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Figueiredo AS, Loureiro JR, Macedo-Ribeiro S, Silveira I. Advances in Nucleotide Repeat Expansion Diseases: Transcription Gets in Phase. Cells 2023; 12:cells12060826. [PMID: 36980167 PMCID: PMC10047669 DOI: 10.3390/cells12060826] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023] Open
Abstract
Unstable DNA repeat expansions and insertions have been found to cause more than 50 neurodevelopmental, neurodegenerative, and neuromuscular disorders. One of the main hallmarks of repeat expansion diseases is the formation of abnormal RNA or protein aggregates in the neuronal cells of affected individuals. Recent evidence indicates that alterations of the dynamic or material properties of biomolecular condensates assembled by liquid/liquid phase separation are critical for the formation of these aggregates. This is a thermodynamically-driven and reversible local phenomenon that condenses macromolecules into liquid-like compartments responsible for compartmentalizing molecules required for vital cellular processes. Disease-associated repeat expansions modulate the phase separation properties of RNAs and proteins, interfering with the composition and/or the material properties of biomolecular condensates and resulting in the formation of abnormal aggregates. Since several repeat expansions have arisen in genes encoding crucial players in transcription, this raises the hypothesis that wide gene expression dysregulation is common to multiple repeat expansion diseases. This review will cover the impact of these mutations in the formation of aberrant aggregates and how they modify gene transcription.
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Affiliation(s)
- Ana S. Figueiredo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
| | - Joana R. Loureiro
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal
| | - Sandra Macedo-Ribeiro
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal
| | - Isabel Silveira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal
- Correspondence: ; Tel.: +351-2240-8800
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Fan C, Chen K, Wang Y, Ball EV, Stenson PD, Mort M, Bacolla A, Kehrer-Sawatzki H, Tainer JA, Cooper DN, Zhao H. Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections. Hum Genet 2023; 142:245-274. [PMID: 36344696 PMCID: PMC10290229 DOI: 10.1007/s00439-022-02500-6] [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: 08/02/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
Abstract
Whilst DNA repeat expansions cause numerous heritable human disorders, their origins and underlying pathological mechanisms are often unclear. We collated a dataset comprising 224 human repeat expansions encompassing 203 different genes, and performed a systematic analysis with respect to key topological features at the DNA, RNA and protein levels. Comparison with controls without known pathogenicity and genomic regions lacking repeats, allowed the construction of the first tool to discriminate repeat regions harboring pathogenic repeat expansions (DPREx). At the DNA level, pathogenic repeat expansions exhibited stronger signals for DNA regulatory factors (e.g. H3K4me3, transcription factor-binding sites) in exons, promoters, 5'UTRs and 5'genes but were not significantly different from controls in introns, 3'UTRs and 3'genes. Additionally, pathogenic repeat expansions were also found to be enriched in non-B DNA structures. At the RNA level, pathogenic repeat expansions were characterized by lower free energy for forming RNA secondary structure and were closer to splice sites in introns, exons, promoters and 5'genes than controls. At the protein level, pathogenic repeat expansions exhibited a preference to form coil rather than other types of secondary structure, and tended to encode surface-located protein domains. Guided by these features, DPREx ( http://biomed.nscc-gz.cn/zhaolab/geneprediction/# ) achieved an Area Under the Curve (AUC) value of 0.88 in a test on an independent dataset. Pathogenic repeat expansions are thus located such that they exert a synergistic influence on the gene expression pathway involving inter-molecular connections at the DNA, RNA and protein levels.
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Affiliation(s)
- Cong Fan
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang West Road, Guangzhou, 500001, People's Republic of China
| | - Ken Chen
- School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 500001, China
| | - Yukai Wang
- School of Life Science, Sun Yat-Sen University, Guangzhou, 500001, China
| | - Edward V Ball
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | | | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang West Road, Guangzhou, 500001, People's Republic of China.
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Lopez-Herdoiza MB, Bauché S, Wilmet B, Le Duigou C, Roussel D, Frah M, Béal J, Devely G, Boluda S, Frick P, Bouteiller D, Dussaud S, Guillabert P, Dalle C, Dumont M, Camuzat A, Saracino D, Barbier M, Bruneteau G, Ravassard P, Neumann M, Nicole S, Le Ber I, Brice A, Latouche M. C9ORF72 knockdown triggers FTD-like symptoms and cell pathology in mice. Front Cell Neurosci 2023; 17:1155929. [PMID: 37138765 PMCID: PMC10149765 DOI: 10.3389/fncel.2023.1155929] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
The GGGGCC intronic repeat expansion within C9ORF72 is the most common genetic cause of ALS and FTD. This mutation results in toxic gain of function through accumulation of expanded RNA foci and aggregation of abnormally translated dipeptide repeat proteins, as well as loss of function due to impaired transcription of C9ORF72. A number of in vivo and in vitro models of gain and loss of function effects have suggested that both mechanisms synergize to cause the disease. However, the contribution of the loss of function mechanism remains poorly understood. We have generated C9ORF72 knockdown mice to mimic C9-FTD/ALS patients haploinsufficiency and investigate the role of this loss of function in the pathogenesis. We found that decreasing C9ORF72 leads to anomalies of the autophagy/lysosomal pathway, cytoplasmic accumulation of TDP-43 and decreased synaptic density in the cortex. Knockdown mice also developed FTD-like behavioral deficits and mild motor phenotypes at a later stage. These findings show that C9ORF72 partial loss of function contributes to the damaging events leading to C9-FTD/ALS.
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Affiliation(s)
| | - Stephanie Bauché
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Baptiste Wilmet
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Caroline Le Duigou
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Delphine Roussel
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Magali Frah
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Jonas Béal
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Gabin Devely
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Susana Boluda
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Petra Frick
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | | | - Sébastien Dussaud
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Pierre Guillabert
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Carine Dalle
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Magali Dumont
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Agnes Camuzat
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Dario Saracino
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Mathieu Barbier
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Gaelle Bruneteau
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | | | - Manuela Neumann
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neuropathology, Tübingen University Hospital, Tübingen, Germany
| | - Sophie Nicole
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Isabelle Le Ber
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Alexis Brice
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Morwena Latouche
- Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
- EPHE, Neurogenetics Team, PSL Research University, Paris, France
- *Correspondence: Morwena Latouche,
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Fourier A, Quadrio I. Proteinopathies associated to repeat expansion disorders. J Neural Transm (Vienna) 2022; 129:173-185. [DOI: 10.1007/s00702-021-02454-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/13/2021] [Indexed: 12/11/2022]
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Loureiro JR, Castro AF, Figueiredo AS, Silveira I. Molecular Mechanisms in Pentanucleotide Repeat Diseases. Cells 2022; 11:cells11020205. [PMID: 35053321 PMCID: PMC8773600 DOI: 10.3390/cells11020205] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 02/01/2023] Open
Abstract
The number of neurodegenerative diseases resulting from repeat expansion has increased extraordinarily in recent years. In several of these pathologies, the repeat can be transcribed in RNA from both DNA strands producing, at least, one toxic RNA repeat that causes neurodegeneration by a complex mechanism. Recently, seven diseases have been found caused by a novel intronic pentanucleotide repeat in distinct genes encoding proteins highly expressed in the cerebellum. These disorders are clinically heterogeneous being characterized by impaired motor function, resulting from ataxia or epilepsy. The role that apparently normal proteins from these mutant genes play in these pathologies is not known. However, recent advances in previously known spinocerebellar ataxias originated by abnormal non-coding pentanucleotide repeats point to a gain of a toxic function by the pathogenic repeat-containing RNA that abnormally forms nuclear foci with RNA-binding proteins. In cells, RNA foci have been shown to be formed by phase separation. Moreover, the field of repeat expansions has lately achieved an extraordinary progress with the discovery that RNA repeats, polyglutamine, and polyalanine proteins are crucial for the formation of nuclear membraneless organelles by phase separation, which is perturbed when they are expanded. This review will cover the amazing advances on repeat diseases.
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Affiliation(s)
- Joana R. Loureiro
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
| | - Ana F. Castro
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Ana S. Figueiredo
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Isabel Silveira
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
- Correspondence: ; Tel.: +351-2240-8800
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Bede P, Chipika RH, Christidi F, Hengeveld JC, Karavasilis E, Argyropoulos GD, Lope J, Li Hi Shing S, Velonakis G, Dupuis L, Doherty MA, Vajda A, McLaughlin RL, Hardiman O. Genotype-associated cerebellar profiles in ALS: focal cerebellar pathology and cerebro-cerebellar connectivity alterations. J Neurol Neurosurg Psychiatry 2021; 92:1197-1205. [PMID: 34168085 PMCID: PMC8522463 DOI: 10.1136/jnnp-2021-326854] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/02/2021] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Cerebellar disease burden and cerebro-cerebellar connectivity alterations are poorly characterised in amyotrophic lateral sclerosis (ALS) despite the likely contribution of cerebellar pathology to the clinical heterogeneity of the condition. METHODS A prospective imaging study has been undertaken with 271 participants to systematically evaluate cerebellar grey and white matter alterations, cerebellar peduncle integrity and cerebro-cerebellar connectivity in ALS. Participants were stratified into four groups: (1) patients testing positive for GGGGCC repeat expansions in C9orf72, (2) patients carrying an intermediate-length repeat expansion in ATXN2, (3) patients without established ALS-associated mutations and (4) healthy controls. Additionally, the cerebellar profile of a single patient with ALS who had an ATXN2 allele length of 62 was evaluated. Cortical thickness, grey matter and white matter volumes were calculated in each cerebellar lobule complemented by morphometric analyses to characterise genotype-associated atrophy patterns. A Bayesian segmentation algorithm was used for superior cerebellar peduncle volumetry. White matter diffusivity parameters were appraised both within the cerebellum and in the cerebellar peduncles. Cerebro-cerebellar connectivity was assessed using deterministic tractography. RESULTS Cerebellar pathology was confined to lobules I-V of the anterior lobe in patients with sporadic ALS in contrast to the considerable posterior lobe and vermis disease burden identified in C9orf72 mutation carriers. Patients with intermediate ATXN2 expansions did not exhibit significant cerebellar pathology. CONCLUSIONS Focal rather than global cerebellar degeneration characterises ALS. Pathognomonic ALS symptoms which are typically attributed to other anatomical regions, such as dysarthria, dysphagia, pseudobulbar affect, eye movement abnormalities and cognitive deficits, may be modulated, exacerbated or partially driven by cerebellar changes in ALS.
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Affiliation(s)
- Peter Bede
- Computational Neuroimaging Group, Trinity College Dublin, Dublin, Ireland
| | | | - Foteini Christidi
- Computational Neuroimaging Group, Trinity College Dublin, Dublin, Ireland
- National and Kapodistrian University of Athens, Athens, Greece
| | | | | | | | - Jasmin Lope
- Computational Neuroimaging Group, Trinity College Dublin, Dublin, Ireland
| | - Stacey Li Hi Shing
- Computational Neuroimaging Group, Trinity College Dublin, Dublin, Ireland
| | | | - Léonie Dupuis
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- University of Central Florida College of Medicine, Orlando, Florida, USA
| | - Mark A Doherty
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Alice Vajda
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Orla Hardiman
- Computational Neuroimaging Group, Trinity College Dublin, Dublin, Ireland
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Semmelink MFW, Steen A, Veenhoff LM. Measuring and Interpreting Nuclear Transport in Neurodegenerative Disease-The Example of C9orf72 ALS. Int J Mol Sci 2021; 22:9217. [PMID: 34502125 PMCID: PMC8431710 DOI: 10.3390/ijms22179217] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 11/25/2022] Open
Abstract
Transport from and into the nucleus is essential to all eukaryotic life and occurs through the nuclear pore complex (NPC). There are a multitude of data supporting a role for nuclear transport in neurodegenerative diseases, but actual transport assays in disease models have provided diverse outcomes. In this review, we summarize how nuclear transport works, which transport assays are available, and what matters complicate the interpretation of their results. Taking a specific type of ALS caused by mutations in C9orf72 as an example, we illustrate these complications, and discuss how the current data do not firmly answer whether the kinetics of nucleocytoplasmic transport are altered. Answering this open question has far-reaching implications, because a positive answer would imply that widespread mislocalization of proteins occurs, far beyond the reported mislocalization of transport reporters, and specific proteins such as FUS, or TDP43, and thus presents a challenge for future research.
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Affiliation(s)
| | | | - Liesbeth M. Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands; (M.F.W.S.); (A.S.)
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Zhou Y, Sood R, Wang Q, Carrington B, Park M, Young AC, Birnbaum D, Liu Z, Ashizawa T, Mullikin JC, Koubeissi MZ, Liu P. Clinical and genomic analysis of a large Chinese family with familial cortical myoclonic tremor with epilepsy and SAMD12 intronic repeat expansion. Epilepsia Open 2021; 6:102-111. [PMID: 33681653 PMCID: PMC7918340 DOI: 10.1002/epi4.12450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 11/07/2020] [Accepted: 11/14/2020] [Indexed: 01/13/2023] Open
Abstract
Objective Our goal was to perform detailed clinical and genomic analysis of a large multigenerational Chinese family with 21 individuals showing symptoms of Familial Cortical Myoclonic Tremor with Epilepsy (FCMTE) that we have followed for over 20 years. Methods Patients were subjected to clinical evaluation, routine EEG, and structural magnetic resonance imaging. Whole exome sequencing, repeat-primed PCR, long-range PCR, and PacBio sequencing were performed to characterize the disease-causing mutation in this family. Results All evaluated patients manifested adult-onset seizures and presented with progressive myoclonic postural tremors starting after the third or fourth decade of life. Seizures typically diminished markedly in frequency with implementation of antiseizure medications but did not completely cease. The electroencephalogram of affected individuals showed generalized or multifocal spikes and slow wave complexes. An expansion of TTTTA motifs with addition of TTTCA motifs in intron 4 of SAMD12 was identified to segregate with the disease phenotype in this family. Furthermore, we found that the mutant allele is unstable and can undergo both contraction and expansion by changes in the number of repeat motifs each time it is passed to the next generation. The size of mutant allele varied from 5 to 5.5 kb with 549-603 copies of TTTTA and 287-343 copies of TTTCA repeat motifs in this family. Significance Our study provides a detailed description of clinical progression of FCMTE symptoms and its management with antiseizure medications. Our method of repeat analysis by PacBio sequencing of long-range PCR products does not require high-quality DNA and hence can be easily applied to other families to elucidate any correlation between the repeat size and phenotypic variables, such as, age of onset, and severity of symptoms.
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Affiliation(s)
- Yongxing Zhou
- Department of NeurologyMedStar St Mary’s Hospital/Georgetown University HospitalMedStar Medical GroupLeonardtownMDUSA
| | - Raman Sood
- Translational and Functional Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Qun Wang
- Epilepsy CenterDepartment of NeurologyBeijing Tiantan HospitalCapital Medical UniversityBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
| | - Blake Carrington
- Translational and Functional Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Morgan Park
- NIH Intramural Sequencing CenterNational Human Genome Research InstituteNational Institutes of HealthRockvilleMDUSA
| | - Alice C. Young
- NIH Intramural Sequencing CenterNational Human Genome Research InstituteNational Institutes of HealthRockvilleMDUSA
| | - Daniel Birnbaum
- Department of NeurologyEinstein Medical CenterPhiladelphiaPAUSA
| | - Zhao Liu
- Division of Pediatric NeurologyChildren's Hospital of IllinoisUniversity of Illinois College of MedicineChicagoILUSA
| | - Tetsuo Ashizawa
- Houston Methodist Neurological Institute and Research InstituteHoustonTXUSA
| | - James C. Mullikin
- NIH Intramural Sequencing CenterNational Human Genome Research InstituteNational Institutes of HealthRockvilleMDUSA
| | - Mohamad Z. Koubeissi
- Epilepsy CenterDepartment of NeurologyGeorge Washington UniversityWashingtonDCUSA
| | - Paul Liu
- Translational and Functional Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
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Mahadevan R, Bhoyar RC, Viswanathan N, Rajagopal RE, Essaki B, Suroliya V, Chelladurai R, Sankaralingam S, Shanmugam G, Vayanakkan S, Shamim U, Mathur A, Jain A, Imran M, Faruq M, Scaria V, Sivasubbu S, Kalyanaraman S. Genomic analysis of patients in a South Indian Community with autosomal dominant cortical tremor, myoclonus and epilepsy suggests a founder repeat expansion mutation in the SAMD12 gene. Brain Commun 2021; 3:fcaa214. [PMID: 33501421 PMCID: PMC7811760 DOI: 10.1093/braincomms/fcaa214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/15/2020] [Accepted: 10/25/2020] [Indexed: 12/11/2022] Open
Abstract
Autosomal Dominant Cortical Tremor, Myoclonus and Epilepsy is a non-progressive disorder characterized by distal tremors. Autosomal Dominant Cortical Tremor, Myoclonus and Epilepsy has been reported globally with different genetic predispositions of autosomal dominant inheritance with a high degree of penetrance. In south India, Autosomal Dominant Cortical Tremor, Myoclonus and Epilepsy has been reported in a large cohort of 48 families, in which the genetic defect was not identified. This report pertains to the whole-genome analysis of four individuals followed by repeat-primed PCR for 102 patients from a familial cohort of 325 individuals. All the patients underwent extensive clinical evaluation including neuropsychological examinations. The whole-genome sequencing was done for two affected and two unaffected individuals, belonging to two different families. The whole-genome sequencing analysis revealed the repeat expansion of TTTTA and TTTCA in intron 4 of the SAMD12 gene located on chromosome 8 in the patients affected with Autosomal Dominant Cortical Tremor, Myoclonus and Epilepsy, whereas the unaffected family members were negative for the similar expansion. Further, the repeat-primed PCR analysis of 102 patients showed the expansion of the TTTCA repeats in the intron 4 of SAMD12 gene. All patients registered for this study belong to a single community called “Nadar” whose nativity is confined to the southern districts of India, with reported unique genetic characteristics. This is the largest and most comprehensive single report on clinically and genetically characterized Autosomal Dominant Cortical Tremor, Myoclonus and Epilepsy patients belonging to a unique ethnic group worldwide.
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Affiliation(s)
- Radha Mahadevan
- Department of Neurology, Tirunelveli Medical College, Tirunelveli 627011, Tamil Nadu, India
| | - Rahul C Bhoyar
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110025, India
| | | | - Raskin Erusan Rajagopal
- Multidisciplinary Research Unit, Tirunelveli Medical College, Tirunelveli 627011, Tamil Nadu, India
| | - Bobby Essaki
- Department of Neurology, Tirunelveli Medical College, Tirunelveli 627011, Tamil Nadu, India
| | - Varun Suroliya
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110025, India
| | - Rachel Chelladurai
- Department of Neurology, Tirunelveli Medical College, Tirunelveli 627011, Tamil Nadu, India
| | | | | | | | - Uzma Shamim
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110025, India
| | - Aradhana Mathur
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110025, India
| | - Abhinav Jain
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110025, India
| | - Mohamed Imran
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110025, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110025, India
| | - Vinod Scaria
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110025, India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110025, India
| | - Shantaraman Kalyanaraman
- Multidisciplinary Research Unit, Tirunelveli Medical College, Tirunelveli 627011, Tamil Nadu, India
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10
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Antisense Transcription across Nucleotide Repeat Expansions in Neurodegenerative and Neuromuscular Diseases: Progress and Mysteries. Genes (Basel) 2020; 11:genes11121418. [PMID: 33261024 PMCID: PMC7760973 DOI: 10.3390/genes11121418] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Unstable repeat expansions and insertions cause more than 30 neurodegenerative and neuromuscular diseases. Remarkably, bidirectional transcription of repeat expansions has been identified in at least 14 of these diseases. More remarkably, a growing number of studies has been showing that both sense and antisense repeat RNAs are able to dysregulate important cellular pathways, contributing together to the observed clinical phenotype. Notably, antisense repeat RNAs from spinocerebellar ataxia type 7, myotonic dystrophy type 1, Huntington's disease and frontotemporal dementia/amyotrophic lateral sclerosis associated genes have been implicated in transcriptional regulation of sense gene expression, acting either at a transcriptional or posttranscriptional level. The recent evidence that antisense repeat RNAs could modulate gene expression broadens our understanding of the pathogenic pathways and adds more complexity to the development of therapeutic strategies for these disorders. In this review, we cover the amazing progress made in the understanding of the pathogenic mechanisms associated with repeat expansion neurodegenerative and neuromuscular diseases with a focus on the impact of antisense repeat transcription in the development of efficient therapies.
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11
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Ramesh N, Daley EL, Gleixner AM, Mann JR, Kour S, Mawrie D, Anderson EN, Kofler J, Donnelly CJ, Kiskinis E, Pandey UB. RNA dependent suppression of C9orf72 ALS/FTD associated neurodegeneration by Matrin-3. Acta Neuropathol Commun 2020; 8:177. [PMID: 33129345 PMCID: PMC7603783 DOI: 10.1186/s40478-020-01060-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/11/2022] Open
Abstract
The most common genetic cause of amyotrophic lateral sclerosis (ALS) is a GGGGCC (G4C2) hexanucleotide repeat expansions in first intron of the C9orf72 gene. The accumulation of repetitive RNA sequences can mediate toxicity potentially through the formation of intranuclear RNA foci that sequester key RNA-binding proteins (RBPs), and non-ATG mediated translation into toxic dipeptide protein repeats. However, the contribution of RBP sequestration to the mechanisms underlying RNA-mediated toxicity remain unknown. Here we show that the ALS-associated RNA-binding protein, Matrin-3 (MATR3), colocalizes with G4C2 RNA foci in patient tissues as well as iPSC-derived motor neurons harboring the C9orf72 mutation. Hyperexpansion of C9 repeats perturbed subcellular distribution and levels of endogenous MATR3 in C9-ALS patient-derived motor neurons. Interestingly, we observed that ectopic expression of human MATR3 strongly mitigates G4C2-mediated neurodegeneration in vivo. MATR3-mediated suppression of C9 toxicity was dependent on the RNA-binding domain of MATR3. Importantly, we found that expression of MATR3 reduced the levels of RAN-translation products in mammalian cells in an RNA-dependent manner. Finally, we have shown that knocking down endogenous MATR3 in C9-ALS patient-derived iPSC neurons decreased the presence of G4C2 RNA foci in the nucleus. Overall, these studies suggest that MATR3 genetically modifies the neuropathological and the pathobiology of C9orf72 ALS through modulating the RNA foci and RAN translation.
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Affiliation(s)
- Nandini Ramesh
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Human Genetics, School of Public Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Elizabeth L Daley
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Amanda M Gleixner
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- LiveLikeLou Center for ALS Research, University of Pittsburgh Brain Institute, Pittsburgh, PA, USA
| | - Jacob R Mann
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Darilang Mawrie
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Julia Kofler
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Christopher J Donnelly
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- LiveLikeLou Center for ALS Research, University of Pittsburgh Brain Institute, Pittsburgh, PA, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Human Genetics, School of Public Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
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12
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Buckner N, Kemp KC, Scott HL, Shi G, Rivers C, Gialeli A, Wong LF, Cordero-LLana O, Allen N, Wilkins A, Uney JB. Abnormal scaffold attachment factor 1 expression and localization in spinocerebellar ataxias and Huntington's chorea. Brain Pathol 2020; 30:1041-1055. [PMID: 32580238 PMCID: PMC8018166 DOI: 10.1111/bpa.12872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
SAFB1 is a DNA and RNA binding protein that is highly expressed in the cerebellum and hippocampus and is involved in the processing of coding and non-coding RNAs, splicing and dendritic function. We analyzed SAFB1 expression in the post-mortem brain tissue of spinocerebellar ataxia (SCA), Huntington's disease (HD), Multiple sclerosis (MS), Parkinson's disease patients and controls. In SCA cases, the expression of SAFB1 in the nucleus was increased and there was abnormal and extensive expression in the cytoplasm where it co-localized with the markers of Purkinje cell injury. Significantly, no SAFB1 expression was found in the cerebellar neurons of the dentate nucleus in control or MS patients; however, in SCA patients, SAFB1 expression was increased significantly in both the nucleus and cytoplasm of dentate neurons. In HD, we found that SAFB1 expression was increased in the nucleus and cytoplasm of striatal neurons; however, there was no SAFB1 staining in the striatal neurons of controls. In PD substantia nigra, we did not see any changes in neuronal SAFB1 expression. iCLIP analysis found that SAFB1 crosslink sites within ATXN1 RNA were adjacent to the start and within the glutamine repeat sequence. Further investigation found increased binding of SAFB1 to pathogenic ATXN1-85Q mRNA. These novel data strongly suggest SAFB1 contributes to the etiology of SCA and Huntington's chorea and that it may be a pathological marker of polyglutamine repeat expansion diseases.
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Affiliation(s)
- Nicola Buckner
- Bristol Medical School, Translational Health Sciences, University of Bristol, Bristol, UK
| | - Kevin C Kemp
- Bristol Medical School, Translational Health Sciences, University of Bristol, Bristol, UK
| | - Helen L Scott
- Bristol Medical School, Translational Health Sciences, University of Bristol, Bristol, UK
| | - Gongyu Shi
- Bristol Medical School, Translational Health Sciences, University of Bristol, Bristol, UK
| | - Caroline Rivers
- Bristol Medical School, Translational Health Sciences, University of Bristol, Bristol, UK
| | - Andriana Gialeli
- Bristol Medical School, Translational Health Sciences, University of Bristol, Bristol, UK
| | - Liang-Fong Wong
- Bristol Medical School, Translational Health Sciences, University of Bristol, Bristol, UK
| | - Oscar Cordero-LLana
- Bristol Medical School, Translational Health Sciences, University of Bristol, Bristol, UK
| | | | - Alastair Wilkins
- Institute of Clinical Neurosciences, Bristol Medical School, Translational Health Sciences, University of Bristol, Bristol, UK
| | - James B Uney
- Bristol Medical School, Translational Health Sciences, University of Bristol, Bristol, UK
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13
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Familial cortical myoclonic tremor with epilepsy: TTTCA/TTTTA repeat expansions and expanding phenotype in two Chinese families. Brain Res 2020; 1737:146796. [PMID: 32194077 DOI: 10.1016/j.brainres.2020.146796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 03/04/2020] [Accepted: 03/14/2020] [Indexed: 02/08/2023]
Abstract
Recently, expanded intronic TTTCA and TTTTA repeat in SAMD12 were identified in families with familial cortical myoclonic tremor with epilepsy (FCMTE). We conducted to this study to clarify the genetic etiology and to describe the clinical, neurophysiologic, and imaging features in two unrelated Chinese families with FCMTE. In this study, we performed the RP-PCR and long-range PCR analysis to examine and verifyTTTCA and TTTTA expansions in five affected members whose severities of cortical tremor, neuropsychology and MRI were also evaluated. Reliable clinical information was collected from another two affected members. Our results revealed that expansions of intronic TTTCA and TTTTA repeats in SAMD12 were both identified in all five affected subjects. All seven affected living patients had cortical tremor with a median age at onset of 16.4 years (range, 10-22 years). Convulsions occurred in 5 of 7 with a median age at onset of 32.4 years (range, 10-42 years). Among five patients evaluated for cortical tremor severity and psychiatric comorbidity, two patients had severe cortical tremor, anxiety and depression. Abnormal brain MRI findings including the possible existence of demyelination, severe atrophy of the cerebral hemisphere and abnormal bilateral symmetrical signals in the globus pallidus were observed in three patients, respectively. These results further expanded the known genotype in two Chinese families affected with FCMTE. Border clinical spectrum needs to be confirmed in future studies from additional FCMTE families genetically diagnosed.
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14
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Nelson PT, Fardo DW, Katsumata Y. The MUC6/AP2A2 Locus and Its Relevance to Alzheimer's Disease: A Review. J Neuropathol Exp Neurol 2020; 79:568-584. [PMID: 32357373 PMCID: PMC7241941 DOI: 10.1093/jnen/nlaa024] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/10/2020] [Indexed: 12/11/2022] Open
Abstract
We recently reported evidence of Alzheimer's disease (AD)-linked genetic variation within the mucin 6 (MUC6) gene on chromosome 11p, nearby the adaptor-related protein complex 2 subunit alpha 2 (AP2A2) gene. This locus has interesting features related to human genomics and clinical research. MUC6 gene variants have been reported to potentially influence viral-including herpesvirus-immunity and the gut microbiome. Within the MUC6 gene is a unique variable number of tandem repeat (VNTR) region. We discovered an association between MUC6 VNTR repeat expansion and AD pathologic severity, particularly tau proteinopathy. Here, we review the relevant literature. The AD-linked VNTR polymorphism may also influence AP2A2 gene expression. AP2A2 encodes a polypeptide component of the adaptor protein complex, AP-2, which is involved in clathrin-coated vesicle function and was previously implicated in AD pathogenesis. To provide background information, we describe some key knowledge gaps in AD genetics research. The "missing/hidden heritability problem" of AD is highlighted. Extensive portions of the human genome, including the MUC6 VNTR, have not been thoroughly evaluated due to limitations of existing high-throughput sequencing technology. We present and discuss additional data, along with cautionary considerations, relevant to the hypothesis that MUC6 repeat expansion influences AD pathogenesis.
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Affiliation(s)
- Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
- Department of Pathology, University of Kentucky, Lexington, Kentucky
| | - David W Fardo
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky
| | - Yuriko Katsumata
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky
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15
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Ishiguro A, Kimura N, Noma T, Shimo-Kon R, Ishihama A, Kon T. Molecular dissection of ALS-linked TDP-43 - involvement of the Gly-rich domain in interaction with G-quadruplex mRNA. FEBS Lett 2020; 594:2254-2265. [PMID: 32337711 DOI: 10.1002/1873-3468.13800] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 12/12/2022]
Abstract
TDP-43 is the major pathogenic protein of amyotrophic lateral sclerosis (ALS). Previously, we identified that TDP-43 interacts with G-quadruplex (G4)-containing RNA and is involved in their long-distance transport in neurons. For the molecular dissection of the TDP-43 and G4-RNA interaction, we analyzed it here in vitro and in cultured cells using a set of 10 mutant TDP-43 proteins from familial and sporadic ALS patients as well as using the TDP-43 C-terminal Gly-rich domain alone. Our results altogether indicate the involvement of the Gly-rich region of TDP-43 in the initial recognition and binding of G4-RNA, which then induces tight binding of TDP-43 with target RNAs, supposedly in conjunction with its RNA recognition motifs.
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Affiliation(s)
- Akira Ishiguro
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Japan
| | - Nobuyuki Kimura
- Section of Cell Biology and Pathology, Department of Alzheimer's Disease Research, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Takashi Noma
- Department of Biological Science, Graduate School of Science, and Faculty of Science Osaka University, Toyonaka, Japan
| | - Rieko Shimo-Kon
- Department of Biological Science, Graduate School of Science, and Faculty of Science Osaka University, Toyonaka, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Japan
| | - Takahide Kon
- Department of Biological Science, Graduate School of Science, and Faculty of Science Osaka University, Toyonaka, Japan
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16
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Rempel IL, Steen A, Veenhoff LM. Poor old pores-The challenge of making and maintaining nuclear pore complexes in aging. FEBS J 2020; 287:1058-1075. [PMID: 31912972 PMCID: PMC7154712 DOI: 10.1111/febs.15205] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/20/2019] [Accepted: 01/06/2020] [Indexed: 12/11/2022]
Abstract
The nuclear pore complex (NPC) is the sole gateway to the nuclear interior, and its function is essential to all eukaryotic life. Controlling the functionality of NPCs is a tremendous challenge for cells. Firstly, NPCs are large structures, and their complex assembly does occasionally go awry. Secondly, once assembled, some components of the NPC persist for an extremely long time and, as a result, are susceptible to accumulate damage. Lastly, a significant proportion of the NPC is composed of intrinsically disordered proteins that are prone to aggregation. In this review, we summarize how the quality of NPCs is guarded in young cells and discuss the current knowledge on the fate of NPCs during normal aging in different tissues and organisms. We discuss the extent to which current data supports a hypothesis that NPCs are poorly maintained during aging of nondividing cells, while in dividing cells the main challenge is related to the assembly of new NPCs. Our survey of current knowledge points toward NPC quality control as an important node in aging of both dividing and nondividing cells. Here, the loss of protein homeostasis during aging is central and the NPC appears to both be impacted by, and to drive, this process.
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Affiliation(s)
- Irina L Rempel
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, The Netherlands
| | - Anton Steen
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, The Netherlands
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17
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Yu ACS, Yim AKY, Chan AYY, Yuen LYP, Au WC, Cheng THT, Lin X, Li JW, Chan LWL, Mok VCT, Chan TF, Chan HYE. A Targeted Gene Panel That Covers Coding, Non-coding and Short Tandem Repeat Regions Improves the Diagnosis of Patients With Neurodegenerative Diseases. Front Neurosci 2019; 13:1324. [PMID: 31920494 PMCID: PMC6917647 DOI: 10.3389/fnins.2019.01324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/26/2019] [Indexed: 12/20/2022] Open
Abstract
Genetic testing for neurodegenerative diseases (NDs) is highly challenging because of genetic heterogeneity and overlapping manifestations. Targeted-gene panels (TGPs), coupled with next-generation sequencing (NGS), can facilitate the profiling of a large repertoire of ND-related genes. Due to the technical limitations inherent in NGS and TGPs, short tandem repeat (STR) variations are often ignored. However, STR expansions are known to cause such NDs as Huntington’s disease and spinocerebellar ataxias type 3 (SCA3). Here, we studied the clinical utility of a custom-made TGP that targets 199 NDs and 311 ND-associated genes on 118 undiagnosed patients. At least one known or likely pathogenic variation was found in 54 patients; 27 patients demonstrated clinical profiles that matched the variants; and 16 patients whose original diagnosis were refined. A high concordance of variant calling were observed when comparing the results from TGP and whole-exome sequencing of four patients. Our in-house STR detection algorithm has reached a specificity of 0.88 and a sensitivity of 0.82 in our SCA3 cohort. This study also uncovered a trove of novel and recurrent variants that may enrich the repertoire of ND-related genetic markers. We propose that a combined comprehensive TGPs-bioinformatics pipeline can improve the clinical diagnosis of NDs.
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Affiliation(s)
- Allen Chi-Shing Yu
- Codex Genetics Limited, Shatin, Hong Kong.,School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Aldrin Kay-Yuen Yim
- Codex Genetics Limited, Shatin, Hong Kong.,Computational and System Biology Program, Washington University School of Medicine, Saint Louis, MO, United States
| | - Anne Yin-Yan Chan
- Division of Neurology, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, China
| | - Liz Y P Yuen
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, China
| | - Wing Chi Au
- Division of Neurology, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, China
| | - Timothy H T Cheng
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, China
| | - Xiao Lin
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | | | - Larry W L Chan
- Alice Ho Miu Ling Nethersole Hospital, Tai Po, Hong Kong
| | - Vincent C T Mok
- Division of Neurology, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, China
| | - Ting-Fung Chan
- Codex Genetics Limited, Shatin, Hong Kong.,School of Life Sciences, The Chinese University of Hong Kong, Shatin, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, China
| | - Ho Yin Edwin Chan
- Codex Genetics Limited, Shatin, Hong Kong.,School of Life Sciences, The Chinese University of Hong Kong, Shatin, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, China
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18
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Ishiura H, Shibata S, Yoshimura J, Suzuki Y, Qu W, Doi K, Almansour MA, Kikuchi JK, Taira M, Mitsui J, Takahashi Y, Ichikawa Y, Mano T, Iwata A, Harigaya Y, Matsukawa MK, Matsukawa T, Tanaka M, Shirota Y, Ohtomo R, Kowa H, Date H, Mitsue A, Hatsuta H, Morimoto S, Murayama S, Shiio Y, Saito Y, Mitsutake A, Kawai M, Sasaki T, Sugiyama Y, Hamada M, Ohtomo G, Terao Y, Nakazato Y, Takeda A, Sakiyama Y, Umeda-Kameyama Y, Shinmi J, Ogata K, Kohno Y, Lim SY, Tan AH, Shimizu J, Goto J, Nishino I, Toda T, Morishita S, Tsuji S. Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease. Nat Genet 2019; 51:1222-1232. [DOI: 10.1038/s41588-019-0458-z] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 05/29/2019] [Indexed: 11/09/2022]
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19
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Cen Z, Jiang Z, Chen Y, Zheng X, Xie F, Yang X, Lu X, Ouyang Z, Wu H, Chen S, Yin H, Qiu X, Wang S, Ding M, Tang Y, Yu F, Li C, Wang T, Ishiura H, Tsuji S, Jiao C, Liu C, Xiao J, Luo W. Intronic pentanucleotide TTTCA repeat insertion in the SAMD12 gene causes familial cortical myoclonic tremor with epilepsy type 1. Brain 2019; 141:2280-2288. [PMID: 29939203 DOI: 10.1093/brain/awy160] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/18/2018] [Indexed: 12/16/2022] Open
Abstract
Familial cortical myoclonic tremor with epilepsy is an autosomal dominant neurodegenerative disease, characterized by cortical tremor and epileptic seizures. Although four subtypes (types 1-4) mapped on different chromosomes (8q24, 2p11.1-q12.2, 5p15.31-p15.1 and 3q26.32-3q28) have been reported, the causative gene has not yet been identified. Here, we report the genetic study in a cohort of 20 Chinese pedigrees with familial cortical myoclonic tremor with epilepsy. Linkage and haplotype analysis in 11 pedigrees revealed maximum two-point logarithm of the odds (LOD) scores from 1.64 to 3.77 (LOD scores in five pedigrees were >3.0) in chromosomal region 8q24 and narrowed the candidate region to an interval of 4.9 Mb. Using whole-genome sequencing, long-range polymerase chain reaction and repeat-primed polymerase chain reaction, we identified an intronic pentanucleotide (TTTCA)n insertion in the SAMD12 gene as the cause, which co-segregated with the disease among the 11 pedigrees mapped on 8q24 and additional seven unmapped pedigrees. Only two pedigrees did not contain the (TTTCA)n insertion. Repeat-primed polymerase chain reaction revealed that the sizes of (TTTCA)n insertion in all affected members were larger than 105 repeats. The same pentanucleotide insertion (ATTTCATTTC)58 has been reported to form RNA foci resulting in neurotoxicity in spinocerebellar ataxia type 37, which suggests the similar pathogenic process in familial cortical myoclonic tremor with epilepsy type 1.
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Affiliation(s)
- Zhidong Cen
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhengwen Jiang
- Genesky Diagnostics Inc, Biobay, SIP, Suzhou, Jiangsu, China
| | - You Chen
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaosheng Zheng
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Intensive Care Unit, Zhejiang Hospital, Hangzhou, Zhejiang, China
| | - Fei Xie
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Neurology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaodong Yang
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Neurology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xingjiao Lu
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Neurology, Zhejiang Hospital, Hangzhou, Zhejiang, China
| | - Zhiyuan Ouyang
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongwei Wu
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Neurology, Lishui People's Hospital, Lishui, Zhejiang, China
| | - Si Chen
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Houmin Yin
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xia Qiu
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shuang Wang
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Meiping Ding
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yelei Tang
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Feng Yu
- Genesky Diagnostics Inc, Biobay, SIP, Suzhou, Jiangsu, China
| | - Caihua Li
- Genesky Biotechnologies Inc., Shanghai, China
| | - Tao Wang
- Genesky Biotechnologies Inc., Shanghai, China
| | - Hiroyuki Ishiura
- Department of Neurology, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shoji Tsuji
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Institute of Medical Genomics, International University of Health and Welfare, Chiba, Japan
| | - Chuan Jiao
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Jianfeng Xiao
- Department of Neurology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Wei Luo
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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20
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Abstract
The spinocerebellar ataxias (SCAs) are a genetically heterogeneous group of autosomal dominantly inherited progressive disorders, the clinical hallmark of which is loss of balance and coordination accompanied by slurred speech; onset is most often in adult life. Genetically, SCAs are grouped as repeat expansion SCAs, such as SCA3/Machado-Joseph disease (MJD), and rare SCAs that are caused by non-repeat mutations, such as SCA5. Most SCA mutations cause prominent damage to cerebellar Purkinje neurons with consecutive cerebellar atrophy, although Purkinje neurons are only mildly affected in some SCAs. Furthermore, other parts of the nervous system, such as the spinal cord, basal ganglia and pontine nuclei in the brainstem, can be involved. As there is currently no treatment to slow or halt SCAs (many SCAs lead to premature death), the clinical care of patients with SCA focuses on managing the symptoms through physiotherapy, occupational therapy and speech therapy. Intense research has greatly expanded our understanding of the pathobiology of many SCAs, revealing that they occur via interrelated mechanisms (including proteotoxicity, RNA toxicity and ion channel dysfunction), and has led to the identification of new targets for treatment development. However, the development of effective therapies is hampered by the heterogeneity of the SCAs; specific therapeutic approaches may be required for each disease.
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21
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Loureiro JR, Oliveira CL, Mota C, Castro AF, Costa C, Loureiro JL, Coutinho P, Martins S, Sequeiros J, Silveira I. Mutational mechanism for DAB1 (ATTTC) n insertion in SCA37: ATTTT repeat lengthening and nucleotide substitution. Hum Mutat 2019; 40:404-412. [PMID: 30588707 DOI: 10.1002/humu.23704] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/28/2018] [Accepted: 12/22/2018] [Indexed: 12/20/2022]
Abstract
Dynamic mutations by microsatellite instability are the molecular basis of a growing number of neuromuscular and neurodegenerative diseases. Repetitive stretches in the human genome may drive pathogenicity, either by expansion above a given threshold, or by insertion of abnormal tracts in nonpathogenic polymorphic repetitive regions, as is the case in spinocerebellar ataxia type 37 (SCA37). We have recently established that this neurodegenerative disease is caused by an (ATTTC)n insertion within an (ATTTT)n in a noncoding region of DAB1. We now investigated the mutational mechanism that originated the (ATTTC)n insertion within an ancestral (ATTTT)n . Approximately 3% of nonpathogenic (ATTTT)n alleles are interspersed by AT-rich motifs, contrarily to mutant alleles that are composed of pure (ATTTT)n and (ATTTC)n stretches. Haplotype studies in unaffected chromosomes suggested that the primary mutational mechanism, leading to the (ATTTC)n insertion, was likely one or more T>C substitutions in an (ATTTT)n pure allele of approximately 200 repeats. Then, the (ATTTC)n expanded in size, originating a deleterious allele in DAB1 that leads to SCA37. This is likely the mutational mechanism in three similar (TTTCA)n insertions responsible for familial myoclonic epilepsy. Because (ATTTT)n tracts are frequent in the human genome, many loci could be at risk for this mutational process.
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Affiliation(s)
- Joana R Loureiro
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal.,ICBAS, Universidade do Porto, Porto, Portugal
| | - Cláudia L Oliveira
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal
| | - Carolina Mota
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal
| | - Ana F Castro
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal
| | - Cristina Costa
- Department of Neurology, Hospital Prof. Doutor Fernando Fonseca, Amadora, Portugal
| | - José L Loureiro
- IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal.,UnIGENe, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Department of Neurology, Hospital São Sebastião, Feira, Portugal
| | - Paula Coutinho
- IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal.,UnIGENe, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sandra Martins
- Population Genetics & Evolution, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Jorge Sequeiros
- IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal.,ICBAS, Universidade do Porto, Porto, Portugal.,UnIGENe, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Isabel Silveira
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal
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22
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Miller SJ, Glatzer JC, Hsieh YC, Rothstein JD. Cortical astroglia undergo transcriptomic dysregulation in the G93A SOD1 ALS mouse model. J Neurogenet 2018; 32:322-335. [PMID: 30398075 PMCID: PMC6444185 DOI: 10.1080/01677063.2018.1513508] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 08/06/2018] [Indexed: 12/13/2022]
Abstract
Astroglia are the most abundant glia cell in the central nervous system, playing essential roles in maintaining homeostasis. Key functions of astroglia include, but are not limited to, neurotransmitter recycling, ion buffering, immune modulation, neurotrophin secretion, neuronal synaptogenesis and elimination, and blood-brain barrier maintenance. In neurological diseases, it is well appreciated that astroglia play crucial roles in the disease pathogenesis. In amyotrophic lateral sclerosis (ALS), a motor neuron degenerative disease, astroglia in the spinal cord and cortex downregulate essential transporters, among other proteins, that exacerbate disease progression. Spinal cord astroglia undergo dramatic transcriptome dysregulation. However, in the cortex, it has not been well studied what effects glia, especially astroglia, have on upper motor neurons in the pathology of ALS. To begin to shed light on the involvement and dysregulation that astroglia undergo in ALS, we isolated pure grey-matter cortical astroglia and subjected them to microarray analysis. We uncovered a vast number of genes that show dysregulation at end-stage in the ALS mouse model, G93A SOD1. Many of these genes play essential roles in ion homeostasis and the Wnt-signaling pathway. Several of these dysregulated genes are common in ALS spinal cord astroglia, while many of them are unique. This database serves as an approach for understanding the significance of dysfunctional genes and pathways in cortical astroglia in the context of motor neuron disease, as well as determining regional astroglia heterogeneity, and providing insight into ALS pathogenesis.
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Affiliation(s)
- Sean J. Miller
- Dept. of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205
- Cellular and Molecular Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205
- The Brain Science Institute, Johns Hopkins University, Baltimore, MD 21205
| | - Jenna C. Glatzer
- Dept. of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205
- Cellular and Molecular Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205
- The Brain Science Institute, Johns Hopkins University, Baltimore, MD 21205
| | - Yi-chun Hsieh
- Dept. of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205
- The Brain Science Institute, Johns Hopkins University, Baltimore, MD 21205
| | - Jeffrey D. Rothstein
- Dept. of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205
- Cellular and Molecular Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205
- The Brain Science Institute, Johns Hopkins University, Baltimore, MD 21205
- Dept. of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205
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23
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Lei XX, Liu Q, Lu Q, Huang Y, Zhou XQ, Sun HY, Wu LW, Cui LY, Zhang X. TTTCA repeat expansion causes familial cortical myoclonic tremor with epilepsy. Eur J Neurol 2018; 26:513-518. [PMID: 30351492 DOI: 10.1111/ene.13848] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 10/12/2018] [Indexed: 01/28/2023]
Abstract
BACKGROUND AND PURPOSE The aim was to investigate whether abnormal TTTTA and TTTCA repeat expansions in introns of SAMD12, TNRC6A and RAPGEF2 are involved in the pathogenesis of familial cortical myoclonic tremor with epilepsy (FCMTE). METHODS Five families diagnosed with FCMTE were included in the current genetic analysis. Whole-exome sequencing was performed in selected patients of each family. TTTTA and TTTCA expansions were examined by repeat-primed polymerase chain reaction. The clinical features of FCMTE were elicited as defined by the common genetic mechanism of 14 patients. RESULTS Abnormal TTTCA expansion was identified and co-segregated in all five FCMTE families, four inserted in SAMD12 and one in RAPGEF2. The insertion of expanded TTTCA was not found in 116 control alleles. TTTTA expansion in SAMD12 was detected in 90.9% (10/11) of patients or mutation carriers; TTTTA expansion in RAPGEF2 was not found. The onset age of myoclonic tremor was 27.4 ± 5.9 (19-37) and epilepsy usually presented around age 34. Focal and generalized seizures were witnessed with various origins recorded by electroencephalogram. Cognitive deficits were not common within the first 3 years after epilepsy onset. Emotional instability was reported by most patients. No patients showed any cerebellar deficits. Valproate added with clonazepam is effective in controlling seizures but cannot guarantee a complete remission of tremor. Repeat length showed intergenerational instability and was inversely correlated with age at onset of myoclonic tremor and epilepsy. CONCLUSIONS TTTCA expansion insertion is associated with FCMTE in Chinese families. The homogenous genetic mechanism allowed for a higher precision of FCMTE description.
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Affiliation(s)
- X X Lei
- Department of Neurology and Laboratory of Clinical Genetics, Peking Union Medical College Hospital (PUMCH), CAMS and PUMC, Beijing, China.,McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing, China
| | - Q Liu
- Department of Neurology and Laboratory of Clinical Genetics, Peking Union Medical College Hospital (PUMCH), CAMS and PUMC, Beijing, China.,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Q Lu
- Department of Neurology and Laboratory of Clinical Genetics, Peking Union Medical College Hospital (PUMCH), CAMS and PUMC, Beijing, China
| | - Y Huang
- Department of Neurology and Laboratory of Clinical Genetics, Peking Union Medical College Hospital (PUMCH), CAMS and PUMC, Beijing, China
| | - X Q Zhou
- Department of Neurology and Laboratory of Clinical Genetics, Peking Union Medical College Hospital (PUMCH), CAMS and PUMC, Beijing, China
| | - H Y Sun
- Department of Neurology and Laboratory of Clinical Genetics, Peking Union Medical College Hospital (PUMCH), CAMS and PUMC, Beijing, China
| | - L W Wu
- Department of Neurology and Laboratory of Clinical Genetics, Peking Union Medical College Hospital (PUMCH), CAMS and PUMC, Beijing, China
| | - L Y Cui
- Department of Neurology and Laboratory of Clinical Genetics, Peking Union Medical College Hospital (PUMCH), CAMS and PUMC, Beijing, China.,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - X Zhang
- Department of Neurology and Laboratory of Clinical Genetics, Peking Union Medical College Hospital (PUMCH), CAMS and PUMC, Beijing, China.,McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing, China.,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
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24
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Abstract
Aging-related neurodegenerative diseases are progressive and fatal neurological diseases that are characterized by irreversible neuron loss and gliosis. With a growing population of aging individuals, there is a pressing need to better understand the basic biology underlying these diseases. Although diverse disease mechanisms have been implicated in neurodegeneration, a common theme of altered RNA processing has emerged as a unifying contributing factor to neurodegenerative disease. RNA processing includes a series of distinct processes, including RNA splicing, transport and stability, as well as the biogenesis of non-coding RNAs. Here, we highlight how some of these mechanisms are altered in neurodegenerative disease, including the mislocalization of RNA-binding proteins and their sequestration induced by microsatellite repeats, microRNA biogenesis alterations and defective tRNA biogenesis, as well as changes to long-intergenic non-coding RNAs. We also highlight potential therapeutic interventions for each of these mechanisms. Summary: In this At a Glance review, Edward Lee and co-authors provide an overview of RNA metabolism defects, including mislocalization of RNA-binding proteins and microRNA biogenesis alterations, that contribute to neurodegenerative disease pathology.
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Affiliation(s)
- Elaine Y Liu
- Translational Neuropathology Research Laboratories, Perelman School of Med. Univ. of Pennsylvania, 613A Stellar Chance Laboratories, Philadelphia, PA 19104, USA
| | - Christopher P Cali
- Translational Neuropathology Research Laboratories, Perelman School of Med. Univ. of Pennsylvania, 613A Stellar Chance Laboratories, Philadelphia, PA 19104, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratories, Perelman School of Med. Univ. of Pennsylvania, 613A Stellar Chance Laboratories, Philadelphia, PA 19104, USA
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25
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Loureiro JR, Oliveira CL, Sequeiros J, Silveira I. A repeat-primed PCR assay for pentanucleotide repeat alleles in spinocerebellar ataxia type 37. J Hum Genet 2018; 63:981-987. [DOI: 10.1038/s10038-018-0474-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/11/2018] [Accepted: 05/17/2018] [Indexed: 11/09/2022]
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26
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Hautbergue GM. RNA Nuclear Export: From Neurological Disorders to Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1007:89-109. [PMID: 28840554 DOI: 10.1007/978-3-319-60733-7_6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The presence of a nuclear envelope, also known as nuclear membrane, defines the structural framework of all eukaryotic cells by separating the nucleus, which contains the genetic material, from the cytoplasm where the synthesis of proteins takes place. Translation of proteins in Eukaryotes is thus dependent on the active transport of DNA-encoded RNA molecules through pores embedded within the nuclear membrane. Several mechanisms are involved in this process generally referred to as RNA nuclear export or nucleocytoplasmic transport of RNA. The regulated expression of genes requires the nuclear export of protein-coding messenger RNA molecules (mRNAs) as well as non-coding RNAs (ncRNAs) together with proteins and pre-assembled ribosomal subunits. The nuclear export of mRNAs is intrinsically linked to the co-transcriptional processing of nascent transcripts synthesized by the RNA polymerase II. This functional coupling is essential for the survival of cells allowing for timely nuclear export of fully processed transcripts, which could otherwise cause the translation of abnormal proteins such as the polymeric repeat proteins produced in some neurodegenerative diseases. Alterations of the mRNA nuclear export pathways can also lead to genome instability and to various forms of cancer. This chapter will describe the molecular mechanisms driving the nuclear export of RNAs with a particular emphasis on mRNAs. It will also review their known alterations in neurological disorders and cancer, and the recent opportunities they offer for the potential development of novel therapeutic strategies.
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Affiliation(s)
- Guillaume M Hautbergue
- RNA Biology Laboratory, Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield, S10 2HQ, UK.
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27
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Abe K. [An early history of Japanese amyotrophic lateral sclerosis (ALS)-related diseases and the current development]. Rinsho Shinkeigaku 2018; 58:141-165. [PMID: 29491329 DOI: 10.5692/clinicalneurol.cn-001095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The present review focuses an early history of Japanese amyotrophic lateral sclerosis (ALS)-related diseases and the current development. In relation to foreign previous reports, five topics are introduced and discussed on ALS with dementia, ALS/Parkinsonism dementia complex (ALS/PDC), familial ALS (FALS), spinal bulbar muscular atrophy (SBMA), and multisystem involvement especially in cerebellar system of ALS including ALS/SCA (spinocerebellar ataxia) crossroad mutation Asidan. This review found the great contribution of Japanese reports on the above five topics, and confirmed the great development of ALS-related diseases over the past 120 years.
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Affiliation(s)
- Koji Abe
- Department of Neurology, Okayama University Medical School
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28
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Seixas AI, Loureiro JR, Costa C, Ordóñez-Ugalde A, Marcelino H, Oliveira CL, Loureiro JL, Dhingra A, Brandão E, Cruz VT, Timóteo A, Quintáns B, Rouleau GA, Rizzu P, Carracedo Á, Bessa J, Heutink P, Sequeiros J, Sobrido MJ, Coutinho P, Silveira I. A Pentanucleotide ATTTC Repeat Insertion in the Non-coding Region of DAB1, Mapping to SCA37, Causes Spinocerebellar Ataxia. Am J Hum Genet 2017; 101:87-103. [PMID: 28686858 DOI: 10.1016/j.ajhg.2017.06.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/13/2017] [Indexed: 01/01/2023] Open
Abstract
Advances in human genetics in recent years have largely been driven by next-generation sequencing (NGS); however, the discovery of disease-related gene mutations has been biased toward the exome because the large and very repetitive regions that characterize the non-coding genome remain difficult to reach by that technology. For autosomal-dominant spinocerebellar ataxias (SCAs), 28 genes have been identified, but only five SCAs originate from non-coding mutations. Over half of SCA-affected families, however, remain without a genetic diagnosis. We used genome-wide linkage analysis, NGS, and repeat analysis to identify an (ATTTC)n insertion in a polymorphic ATTTT repeat in DAB1 in chromosomal region 1p32.2 as the cause of autosomal-dominant SCA; this region has been previously linked to SCA37. The non-pathogenic and pathogenic alleles have the configurations [(ATTTT)7-400] and [(ATTTT)60-79(ATTTC)31-75(ATTTT)58-90], respectively. (ATTTC)n insertions are present on a distinct haplotype and show an inverse correlation between size and age of onset. In the DAB1-oriented strand, (ATTTC)n is located in 5' UTR introns of cerebellar-specific transcripts arising mostly during human fetal brain development from the usage of alternative promoters, but it is maintained in the adult cerebellum. Overexpression of the transfected (ATTTC)58 insertion, but not (ATTTT)n, leads to abnormal nuclear RNA accumulation. Zebrafish embryos injected with RNA of the (AUUUC)58 insertion, but not (AUUUU)n, showed lethal developmental malformations. Together, these results establish an unstable repeat insertion in DAB1 as a cause of cerebellar degeneration; on the basis of the genetic and phenotypic evidence, we propose this mutation as the molecular basis for SCA37.
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29
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Hautbergue GM, Castelli LM, Ferraiuolo L, Sanchez-Martinez A, Cooper-Knock J, Higginbottom A, Lin YH, Bauer CS, Dodd JE, Myszczynska MA, Alam SM, Garneret P, Chandran JS, Karyka E, Stopford MJ, Smith EF, Kirby J, Meyer K, Kaspar BK, Isaacs AM, El-Khamisy SF, De Vos KJ, Ning K, Azzouz M, Whitworth AJ, Shaw PJ. SRSF1-dependent nuclear export inhibition of C9ORF72 repeat transcripts prevents neurodegeneration and associated motor deficits. Nat Commun 2017; 8:16063. [PMID: 28677678 PMCID: PMC5504286 DOI: 10.1038/ncomms16063] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 05/24/2017] [Indexed: 12/13/2022] Open
Abstract
Hexanucleotide repeat expansions in the C9ORF72 gene are the commonest known genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. Expression of repeat transcripts and dipeptide repeat proteins trigger multiple mechanisms of neurotoxicity. How repeat transcripts get exported from the nucleus is unknown. Here, we show that depletion of the nuclear export adaptor SRSF1 prevents neurodegeneration and locomotor deficits in a Drosophila model of C9ORF72-related disease. This intervention suppresses cell death of patient-derived motor neuron and astrocytic-mediated neurotoxicity in co-culture assays. We further demonstrate that either depleting SRSF1 or preventing its interaction with NXF1 specifically inhibits the nuclear export of pathological C9ORF72 transcripts, the production of dipeptide-repeat proteins and alleviates neurotoxicity in Drosophila, patient-derived neurons and neuronal cell models. Taken together, we show that repeat RNA-sequestration of SRSF1 triggers the NXF1-dependent nuclear export of C9ORF72 transcripts retaining expanded hexanucleotide repeats and reveal a novel promising therapeutic target for neuroprotection.
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Affiliation(s)
- Guillaume M. Hautbergue
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Lydia M. Castelli
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Laura Ferraiuolo
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Alvaro Sanchez-Martinez
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Adrian Higginbottom
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Claudia S. Bauer
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Jennifer E. Dodd
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Monika A. Myszczynska
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Sarah M. Alam
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Pierre Garneret
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Jayanth S. Chandran
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Evangelia Karyka
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Matthew J. Stopford
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Emma F. Smith
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Kathrin Meyer
- Nationwide Children’s Research Institute, Department of Pediatrics, The Ohio State University, 700 Children’s Drive, Rm. WA3022, Columbus, Ohio 43205, USA
| | - Brian K. Kaspar
- Nationwide Children’s Research Institute, Department of Pediatrics, The Ohio State University, 700 Children’s Drive, Rm. WA3022, Columbus, Ohio 43205, USA
| | - Adrian M. Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Sherif F. El-Khamisy
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
| | - Kurt J. De Vos
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Ke Ning
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Mimoun Azzouz
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Alexander J. Whitworth
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
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