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Solana-Balaguer J, Garcia-Segura P, Campoy-Campos G, Chicote-González A, Fernández-Irigoyen J, Santamaría E, Pérez-Navarro E, Masana M, Alberch J, Malagelada C. Motor skill learning modulates striatal extracellular vesicles' content in a mouse model of Huntington's disease. Cell Commun Signal 2024; 22:321. [PMID: 38863004 PMCID: PMC11167907 DOI: 10.1186/s12964-024-01693-9] [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: 03/05/2024] [Accepted: 05/29/2024] [Indexed: 06/13/2024] Open
Abstract
Huntington's disease (HD) is a neurological disorder caused by a CAG expansion in the Huntingtin gene (HTT). HD pathology mostly affects striatal medium-sized spiny neurons and results in an altered cortico-striatal function. Recent studies report that motor skill learning, and cortico-striatal stimulation attenuate the neuropathology in HD, resulting in an amelioration of some motor and cognitive functions. During physical training, extracellular vesicles (EVs) are released in many tissues, including the brain, as a potential means for inter-tissue communication. To investigate how motor skill learning, involving acute physical training, modulates EVs crosstalk between cells in the striatum, we trained wild-type (WT) and R6/1 mice, the latter with motor and cognitive deficits, on the accelerating rotarod test, and we isolated their striatal EVs. EVs from R6/1 mice presented alterations in the small exosome population when compared to WT. Proteomic analyses revealed that striatal R6/1 EVs recapitulated signaling and energy deficiencies present in HD. Motor skill learning in R6/1 mice restored the amount of EVs and their protein content in comparison to naïve R6/1 mice. Furthermore, motor skill learning modulated crucial pathways in metabolism and neurodegeneration. All these data provide new insights into the pathogenesis of HD and put striatal EVs in the spotlight to understand the signaling and metabolic alterations in neurodegenerative diseases. Moreover, our results suggest that motor learning is a crucial modulator of cell-to-cell communication in the striatum.
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Affiliation(s)
- Júlia Solana-Balaguer
- Departament de Biomedicina, Institut de Neurociències, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Casanova 143, North Wing, 3rd Floor, Barcelona, Catalonia, 08036, Spain.
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain.
| | - Pol Garcia-Segura
- Departament de Biomedicina, Institut de Neurociències, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Casanova 143, North Wing, 3rd Floor, Barcelona, Catalonia, 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Genís Campoy-Campos
- Departament de Biomedicina, Institut de Neurociències, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Casanova 143, North Wing, 3rd Floor, Barcelona, Catalonia, 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Almudena Chicote-González
- Departament de Biomedicina, Institut de Neurociències, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Casanova 143, North Wing, 3rd Floor, Barcelona, Catalonia, 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | | | - Enrique Santamaría
- Proteored-ISCIII, Proteomics Unit, Departamento de Salud, UPNA, Navarrabiomed, Pamplona, IdiSNA, Spain
| | - Esther Pérez-Navarro
- Departament de Biomedicina, Institut de Neurociències, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Casanova 143, North Wing, 3rd Floor, Barcelona, Catalonia, 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mercè Masana
- Departament de Biomedicina, Institut de Neurociències, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Casanova 143, North Wing, 3rd Floor, Barcelona, Catalonia, 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Jordi Alberch
- Departament de Biomedicina, Institut de Neurociències, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Casanova 143, North Wing, 3rd Floor, Barcelona, Catalonia, 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Cristina Malagelada
- Departament de Biomedicina, Institut de Neurociències, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Casanova 143, North Wing, 3rd Floor, Barcelona, Catalonia, 08036, Spain.
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain.
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Regio S, Vachey G, Goñi E, Duarte F, Rybarikova M, Sipion M, Rey M, Huarte M, Déglon N. Revisiting the outcome of adult wild-type Htt inactivation in the context of HTT-lowering strategies for Huntington's disease. Brain Commun 2023; 5:fcad344. [PMID: 38116140 PMCID: PMC10729863 DOI: 10.1093/braincomms/fcad344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/11/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023] Open
Abstract
Huntingtin-lowering strategies are central to therapeutic approaches for Huntington's disease. Recent studies reported the induction of age- and cell type-specific phenotypes by conditional huntingtin knockout, but these experimental conditions did not precisely mimic huntingtin-lowering or gene-editing conditions in terms of the cells targeted and brain distribution, and no transcriptional profiles were provided. Here, we used the adeno-associated delivery system commonly used in CNS gene therapy programmes and the self-inactivating KamiCas9 gene-editing system to investigate the long-term consequences of wild-type mouse huntingtin inactivation in adult neurons and, thus, the feasibility and safety of huntingtin inactivation in these cells. Behavioural and neuropathological analyses and single-nuclei RNA sequencing indicated that huntingtin editing in 77% of striatal neurons and 16% of cortical projecting neurons in adult mice induced no behavioural deficits or cellular toxicity. Single-nuclei RNA sequencing in 11.5-month-old animals showed that huntingtin inactivation did not alter striatal-cell profiles or proportions. Few differentially expressed genes were identified and Augur analysis confirmed an extremely limited response to huntingtin inactivation in all cell types. Our results therefore indicate that wild-type huntingtin inactivation in adult striatal and projection neurons is well tolerated in the long term.
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Affiliation(s)
- Sara Regio
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Department of Clinical Neurosciences (DNC), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Neuroscience Research Center (CRN), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
| | - Gabriel Vachey
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Department of Clinical Neurosciences (DNC), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Neuroscience Research Center (CRN), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
| | - Enrique Goñi
- Center for Applied Medical Research, University of Navarra, Pamplona 31008, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona 31008, Spain
| | - Fabio Duarte
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Department of Clinical Neurosciences (DNC), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Neuroscience Research Center (CRN), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
| | - Margareta Rybarikova
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Department of Clinical Neurosciences (DNC), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Neuroscience Research Center (CRN), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
| | - Mélanie Sipion
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Department of Clinical Neurosciences (DNC), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Neuroscience Research Center (CRN), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
| | - Maria Rey
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Department of Clinical Neurosciences (DNC), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Neuroscience Research Center (CRN), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
| | - Maite Huarte
- Center for Applied Medical Research, University of Navarra, Pamplona 31008, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona 31008, Spain
| | - Nicole Déglon
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Department of Clinical Neurosciences (DNC), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
- Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Neuroscience Research Center (CRN), Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne 1011, Switzerland
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Karayel-Basar M, Uras I, Kiris I, Baykal AT. Detection of proteomic alterations at different stages in a Huntington's disease mouse model via matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging. Eur J Neurosci 2023; 58:2985-3002. [PMID: 37525529 DOI: 10.1111/ejn.16103] [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: 02/19/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 08/02/2023]
Abstract
Huntington's disease (HD) is a progressive and irreversible neurodegenerative disease leading to the inability to carry out daily activities and for which no cure exists. The underlying mechanisms of the disease have not been fully elucidated yet. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) allows the spatial information of proteins to be obtained upon the tissue sections without homogenisation. In this study, we aimed to examine proteomic alterations in the brain tissue of an HD mouse model with MALDI-MSI coupled to LC-MS/MS system. We used 3-, 6- and 12-month-old YAC128 mice representing pre-stage, mild stage and pathological stage of the HD and their non-transgenic littermates, respectively. The intensity levels of 89 proteins were found to be significantly different in YAC128 in comparison to their control mice in the pre-stage, 83 proteins in the mild stage, and 82 proteins in the pathological stage. Among them, Tau, EF2, HSP70, and NogoA proteins were validated with western blot analysis. In conclusion, the results of this study have provided remarkable new information about the spatial proteomic alterations in the HD mouse model, and we suggest that MALDI-MSI is an excellent technique for identifying such regional proteomic changes and could offer new perspectives in examining complex diseases.
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Affiliation(s)
- Merve Karayel-Basar
- Department of Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Irep Uras
- Department of Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Irem Kiris
- Department of Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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4
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Li J, Amoh BK, McCormick E, Tarkunde A, Zhu KF, Perez A, Mair M, Moore J, Shulman JM, Al-Ramahi I, Botas J. Integration of transcriptome-wide association study with neuronal dysfunction assays provides functional genomics evidence for Parkinson's disease genes. Hum Mol Genet 2023; 32:685-695. [PMID: 36173927 PMCID: PMC9896475 DOI: 10.1093/hmg/ddac230] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies (GWAS) have markedly advanced our understanding of the genetics of Parkinson's disease (PD), but they currently do not account for the full heritability of PD. In many cases it is difficult to unambiguously identify a specific gene within each locus because GWAS does not provide functional information on the identified candidate loci. Here we present an integrative approach that combines transcriptome-wide association study (TWAS) with high-throughput neuronal dysfunction analyses in Drosophila to discover and validate candidate PD genes. We identified 160 candidate genes whose misexpression is associated with PD risk via TWAS. Candidates were validated using orthogonal in silico methods and found to be functionally related to PD-associated pathways (i.e. endolysosome). We then mimicked these TWAS-predicted transcriptomic alterations in a Drosophila PD model and discovered that 50 candidates can modulate α-Synuclein(α-Syn)-induced neurodegeneration, allowing us to nominate new genes in previously known PD loci. We also uncovered additional novel PD candidate genes within GWAS suggestive loci (e.g. TTC19, ADORA2B, LZTS3, NRBP1, HN1L), which are also supported by clinical and functional evidence. These findings deepen our understanding of PD, and support applying our integrative approach to other complex trait disorders.
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Affiliation(s)
- Jiayang Li
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Bismark Kojo Amoh
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Emma McCormick
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Akash Tarkunde
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Katy Fan Zhu
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alma Perez
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Megan Mair
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Justin Moore
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Joshua M Shulman
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Center for Alzheimer’s and Neurodegenerative Diseases, Baylor College of Medicine, Houston, TX, USA
| | - Ismael Al-Ramahi
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Alzheimer’s and Neurodegenerative Diseases, Baylor College of Medicine, Houston, TX, USA
| | - Juan Botas
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Alzheimer’s and Neurodegenerative Diseases, Baylor College of Medicine, Houston, TX, USA
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5
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Reyes-Ortiz AM, Abud EM, Burns MS, Wu J, Hernandez SJ, McClure N, Wang KQ, Schulz CJ, Miramontes R, Lau A, Michael N, Miyoshi E, Van Vactor D, Reidling JC, Blurton-Jones M, Swarup V, Poon WW, Lim RG, Thompson LM. Single-nuclei transcriptome analysis of Huntington disease iPSC and mouse astrocytes implicates maturation and functional deficits. iScience 2023; 26:105732. [PMID: 36590162 PMCID: PMC9800269 DOI: 10.1016/j.isci.2022.105732] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/13/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
Huntington disease (HD) is a neurodegenerative disorder caused by expanded CAG repeats in the huntingtin gene that alters cellular homeostasis, particularly in the striatum and cortex. Astrocyte signaling that establishes and maintains neuronal functions are often altered under pathological conditions. We performed single-nuclei RNA-sequencing on human HD patient-induced pluripotent stem cell (iPSC)-derived astrocytes and on striatal and cortical tissue from R6/2 HD mice to investigate high-resolution HD astrocyte cell state transitions. We observed altered maturation and glutamate signaling in HD human and mouse astrocytes. Human HD astrocytes also showed upregulated actin-mediated signaling, suggesting that some states may be cell-autonomous and human specific. In both species, astrogliogenesis transcription factors may drive HD astrocyte maturation deficits, which are supported by rescued climbing deficits in HD drosophila with NFIA knockdown. Thus, dysregulated HD astrocyte states may induce dysfunctional astrocytic properties, in part due to maturation deficits influenced by astrogliogenesis transcription factor dysregulation.
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Affiliation(s)
- Andrea M. Reyes-Ortiz
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92617, USA
| | - Edsel M. Abud
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92617, USA
| | - Mara S. Burns
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92617, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92617, USA
| | - Sarah J. Hernandez
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92617, USA
| | - Nicolette McClure
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92617, USA
| | - Keona Q. Wang
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92617, USA
| | - Corey J. Schulz
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92617, USA
| | - Ricardo Miramontes
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92617, USA
| | - Alice Lau
- Department of Psychiatry & Human Behavior, University of California, Irvine, Irvine, CA 92617, USA
| | - Neethu Michael
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92617, USA
| | - Emily Miyoshi
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92617, USA
| | - David Van Vactor
- Harvard Medical School, Department of Cell Biology, Boston, MA 02115, USA
| | - John C. Reidling
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92617, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92617, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92617, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92617, USA
| | - Vivek Swarup
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92617, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92617, USA
| | - Wayne W. Poon
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92617, USA
| | - Ryan G. Lim
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92617, USA
| | - Leslie M. Thompson
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92617, USA
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92617, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92617, USA
- Department of Psychiatry & Human Behavior, University of California, Irvine, Irvine, CA 92617, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92617, USA
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Brandebura AN, Paumier A, Onur TS, Allen NJ. Astrocyte contribution to dysfunction, risk and progression in neurodegenerative disorders. Nat Rev Neurosci 2023; 24:23-39. [PMID: 36316501 DOI: 10.1038/s41583-022-00641-1] [Citation(s) in RCA: 92] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
Abstract
There is increasing appreciation that non-neuronal cells contribute to the initiation, progression and pathology of diverse neurodegenerative disorders. This Review focuses on the role of astrocytes in disorders including Alzheimer disease, Parkinson disease, Huntington disease and amyotrophic lateral sclerosis. The important roles astrocytes have in supporting neuronal function in the healthy brain are considered, along with studies that have demonstrated how the physiological properties of astrocytes are altered in neurodegenerative disorders and may explain their contribution to neurodegeneration. Further, the question of whether in neurodegenerative disorders with specific genetic mutations these mutations directly impact on astrocyte function, and may suggest a driving role for astrocytes in disease initiation, is discussed. A summary of how astrocyte transcriptomic and proteomic signatures are altered during the progression of neurodegenerative disorders and may relate to functional changes is provided. Given the central role of astrocytes in neurodegenerative disorders, potential strategies to target these cells for future therapeutic avenues are discussed.
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Affiliation(s)
- Ashley N Brandebura
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Adrien Paumier
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Tarik S Onur
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nicola J Allen
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
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7
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Ding Y, Xing D, Fei Y, Lu B. Emerging degrader technologies engaging lysosomal pathways. Chem Soc Rev 2022; 51:8832-8876. [PMID: 36218065 PMCID: PMC9620493 DOI: 10.1039/d2cs00624c] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Indexed: 08/24/2023]
Abstract
Targeted protein degradation (TPD) provides unprecedented opportunities for drug discovery. While the proteolysis-targeting chimera (PROTAC) technology has already entered clinical trials and changed the landscape of small-molecule drugs, new degrader technologies harnessing alternative degradation machineries, especially lysosomal pathways, have emerged and broadened the spectrum of degradable targets. We have recently proposed the concept of autophagy-tethering compounds (ATTECs) that hijack the autophagy protein microtubule-associated protein 1A/1B light chain 3 (LC3) for targeted degradation. Other groups also reported degrader technologies engaging lysosomal pathways through different mechanisms including AUTACs, AUTOTACs, LYTACs and MoDE-As. In this review, we analyse and discuss ATTECs along with other lysosomal-relevant degrader technologies. Finally, we will briefly summarize the current status of these degrader technologies and envision possible future studies.
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Affiliation(s)
- Yu Ding
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Life Sciences, Fudan University, Shanghai, China.
| | - Dong Xing
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, China.
| | - Boxun Lu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Life Sciences, Fudan University, Shanghai, China.
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8
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Altered activity-regulated H3K9 acetylation at TGF-beta signaling genes during egocentric memory in Huntington's disease. Prog Neurobiol 2022; 219:102363. [PMID: 36179935 DOI: 10.1016/j.pneurobio.2022.102363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/25/2022] [Accepted: 09/24/2022] [Indexed: 11/21/2022]
Abstract
Molecular mechanisms underlying cognitive deficits in Huntington's disease (HD), a striatal neurodegenerative disorder, are unknown. Here, we generated ChIPseq, 4Cseq and RNAseq data on striatal tissue of HD and control mice during striatum-dependent egocentric memory process. Multi-omics analyses showed altered activity-dependent epigenetic gene reprogramming of neuronal and glial genes regulating striatal plasticity in HD mice, which correlated with memory deficit. First, our data reveal that spatial chromatin re-organization and transcriptional induction of BDNF-related markers, regulating neuronal plasticity, were reduced since memory acquisition in the striatum of HD mice. Second, our data show that epigenetic memory implicating H3K9 acetylation, which established during late phase of memory process (e.g. during consolidation/recall) and contributed to glia-mediated, TGFβ-dependent plasticity, was compromised in HD mouse striatum. Specifically, memory-dependent regulation of H3K9 acetylation was impaired at genes controlling extracellular matrix and myelination. Our study investigating the interplay between epigenetics and memory identifies H3K9 acetylation and TGFβ signaling as new targets of striatal plasticity, which might offer innovative leads to improve HD.
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Lagisetty Y, Bourquard T, Al-Ramahi I, Mangleburg CG, Mota S, Soleimani S, Shulman JM, Botas J, Lee K, Lichtarge O. Identification of risk genes for Alzheimer's disease by gene embedding. CELL GENOMICS 2022; 2:100162. [PMID: 36268052 PMCID: PMC9581494 DOI: 10.1016/j.xgen.2022.100162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Most disease-gene association methods do not account for gene-gene interactions, even though these play a crucial role in complex, polygenic diseases like Alzheimer's disease (AD). To discover new genes whose interactions may contribute to pathology, we introduce GeneEMBED. This approach compares the functional perturbations induced in gene interaction network neighborhoods by coding variants from disease versus healthy subjects. In two independent AD cohorts of 5,169 exomes and 969 genomes, GeneEMBED identified novel candidates. These genes were differentially expressed in post mortem AD brains and modulated neurological phenotypes in mice. Four that were differentially overexpressed and modified neurodegeneration in vivo are PLEC, UTRN, TP53, and POLD1. Notably, TP53 and POLD1 are involved in DNA break repair and inhibited by approved drugs. While these data show proof of concept in AD, GeneEMBED is a general approach that should be broadly applicable to identify genes relevant to risk mechanisms and therapy of other complex diseases.
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Affiliation(s)
- Yashwanth Lagisetty
- Department of Biology and Pharmacology, UTHealth McGovern Medical School, Houston, TX 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas Bourquard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ismael Al-Ramahi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA,Center for Alzheimer’s and Neurodegenerative Diseases, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carl Grant Mangleburg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Samantha Mota
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shirin Soleimani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joshua M. Shulman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA,Center for Alzheimer’s and Neurodegenerative Diseases, Baylor College of Medicine, Houston, TX 77030, USA,Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA,Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Juan Botas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA,Center for Alzheimer’s and Neurodegenerative Diseases, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kwanghyuk Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Center for Alzheimer’s and Neurodegenerative Diseases, Baylor College of Medicine, Houston, TX 77030, USA,Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX 77030, USA,Corresponding author
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10
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Chongtham A, Yoo JH, Chin TM, Akingbesote ND, Huda A, Marsh JL, Khoshnan A. Gut Bacteria Regulate the Pathogenesis of Huntington's Disease in Drosophila Model. Front Neurosci 2022; 16:902205. [PMID: 35757549 PMCID: PMC9215115 DOI: 10.3389/fnins.2022.902205] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022] Open
Abstract
Changes in the composition of gut microbiota are implicated in the pathogenesis of several neurodegenerative disorders. Here, we investigated whether gut bacteria affect the progression of Huntington’s disease (HD) in transgenic Drosophila melanogaster (fruit fly) models expressing full-length or N-terminal fragments of human mutant huntingtin (HTT) protein. We find that elimination of commensal gut bacteria by antibiotics reduces the aggregation of amyloidogenic N-terminal fragments of HTT and delays the development of motor defects. Conversely, colonization of HD flies with Escherichia coli (E. coli), a known pathobiont of human gut with links to neurodegeneration and other morbidities, accelerates HTT aggregation, aggravates immobility, and shortens lifespan. Similar to antibiotics, treatment of HD flies with small compounds such as luteolin, a flavone, or crocin a beta-carotenoid, ameliorates disease phenotypes, and promotes survival. Crocin prevents colonization of E. coli in the gut and alters the levels of commensal bacteria, which may be linked to its protective effects. The opposing effects of E. coli and crocin on HTT aggregation, motor defects, and survival in transgenic Drosophila models support the involvement of gut-brain networks in the pathogenesis of HD.
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Affiliation(s)
- Anjalika Chongtham
- Biology and Bioengineering, California Institute of Technology (Caltech), Pasadena, CA, United States
| | - Jung Hyun Yoo
- Biology and Bioengineering, California Institute of Technology (Caltech), Pasadena, CA, United States
| | - Theodore M Chin
- Biology and Bioengineering, California Institute of Technology (Caltech), Pasadena, CA, United States
| | - Ngozi D Akingbesote
- Biology and Bioengineering, California Institute of Technology (Caltech), Pasadena, CA, United States
| | - Ainul Huda
- Biology and Bioengineering, California Institute of Technology (Caltech), Pasadena, CA, United States
| | - J Lawrence Marsh
- Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States
| | - Ali Khoshnan
- Biology and Bioengineering, California Institute of Technology (Caltech), Pasadena, CA, United States
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11
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Costa MD, Maciel P. Modifier pathways in polyglutamine (PolyQ) diseases: from genetic screens to drug targets. Cell Mol Life Sci 2022; 79:274. [PMID: 35503478 PMCID: PMC11071829 DOI: 10.1007/s00018-022-04280-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/14/2022] [Accepted: 03/30/2022] [Indexed: 12/17/2022]
Abstract
Polyglutamine (PolyQ) diseases include a group of inherited neurodegenerative disorders caused by unstable expansions of CAG trinucleotide repeats in the coding region of specific genes. Such genetic alterations produce abnormal proteins containing an unusually long PolyQ tract that renders them more prone to aggregate and cause toxicity. Although research in the field in the last years has contributed significantly to the knowledge of the biological mechanisms implicated in these diseases, effective treatments are still lacking. In this review, we revisit work performed in models of PolyQ diseases, namely the yeast Saccharomyces cerevisiae, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and provide a critical overview of the high-throughput unbiased genetic screens that have been performed using these systems to identify novel genetic modifiers of PolyQ diseases. These approaches have revealed a wide variety of cellular processes that modulate the toxicity and aggregation of mutant PolyQ proteins, reflecting the complexity of these disorders and demonstrating how challenging the development of therapeutic strategies can be. In addition to the unbiased large-scale genetic screenings in non-vertebrate models, complementary studies in mammalian systems, closer to humans, have contributed with novel genetic modifiers of PolyQ diseases, revealing neuronal function and inflammation as key disease modulators. A pathway enrichment analysis, using the human orthologues of genetic modifiers of PolyQ diseases clustered modifier genes into major themes translatable to the human disease context, such as protein folding and transport as well as transcription regulation. Innovative genetic strategies of genetic manipulation, together with significant advances in genomics and bioinformatics, are taking modifier genetic studies to more realistic disease contexts. The characterization of PolyQ disease modifier pathways is of extreme relevance to reveal novel therapeutic possibilities to delay disease onset and progression in patients.
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Affiliation(s)
- Marta Daniela Costa
- School of Medicine, Life and Health Sciences Research Institute (ICVS), University of Minho, 4710-057, Braga, Portugal
- ICVS/3Bs-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Patrícia Maciel
- School of Medicine, Life and Health Sciences Research Institute (ICVS), University of Minho, 4710-057, Braga, Portugal.
- ICVS/3Bs-PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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12
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Greco TM, Secker C, Ramos ES, Federspiel JD, Liu JP, Perez AM, Al-Ramahi I, Cantle JP, Carroll JB, Botas J, Zeitlin SO, Wanker EE, Cristea IM. Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease. Cell Syst 2022; 13:304-320.e5. [PMID: 35148841 PMCID: PMC9317655 DOI: 10.1016/j.cels.2022.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/18/2021] [Accepted: 01/24/2022] [Indexed: 12/13/2022]
Abstract
Huntington disease (HD) is a monogenic neurodegenerative disorder with one causative gene, huntingtin (HTT). Yet, HD pathobiology is multifactorial, suggesting that cellular factors influence disease progression. Here, we define HTT protein-protein interactions (PPIs) perturbed by the mutant protein with expanded polyglutamine in the mouse striatum, a brain region with selective HD vulnerability. Using metabolically labeled tissues and immunoaffinity purification-mass spectrometry, we establish that polyglutamine-dependent modulation of HTT PPI abundances and relative stability starts at an early stage of pathogenesis in a Q140 HD mouse model. We identify direct and indirect PPIs that are also genetic disease modifiers using in-cell two-hybrid and behavioral assays in HD human cell and Drosophila models, respectively. Validated, disease-relevant mHTT-dependent interactions encompass mediators of synaptic neurotransmission (SNAREs and glutamate receptors) and lysosomal acidification (V-ATPase). Our study provides a resource for understanding mHTT-dependent dysfunction in cortico-striatal cellular networks, partly through impaired synaptic communication and endosomal-lysosomal system. A record of this paper's Transparent Peer Review process is included in the supplemental information.
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Affiliation(s)
- Todd M Greco
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ, USA
| | - Christopher Secker
- Neuroproteomics, Max Delbrück Centre for Molecular Medicine, Berlin, Germany
| | - Eduardo Silva Ramos
- Neuroproteomics, Max Delbrück Centre for Molecular Medicine, Berlin, Germany
| | - Joel D Federspiel
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ, USA
| | - Jeh-Ping Liu
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Alma M Perez
- Jan and Dan Duncan Neurological Research Institute, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ismael Al-Ramahi
- Jan and Dan Duncan Neurological Research Institute, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey P Cantle
- Department of Psychology, Western Washington University, Bellingham, WA, USA
| | - Jeffrey B Carroll
- Department of Psychology, Western Washington University, Bellingham, WA, USA
| | - Juan Botas
- Jan and Dan Duncan Neurological Research Institute, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Scott O Zeitlin
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Centre for Molecular Medicine, Berlin, Germany
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ, USA.
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13
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Kluever V, Fornasiero EF. Principles of brain aging: Status and challenges of modeling human molecular changes in mice. Ageing Res Rev 2021; 72:101465. [PMID: 34555542 DOI: 10.1016/j.arr.2021.101465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 01/22/2023]
Abstract
Due to the extension of human life expectancy, the prevalence of cognitive impairment is rising in the older portion of society. Developing new strategies to delay or attenuate cognitive decline is vital. For this purpose, it is imperative to understand the cellular and molecular events at the basis of brain aging. While several organs are directly accessible to molecular analysis through biopsies, the brain constitutes a notable exception. Most of the molecular studies are performed on postmortem tissues, where cell death and tissue damage have already occurred. Hence, the study of the molecular aspects of cognitive decline largely relies on animal models and in particular on small mammals such as mice. What have we learned from these models? Do these animals recapitulate the changes observed in humans? What should we expect from future mouse studies? In this review we answer these questions by summarizing the state of the research that has addressed cognitive decline in mice from several perspectives, including genetic manipulation and omics strategies. We conclude that, while extremely valuable, mouse models have limitations that can be addressed by the optimal design of future studies and by ensuring that results are cross-validated in the human context.
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14
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Bailus BJ, Scheeler SM, Simons J, Sanchez MA, Tshilenge KT, Creus-Muncunill J, Naphade S, Lopez-Ramirez A, Zhang N, Lakshika Madushani K, Moroz S, Loureiro A, Schreiber KH, Hausch F, Kennedy BK, Ehrlich ME, Ellerby LM. Modulating FKBP5/FKBP51 and autophagy lowers HTT (huntingtin) levels. Autophagy 2021; 17:4119-4140. [PMID: 34024231 PMCID: PMC8726715 DOI: 10.1080/15548627.2021.1904489] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 12/14/2022] Open
Abstract
Current disease-modifying therapies for Huntington disease (HD) focus on lowering mutant HTT (huntingtin; mHTT) levels, and the immunosuppressant drug rapamycin is an intriguing therapeutic for aging and neurological disorders. Rapamycin interacts with FKBP1A/FKBP12 and FKBP5/FKBP51, inhibiting the MTORC1 complex and increasing cellular clearance mechanisms. Whether the levels of FKBP (FK506 binding protein) family members are altered in HD models and if these proteins are potential therapeutic targets for HD have not been investigated. Here, we found levels of FKBP5 are significantly reduced in HD R6/2 and zQ175 mouse models and human HD isogenic neural stem cells and medium spiny neurons derived from induced pluripotent stem cells. Moreover, FKBP5 interacts and colocalizes with HTT in the striatum and cortex of zQ175 mice and controls. Importantly, when we decreased FKBP5 levels or activity by genetic or pharmacological approaches, we observed reduced levels of mHTT in our isogenic human HD stem cell model. Decreasing FKBP5 levels by siRNA or pharmacological inhibition increased LC3-II levels and macroautophagic/autophagic flux, suggesting autophagic cellular clearance mechanisms are responsible for mHTT lowering. Unlike rapamycin, the effect of pharmacological inhibition with SAFit2, an inhibitor of FKBP5, is MTOR independent. Further, in vivo treatment for 2 weeks with SAFit2, results in reduced HTT levels in both HD R6/2 and zQ175 mouse models. Our studies establish FKBP5 as a protein involved in the pathogenesis of HD and identify FKBP5 as a potential therapeutic target for HD.Abbreviations : ACTB/β-actin: actin beta; AD: Alzheimer disease; BafA1: bafilomycin A1; BCA: bicinchoninic acid; BBB: blood brain barrier; BSA: bovine serum albumin; CoIP: co-immunoprecipitation; DMSO: dimethyl sulfoxide; DTT: dithiothreitol; FKBPs: FK506 binding proteins; HD: Huntington disease; HTT: huntingtin; iPSC: induced pluripotent stem cells; MAP1LC3/LC3:microtubule associated protein 1 light chain 3; MAPT/tau: microtubule associated protein tau; MES: 2-ethanesulfonic acid; MOPS: 3-(N-morphorlino)propanesulfonic acid); MSN: medium spiny neurons; mHTT: mutant huntingtin; MTOR: mechanistic target of rapamycin kinase; NSC: neural stem cells; ON: overnight; PD: Parkinson disease; PPIase: peptidyl-prolyl cis/trans-isomerases; polyQ: polyglutamine; PPP1R1B/DARPP-32: protein phosphatase 1 regulatory inhibitor subunit 1B; PTSD: post-traumatic stress disorder; RT: room temperature; SQSTM1/p62: sequestosome 1; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; TBST:Tris-buffered saline, 0.1% Tween 20; TUBA: tubulin; ULK1: unc-51 like autophagy activating kinase 1; VCL: vinculin; WT: littermate controls.
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Affiliation(s)
- Barbara J. Bailus
- The Buck Institute for Research on Aging, Novato, CA, USA
- School of Pharmacy and Health Sciences, Keck Graduate Institute, Claremont, CA, USA
| | - Stephen M. Scheeler
- The Buck Institute for Research on Aging, Novato, CA, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Jesse Simons
- The Buck Institute for Research on Aging, Novato, CA, USA
| | | | | | | | - Swati Naphade
- The Buck Institute for Research on Aging, Novato, CA, USA
| | | | - Ningzhe Zhang
- The Buck Institute for Research on Aging, Novato, CA, USA
| | | | | | | | | | - Felix Hausch
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Brian K. Kennedy
- The Buck Institute for Research on Aging, Novato, CA, USA
- Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University Singapore, Singapore
- Centre for Healthy Longevity, National University Health System, Singapore
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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15
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Developmental defects in Huntington's disease show that axonal growth and microtubule reorganization require NUMA1. Neuron 2021; 110:36-50.e5. [PMID: 34793694 DOI: 10.1016/j.neuron.2021.10.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 09/14/2021] [Accepted: 10/21/2021] [Indexed: 01/09/2023]
Abstract
Although the classic symptoms of Huntington's disease (HD) manifest in adulthood, neural progenitor cell behavior is already abnormal by 13 weeks' gestation. To determine how these developmental defects evolve, we turned to cell and mouse models. We found that layer II/III neurons that normally connect the hemispheres are limited in their growth in HD by microtubule bundling defects within the axonal growth cone, so that fewer axons cross the corpus callosum. Proteomic analyses of the growth cones revealed that NUMA1 (nuclear/mitotic apparatus protein 1) is downregulated in HD by miR-124. Suppressing NUMA1 in wild-type cells recapitulates the microtubule and axonal growth defects of HD, whereas raising NUMA1 levels with antagomiR-124 or stabilizing microtubules with epothilone B restores microtubule organization and rescues axonal growth. NUMA1 therefore regulates the microtubule network in the growth cone, and HD, which is traditionally conceived as a disease of intracellular trafficking, also disturbs the cytoskeletal network.
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16
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Onur TS, Laitman A, Zhao H, Keyho R, Kim H, Wang J, Mair M, Wang H, Li L, Perez A, de Haro M, Wan YW, Allen G, Lu B, Al-Ramahi I, Liu Z, Botas J. Downregulation of glial genes involved in synaptic function mitigates Huntington's disease pathogenesis. eLife 2021; 10:64564. [PMID: 33871358 PMCID: PMC8149125 DOI: 10.7554/elife.64564] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/19/2021] [Indexed: 01/01/2023] Open
Abstract
Most research on neurodegenerative diseases has focused on neurons, yet glia help form and maintain the synapses whose loss is so prominent in these conditions. To investigate the contributions of glia to Huntington's disease (HD), we profiled the gene expression alterations of Drosophila expressing human mutant Huntingtin (mHTT) in either glia or neurons and compared these changes to what is observed in HD human and HD mice striata. A large portion of conserved genes are concordantly dysregulated across the three species; we tested these genes in a high-throughput behavioral assay and found that downregulation of genes involved in synapse assembly mitigated pathogenesis and behavioral deficits. To our surprise, reducing dNRXN3 function in glia was sufficient to improve the phenotype of flies expressing mHTT in neurons, suggesting that mHTT's toxic effects in glia ramify throughout the brain. This supports a model in which dampening synaptic function is protective because it attenuates the excitotoxicity that characterizes HD. When a neuron dies, through injury or disease, the body loses all communication that passes through it. The brain compensates by rerouting the flow of information through other neurons in the network. Eventually, if the loss of neurons becomes too great, compensation becomes impossible. This process happens in Alzheimer's, Parkinson's, and Huntington's disease. In the case of Huntington's disease, the cause is mutation to a single gene known as huntingtin. The mutation is present in every cell in the body but causes particular damage to parts of the brain involved in mood, thinking and movement. Neurons and other cells respond to mutations in the huntingtin gene by turning the activities of other genes up or down, but it is not clear whether all of these changes contribute to the damage seen in Huntington's disease. In fact, it is possible that some of the changes are a result of the brain trying to protect itself. So far, most research on this subject has focused on neurons because the huntingtin gene plays a role in maintaining healthy neuronal connections. But, given that all cells carry the mutated gene, it is likely that other cells are also involved. The glia are a diverse group of cells that support the brain, providing care and sustenance to neurons. These cells have a known role in maintaining the connections between neurons and may also have play a role in either causing or correcting the damage seen in Huntington's disease. The aim of Onur et al. was to find out which genes are affected by having a mutant huntingtin gene in neurons or glia, and whether severity of Huntington’s disease improved or worsened when the activity of these genes changed. First, Onur et al. identified genes affected by mutant huntingtin by comparing healthy human brains to the brains of people with Huntington's disease. Repeating the same comparison in mice and fruit flies identified genes affected in the same way across all three species, revealing that, in Huntington's disease, the brain dials down glial cell genes involved in maintaining neuronal connections. To find out how these changes in gene activity affect disease severity and progression, Onur et al. manipulated the activity of each of the genes they had identified in fruit flies that carried mutant versions of huntingtin either in neurons, in glial cells or in both cell types. They then filmed the flies to see the effects of the manipulation on movement behaviors, which are affected by Huntington’s disease. This revealed that purposely lowering the activity of the glial genes involved in maintaining connections between neurons improved the symptoms of the disease, but only in flies who had mutant huntingtin in their glial cells. This indicates that the drop in activity of these genes observed in Huntington’s disease is the brain trying to protect itself. This work suggests that it is important to include glial cells in studies of neurological disorders. It also highlights the fact that changes in gene expression as a result of a disease are not always bad. Many alterations are compensatory, and try to either make up for or protect cells affected by the disease. Therefore, it may be important to consider whether drugs designed to treat a condition by changing levels of gene activity might undo some of the body's natural protection. Working out which changes drive disease and which changes are protective will be essential for designing effective treatments.
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Affiliation(s)
- Tarik Seref Onur
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States.,Genetics & Genomics Graduate Program, Baylor College of Medicine, Houston, United States
| | - Andrew Laitman
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States.,Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, United States.,Department of Pediatrics, Baylor College of Medicine, Houston, United States
| | - He Zhao
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States
| | - Ryan Keyho
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States
| | - Hyemin Kim
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States
| | - Jennifer Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States
| | - Megan Mair
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States.,Genetics & Genomics Graduate Program, Baylor College of Medicine, Houston, United States
| | - Huilan Wang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Lifang Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States
| | - Alma Perez
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States
| | - Maria de Haro
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States
| | - Genevera Allen
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States.,Departments of Electrical & Computer Engineering, Statistics and Computer Science, Rice University, Houston, United States
| | - Boxun Lu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Ismael Al-Ramahi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States.,Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, United States.,Department of Pediatrics, Baylor College of Medicine, Houston, United States
| | - Juan Botas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, United States.,Genetics & Genomics Graduate Program, Baylor College of Medicine, Houston, United States.,Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, United States
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17
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Virlogeux A, Scaramuzzino C, Lenoir S, Carpentier R, Louessard M, Genoux A, Lino P, Hinckelmann MV, Perrier AL, Humbert S, Saudou F. Increasing brain palmitoylation rescues behavior and neuropathology in Huntington disease mice. SCIENCE ADVANCES 2021; 7:7/14/eabb0799. [PMID: 33789888 PMCID: PMC8011966 DOI: 10.1126/sciadv.abb0799] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/11/2021] [Indexed: 05/02/2023]
Abstract
Huntington disease (HD) damages the corticostriatal circuitry in large part by impairing transport of brain-derived neurotrophic factor (BDNF). We hypothesized that improving vesicular transport of BDNF could slow or prevent disease progression. We therefore performed selective proteomic analysis of vesicles transported within corticostriatal projecting neurons followed by in silico screening and identified palmitoylation as a pathway that could restore defective huntingtin-dependent trafficking. Using a synchronized trafficking assay and an HD network-on-a-chip, we found that increasing brain palmitoylation via ML348, which inhibits the palmitate-removing enzyme acyl-protein thioesterase 1 (APT1), restores axonal transport, synapse homeostasis, and survival signaling to wild-type levels without toxicity. In human HD induced pluripotent stem cell-derived cortical neurons, ML348 increased BDNF trafficking. In HD knock-in mice, it efficiently crossed the blood-brain barrier to restore palmitoylation levels and reverse neuropathology, locomotor deficits, and anxio-depressive behaviors. APT1 and its inhibitor ML348 thus hold therapeutic interest for HD.
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Affiliation(s)
- Amandine Virlogeux
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neuroscience, GIN, 38000, Grenoble, France
| | - Chiara Scaramuzzino
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neuroscience, GIN, 38000, Grenoble, France
| | - Sophie Lenoir
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neuroscience, GIN, 38000, Grenoble, France
| | - Rémi Carpentier
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neuroscience, GIN, 38000, Grenoble, France
| | | | - Aurélie Genoux
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neuroscience, GIN, 38000, Grenoble, France
| | - Patricia Lino
- INSERM U861, UEVE, I-STEM, AFM, 91100, Corbeil-Essonnes, France
| | - Maria-Victoria Hinckelmann
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neuroscience, GIN, 38000, Grenoble, France
| | - Anselme L Perrier
- INSERM U861, UEVE, I-STEM, AFM, 91100, Corbeil-Essonnes, France
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Direction de la Recherche Fondamentale, Institut François Jacob, Molecular Imaging Center (MIRCen), CNRS UMR 9199, Université Paris-Saclay, 92265, Fontenay-aux-Roses, France
| | - Sandrine Humbert
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neuroscience, GIN, 38000, Grenoble, France
| | - Frédéric Saudou
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neuroscience, GIN, 38000, Grenoble, France.
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18
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Megret L, Gris B, Sasidharan Nair S, Cevost J, Wertz M, Aaronson J, Rosinski J, Vogt TF, Wilkinson H, Heiman M, Neri C. Shape deformation analysis reveals the temporal dynamics of cell-type-specific homeostatic and pathogenic responses to mutant huntingtin. eLife 2021; 10:64984. [PMID: 33618800 PMCID: PMC7901871 DOI: 10.7554/elife.64984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/31/2021] [Indexed: 01/06/2023] Open
Abstract
Loss of cellular homeostasis has been implicated in the etiology of several neurodegenerative diseases (NDs). However, the molecular mechanisms that underlie this loss remain poorly understood on a systems level in each case. Here, using a novel computational approach to integrate dimensional RNA-seq and in vivo neuron survival data, we map the temporal dynamics of homeostatic and pathogenic responses in four striatal cell types of Huntington’s disease (HD) model mice. This map shows that most pathogenic responses are mitigated and most homeostatic responses are decreased over time, suggesting that neuronal death in HD is primarily driven by the loss of homeostatic responses. Moreover, different cell types may lose similar homeostatic processes, for example, endosome biogenesis and mitochondrial quality control in Drd1-expressing neurons and astrocytes. HD relevance is validated by human stem cell, genome-wide association study, and post-mortem brain data. These findings provide a new paradigm and framework for therapeutic discovery in HD and other NDs.
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Affiliation(s)
- Lucile Megret
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, INSERM ERL U1164, Paris, France
| | - Barbara Gris
- Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire Jacques-Louis Lyons (LJLL), Paris, France
| | - Satish Sasidharan Nair
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, INSERM ERL U1164, Paris, France
| | - Jasmin Cevost
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, INSERM ERL U1164, Paris, France
| | - Mary Wertz
- MIT, Broad Institute, MIT, Picower Institute for Learning and Memory, Cambridge, United States
| | | | | | | | | | - Myriam Heiman
- MIT, Broad Institute, MIT, Picower Institute for Learning and Memory, Cambridge, United States
| | - Christian Neri
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, INSERM ERL U1164, Paris, France
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19
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Mangleburg CG, Wu T, Yalamanchili HK, Guo C, Hsieh YC, Duong DM, Dammer EB, De Jager PL, Seyfried NT, Liu Z, Shulman JM. Integrated analysis of the aging brain transcriptome and proteome in tauopathy. Mol Neurodegener 2020; 15:56. [PMID: 32993812 PMCID: PMC7526226 DOI: 10.1186/s13024-020-00405-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 09/18/2020] [Indexed: 01/09/2023] Open
Abstract
Background Tau neurofibrillary tangle pathology characterizes Alzheimer’s disease and other neurodegenerative tauopathies. Brain gene expression profiles can reveal mechanisms; however, few studies have systematically examined both the transcriptome and proteome or differentiated Tau- versus age-dependent changes. Methods Paired, longitudinal RNA-sequencing and mass-spectrometry were performed in a Drosophila model of tauopathy, based on pan-neuronal expression of human wildtype Tau (TauWT) or a mutant form causing frontotemporal dementia (TauR406W). Tau-induced, differentially expressed transcripts and proteins were examined cross-sectionally or using linear regression and adjusting for age. Hierarchical clustering was performed to highlight network perturbations, and we examined overlaps with human brain gene expression profiles in tauopathy. Results TauWT induced 1514 and 213 differentially expressed transcripts and proteins, respectively. TauR406W had a substantially greater impact, causing changes in 5494 transcripts and 697 proteins. There was a ~ 70% overlap between age- and Tau-induced changes and our analyses reveal pervasive bi-directional interactions. Strikingly, 42% of Tau-induced transcripts were discordant in the proteome, showing opposite direction of change. Tau-responsive gene expression networks strongly implicate innate immune activation. Cross-species analyses pinpoint human brain gene perturbations specifically triggered by Tau pathology and/or aging, and further differentiate between disease amplifying and protective changes. Conclusions Our results comprise a powerful, cross-species functional genomics resource for tauopathy, revealing Tau-mediated disruption of gene expression, including dynamic, age-dependent interactions between the brain transcriptome and proteome.
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Affiliation(s)
- Carl Grant Mangleburg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Timothy Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hari K Yalamanchili
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Caiwei Guo
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yi-Chen Hsieh
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and Taub Institute for the study of Alzheimer's disease and the aging brain, Columbia University Medical Center, New York, NY, 10032, USA.,Cell Circuits Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, 1250 Moursund St., Suite N.1150, Houston, TX, 77030, USA
| | - Joshua M Shulman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA. .,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, 1250 Moursund St., Suite N.1150, Houston, TX, 77030, USA. .,Department of Neurology, Baylor College of Medicine, Houston, TX, 77030, USA.
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20
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Bigan E, Sasidharan Nair S, Lejeune FX, Fragnaud H, Parmentier F, Mégret L, Verny M, Aaronson J, Rosinski J, Neri C. Genetic cooperativity in multi-layer networks implicates cell survival and senescence in the striatum of Huntington's disease mice synchronous to symptoms. Bioinformatics 2020; 36:186-196. [PMID: 31228193 PMCID: PMC6956776 DOI: 10.1093/bioinformatics/btz514] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 06/11/2019] [Accepted: 06/18/2019] [Indexed: 02/06/2023] Open
Abstract
Motivation Huntington’s disease (HD) may evolve through gene deregulation. However, the impact of gene deregulation on the dynamics of genetic cooperativity in HD remains poorly understood. Here, we built a multi-layer network model of temporal dynamics of genetic cooperativity in the brain of HD knock-in mice (allelic series of Hdh mice). To enhance biological precision and gene prioritization, we integrated three complementary families of source networks, all inferred from the same RNA-seq time series data in Hdh mice, into weighted-edge networks where an edge recapitulates path-length variation across source-networks and age-points. Results Weighted edge networks identify two consecutive waves of tight genetic cooperativity enriched in deregulated genes (critical phases), pre-symptomatically in the cortex, implicating neurotransmission, and symptomatically in the striatum, implicating cell survival (e.g. Hipk4) intertwined with cell proliferation (e.g. Scn4b) and cellular senescence (e.g. Cdkn2a products) responses. Top striatal weighted edges are enriched in modulators of defective behavior in invertebrate models of HD pathogenesis, validating their relevance to neuronal dysfunction in vivo. Collectively, these findings reveal highly dynamic temporal features of genetic cooperativity in the brain of Hdh mice where a 2-step logic highlights the importance of cellular maintenance and senescence in the striatum of symptomatic mice, providing highly prioritized targets. Availability and implementation Weighted edge network analysis (WENA) data and source codes for performing spectral decomposition of the signal (SDS) and WENA analysis, both written using Python, are available at http://www.broca.inserm.fr/HD-WENA/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Erwan Bigan
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | - Satish Sasidharan Nair
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | - François-Xavier Lejeune
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | - Hélissande Fragnaud
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | - Frédéric Parmentier
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | - Lucile Mégret
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | - Marc Verny
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | | | | | - Christian Neri
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
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21
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Pham M, Lichtarge O. Graph-based information diffusion method for prioritizing functionally related genes in protein-protein interaction networks. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2020; 25:439-450. [PMID: 31797617 PMCID: PMC7043368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Shortest path length methods are routinely used to validate whether genes of interest are functionally related to each other based on biological network information. However, the methods are computationally intensive, impeding extensive utilization of network information. In addition, non-weighted shortest path length approach, which is more frequently used, often treat all network connections equally without taking into account of confidence levels of the associations. On the other hand, graph-based information diffusion method, which employs both the presence and confidence weights of network edges, can efficiently explore large networks and has previously detected meaningful biological patterns. Therefore, in this study, we hypothesized that the graph-based information diffusion method could prioritize genes with relevant functions more efficiently and accurately than the shortest path length approaches. We demonstrated that the graph-based information diffusion method substantially differentiated not only genes participating in same biological pathways (p << 0.0001) but also genes associated with specific human drug-induced clinical symptoms (p << 0.0001) from random. Furthermore, the diffusion method prioritized these functionally related genes faster and more accurately than the shortest path length approaches (pathways: p = 2.7e-28, clinical symptoms: p = 0.032). These data show the graph-based information diffusion method can be routinely used for robust prioritization of functionally related genes, facilitating efficient network validation and hypothesis generation, especially for human phenotype-specific genes.
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Affiliation(s)
- Minh Pham
- Integrative Molecular and Biomedical Sciences Graduate Program, and Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA,
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22
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Creus-Muncunill J, Ehrlich ME. Cell-Autonomous and Non-cell-Autonomous Pathogenic Mechanisms in Huntington's Disease: Insights from In Vitro and In Vivo Models. Neurotherapeutics 2019; 16:957-978. [PMID: 31529216 PMCID: PMC6985401 DOI: 10.1007/s13311-019-00782-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Huntington's disease (HD) is an autosomal dominant disorder caused by an expansion in the trinucleotide CAG repeat in exon-1 in the huntingtin gene, located on chromosome 4. When the number of trinucleotide CAG exceeds 40 repeats, disease invariably is manifested, characterized by motor, cognitive, and psychiatric symptoms. The huntingtin (Htt) protein and its mutant form (mutant huntingtin, mHtt) are ubiquitously expressed but although multiple brain regions are affected, the most vulnerable brain region is the striatum. Striatal medium-sized spiny neurons (MSNs) preferentially degenerate, followed by the cortical pyramidal neurons located in layers V and VI. Proposed HD pathogenic mechanisms include, but are not restricted to, excitotoxicity, neurotrophic support deficits, collapse of the protein degradation mechanisms, mitochondrial dysfunction, transcriptional alterations, and disorders of myelin. Studies performed in cell type-specific and regionally selective HD mouse models implicate both MSN cell-autonomous properties and cell-cell interactions, particularly corticostriatal but also with non-neuronal cell types. Here, we review the intrinsic properties of MSNs that contribute to their selective vulnerability and in addition, we discuss how astrocytes, microglia, and oligodendrocytes, together with aberrant corticostriatal connectivity, contribute to HD pathophysiology. In addition, mHtt causes cell-autonomous dysfunction in cell types other than MSNs. These findings have implications in terms of therapeutic strategies aimed at preventing neuronal dysfunction and degeneration.
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Affiliation(s)
- Jordi Creus-Muncunill
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, 10029, USA
| | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, 10029, USA.
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23
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Paul BD, Snyder SH. Impaired Redox Signaling in Huntington's Disease: Therapeutic Implications. Front Mol Neurosci 2019; 12:68. [PMID: 30941013 PMCID: PMC6433839 DOI: 10.3389/fnmol.2019.00068] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/04/2019] [Indexed: 12/22/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disease triggered by expansion of polyglutamine repeats in the protein huntingtin. Mutant huntingtin (mHtt) aggregates and elicits toxicity by multiple mechanisms which range from dysregulated transcription to disturbances in several metabolic pathways in both the brain and peripheral tissues. Hallmarks of HD include elevated oxidative stress and imbalanced redox signaling. Disruption of antioxidant defense mechanisms, involving antioxidant molecules and enzymes involved in scavenging or reversing oxidative damage, have been linked to the pathophysiology of HD. In addition, mitochondrial function is compromised in HD leading to impaired bioenergetics and elevated production of free radicals in cells. However, the exact mechanisms linking redox imbalance to neurodegeneration are still elusive. This review will focus on the current understanding of aberrant redox homeostasis in HD and potential therapeutic interventions.
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Affiliation(s)
- Bindu D Paul
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Solomon H Snyder
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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24
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Friedrich J, Kordasiewicz HB, O'Callaghan B, Handler HP, Wagener C, Duvick L, Swayze EE, Rainwater O, Hofstra B, Benneyworth M, Nichols-Meade T, Yang P, Chen Z, Ortiz JP, Clark HB, Öz G, Larson S, Zoghbi HY, Henzler C, Orr HT. Antisense oligonucleotide-mediated ataxin-1 reduction prolongs survival in SCA1 mice and reveals disease-associated transcriptome profiles. JCI Insight 2018; 3:123193. [PMID: 30385727 PMCID: PMC6238731 DOI: 10.1172/jci.insight.123193] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/19/2018] [Indexed: 12/22/2022] Open
Abstract
Spinocerebellar ataxia type 1 (SCA1) is a dominantly inherited ataxia caused by expansion of a translated CAG repeat encoding a glutamine tract in the ataxin-1 (ATXN1) protein. Despite advances in understanding the pathogenesis of SCA1, there are still no therapies to alter its progressive fatal course. RNA-targeting approaches have improved disease symptoms in preclinical rodent models of several neurological diseases. Here, we investigated the therapeutic capability of an antisense oligonucleotide (ASO) targeting mouse Atxn1 in Atxn1154Q/2Q-knockin mice that manifest motor deficits and premature lethality. Following a single ASO treatment at 5 weeks of age, mice demonstrated rescue of these disease-associated phenotypes. RNA-sequencing analysis of genes with expression restored to WT levels in ASO-treated Atxn1154Q/2Q mice was used to demonstrate molecular differences between SCA1 pathogenesis in the cerebellum and disease in the medulla. Finally, select neurochemical abnormalities detected by magnetic resonance spectroscopy in vehicle-treated Atxn1154Q/2Q mice were reversed in the cerebellum and brainstem (a region containing the pons and the medulla) of ASO-treated Atxn1154Q/2Q mice. Together, these findings support the efficacy and therapeutic importance of directly targeting ATXN1 RNA expression as a strategy for treating both motor deficits and lethality in SCA1.
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Affiliation(s)
- Jillian Friedrich
- Institute for Translational Neuroscience and.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Brennon O'Callaghan
- Institute for Translational Neuroscience and.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hillary P Handler
- Institute for Translational Neuroscience and.,Graduate Program in Neuroscience
| | - Carmen Wagener
- Institute for Translational Neuroscience and.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Lisa Duvick
- Institute for Translational Neuroscience and.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Orion Rainwater
- Institute for Translational Neuroscience and.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Bente Hofstra
- Institute for Translational Neuroscience and.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | | | | | - Praseuth Yang
- Institute for Translational Neuroscience and.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Zhao Chen
- Institute for Translational Neuroscience and.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Judit Perez Ortiz
- Institute for Translational Neuroscience and.,Graduate Program in Neuroscience
| | - H Brent Clark
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Gülin Öz
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sarah Larson
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Huda Y Zoghbi
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital and Department of Molecular and Human Genetics, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - Christine Henzler
- Research Informatics Support Systems Bioinformatics, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Harry T Orr
- Institute for Translational Neuroscience and.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
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