1
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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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2
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Mah CK, Ahmed N, Lopez NA, Lam DC, Pong A, Monell A, Kern C, Han Y, Prasad G, Cesnik AJ, Lundberg E, Zhu Q, Carter H, Yeo GW. Bento: a toolkit for subcellular analysis of spatial transcriptomics data. Genome Biol 2024; 25:82. [PMID: 38566187 PMCID: PMC11289963 DOI: 10.1186/s13059-024-03217-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell-cell interactions, and spatial expression patterns, they are limited to the multicellular scale. We present Bento, a Python toolkit that takes advantage of single-molecule information to enable spatial analysis at the subcellular scale. Bento ingests molecular coordinates and segmentation boundaries to perform three analyses: defining subcellular domains, annotating localization patterns, and quantifying gene-gene colocalization. We demonstrate MERFISH, seqFISH + , Molecular Cartography, and Xenium datasets. Bento is part of the open-source Scverse ecosystem, enabling integration with other single-cell analysis tools.
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Affiliation(s)
- Clarence K Mah
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center, La Jolla, CA, USA
| | - Noorsher Ahmed
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center, La Jolla, CA, USA
| | - Nicole A Lopez
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Dylan C Lam
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Avery Pong
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alexander Monell
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Colin Kern
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Yuanyuan Han
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Gino Prasad
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Anthony J Cesnik
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Emma Lundberg
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Quan Zhu
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Institute Innovation Center, La Jolla, CA, USA.
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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3
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Kiessling P, Kuppe C. Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases. Genome Med 2024; 16:14. [PMID: 38238823 PMCID: PMC10795303 DOI: 10.1186/s13073-024-01282-y] [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: 08/15/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome in parallel or even the same tissue section. This review focuses on the recent advancements in spatial multi-omics technologies, including novel data modalities and computational approaches. We discuss the advancements in low-resolution and high-resolution spatial multi-omics methods which can resolve up to 10,000 of individual molecules at subcellular level. By applying and integrating these techniques, researchers have recently gained valuable insights into the molecular circuits and mechanisms which govern cell biology along the cardiovascular disease spectrum. We provide an overview of current data analysis approaches, with a focus on data integration of multi-omic datasets, highlighting strengths and weaknesses of various computational pipelines. These tools play a crucial role in analyzing and interpreting spatial multi-omics datasets, facilitating the discovery of new findings, and enhancing translational cardiovascular research. Despite nontrivial challenges, such as the need for standardization of experimental setups, data analysis, and improved computational tools, the application of spatial multi-omics holds tremendous potential in revolutionizing our understanding of human disease processes and the identification of novel biomarkers and therapeutic targets. Exciting opportunities lie ahead for the spatial multi-omics field and will likely contribute to the advancement of personalized medicine for cardiovascular diseases.
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Affiliation(s)
- Paul Kiessling
- Department of Nephrology, Rheumatology, and Clinical Immunology, University Hospital RWTH Aachen, Aachen, Germany
| | - Christoph Kuppe
- Department of Nephrology, Rheumatology, and Clinical Immunology, University Hospital RWTH Aachen, Aachen, Germany.
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4
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Savulescu AF, Doxakis E. Editorial: RNA binding proteins in neuroscience. Front Mol Neurosci 2023; 16:1340721. [PMID: 38115823 PMCID: PMC10728815 DOI: 10.3389/fnmol.2023.1340721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Affiliation(s)
- Anca F. Savulescu
- Division of Chemical, Systems and Synthetic Biology, Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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5
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Trujillo-Del Río C, Tortajada-Pérez J, Gómez-Escribano AP, Casterá F, Peiró C, Millán JM, Herrero MJ, Vázquez-Manrique RP. Metformin to treat Huntington disease: a pleiotropic drug against a multi-system disorder. Mech Ageing Dev 2022; 204:111670. [DOI: 10.1016/j.mad.2022.111670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 12/17/2022]
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6
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Nuclear and cytoplasmic huntingtin inclusions exhibit distinct biochemical composition, interactome and ultrastructural properties. Nat Commun 2021; 12:6579. [PMID: 34772920 PMCID: PMC8589980 DOI: 10.1038/s41467-021-26684-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/11/2021] [Indexed: 12/20/2022] Open
Abstract
Despite the strong evidence linking the aggregation of the Huntingtin protein (Htt) to the pathogenesis of Huntington's disease (HD), the mechanisms underlying Htt aggregation and neurodegeneration remain poorly understood. Herein, we investigated the ultrastructural properties and protein composition of Htt cytoplasmic and nuclear inclusions in mammalian cells and primary neurons overexpressing mutant exon1 of the Htt protein. Our findings provide unique insight into the ultrastructural properties of cytoplasmic and nuclear Htt inclusions and their mechanisms of formation. We show that Htt inclusion formation and maturation are complex processes that, although initially driven by polyQ-dependent Htt aggregation, also involve the polyQ and PRD domain-dependent sequestration of lipids and cytoplasmic and cytoskeletal proteins related to HD dysregulated pathways; the recruitment and accumulation of remodeled or dysfunctional membranous organelles, and the impairment of the protein quality control and degradation machinery. We also show that nuclear and cytoplasmic Htt inclusions exhibit distinct biochemical compositions and ultrastructural properties, suggesting different mechanisms of aggregation and toxicity.
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7
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Wei H, Dong X, You Y, Hai B, Duran RCD, Wu X, Kharas N, Wu JQ. OLIG2 regulates lncRNAs and its own expression during oligodendrocyte lineage formation. BMC Biol 2021; 19:132. [PMID: 34172044 PMCID: PMC8235854 DOI: 10.1186/s12915-021-01057-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 05/27/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Oligodendrocytes, responsible for axon ensheathment, are critical for central nervous system (CNS) development, function, and diseases. OLIG2 is an important transcription factor (TF) that acts during oligodendrocyte development and performs distinct functions at different stages. Previous studies have shown that lncRNAs (long non-coding RNAs; > 200 bp) have important functions during oligodendrocyte development, but their roles have not been systematically characterized and their regulation is not yet clear. RESULTS We performed an integrated study of genome-wide OLIG2 binding and the epigenetic modification status of both coding and non-coding genes during three stages of oligodendrocyte differentiation in vivo: neural stem cells (NSCs), oligodendrocyte progenitor cells (OPCs), and newly formed oligodendrocytes (NFOs). We found that 613 lncRNAs have OLIG2 binding sites and are expressed in at least one cell type, which can potentially be activated or repressed by OLIG2. Forty-eight of them have increased expression in oligodendrocyte lineage cells. Predicting lncRNA functions by using a "guilt-by-association" approach revealed that the functions of these 48 lncRNAs were enriched in "oligodendrocyte development and differentiation." Additionally, bivalent genes are known to play essential roles during embryonic stem cell differentiation. We identified bivalent genes in NSCs, OPCs, and NFOs and found that some bivalent genes bound by OLIG2 are dynamically regulated during oligodendrocyte development. Importantly, we unveiled a previously unknown mechanism that, in addition to transcriptional regulation via DNA binding, OLIG2 could self-regulate through the 3' UTR of its own mRNA. CONCLUSIONS Our studies have revealed the missing links in the mechanisms regulating oligodendrocyte development at the transcriptional level and after transcription. The results of our research have improved the understanding of fundamental cell fate decisions during oligodendrocyte lineage formation, which can enable insights into demyelination diseases and regenerative medicine.
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Affiliation(s)
- Haichao Wei
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | - Xiaomin Dong
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | - Yanan You
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | - Bo Hai
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | - Raquel Cuevas-Diaz Duran
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA.,Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, N.L., Mexico
| | - Xizi Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | - Natasha Kharas
- Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA. .,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA. .,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
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8
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Eshraghi M, Karunadharma PP, Blin J, Shahani N, Ricci EP, Michel A, Urban NT, Galli N, Sharma M, Ramírez-Jarquín UN, Florescu K, Hernandez J, Subramaniam S. Mutant Huntingtin stalls ribosomes and represses protein synthesis in a cellular model of Huntington disease. Nat Commun 2021; 12:1461. [PMID: 33674575 PMCID: PMC7935949 DOI: 10.1038/s41467-021-21637-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 01/29/2021] [Indexed: 02/08/2023] Open
Abstract
The polyglutamine expansion of huntingtin (mHTT) causes Huntington disease (HD) and neurodegeneration, but the mechanisms remain unclear. Here, we found that mHtt promotes ribosome stalling and suppresses protein synthesis in mouse HD striatal neuronal cells. Depletion of mHtt enhances protein synthesis and increases the speed of ribosomal translocation, while mHtt directly inhibits protein synthesis in vitro. Fmrp, a known regulator of ribosome stalling, is upregulated in HD, but its depletion has no discernible effect on protein synthesis or ribosome stalling in HD cells. We found interactions of ribosomal proteins and translating ribosomes with mHtt. High-resolution global ribosome footprint profiling (Ribo-Seq) and mRNA-Seq indicates a widespread shift in ribosome occupancy toward the 5' and 3' end and unique single-codon pauses on selected mRNA targets in HD cells, compared to controls. Thus, mHtt impedes ribosomal translocation during translation elongation, a mechanistic defect that can be exploited for HD therapeutics.
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Affiliation(s)
- Mehdi Eshraghi
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Pabalu P. Karunadharma
- grid.214007.00000000122199231The Scripps Research Institute, Genomic Core, Jupiter, FL USA
| | - Juliana Blin
- grid.462957.b0000 0004 0598 0706Laboratory of Biology and Cellular Modelling at Ecole Normale Supérieure of Lyon, RNA Metabolism in Immunity and Infection Lab, LBMC, Lyon, France
| | - Neelam Shahani
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Emiliano P. Ricci
- grid.462957.b0000 0004 0598 0706Laboratory of Biology and Cellular Modelling at Ecole Normale Supérieure of Lyon, RNA Metabolism in Immunity and Infection Lab, LBMC, Lyon, France
| | | | | | - Nicole Galli
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Manish Sharma
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Uri Nimrod Ramírez-Jarquín
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Katie Florescu
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Jennifer Hernandez
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
| | - Srinivasa Subramaniam
- grid.214007.00000000122199231The Scripps Research Institute, Department of Neuroscience, Jupiter, FL USA
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9
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Maiuri T, Truant R. Single Cell Technologies Define New Therapeutic Avenues for Huntington's Disease. Neuron 2020; 107:768-769. [PMID: 32910889 DOI: 10.1016/j.neuron.2020.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Using two independent single-cell transcriptomics technologies, Lee et al. have cataloged transcriptional changes in the subset of striatal neurons hit hardest in Huntington's disease. One downregulated pathway, oxidative phosphorylation, may also explain their observed release of mitochondrial-encoded RNAs.
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Affiliation(s)
- Tamara Maiuri
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N3Z5, Canada
| | - Ray Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N3Z5, Canada.
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10
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Joag H, Ghatpande V, Desai M, Sarkar M, Raina A, Shinde M, Chitale R, Deo A, Bose T, Majumdar A. A role of cellular translation regulation associated with toxic Huntingtin protein. Cell Mol Life Sci 2020; 77:3657-3670. [PMID: 31796991 PMCID: PMC11105026 DOI: 10.1007/s00018-019-03392-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 11/29/2022]
Abstract
Huntington's disease (HD) is a severe neurodegenerative disorder caused by poly Q repeat expansion in the Huntingtin (Htt) gene. While the Htt amyloid aggregates are known to affect many cellular processes, their role in translation has not been addressed. Here we report that pathogenic Htt expression causes a protein synthesis deficit in cells. We find a functional prion-like protein, the translation regulator Orb2, to be sequestered by Htt aggregates in cells. Co-expression of Orb2 can partially rescue the lethality associated with poly Q expanded Htt. These findings can be relevant for HD as human homologs of Orb2 are also sequestered by pathogenic Htt aggregates. Our work suggests that translation dysfunction is one of the contributors to the pathogenesis of HD and new therapies targeting protein synthesis pathways might help to alleviate disease symptoms.
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Affiliation(s)
- Hiranmay Joag
- National Centre for Cell Science, S. P. Pune University, Pune, India
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | | | - Meghal Desai
- National Centre for Cell Science, S. P. Pune University, Pune, India
| | - Maitheli Sarkar
- National Centre for Cell Science, S. P. Pune University, Pune, India
| | - Anshu Raina
- National Centre for Cell Science, S. P. Pune University, Pune, India
| | - Mrunalini Shinde
- Institute of Bioinformatics and Biotechnology, S. P. Pune University, Pune, India
| | - Ruta Chitale
- Institute of Bioinformatics and Biotechnology, S. P. Pune University, Pune, India
| | - Ankita Deo
- Institute of Bioinformatics and Biotechnology, S. P. Pune University, Pune, India
| | - Tania Bose
- Institute of Bioinformatics and Biotechnology, S. P. Pune University, Pune, India.
| | - Amitabha Majumdar
- National Centre for Cell Science, S. P. Pune University, Pune, India.
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11
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Mori S, Honda H, Ishii T, Yoshimura M, Sasagasako N, Suzuki SO, Taniwaki T, Iwaki T. Expanded polyglutamine impairs normal nuclear distribution of fused in sarcoma and poly (rC)‐binding protein 1 in Huntington's disease. Neuropathology 2019; 39:358-367. [DOI: 10.1111/neup.12600] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/25/2019] [Accepted: 08/08/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Shinichiro Mori
- Department of NeuropathologyGraduate School of Medical Sciences, Kyushu University Fukuoka Japan
- Department of Neurology, Division of Respirology, Neurology and Rheumatology, Department of MedicineKurume University School of Medicine Kurume Japan
| | - Hiroyuki Honda
- Department of NeuropathologyGraduate School of Medical Sciences, Kyushu University Fukuoka Japan
| | - Takashi Ishii
- Department of BiochemistryFukuoka Dental College Fukuoka Japan
| | - Motoi Yoshimura
- Department of NeuropathologyGraduate School of Medical Sciences, Kyushu University Fukuoka Japan
| | - Naokazu Sasagasako
- Department of NeurologyNeuro‐Muscular Center, National Omuta Hospital Omuta Japan
| | - Satoshi O. Suzuki
- Department of NeuropathologyGraduate School of Medical Sciences, Kyushu University Fukuoka Japan
| | - Takayuki Taniwaki
- Department of Neurology, Division of Respirology, Neurology and Rheumatology, Department of MedicineKurume University School of Medicine Kurume Japan
| | - Toru Iwaki
- Department of NeuropathologyGraduate School of Medical Sciences, Kyushu University Fukuoka Japan
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12
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Sap KA, Guler AT, Bezstarosti K, Bury AE, Juenemann K, Demmers JA, Reits EA. Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains. Mol Cell Proteomics 2019; 18:1705-1720. [PMID: 31138642 PMCID: PMC6731087 DOI: 10.1074/mcp.ra119.001486] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/21/2019] [Indexed: 01/31/2023] Open
Abstract
Huntington's disease is caused by a polyglutamine repeat expansion in the huntingtin protein which affects the function and folding of the protein, and results in intracellular protein aggregates. Here, we examined whether this mutation leads to altered ubiquitination of huntingtin and other proteins in both soluble and insoluble fractions of brain lysates of the Q175 knock-in Huntington's disease mouse model and the Q20 wild-type mouse model. Ubiquitination sites are detected by identification of Gly-Gly (diGly) remnant motifs that remain on modified lysine residues after digestion. We identified K6, K9, K132, K804, and K837 as endogenous ubiquitination sites of soluble huntingtin, with wild-type huntingtin being mainly ubiquitinated at K132, K804, and K837. Mutant huntingtin protein levels were strongly reduced in the soluble fraction whereas K6 and K9 were mainly ubiquitinated. In the insoluble fraction increased levels of huntingtin K6 and K9 diGly sites were observed for mutant huntingtin as compared with wild type. Besides huntingtin, proteins with various roles, including membrane organization, transport, mRNA processing, gene transcription, translation, catabolic processes and oxidative phosphorylation, were differently expressed or ubiquitinated in wild-type and mutant huntingtin brain tissues. Correlating protein and diGly site fold changes in the soluble fraction revealed that diGly site abundances of most of the proteins were not related to protein fold changes, indicating that these proteins were differentially ubiquitinated in the Q175 mice. In contrast, both the fold change of the protein level and diGly site level were increased for several proteins in the insoluble fraction, including ubiquitin, ubiquilin-2, sequestosome-1/p62 and myo5a. Our data sheds light on putative novel proteins involved in different cellular processes as well as their ubiquitination status in Huntington's disease, which forms the basis for further mechanistic studies to understand the role of differential ubiquitination of huntingtin and ubiquitin-regulated processes in Huntington's disease.
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Affiliation(s)
- Karen A Sap
- ‡Department of Medical Biology, Amsterdam UMC, location AMC, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Arzu Tugce Guler
- ‡Department of Medical Biology, Amsterdam UMC, location AMC, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Karel Bezstarosti
- §Department of Biochemistry, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Aleksandra E Bury
- ‡Department of Medical Biology, Amsterdam UMC, location AMC, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Katrin Juenemann
- ¶Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin, Robert-Roessle-St. 10 13089 Berlin, Germany
| | - JeroenA A Demmers
- §Department of Biochemistry, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Eric A Reits
- ‡Department of Medical Biology, Amsterdam UMC, location AMC, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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Coudert L, Nonaka T, Bernard E, Hasegawa M, Schaeffer L, Leblanc P. Phosphorylated and aggregated TDP-43 with seeding properties are induced upon mutant Huntingtin (mHtt) polyglutamine expression in human cellular models. Cell Mol Life Sci 2019; 76:2615-2632. [PMID: 30863908 PMCID: PMC11105362 DOI: 10.1007/s00018-019-03059-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 02/06/2019] [Accepted: 03/01/2019] [Indexed: 12/14/2022]
Abstract
The Tar DNA-Binding Protein 43 (TDP-43) and its phosphorylated isoform (pTDP-43) are the major components associated with ubiquitin positive/Tau-negative inclusions found in neurons and glial cells of patients suffering of amyotrophic lateral sclerosis (ALS) or frontotemporal lobar degeneration-TDP-43 (FTLD-TDP). Many studies have revealed that TDP-43 is also in the protein inclusions associated with neurodegenerative conditions other than ALS and FTLD-TDP, thus suggesting that this protein may be involved in the pathogenesis of a variety of neurological disorders. In brains of Huntington-affected patients, pTDP-43 aggregates were shown to co-localize with mutant Huntingtin (mHtt) inclusions. Here, we show that expression of mHtt carrying 80-97 polyglutamines repeats in human cell cultures induces the aggregation and the phosphorylation of endogenous TDP-43, whereas non-pathological Htt with 25 polyglutamines repeats has no effect. Mutant Htt aggregation precedes accumulation of pTDP-43 and pTDP-43 co-localizes with mHtt inclusions reminding what it was previously described in brains of Huntington-affected patients. Detergent-insoluble fractions from cells expressing mHtt and containing mHtt-pTDP-43 co-aggregates can function as seeds for further TDP-43 aggregation in human cell culture. The human cellular prion protein PrPC was previously identified as a negative modulator of mHtt aggregation; here, we show that PrPC-mediated reduction of mHtt aggregation is tightly correlated with a decrease of TDP-43 aggregation and phosphorylation, thus confirming the close relationships between TDP-43 and mHtt.
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Affiliation(s)
- Laurent Coudert
- Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217, Faculté de Médecine Rockefeller, Université Claude Bernard Lyon I, 8 Avenue Rockefeller, 69373, Lyon Cedex 08, France
| | - Takashi Nonaka
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Emilien Bernard
- Hospices Civils de Lyon, Hôpital Neurologique Pierre-Wertheimer, Service de Neurologie C et Centre SLA de Lyon, Bron, France
- Université de Lyon, Faculté de Médecine Lyon Sud Charles Mérieux, Lyon, France
| | - Masato Hasegawa
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Laurent Schaeffer
- Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217, Faculté de Médecine Rockefeller, Université Claude Bernard Lyon I, 8 Avenue Rockefeller, 69373, Lyon Cedex 08, France
| | - Pascal Leblanc
- Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217, Faculté de Médecine Rockefeller, Université Claude Bernard Lyon I, 8 Avenue Rockefeller, 69373, Lyon Cedex 08, France.
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Reduced mitochondrial fusion and Huntingtin levels contribute to impaired dendritic maturation and behavioral deficits in Fmr1-mutant mice. Nat Neurosci 2019; 22:386-400. [PMID: 30742117 PMCID: PMC6556892 DOI: 10.1038/s41593-019-0338-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/09/2019] [Indexed: 12/26/2022]
Abstract
Fragile X syndrome results from a loss of the RNA-binding protein fragile X mental retardation protein (FMRP). How FMRP regulates neuronal development and function remains unclear. Here we show that FMRP-deficient immature neurons exhibit impaired dendritic maturation, altered expression of mitochondrial genes, fragmented mitochondria, impaired mitochondrial function, and increased oxidative stress. Enhancing mitochondrial fusion partially rescued dendritic abnormalities in FMRP-deficient immature neurons. We show that FMRP deficiency leads to reduced Htt mRNA and protein levels and that HTT mediates FMRP regulation of mitochondrial fusion and dendritic maturation. Mice with hippocampal Htt knockdown and Fmr1-knockout mice showed similar behavioral deficits that could be rescued by treatment with a mitochondrial fusion compound. Our data unveil mitochondrial dysfunction as a contributor to the impaired dendritic maturation of FMRP-deficient neurons and suggest a role for interactions between FMRP and HTT in the pathogenesis of fragile X syndrome.
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Abstract
Huntingtin (HTT) is an essential protein during early embryogenesis and the development of the central nervous system (CNS). Conditional knock-out of mouse Huntingtin (Htt) expression in the CNS beginning during neural development, as well as reducing Htt expression only during embryonic and early postnatal stages, results in neurodegeneration in the adult brain. These findings suggest that HTT is important for the development and/or maintenance of the CNS, but they do not address the question of whether HTT is required specifically in the adult CNS for its normal functions and/or homeostasis. Recently, it was reported that although removing Htt expression in young adult mice causes lethality due to acute pancreatitis, loss of Htt expression in the adult brain is well tolerated and does not result in either motor deficits or neurodegeneration for up to 7 months after Htt inactivation. However, recent studies have also demonstrated that HTT participates in several cellular functions that are important for neuronal homeostasis and survival including sensing reactive oxygen species (ROS), DNA damage repair, and stress responses, in addition to its role in selective macroautophagy. In this review, HTT's functions in development and in the adult CNS will be discussed in the context of these recent discoveries, together with a discussion of their potential impact on the design of therapeutic strategies for Huntington's disease (HD) aimed at lowering total HTT expression.
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Affiliation(s)
| | - Scott O. Zeitlin
- Correspondence to: Scott O. Zeitlin, Ph.D., Department of Neuroscience, University of Virginia School of Medicine, 409 Lane Rd., Box 801392, MR4-5022, Charlottesville, VA 22908, USA. Tel.: +1 434 924 5011; Fax: +1 434 982 4380; E-mail:
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