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Olmos V, Thompson EN, Gogia N, Luttik K, Veeranki V, Ni L, Sim S, Chen K, Krause DS, Lim J. Dysregulation of alternative splicing in spinocerebellar ataxia type 1. Hum Mol Genet 2024; 33:138-149. [PMID: 37802886 PMCID: PMC10979408 DOI: 10.1093/hmg/ddad170] [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: 06/30/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023] Open
Abstract
Spinocerebellar ataxia type 1 is caused by an expansion of the polyglutamine tract in ATAXIN-1. Ataxin-1 is broadly expressed throughout the brain and is involved in regulating gene expression. However, it is not yet known if mutant ataxin-1 can impact the regulation of alternative splicing events. We performed RNA sequencing in mouse models of spinocerebellar ataxia type 1 and identified that mutant ataxin-1 expression abnormally leads to diverse splicing events in the mouse cerebellum of spinocerebellar ataxia type 1. We found that the diverse splicing events occurred in a predominantly cell autonomous manner. A majority of the transcripts with misregulated alternative splicing events were previously unknown, thus allowing us to identify overall new biological pathways that are distinctive to those affected by differential gene expression in spinocerebellar ataxia type 1. We also provide evidence that the splicing factor Rbfox1 mediates the effect of mutant ataxin-1 on misregulated alternative splicing and that genetic manipulation of Rbfox1 expression modifies neurodegenerative phenotypes in a Drosophila model of spinocerebellar ataxia type 1 in vivo. Together, this study provides novel molecular mechanistic insight into the pathogenesis of spinocerebellar ataxia type 1 and identifies potential therapeutic strategies for spinocerebellar ataxia type 1.
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Affiliation(s)
- Victor Olmos
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
| | - Evrett N Thompson
- Department of Cell Biology, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
- Yale Stem Cell Center, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
| | - Neha Gogia
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
| | - Kimberly Luttik
- Interdepartmental Neuroscience Program, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Vaishnavi Veeranki
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
| | - Luhan Ni
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
| | - Serena Sim
- Yale College, 433 Temple Street, New Haven, CT 06510, United States
| | - Kelly Chen
- Yale College, 433 Temple Street, New Haven, CT 06510, United States
| | - Diane S Krause
- Department of Cell Biology, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
- Yale Stem Cell Center, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
- Department of Pathology, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
- Department of Laboratory Medicine, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
| | - Janghoo Lim
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
- Yale Stem Cell Center, Yale School of Medicine, 10 Amistad Street, New Haven, CT 06510, United States
- Interdepartmental Neuroscience Program, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, United States
- Wu Tsai Institute, Yale School of Medicine, 100 College, New Haven, CT 06510, United States
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2
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Johnson SL, Tsou WL, Prifti MV, Harris AL, Todi SV. A survey of protein interactions and posttranslational modifications that influence the polyglutamine diseases. Front Mol Neurosci 2022; 15:974167. [PMID: 36187346 PMCID: PMC9515312 DOI: 10.3389/fnmol.2022.974167] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/27/2022] [Indexed: 01/20/2023] Open
Abstract
The presence and aggregation of misfolded proteins has deleterious effects in the nervous system. Among the various diseases caused by misfolded proteins is the family of the polyglutamine (polyQ) disorders. This family comprises nine members, all stemming from the same mutation—the abnormal elongation of a polyQ repeat in nine different proteins—which causes protein misfolding and aggregation, cellular dysfunction and disease. While it is the same type of mutation that causes them, each disease is distinct: it is influenced by regions and domains that surround the polyQ repeat; by proteins with which they interact; and by posttranslational modifications they receive. Here, we overview the role of non-polyQ regions that control the pathogenicity of the expanded polyQ repeat. We begin by introducing each polyQ disease, the genes affected, and the symptoms experienced by patients. Subsequently, we provide a survey of protein-protein interactions and posttranslational modifications that regulate polyQ toxicity. We conclude by discussing shared processes and pathways that bring some of the polyQ diseases together and may serve as common therapeutic entry points for this family of incurable disorders.
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Affiliation(s)
- Sean L. Johnson
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Matthew V. Prifti
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Autumn L. Harris
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
- Maximizing Access to Research Careers (MARC) Program, Wayne State University, Detroit, MI, United States
| | - Sokol V. Todi
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
- Maximizing Access to Research Careers (MARC) Program, Wayne State University, Detroit, MI, United States
- Department of Neurology, Wayne State University, Detroit, MI, United States
- *Correspondence: Sokol V. Todi,
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Marklein B, Jenning M, Konthur Z, Häupl T, Welzel F, Nonhoff U, Krobitsch S, Mulder DM, Koenders MI, Joshua V, Cope AP, Shlomchik MJ, Anders HJ, Burmester GR, Hensvold A, Catrina AI, Rönnelid J, Steiner G, Skriner K. The citrullinated/native index of autoantibodies against hnRNP-DL predicts an individual "window of treatment success" in RA patients. Arthritis Res Ther 2021; 23:239. [PMID: 34521462 PMCID: PMC8439038 DOI: 10.1186/s13075-021-02603-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is a need for biomarker to identify patients "at risk" for rheumatoid arthritis (risk-RA) and to better predict the therapeutic response and in this study we tested the hypothesis that novel native and citrullinated heterogeneous nuclear ribonucleoprotein (hnRNP)-DL autoantibodies could be possible biomarkers. METHODS Using protein macroarray and ELISA, epitope recognition against hnRNP-DL was analysed in sera from different developed RA disease and diagnosed SLE patients. Toll-like receptor (TLR) 7/9 and myeloid differentiation primary response gene 88 (MyD88)-dependency were studied in sera from murine disease models. HnRNP-DL expression in cultivated cells and synovial tissue was analysed by indirect immunofluorescence, immunoblot and immunohistochemistry. RESULTS HnRNP-DL was highly expressed in stress granules, citrullinated in the rheumatoid joint and targeted by autoantibodies either as native or citrullinated proteins in patient subsets with different developed RA disease. Structural citrullination dependent epitopes (SCEs) of hnRNP-DL were detected in 58% of the SLE patients although 98% of these sera were α-CCP-2-negative. To obtain a specific citrullinated signal value, we subtracted the native antibody value from the citrullinated signal. The citrullinated/native index of autoantibodies against hnRNP-DL (CNDL-Index) was identified as a new value for an "individual window of treatment success" in early RA and for the detection of RF IgM/α-CCP-2 seronegative RA patients (24-46%). Negative CNDL-index was found in SLE patients, risk-RA and early RA cohorts such as EIRA where the majority of these patients are DAS28-responders to methotrexate (MTX) treatment (87%). High positive CNDL-values were associated with more severe RA, shared epitope and parenchymal changes in the lung. Specifically, native α-hnRNP-DL is TLR7/9-dependent, associated with pain and ROC analysis revealed an association to initial MTX or etanercept treatment response, especially in seronegative RA patients. CONCLUSION CNDL-index defines people at risk to develop RA and the "window of treatment success" thereby closing the sensitivity gap in RA.
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Affiliation(s)
- Bianka Marklein
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Charite Campus Mitte, Rheumatologisches Forschungslabor - AG Skriner, Chariteplatz 1 (intern Virchowweg 11, 5.OG, R011), 10117, Berlin, Germany
| | - Madeleine Jenning
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Charite Campus Mitte, Rheumatologisches Forschungslabor - AG Skriner, Chariteplatz 1 (intern Virchowweg 11, 5.OG, R011), 10117, Berlin, Germany
- German Rheumatism Research Centre, Leibniz Institute, 10117, Berlin, Germany
| | - Zoltán Konthur
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Analytical Chemistry (Dpt.1), Bundesanstalt für Materialforschung und-prüfung (BAM), Berlin, Germany
| | - Thomas Häupl
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Charite Campus Mitte, Rheumatologisches Forschungslabor - AG Skriner, Chariteplatz 1 (intern Virchowweg 11, 5.OG, R011), 10117, Berlin, Germany
| | | | - Ute Nonhoff
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Debbie M Mulder
- Department of Experimental Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marije I Koenders
- Department of Experimental Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vijay Joshua
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Andrew P Cope
- Centre for Rheumatic Diseases, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Mark J Shlomchik
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Hans-Joachim Anders
- Medical Clinic and Policlinic IV, Nephrological Center, Ludwig-Maximilian-University Hospital, Munich, Germany
| | - Gerd R Burmester
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Charite Campus Mitte, Rheumatologisches Forschungslabor - AG Skriner, Chariteplatz 1 (intern Virchowweg 11, 5.OG, R011), 10117, Berlin, Germany
| | - Aase Hensvold
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Academic Specialist Center, Center for Rheumatology, Stockholm Health Region, Stockholm, Sweden
| | - Anca I Catrina
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Rönnelid
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Günter Steiner
- Division of Rheumatology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Cluster for Arthritis and Rehabilitation, Vienna, Austria
| | - Karl Skriner
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Charite Campus Mitte, Rheumatologisches Forschungslabor - AG Skriner, Chariteplatz 1 (intern Virchowweg 11, 5.OG, R011), 10117, Berlin, Germany.
- German Rheumatism Research Centre, Leibniz Institute, 10117, Berlin, Germany.
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Lastres-Becker I, Nonis D, Nowock J, Auburger G. New alternative splicing variants of the ATXN2 transcript. Neurol Res Pract 2019; 1:22. [PMID: 33324888 PMCID: PMC7650068 DOI: 10.1186/s42466-019-0025-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/09/2019] [Indexed: 12/12/2022] Open
Abstract
Background Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant disorder with progressive degeneration of cerebellar Purkinje cells and selective loss of neurons in the brainstem. This neurodegenerative disorder is caused by the expansion of a polyglutamine domain in ataxin-2. Ataxin-2 is composed of 1312 amino acids, has a predicted molecular weight of 150-kDa and is widely expressed in neuronal and non-neuronal tissues. To date, the putative functions of ataxin-2 on mRNA translation and endocytosis remain ill-defined. Differential splicing with a lack of exons 10 and 21 was described in humans, and additional splicing of exon 11 in mice. In this study, we observed that the molecular size of transfected full-length wild-type ataxin-2 (22 glutamines) is different from endogenous ataxin-2 and that this variation could not be explained by the previously published splice variants alone. Methods Quantitative immunoblots and qualitative reverse-transcriptase polymerase-chain-reaction (RT-PCR) were used to characterize isoform variants, before sequencing was employed for validation. Results We report the characterization of further splice variants of ataxin-2 in different human cell lines and in mouse and human brain. Using RT-PCR from cell lines HeLa, HEK293 and COS-7 throughout the open reading frame of ataxin-2 together with PCR-sequencing, we found novel splice variants lacking exon 12 and exon 24. These findings were corroborated in murine and human brain. The splice variants were also found in human skin fibroblasts from SCA2 patients and controls, indicating that the polyglutamine expansion does not abolish the splicing. Conclusions Given that Ataxin-2 interacts with crucial splice modulators such as TDP-43 and modulates the risk of Amyotrophic Lateral Sclerosis, its own splice isoforms may become relevant in brain tissue to monitor the RNA processing during disease progression and neuroprotective therapy.
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Affiliation(s)
- Isabel Lastres-Becker
- Experimental Neurology, Goethe University Medical Faculty, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany.,Present address: Department of Biochemistry, Faculty of Medicine, Universidad Autonoma of Madrid, Madrid, Spain
| | - David Nonis
- Experimental Neurology, Goethe University Medical Faculty, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Joachim Nowock
- Experimental Neurology, Goethe University Medical Faculty, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Georg Auburger
- Experimental Neurology, Goethe University Medical Faculty, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
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5
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Adegbuyiro A, Sedighi F, Pilkington AW, Groover S, Legleiter J. Proteins Containing Expanded Polyglutamine Tracts and Neurodegenerative Disease. Biochemistry 2017; 56:1199-1217. [PMID: 28170216 DOI: 10.1021/acs.biochem.6b00936] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Several hereditary neurological and neuromuscular diseases are caused by an abnormal expansion of trinucleotide repeats. To date, there have been 10 of these trinucleotide repeat disorders associated with an expansion of the codon CAG encoding glutamine (Q). For these polyglutamine (polyQ) diseases, there is a critical threshold length of the CAG repeat required for disease, and further expansion beyond this threshold is correlated with age of onset and symptom severity. PolyQ expansion in the translated proteins promotes their self-assembly into a variety of oligomeric and fibrillar aggregate species that accumulate into the hallmark proteinaceous inclusion bodies associated with each disease. Here, we review aggregation mechanisms of proteins with expanded polyQ-tracts, structural consequences of expanded polyQ ranging from monomers to fibrillar aggregates, the impact of protein context and post-translational modifications on aggregation, and a potential role for lipid membranes in aggregation. As the pathogenic mechanisms that underlie these disorders are often classified as either a gain of toxic function or loss of normal protein function, some toxic mechanisms associated with mutant polyQ tracts will also be discussed.
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Affiliation(s)
- Adewale Adegbuyiro
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Faezeh Sedighi
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Albert W Pilkington
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Sharon Groover
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States.,Blanchette Rockefeller Neurosciences Institute, Robert C. Byrd Health Sciences Center, P.O. Box 9304, West Virginia University , Morgantown, West Virginia 26506, United States.,NanoSAFE, P.O. Box 6223, West Virginia University , Morgantown, West Virginia 26506, United States
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de Chiara C, Pastore A. Kaleidoscopic protein-protein interactions in the life and death of ataxin-1: new strategies against protein aggregation. Trends Neurosci 2014; 37:211-8. [PMID: 24636457 PMCID: PMC3988977 DOI: 10.1016/j.tins.2014.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 01/26/2014] [Accepted: 02/06/2014] [Indexed: 12/11/2022]
Abstract
Understanding how proteins protect themselves from aberrant aggregation is of primary interest for understanding basic biology, protein biochemistry, and human disease. We discuss the paradigmatic example of ataxin-1 (Atx1), the protein responsible for neurodegenerative spinocerebellar ataxia type 1 (SCA1). This disease is part of the increasing family of pathologies caused by protein aggregation and misfolding. We discuss the importance of protein-protein interactions not only in the nonpathological function of Atx1 but also in protecting the protein from aggregation and misfolding. The lessons learned from Atx1 may lead to a more general understanding of the cell's protective strategies against aggregation. The obtained knowledge may suggest a new perspective for designing specific therapeutic strategies for the cure of misfolding diseases.
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Affiliation(s)
- Cesira de Chiara
- National Institute for Medical Research (NIMR), Medical Research Council (MRC), The Ridgeway, London NW7 1AA, UK
| | - Annalisa Pastore
- Department of Clinical Neurosciences, King's College London, Denmark Hill Campus, London, UK.
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Kaehler C, Isensee J, Nonhoff U, Terrey M, Hucho T, Lehrach H, Krobitsch S. Ataxin-2-like is a regulator of stress granules and processing bodies. PLoS One 2012; 7:e50134. [PMID: 23209657 PMCID: PMC3507954 DOI: 10.1371/journal.pone.0050134] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 10/17/2012] [Indexed: 12/15/2022] Open
Abstract
Paralogs for several proteins implicated in neurodegenerative disorders have been identified and explored to further facilitate the identification of molecular mechanisms contributing to disease pathogenesis. For the disease-causing protein in spinocerebellar ataxia type 2, ataxin-2, a paralog of unknown function, termed ataxin-2-like, has been described. We discovered that ataxin-2-like associates with known interaction partners of ataxin-2, the RNA helicase DDX6 and the poly(A)-binding protein, and with ataxin-2 itself. Furthermore, we found that ataxin-2-like is a component of stress granules. Interestingly, sole ataxin-2-like overexpression led to the induction of stress granules, while a reduction of stress granules was detected in case of a low ataxin-2-like level. Finally, we observed that overexpression of ataxin-2-like as well as its reduction has an impact on the presence of microscopically visible processing bodies. Thus, our results imply a functional overlap between ataxin-2-like and ataxin-2, and further indicate a role for ataxin-2-like in the regulation of stress granules and processing bodies.
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Affiliation(s)
- Christian Kaehler
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Free University Berlin, Department of Biology, Chemistry and Pharmacy, Berlin, Germany
| | - Jörg Isensee
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Universitätsklinik Köln, Klinik für Anästhesiologie und Operative Intensivmedizin, Experimentelle Anästhesiologie und Schmerzforschung, Cologne, Germany
| | - Ute Nonhoff
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Markus Terrey
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tim Hucho
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Universitätsklinik Köln, Klinik für Anästhesiologie und Operative Intensivmedizin, Experimentelle Anästhesiologie und Schmerzforschung, Cologne, Germany
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sylvia Krobitsch
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
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