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Ciechanowska A, Mika J. CC Chemokine Family Members' Modulation as a Novel Approach for Treating Central Nervous System and Peripheral Nervous System Injury-A Review of Clinical and Experimental Findings. Int J Mol Sci 2024; 25:3788. [PMID: 38612597 PMCID: PMC11011591 DOI: 10.3390/ijms25073788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/18/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Despite significant progress in modern medicine and pharmacology, damage to the nervous system with various etiologies still poses a challenge to doctors and scientists. Injuries lead to neuroimmunological changes in the central nervous system (CNS), which may result in both secondary damage and the development of tactile and thermal hypersensitivity. In our review, based on the analysis of many experimental and clinical studies, we indicate that the mechanisms occurring both at the level of the brain after direct damage and at the level of the spinal cord after peripheral nerve damage have a common immunological basis. This suggests that there are opportunities for similar pharmacological therapeutic interventions in the damage of various etiologies. Experimental data indicate that after CNS/PNS damage, the levels of 16 among the 28 CC-family chemokines, i.e., CCL1, CCL2, CCL3, CCL4, CCL5, CCL6, CCL7, CCL8, CCL9, CCL11, CCL12, CCL17, CCL19, CCL20, CCL21, and CCL22, increase in the brain and/or spinal cord and have strong proinflammatory and/or pronociceptive effects. According to the available literature data, further investigation is still needed for understanding the role of the remaining chemokines, especially six of them which were found in humans but not in mice/rats, i.e., CCL13, CCL14, CCL15, CCL16, CCL18, and CCL23. Over the past several years, the results of studies in which available pharmacological tools were used indicated that blocking individual receptors, e.g., CCR1 (J113863 and BX513), CCR2 (RS504393, CCX872, INCB3344, and AZ889), CCR3 (SB328437), CCR4 (C021 and AZD-2098), and CCR5 (maraviroc, AZD-5672, and TAK-220), has beneficial effects after damage to both the CNS and PNS. Recently, experimental data have proved that blockades exerted by double antagonists CCR1/3 (UCB 35625) and CCR2/5 (cenicriviroc) have very good anti-inflammatory and antinociceptive effects. In addition, both single (J113863, RS504393, SB328437, C021, and maraviroc) and dual (cenicriviroc) chemokine receptor antagonists enhanced the analgesic effect of opioid drugs. This review will display the evidence that a multidirectional strategy based on the modulation of neuronal-glial-immune interactions can significantly improve the health of patients after CNS and PNS damage by changing the activity of chemokines belonging to the CC family. Moreover, in the case of pain, the combined administration of such antagonists with opioid drugs could reduce therapeutic doses and minimize the risk of complications.
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Affiliation(s)
| | - Joanna Mika
- Department of Pain Pharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, 12 Smetna Str., 31-343 Kraków, Poland;
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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García Morato J, Gloeckner CJ, Kahle PJ. Proteomics elucidating physiological and pathological functions of TDP-43. Proteomics 2023; 23:e2200410. [PMID: 37671599 DOI: 10.1002/pmic.202200410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
Trans-activation response DNA binding protein of 43 kDa (TDP-43) regulates a great variety of cellular processes in the nucleus and cytosol. In addition, a defined subset of neurodegenerative diseases is characterized by nuclear depletion of TDP-43 as well as cytosolic mislocalization and aggregation. To perform its diverse functions TDP-43 can associate with different ribonucleoprotein complexes. Combined with transcriptomics, MS interactome studies have unveiled associations between TDP-43 and the spliceosome machinery, polysomes and RNA granules. Moreover, the highly dynamic, low-valency interactions regulated by its low-complexity domain calls for innovative proximity labeling methodologies. In addition to protein partners, the analysis of post-translational modifications showed that they may play a role in the nucleocytoplasmic shuttling, RNA binding, liquid-liquid phase separation and protein aggregation of TDP-43. Here we review the various TDP-43 ribonucleoprotein complexes characterized so far, how they contribute to the diverse functions of TDP-43, and roles of post-translational modifications. Further understanding of the fluid dynamic properties of TDP-43 in ribonucleoprotein complexes, RNA granules, and self-assemblies will advance the understanding of RNA processing in cells and perhaps help to develop novel therapeutic approaches for TDPopathies.
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Affiliation(s)
- Jorge García Morato
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Christian Johannes Gloeckner
- Research Group Functional Neuroproteomics, German Center of Neurodegenerative Diseases, Tübingen, Germany
- Core Facility for Medical Bioanalytics, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Philipp J Kahle
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Department of Biochemistry, University of Tübingen, Tübingen, Germany
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Ortiz GG, Ramírez-Jirano J, Arizaga RL, Delgado-Lara DLC, Torres-Sánchez ED. Frontotemporal-TDP and LATE Neurocognitive Disorders: A Pathophysiological and Genetic Approach. Brain Sci 2023; 13:1474. [PMID: 37891841 PMCID: PMC10605418 DOI: 10.3390/brainsci13101474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/07/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Frontotemporal lobar degeneration (FTLD) belongs to a heterogeneous group of highly complex neurodegenerative diseases and represents the second cause of presenile dementia in individuals under 65. Frontotemporal-TDP is a subgroup of frontotemporal dementia characterized by the aggregation of abnormal protein deposits, predominantly transactive response DNA-binding protein 43 (TDP-43), in the frontal and temporal brain regions. These deposits lead to progressive degeneration of neurons resulting in cognitive and behavioral impairments. Limbic age-related encephalopathy (LATE) pertains to age-related cognitive decline primarily affecting the limbic system, which is crucial for memory, emotions, and learning. However, distinct, emerging research suggests a potential overlap in pathogenic processes, with some cases of limbic encephalopathy displaying TDP-43 pathology. Genetic factors play a pivotal role in both disorders. Mutations in various genes, such as progranulin (GRN) and chromosome 9 open reading frame 72 (C9orf72), have been identified as causative in frontotemporal-TDP. Similarly, specific genetic variants have been associated with an increased risk of developing LATE. Understanding these genetic links provides crucial insights into disease mechanisms and the potential for targeted therapies.
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Affiliation(s)
- Genaro Gabriel Ortiz
- Department of Philosophical and Methodological Disciplines, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Jalisco, Mexico;
- Postgraduate Gerontology Program, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Javier Ramírez-Jirano
- Neurosciences Division, Western Biomedical Research Center, Mexican Social Security Institute, IMSS, Guadalajara 44340, Jalisco, Mexico;
| | - Raul L. Arizaga
- Public Health Department, School of Medicine, University of Buenos Aires, Buenos Aires C1121ABG, Argentina;
| | - Daniela L. C. Delgado-Lara
- Department of Philosophical and Methodological Disciplines, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Jalisco, Mexico;
- Departamento Académico de Formación Universitaria, Ciencias de la Salud, Universidad Autónoma de Guadalajara, Zapopan 45129, Jalisco, Mexico
| | - Erandis D. Torres-Sánchez
- Department of Medical and Life Sciences, University Center of la Cienega, University of Guadalajara, Ocotlan 47820, Jalisco, Mexico
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Piol D, Robberechts T, Da Cruz S. Lost in local translation: TDP-43 and FUS in axonal/neuromuscular junction maintenance and dysregulation in amyotrophic lateral sclerosis. Neuron 2023; 111:1355-1380. [PMID: 36963381 DOI: 10.1016/j.neuron.2023.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/21/2022] [Accepted: 02/16/2023] [Indexed: 03/26/2023]
Abstract
Key early features of amyotrophic lateral sclerosis (ALS) are denervation of neuromuscular junctions and axonal degeneration. Motor neuron homeostasis relies on local translation through controlled regulation of axonal mRNA localization, transport, and stability. Yet the composition of the local transcriptome, translatome (mRNAs locally translated), and proteome during health and disease remains largely unexplored. This review covers recent discoveries on axonal translation as a critical mechanism for neuronal maintenance/survival. We focus on two RNA binding proteins, transactive response DNA binding protein-43 (TDP-43) and fused in sarcoma (FUS), whose mutations cause ALS and frontotemporal dementia (FTD). Emerging evidence points to their essential role in the maintenance of axons and synapses, including mRNA localization, transport, and local translation, and whose dysfunction may contribute to ALS. Finally, we describe recent advances in omics-based approaches mapping compartment-specific local RNA and protein compositions, which will be invaluable to elucidate fundamental local processes and identify key targets for therapy development.
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Affiliation(s)
- Diana Piol
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Tessa Robberechts
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Sandrine Da Cruz
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium.
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McGoldrick P, Lau A, You Z, Durcan TM, Robertson J. Loss of C9orf72 perturbs the Ran-GTPase gradient and nucleocytoplasmic transport, generating compositionally diverse Importin β-1 granules. Cell Rep 2023; 42:112134. [PMID: 36821445 DOI: 10.1016/j.celrep.2023.112134] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/05/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
A hexanucleotide (GGGGCC)n repeat expansion in C9orf72 causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), eliciting toxic effects through generation of RNA foci, dipeptide repeat proteins, and/or loss of C9orf72 protein. Defects in nucleocytoplasmic transport (NCT) have been implicated as a pathogenic mechanism underlying repeat expansion toxicity. Here, we show that loss of C9orf72 disrupts the Ran-GTPase gradient and NCT in vitro and in vivo. NCT disruption in vivo is enhanced by the presence of compositionally different types of cytoplasmic Importin β-1 granule that exhibit neuronal subtype-specific properties. We show that the abundance of Importin β-1 granules is increased in the context of C9orf72 deficiency, disrupting interactions with nuclear pore complex proteins. These granules appear to associate with the nuclear envelope and are co-immunoreactive for G3BP1 and K63-ubiquitin. These findings link loss of C9orf72 protein to gain-of-function mechanisms and defects in NCT.
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Affiliation(s)
- Philip McGoldrick
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada.
| | - Agnes Lau
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Zhipeng You
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada
| | - Thomas M Durcan
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada; Department of Laboratory Medicine and Pathobiology, 27 King's College Circle, Toronto, ON M5S 1A1, Canada.
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de Luna N, Carbayo Á, Dols-Icardo O, Turon-Sans J, Reyes-Leiva D, Illan-Gala I, Jericó I, Pagola-Lorz I, Lleixà C, Querol L, Rubio-Guerra S, Alcolea D, Fortea J, Lleó A, Cortés-Vicente E, Rojas-Garcia R. Neuroinflammation-Related Proteins NOD2 and Spp1 Are Abnormally Upregulated in Amyotrophic Lateral Sclerosis. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2022; 10:10/2/e200072. [PMID: 36460480 PMCID: PMC9720732 DOI: 10.1212/nxi.0000000000200072] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/13/2022] [Indexed: 12/04/2022]
Abstract
BACKGROUND AND OBJECTIVES Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of unknown etiology and poorly understood pathophysiology. There is no specific biomarker either for diagnosis or prognosis. The aim of our study was to investigate differentially expressed proteins in the CSF and serum from patients with ALS to determine their role in the disease process and evaluate their utility as diagnostic or prognostic biomarkers. METHODS We performed mass spectrometry in the CSF from 3 patients with ALS and 3 healthy controls (HCs). The results were compared with motor cortex dysregulated transcripts obtained from 11patients with sporadic ALS and 8 HCs. Candidate proteins were tested using ELISA in the serum of 123 patients with ALS, 30 patients with Alzheimer disease (AD), 28 patients with frontotemporal dementia (FTD), and 102 HCs. Patients with ALS, AD, and FTD were prospectively recruited from January 2003 to December 2020. A group of age-matched HCs was randomly selected from the Sant Pau Initiative on Neurodegeneration cohort of the Sant Pau Memory Unit. RESULTS Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) and osteopontin (Spp1) were differentially expressed in the CSF and the motor cortex transcriptome of patients with ALS compared with that in HCs (p < 0.05). NOD2 and Spp1 levels were significantly higher in sera from patients with ALS than in HCs (p < 0.001). Receiver operating characteristic analysis showed an area under the curve of 0.63 for NOD2 and 0.81 for Spp1. NOD2 levels were significantly lower in patients with AD and FTD than in patients with ALS (p < 0.0001), but we found no significant differences in Spp1 levels between patients with ALS, AD (p = 0.51), and FTD (p = 0.42). We found a negative correlation between Spp1 levels and ALS functional rating scale (r = -0.24, p = 0.009). DISCUSSION Our discovery-based approach identified NOD2 as a novel biomarker in ALS and adds evidence to the contribution of Spp1 in the disease process. Both proteins are involved in innate immunity and autophagy and are increased in the serum from patients with ALS. Our data support a relevant role of neuroinflammation in the pathophysiology of the disease and may identify targets for disease-modifying treatments in ALS. Further longitudinal studies should investigate the diagnostic and prognostic value of NOD2 and Spp1 in clinical practice.
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Affiliation(s)
- Noemí de Luna
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Álvaro Carbayo
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Oriol Dols-Icardo
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Janina Turon-Sans
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - David Reyes-Leiva
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Ignacio Illan-Gala
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Ivonne Jericó
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Inma Pagola-Lorz
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Cinta Lleixà
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Luis Querol
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Sara Rubio-Guerra
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Daniel Alcolea
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Juan Fortea
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Alberto Lleó
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Elena Cortés-Vicente
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.)
| | - Ricardo Rojas-Garcia
- From the Neuromuscular Diseases Laboratory (N.d.C., A.C., D.R.-L., C.L., L.Q., E.C.-V., R.R.-G.), Institut de Recerca Hospital de la Santa Creu i Sant Pau (IIB Sant-Pau), Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (N.d.C., A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Madrid; Motor Neuron Diseases Clinic (A.C., J.T.-S., D.R.-L., L.Q., E.C.-V., R.R.-G.), Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Departament de Medicina, Universitat Autònoma de Barcelona; Sant Pau Memory Unit (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (O.D.-I., I.I.-G., S.R.-G., D.A., J.F., A.L.), Madrid, Spain; and Neuromuscular and Motor Neuron Diseases Research Group-Health Research Institute of Navarra (IdisNA) (I.J., I.P.-L.).
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8
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Sušjan-Leite P, Ramuta TŽ, Boršić E, Orehek S, Hafner-Bratkovič I. Supramolecular organizing centers at the interface of inflammation and neurodegeneration. Front Immunol 2022; 13:940969. [PMID: 35979366 PMCID: PMC9377691 DOI: 10.3389/fimmu.2022.940969] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
The pathogenesis of neurodegenerative diseases involves the accumulation of misfolded protein aggregates. These deposits are both directly toxic to neurons, invoking loss of cell connectivity and cell death, and recognized by innate sensors that upon activation release neurotoxic cytokines, chemokines, and various reactive species. This neuroinflammation is propagated through signaling cascades where activated sensors/receptors, adaptors, and effectors associate into multiprotein complexes known as supramolecular organizing centers (SMOCs). This review provides a comprehensive overview of the SMOCs, involved in neuroinflammation and neurotoxicity, such as myddosomes, inflammasomes, and necrosomes, their assembly, and evidence for their involvement in common neurodegenerative diseases. We discuss the multifaceted role of neuroinflammation in the progression of neurodegeneration. Recent progress in the understanding of particular SMOC participation in common neurodegenerative diseases such as Alzheimer's disease offers novel therapeutic strategies for currently absent disease-modifying treatments.
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Affiliation(s)
- Petra Sušjan-Leite
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Taja Železnik Ramuta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Elvira Boršić
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Sara Orehek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Iva Hafner-Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
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9
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Bjork RT, Mortimore NP, Loganathan S, Zarnescu DC. Dysregulation of Translation in TDP-43 Proteinopathies: Deficits in the RNA Supply Chain and Local Protein Production. Front Neurosci 2022; 16:840357. [PMID: 35321094 PMCID: PMC8935057 DOI: 10.3389/fnins.2022.840357] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/09/2022] [Indexed: 12/19/2022] Open
Abstract
Local control of gene expression provides critical mechanisms for regulating development, maintenance and plasticity in the nervous system. Among the strategies known to govern gene expression locally, mRNA transport and translation have emerged as essential for a neuron’s ability to navigate developmental cues, and to establish, strengthen and remove synaptic connections throughout lifespan. Substantiating the role of RNA processing in the nervous system, several RNA binding proteins have been implicated in both developmental and age dependent neurodegenerative disorders. Of these, TDP-43 is an RNA binding protein that has emerged as a common denominator in amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD) and related disorders due to the identification of causative mutations altering its function and its accumulation in cytoplasmic aggregates observed in a significant fraction of ALS/FTD cases, regardless of etiology. TDP-43 is involved in multiple aspects of RNA processing including splicing, transport and translation. Given that one of the early events in disease pathogenesis is mislocalization from the nucleus to the cytoplasm, several studies have focused on elucidating the pathogenic role of TDP-43 in cytoplasmic translation. Here we review recent findings describing TDP-43 translational targets and potential mechanisms of translation dysregulation in TDP-43 proteinopathies across multiple experimental models including cultured cells, flies, mice and patient derived neurons.
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Affiliation(s)
- Reed T. Bjork
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, United States
- Neuroscience Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, United States
| | - Nicholas P. Mortimore
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, United States
| | | | - Daniela C. Zarnescu
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, United States
- *Correspondence: Daniela C. Zarnescu,
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10
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Castelli LM, Benson BC, Huang WP, Lin YH, Hautbergue GM. RNA Helicases in Microsatellite Repeat Expansion Disorders and Neurodegeneration. Front Genet 2022; 13:886563. [PMID: 35646086 PMCID: PMC9133428 DOI: 10.3389/fgene.2022.886563] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
Short repeated sequences of 3-6 nucleotides are causing a growing number of over 50 microsatellite expansion disorders, which mainly present with neurodegenerative features. Although considered rare diseases in relation to the relatively low number of cases, these primarily adult-onset conditions, often debilitating and fatal in absence of a cure, collectively pose a large burden on healthcare systems in an ageing world population. The pathological mechanisms driving disease onset are complex implicating several non-exclusive mechanisms of neuronal injury linked to RNA and protein toxic gain- and loss- of functions. Adding to the complexity of pathogenesis, microsatellite repeat expansions are polymorphic and found in coding as well as in non-coding regions of genes. They form secondary and tertiary structures involving G-quadruplexes and atypical helices in repeated GC-rich sequences. Unwinding of these structures by RNA helicases plays multiple roles in the expression of genes including repeat-associated non-AUG (RAN) translation of polymeric-repeat proteins with aggregating and cytotoxic properties. Here, we will briefly review the pathogenic mechanisms mediated by microsatellite repeat expansions prior to focus on the RNA helicases eIF4A, DDX3X and DHX36 which act as modifiers of RAN translation in C9ORF72-linked amyotrophic lateral sclerosis/frontotemporal dementia (C9ORF72-ALS/FTD) and Fragile X-associated tremor/ataxia syndrome (FXTAS). We will further review the RNA helicases DDX5/17, DHX9, Dicer and UPF1 which play additional roles in the dysregulation of RNA metabolism in repeat expansion disorders. In addition, we will contrast these with the roles of other RNA helicases such as DDX19/20, senataxin and others which have been associated with neurodegeneration independently of microsatellite repeat expansions. Finally, we will discuss the challenges and potential opportunities that are associated with the targeting of RNA helicases for the development of future therapeutic approaches.
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Affiliation(s)
- Lydia M Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Bridget C Benson
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Wan-Ping Huang
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom.,Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom.,Healthy Lifespan Institute (HELSI), University of Sheffield, Sheffield, United Kingdom
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11
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Cozzolino F, Iacobucci I, Monaco V, Monti M. Protein-DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era. J Proteome Res 2021; 20:3018-3030. [PMID: 33961438 PMCID: PMC8280749 DOI: 10.1021/acs.jproteome.1c00074] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
The fields of application
of functional proteomics are not limited
to the study of protein–protein interactions; they also extend
to those involving protein complexes that bind DNA or RNA. These interactions
affect fundamental processes such as replication, transcription, and
repair in the case of DNA, as well as transport, translation, splicing,
and silencing in the case of RNA. Analytical or preparative experimental
approaches, both in vivo and in vitro, have been developed to isolate and identify DNA/RNA binding proteins
by exploiting the advantage of the affinity shown by these proteins
toward a specific oligonucleotide sequence. The present review proposes
an overview of the approaches most commonly employed in proteomics
applications for the identification of nucleic acid-binding proteins,
such as affinity purification (AP) protocols, EMSA, chromatin purification
methods, and CRISPR-based chromatin affinity purification, which are
generally associated with mass spectrometry methodologies for the
unbiased protein identification.
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Affiliation(s)
- Flora Cozzolino
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy.,CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Ilaria Iacobucci
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy.,CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vittoria Monaco
- CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.,Interuniversity Consortium National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro, 305-00136 Rome, Italy
| | - Maria Monti
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy.,CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
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12
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Arzalluz-Luque Á, Cabrera JL, Skottman H, Benguria A, Bolinches-Amorós A, Cuenca N, Lupo V, Dopazo A, Tarazona S, Delás B, Carballo M, Pascual B, Hernan I, Erceg S, Lukovic D. Mutant PRPF8 Causes Widespread Splicing Changes in Spliceosome Components in Retinitis Pigmentosa Patient iPSC-Derived RPE Cells. Front Neurosci 2021; 15:636969. [PMID: 33994920 PMCID: PMC8116631 DOI: 10.3389/fnins.2021.636969] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/25/2021] [Indexed: 11/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is a rare, progressive disease that affects photoreceptors and retinal pigment epithelial (RPE) cells with blindness as a final outcome. Despite high medical and social impact, there is currently no therapeutic options to slow down the progression of or cure the disease. The development of effective therapies was largely hindered by high genetic heterogeneity, inaccessible disease tissue, and unfaithful model organisms. The fact that components of ubiquitously expressed splicing factors lead to the retina-specific disease is an additional intriguing question. Herein, we sought to correlate the retinal cell-type-specific disease phenotype with the splicing profile shown by a patient with autosomal recessive RP, caused by a mutation in pre-mRNA splicing factor 8 (PRPF8). In order to get insight into the role of PRPF8 in homeostasis and disease, we capitalize on the ability to generate patient-specific RPE cells and reveal differentially expressed genes unique to RPE cells. We found that spliceosomal complex and ribosomal functions are crucial in determining cell-type specificity through differential expression and alternative splicing (AS) and that PRPF8 mutation causes global changes in splice site selection and exon inclusion that particularly affect genes involved in these cellular functions. This finding corroborates the hypothesis that retinal tissue identity is conferred by a specific splicing program and identifies retinal AS events as a framework toward the design of novel therapeutic opportunities.
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Affiliation(s)
- Ángeles Arzalluz-Luque
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, València, Spain
| | - Jose Luis Cabrera
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC). Madrid, Spain
| | - Heli Skottman
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alberto Benguria
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC). Madrid, Spain
| | - Arantxa Bolinches-Amorós
- Stem Cells Therapies in Neurodegenerative Diseases Lab, Research Center Principe Felipe, Valencia, Spain
- National Stem Cell Bank-Valencia Node, Research Center Principe Felipe, Valencia, Spain
| | - Nicolás Cuenca
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Vincenzo Lupo
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
- Rare Diseases Joint Units, IIS La Fe-CIPF, Valencia, Spain
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC). Madrid, Spain
| | - Sonia Tarazona
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, València, Spain
| | - Bárbara Delás
- Unitat de Genética Molecular, Hospital de Terrassa, Terrassa, Spain
| | - Miguel Carballo
- Unitat de Genética Molecular, Hospital de Terrassa, Terrassa, Spain
| | - Beatriz Pascual
- Unitat de Genética Molecular, Hospital de Terrassa, Terrassa, Spain
| | - Imma Hernan
- Unitat de Genética Molecular, Hospital de Terrassa, Terrassa, Spain
| | - Slaven Erceg
- Stem Cells Therapies in Neurodegenerative Diseases Lab, Research Center Principe Felipe, Valencia, Spain
- National Stem Cell Bank-Valencia Node, Research Center Principe Felipe, Valencia, Spain
- Rare Diseases Joint Units, IIS La Fe-CIPF, Valencia, Spain
- Department of Neuroregeneration, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
| | - Dunja Lukovic
- Rare Diseases Joint Units, IIS La Fe-CIPF, Valencia, Spain
- Retinal Degeneration Lab, Research Centre Principe Felipe, Valencia, Spain
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13
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Lehmkuhl EM, Loganathan S, Alsop E, Blythe AD, Kovalik T, Mortimore NP, Barrameda D, Kueth C, Eck RJ, Siddegowda BB, Joardar A, Ball H, Macias ME, Bowser R, Van Keuren-Jensen K, Zarnescu DC. TDP-43 proteinopathy alters the ribosome association of multiple mRNAs including the glypican Dally-like protein (Dlp)/GPC6. Acta Neuropathol Commun 2021; 9:52. [PMID: 33762006 PMCID: PMC7992842 DOI: 10.1186/s40478-021-01148-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/06/2021] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a genetically heterogeneous neurodegenerative disease in which 97% of patients exhibit cytoplasmic aggregates containing the RNA binding protein TDP-43. Using tagged ribosome affinity purifications in Drosophila models of TDP-43 proteinopathy, we identified TDP-43 dependent translational alterations in motor neurons impacting the spliceosome, pentose phosphate and oxidative phosphorylation pathways. A subset of the mRNAs with altered ribosome association are also enriched in TDP-43 complexes suggesting that they may be direct targets. Among these, dlp mRNA, which encodes the glypican Dally like protein (Dlp)/GPC6, a wingless (Wg/Wnt) signaling regulator is insolubilized both in flies and patient tissues with TDP-43 pathology. While Dlp/GPC6 forms puncta in the Drosophila neuropil and ALS spinal cords, it is reduced at the neuromuscular synapse in flies suggesting compartment specific effects of TDP-43 proteinopathy. These findings together with genetic interaction data show that Dlp/GPC6 is a novel, physiologically relevant target of TDP-43 proteinopathy.
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Affiliation(s)
- Erik M. Lehmkuhl
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Suvithanandhini Loganathan
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Eric Alsop
- Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ 85004 USA
| | - Alexander D. Blythe
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Tina Kovalik
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Rd, Phoenix, AZ 85013 USA
| | - Nicholas P. Mortimore
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Dianne Barrameda
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Chuol Kueth
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Randall J. Eck
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Bhavani B. Siddegowda
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Archi Joardar
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Hannah Ball
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Maria E. Macias
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
| | - Robert Bowser
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Rd, Phoenix, AZ 85013 USA
| | | | - Daniela C. Zarnescu
- Department of Cellular and Molecular Biology, University of Arizona, 1007 E. Lowell St, LSS RM 548A, Tucson, AZ 85721 USA
- Department of Neuroscience, University of Arizona, 1040 4th St, Tucson, AZ 85721 USA
- Department of Neurology, University of Arizona, 1501 N Campbell Ave, Tucson, AZ 85724 USA
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14
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Buratti E. Trends in Understanding the Pathological Roles of TDP-43 and FUS Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1281:243-267. [PMID: 33433879 DOI: 10.1007/978-3-030-51140-1_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Following the discovery of TDP-43 and FUS involvement in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD), the major challenge in the field has been to understand their physiological functions, both in normal and disease conditions. The hope is that this knowledge will improve our understanding of disease and lead to the development of effective therapeutic options. Initially, the focus has been directed at characterizing the role of these proteins in the control of RNA metabolism, because the main function of TDP-43 and FUS is to bind coding and noncoding RNAs to regulate their life cycle within cells. As a result, we now have an in-depth picture of the alterations that occur in RNA metabolism following their aggregation in various ALS/FTLD models and, to a somewhat lesser extent, in patients' brains. In parallel, progress has been made with regard to understanding how aggregation of these proteins occurs in neurons, how it can spread in different brain regions, and how these changes affect various metabolic cellular pathways to result in neuronal death. The aim of this chapter will be to provide a general overview of the trending topics in TDP-43 and FUS investigations and to highlight what might represent the most promising avenues of research in the years to come.
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Affiliation(s)
- Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.
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15
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Mesquida-Veny F, Del Río JA, Hervera A. Macrophagic and microglial complexity after neuronal injury. Prog Neurobiol 2020; 200:101970. [PMID: 33358752 DOI: 10.1016/j.pneurobio.2020.101970] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/12/2020] [Accepted: 12/06/2020] [Indexed: 12/14/2022]
Abstract
Central nervous system (CNS) injuries do not heal properly in contrast to normal tissue repair, in which functional recovery typically occurs. The reason for this dichotomy in wound repair is explained in part by macrophage and microglial malfunction, affecting both the extrinsic and intrinsic barriers to appropriate axonal regeneration. In normal healing tissue, macrophages promote the repair of injured tissue by regulating transitions through different phases of the healing response. In contrast, inflammation dominates the outcome of CNS injury, often leading to secondary damage. Therefore, an understanding of the molecular mechanisms underlying this dichotomy is critical to advance in neuronal repair therapies. Recent studies highlight the plasticity and complexity of macrophages and microglia beyond the classical view of the M1/M2 polarization paradigm. This plasticity represents an in vivo continuous spectrum of phenotypes with overlapping functions and markers. Moreover, macrophage and microglial plasticity affect many events essential for neuronal regeneration after injury, such as myelin and cell debris clearance, inflammation, release of cytokines, and trophic factors, affecting both intrinsic neuronal properties and extracellular matrix deposition. Until recently, this complexity was overlooked in the translation of therapies modulating these responses for the treatment of neuronal injuries. However, recent studies have shed important light on the underlying molecular mechanisms of this complexity and its transitions and effects on regenerative events. Here we review the complexity of macrophages and microglia after neuronal injury and their roles in regeneration, as well as the underlying molecular mechanisms, and we discuss current challenges and future opportunities for treatment.
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Affiliation(s)
- Francina Mesquida-Veny
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; Department of Cell Biology, Physiology and Immunology, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain; Institute of Neuroscience, University of Barcelona, 08028 Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - José Antonio Del Río
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; Department of Cell Biology, Physiology and Immunology, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain; Institute of Neuroscience, University of Barcelona, 08028 Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Arnau Hervera
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; Department of Cell Biology, Physiology and Immunology, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain; Institute of Neuroscience, University of Barcelona, 08028 Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain.
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16
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Marques RF, Engler JB, Küchler K, Jones RA, Lingner T, Salinas G, Gillingwater TH, Friese MA, Duncan KE. Motor neuron translatome reveals deregulation of SYNGR4 and PLEKHB1 in mutant TDP-43 amyotrophic lateral sclerosis models. Hum Mol Genet 2020; 29:2647-2661. [PMID: 32686835 PMCID: PMC7530531 DOI: 10.1093/hmg/ddaa140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/18/2020] [Accepted: 06/30/2020] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable neurological disease with progressive loss of motor neuron (MN) function in the brain and spinal cord. Mutations in TARDBP, encoding the RNA-binding protein TDP-43, are one cause of ALS, and TDP-43 mislocalization in MNs is a key pathological feature of >95% of ALS cases. While numerous studies support altered RNA regulation by TDP-43 as a major cause of disease, specific changes within MNs that trigger disease onset remain unclear. Here, we combined translating ribosome affinity purification (TRAP) with RNA sequencing to identify molecular changes in spinal MNs of TDP-43-driven ALS at motor symptom onset. By comparing the MN translatome of hTDP-43A315T mice to littermate controls and to mice expressing wild type hTDP-43, we identified hundreds of mRNAs that were selectively up- or downregulated in MNs. We validated the deregulated candidates Tex26, Syngr4, and Plekhb1 mRNAs in an independent TRAP experiment. Moreover, by quantitative immunostaining of spinal cord MNs, we found corresponding protein level changes for SYNGR4 and PLEKHB1. We also observed these changes in spinal MNs of an independent ALS mouse model caused by a different patient mutant allele of TDP-43, suggesting that they are general features of TDP-43-driven ALS. Thus, we identified SYNGR4 and PLEKHB1 to be deregulated in MNs at motor symptom onset in TDP-43-driven ALS models. This spatial and temporal pattern suggests that these proteins could be functionally important for driving the transition to the symptomatic phase of the disease.
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Affiliation(s)
- Rita F Marques
- Neuronal Translational Control Research Group, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Jan B Engler
- Institute of Neuroimmunology and Multiple Sclerosis, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Katrin Küchler
- Neuronal Translational Control Research Group, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Ross A Jones
- Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom
| | - Thomas Lingner
- NGS—Integrative Genomics Core Unit (NIG), Institute of Human Genetics, University Medical Center Göttingen, Göttingen 37077, Germany
| | - Gabriela Salinas
- NGS—Integrative Genomics Core Unit (NIG), Institute of Human Genetics, University Medical Center Göttingen, Göttingen 37077, Germany
| | - Thomas H Gillingwater
- Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom
| | - Manuel A Friese
- Institute of Neuroimmunology and Multiple Sclerosis, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Kent E Duncan
- Neuronal Translational Control Research Group, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
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17
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Wei M, Ge H, Shao C, Yan X, Nie H, Duan H, Liao X, Zhang M, Chen Y, Zhang D, Dong Z. Chromosome-Level Clam Genome Helps Elucidate the Molecular Basis of Adaptation to a Buried Lifestyle. iScience 2020; 23:101148. [PMID: 32454450 PMCID: PMC7251785 DOI: 10.1016/j.isci.2020.101148] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/10/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Bivalve mollusks are economically important invertebrates that exhibit marked diversity in benthic lifestyle and provide valuable resources for understanding the molecular basis of adaptation to benthic life. In this report, we present a high-quality, chromosome-anchored reference genome of the Venus clam, Cyclina sinensis. The chromosome-level genome was assembled by Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, 10× Genomics, and high-throughput chromosome conformation capture technologies. The final genome assembly of C. sinensis is 903.2 Mb in size, with a contig N50 size of 2.6 Mb and a scaffold N50 size of 46.5 Mb. Enrichment analyses of significantly expanded and positively selected genes suggested evolutionary adaptation of this clam to buried life. In addition, a change in shell color represents another mechanism of adaptation to burial in sediment. The high-quality genome generated in this work provides a valuable resource for investigating the molecular mechanisms of adaptation to buried lifestyle. A chromosome-level assembly for clam genome is provided The evolutionary order of bivalve adductor muscle is from double to single The work suggests evolutionary adaptations to a buried lifestyle Change of shell color represents another mechanism of adaptation to burial in sediment
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Affiliation(s)
- Min Wei
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Hongxing Ge
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Changwei Shao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiwu Yan
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Haibao Duan
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xiaoting Liao
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Min Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yihua Chen
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Dongdong Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Zhiguo Dong
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
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18
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Ciechanowska A, Popiolek-Barczyk K, Pawlik K, Ciapała K, Oggioni M, Mercurio D, De Simoni MG, Mika J. Changes in macrophage inflammatory protein-1 (MIP-1) family members expression induced by traumatic brain injury in mice. Immunobiology 2020; 225:151911. [PMID: 32059938 DOI: 10.1016/j.imbio.2020.151911] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/15/2020] [Accepted: 01/31/2020] [Indexed: 12/14/2022]
Abstract
A deep knowledge of the profound immunological response induced by traumatic brain injury (TBI) raises the possibility of novel therapeutic interventions. Existing studies have highlighted the important roles of C-C motif ligands in the development of neuroinflammation after brain injury; however, the participation of macrophage inflammatory protein-1 (MIP-1) family members in this phenomenon is still undefined. Therefore, the goal of our study was to evaluate changes in macrophage inflammatory protein-1 (MIP-1) family members (CCL3, CCL4, and CCL9) and their receptors (CCR1 and CCR5) in a mouse model of TBI (induced by controlled cortical impact (CCI)). We also investigated the pattern of activation of immunological cells (such as neutrophils, microglia and astroglia), which on one hand express CCR1/CCR5, and on the other hand might be a source of the tested chemokines in the injured brain. We investigated changes in mRNA (RT-qPCR) and/or protein (ELISA and Western blot) expression in brain structures (the cortex, hippocampus, thalamus, and striatum) at different time points (24 h, 4 days, 7 days, 2 weeks, and/or 5 weeks) after trauma. Our time-course studies revealed the upregulation of the mRNA expression of all members of the MIP-1 family (CCL3, CCL4, and CCL9) in all tested brain structures, mainly in the early stages after injury. A similar pattern of activation was observed at the protein level in the cortex and thalamus, where the strongest activation was observed 1 day after CCI; however, we did not observe any change in CCL3 in the thalamus. Analyses of CCR1 and CCR5 demonstrated the upregulation of the mRNA expression of both receptors in all tested cerebral structures, mainly in the early phases post injury (24 h, 4 days and 7 days). Protein analysis showed the upregulation of CCR1 and CCR5 in the thalamus 24 h after TBI, but we did not detect any change in the cortex. We also observed the upregulation of neutrophil marker (MPO) at the early time points (24 h and 7 days) in the cortex, while the profound activation of microglia (IBA-1) and astroglia (GFAP) was observed mainly on day 7. Our findings highlight for the first time that CCL3, CCL4, CCL9 and their receptors offer promising targets for influencing secondary neuronal injury and improving TBI therapy. The results suggest that the MIP-1 family is an important target for pharmacological intervention for brain injury.
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Affiliation(s)
- Agata Ciechanowska
- Department of Pain Pharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Katarzyna Popiolek-Barczyk
- Department of Pain Pharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Katarzyna Pawlik
- Department of Pain Pharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Katarzyna Ciapała
- Department of Pain Pharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Marco Oggioni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Neuroscience, Milan, Italy
| | - Domenico Mercurio
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Neuroscience, Milan, Italy
| | - Maria-Grazia De Simoni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Neuroscience, Milan, Italy
| | - Joanna Mika
- Department of Pain Pharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland.
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19
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Beesley J, Sivakumaran H, Moradi Marjaneh M, Lima LG, Hillman KM, Kaufmann S, Tuano N, Hussein N, Ham S, Mukhopadhyay P, Kazakoff S, Lee JS, Michailidou K, Barnes DR, Antoniou AC, Fachal L, Dunning AM, Easton DF, Waddell N, Rosenbluh J, Möller A, Chenevix-Trench G, French JD, Edwards SL. Chromatin interactome mapping at 139 independent breast cancer risk signals. Genome Biol 2020; 21:8. [PMID: 31910858 PMCID: PMC6947858 DOI: 10.1186/s13059-019-1877-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 11/01/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified 196 high confidence independent signals associated with breast cancer susceptibility. Variants within these signals frequently fall in distal regulatory DNA elements that control gene expression. RESULTS We designed a Capture Hi-C array to enrich for chromatin interactions between the credible causal variants and target genes in six human mammary epithelial and breast cancer cell lines. We show that interacting regions are enriched for open chromatin, histone marks for active enhancers, and transcription factors relevant to breast biology. We exploit this comprehensive resource to identify candidate target genes at 139 independent breast cancer risk signals and explore the functional mechanism underlying altered risk at the 12q24 risk region. CONCLUSIONS Our results demonstrate the power of combining genetics, computational genomics, and molecular studies to rationalize the identification of key variants and candidate target genes at breast cancer GWAS signals.
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Affiliation(s)
- Jonathan Beesley
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Haran Sivakumaran
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Mahdi Moradi Marjaneh
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Current address: UK Dementia Research Institute, Imperial College London, London, UK
| | - Luize G Lima
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kristine M Hillman
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Susanne Kaufmann
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Natasha Tuano
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Nehal Hussein
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Sunyoung Ham
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Pamela Mukhopadhyay
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Stephen Kazakoff
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jason S Lee
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Daniel R Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Nicola Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Joseph Rosenbluh
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Andreas Möller
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Juliet D French
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
| | - Stacey L Edwards
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
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20
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Goldstein O, Kedmi M, Gana-Weisz M, Twito S, Nefussy B, Vainer B, Fainmesser Y, Abraham A, Nayshool O, Orr-Urtreger A, Drory VE. Rare homozygosity in amyotrophic lateral sclerosis suggests the contribution of recessive variants to disease genetics. J Neurol Sci 2019; 402:62-68. [DOI: 10.1016/j.jns.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/02/2019] [Accepted: 05/07/2019] [Indexed: 02/06/2023]
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21
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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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22
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Ran XQ, Pan H, Huang SH, Liu C, Niu X, Li S, Wang JF. Copy number variations of MTHFSD gene across pig breeds and its association with litter size traits in Chinese indigenous Xiang pig. J Anim Physiol Anim Nutr (Berl) 2018; 102:1320-1327. [PMID: 29797367 DOI: 10.1111/jpn.12922] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/15/2018] [Accepted: 04/15/2018] [Indexed: 12/14/2022]
Abstract
Copy number variation (CNV) is a major proportion of genetic variation, which changes the gene structure and dosage and affects gene expression and function. To validate the presence and the function of CNV in pig, we used real-time quantitative polymerase chain reaction (qPCR) method to validate a 496 kb CNV region comprising MTHFSD gene on chromosome 6 of Xiang pig detected by single nucleotide polymorphism (SNP) array. Then we investigated the distribution of the MTHFSD CNV in a total of 545 pigs in four breeds. About 46.2% and 32.7% individuals in the four pig breeds were detected to be types of loss and gain of MTHFSD locus. The relative copy numbers of MTHFSD gene showed the largest variation range (0-55 copies) in the Xiang pig population. The copy numbers of MTHFSD gene presented the positive correlations with the transcript level of MTHFSD gene in adult ovaries. Statistical analysis indicated that CNVs of MTHFSD gene was significantly changed the litter size traits of Xiang pigs, and the individuals with CNV gain showed more litter size than the CNV loss pigs. We have reasons to believe that the MTHFSD as RNA-binding protein play an important role in pig reproduction as a result of regulating MTHFS mRNA metabolism.
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Affiliation(s)
- Xue-Qin Ran
- College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Hua Pan
- College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Shi-Hui Huang
- College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Chang Liu
- College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Xi Niu
- College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Sheng Li
- College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Jia-Fu Wang
- College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Tongren University, Tongren, China
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23
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Handley EE, Pitman KA, Dawkins E, Young KM, Clark RM, Jiang TC, Turner BJ, Dickson TC, Blizzard CA. Synapse Dysfunction of Layer V Pyramidal Neurons Precedes Neurodegeneration in a Mouse Model of TDP-43 Proteinopathies. Cereb Cortex 2018; 27:3630-3647. [PMID: 27496536 DOI: 10.1093/cercor/bhw185] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
TDP-43 is a major protein component of pathological neuronal inclusions that are present in frontotemporal dementia and amyotrophic lateral sclerosis. We report that TDP-43 plays an important role in dendritic spine formation in the cortex. The density of spines on YFP+ pyramidal neurons in both the motor and somatosensory cortex of Thy1-YFP mice, increased significantly from postnatal day 30 (P30), to peak at P60, before being pruned by P90. By comparison, dendritic spine density was significantly reduced in the motor cortex of Thy1-YFP::TDP-43A315T transgenic mice prior to symptom onset (P60), and in the motor and somatosensory cortex at symptom onset (P90). Morphological spine-type analysis revealed that there was a significant impairment in the development of basal mushroom spines in the motor cortex of Thy1-YFP::TDP-43A315T mice compared to Thy1-YFP control. Furthermore, reductions in spine density corresponded to mislocalisation of TDP-43 immunoreactivity and lowered efficacy of synaptic transmission as determined by electrophysiology at P60. We conclude that mutated TDP-43 has a significant pathological effect at the dendritic spine that is associated with attenuated neural transmission.
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Affiliation(s)
- Emily E Handley
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Kimberley A Pitman
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Edgar Dawkins
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Kaylene M Young
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Rosemary M Clark
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Tongcui C Jiang
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Bradley J Turner
- Florey Institute for Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Tracey C Dickson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Catherine A Blizzard
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
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24
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Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes. G3-GENES GENOMES GENETICS 2018; 8:859-873. [PMID: 29378821 PMCID: PMC5844307 DOI: 10.1534/g3.117.300508] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Domesticated species exhibit a suite of behavioral, endocrinological, and morphological changes referred to as "domestication syndrome." These changes may include a reduction in reactivity of the hypothalamic-pituitary-adrenal (HPA) axis and specifically reduced adrenocorticotropic hormone release from the anterior pituitary. To investigate the biological mechanisms targeted during domestication, we investigated gene expression in the pituitaries of experimentally domesticated foxes (Vulpes vulpes). RNA was sequenced from the anterior pituitary of six foxes selectively bred for tameness ("tame foxes") and six foxes selectively bred for aggression ("aggressive foxes"). Expression, splicing, and network differences identified between the two lines indicated the importance of genes related to regulation of exocytosis, specifically mediated by cAMP, organization of pseudopodia, and cell motility. These findings provide new insights into biological mechanisms that may have been targeted when these lines of foxes were selected for behavior and suggest new directions for research into HPA axis regulation and the biological underpinnings of domestication.
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25
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Gao J, Wang L, Huntley ML, Perry G, Wang X. Pathomechanisms of TDP-43 in neurodegeneration. J Neurochem 2018; 146:10.1111/jnc.14327. [PMID: 29486049 PMCID: PMC6110993 DOI: 10.1111/jnc.14327] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/08/2018] [Accepted: 02/20/2018] [Indexed: 12/11/2022]
Abstract
Neurodegeneration, a term that refers to the progressive loss of structure and function of neurons, is a feature of many neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD), Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). There is no cure or treatment available that can prevent or reverse neurodegenerative conditions. The causes of neurodegeneration in these diseases remain largely unknown; yet, an extremely small proportion of these devastating diseases are associated with genetic mutations in proteins involved in a wide range of cellular pathways and processes. Over the past decade, it has become increasingly clear that the most notable neurodegenerative diseases, such as ALS, FTLD, and AD, share a common prominent pathological feature known as TAR DNA-binding protein 43 (TDP-43) proteinopathy, which is usually characterized by the presence of aberrant phosphorylation, ubiquitination, cleavage and/or nuclear depletion of TDP-43 in neurons and glial cells. The role of TDP-43 as a neurotoxicity trigger has been well documented in different in vitro and in vivo experimental models. As such, the investigation of TDP-43 pathomechanisms in various major neurodegenerative diseases is on the rise. Here, after a discussion of stages of TDP-43 proteinopathy during disease progression in various major neurodegenerative diseases, we review previous and most recent studies about the potential pathomechanisms with a particular emphasis on ALS, FTLD, and AD, and discuss the possibility of targeting TDP-43 as a common therapeutic approach to treat neurodegenerative diseases.
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Affiliation(s)
- Ju Gao
- Departments of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Luwen Wang
- Departments of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mikayla L. Huntley
- Departments of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - George Perry
- College of Sciences, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Xinglong Wang
- Departments of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
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26
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Bakkar N, Kovalik T, Lorenzini I, Spangler S, Lacoste A, Sponaugle K, Ferrante P, Argentinis E, Sattler R, Bowser R. Artificial intelligence in neurodegenerative disease research: use of IBM Watson to identify additional RNA-binding proteins altered in amyotrophic lateral sclerosis. Acta Neuropathol 2018; 135:227-247. [PMID: 29134320 PMCID: PMC5773659 DOI: 10.1007/s00401-017-1785-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/04/2017] [Accepted: 11/04/2017] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease with no effective treatments. Numerous RNA-binding proteins (RBPs) have been shown to be altered in ALS, with mutations in 11 RBPs causing familial forms of the disease, and 6 more RBPs showing abnormal expression/distribution in ALS albeit without any known mutations. RBP dysregulation is widely accepted as a contributing factor in ALS pathobiology. There are at least 1542 RBPs in the human genome; therefore, other unidentified RBPs may also be linked to the pathogenesis of ALS. We used IBM Watson® to sieve through all RBPs in the genome and identify new RBPs linked to ALS (ALS-RBPs). IBM Watson extracted features from published literature to create semantic similarities and identify new connections between entities of interest. IBM Watson analyzed all published abstracts of previously known ALS-RBPs, and applied that text-based knowledge to all RBPs in the genome, ranking them by semantic similarity to the known set. We then validated the Watson top-ten-ranked RBPs at the protein and RNA levels in tissues from ALS and non-neurological disease controls, as well as in patient-derived induced pluripotent stem cells. 5 RBPs previously unlinked to ALS, hnRNPU, Syncrip, RBMS3, Caprin-1 and NUPL2, showed significant alterations in ALS compared to controls. Overall, we successfully used IBM Watson to help identify additional RBPs altered in ALS, highlighting the use of artificial intelligence tools to accelerate scientific discovery in ALS and possibly other complex neurological disorders.
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Affiliation(s)
- Nadine Bakkar
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Tina Kovalik
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Ileana Lorenzini
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | | | | | - Kyle Sponaugle
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Philip Ferrante
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | | | - Rita Sattler
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Robert Bowser
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA.
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27
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Dong X, Cong S. Identification of differentially expressed genes and regulatory relationships in Huntington's disease by bioinformatics analysis. Mol Med Rep 2018; 17:4317-4326. [PMID: 29328442 PMCID: PMC5802203 DOI: 10.3892/mmr.2018.8410] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/20/2017] [Indexed: 12/14/2022] Open
Abstract
Huntington's disease (HD) is an inherited, progressive neurodegenerative disease caused by a CAG expansion in the huntingtin (HTT) gene; various dysfunctions of biological processes in HD have been proposed. However, at present the exact pathogenesis of HD is not fully understood. The present study aimed to explore the pathogenesis of HD using a computational bioinformatics analysis of gene expression. GSE11358 was downloaded from the Gene Expression Omnibus andthe differentially expressed genes (DEGs) in the mutant HTT knock-in cell model STHdhQ111/Q111 were predicted. DEGs between the HD and control samples were screened using the limma package in R. Functional and pathway enrichment analyses were conducted using the database for annotation, visualization and integrated discovery software. A protein-protein interaction (PPI) network was established by the search tool for the retrieval of interacting genes and visualized by Cytoscape. Module analysis of the PPI network was performed utilizing MCODE. A total of 471 DEGs were identified, including ribonuclease A family member 4 (RNASE4). In addition, 41 significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways, as well as several significant Gene Ontology terms (including cytokine-cytokine receptor interaction and cytosolic DNA-sensing) were identified. A total of 18 significant modules were identified from the PPI network. Furthermore, a novel transcriptional regulatory relationship was identified, namely signal transducer and activator of transcription 3 (STAT3), which is regulated by miRNA-124 in HD. In conclusion, deregulation of 18 critical genes may contribute to the occurrence of HD. RNASE4, STAT3, and miRNA-124 may have a regulatory association with the pathological mechanisms in HD.
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Affiliation(s)
- Xiaoyu Dong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Shuyan Cong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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28
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Shenouda M, Zhang AB, Weichert A, Robertson J. Mechanisms Associated with TDP-43 Neurotoxicity in ALS/FTLD. ADVANCES IN NEUROBIOLOGY 2018; 20:239-263. [PMID: 29916022 DOI: 10.1007/978-3-319-89689-2_9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The discovery of TDP-43 as a major disease protein in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) was first made in 2006. Prior to 2006 there were only 11 publications related to TDP-43, now there are over 2000, indicating the importance of TDP-43 to unraveling the complex molecular mechanisms that underpin the pathogenesis of ALS/FTLD. Subsequent to this discovery, TDP-43 pathology was also found in other neurodegenerative diseases, including Alzheimer's disease, the significance of which is still in the early stages of exploration. TDP-43 is a predominantly nuclear DNA/RNA-binding protein, one of a number of RNA-binding proteins that are now known to be linked with ALS/FTLD, including Fused in Sarcoma (FUS), heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), and heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1). However, what sets TDP-43 apart is the vast number of cases in which TDP-43 pathology is present, providing a point of convergence, the understanding of which could lead to broadly applicable therapeutics. Here we will focus on TDP-43 in ALS/FTLD, its nuclear and cytoplasmic functions, and consequences should these functions go awry.
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Affiliation(s)
- Marc Shenouda
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5T 2S8, Canada
| | - Ashley B Zhang
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5T 2S8, Canada
| | - Anna Weichert
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5T 2S8, Canada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5T 2S8, Canada.
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29
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Tennakoon A, Katharesan V, Johnson IP. Brainstem cytokine changes in healthy ageing and Motor Neurone Disease. J Neurol Sci 2017; 381:192-199. [PMID: 28991679 DOI: 10.1016/j.jns.2017.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 07/12/2017] [Accepted: 08/08/2017] [Indexed: 11/18/2022]
Abstract
Neuroinflammation is linked to healthy ageing, but its role in the development of age-related neurodegenerative diseases is unclear. In this pilot study we used a multiplex assay approach to compare 27 cytokines in 6 young adult and 6 ageing control brainstems with those in 6 MND brainstems. We report that healthy ageing is associated with significantly increased brainstem levels of IL-1β, IP-10 and MIP-1β which co-localise immunocytochemically to astrocytes. MND brainstem is also characterised by a general increase in both pro- and anti-cytokine levels, but fails to show the expected age-related increase in MIP-1β and IP-10. This pilot study is the first to show that MND is associated with a failure of specific features of the normal age-related neuroinflammatory process. We suggest that our pilot data indicates that neuroinflammation during healthy ageing may not always be detrimental to motoneuronal survival and that age-related neurodegenerative diseases, such as MND, may instead result from defective neuroinflammation.
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Affiliation(s)
- Anuradha Tennakoon
- Discipline of Anatomy and Pathology, The University of Adelaide, SA5005, Australia
| | - Viythia Katharesan
- Discipline of Anatomy and Pathology, The University of Adelaide, SA5005, Australia
| | - Ian P Johnson
- Discipline of Anatomy and Pathology, The University of Adelaide, SA5005, Australia.
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30
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McKeever PM, Kim T, Hesketh AR, MacNair L, Miletic D, Favrin G, Oliver SG, Zhang Z, St George-Hyslop P, Robertson J. Cholinergic neuron gene expression differences captured by translational profiling in a mouse model of Alzheimer's disease. Neurobiol Aging 2017; 57:104-119. [PMID: 28628896 DOI: 10.1016/j.neurobiolaging.2017.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/25/2017] [Accepted: 05/12/2017] [Indexed: 12/14/2022]
Abstract
Cholinergic neurotransmission is impaired in Alzheimer's disease (AD), and loss of basal forebrain cholinergic neurons is a key component of disease pathogenicity and symptomatology. To explore the molecular basis of this cholinergic dysfunction, we paired translating ribosome affinity purification (TRAP) with RNA sequencing (TRAP-Seq) to identify the actively translating mRNAs in anterior forebrain cholinergic neurons in the TgCRND8 mouse model of AD. Bioinformatic analyses revealed the downregulation of 67 of 71 known cholinergic-related transcripts, consistent with cholinergic neuron dysfunction in TgCRND8 mice, as well as transcripts related to oxidative phosphorylation, neurotrophins, and ribosomal processing. Upregulated transcripts included those related to axon guidance, glutamatergic synapses and kinase activity and included AD-risk genes Sorl1 and Ptk2b. In contrast, the total transcriptome of the anterior forebrain showed upregulation in cytokine signaling, microglia, and immune system pathways, including Trem2, Tyrobp, and Inpp5d. Hence, TRAP-Seq clearly distinguished the differential gene expression alterations occurring in cholinergic neurons of TgCRND8 mice compared with wild-type littermates, providing novel candidate pathways to explore for therapeutic development in AD.
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Affiliation(s)
- Paul M McKeever
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - TaeHyung Kim
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada; Department of Computer Science, University of Toronto, Toronto, Canada
| | - Andrew R Hesketh
- Department of Biochemistry, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Laura MacNair
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Denise Miletic
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Canada
| | - Giorgio Favrin
- Department of Biochemistry, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Stephen G Oliver
- Department of Biochemistry, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Zhaolei Zhang
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada; Department of Computer Science, University of Toronto, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Peter St George-Hyslop
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Canada; Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.
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31
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Ederle H, Dormann D. TDP-43 and FUS en route from the nucleus to the cytoplasm. FEBS Lett 2017; 591:1489-1507. [PMID: 28380257 DOI: 10.1002/1873-3468.12646] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/24/2017] [Accepted: 04/02/2017] [Indexed: 12/13/2022]
Abstract
Misfolded or mislocalized RNA-binding proteins (RBPs) and, consequently, altered mRNA processing, can cause neuronal dysfunction, eventually leading to neurodegeneration. Two prominent examples are the RBPs TAR DNA-binding protein of 43 kDa (TDP-43) and fused in sarcoma (FUS), which form pathological messenger ribonucleoprotein aggregates in patients suffering from amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), two devastating neurodegenerative disorders. Here, we review the multiple functions of TDP-43 and FUS in mRNA processing, both in the nucleus and in the cytoplasm. We discuss how TDP-43 and FUS may exit the nucleus and how defects in both nuclear and cytosolic mRNA processing events, and possibly nuclear export defects, may contribute to neurodegeneration and ALS/FTD pathogenesis.
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Affiliation(s)
- Helena Ederle
- BioMedical Center (BMC), Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.,Graduate School of Systemic Neurosciences (GSN), Planegg-Martinsried, Germany
| | - Dorothee Dormann
- BioMedical Center (BMC), Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.,Graduate School of Systemic Neurosciences (GSN), Planegg-Martinsried, Germany.,Munich Cluster for Systems Neurology (SyNergy), Germany
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32
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Ratti A, Buratti E. Physiological functions and pathobiology of TDP-43 and FUS/TLS proteins. J Neurochem 2016; 138 Suppl 1:95-111. [PMID: 27015757 DOI: 10.1111/jnc.13625] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/19/2016] [Accepted: 03/22/2016] [Indexed: 12/12/2022]
Abstract
The multiple roles played by RNA binding proteins in neurodegeneration have become apparent following the discovery of TAR DNA binding protein 43 kDa (TDP-43) and fused in sarcoma/translocated in liposarcoma (FUS/TLS) involvement in amyotrophic lateral sclerosis and frontotemporal lobar dementia. In these two diseases, the majority of patients display the presence of aggregated forms of one of these proteins in their brains. The study of their functional properties currently represents a very promising target for developing the effective therapeutic options that are still lacking. This aim, however, must be preceded by an accurate evaluation of TDP-43 and FUS/TLS biological functions, both in physiological and disease conditions. Recent findings have uncovered several aspects of RNA metabolism that can be affected by misregulation of these two proteins. Progress has also been made in starting to understand how the aggregation of these proteins occurs and spreads from cell to cell. The aim of this review will be to provide a general overview of TDP-43 and FUS/TLS proteins and to highlight their physiological functions. At present, the emerging picture is that TDP-43 and FUS/TLS control several aspects of an mRNA's life, but they can also participate in DNA repair processes and in non-coding RNA metabolism. Although their regulatory activities are similar, they regulate mainly distinct RNA targets and show different pathogenetic mechanisms in amyotrophic lateral sclerosis/frontotemporal lobar dementia diseases. The identification of key events in these processes represents today the best chance of finding targetable options for therapeutic approaches that might actually make a difference at the clinical level. The two major RNA Binding Proteins involved in Amyotrophic Lateral Sclerosisi and Frontotemporal Dementia are TDP-43 and FUST/TLS. Both proteins are involved in regulating all aspects of RNA and RNA life cycle within neurons, from transcription, processing, and transport/stability to the formation of cytoplasmic and nuclear stress granules. For this reason, the aberrant aggregation of these factors during disease can impair multiple RNA metabolic pathways and eventually lead to neuronal death/inactivation. The purpose of this review is to provide an up-to-date perspective on what we know about this issue at the molecular level. This article is part of the Frontotemporal Dementia special issue.
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Affiliation(s)
- Antonia Ratti
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, Milan, Italy.,Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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33
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Bowden HA, Dormann D. Altered mRNP granule dynamics in FTLD pathogenesis. J Neurochem 2016; 138 Suppl 1:112-33. [PMID: 26938019 DOI: 10.1111/jnc.13601] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 12/13/2022]
Abstract
In neurons, RNA-binding proteins (RBPs) play a key role in post-transcriptional gene regulation, for example alternative splicing, mRNA localization in neurites and local translation upon synaptic stimulation. There is increasing evidence that defective or mislocalized RBPs - and consequently altered mRNA processing - lead to neuronal dysfunction and cause neurodegeneration, including frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Cytosolic RBP aggregates containing TAR DNA-binding protein of 43 kDa (TDP-43) or fused in sarcoma (FUS) are a common hallmark of both disorders. There is mounting evidence that translationally silent mRNP granules, such as stress granules or transport granules, play an important role in the formation of these RBP aggregates. These granules are thought to be 'catalytic convertors' of RBP aggregation by providing a high local concentration of RBPs. As recently shown in vitro, RBPs that contain a so-called low-complexity domain start to 'solidify' and eventually aggregate at high protein concentrations. The same may happen in mRNP granules in vivo, leading to 'solidified' granules that lose their dynamic properties and ability to fulfill their physiological functions. This may result in a disturbed stress response, altered mRNA transport and local translation, and formation of pathological TDP-43 or FUS aggregates, all of which may contribute to neuronal dysfunction and neurodegeneration. Here, we discuss the general functional properties of these mRNP granules, how their dynamics may be disrupted in frontotemporal lobar degeneration/amyotrophic lateral sclerosis, for example by loss or gain of function of TDP-43 and FUS, and how this may contribute to the development of RBP aggregates and neurotoxicity. In this review, we discuss how dynamic mRNP granules, such as stress granules or neuronal transport granules, may be converted into pathological aggregates containing misfolded RNA-binding proteins (RBPs), such as TDP-43 and FUS. Abnormal interactions between low-complexity domains in RBPs may cause dynamic mRNP granules to solidify and become dysfunctional. This may result in a disturbed stress response, altered mRNA transport and local translation, as well as RBP aggregation, all of which may contribute to neuronal dysfunction and neurodegeneration.
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Affiliation(s)
- Hilary A Bowden
- Graduate School of Systemic Neurosciences (GSN), Planegg-Martinsried, Germany
| | - Dorothee Dormann
- BioMedical Center (BMC), Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.,Graduate School of Systemic Neurosciences (GSN), Planegg-Martinsried, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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