1
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Fote GM, Eapen VV, Lim RG, Yu C, Salazar L, McClure NR, McKnight J, Nguyen TB, Heath MC, Lau AL, Villamil MA, Miramontes R, Kratter IH, Finkbeiner S, Reidling JC, Paulo JA, Kaiser P, Huang L, Housman DE, Thompson LM, Steffan JS. Huntingtin contains an ubiquitin-binding domain and regulates lysosomal targeting of mitochondrial and RNA-binding proteins. Proc Natl Acad Sci U S A 2024; 121:e2319091121. [PMID: 39074279 PMCID: PMC11317567 DOI: 10.1073/pnas.2319091121] [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: 11/20/2023] [Accepted: 06/20/2024] [Indexed: 07/31/2024] Open
Abstract
Understanding the normal function of the Huntingtin (HTT) protein is of significance in the design and implementation of therapeutic strategies for Huntington's disease (HD). Expansion of the CAG repeat in the HTT gene, encoding an expanded polyglutamine (polyQ) repeat within the HTT protein, causes HD and may compromise HTT's normal activity contributing to HD pathology. Here, we investigated the previously defined role of HTT in autophagy specifically through studying HTT's association with ubiquitin. We find that HTT interacts directly with ubiquitin in vitro. Tandem affinity purification was used to identify ubiquitinated and ubiquitin-associated proteins that copurify with a HTT N-terminal fragment under basal conditions. Copurification is enhanced by HTT polyQ expansion and reduced by mimicking HTT serine 421 phosphorylation. The identified HTT-interacting proteins include RNA-binding proteins (RBPs) involved in mRNA translation, proteins enriched in stress granules, the nuclear proteome, the defective ribosomal products (DRiPs) proteome and the brain-derived autophagosomal proteome. To determine whether the proteins interacting with HTT are autophagic targets, HTT knockout (KO) cells and immunoprecipitation of lysosomes were used to investigate autophagy in the absence of HTT. HTT KO was associated with reduced abundance of mitochondrial proteins in the lysosome, indicating a potential compromise in basal mitophagy, and increased lysosomal abundance of RBPs which may result from compensatory up-regulation of starvation-induced macroautophagy. We suggest HTT is critical for appropriate basal clearance of mitochondrial proteins and RBPs, hence reduced HTT proteostatic function with mutation may contribute to the neuropathology of HD.
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Affiliation(s)
- Gianna M. Fote
- Department of Biological Chemistry, UC Irvine School of Medicine, Irvine, CA92697
- Department of Neurological Surgery, UC Irvine School of Medicine, Orange, CA92868
| | - Vinay V. Eapen
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
- Casma Therapeutics, Cambridge, MA02139
| | - Ryan G. Lim
- The University of California Irvine Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA92697
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, CA92697
| | - Lisa Salazar
- Department of Psychiatry and Human Behavior, UC Irvine School of Medicine, Orange, CA92868
| | - Nicolette R. McClure
- Department of Neurobiology and Behavior, University of California, Irvine, CA92697
| | - Jharrayne McKnight
- Department of Neurobiology and Behavior, University of California, Irvine, CA92697
| | - Thai B. Nguyen
- Department of Neurobiology and Behavior, University of California, Irvine, CA92697
| | - Marie C. Heath
- Department of Neurobiology and Behavior, University of California, Irvine, CA92697
| | - Alice L. Lau
- Department of Psychiatry and Human Behavior, UC Irvine School of Medicine, Orange, CA92868
| | - Mark A. Villamil
- Department of Biological Chemistry, UC Irvine School of Medicine, Irvine, CA92697
| | - Ricardo Miramontes
- Department of Psychiatry and Human Behavior, UC Irvine School of Medicine, Orange, CA92868
| | - Ian H. Kratter
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA94158
- Stanford Brain Stimulation Lab, Stanford, CA94304
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA94304
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA94158
- Department of Physiology, University of California, San Francisco, CA94158
- Department of Neurology, University of California, San Francisco, CA94158
| | - Jack C. Reidling
- The University of California Irvine Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA92697
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Peter Kaiser
- Department of Biological Chemistry, UC Irvine School of Medicine, Irvine, CA92697
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, CA92697
| | - David E. Housman
- Koch Institute for Integrative Cancer Research, The Massachusetts Institute of Technology, Cambridge, MA02139
| | - Leslie M. Thompson
- Department of Biological Chemistry, UC Irvine School of Medicine, Irvine, CA92697
- The University of California Irvine Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA92697
- Department of Psychiatry and Human Behavior, UC Irvine School of Medicine, Orange, CA92868
- Department of Neurobiology and Behavior, University of California, Irvine, CA92697
- Center for Epigenetics and Metabolism, University of California, Irvine School of Medicine, University of California, Irvine, CA92697
| | - Joan S. Steffan
- The University of California Irvine Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA92697
- Department of Psychiatry and Human Behavior, UC Irvine School of Medicine, Orange, CA92868
- Center for Epigenetics and Metabolism, University of California, Irvine School of Medicine, University of California, Irvine, CA92697
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Yadav M, Harding RJ, Li T, Xu X, Gall-Duncan T, Khan M, Bardile CF, Sequiera GL, Duan S, Chandrasekaran R, Pan A, Bu J, Yamazaki T, Hirose T, Prinos P, Tippett L, Turner C, Curtis MA, Faull RL, Pouladi MA, Pearson CE, He HH, Arrowsmith CH. Huntingtin is an RNA binding protein and participates in NEAT1-mediated paraspeckles. SCIENCE ADVANCES 2024; 10:eado5264. [PMID: 39028820 PMCID: PMC11259171 DOI: 10.1126/sciadv.ado5264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/14/2024] [Indexed: 07/21/2024]
Abstract
Huntingtin protein, mutated in Huntington's disease, is implicated in nucleic acid-mediated processes, yet the evidence for direct huntingtin-nucleic acid interaction is limited. Here, we show wild-type and mutant huntingtin copurify with nucleic acids, primarily RNA, and interact directly with G-rich RNAs in in vitro assays. Huntingtin RNA-immunoprecipitation sequencing from patient-derived fibroblasts and neuronal progenitor cells expressing wild-type and mutant huntingtin revealed long noncoding RNA NEAT1 as a significantly enriched transcript. Altered NEAT1 levels were evident in Huntington's disease cells and postmortem brain tissues, and huntingtin knockdown decreased NEAT1 levels. Huntingtin colocalized with NEAT1 in paraspeckles, and we identified a high-affinity RNA motif preferred by huntingtin. This study highlights NEAT1 as a huntingtin interactor, demonstrating huntingtin's involvement in RNA-mediated functions and paraspeckle regulation.
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Affiliation(s)
- Manisha Yadav
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Rachel J. Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Tiantian Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Xin Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Terence Gall-Duncan
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mahreen Khan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Costanza Ferrari Bardile
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Djavad Mowafaghian Centre for Brain Health, Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Glen L. Sequiera
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Djavad Mowafaghian Centre for Brain Health, Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Shili Duan
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Anni Pan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jiachuan Bu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Panagiotis Prinos
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Lynette Tippett
- School of Psychology, University of Auckland, Auckland, New Zealand
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Clinton Turner
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Anatomical Pathology, Pathology and Laboratory Medicine, Auckland City Hospital, Auckland, New Zealand
| | - Maurice A. Curtis
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Richard L.M. Faull
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Mahmoud A. Pouladi
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Djavad Mowafaghian Centre for Brain Health, Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Christopher E. Pearson
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Housheng Hansen He
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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3
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Seefelder M, Kochanek S, Klein FAC. ProteinCoLoc streamlines Bayesian analysis of colocalization in microscopic images. Sci Rep 2024; 14:13277. [PMID: 38858475 PMCID: PMC11164984 DOI: 10.1038/s41598-024-63884-1] [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: 01/26/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
Colocalization, the spatial overlap of molecular entities, is often key to support their involvement in common functions. Existing colocalization tools, however, face limitations, particularly because of their basic statistical analysis and their low-throughput manual entry processes making them unsuitable for automation and potentially introducing bias. These shortcomings underscore the need for user-friendly tools streamlining colocalization assessments and enabling their robust and automated quantitative analyses. We have developed ProteinCoLoc, an innovative software designed for automated high-throughput colocalization analyses and incorporating advanced statistical features such as Bayesian modelling, automatic background detection and localised correlation analysis. ProteinCoLoc rationalises colocalization assessments without manual input, comes with a user-friendly graphical user interface and provides various analytics allowing to study and locally quantify colocalization. This easy-to-use application presents numerous advantages, including a direct comparison with controls employing a Bayesian model and the analysis of local correlation patterns, while reducing hands-on time through automatic background detection. The software was validated while studying the colocalization pattern of two proteins forming a stable complex: the huntingtin protein (HTT) and its partner huntingtin-associated protein 40 (HAP40). Our results showcase the software's capacity to quantitatively assess colocalizations. ProteinCoLoc is available both as a Julia package and as a compiled software ( https://github.com/ma-seefelder/ProteinCoLoc ).
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Affiliation(s)
- Manuel Seefelder
- Department of Gene Therapy, Ulm University, 89081, Ulm, Germany.
| | - Stefan Kochanek
- Department of Gene Therapy, Ulm University, 89081, Ulm, Germany
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Dickmann CGF, Milicevic Sephton S, Barker RA, Aigbirhio FI. PET Ligands for Imaging Mutant Huntingtin Aggregates: A Case Study in Non-For-Profit Scientific Management. Chembiochem 2024; 25:e202400152. [PMID: 38695673 DOI: 10.1002/cbic.202400152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/02/2024] [Indexed: 06/13/2024]
Abstract
Positron emission tomography imaging of misfolded proteins with high-affinity and selective radioligands has played a vital role in expanding our knowledge of neurodegenerative diseases such as Parkinson's and Alzheimer's disease. The pathogenesis of Huntington's disease, a CAG trinucleotide repeat disorder, is similarly linked to the presence of protein fibrils formed from mutant huntingtin (mHTT) protein. Development of mHTT fibril-specific radioligands has been limited by the lack of structural knowledge around mHTT and a dearth of available hit compounds for medicinal chemistry refinement. Over the past decade, the CHDI Foundation, a non-for-profit scientific management organisation has orchestrated a large-scale screen of small molecules to identify high affinity ligands of mHTT, with lead compounds now reaching clinical maturity. Here we describe the mHTT radioligands developed to date and opportunities for further improvement of this radiotracer class.
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Affiliation(s)
- Catherine G F Dickmann
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Selena Milicevic Sephton
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Roger A Barker
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Franklin I Aigbirhio
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
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5
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Bonsor M, Ammar O, Schnoegl S, Wanker EE, Silva Ramos E. Polyglutamine disease proteins: Commonalities and differences in interaction profiles and pathological effects. Proteomics 2024; 24:e2300114. [PMID: 38615323 DOI: 10.1002/pmic.202300114] [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: 11/30/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024]
Abstract
Currently, nine polyglutamine (polyQ) expansion diseases are known. They include spinocerebellar ataxias (SCA1, 2, 3, 6, 7, 17), spinal and bulbar muscular atrophy (SBMA), dentatorubral-pallidoluysian atrophy (DRPLA), and Huntington's disease (HD). At the root of these neurodegenerative diseases are trinucleotide repeat mutations in coding regions of different genes, which lead to the production of proteins with elongated polyQ tracts. While the causative proteins differ in structure and molecular mass, the expanded polyQ domains drive pathogenesis in all these diseases. PolyQ tracts mediate the association of proteins leading to the formation of protein complexes involved in gene expression regulation, RNA processing, membrane trafficking, and signal transduction. In this review, we discuss commonalities and differences among the nine polyQ proteins focusing on their structure and function as well as the pathological features of the respective diseases. We present insights from AlphaFold-predicted structural models and discuss the biological roles of polyQ-containing proteins. Lastly, we explore reported protein-protein interaction networks to highlight shared protein interactions and their potential relevance in disease development.
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Affiliation(s)
- Megan Bonsor
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Orchid Ammar
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Sigrid Schnoegl
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Erich E Wanker
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Eduardo Silva Ramos
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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6
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Chen L, Qin Y, Guo T, Zhu W, Lin J, Xing T, Duan X, Zhang Y, Ruan E, Li X, Yin P, Li S, Li XJ, Yang S. HAP40 modulates mutant Huntingtin aggregation and toxicity in Huntington's disease mice. Cell Death Dis 2024; 15:337. [PMID: 38744826 PMCID: PMC11094052 DOI: 10.1038/s41419-024-06716-4] [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: 09/08/2023] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
Huntington's disease (HD) is a monogenic neurodegenerative disease, caused by the CAG trinucleotide repeat expansion in exon 1 of the Huntingtin (HTT) gene. The HTT gene encodes a large protein known to interact with many proteins. Huntingtin-associated protein 40 (HAP40) is one that shows high binding affinity with HTT and functions to maintain HTT conformation in vitro. However, the potential role of HAP40 in HD pathogenesis remains unknown. In this study, we found that the expression level of HAP40 is in parallel with HTT but inversely correlates with mutant HTT aggregates in mouse brains. Depletion of endogenous HAP40 in the striatum of HD140Q knock-in (KI) mice leads to enhanced mutant HTT aggregation and neuronal loss. Consistently, overexpression of HAP40 in the striatum of HD140Q KI mice reduced mutant HTT aggregation and ameliorated the behavioral deficits. Mechanistically, HAP40 preferentially binds to mutant HTT and promotes Lysine 48-linked ubiquitination of mutant HTT. Our results revealed that HAP40 is an important regulator of HTT protein homeostasis in vivo and hinted at HAP40 as a therapeutic target in HD treatment.
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Affiliation(s)
- Laiqiang Chen
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
| | - Yiyang Qin
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
| | - Tingting Guo
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Wenzhen Zhu
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Jingpan Lin
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Tingting Xing
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Xuezhi Duan
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Yiran Zhang
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Eshu Ruan
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Xiang Li
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Peng Yin
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
| | - Shihua Li
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
| | - Xiao-Jiang Li
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China.
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China.
| | - Su Yang
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China.
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China.
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7
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van der Wel PC. Solid-state nuclear magnetic resonance in the structural study of polyglutamine aggregation. Biochem Soc Trans 2024; 52:719-731. [PMID: 38563485 PMCID: PMC11088915 DOI: 10.1042/bst20230731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/06/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024]
Abstract
The aggregation of proteins into amyloid-like fibrils is seen in many neurodegenerative diseases. Recent years have seen much progress in our understanding of these misfolded protein inclusions, thanks to advances in techniques such as solid-state nuclear magnetic resonance (ssNMR) spectroscopy and cryogenic electron microscopy (cryo-EM). However, multiple repeat-expansion-related disorders have presented special challenges to structural elucidation. This review discusses the special role of ssNMR analysis in the study of protein aggregates associated with CAG repeat expansion disorders. In these diseases, the misfolding and aggregation affect mutant proteins with expanded polyglutamine segments. The most common disorder, Huntington's disease (HD), is connected to the mutation of the huntingtin protein. Since the discovery of the genetic causes for HD in the 1990s, steady progress in our understanding of the role of protein aggregation has depended on the integrative and interdisciplinary use of multiple types of structural techniques. The heterogeneous and dynamic features of polyQ protein fibrils, and in particular those formed by huntingtin N-terminal fragments, have made these aggregates into challenging targets for structural analysis. ssNMR has offered unique insights into many aspects of these amyloid-like aggregates. These include the atomic-level structure of the polyglutamine core, but also measurements of dynamics and solvent accessibility of the non-core flanking domains of these fibrils' fuzzy coats. The obtained structural insights shed new light on pathogenic mechanisms behind this and other protein misfolding diseases.
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8
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Ratovitski T, Kamath SV, O'Meally RN, Gosala K, Holland CD, Jiang M, Cole RN, Ross CA. Arginine methylation of RNA-binding proteins is impaired in Huntington's disease. Hum Mol Genet 2023; 32:3006-3025. [PMID: 37535888 PMCID: PMC10549789 DOI: 10.1093/hmg/ddad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023] Open
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG repeat expansion in the HD gene, coding for huntingtin protein (HTT). Mechanisms of HD cellular pathogenesis remain undefined and likely involve disruptions in many cellular processes and functions presumably mediated by abnormal protein interactions of mutant HTT. We previously found HTT interaction with several protein arginine methyl-transferase (PRMT) enzymes. Protein arginine methylation mediated by PRMT enzymes is an important post-translational modification with an emerging role in neurodegeneration. We found that normal (but not mutant) HTT can facilitate the activity of PRMTs in vitro and the formation of arginine methylation complexes. These interactions appear to be disrupted in HD neurons. This suggests an additional functional role for HTT/PRMT interactions, not limited to substrate/enzyme relationship, which may result in global changes in arginine protein methylation in HD. Our quantitative analysis of striatal precursor neuron proteome indicated that arginine protein methylation is significantly altered in HD. We identified a cluster highly enriched in RNA-binding proteins with reduced arginine methylation, which is essential to their function in RNA processing and splicing. We found that several of these proteins interact with HTT, and their RNA-binding and localization are affected in HD cells likely due to a compromised arginine methylation and/or abnormal interactions with mutant HTT. These studies reveal a potential new mechanism for disruption of RNA processing in HD, involving a direct interaction of HTT with methyl-transferase enzymes and modulation of their activity and highlighting methylation of arginine as potential new therapeutic target for HD.
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Affiliation(s)
- Tamara Ratovitski
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Siddhi V Kamath
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Robert N O'Meally
- Department of Biological Chemistry, Mass Spectrometry and Proteomics Facility, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Keerthana Gosala
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Chloe D Holland
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Mali Jiang
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Robert N Cole
- Department of Biological Chemistry, Mass Spectrometry and Proteomics Facility, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Christopher A Ross
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
- Departments of Neurology, Neuroscience and Pharmacology, Johns Hopkins University, Baltimore, MD 21287, USA
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9
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Liu L, Malagu K, Haughan AF, Khetarpal V, Stott AJ, Esmieu W, Vater HD, Webster SJ, Van de Poël AJ, Clissold C, Cosgrove B, Sutton B, Spencer JA, Breccia P, Gancia E, Bonomo S, Ladduwahetty T, Lazari O, Patel H, Atton HC, Clifton S, Mota DM, Magnani D, O'Neill A, Stebbeds M, Macabuag N, Todd D, Herva ME, Mitchell P, Visser M, Compte Sancerni S, Grand Moursel L, da Silva M, Kritikou E, Heikkinen TT, Bolkvadze T, Fodale V, Spadafora D, Daldin M, Bresciani A, Mangette JE, Doherty EM, Lee MR, Herbst T, Monteagudo E, Macdonald D, Plotnikov NV, Chambers M, McAllister G, Muňoz-Sanjuan I, Dominguez C. Identification and Optimization of RNA-Splicing Modulators as Huntingtin Protein-Lowering Agents for the Treatment of Huntington's Disease. J Med Chem 2023; 66:13205-13246. [PMID: 37712656 DOI: 10.1021/acs.jmedchem.3c01173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Huntington's disease (HD) is caused by an expanded CAG trinucleotide repeat in exon 1 of the huntingtin (HTT) gene. We report the design of a series of HTT pre-mRNA splicing modulators that lower huntingtin (HTT) protein, including the toxic mutant huntingtin (mHTT), by promoting insertion of a pseudoexon containing a premature termination codon at the exon 49-50 junction. The resulting transcript undergoes nonsense-mediated decay, leading to a reduction of HTT mRNA transcripts and protein levels. The starting benzamide core was modified to pyrazine amide and further optimized to give a potent, CNS-penetrant, and orally bioavailable HTT-splicing modulator 27. This compound reduced canonical splicing of the HTT RNA exon 49-50 and demonstrated significant HTT-lowering in both human HD stem cells and mouse BACHD models. Compound 27 is a structurally diverse HTT-splicing modulator that may help understand the mechanism of adverse effects such as peripheral neuropathy associated with branaplam.
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Affiliation(s)
- Longbin Liu
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Karine Malagu
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Alan F Haughan
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Vinod Khetarpal
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Andrew J Stott
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - William Esmieu
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Huw D Vater
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Stephen J Webster
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Amanda J Van de Poël
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Cole Clissold
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Brett Cosgrove
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Benjamin Sutton
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Jonathan A Spencer
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Perla Breccia
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Emanuela Gancia
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Silvia Bonomo
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Tammy Ladduwahetty
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Ovadia Lazari
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Hiral Patel
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Helen C Atton
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Steve Clifton
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Daniel M Mota
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Dario Magnani
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Amy O'Neill
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Marta Stebbeds
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Natsuko Macabuag
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Daniel Todd
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Maria E Herva
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Philip Mitchell
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Mijke Visser
- Charles River, Darwinweg 24, 2333 CR Leiden, The Netherlands
| | | | | | - Marta da Silva
- Charles River, Darwinweg 24, 2333 CR Leiden, The Netherlands
| | - Eva Kritikou
- Charles River, Darwinweg 24, 2333 CR Leiden, The Netherlands
| | | | | | | | | | | | | | | | - Elizabeth M Doherty
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Matthew R Lee
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Todd Herbst
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Edith Monteagudo
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Douglas Macdonald
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Nikolay V Plotnikov
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Mark Chambers
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - George McAllister
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Ignacio Muňoz-Sanjuan
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Celia Dominguez
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
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Alteen MG, Deme JC, Alvarez CP, Loppnau P, Hutchinson A, Seitova A, Chandrasekaran R, Silva Ramos E, Secker C, Alqazzaz M, Wanker EE, Lea SM, Arrowsmith CH, Harding RJ. Delineation of functional subdomains of Huntingtin protein and their interaction with HAP40. Structure 2023; 31:1121-1131.e6. [PMID: 37390814 PMCID: PMC10527579 DOI: 10.1016/j.str.2023.06.002] [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: 01/26/2023] [Revised: 04/14/2023] [Accepted: 06/05/2023] [Indexed: 07/02/2023]
Abstract
The huntingtin (HTT) protein plays critical roles in numerous cellular pathways by functioning as a scaffold for its many interaction partners and HTT knock out is embryonic lethal. Interrogation of HTT function is complicated by the large size of this protein so we studied a suite of structure-rationalized subdomains to investigate the structure-function relationships within the HTT-HAP40 complex. Protein samples derived from the subdomain constructs were validated using biophysical methods and cryo-electron microscopy, revealing they are natively folded and can complex with validated binding partner, HAP40. Derivatized versions of these constructs enable protein-protein interaction assays in vitro, with biotin tags, and in cells, with luciferase two-hybrid assay-based tags, which we use in proof-of-principle analyses to further interrogate the HTT-HAP40 interaction. These open-source biochemical tools enable studies of fundamental HTT biochemistry and biology, will aid the discovery of macromolecular or small-molecule binding partners and help map interaction sites across this large protein.
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Affiliation(s)
- Matthew G Alteen
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; POINT Biopharma, 22 St Clair Avenue E Suite 1201, Toronto, ON M4T 2S3, Canada
| | - Justin C Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Claudia P Alvarez
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; SCIEX, 71 Four Valley Dr, Vaughan, ON L4K 4V8, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Renu Chandrasekaran
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Eduardo Silva Ramos
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Christopher Secker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Mona Alqazzaz
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
| | - Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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11
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Liu L, Tong H, Sun Y, Chen X, Yang T, Zhou G, Li XJ, Li S. Huntingtin Interacting Proteins and Pathological Implications. Int J Mol Sci 2023; 24:13060. [PMID: 37685866 PMCID: PMC10488016 DOI: 10.3390/ijms241713060] [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: 07/06/2023] [Revised: 08/08/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Huntington's disease (HD) is caused by an expansion of a CAG repeat in the gene that encodes the huntingtin protein (HTT). The exact function of HTT is still not fully understood, and previous studies have mainly focused on identifying proteins that interact with HTT to gain insights into its function. Numerous HTT-interacting proteins have been discovered, shedding light on the functions and structure of HTT. Most of these proteins interact with the N-terminal region of HTT. Among the various HTT-interacting proteins, huntingtin-associated protein 1 (HAP1) and HTT-interacting protein 1 (HIP1) have been extensively studied. Recent research has uncovered differences in the distribution of HAP1 in monkey and human brains compared with mice. This finding suggests that there may be species-specific variations in the regulation and function of HTT-interacting proteins. Understanding these differences could provide crucial insights into the development of HD. In this review, we will focus on the recent advancements in the study of HTT-interacting proteins, with particular attention to the differential distributions of HTT and HAP1 in larger animal models.
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Affiliation(s)
| | | | | | | | | | | | | | - Shihua Li
- Guangdong Key Laboratory of Non-Human Primate Research, Key Laboratory of Central Nervous System Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510623, China; (L.L.); (H.T.); (Y.S.); (X.C.); (T.Y.); (G.Z.); (X.-J.L.)
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12
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Helabad MB, Matlahov I, Daldrop JO, Jain G, van der Wel PC, Miettinen MS. Integrative determination of the atomic structure of mutant huntingtin exon 1 fibrils from Huntington's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.549993. [PMID: 37502911 PMCID: PMC10370190 DOI: 10.1101/2023.07.21.549993] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Neurodegeneration in Huntington's disease (HD) is accompanied by the aggregation of fragments of the mutant huntingtin protein, a biomarker of disease progression. A particular pathogenic role has been attributed to the aggregation-prone huntingtin exon 1 (HttEx1) fragment, whose polyglutamine (polyQ) segment is expanded. Unlike amyloid fibrils from Parkinson's and Alzheimer's diseases, the atomic-level structure of HttEx1 fibrils has remained unknown, limiting diagnostic and treatment efforts. We present and analyze the structure of fibrils formed by polyQ peptides and polyQ-expanded HttEx1. Atomic-resolution perspectives are enabled by an integrative analysis and unrestrained all-atom molecular dynamics (MD) simulations incorporating experimental data from electron microscopy (EM), solid-state NMR, and other techniques. Visualizing the HttEx1 subdomains in atomic detail helps explaining the biological properties of these protein aggregates, as well as paves the way for targeting them for detection and degradation.
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Affiliation(s)
- Mahdi Bagherpoor Helabad
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
- Institute for Drug Discovery, Leipzig University Medical Center, 04103 Leipzig, Germany
| | - Irina Matlahov
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Jan O. Daldrop
- Fachbereich Physik, Freie Universitä t Berlin, 14195 Berlin, Germany
| | - Greeshma Jain
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | | | - Markus S. Miettinen
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
- Fachbereich Physik, Freie Universitä t Berlin, 14195 Berlin, Germany
- Department of Chemistry, University of Bergen, 5007 Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
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13
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Barbosa Pereira PJ, Manso JA, Macedo-Ribeiro S. The structural plasticity of polyglutamine repeats. Curr Opin Struct Biol 2023; 80:102607. [PMID: 37178477 DOI: 10.1016/j.sbi.2023.102607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/15/2023]
Abstract
From yeast to humans, polyglutamine (polyQ) repeat tracts are found frequently in the proteome and are particularly prominent in the activation domains of transcription factors. PolyQ is a polymorphic motif that modulates functional protein-protein interactions and aberrant self-assembly. Expansion of the polyQ repeated sequences beyond critical physiological repeat length thresholds triggers self-assembly and is linked to severe pathological implications. This review provides an overview of the current knowledge on the structures of polyQ tracts in the soluble and aggregated states and discusses the influence of neighboring regions on polyQ secondary structure, aggregation, and fibril morphologies. The influence of the genetic context of the polyQ-encoding trinucleotides is briefly discussed as a challenge for future endeavors in this field.
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Affiliation(s)
- Pedro José Barbosa Pereira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.
| | - José A Manso
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
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14
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Denis HL, Alpaugh M, Alvarez CP, Fenyi A, Barker RA, Chouinard S, Arrowsmith CH, Melki R, Labib R, Harding RJ, Cicchetti F. Detection of antibodies against the huntingtin protein in human plasma. Cell Mol Life Sci 2023; 80:45. [PMID: 36651994 PMCID: PMC9849309 DOI: 10.1007/s00018-023-04687-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023]
Abstract
Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder resulting from a CAG expansion in the huntingtin (HTT) gene, which leads to the production and accumulation of mutant huntingtin (mHTT). While primarily considered a disorder of the central nervous system, multiple changes have been described to occur throughout the body, including activation of the immune system. In other neurodegenerative disorders, activation of the immune system has been shown to include the production of antibodies against disease-associated pathological proteins. However, the existence of mHTT-targeted antibodies has never been reported. In this study, we assessed the presence and titer of antibodies recognizing HTT/mHTT in patients with HD (n = 66) and age- and gender-matched healthy controls (n = 66) using a combination of Western blotting and ELISA. Together, these analyses revealed that antibodies capable of recognizing HTT/mHTT were detectable in the plasma samples of all participants, including healthy controls. When antibody levels were monitored at different disease stages, it was observed that antibodies against full-length mHTT were highest in patients with severe disease while antibodies against HTTExon1 were elevated in patients with mild disease. Combined, these results suggest that antibodies detecting different forms of mHTT peak at different disease stages.
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Affiliation(s)
- Hélèna L Denis
- Centre de Recherche du CHU de Québec, Axe Neurosciences, T2-07, 2705, Boulevard Laurier, Québec, QC, G1V 4G2, Canada
- Département de Psychiatrie and Neurosciences, Université Laval, Québec, QC, Canada
| | - Melanie Alpaugh
- Centre de Recherche du CHU de Québec, Axe Neurosciences, T2-07, 2705, Boulevard Laurier, Québec, QC, G1V 4G2, Canada
- Département de Psychiatrie and Neurosciences, Université Laval, Québec, QC, Canada
| | - Claudia P Alvarez
- Structural Genomics Consortium, University of Toronto, MaRS Building Suite 700, 101 College Street, Toronto, ON, M5G1L7, Canada
| | - Alexis Fenyi
- Laboratory of Neurodegenerative Diseases, Institut François Jacob, MIRCen, CEA, CNRS, Fontenay-Aux-Roses, France
| | - Roger A Barker
- John van Geest Center for Brain Repair, University of Cambridge, Cambridge, UK
| | - Sylvain Chouinard
- Centre Hospitalier Universitaire de Montréal-Hôtel Dieu, Movement Disorders Unit, CHUM, Montréal, QC, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, MaRS Building Suite 700, 101 College Street, Toronto, ON, M5G1L7, Canada
- Department of Medical Biophysics, University of Toronto and Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Ronald Melki
- Laboratory of Neurodegenerative Diseases, Institut François Jacob, MIRCen, CEA, CNRS, Fontenay-Aux-Roses, France
| | - Richard Labib
- Department of Mathematical and Industrial Engineering, Polytechnique Montréal, Montréal, QC, Canada
| | - Rachel J Harding
- Structural Genomics Consortium, University of Toronto, MaRS Building Suite 700, 101 College Street, Toronto, ON, M5G1L7, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
| | - Francesca Cicchetti
- Centre de Recherche du CHU de Québec, Axe Neurosciences, T2-07, 2705, Boulevard Laurier, Québec, QC, G1V 4G2, Canada.
- Département de Psychiatrie and Neurosciences, Université Laval, Québec, QC, Canada.
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15
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Lee Y, Kim H, Barker D, Vijayvargia R, Atwal RS, Specht H, Keshishian H, Carr SA, Lee R, Kwak S, Hyun KG, Loupe J, MacDonald ME, Song JJ, Seong IS. Huntingtin turnover: modulation of huntingtin degradation by cAMP-dependent protein kinase A (PKA) phosphorylation of C-HEAT domain Ser2550. Hum Mol Genet 2023; 32:30-45. [PMID: 35908190 DOI: 10.1093/hmg/ddac165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 01/25/2023] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by an inherited unstable HTT CAG repeat that expands further, thereby eliciting a disease process that may be initiated by polyglutamine-expanded huntingtin or a short polyglutamine-product. Phosphorylation of selected candidate residues is reported to mediate polyglutamine-fragment degradation and toxicity. Here to support the discovery of phosphosites involved in the life-cycle of (full-length) huntingtin, we employed mass spectrometry-based phosphoproteomics to systematically identify sites in purified huntingtin and in the endogenous protein by proteomic and phosphoproteomic analyses of members of an HD neuronal progenitor cell panel. Our results bring total huntingtin phosphosites to 95, with more located in the N-HEAT domain relative to numbers in the Bridge and C-HEAT domains. Moreover, phosphorylation of C-HEAT Ser2550 by cAMP-dependent protein kinase (PKA), the top hit in kinase activity screens, was found to hasten huntingtin degradation, such that levels of the catalytic subunit (PRKACA) were inversely related to huntingtin levels. Taken together, these findings highlight categories of phosphosites that merit further study and provide a phosphosite kinase pair (pSer2550-PKA) with which to investigate the biological processes that regulate huntingtin degradation and thereby influence the steady state levels of huntingtin in HD cells.
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Affiliation(s)
- Yejin Lee
- Department of Biological Sciences, KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.,Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Hyeongju Kim
- Department of Biological Sciences, KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Douglas Barker
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Ravi Vijayvargia
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Ranjit Singh Atwal
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Harrison Specht
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Hasmik Keshishian
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Ramee Lee
- CHDI Management/CHDI Foundation, Princeton, NJ 08540, USA
| | - Seung Kwak
- CHDI Management/CHDI Foundation, Princeton, NJ 08540, USA
| | - Kyung-Gi Hyun
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Jacob Loupe
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Marcy E MacDonald
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Ji-Joon Song
- Department of Biological Sciences, KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Ihn Sik Seong
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
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16
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Kennedy MA, Greco TM, Song B, Cristea IM. HTT-OMNI: A Web-based Platform for Huntingtin Interaction Exploration and Multi-omics Data Integration. Mol Cell Proteomics 2022; 21:100275. [PMID: 35932982 PMCID: PMC9540350 DOI: 10.1016/j.mcpro.2022.100275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 01/18/2023] Open
Abstract
Huntington's disease (HD) is a progressive neurological disorder that is caused by polyglutamine expansion of the huntingtin (HTT) protein. With the hope to uncover key modifiers of disease, a focus of the field of HD research has been on characterizing HTT-interacting proteins (HIPs) and the effect of the HTT polyglutamine expansion on the cellular omics landscape. However, while hundreds of studies have uncovered over 3000 potential HIPs to date, a means to interrogate these complementary interaction and omics datasets does not exist. The lack of a unified platform for exploring this breadth of potential HIPs and associated omics data represents a substantial barrier toward understanding the impact of HTT polyQ expansion and identifying interactions proximal to HD pathogenesis. Here, we describe the development of a web-based platform called HTT-OMNI (HTT OMics and Network Integration). This application facilitates the visualization and exploration of ∼3400 potential HTT interactors (from the HINT database) and their associated polyQ-dependent omics measurements, such as transcriptome and proteome abundances. Additionally, HTT-OMNI allows for the integration of user-generated datasets with existing HIPs and omic measurements. We first demonstrate the utility of HTT-OMNI for filtering existing HTT PPIs based on a variety of experimental metadata parameters, highlighting its capacity to select for HIPs detected in specific model organisms and tissues. Next, we leverage our application to visualize the relationships between HTT PPIs, genetic disease modifiers, and their multiomic landscape. Finally, we generate and analyze a previously unreported dataset of HTT PPIs, aimed at defining tissue-specific HTT interactions and the polyQ-dependent modulation of their relative stabilities in the cortex and striatum of HD mouse models.
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17
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Seefelder M, Klein FAC, Landwehrmeyer B, Fernández-Busnadiego R, Kochanek S. Huntingtin and Its Partner Huntingtin-Associated Protein 40: Structural and Functional Considerations in Health and Disease. J Huntingtons Dis 2022; 11:227-242. [PMID: 35871360 PMCID: PMC9484127 DOI: 10.3233/jhd-220543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the discovery of the mutation causing Huntington’s disease (HD) in 1993, it has been debated whether an expanded polyglutamine (polyQ) stretch affects the properties of the huntingtin (HTT) protein and thus contributes to the pathological mechanisms responsible for HD. Here we review the current knowledge about the structure of HTT, alone (apo-HTT) or in a complex with Huntingtin-Associated Protein 40 (HAP40), the influence of polyQ-length variation on apo-HTT and the HTT-HAP40 complex, and the biology of HAP40. Phylogenetic analyses suggest that HAP40 performs essential functions. Highlighting the relevance of its interaction with HTT, HAP40 is one of the most abundant partners copurifying with HTT and is rapidly degraded, when HTT levels are reduced. As the levels of both proteins decrease during disease progression, HAP40 could also be a biomarker for HD. Whether declining HAP40 levels contribute to disease etiology is an open question. Structural studies have shown that the conformation of apo-HTT is less constrained but resembles that adopted in the HTT-HAP40 complex, which is exceptionally stable because of extensive interactions between HAP40 and the three domains of HTT. The complex— and to some extent apo-HTT— resists fragmentation after limited proteolysis. Unresolved regions of apo-HTT, constituting about 25% of the protein, are the main sites of post-translational modifications and likely have major regulatory functions. PolyQ elongation does not substantially alter the structure of HTT, alone or when associated with HAP40. Particularly, polyQ above the disease length threshold does not induce drastic conformational changes in full-length HTT. Therefore, models of HD pathogenesis stating that polyQ expansion drastically alters HTT properties should be reconsidered.
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Affiliation(s)
| | | | | | - Rubén Fernández-Busnadiego
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
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Babi M, Neuman K, Peng CY, Maiuri T, Suart CE, Truant R. Recent Microscopy Advances and the Applications to Huntington’s Disease Research. J Huntingtons Dis 2022; 11:269-280. [PMID: 35848031 PMCID: PMC9484089 DOI: 10.3233/jhd-220536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Huntingtin is a 3144 amino acid protein defined as a scaffold protein with many intracellular locations that suggest functions in these compartments. Expansion of the CAG DNA tract in the huntingtin first exon is the cause of Huntington’s disease. An important tool in understanding the biological functions of huntingtin is molecular imaging at the single-cell level by microscopy and nanoscopy. The evolution of these technologies has accelerated since the Nobel Prize in Chemistry was awarded in 2014 for super-resolution nanoscopy. We are in a new era of light imaging at the single-cell level, not just for protein location, but also for protein conformation and biochemical function. Large-scale microscopy-based screening is also being accelerated by a coincident development of machine-based learning that offers a framework for truly unbiased data acquisition and analysis at very large scales. This review will summarize the newest technologies in light, electron, and atomic force microscopy in the context of unique challenges with huntingtin cell biology and biochemistry.
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Affiliation(s)
- Mouhanad Babi
- McMaster Centre for Advanced Light Microscopy (CALM) McMaster University, Hamilton, Canada
| | - Kaitlyn Neuman
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Christina Y. Peng
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Tamara Maiuri
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Celeste E. Suart
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Ray Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- McMaster Centre for Advanced Light Microscopy (CALM) McMaster University, Hamilton, Canada
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19
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Molecular Pathophysiological Mechanisms in Huntington's Disease. Biomedicines 2022; 10:biomedicines10061432. [PMID: 35740453 PMCID: PMC9219859 DOI: 10.3390/biomedicines10061432] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
Huntington’s disease is an inherited neurodegenerative disease described 150 years ago by George Huntington. The genetic defect was identified in 1993 to be an expanded CAG repeat on exon 1 of the huntingtin gene located on chromosome 4. In the following almost 30 years, a considerable amount of research, using mainly animal models or in vitro experiments, has tried to unravel the complex molecular cascades through which the transcription of the mutant protein leads to neuronal loss, especially in the medium spiny neurons of the striatum, and identified excitotoxicity, transcriptional dysregulation, mitochondrial dysfunction, oxidative stress, impaired proteostasis, altered axonal trafficking and reduced availability of trophic factors to be crucial contributors. This review discusses the pathogenic cascades described in the literature through which mutant huntingtin leads to neuronal demise. However, due to the ubiquitous presence of huntingtin, astrocytes are also dysfunctional, and neuroinflammation may additionally contribute to Huntington’s disease pathology. The quest for therapies to delay the onset and reduce the rate of Huntington’s disease progression is ongoing, but is based on findings from basic research.
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