhou Y, Fu XD. The RNA binding protein EWS is broadly involved in the regulation of pri-miRNA processing in mammalian cells. Nucleic Acids Res 2019; 45:12481-12495. [PMID: 30053258 PMCID: PMC5716145 DOI: 10.1093/nar/gkx912] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 09/27/2017] [Indexed: 12/13/2022] Open
Abstract
The Ewing Sarcoma protein (EWS) is a multifaceted RNA binding protein (RBP) with established roles in transcription, pre-mRNA processing and DNA damage response. By generating high quality EWS-RNA interactome, we uncovered its specific and prevalent interaction with a large subset of primary microRNAs (pri-miRNAs) in mammalian cells. Knockdown of EWS reduced, whereas overexpression enhanced, the expression of its target miRNAs. Biochemical analysis revealed that multiple elements in target pri-miRNAs, including the sequences flanking the stem-loop region, contributed to high affinity EWS binding and sequence swap experiments between target and non-target demonstrated that the flanking sequences provided the specificity for enhanced pri-miRNA processing by the Microprocessor Drosha/DGCR8. Interestingly, while repressing Drosha expression, as reported earlier, we found that EWS was able to enhance the recruitment of Drosha to chromatin. Together, these findings suggest that EWS may positively and negatively regulate miRNA biogenesis via distinct mechanisms, thus providing a new foundation to understand the function of EWS in development and disease.
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Affiliation(s)
- Huiwu Ouyang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kai Zhang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kristi Fox-Walsh
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Yang Yang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Huang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hairi Li
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Yu Zhou
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Institue of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Xiang-Dong Fu
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
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63
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Birsa N, Bentham MP, Fratta P. Cytoplasmic functions of TDP-43 and FUS and their role in ALS. Semin Cell Dev Biol 2019; 99:193-201. [PMID: 31132467 DOI: 10.1016/j.semcdb.2019.05.023] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/06/2019] [Accepted: 05/23/2019] [Indexed: 02/08/2023]
Abstract
TAR DNA-binding protein of 43 kDa (TDP-43) and fused in sarcoma (FUS) are RNA binding proteins (RBPs) primarily located in the nucleus, and involved in numerous aspects of RNA metabolism. Both proteins can be found to be depleted from the nucleus and accumulated in cytoplasmic inclusions in two major neurodegenerative conditions, amyotrophic lateral sclerosis and frontotemporal dementia. Recent evidences suggest that, in addition to their nuclear functions, both TDP-43 and FUS are involved in multiple processes in the cytoplasm, including mRNA stability and transport, translation, the stress response, mitochondrial function and autophagy regulation. Here, we review the most recent advances in understanding their functions in the cytoplasm and how these are affected in disease.
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Affiliation(s)
- Nicol Birsa
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
| | - Matthew Peter Bentham
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK; MRC Centre for Neuromuscular Disease, Queen Square, London, WC1N 3BG, UK.
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64
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Tung YT, Peng KC, Chen YC, Yen YP, Chang M, Thams S, Chen JA. Mir-17∼92 Confers Motor Neuron Subtype Differential Resistance to ALS-Associated Degeneration. Cell Stem Cell 2019; 25:193-209.e7. [PMID: 31155482 DOI: 10.1016/j.stem.2019.04.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 01/14/2019] [Accepted: 04/22/2019] [Indexed: 12/11/2022]
Abstract
Progressive degeneration of motor neurons (MNs) is the hallmark of amyotrophic lateral sclerosis (ALS). Limb-innervating lateral motor column MNs (LMC-MNs) seem to be particularly vulnerable and are among the first MNs affected in ALS. Here, we report association of this differential susceptibility with reduced expression of the mir-17∼92 cluster in LMC-MNs prior to disease onset. Reduced mir-17∼92 is accompanied by elevated nuclear PTEN in spinal MNs of presymptomatic SOD1G93A mice. Selective dysregulation of the mir-17∼92/nuclear PTEN axis in degenerating SOD1G93A LMC-MNs was confirmed in a double-transgenic embryonic stem cell system and recapitulated in human SOD1+/L144F-induced pluripotent stem cell (iPSC)-derived MNs. We further show that overexpression of mir-17∼92 significantly rescues human SOD1+/L144F MNs, and intrathecal delivery of adeno-associated virus (AAV)9-mir-17∼92 improves motor deficits and survival in SOD1G93A mice. Thus, mir-17∼92 may have value as a prognostic marker of MN degeneration and is a candidate therapeutic target in SOD1-linked ALS. VIDEO ABSTRACT.
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Affiliation(s)
- Ying-Tsen Tung
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan.
| | - Kuan-Chih Peng
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yen-Chung Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ya-Ping Yen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Mien Chang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Sebastian Thams
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jun-An Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan.
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65
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Increased FUS levels in astrocytes leads to astrocyte and microglia activation and neuronal death. Sci Rep 2019; 9:4572. [PMID: 30872738 PMCID: PMC6418113 DOI: 10.1038/s41598-019-41040-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/25/2019] [Indexed: 12/12/2022] Open
Abstract
Mutations of Fused in sarcoma (FUS), a ribonucleoprotein involved in RNA metabolism, have been found associated with both familial and sporadic cases of amyotrophic lateral sclerosis (ALS). Notably, besides mutations in the coding sequence, also mutations into the 3′ untranslated region, leading to increased levels of the wild-type protein, have been associated with neuronal death and ALS pathology, in ALS models and patients. The mechanistic link between altered FUS levels and ALS-related neurodegeneration is far to be elucidated, as well as the consequences of elevated FUS levels in the modulation of the inflammatory response sustained by glial cells, a well-recognized player in ALS progression. Here, we studied the effect of wild-type FUS overexpression on the responsiveness of mouse and human neural progenitor-derived astrocytes to a pro-inflammatory stimulus (IL1β) used to mimic an inflammatory environment. We found that astrocytes with increased FUS levels were more sensitive to IL1β, as shown by their enhanced expression of inflammatory genes, compared with control astrocytes. Moreover, astrocytes overexpressing FUS promoted neuronal cell death and pro-inflammatory microglia activation. We conclude that overexpression of wild-type FUS intrinsically affects astrocyte reactivity and drives their properties toward pro-inflammatory and neurotoxic functions, suggesting that a non-cell autonomous mechanism can support neurodegeneration in FUS-mutated animals and patients.
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66
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Bajczyk M, Bhat SS, Szewc L, Szweykowska-Kulinska Z, Jarmolowski A, Dolata J. Novel Nuclear Functions of Arabidopsis ARGONAUTE1: Beyond RNA Interference. PLANT PHYSIOLOGY 2019; 179:1030-1039. [PMID: 30606888 PMCID: PMC6393810 DOI: 10.1104/pp.18.01351] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/21/2018] [Indexed: 05/04/2023]
Abstract
Argonaute1 activity is not limited to the cytoplasm and has been found to be associated with the regulation of gene expression in the nucleus and to be tightly associated with chromatin and transcription.
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Affiliation(s)
- Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Susheel Sagar Bhat
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Lukasz Szewc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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67
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Butti Z, Patten SA. RNA Dysregulation in Amyotrophic Lateral Sclerosis. Front Genet 2019; 9:712. [PMID: 30723494 PMCID: PMC6349704 DOI: 10.3389/fgene.2018.00712] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/20/2018] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common adult-onset motor neuron disease and is characterized by the degeneration of upper and lower motor neurons. It has become increasingly clear that RNA dysregulation is a key contributor to ALS pathogenesis. The major ALS genes SOD1, TARDBP, FUS, and C9orf72 are involved in aspects of RNA metabolism processes such as mRNA transcription, alternative splicing, RNA transport, mRNA stabilization, and miRNA biogenesis. In this review, we highlight the current understanding of RNA dysregulation in ALS pathogenesis involving these major ALS genes and discuss the potential of therapeutic strategies targeting disease RNAs for treating ALS.
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Affiliation(s)
- Zoe Butti
- INRS-Institut Armand-Frappier, National Institute of Scientific Research, Laval, QC, Canada
| | - Shunmoogum A Patten
- INRS-Institut Armand-Frappier, National Institute of Scientific Research, Laval, QC, Canada
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68
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An H, Skelt L, Notaro A, Highley JR, Fox AH, La Bella V, Buchman VL, Shelkovnikova TA. ALS-linked FUS mutations confer loss and gain of function in the nucleus by promoting excessive formation of dysfunctional paraspeckles. Acta Neuropathol Commun 2019; 7:7. [PMID: 30642400 PMCID: PMC6330737 DOI: 10.1186/s40478-019-0658-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/07/2019] [Indexed: 12/13/2022] Open
Abstract
Mutations in the FUS gene cause amyotrophic lateral sclerosis (ALS-FUS). Mutant FUS is known to confer cytoplasmic gain of function but its effects in the nucleus are less understood. FUS is an essential component of paraspeckles, subnuclear bodies assembled on a lncRNA NEAT1. Paraspeckles may play a protective role specifically in degenerating spinal motor neurons. However it is still unknown how endogenous levels of mutant FUS would affect NEAT1/paraspeckles. Using novel cell lines with the FUS gene modified by CRISPR/Cas9 and human patient fibroblasts, we found that endogenous levels of mutant FUS cause accumulation of NEAT1 isoforms and paraspeckles. However, despite only mild cytoplasmic mislocalisation of FUS, paraspeckle integrity is compromised in these cells, as confirmed by reduced interaction of mutant FUS with core paraspeckle proteins NONO and SFPQ and increased NEAT1 extractability. This results in NEAT1 localisation outside paraspeckles, especially prominent under conditions of paraspeckle-inducing stress. Consistently, paraspeckle-dependent microRNA production, a readout for functionality of paraspeckles, is impaired in cells expressing mutant FUS. In line with the cellular data, we observed paraspeckle hyper-assembly in spinal neurons of ALS-FUS patients. Therefore, despite largely preserving its nuclear localisation, mutant FUS leads to loss (dysfunctional paraspeckles) and gain (excess of free NEAT1) of function in the nucleus. Perturbed fine structure and functionality of paraspeckles accompanied by accumulation of non-paraspeckle NEAT1 may contribute to the disease severity in ALS-FUS.
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Affiliation(s)
- Haiyan An
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX UK
| | - Lucy Skelt
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX UK
| | - Antonietta Notaro
- ALS Clinical Research Center and Laboratory of Neurochemistry, Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Palermo, Italy
| | - J. Robin Highley
- The Sheffield Institute for Translational Neuroscience, Sheffield, S10 2HQ UK
| | - Archa H. Fox
- School of Human Sciences, School of Molecular Sciences and Harry Perkins Institute of Medical Research, University of Western Australia, Crawley, 6009 Australia
| | - Vincenzo La Bella
- ALS Clinical Research Center and Laboratory of Neurochemistry, Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Palermo, Italy
| | - Vladimir L. Buchman
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX UK
- Institute of Physiologically Active Compounds RAS, Chernogolovka, Russian Federation 142432
| | - Tatyana A. Shelkovnikova
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX UK
- Institute of Physiologically Active Compounds RAS, Chernogolovka, Russian Federation 142432
- Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT UK
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69
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Zhang T, Wu YC, Mullane P, Ji YJ, Liu H, He L, Arora A, Hwang HY, Alessi AF, Niaki AG, Periz G, Guo L, Wang H, Elkayam E, Joshua-Tor L, Myong S, Kim JK, Shorter J, Ong SE, Leung AKL, Wang J. FUS Regulates Activity of MicroRNA-Mediated Gene Silencing. Mol Cell 2019; 69:787-801.e8. [PMID: 29499134 DOI: 10.1016/j.molcel.2018.02.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/22/2017] [Accepted: 01/31/2018] [Indexed: 12/13/2022]
Abstract
MicroRNA-mediated gene silencing is a fundamental mechanism in the regulation of gene expression. It remains unclear how the efficiency of RNA silencing could be influenced by RNA-binding proteins associated with the microRNA-induced silencing complex (miRISC). Here we report that fused in sarcoma (FUS), an RNA-binding protein linked to neurodegenerative diseases including amyotrophic lateral sclerosis (ALS), interacts with the core miRISC component AGO2 and is required for optimal microRNA-mediated gene silencing. FUS promotes gene silencing by binding to microRNA and mRNA targets, as illustrated by its action on miR-200c and its target ZEB1. A truncated mutant form of FUS that leads its carriers to an aggressive form of ALS, R495X, impairs microRNA-mediated gene silencing. The C. elegans homolog fust-1 also shares a conserved role in regulating the microRNA pathway. Collectively, our results suggest a role for FUS in regulating the activity of microRNA-mediated silencing.
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Affiliation(s)
- Tao Zhang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yen-Ching Wu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Patrick Mullane
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yon Ju Ji
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Honghe Liu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lu He
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Amit Arora
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ho-Yon Hwang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Amelia F Alessi
- Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Amirhossein G Niaki
- Department of Biophysics, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Goran Periz
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lin Guo
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hejia Wang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elad Elkayam
- Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Leemor Joshua-Tor
- Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sua Myong
- Department of Biophysics, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - John K Kim
- Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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70
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Abstract
MicroRNAs (miRNAs) are important regulators of gene expression that bind complementary target mRNAs and repress their expression. Precursor miRNA molecules undergo nuclear and cytoplasmic processing events, carried out by the endoribonucleases DROSHA and DICER, respectively, to produce mature miRNAs that are loaded onto the RISC (RNA-induced silencing complex) to exert their biological function. Regulation of mature miRNA levels is critical in development, differentiation, and disease, as demonstrated by multiple levels of control during their biogenesis cascade. Here, we will focus on post-transcriptional mechanisms and will discuss the impact of cis-acting sequences in precursor miRNAs, as well as trans-acting factors that bind to these precursors and influence their processing. In particular, we will highlight the role of general RNA-binding proteins (RBPs) as factors that control the processing of specific miRNAs, revealing a complex layer of regulation in miRNA production and function.
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Affiliation(s)
- Gracjan Michlewski
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Zhejiang 314400, P.R. China
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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71
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De Paola E, Verdile V, Paronetto MP. Dysregulation of microRNA metabolism in motor neuron diseases: Novel biomarkers and potential therapeutics. Noncoding RNA Res 2018; 4:15-22. [PMID: 30891533 PMCID: PMC6404378 DOI: 10.1016/j.ncrna.2018.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/11/2022] Open
Abstract
In the last 15 years, several classes of small regulatory RNAs have been identified, uncovering the widespread impact of non-coding elements in the human genome on cell homeostasis and human diseases. MicroRNAs (miRNAs) are a family of small, non-coding RNAs, which exert silencing of mRNA targets in a sequence-dependent fashion. Many miRNAs are specifically expressed in the central nervous system, where they display roles in differentiation, neuronal survival, neuronal plasticity and learning. On the other hand, deregulated miRNA/mRNA expression networks are deeply involved in neurodegeneration. Recent findings suggest a role for miRNAs in the pathogenesis of motor neuron diseases. In particular, cell-specific changes in miRNA profile are involved in the motor neuron disease phenotype and might be implicated in their selective vulnerability. Exploitation of noncoding RNAs, in particular miRNAs, for therapeutic strategies is being assessed for implementing current therapies. In this regard, the neuroprotective potential of certain miRNAs could represent a promising potential tool to improve therapies for motor-neuron diseases. This review focuses on emerging roles of miRNAs in motor neuron diseases and on their impact on neuron life-span and integrity.
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Affiliation(s)
- Elisa De Paola
- University of Rome "Foro Italico", Piazza Lauro de Bosis 15, 00135, Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143, Rome, Italy
| | - Veronica Verdile
- University of Rome "Foro Italico", Piazza Lauro de Bosis 15, 00135, Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143, Rome, Italy
| | - Maria Paola Paronetto
- University of Rome "Foro Italico", Piazza Lauro de Bosis 15, 00135, Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143, Rome, Italy
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72
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Trabucchi M, Mategot R. Subcellular Heterogeneity of the microRNA Machinery. Trends Genet 2018; 35:15-28. [PMID: 30503571 DOI: 10.1016/j.tig.2018.10.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/20/2018] [Accepted: 10/26/2018] [Indexed: 01/09/2023]
Abstract
Different methods have recently been developed to understand the subcellular localization and role of microRNAs (miRNAs) as well as small RNAs associated with Argonaute (AGO) proteins. The heterogeneity of the protein complexes associated with miRNAs, along with their subcellular localization, provides clues into their biochemical mechanism of function. Subcellular diversity indicates that miRNAs localized to different cellular regions could have different functions, including transcriptional regulation on chromatin or post-transcriptional control, providing global regulation of gene expression by miRNAs. Herein, I review the current knowledge and most recent discoveries relating to the subcellular function of miRNAs and other AGO-associated small RNAs, revealing the emergence of a multitude of functions of the miRNA pathway to control different steps of the gene expression program(s).
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Affiliation(s)
- Michele Trabucchi
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France; Université Côte d'Azur, Inserm, C3M, Nice, France.
| | - Raphael Mategot
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France; Université Côte d'Azur, Inserm, C3M, Nice, France
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73
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MicroRNAs as Biomarkers in Amyotrophic Lateral Sclerosis. Cells 2018; 7:cells7110219. [PMID: 30463376 PMCID: PMC6262636 DOI: 10.3390/cells7110219] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/15/2018] [Accepted: 11/17/2018] [Indexed: 12/30/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable and fatal disorder characterized by the progressive loss of motor neurons in the cerebral cortex, brain stem, and spinal cord. Sporadic ALS form accounts for the majority of patients, but in 1–13.5% of cases the disease is inherited. The diagnosis of ALS is mainly based on clinical assessment and electrophysiological examinations with a history of symptom progression and is then made with a significant delay from symptom onset. Thus, the identification of biomarkers specific for ALS could be of a fundamental importance in the clinical practice. An ideal biomarker should display high specificity and sensitivity for discriminating ALS from control subjects and from ALS-mimics and other neurological diseases, and should then monitor disease progression within individual patients. microRNAs (miRNAs) are considered promising biomarkers for neurodegenerative diseases, since they are remarkably stable in human body fluids and can reflect physiological and pathological processes relevant for ALS. Here, we review the state of the art of miRNA biomarker identification for ALS in cerebrospinal fluid (CSF), blood and muscle tissue; we discuss advantages and disadvantages of different approaches, and underline the limits but also the great potential of this research for future practical applications.
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An H, Williams NG, Shelkovnikova TA. NEAT1 and paraspeckles in neurodegenerative diseases: A missing lnc found? Noncoding RNA Res 2018; 3:243-252. [PMID: 30533572 PMCID: PMC6257911 DOI: 10.1016/j.ncrna.2018.11.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/13/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative diseases are among the most common causes of disability worldwide. Although neurodegenerative diseases are heterogeneous in both their clinical features and the underlying physiology, they are all characterised by progressive loss of specific neuronal populations. Recent experimental evidence suggests that long non-coding RNAs (lncRNAs) play important roles in the CNS in health and disease. Nuclear Paraspeckle Assembly Transcript 1 (NEAT1) is an abundant, ubiquitously expressed lncRNA, which forms a scaffold for a specific RNA granule in the nucleus, or nuclear body, the paraspeckle. Paraspeckles act as molecular hubs for cellular processes commonly affected by neurodegeneration. Transcriptomic analyses of the diseased human tissue have revealed altered NEAT1 levels in the CNS in major neurodegenerative disorders as well as in some disease models. Although it is clear that changes in NEAT1 expression (and in some cases, paraspeckle assembly) accompany neuronal damage, our understanding of NEAT1 contribution to the disease pathogenesis is still rudimentary. In this review, we have summarised the available knowledge on NEAT1 involvement in the molecular processes linked to neurodegeneration and on NEAT1 dysregulation in this type of disease, with a special focus on amyotrophic lateral sclerosis. The goal of this review is to attract the attention of researchers in the field of neurodegeneration to NEAT1 and paraspeckles.
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Affiliation(s)
- Haiyan An
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Non G Williams
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Tatyana A Shelkovnikova
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
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75
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Treiber T, Treiber N, Meister G. Regulation of microRNA biogenesis and its crosstalk with other cellular pathways. Nat Rev Mol Cell Biol 2018; 20:5-20. [DOI: 10.1038/s41580-018-0059-1] [Citation(s) in RCA: 628] [Impact Index Per Article: 104.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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76
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Jawaid A, Woldemichael BT, Kremer EA, Laferriere F, Gaur N, Afroz T, Polymenidou M, Mansuy IM. Memory Decline and Its Reversal in Aging and Neurodegeneration Involve miR-183/96/182 Biogenesis. Mol Neurobiol 2018; 56:3451-3462. [PMID: 30128653 DOI: 10.1007/s12035-018-1314-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/09/2018] [Indexed: 01/31/2023]
Abstract
Aging is characterized by progressive memory decline that can lead to dementia when associated with neurodegeneration. Here, we show in mice that aging-related memory decline involves defective biogenesis of microRNAs (miRNAs), in particular miR-183/96/182 cluster, resulting from increased protein phosphatase 1 (PP1) and altered receptor SMAD (R-SMAD) signaling. Correction of the defect by miR-183/96/182 overexpression in hippocampus or by environmental enrichment that normalizes PP1 activity restores memory in aged animals. Regulation of miR-183/96/182 biogenesis is shown to involve the neurodegeneration-related RNA-binding proteins TDP-43 and FUS. Similar alterations in miR-183/96/182, PP1, and R-SMADs are observed in the brains of patients with amyotrophic lateral sclerosis (ALS) or frontotemporal lobar degeneration (FTLD), two neurodegenerative diseases with pathological aggregation of TDP-43. Overall, these results identify new mechanistic links between miR-183/96/182, PP1, TDP-43, and FUS in age-related memory deficits and their reversal.
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Affiliation(s)
- Ali Jawaid
- Laboratory of Neuroepigenetics, Neuroscience Center Zürich, University of Zurich (UZH) and Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Bisrat T Woldemichael
- Laboratory of Neuroepigenetics, Neuroscience Center Zürich, University of Zurich (UZH) and Swiss Federal Institute of Technology (ETH), Zurich, Switzerland.,Icahn school of medicine at Mount Sinai, New York, USA
| | - Eloïse A Kremer
- Laboratory of Neuroepigenetics, Neuroscience Center Zürich, University of Zurich (UZH) and Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Florent Laferriere
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Niharika Gaur
- Laboratory of Neuroepigenetics, Neuroscience Center Zürich, University of Zurich (UZH) and Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Tariq Afroz
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Isabelle M Mansuy
- Laboratory of Neuroepigenetics, Neuroscience Center Zürich, University of Zurich (UZH) and Swiss Federal Institute of Technology (ETH), Zurich, Switzerland.
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Ravanidis S, Kattan FG, Doxakis E. Unraveling the Pathways to Neuronal Homeostasis and Disease: Mechanistic Insights into the Role of RNA-Binding Proteins and Associated Factors. Int J Mol Sci 2018; 19:ijms19082280. [PMID: 30081499 PMCID: PMC6121432 DOI: 10.3390/ijms19082280] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 07/26/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
The timing, dosage and location of gene expression are fundamental determinants of brain architectural complexity. In neurons, this is, primarily, achieved by specific sets of trans-acting RNA-binding proteins (RBPs) and their associated factors that bind to specific cis elements throughout the RNA sequence to regulate splicing, polyadenylation, stability, transport and localized translation at both axons and dendrites. Not surprisingly, misregulation of RBP expression or disruption of its function due to mutations or sequestration into nuclear or cytoplasmic inclusions have been linked to the pathogenesis of several neuropsychiatric and neurodegenerative disorders such as fragile-X syndrome, autism spectrum disorders, spinal muscular atrophy, amyotrophic lateral sclerosis and frontotemporal dementia. This review discusses the roles of Pumilio, Staufen, IGF2BP, FMRP, Sam68, CPEB, NOVA, ELAVL, SMN, TDP43, FUS, TAF15, and TIA1/TIAR in RNA metabolism by analyzing their specific molecular and cellular function, the neurological symptoms associated with their perturbation, and their axodendritic transport/localization along with their target mRNAs as part of larger macromolecular complexes termed ribonucleoprotein (RNP) granules.
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Affiliation(s)
- Stylianos Ravanidis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Fedon-Giasin Kattan
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Epaminondas Doxakis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
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78
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Rad N, Weiss MD. MicroRNAS: Mapping out the road to
amyotrophic lateral sclerosis. Muscle Nerve 2018; 58:189-190. [DOI: 10.1002/mus.26141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/09/2018] [Accepted: 04/12/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Nassim Rad
- Department of Rehabilitation MedicineUniversity of WashingtonSeattle Washington USA
| | - Michael D. Weiss
- Division of Neuromuscular Diseases, Department of NeurologyUniversity of WashingtonSeattle Washington USA
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Macro roles for microRNAs in neurodegenerative diseases. Noncoding RNA Res 2018; 3:154-159. [PMID: 30175288 PMCID: PMC6114258 DOI: 10.1016/j.ncrna.2018.07.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/24/2018] [Accepted: 07/30/2018] [Indexed: 02/07/2023] Open
Abstract
Neurodegenerative diseases (NDs) are typically adult-onset progressive disorders that perturb neuronal function, plasticity and health that arise through a host of one or more genetic and/or environmental factors. Over the last decade, numerous studies have shown that mutations in RNA binding proteins and changes in miRNA profiles within the brain are significantly altered during the progression towards NDs – suggesting miRNAs may be one of these contributing factors. Interestingly, the molecular and cellular functions of miRNAs in NDs is largely understudied and could remain a possible avenue for exploring therapeutic treatments for various NDs. In this review, I describe findings which have implicated miRNAs in various NDs and discuss how future studies focused around miRNA-mediated gene silencing could aid in furthering our understanding of maintaining a healthy brain.
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MicroRNA expression analysis identifies a subset of downregulated miRNAs in ALS motor neuron progenitors. Sci Rep 2018; 8:10105. [PMID: 29973608 PMCID: PMC6031650 DOI: 10.1038/s41598-018-28366-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/18/2018] [Indexed: 02/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurological disorder that is characterized by a progressive degeneration of motor neurons (MNs). The pathomechanism underlying the disease is largely unknown, even though increasing evidence suggests that RNA metabolism, including microRNAs (miRNAs) may play an important role. In this study, human ALS induced pluripotent stem cells were differentiated into MN progenitors and their miRNA expression profiles were compared to those of healthy control cells. We identified 15 downregulated miRNAs in patients’ cells. Gene ontology and molecular pathway enrichment analysis indicated that the predicted target genes of the differentially expressed miRNAs were involved in neurodegeneration-related pathways. Among the 15 examined miRNAs, miR-34a and miR504 appeared particularly relevant due to their involvement in the p53 pathway, synaptic vesicle regulation and general involvement in neurodegenerative diseases. Taken together our results demonstrate that the neurodegenerative phenotype in ALS can be associated with a dysregulation of miRNAs involved in the control of disease-relevant genetic pathways, suggesting that targeting entire gene networks can be a potential strategy to treat complex diseases such as ALS.
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81
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Splicing factors as regulators of miRNA biogenesis – links to human disease. Semin Cell Dev Biol 2018; 79:113-122. [DOI: 10.1016/j.semcdb.2017.10.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/09/2017] [Accepted: 10/09/2017] [Indexed: 12/16/2022]
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82
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Yokoi S, Udagawa T, Fujioka Y, Honda D, Okado H, Watanabe H, Katsuno M, Ishigaki S, Sobue G. 3'UTR Length-Dependent Control of SynGAP Isoform α2 mRNA by FUS and ELAV-like Proteins Promotes Dendritic Spine Maturation and Cognitive Function. Cell Rep 2018; 20:3071-3084. [PMID: 28954225 DOI: 10.1016/j.celrep.2017.08.100] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/19/2017] [Accepted: 08/29/2017] [Indexed: 12/13/2022] Open
Abstract
FUS is an RNA-binding protein associated with frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Previous reports have demonstrated intrinsic roles of FUS in synaptic function. However, the mechanism underlying FUS's regulation of synaptic morphology has remained unclear. We found that reduced mature spines after FUS depletion were associated with the internalization of PSD-95 within the dendritic shaft. Mass spectrometry of PSD-95-interacting proteins identified SynGAP, whose expression decreased after FUS depletion. Moreover, FUS and the ELAV-like proteins ELAVL4 and ELAVL1 control SynGAP mRNA stability in a 3'UTR length-dependent manner, resulting in the stable expression of the alternatively spliced SynGAP isoform α2. Finally, abnormal spine maturation and FTLD-like behavioral deficits in FUS-knockout mice were ameliorated by SynGAP α2. Our findings establish an important link between FUS and ELAVL proteins for mRNA stability control and indicate that this mechanism is crucial for the maintenance of synaptic morphology and cognitive function.
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Affiliation(s)
- Satoshi Yokoi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Tsuyoshi Udagawa
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan.
| | - Yusuke Fujioka
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Daiyu Honda
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Haruo Okado
- Department of Brain Development and Neural Regeneration, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan
| | - Hirohisa Watanabe
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Research Division of Dementia and Neurodegenerative Disease, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Shinsuke Ishigaki
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Department of Therapeutics for Intractable Neurological Disorders, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan.
| | - Gen Sobue
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Research Division of Dementia and Neurodegenerative Disease, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan.
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83
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A stress-induced response complex (SIRC) shuttles miRNAs, siRNAs, and oligonucleotides to the nucleus. Proc Natl Acad Sci U S A 2018; 115:E5756-E5765. [PMID: 29866826 PMCID: PMC6016802 DOI: 10.1073/pnas.1721346115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The deregulation of miRNA function is critical in the pathogenesis of cancer and other diseases. miRNAs and other noncoding RNAs (ncRNAs) tightly regulate gene expression, often in the cell nucleus. Heretofore, there has been no understanding that there exists a general shuttling mechanism that brings miRNAs, in addition to therapeutic oligonucleotides and siRNAs, from the cytoplasm into the nucleus. We have identified this shuttling mechanism, which occurs in response to cell stress. Nuclear imported miRNAs are functional, can potentially alter gene expression, and participate in cell stress response mechanisms. This shuttling mechanism can be augmented to target specific RNAs, including miRNA sponges, and long ncRNAs like Malat-1, which have been implicated in promoting tumor metastasis. Although some information is available for specific subsets of miRNAs and several factors have been shown to bind oligonucleotides (ONs), no general transport mechanism for these molecules has been identified to date. In this work, we demonstrate that the nuclear transport of ONs, siRNAs, and miRNAs responds to cellular stress. Furthermore, we have identified a stress-induced response complex (SIRC), which includes Ago-1 and Ago-2 in addition to the transcription and splicing regulators YB1, CTCF, FUS, Smad1, Smad3, and Smad4. The SIRC transports endogenous miRNAs, siRNAs, and ONs to the nucleus. We show that cellular stress can significantly increase ON- or siRNA-directed splicing switch events and endogenous miRNA targeting of nuclear RNAs.
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84
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Shelkovnikova TA, Kukharsky MS, An H, Dimasi P, Alexeeva S, Shabir O, Heath PR, Buchman VL. Protective paraspeckle hyper-assembly downstream of TDP-43 loss of function in amyotrophic lateral sclerosis. Mol Neurodegener 2018; 13:30. [PMID: 29859124 PMCID: PMC5984788 DOI: 10.1186/s13024-018-0263-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/25/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Paraspeckles are subnuclear bodies assembled on a long non-coding RNA (lncRNA) NEAT1. Their enhanced formation in spinal neurons of sporadic amyotrophic lateral sclerosis (ALS) patients has been reported but underlying mechanisms are unknown. The majority of ALS cases are characterized by TDP-43 proteinopathy. In current study we aimed to establish whether and how TDP-43 pathology may augment paraspeckle assembly. METHODS Paraspeckle formation in human samples was analysed by RNA-FISH and laser capture microdissection followed by qRT-PCR. Mechanistic studies were performed in stable cell lines, mouse primary neurons and human embryonic stem cell-derived neurons. Loss and gain of function for TDP-43 and other microRNA pathway factors were modelled by siRNA-mediated knockdown and protein overexpression. RESULTS We show that de novo paraspeckle assembly in spinal neurons and glial cells is a hallmark of both sporadic and familial ALS with TDP-43 pathology. Mechanistically, loss of TDP-43 but not its cytoplasmic accumulation or aggregation augments paraspeckle assembly in cultured cells. TDP-43 is a component of the microRNA machinery, and recently, paraspeckles have been shown to regulate pri-miRNA processing. Consistently, downregulation of core protein components of the miRNA pathway also promotes paraspeckle assembly. In addition, depletion of these proteins or TDP-43 results in accumulation of endogenous dsRNA and activation of type I interferon response which also stimulates paraspeckle formation. We demonstrate that human or mouse neurons in vitro lack paraspeckles, but a synthetic dsRNA is able to trigger their de novo formation. Finally, paraspeckles are protective in cells with compromised microRNA/dsRNA metabolism, and their assembly can be promoted by a small-molecule microRNA enhancer. CONCLUSIONS Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA.
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Affiliation(s)
| | - Michail S Kukharsky
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.,Institute of Physiologically Active Compounds Russian Academy of Sciences, 1 Severniy proezd, Chernogolovka, Moscow Region, Russian Federation, 142432
| | - Haiyan An
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Pasquale Dimasi
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Svetlana Alexeeva
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Osman Shabir
- The Sheffield Institute for Translational Neuroscience, 385A Glossop Road, Sheffield, S10 2HQ, UK
| | - Paul R Heath
- The Sheffield Institute for Translational Neuroscience, 385A Glossop Road, Sheffield, S10 2HQ, UK
| | - Vladimir L Buchman
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.,Institute of Physiologically Active Compounds Russian Academy of Sciences, 1 Severniy proezd, Chernogolovka, Moscow Region, Russian Federation, 142432
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85
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Neuronal activity regulates DROSHA via autophagy in spinal muscular atrophy. Sci Rep 2018; 8:7907. [PMID: 29784949 PMCID: PMC5962575 DOI: 10.1038/s41598-018-26347-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 05/10/2018] [Indexed: 02/06/2023] Open
Abstract
Dysregulated miRNA expression and mutation of genes involved in miRNA biogenesis have been reported in motor neuron diseases including spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS). Therefore, identifying molecular mechanisms governing miRNA expression is important to understand these diseases. Here, we report that expression of DROSHA, which is a critical enzyme in the microprocessor complex and essential for miRNA biogenesis, is reduced in motor neurons from an SMA mouse model. We show that DROSHA is degraded by neuronal activity induced autophagy machinery, which is also dysregulated in SMA. Blocking neuronal activity or the autophagy-lysosome pathway restores DROSHA levels in SMA motor neurons. Moreover, reducing DROSHA levels enhances axonal growth. As impaired axonal growth is a well described phenotype of SMA motor neurons, these data suggest that DROSHA reduction by autophagy may mitigate the phenotype of SMA. In summary, these findings suggest that autophagy regulates RNA metabolism and neuronal growth via the DROSHA/miRNA pathway and this pathway is dysregulated in SMA.
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86
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Synaptic Paths to Neurodegeneration: The Emerging Role of TDP-43 and FUS in Synaptic Functions. Neural Plast 2018; 2018:8413496. [PMID: 29755516 PMCID: PMC5925147 DOI: 10.1155/2018/8413496] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 02/08/2018] [Accepted: 02/27/2018] [Indexed: 12/13/2022] Open
Abstract
TAR DNA-binding protein-43 KDa (TDP-43) and fused in sarcoma (FUS) as the defining pathological hallmarks for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), coupled with ALS-FTD-causing mutations in both genes, indicate that their dysfunctions damage the motor system and cognition. On the molecular level, TDP-43 and FUS participate in the biogenesis and metabolism of coding and noncoding RNAs as well as in the transport and translation of mRNAs as part of cytoplasmic mRNA-ribonucleoprotein (mRNP) granules. Intriguingly, many of the RNA targets of TDP-43 and FUS are involved in synaptic transmission and plasticity, indicating that synaptic dysfunction could be an early event contributing to motor and cognitive deficits in ALS and FTD. Furthermore, the ability of the low-complexity prion-like domains of TDP-43 and FUS to form liquid droplets suggests a potential mechanism for mRNP assembly and conversion. This review will discuss the role of TDP-43 and FUS in RNA metabolism, with an emphasis on the involvement of this process in synaptic function and neuroprotection. This will be followed by a discussion of the potential phase separation mechanism for forming RNP granules and pathological inclusions.
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87
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Differential expression of microRNAs and other small RNAs in muscle tissue of patients with ALS and healthy age-matched controls. Sci Rep 2018; 8:5609. [PMID: 29618798 PMCID: PMC5884852 DOI: 10.1038/s41598-018-23139-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 03/05/2018] [Indexed: 02/08/2023] Open
Abstract
Amyotrophic lateral sclerosis is a late-onset disorder primarily affecting motor neurons and leading to progressive and lethal skeletal muscle atrophy. Small RNAs, including microRNAs (miRNAs), can serve as important regulators of gene expression and can act both globally and in a tissue-/cell-type-specific manner. In muscle, miRNAs called myomiRs govern important processes and are deregulated in various disorders. Several myomiRs have shown promise for therapeutic use in cellular and animal models of ALS; however, the exact miRNA species differentially expressed in muscle tissue of ALS patients remain unknown. Following small RNA-Seq, we compared the expression of small RNAs in muscle tissue of ALS patients and healthy age-matched controls. The identified snoRNAs, mtRNAs and other small RNAs provide possible molecular links between insulin signaling and ALS. Furthermore, the identified miRNAs are predicted to target proteins that are involved in both normal processes and various muscle disorders and indicate muscle tissue is undergoing active reinnervation/compensatory attempts thus providing targets for further research and therapy development in ALS.
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88
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Matamala JM, Arias-Carrasco R, Sanchez C, Uhrig M, Bargsted L, Matus S, Maracaja-Coutinho V, Abarzua S, van Zundert B, Verdugo R, Manque P, Hetz C. Genome-wide circulating microRNA expression profiling reveals potential biomarkers for amyotrophic lateral sclerosis. Neurobiol Aging 2018; 64:123-138. [DOI: 10.1016/j.neurobiolaging.2017.12.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/18/2017] [Accepted: 12/21/2017] [Indexed: 12/17/2022]
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89
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Raheja R, Regev K, Healy BC, Mazzola MA, Beynon V, Von Glehn F, Paul A, Diaz-Cruz C, Gholipour T, Glanz BI, Kivisakk P, Chitnis T, Weiner HL, Berry JD, Gandhi R. Correlating serum micrornas and clinical parameters in amyotrophic lateral sclerosis. Muscle Nerve 2018; 58:261-269. [PMID: 29466830 DOI: 10.1002/mus.26106] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 02/12/2018] [Accepted: 02/17/2018] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Amyotrophic lateral sclerosis (ALS) is a debilitating neurologic disorder with poor survival rates and no clear biomarkers for disease diagnosis and prognosis. METHODS We compared serum microRNA (miRNA) expression from patients with ALS with healthy controls and patients with multiple sclerosis and Alzheimer disease. We also correlated miRNA expression in cross-sectional and longitudinal cohorts of ALS patients with clinical parameters. RESULTS We identified 7 miRNAs (miR-192-5p, miR-192-3p, miR-1, miR-133a-3p, miR-133b, miR-144-5p, miR-19a-3p) that were upregulated and 6 miRNAs (miR-320c, miR-320a, let-7d-3p, miR-425-5p, miR-320b, miR-139-5p) that were downregulated in patients with ALS compared with healthy controls, patients with Alzheimer disease, and patients with multiple sclerosis. Changes in 4 miRNAs (miR-136-3p, miR-30b-5p, miR-331-3p, miR-496) correlated positively and change in 1 miRNA (miR-2110) correlated negatively with changes in clinical parameters in longitudinal analysis. DISCUSSION Our findings identified serum miRNAs that can serve as biomarkers for ALS diagnosis and progression. Muscle Nerve 58: 261-269, 2018.
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Affiliation(s)
- Radhika Raheja
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Keren Regev
- Department of Neurology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Brian C Healy
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Maria Antonietta Mazzola
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Vanessa Beynon
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Felipe Von Glehn
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Anu Paul
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Camilo Diaz-Cruz
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Taha Gholipour
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bonnie I Glanz
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pia Kivisakk
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tanuja Chitnis
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Howard L Weiner
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - James D Berry
- Department of Neurology, Neurological Clinical Research Institute, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Roopali Gandhi
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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90
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A Regulatory Circuitry Between Gria2, miR-409, and miR-495 Is Affected by ALS FUS Mutation in ESC-Derived Motor Neurons. Mol Neurobiol 2018; 55:7635-7651. [PMID: 29430619 PMCID: PMC6132778 DOI: 10.1007/s12035-018-0884-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/08/2018] [Indexed: 12/12/2022]
Abstract
Mutations in fused in sarcoma (FUS) cause amyotrophic lateral sclerosis (ALS). FUS is a multifunctional protein involved in the biogenesis and activity of several types of RNAs, and its role in the pathogenesis of ALS may involve both direct effects of disease-associated mutations through gain- and loss-of-function mechanisms and indirect effects due to the cross talk between different classes of FUS-dependent RNAs. To explore how FUS mutations impinge on motor neuron-specific RNA-based circuitries, we performed transcriptome profiling of small and long RNAs of motor neurons (MNs) derived from mouse embryonic stem cells carrying a FUS-P517L knock-in mutation, which is equivalent to human FUS-P525L, associated with a severe and juvenile-onset form of ALS. Combining ontological, predictive and molecular analyses, we found an inverse correlation between several classes of deregulated miRNAs and their corresponding mRNA targets in both homozygous and heterozygous P517L MNs. We validated a circuitry in which the upregulation of miR-409-3p and miR-495-3p, belonging to a brain-specific miRNA subcluster implicated in several neurodevelopmental disorders, produced the downregulation of Gria2, a subunit of the glutamate α‐amino‐3‐hydroxy‐5‐methyl-4-isoxazole propionic acid (AMPA) receptor with a significant role in excitatory neurotransmission. Moreover, we found that FUS was involved in mediating such miRNA repression. Gria2 alteration has been proposed to be implicated in MN degeneration, through disturbance of Ca2+ homeostasis, which triggers a cascade of damaging “excitotoxic” events. The molecular cross talk identified highlights a role for FUS in excitotoxicity and in miRNA-dependent regulation of Gria2. This circuitry also proved to be deregulated in heterozygosity, which matches the human condition perfectly.
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91
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Weskamp K, Barmada SJ. TDP43 and RNA instability in amyotrophic lateral sclerosis. Brain Res 2018; 1693:67-74. [PMID: 29395044 DOI: 10.1016/j.brainres.2018.01.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/09/2018] [Accepted: 01/12/2018] [Indexed: 12/13/2022]
Abstract
The nuclear RNA-binding protein TDP43 is integrally involved in RNA processing. In accord with this central function, TDP43 levels are tightly regulated through a negative feedback loop, in which TDP43 recognizes its own RNA transcript, destabilizes it, and reduces new TDP43 protein production. In the neurodegenerative disorder amyotrophic lateral sclerosis (ALS), cytoplasmic mislocalization and accumulation of TDP43 disrupt autoregulation; conversely, inefficient TDP43 autoregulation can lead to cytoplasmic TDP43 deposition and subsequent neurodegeneration. Because TDP43 plays a multifaceted role in maintaining RNA metabolism, its mislocalization and accumulation interrupt several RNA processing pathways that in turn affect RNA stability and gene expression. TDP43-mediated disruption of these pathways-including alternative mRNA splicing, non-coding RNA processing, and RNA granule dynamics-may directly or indirectly contribute to ALS pathogenesis. Therefore, strategies that restore effective TDP43 autoregulation may ultimately prevent neurodegeneration in ALS and related disorders.
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Affiliation(s)
- Kaitlin Weskamp
- Neuroscience Graduate Program and Department of Neurology, University of Michigan School of Medicine, Ann Arbor, MI, United States
| | - Sami J Barmada
- Neuroscience Graduate Program and Department of Neurology, University of Michigan School of Medicine, Ann Arbor, MI, United States.
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92
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Svetoni F, De Paola E, La Rosa P, Mercatelli N, Caporossi D, Sette C, Paronetto MP. Post-transcriptional regulation of FUS and EWS protein expression by miR-141 during neural differentiation. Hum Mol Genet 2018; 26:2732-2746. [PMID: 28453628 DOI: 10.1093/hmg/ddx160] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/21/2017] [Indexed: 12/31/2022] Open
Abstract
Brain development involves proliferation, migration and specification of neural progenitor cells, culminating in neuronal circuit formation. Mounting evidence indicates that improper regulation of RNA binding proteins (RBPs), including members of the FET (FUS, EWS, TAF15) family, results in defective cortical development and/or neurodegenerative disorders. However, in spite of their physiological relevance, the precise pattern of FET protein expression in developing neurons is largely unknown. Herein, we found that FUS, EWS and TAF15 expression is differentially regulated during brain development, both in time and in space. In particular, our study identifies a fine-tuned regulation of FUS and EWS during neuronal differentiation, whereas TAF15 appears to be more constitutively expressed. Mechanistically FUS and EWS protein expression is regulated at the post-transcriptional level during neuron differentiation and brain development. Moreover, we identified miR-141 as a key regulator of these FET proteins that modulate their expression levels in differentiating neuronal cells. Thus, our studies uncover a novel link between post-transcriptional regulation of FET proteins expression and neurogenesis.
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Affiliation(s)
- Francesca Svetoni
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Elisa De Paola
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Piergiorgio La Rosa
- Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Neri Mercatelli
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Daniela Caporossi
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy
| | - Claudio Sette
- Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
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93
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Russell AP, Ghobrial L, Ngo S, Yerbury J, Zacharewicz E, Chung R, Lamon S. Dysregulation of microRNA biogenesis machinery and microRNA/RNA ratio in skeletal muscle of amyotrophic lateral sclerosis mice. Muscle Nerve 2017; 57:838-847. [PMID: 29236291 DOI: 10.1002/mus.26039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2017] [Indexed: 12/12/2022]
Abstract
INTRODUCTION The pathology of amyotrophic lateral sclerosis (ALS) is associated with impaired RNA processing and microRNA (miRNA) dysregulation. Here we investigate the regulation of the members of the miRNA biogenesis pathways and total miRNA levels at different stages of the disease. METHODS Muscle, brain, and spinal cord tissue were obtained from presymptomatic, symptomatic, and end-stage superoxide dismutase 1 (SOD1)G93A mice. miRNA and transcript levels were measured by quantitative polymerase chain reaction. RESULTS As the diseases progresses, several genes involved in miRNA biogenesis as well as the miRNA/total RNA (totRNA) ratio increased in the tibialis anterior (TA) muscle but not in the soleus or in neural tissue. DISCUSSION We propose that a dysregulation in the miRNA/totRNA ratio in the TA muscle from SOD1G93A mice reflects a pathological increase in miRNA biogenesis machinery. Alterations in the miRNA/totRNA ratio influence the levels of reference noncoding RNAs and may therefore potentially compromise the accuracy of commonly used miRNA normalization strategies. Muscle Nerve 57: 838-847, 2018.
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Affiliation(s)
- Aaron P Russell
- Institute for Physical Activity and Nutrition (IPAN), Deakin University, Geelong, Australia
| | - Lobna Ghobrial
- Institute for Physical Activity and Nutrition (IPAN), Deakin University, Geelong, Australia
| | - Shyuan Ngo
- Australian Institute for Bioengineering and Nanotechnology, Australia Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Justin Yerbury
- Illawarra Health & Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Evelyn Zacharewicz
- Institute for Physical Activity and Nutrition (IPAN), Deakin University, Geelong, Australia
| | - Roger Chung
- Department of Biomedical Sciences, Macquarie University, Sydney, Australia
| | - Séverine Lamon
- Institute for Physical Activity and Nutrition (IPAN), Deakin University, Geelong, Australia
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Abstract
DROSHA is the catalytic subunit of the Microprocessor complex, which initiates microRNA (miRNA) maturation in the nucleus by recognizing and cleaving hairpin precursors embedded in primary transcripts. However, accumulating evidence suggests that not all hairpin substrates of DROSHA are associated with the generation of functional small RNAs. By targeting those hairpins, DROSHA regulates diverse aspects of RNA metabolism across the transcriptome, serves as a line of defense against the expression of potentially deleterious elements, and permits cell fate determination and differentiation. DROSHA is also versatile in the way that it executes these noncanonical functions, occasionally depending on its RNA-binding activity rather than its catalytic activity. Herein, we discuss the functional and mechanistic diversity of DROSHA beyond the miRNA biogenesis pathway in light of recent findings.
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Affiliation(s)
- Dooyoung Lee
- a Department of Agricultural Biotechnology , Seoul National University , Seoul , Republic of Korea
| | - Chanseok Shin
- a Department of Agricultural Biotechnology , Seoul National University , Seoul , Republic of Korea.,b Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute , Seoul National University , Seoul , Republic of Korea
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95
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Zheng Q, Yang HJ, Yuan YA. Autoantigen La Regulates MicroRNA Processing from Stem–Loop Precursors by Association with DGCR8. Biochemistry 2017; 56:6098-6110. [DOI: 10.1021/acs.biochem.7b00693] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Quan Zheng
- Department
of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Hai-Jie Yang
- Department
of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Y. Adam Yuan
- Department
of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
- National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Suzhou, Jiangsu 215123, China
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96
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De Santis R, Santini L, Colantoni A, Peruzzi G, de Turris V, Alfano V, Bozzoni I, Rosa A. FUS Mutant Human Motoneurons Display Altered Transcriptome and microRNA Pathways with Implications for ALS Pathogenesis. Stem Cell Reports 2017; 9:1450-1462. [PMID: 28988989 PMCID: PMC5830977 DOI: 10.1016/j.stemcr.2017.09.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 12/13/2022] Open
Abstract
The FUS gene has been linked to amyotrophic lateral sclerosis (ALS). FUS is a ubiquitous RNA-binding protein, and the mechanisms leading to selective motoneuron loss downstream of ALS-linked mutations are largely unknown. We report the transcriptome analysis of human purified motoneurons, obtained from FUS wild-type or mutant isogenic induced pluripotent stem cells (iPSCs). Gene ontology analysis of differentially expressed genes identified significant enrichment of pathways previously associated to sporadic ALS and other neurological diseases. Several microRNAs (miRNAs) were also deregulated in FUS mutant motoneurons, including miR-375, involved in motoneuron survival. We report that relevant targets of miR-375, including the neural RNA-binding protein ELAVL4 and apoptotic factors, are aberrantly increased in FUS mutant motoneurons. Characterization of transcriptome changes in the cell type primarily affected by the disease contributes to the definition of the pathogenic mechanisms of FUS-linked ALS.
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Affiliation(s)
- Riccardo De Santis
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Laura Santini
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessio Colantoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Valeria de Turris
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Vincenzo Alfano
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Irene Bozzoni
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Institute Pasteur Fondazione Cenci-Bolognetti, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessandro Rosa
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
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97
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Novel miR-b2122 regulates several ALS-related RNA-binding proteins. Mol Brain 2017; 10:46. [PMID: 28969660 PMCID: PMC5625648 DOI: 10.1186/s13041-017-0326-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/14/2017] [Indexed: 02/08/2023] Open
Abstract
Common pathological features of amyotrophic lateral sclerosis (ALS) include cytoplasmic aggregation of several RNA-binding proteins. Out of these RNA-binding proteins, TDP-43, FUS/TLS and RGNEF have been shown to co-aggregate with one another within motor neurons of sporadic ALS (sALS) patients, suggesting that there may be a common regulatory network disrupted. MiRNAs have been a recent focus in ALS research as they have been identified to be globally down-regulated in the spinal cord of ALS patients. The objective of this study was to identify if there are miRNA(s) dysregulated in sALS that are responsible for regulating the TDP-43, FUS/TLS and RGNEF network. In this study, we identify miR-194 and miR-b2122 to be significantly down-regulated in sALS patients, and were predicted to regulate TARDBP, FUS/TLS and RGNEF expression. Reporter gene assays and RT-qPCR revealed that miR-b2122 down-regulates the reporter gene through direct interactions with either the TARDBP, FUS/TLS, or RGNEF 3’UTR, while miR-194 down-regulates firefly expression when it contained either the TARDBP or FUS/TLS 3’UTR. Further, we showed that miR-b2122 regulates endogenous expression of all three of these genes in a neuronal-derived cell line. Also, an ALS-associated mutation in the FUS/TLS 3’UTR ablates the ability of miR-b2122 to regulate reporter gene linked to FUS/TLS 3’UTR, and sALS samples which showed a down-regulation in miR-b2122 also showed an increase in FUS/TLS protein expression. Overall, we have identified a novel miRNA that is down-regulated in sALS that appears to be a central regulator of disease-related RNA-binding proteins, and thus its dysregulation likely contributes to TDP-43, FUS/TLS and RGNEF pathogenesis in sALS.
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98
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Treiber T, Treiber N, Plessmann U, Harlander S, Daiß JL, Eichner N, Lehmann G, Schall K, Urlaub H, Meister G. A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis. Mol Cell 2017; 66:270-284.e13. [PMID: 28431233 DOI: 10.1016/j.molcel.2017.03.014] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/22/2016] [Accepted: 03/20/2017] [Indexed: 12/19/2022]
Abstract
During microRNA (miRNA) biogenesis, two endonucleolytic reactions convert stem-loop-structured precursors into mature miRNAs. These processing steps can be posttranscriptionally regulated by RNA-binding proteins (RBPs). Here, we have used a proteomics-based pull-down approach to map and characterize the interactome of a multitude of pre-miRNAs. We identify ∼180 RBPs that interact specifically with distinct pre-miRNAs. For functional validation, we combined RNAi and CRISPR/Cas-mediated knockout experiments to analyze RBP-dependent changes in miRNA levels. Indeed, a large number of the investigated candidates, including splicing factors and other mRNA processing proteins, have effects on miRNA processing. As an example, we show that TRIM71/LIN41 is a potent regulator of miR-29a processing and its inactivation directly affects miR-29a targets. We provide an extended database of RBPs that interact with pre-miRNAs in extracts of different cell types, highlighting a widespread layer of co- and posttranscriptional regulation of miRNA biogenesis.
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Affiliation(s)
- Thomas Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Uwe Plessmann
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute of Biophysical Chemistry, 37077 Göttingen, Germany
| | - Simone Harlander
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Julia-Lisa Daiß
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Norbert Eichner
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Gerhard Lehmann
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Kevin Schall
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute of Biophysical Chemistry, 37077 Göttingen, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany.
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99
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Kuang L, Kamelgarn M, Arenas A, Gal J, Taylor D, Gong W, Brown M, St Clair D, Kasarskis EJ, Zhu H. Clinical and experimental studies of a novel P525R FUS mutation in amyotrophic lateral sclerosis. NEUROLOGY-GENETICS 2017; 3:e172. [PMID: 28812062 PMCID: PMC5546284 DOI: 10.1212/nxg.0000000000000172] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/16/2017] [Indexed: 12/13/2022]
Abstract
Objective: To describe the clinical features of a novel fused in sarcoma (FUS) mutation in a young adult female amyotrophic lateral sclerosis (ALS) patient with rapid progression of weakness and to experimentally validate the consequences of the P525R mutation in cellular neuronal models. Methods: We conducted sequencing of genomic DNA from the index patient and her family members. Immunocytochemistry was performed in various cellular models to determine whether the newly identified P525R mutant FUS protein accumulated in cytoplasmic inclusions. Clinical features of the index patient were compared with 19 other patients with ALS carrying the P525L mutation in the same amino acid position. Results: A novel mutation c.1574C>G (p.525P>R) in the FUS gene was identified in the index patient. The clinical symptoms are similar to those in familial ALS patients with the P525L mutation at the same position. The P525R mutant FUS protein showed cytoplasmic localization and formed large stress granule–like cytoplasmic inclusions in multiple cellular models. Conclusions: The clinical features of the patient and the cytoplasmic inclusions of the P525R mutant FUS protein strengthen the notion that mutations at position 525 of the FUS protein result in a coherent phenotype characterized by juvenile or young adult onset, rapid progression, variable positive family history, and female preponderance.
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Affiliation(s)
- Lisha Kuang
- Molecular and Cellular Biochemistry (L.K., J.G., H.Z.), Department of Toxicology and Cancer Biology (M.K., A.A., D.S.C., H.Z.), and Department of Neurology (D.T., E.J.K.), College of Medicine, University of Kentucky, Lexington; Hefei National Laboratory for Physical Sciences at the Microscale (W.G.), University of Science and Technology of China, Anhui; Department of Neurology (M.B.), University of Louisville; and Research and Development (E.J.K., H.Z.), Lexington VA Medical Center, KY
| | - Marisa Kamelgarn
- Molecular and Cellular Biochemistry (L.K., J.G., H.Z.), Department of Toxicology and Cancer Biology (M.K., A.A., D.S.C., H.Z.), and Department of Neurology (D.T., E.J.K.), College of Medicine, University of Kentucky, Lexington; Hefei National Laboratory for Physical Sciences at the Microscale (W.G.), University of Science and Technology of China, Anhui; Department of Neurology (M.B.), University of Louisville; and Research and Development (E.J.K., H.Z.), Lexington VA Medical Center, KY
| | - Alexandra Arenas
- Molecular and Cellular Biochemistry (L.K., J.G., H.Z.), Department of Toxicology and Cancer Biology (M.K., A.A., D.S.C., H.Z.), and Department of Neurology (D.T., E.J.K.), College of Medicine, University of Kentucky, Lexington; Hefei National Laboratory for Physical Sciences at the Microscale (W.G.), University of Science and Technology of China, Anhui; Department of Neurology (M.B.), University of Louisville; and Research and Development (E.J.K., H.Z.), Lexington VA Medical Center, KY
| | - Jozsef Gal
- Molecular and Cellular Biochemistry (L.K., J.G., H.Z.), Department of Toxicology and Cancer Biology (M.K., A.A., D.S.C., H.Z.), and Department of Neurology (D.T., E.J.K.), College of Medicine, University of Kentucky, Lexington; Hefei National Laboratory for Physical Sciences at the Microscale (W.G.), University of Science and Technology of China, Anhui; Department of Neurology (M.B.), University of Louisville; and Research and Development (E.J.K., H.Z.), Lexington VA Medical Center, KY
| | - Deborah Taylor
- Molecular and Cellular Biochemistry (L.K., J.G., H.Z.), Department of Toxicology and Cancer Biology (M.K., A.A., D.S.C., H.Z.), and Department of Neurology (D.T., E.J.K.), College of Medicine, University of Kentucky, Lexington; Hefei National Laboratory for Physical Sciences at the Microscale (W.G.), University of Science and Technology of China, Anhui; Department of Neurology (M.B.), University of Louisville; and Research and Development (E.J.K., H.Z.), Lexington VA Medical Center, KY
| | - Weiming Gong
- Molecular and Cellular Biochemistry (L.K., J.G., H.Z.), Department of Toxicology and Cancer Biology (M.K., A.A., D.S.C., H.Z.), and Department of Neurology (D.T., E.J.K.), College of Medicine, University of Kentucky, Lexington; Hefei National Laboratory for Physical Sciences at the Microscale (W.G.), University of Science and Technology of China, Anhui; Department of Neurology (M.B.), University of Louisville; and Research and Development (E.J.K., H.Z.), Lexington VA Medical Center, KY
| | - Martin Brown
- Molecular and Cellular Biochemistry (L.K., J.G., H.Z.), Department of Toxicology and Cancer Biology (M.K., A.A., D.S.C., H.Z.), and Department of Neurology (D.T., E.J.K.), College of Medicine, University of Kentucky, Lexington; Hefei National Laboratory for Physical Sciences at the Microscale (W.G.), University of Science and Technology of China, Anhui; Department of Neurology (M.B.), University of Louisville; and Research and Development (E.J.K., H.Z.), Lexington VA Medical Center, KY
| | - Daret St Clair
- Molecular and Cellular Biochemistry (L.K., J.G., H.Z.), Department of Toxicology and Cancer Biology (M.K., A.A., D.S.C., H.Z.), and Department of Neurology (D.T., E.J.K.), College of Medicine, University of Kentucky, Lexington; Hefei National Laboratory for Physical Sciences at the Microscale (W.G.), University of Science and Technology of China, Anhui; Department of Neurology (M.B.), University of Louisville; and Research and Development (E.J.K., H.Z.), Lexington VA Medical Center, KY
| | - Edward J Kasarskis
- Molecular and Cellular Biochemistry (L.K., J.G., H.Z.), Department of Toxicology and Cancer Biology (M.K., A.A., D.S.C., H.Z.), and Department of Neurology (D.T., E.J.K.), College of Medicine, University of Kentucky, Lexington; Hefei National Laboratory for Physical Sciences at the Microscale (W.G.), University of Science and Technology of China, Anhui; Department of Neurology (M.B.), University of Louisville; and Research and Development (E.J.K., H.Z.), Lexington VA Medical Center, KY
| | - Haining Zhu
- Molecular and Cellular Biochemistry (L.K., J.G., H.Z.), Department of Toxicology and Cancer Biology (M.K., A.A., D.S.C., H.Z.), and Department of Neurology (D.T., E.J.K.), College of Medicine, University of Kentucky, Lexington; Hefei National Laboratory for Physical Sciences at the Microscale (W.G.), University of Science and Technology of China, Anhui; Department of Neurology (M.B.), University of Louisville; and Research and Development (E.J.K., H.Z.), Lexington VA Medical Center, KY
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100
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Louloupi A, Ntini E, Liz J, Ørom UA. Microprocessor dynamics shows co- and post-transcriptional processing of pri-miRNAs. RNA (NEW YORK, N.Y.) 2017; 23:892-898. [PMID: 28250203 PMCID: PMC5435862 DOI: 10.1261/rna.060715.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/21/2017] [Indexed: 05/05/2023]
Abstract
miRNAs are small regulatory RNAs involved in the regulation of translation of target transcripts. miRNA biogenesis is a multistep process starting with the cleavage of the primary miRNA transcript in the nucleus by the Microprocessor complex. Endogenous processing of pri-miRNAs is challenging to study and the in vivo kinetics of this process is not known. Here, we present a method for determining the processing kinetics of pri-miRNAs within intact cells over time, using a pulse-chase approach to label transcribed RNA during 15 min, and follow the processing within a 1-hour window after labeling with bromouridine. We show that pri-miRNAs exhibit different processing kinetics ranging from fast over intermediate to slow processing, and we provide evidence that pri-miRNA processing can occur both cotranscriptionally and post-transcriptionally.
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Affiliation(s)
- Annita Louloupi
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Evgenia Ntini
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Julia Liz
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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