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Negrutskii BS, Porubleva LV, Malinowska A, Novosylna OV, Dadlez M, Knudsen CR. Understanding functions of eEF1 translation elongation factors beyond translation. A proteomic approach. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:67-99. [PMID: 38220433 DOI: 10.1016/bs.apcsb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Mammalian translation elongation factors eEF1A1 and eEF1A2 are 92% homologous isoforms whose mutually exclusive tissue-specific expression is regulated during development. The isoforms have similar translation functionality, but show differences in spatial organization and participation in various processes, such as oncogenesis and virus reproduction. The differences may be due to their ability to interact with isoform-specific partner proteins. We used the identified sets of eEF1A1 or eEF1A2 partner proteins to identify cell complexes and/or processes specific to one particular isoform. As a result, we found isoform-specific interactions reflecting the involvement of different eEF1A isoforms in different cellular processes, including actin-related, chromatin-remodeling, ribonuclease H2, adenylyl cyclase, and Cul3-RING ubiquitin ligase complexes as well as initiation of mitochondrial transcription. An essential by-product of our analysis is the elucidation of a number of cellular processes beyond protein biosynthesis, where both isoforms appear to participate such as large ribosomal subunit biogenesis, mRNA splicing, DNA mismatch repair, 26S proteasome activity, P-body and exosomes formation, protein targeting to the membrane. This information suggests that a relatively high content of eEF1A in the cell may be necessary not only to maintain efficient translation, but also to ensure its participation in various cellular processes, where some roles of eEF1A have not yet been described. We believe that the data presented here will be useful for deciphering new auxiliary functions of eEF1A and its isoforms, and provide a new look at the known non-canonical functions of this main component of the human translation-elongation machinery.
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Affiliation(s)
- Boris S Negrutskii
- Institute of Molecular Biology and Genetics, Kyiv, Ukraine; Aarhus Institute of Advanced Sciences, Høegh-Guldbergs, Aarhus C, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen, Aarhus C, Denmark.
| | | | - Agata Malinowska
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego, Warsaw, Poland
| | | | - Michal Dadlez
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego, Warsaw, Poland
| | - Charlotte R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen, Aarhus C, Denmark
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2
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Kurosaki T, Ashizawa T. The genetic and molecular features of the intronic pentanucleotide repeat expansion in spinocerebellar ataxia type 10. Front Genet 2022; 13:936869. [PMID: 36199580 PMCID: PMC9528567 DOI: 10.3389/fgene.2022.936869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is characterized by progressive cerebellar neurodegeneration and, in many patients, epilepsy. This disease mainly occurs in individuals with Indigenous American or East Asian ancestry, with strong evidence supporting a founder effect. The mutation causing SCA10 is a large expansion in an ATTCT pentanucleotide repeat in intron 9 of the ATXN10 gene. The ATTCT repeat is highly unstable, expanding to 280–4,500 repeats in affected patients compared with the 9–32 repeats in normal individuals, one of the largest repeat expansions causing neurological disorders identified to date. However, the underlying molecular basis of how this huge repeat expansion evolves and contributes to the SCA10 phenotype remains largely unknown. Recent progress in next-generation DNA sequencing technologies has established that the SCA10 repeat sequence has a highly heterogeneous structure. Here we summarize what is known about the structure and origin of SCA10 repeats, discuss the potential contribution of variant repeats to the SCA10 disease phenotype, and explore how this information can be exploited for therapeutic benefit.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
- Center for RNA Biology, University of Rochester, Rochester, NY, United States
- *Correspondence: Tatsuaki Kurosaki, ; Tetsuo Ashizawa,
| | - Tetsuo Ashizawa
- Stanley H. Appel Department of Neurology, Houston Methodist Research Institute and Weil Cornell Medical College at Houston Methodist Houston, TX, United States
- *Correspondence: Tatsuaki Kurosaki, ; Tetsuo Ashizawa,
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3
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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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Bentley-Ford MR, Andersen RS, Croyle MJ, Haycraft CJ, Clearman KR, Foote JB, Reiter JF, Yoder BK. ATXN10 Is Required for Embryonic Heart Development and Maintenance of Epithelial Cell Phenotypes in the Adult Kidney and Pancreas. Front Cell Dev Biol 2021; 9:705182. [PMID: 34970537 PMCID: PMC8712648 DOI: 10.3389/fcell.2021.705182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Atxn10 is a gene known for its role in cytokinesis and is associated with spinocerebellar ataxia (SCA10), a slowly progressing cerebellar syndrome caused by an intragenic pentanucleotide repeat expansion. Atxn10 is also implicated in the ciliopathy syndromes nephronophthisis (NPHP) and Joubert syndrome (JBTS), which are caused by the disruption of cilia function leading to nephron loss, impaired renal function, and cerebellar hypoplasia. How Atxn10 disruption contributes to these disorders remains unknown. Here, we generated Atxn10 congenital and conditional mutant mouse models. Our data indicate that while ATXN10 protein can be detected around the base of the cilium as well as in the cytosol, its loss does not cause overt changes in cilia formation or morphology. Congenital loss of Atxn10 results in embryonic lethality around E10.5 associated with pericardial effusion and loss of trabeculation. Similarly, tissue-specific loss of ATXN10 in the developing endothelium (Tie2-Cre) and myocardium (cTnT-Cre) also results in embryonic lethality with severe cardiac malformations occurring in the latter. Using an inducible Cagg-CreER to disrupt ATXN10 systemically at postnatal stages, we show that ATXN10 is also required for survival in adult mice. Loss of ATXN10 results in severe pancreatic and renal abnormalities leading to lethality within a few weeks post ATXN10 deletion in adult mice. Evaluation of these phenotypes further identified rapid epithelial-to-mesenchymal transition (EMT) in these tissues. In the pancreas, the phenotype includes signs of both acinar to ductal metaplasia and EMT with aberrant cilia formation and severe defects in glucose homeostasis related to pancreatic insufficiency or defects in feeding or nutrient intake. Collectively, this study identifies ATXN10 as an essential protein for survival.
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Affiliation(s)
- Melissa R. Bentley-Ford
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Reagan S. Andersen
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mandy J. Croyle
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Courtney J. Haycraft
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kelsey R. Clearman
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jeremy B. Foote
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jeremy F. Reiter
- Department of Biochemistry and Biophysics, University of Alabama at Birmingham, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, United States
| | - Bradley K. Yoder
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
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5
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Ataxin-10 Inhibits TNF- α-Induced Endothelial Inflammation via Suppressing Interferon Regulatory Factor-1. Mediators Inflamm 2021; 2021:7042148. [PMID: 34858081 PMCID: PMC8632433 DOI: 10.1155/2021/7042148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/01/2021] [Indexed: 02/08/2023] Open
Abstract
Endothelial inflammation is a crucial event in the initiation of atherosclerosis. Here, we identify Ataxin-10 protein as a novel negative modulator of endothelial activation by suppressing IRF-1 transcription activity. The protein level of Ataxin-10 is relatively higher in human vascular endothelial cells, which can be significantly suppressed by TNF-α in both HUVECs and HLMECs. Overexpression of Ataxin-10 markedly inhibited the mRNA expressions of VCAM-1 and several cytokines including MCP-1, CXCL-1, CCL-5, and TNF-α; thus, it can also suppress monocyte adhesion to endothelial cells. Accordingly, Ataxin-10 silencing promoted endothelial inflammation. However, Ataxin-10 did not affect the MAPK/NF-κB signaling pathway stimulated by TNF-α in HUVECs. Using the yeast two-hybrid assay, we found that Ataxin-10 can directly bind to interferon regulatory factor-1 (IRF-1). Upon TNF-α stimulation, Ataxin-10 promoted the cytoplasmic localization of IRF-1, which inhibited the transcription of VCAM-1. Moreover, knockdown of IRF-1 can eliminate the effect of Ataxin-10 on the expression of VCAM-1 in HUVECs induced by TNF-α. Taken together, these results indicate that Ataxin-10 inhibits endothelial cell activation and may serve as a promising therapeutic target for some vascular inflammatory-related diseases such as atherosclerosis.
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6
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Molecular genetics of renal ciliopathies. Biochem Soc Trans 2021; 49:1205-1220. [PMID: 33960378 DOI: 10.1042/bst20200791] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/25/2022]
Abstract
Renal ciliopathies are a heterogenous group of inherited disorders leading to an array of phenotypes that include cystic kidney disease and renal interstitial fibrosis leading to progressive chronic kidney disease and end-stage kidney disease. The renal tubules are lined with epithelial cells that possess primary cilia that project into the lumen and act as sensory and signalling organelles. Mutations in genes encoding ciliary proteins involved in the structure and function of primary cilia cause ciliopathy syndromes and affect many organ systems including the kidney. Recognised disease phenotypes associated with primary ciliopathies that have a strong renal component include autosomal dominant and recessive polycystic kidney disease and their various mimics, including atypical polycystic kidney disease and nephronophthisis. The molecular investigation of inherited renal ciliopathies often allows a precise diagnosis to be reached where renal histology and other investigations have been unhelpful and can help in determining kidney prognosis. With increasing molecular insights, it is now apparent that renal ciliopathies form a continuum of clinical phenotypes with disease entities that have been classically described as dominant or recessive at both extremes of the spectrum. Gene-dosage effects, hypomorphic alleles, modifier genes and digenic inheritance further contribute to the genetic complexity of these disorders. This review will focus on recent molecular genetic advances in the renal ciliopathy field with a focus on cystic kidney disease phenotypes and the genotypes that lead to them. We discuss recent novel insights into underlying disease mechanisms of renal ciliopathies that might be amenable to therapeutic intervention.
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7
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Ng SS, Park JE, Meng W, Chen CP, Kalaria RN, McCarthy NE, Sze SK. Pulsed SILAM Reveals In Vivo Dynamics of Murine Brain Protein Translation. ACS OMEGA 2020; 5:13528-13540. [PMID: 32566817 PMCID: PMC7301365 DOI: 10.1021/acsomega.9b04439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
Identification of proteins that are synthesized de novo in response to specific microenvironmental cues is critical for understanding molecular mechanisms that underpin vital physiological processes and pathologies. Here, we report that a brief period of SILAM (Stable Isotope Labeling of Mammals) diet enables the determination of biological functions corresponding to actively translating proteins in the mouse brain. Our results demonstrate that the synapse, dendrite, and myelin sheath are highly active neuronal structures that display rapid protein synthesis, producing key mediators of chemical signaling as well as nutrient sensing, lipid metabolism, and amyloid precursor protein processing/stability. Together, these findings confirm that protein metabolic activity varies significantly between brain functional units in vivo. Our data indicate that pulsed SILAM approaches can unravel complex protein expression dynamics in the murine brain and identify active synthetic pathways and associated functions that are likely impaired in neurodegenerative diseases.
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Affiliation(s)
- Ser Sue Ng
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang Drive, 637551 Singapore
| | - Jung Eun Park
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang Drive, 637551 Singapore
| | - Wei Meng
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang Drive, 637551 Singapore
| | - Christopher P. Chen
- Memory,
Aging and Cognition Centre, National University
Health System, 1E Kent
Ridge Road, 119228 Singapore
- Department
of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Blk MD3, 16 Medical Drive, 117600 Singapore
| | - Raj N. Kalaria
- Institute
of Neuroscience, Campus for Ageing and Vitality, Newcastle University, Newcastle
upon Tyne NE4 5PL, U.K.
| | - Neil E. McCarthy
- Centre
for Immunobiology, The Blizard Institute, Bart’s and The London
School of Medicine and Dentistry, Queen
Mary University of London, 4 Newark St, London E1
2AT, U.K.
| | - Siu Kwan Sze
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang Drive, 637551 Singapore
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8
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Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Syst 2020; 10:333-350.e14. [PMID: 32325033 PMCID: PMC7938770 DOI: 10.1016/j.cels.2020.03.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 11/25/2019] [Accepted: 03/20/2020] [Indexed: 12/12/2022]
Abstract
Connectivity webs mediate the unique biology of the mammalian brain. Yet, while cell circuit maps are increasingly available, knowledge of their underlying molecular networks remains limited. Here, we applied multi-dimensional biochemical fractionation with mass spectrometry and machine learning to survey endogenous macromolecules across the adult mouse brain. We defined a global "interactome" comprising over one thousand multi-protein complexes. These include hundreds of brain-selective assemblies that have distinct physical and functional attributes, show regional and cell-type specificity, and have links to core neurological processes and disorders. Using reciprocal pull-downs and a transgenic model, we validated a putative 28-member RNA-binding protein complex associated with amyotrophic lateral sclerosis, suggesting a coordinated function in alternative splicing in disease progression. This brain interaction map (BraInMap) resource facilitates mechanistic exploration of the unique molecular machinery driving core cellular processes of the central nervous system. It is publicly available and can be explored here https://www.bu.edu/dbin/cnsb/mousebrain/.
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Affiliation(s)
- Reza Pourhaghighi
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Peter E A Ash
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - Sadhna Phanse
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Regina, Regina, SK, Canada; Center for Network Systems Biology, Boston University, Boston, MA, USA
| | - Florian Goebels
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Lucas Z M Hu
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Siwei Chen
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Yingying Zhang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Shayne D Wierbowski
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Samantha Boudeau
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | | | - Ramy H Malty
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Edyta Malolepsza
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
| | - Kalliopi Tsafou
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
| | - Aparna Nathan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
| | - Graham Cromar
- Program in Molecular Medicine, Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Hongbo Guo
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Ali Al Abdullatif
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - Daniel J Apicco
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - Lindsay A Becker
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Stefan M Pulst
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | - Ahmed Youssef
- Program in Bioinformatics, Boston University, Boston, MA, USA; Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA, USA
| | - Ryan Hekman
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA, USA
| | - Pierre C Havugimana
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA, USA; Departments of Biochemistry and Biology, Boston University, Boston, MA, USA
| | - Carl A White
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA, USA
| | - Benjamin C Blum
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA, USA
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS, Milan, Italy
| | - Camron D Bryant
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - John Parkinson
- Program in Molecular Medicine, Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Kasper Lage
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Haiyuan Yu
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Gary D Bader
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Benjamin Wolozin
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA; Department of Neurology, Boston University School of Medicine, Boston, MA, USA; Program in Neuroscience, Boston University, Boston, MA, USA.
| | - Andrew Emili
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Program in Bioinformatics, Boston University, Boston, MA, USA; Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA, USA; Departments of Biochemistry and Biology, Boston University, Boston, MA, USA.
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9
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Borghini L, Png E, Binder A, Wright VJ, Pinnock E, de Groot R, Hazelzet J, Emonts M, Van der Flier M, Schlapbach LJ, Anderson S, Secka F, Salas A, Fink C, Carrol ED, Pollard AJ, Coin LJ, Kuijpers TW, Martinon-Torres F, Zenz W, Levin M, Hibberd ML, Davila S. Identification of regulatory variants associated with genetic susceptibility to meningococcal disease. Sci Rep 2019; 9:6966. [PMID: 31061469 PMCID: PMC6502852 DOI: 10.1038/s41598-019-43292-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/17/2019] [Indexed: 12/30/2022] Open
Abstract
Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remains challenging. Here, we employed a novel approach to interrogate the genetic risk of such polymorphisms in a more systematic way by targeting specific regulatory regions relevant for the phenotype studied. We applied this method to meningococcal disease susceptibility, using the DNA binding pattern of RELA – a NF-kB subunit, master regulator of the response to infection – under bacterial stimuli in nasopharyngeal epithelial cells. We designed a custom panel to cover these RELA binding sites and used it for targeted sequencing in cases and controls. Variant calling and association analysis were performed followed by validation of candidate polymorphisms by genotyping in three independent cohorts. We identified two new polymorphisms, rs4823231 and rs11913168, showing signs of association with meningococcal disease susceptibility. In addition, using our genomic data as well as publicly available resources, we found evidences for these SNPs to have potential regulatory effects on ATXN10 and LIF genes respectively. The variants and related candidate genes are relevant for infectious diseases and may have important contribution for meningococcal disease pathology. Finally, we described a novel genetic association approach that could be applied to other phenotypes.
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Affiliation(s)
- Lisa Borghini
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore. .,Infectious diseases, Genome Institute of Singapore, Singapore, Singapore.
| | - Eileen Png
- Infectious diseases, Genome Institute of Singapore, Singapore, Singapore
| | - Alexander Binder
- Department of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Victoria J Wright
- Section for Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - Ellie Pinnock
- Micropathology Ltd, University of Warwick, Warwick, UK
| | - Ronald de Groot
- Department of Pediatrics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan Hazelzet
- Department of Pediatrics, Erasmus Medical Center-Sophia Children's hospital, University Medical Center, Rotterdam, The Netherlands
| | - Marieke Emonts
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom.,Paediatric Infectious Diseases and Immunology Department, Newcastle upon Tyne Hospitals Foundation Trust, Great North Children's Hospital, Newcastle upon Tyne, United Kingdom
| | - Michiel Van der Flier
- Department of Pediatrics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Luregn J Schlapbach
- Faculty of Medicine, The University of Queensland, Brisbane, Australia.,Paediatric Critical Care Research Group, Mater Research Institute, University of Queensland, Brisbane, Australia.,Paediatric Intensive Care Unit, Lady Cilento Children's Hospital, Brisbane, Australia.,Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Fatou Secka
- Medical Research Council Unit Gambia, Banjul, The Gambia
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Colin Fink
- Micropathology Ltd, University of Warwick, Warwick, UK
| | - Enitan D Carrol
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Lachlan J Coin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Taco W Kuijpers
- Division of Pediatric Hematology, Immunology and Infectious diseases, Emma Children's Hospital Academic Medical Center, Amsterdam, The Netherlands
| | - Federico Martinon-Torres
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - Werner Zenz
- Department of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Michael Levin
- Section for Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - Martin L Hibberd
- Infectious diseases, Genome Institute of Singapore, Singapore, Singapore.,Infectious and Tropical Disease, London School of Hygiene & Tropical Medicine, London, UK
| | - Sonia Davila
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore. .,SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore. .,Duke-NUS Medical School, Singapore, Singapore.
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10
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Tian J, Shi Y, Nai S, Geng Q, Zhang L, Wei GH, Xu X, Li J. Ataxin-10 is involved in Golgi membrane dynamics. J Genet Genomics 2017; 44:549-552. [PMID: 29169923 DOI: 10.1016/j.jgg.2017.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/18/2022]
Affiliation(s)
- Jie Tian
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China; Molecular & Environmental Plant Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Yingxin Shi
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Shanshan Nai
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Qizhi Geng
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Leiliang Zhang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu 90014, Finland
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China; Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen 518060, China.
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China.
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11
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Kollipara L, Buchkremer S, Coraspe JAG, Hathazi D, Senderek J, Weis J, Zahedi RP, Roos A. In-depth phenotyping of lymphoblastoid cells suggests selective cellular vulnerability in Marinesco-Sjögren syndrome. Oncotarget 2017; 8:68493-68516. [PMID: 28978133 PMCID: PMC5620273 DOI: 10.18632/oncotarget.19663] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/28/2017] [Indexed: 12/18/2022] Open
Abstract
SIL1 is a ubiquitous protein of the Endoplasmic Reticulum (ER) acting as a co-chaperone for the ER-resident chaperone, BiP. Recessive mutations of the corresponding gene lead to vulnerability of skeletal muscle and central nervous system in man (Marinesco-Sjögren syndrome; MSS) and mouse. However, it is still unclear how loss of ubiquitous SIL1 leads to selective vulnerability of the nervous system and skeletal muscle whereas other cells and organs are protected from clinical manifestations. In this study we aimed to disentangle proteins participating in selective vulnerability of SIL1-deficient cells and tissues: morphological examination of MSS patient-derived lymphoblastoid cells revealed altered organelle structures (ER, nucleus and mitochondria) thus showing subclinical vulnerability. To correlate structural perturbations with biochemical changes and to identify proteins potentially preventing phenotypical manifestation, proteomic studies have been carried out. Results of proteomic profiling are in line with the morphological findings and show affection of nuclear, mitochondrial and cytoskeletal proteins as well as of such responsible for cellular viability. Moreover, expression patterns of proteins known to be involved in neuromuscular disorders or in development and function of the nervous system were altered. Paradigmatic findings were confirmed by immunohistochemistry of splenic lymphocytes and the cerebellum of SIL1-deficient mice. Ataxin-10, identified with increased abundance in our proteome profile, is necessary for the neuronal survival but also controls muscle fiber apoptosis, thus declaring this protein as a plausible candidate for selective tissue vulnerability. Our combined results provide first insights into the molecular causes of selective cell and tissue vulnerability defining the MSS phenotype.
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Affiliation(s)
- Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften-ISAS -e.V., 44227 Dortmund, Germany
| | - Stephan Buchkremer
- Institute of Neuropathology, University Hospital Aachen, RWTH Aachen, 5274 Aachen, Germany
| | | | - Denisa Hathazi
- Leibniz-Institut für Analytische Wissenschaften-ISAS -e.V., 44227 Dortmund, Germany
| | - Jan Senderek
- Friedrich-Baur-Institute, Medical Faculty, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - Joachim Weis
- Institute of Neuropathology, University Hospital Aachen, RWTH Aachen, 5274 Aachen, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS -e.V., 44227 Dortmund, Germany
| | - Andreas Roos
- Leibniz-Institut für Analytische Wissenschaften-ISAS -e.V., 44227 Dortmund, Germany.,Institute of Neuropathology, University Hospital Aachen, RWTH Aachen, 5274 Aachen, Germany.,The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
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12
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Bitsika V, Duveau V, Simon-Areces J, Mullen W, Roucard C, Makridakis M, Mermelekas G, Savvopoulos P, Depaulis A, Vlahou A. High-Throughput LC–MS/MS Proteomic Analysis of a Mouse Model of Mesiotemporal Lobe Epilepsy Predicts Microglial Activation Underlying Disease Development. J Proteome Res 2016; 15:1546-62. [DOI: 10.1021/acs.jproteome.6b00003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Vasiliki Bitsika
- Biotechnology
Division, Biomedical Research Foundation, Academy of Athens, Soranou
Efessiou 4, 11527 Athens, Greece
| | | | - Julia Simon-Areces
- Inserm,
U1216, Grenoble-Institut des Neurosciences, F-38000 Grenoble, France
| | - William Mullen
- BHF
Glasgow Cardiovascular Research Centre, University of Glasgow, G12 8QQ Glasgow, United Kingdom
| | | | - Manousos Makridakis
- Biotechnology
Division, Biomedical Research Foundation, Academy of Athens, Soranou
Efessiou 4, 11527 Athens, Greece
| | - George Mermelekas
- Biotechnology
Division, Biomedical Research Foundation, Academy of Athens, Soranou
Efessiou 4, 11527 Athens, Greece
| | - Pantelis Savvopoulos
- Biotechnology
Division, Biomedical Research Foundation, Academy of Athens, Soranou
Efessiou 4, 11527 Athens, Greece
| | - Antoine Depaulis
- Inserm,
U1216, Grenoble-Institut des Neurosciences, F-38000 Grenoble, France
| | - Antonia Vlahou
- Biotechnology
Division, Biomedical Research Foundation, Academy of Athens, Soranou
Efessiou 4, 11527 Athens, Greece
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13
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Tian J, Tian C, Ding Y, Li Z, Geng Q, Xiahou Z, Wang J, Hou W, Liao J, Dong MQ, Xu X, Li J. Aurora B-dependent phosphorylation of Ataxin-10 promotes the interaction between Ataxin-10 and Plk1 in cytokinesis. Sci Rep 2015; 5:8360. [PMID: 25666058 PMCID: PMC4322367 DOI: 10.1038/srep08360] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 01/19/2015] [Indexed: 11/09/2022] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurologic disorder caused by ATTCT expansion in the ATXN10 gene. Previous investigations have identified that depletion of Ataxin-10, the gene product, leads to cellular apoptosis and cytokinesis failure. Herein we identify the mitotic kinase Aurora B as an Ataxin-10 interacting partner. Aurora B interacts with and phosphorylates Ataxin-10 at S12, as evidenced by in vitro kinase and mass spectrometry analysis. Both endogenous and S12-phosphorylated Ataxin-10 localizes to the midbody during cytokinesis, and cytokinetic defects induced by inhibition of ATXN10 expression is not rescued by the S12A mutant. Inhibition of Aurora B or expression of the S12A mutant renders reduced interaction between Ataxin-10 and polo-like kinase 1 (Plk1), a kinase previously identified to regulate Ataxin-10 in cytokinesis. Taken together, we propose a model that Aurora B phosphorylates Ataxin-10 at S12 to promote the interaction between Ataxin-10 and Plk1 in cytokinesis. These findings identify an Aurora B-dependent mechanism that implicates Ataxin-10 in cytokinesis.
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Affiliation(s)
- Jie Tian
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Chuan Tian
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yuehe Ding
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhe Li
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Qizhi Geng
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Zhikai Xiahou
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jue Wang
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Wenya Hou
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ji Liao
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing 100048, China
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14
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Cheng X, Gan L, Zhao J, Chen M, Liu Y, Wang Y. Changes in Ataxin-10 Expression after Sciatic Nerve Crush in Adult Rats. Neurochem Res 2013; 38:1013-21. [DOI: 10.1007/s11064-013-1011-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/19/2013] [Accepted: 02/23/2013] [Indexed: 01/22/2023]
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15
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Transgenic models of spinocerebellar ataxia type 10: modeling a repeat expansion disorder. Genes (Basel) 2012; 3:481-491. [PMID: 24533179 PMCID: PMC3899997 DOI: 10.3390/genes3030481] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 07/24/2012] [Accepted: 07/26/2012] [Indexed: 01/01/2023] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurodegenerative disease with a spectrum of phenotypes. SCA10 is caused by a pentanucleotide repeat expansion of the ATTCT motif within intron 9 of ATAXIN 10 (ATXN10). Patients present with cerebellar ataxia; however, a subset also develops epileptic seizures which significantly contribute to the morbidity and mortality of the disease. Past research from our lab has demonstrated that epileptic SCA10 patients predominantly originate from or have ancestral ties to Mexico. In addition, a large proportion of epileptic SCA10 patients carry repeat interruptions within their SCA10 expansion. This paper outlines the variability in SCA10 phenotypes and our attempts to model these phenotypes using transgenic mouse models and highlights the benefits of using a transgenic model organism to understand the pathological mechanisms of a human disease.
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16
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Affiliation(s)
- Tetsuo Ashizawa
- Department of Neurology, Evelyn & WIlliam L. McKinght Brain Institute, University of Florida, Gainesville, FL, USA.
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17
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White M, Xia G, Gao R, Wakamiya M, Sarkar PS, McFarland K, Ashizawa T. Transgenic mice with SCA10 pentanucleotide repeats show motor phenotype and susceptibility to seizure: a toxic RNA gain-of-function model. J Neurosci Res 2011; 90:706-14. [PMID: 22065565 DOI: 10.1002/jnr.22786] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Revised: 08/04/2011] [Accepted: 08/16/2011] [Indexed: 11/11/2022]
Abstract
Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurodegenerative disorder manifested by ataxia and seizure. SCA10 is caused by a large expansion of an intronic ATTCT pentanucleotide repeat in the ATXN10 gene. We have recently postulated a toxic RNA-mediated gain of function in the pathogenesis of spinal cerebellar ataxia type 10 (SCA10). The spliced intron-9 RNA containing the expanded AUUCU repeat aggregates in SCA10 cells and sequesters hnRNP K. hnRNP K sequestration triggers the translocation of protein kinase Cδ (PKCδ) to mitochondria, leading to activation of caspase-3 and apoptosis. To confirm the toxic RNA-mediated gain of function, we generated a new transgenic mouse model in which the expanded pentanucleotide repeats are constructed in the 3'-untranslated region (3'UTR) to ensure transcription without translation of the repeat. We constructed an artificial transgene containing the SCA10 (ATTCT)(500) track within the 3'UTR of the LacZ gene driven by the rat prion promoter (PrP) and used this to generate a new transgenic mouse model for SCA10. We then examined these mice for neurological phenotypes and histopathological, molecular, and cellular changes. The transgenic mice showed irregular gait and increased seizure susceptibility at the age of 6 months, resembling the clinical phenotype of SCA10. The cerebral cortex, hippocampus, and pontine nuclei showed neuronal loss. The brains of these animals also showed molecular and cellular changes similar to those previously found in an SCA10 cell model. Expression of the expanded SCA10 AUUCU repeat within the 3'UTR of a gene results in neuronal loss with associated gait abnormalities and increased seizure susceptibility phenotypes, which resemble those seen in SCA10 patients. Moreover, these results bolster the idea that the SCA10 disease mechanism is mediated by a toxic RNA gain-of-function mutation of the expanded AUUCU repeat.
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Affiliation(s)
- Misti White
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, USA
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18
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Sang L, Miller JJ, Corbit KC, Giles RH, Brauer MJ, Otto EA, Baye LM, Wen X, Scales SJ, Kwong M, Huntzicker EG, Sfakianos MK, Sandoval W, Bazan JF, Kulkarni P, Garcia-Gonzalo FR, Seol AD, O'Toole JF, Held S, Reutter HM, Lane WS, Rafiq MA, Noor A, Ansar M, Devi ARR, Sheffield VC, Slusarski DC, Vincent JB, Doherty DA, Hildebrandt F, Reiter JF, Jackson PK. Mapping the NPHP-JBTS-MKS protein network reveals ciliopathy disease genes and pathways. Cell 2011; 145:513-28. [PMID: 21565611 DOI: 10.1016/j.cell.2011.04.019] [Citation(s) in RCA: 455] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 03/16/2011] [Accepted: 04/27/2011] [Indexed: 12/18/2022]
Abstract
Nephronophthisis (NPHP), Joubert (JBTS), and Meckel-Gruber (MKS) syndromes are autosomal-recessive ciliopathies presenting with cystic kidneys, retinal degeneration, and cerebellar/neural tube malformation. Whether defects in kidney, retinal, or neural disease primarily involve ciliary, Hedgehog, or cell polarity pathways remains unclear. Using high-confidence proteomics, we identified 850 interactors copurifying with nine NPHP/JBTS/MKS proteins and discovered three connected modules: "NPHP1-4-8" functioning at the apical surface, "NPHP5-6" at centrosomes, and "MKS" linked to Hedgehog signaling. Assays for ciliogenesis and epithelial morphogenesis in 3D renal cultures link renal cystic disease to apical organization defects, whereas ciliary and Hedgehog pathway defects lead to retinal or neural deficits. Using 38 interactors as candidates, linkage and sequencing analysis of 250 patients identified ATXN10 and TCTN2 as new NPHP-JBTS genes, and our Tctn2 mouse knockout shows neural tube and Hedgehog signaling defects. Our study further illustrates the power of linking proteomic networks and human genetics to uncover critical disease pathways.
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Affiliation(s)
- Liyun Sang
- Genentech Inc., South San Francisco, CA 94080, USA
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19
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Rovillain E, Mansfield L, Lord CJ, Ashworth A, Jat PS. An RNA interference screen for identifying downstream effectors of the p53 and pRB tumour suppressor pathways involved in senescence. BMC Genomics 2011; 12:355. [PMID: 21740549 PMCID: PMC3161017 DOI: 10.1186/1471-2164-12-355] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 07/08/2011] [Indexed: 12/28/2022] Open
Abstract
Background Cellular senescence is an irreversible cell cycle arrest that normal cells undergo in response to progressive shortening of telomeres, changes in telomeric structure, oncogene activation or oxidative stress and acts as an important tumour suppressor mechanism. Results To identify the downstream effectors of the p53-p21 and p16-pRB tumour suppressor pathways crucial for mediating entry into senescence, we have carried out a loss-of-function RNA interference screen in conditionally immortalised human fibroblasts that can be induced to rapidly undergo senescence, whereas in primary cultures senescence is stochastic and occurs asynchronously. These cells are immortal but undergo a rapid irreversible arrest upon activation of the p53-p21 and p16-pRB pathways that can be readily bypassed upon their inactivation. The primary screen identified 112 known genes including p53 and another 29 shRNAmirs targetting as yet unidentified loci. Comparison of these known targets with genes known to be up-regulated upon senescence in these cells, by micro-array expression profiling, identified 4 common genes TMEM9B, ATXN10, LAYN and LTBP2/3. Direct silencing of these common genes, using lentiviral shRNAmirs, bypassed senescence in the conditionally immortalised cells. Conclusion The senescence bypass screen identified TMEM9B, ATXN10, LAYN and LTBP2/3 as novel downstream effectors of the p53-p21 and p16-pRB tumour suppressor pathways. Although none of them has previously been linked to cellular senescence, TMEM9B has been suggested to be an upstream activator of NF-κB signalling which has been found to have a causal role in promoting senescence. Future studies will focus on determining on how many of the other primary hits also have a casual role in senescence and what is the mechanism of action.
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Affiliation(s)
- Emilie Rovillain
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
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20
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Teive HAG, Munhoz RP, Arruda WO, Raskin S, Werneck LC, Ashizawa T. Spinocerebellar ataxia type 10 - A review. Parkinsonism Relat Disord 2011; 17:655-61. [PMID: 21531163 DOI: 10.1016/j.parkreldis.2011.04.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 04/02/2011] [Accepted: 04/03/2011] [Indexed: 10/18/2022]
Abstract
Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant inherited ataxia caused by an expanded ATTCT pentanucleotide repeat in intron 9 of the ATXN10 gene, on chromosome 22q13.3. SCA10 represents a rare form of SCA, until now only described in Latin America, particularly in Mexico, Brazil, Argentina and Venezuela. In Mexico and Brazil SCA10 represents the second most common type of autosomal dominant cerebellar ataxia. The phenotype described in Mexico, is characterized by the association of cerebellar ataxia with epilepsy, while in Brazil the SCA10 phenotype is that of a pure cerebellar ataxia. As yet unidentified genotypic variables may account for this phenotypic difference.
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Affiliation(s)
- Hélio A G Teive
- Movement Disorders Unit, Neurology Service, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, PR, Brazil.
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Boulisfane N, Choleza M, Rage F, Neel H, Soret J, Bordonné R. Impaired minor tri-snRNP assembly generates differential splicing defects of U12-type introns in lymphoblasts derived from a type I SMA patient. Hum Mol Genet 2010; 20:641-8. [PMID: 21098506 DOI: 10.1093/hmg/ddq508] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The survival of motor neuron (SMN) protein is essential for cytoplasmic assembly of spliceosomal snRNPs. Although the normal proportion of endogenous snRNAs is unevenly altered in spinal muscular atrophy (SMA) tissues, the biogenesis of individual snRNPs is not dramatically affected in SMN-deficient cells. The SMN protein is also required for normal Cajal body (CB) formation, but the functional consequences of CB disruption upon SMN deficiency have not yet been analyzed at the level of macromolecular snRNPs assembly. Here, we show that the SMN protein is required for tri-snRNPs formation and that the level of the minor U4atac/U6atac/U5 tri-snRNPs is dramatically decreased in lymphoblasts derived from a patient suffering from a severe form of SMA. We found also that splicing of some, but not all, minor introns is inhibited in these cells, demonstrating links between SMN deficiency and differential alterations of splicing events mediated by the minor spliceosome. Our results suggest that SMA might result from the inefficient splicing of one or only a few pre-mRNAs carrying minor introns and coding for proteins required for motor neurons function and/or organization.
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Affiliation(s)
- Nawal Boulisfane
- Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS UMR 5535/IFR122, Université Montpellier I and II,1919 route de Mende, 34293 Montpellier Cedex 5, France
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22
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White MC, Gao R, Xu W, Mandal SM, Lim JG, Hazra TK, Wakamiya M, Edwards SF, Raskin S, Teive HAG, Zoghbi HY, Sarkar PS, Ashizawa T. Inactivation of hnRNP K by expanded intronic AUUCU repeat induces apoptosis via translocation of PKCdelta to mitochondria in spinocerebellar ataxia 10. PLoS Genet 2010; 6:e1000984. [PMID: 20548952 PMCID: PMC2883596 DOI: 10.1371/journal.pgen.1000984] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 05/12/2010] [Indexed: 01/20/2023] Open
Abstract
We have identified a large expansion of an ATTCT repeat within intron 9 of ATXN10 on chromosome 22q13.31 as the genetic mutation of spinocerebellar ataxia type 10 (SCA10). Our subsequent studies indicated that neither a gain nor a loss of function of ataxin 10 is likely the major pathogenic mechanism of SCA10. Here, using SCA10 cells, and transfected cells and transgenic mouse brain expressing expanded intronic AUUCU repeats as disease models, we show evidence for a key pathogenic molecular mechanism of SCA10. First, we studied the fate of the mutant repeat RNA by in situ hybridization. A Cy3-(AGAAU)10 riboprobe detected expanded AUUCU repeats aggregated in foci in SCA10 cells. Pull-down and co-immunoprecipitation data suggested that expanded AUUCU repeats within the spliced intronic sequence strongly bind to hnRNP K. Co-localization of hnRNP K and the AUUCU repeat aggregates in the transgenic mouse brain and transfected cells confirmed this interaction. To examine the impact of this interaction on hnRNP K function, we performed RT–PCR analysis of a splicing-regulatory target of hnRNP K, and found diminished hnRNP K activity in SCA10 cells. Cells expressing expanded AUUCU repeats underwent apoptosis, which accompanied massive translocation of PKCδ to mitochondria and activation of caspase 3. Importantly, siRNA–mediated hnRNP K deficiency also caused the same apoptotic event in otherwise normal cells, and over-expression of hnRNP K rescued cells expressing expanded AUUCU repeats from apoptosis, suggesting that the loss of function of hnRNP K plays a key role in cell death of SCA10. These results suggest that the expanded AUUCU–repeat in the intronic RNA undergoes normal transcription and splicing, but causes apoptosis via an activation cascade involving a loss of hnRNP K activities, massive translocation of PKCδ to mitochondria, and caspase 3 activation. In an earlier study, we showed that the mutation of spinocerebellar ataxia 10 (SCA10) is an enormous expansion of a gene segment, which contains a tandemly repeated 5-base (ATTCT) unit. Since SCA10 is the only known human disease that is proven to be caused by 5-base repeat expansion, it is important to learn how this novel class of mutation causes the disease. We found that the mutation produces an expanded RNA repeat, which aberrantly accumulates in SCA10 cells and interacts with a major RNA–binding protein. When we expressed expanded RNA repeats or decreased the RNA–binding protein level in cultured cells, either of these manipulations produced a specific type of cell death that is associated with a massive transfer of a key enzyme called protein kinase C delta to mitochondria. We also showed that either blocking the expanded AUUCU repeat or replenishing hnRNP K rescues cells from the cell death induced by the SCA10 mutation. Together, we conclude that the mutant RNA inactivates hnRNP K and kills cells by triggering the specific cell-death mechanism. Our data provide important clues for therapeutic intervention in SCA10.
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Affiliation(s)
- Misti C. White
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Rui Gao
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Weidong Xu
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Santi M. Mandal
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jung G. Lim
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tapas K. Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Maki Wakamiya
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sharon F. Edwards
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Salmo Raskin
- Center for Health and Biological Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | | | - Huda Y. Zoghbi
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, United States of America
| | - Partha S. Sarkar
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tetsuo Ashizawa
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Neurology, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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23
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The ATTCT repeats of spinocerebellar ataxia type 10 display strong nucleosome assembly which is enhanced by repeat interruptions. Gene 2009; 434:29-34. [DOI: 10.1016/j.gene.2008.12.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 12/07/2008] [Accepted: 12/15/2008] [Indexed: 12/19/2022]
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24
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Genetics and Pathogenesis of Inherited Ataxias and Spastic Paraplegias. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 652:263-96. [DOI: 10.1007/978-90-481-2813-6_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Abstract
PURPOSE OF REVIEW Here we discuss recent advances regarding the molecular genetic basis of dominantly inherited ataxias. RECENT FINDINGS Important recent observations include insights into the mechanisms by which expanded polyglutamine causes cerebellar degeneration; new findings regarding how noncoding expansions may cause disease; the discovery that conventional (i.e. nonrepeat) mutations underlie recently identified ataxias; and growing recognition that multiple biological pathways, when perturbed, can cause cerebellar degeneration. SUMMARY The dominant ataxias, also known as spinocerebellar ataxias, continue to grow in number. Here we review the major categories of spinocerebellar ataxias: expanded polyglutamine ataxias; noncoding repeat ataxias; and ataxias caused by conventional mutations. After discussing features shared by these disorders, we present recent evidence supporting a toxic protein mechanism for the polyglutamine spinocerebellar ataxias and the recognition that both protein misfolding and perturbations in nuclear events represent key events in pathogenesis. Less is known about pathogenic mechanisms in spinocerebellar ataxias due to noncoding repeats, though a toxic RNA effect remains possible. Newly discovered, conventional mutations in spinocerebellar ataxias suggest a wide range of biological pathways can be disrupted to cause progressive ataxia. Finally, we discuss how new mechanistic insights can drive the push toward preventive treatment.
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Affiliation(s)
- Bing-wen Soong
- Department of Neurology, National Yang-Ming University School of Medicine, The Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
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Chen R, Chang PA, Long DX, Liu CY, Yang L, Wu YJ. G protein beta2 subunit interacts directly with neuropathy target esterase and regulates its activity. Int J Biochem Cell Biol 2006; 39:124-32. [PMID: 16978909 DOI: 10.1016/j.biocel.2006.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Revised: 08/09/2006] [Accepted: 08/10/2006] [Indexed: 11/26/2022]
Abstract
Neuropathy target esterase (NTE) was identified as the primary target of organophosphate compounds that cause a delayed neuropathy with degeneration of nerve axons. NTE is a novel phospholipase B anchored to the cytoplasmic face of endoplasmic reticulum and essential for embryonic and nervous development. However, little is known about the regulation of NTE. A human fetal brain cDNA library was screened for proteins that interact with NTE, Gbeta2 and Gbeta2-like I subunits were found to be able to bind the C-terminal of NTE in yeast. The interaction of Gbeta2 and NTE was confirmed by in vivo co-immunoprecipitation analysis in COS7 cells. Furthermore, depletion of Gbeta2 by RNA interference down regulated the activity of NTE but not its expression level. In addition, the activity of NTE was down regulated by the G protein signal pathway influencing factor, pertussis toxin, treatment in vivo. These findings suggest that Gbeta2 may play a significant role in maintaining the activity of NTE.
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Affiliation(s)
- Rui Chen
- Laboratory of Molecular Toxicology, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, PR China
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