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Speidell A, Bin Abid N, Yano H. Brain-Derived Neurotrophic Factor Dysregulation as an Essential Pathological Feature in Huntington's Disease: Mechanisms and Potential Therapeutics. Biomedicines 2023; 11:2275. [PMID: 37626771 PMCID: PMC10452871 DOI: 10.3390/biomedicines11082275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Brain-derived neurotrophic factor (BDNF) is a major neurotrophin whose loss or interruption is well established to have numerous intersections with the pathogenesis of progressive neurological disorders. There is perhaps no greater example of disease pathogenesis resulting from the dysregulation of BDNF signaling than Huntington's disease (HD)-an inherited neurodegenerative disorder characterized by motor, psychiatric, and cognitive impairments associated with basal ganglia dysfunction and the ultimate death of striatal projection neurons. Investigation of the collection of mechanisms leading to BDNF loss in HD highlights this neurotrophin's importance to neuronal viability and calls attention to opportunities for therapeutic interventions. Using electronic database searches of existing and forthcoming research, we constructed a literature review with the overarching goal of exploring the diverse set of molecular events that trigger BDNF dysregulation within HD. We highlighted research that investigated these major mechanisms in preclinical models of HD and connected these studies to those evaluating similar endpoints in human HD subjects. We also included a special focus on the growing body of literature detailing key transcriptomic and epigenetic alterations that affect BDNF abundance in HD. Finally, we offer critical evaluation of proposed neurotrophin-directed therapies and assessed clinical trials seeking to correct BDNF expression in HD individuals.
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Affiliation(s)
- Andrew Speidell
- Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.S.); (N.B.A.)
| | - Noman Bin Abid
- Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.S.); (N.B.A.)
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.S.); (N.B.A.)
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
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2
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Tano V, Utami KH, Yusof NABM, Bégin J, Tan WWL, Pouladi MA, Langley SR. Widespread dysregulation of mRNA splicing implicates RNA processing in the development and progression of Huntington's disease. EBioMedicine 2023; 94:104720. [PMID: 37481821 PMCID: PMC10393612 DOI: 10.1016/j.ebiom.2023.104720] [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: 02/02/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND In Huntington's disease (HD), a CAG repeat expansion mutation in the Huntingtin (HTT) gene drives a gain-of-function toxicity that disrupts mRNA processing. Although dysregulation of gene splicing has been shown in human HD post-mortem brain tissue, post-mortem analyses are likely confounded by cell type composition changes in late-stage HD, limiting the ability to identify dysregulation related to early pathogenesis. METHODS To investigate gene splicing changes in early HD, we performed alternative splicing analyses coupled with a proteogenomics approach to identify early CAG length-associated splicing changes in an established isogenic HD cell model. FINDINGS We report widespread neuronal differentiation stage- and CAG length-dependent splicing changes, and find an enrichment of RNA processing, neuronal function, and epigenetic modification-related genes with mutant HTT-associated splicing. When integrated with a proteomics dataset, we identified several of these differential splicing events at the protein level. By comparing with human post-mortem and mouse model data, we identified common patterns of altered splicing from embryonic stem cells through to post-mortem striatal tissue. INTERPRETATION We show that widespread splicing dysregulation in HD occurs in an early cell model of neuronal development. Importantly, we observe HD-associated splicing changes in our HD cell model that were also identified in human HD striatum and mouse model HD striatum, suggesting that splicing-associated pathogenesis possibly occurs early in neuronal development and persists to later stages of disease. Together, our results highlight splicing dysregulation in HD which may lead to disrupted neuronal function and neuropathology. FUNDING This research is supported by the Lee Kong Chian School of Medicine, Nanyang Technological University Singapore Nanyang Assistant Professorship Start-Up Grant, the Singapore Ministry of Education under its Singapore Ministry of Education Academic Research Fund Tier 1 (RG23/22), the BC Children's Hospital Research Institute Investigator Grant Award (IGAP), and a Scholar Award from the Michael Smith Health Research BC.
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Affiliation(s)
- Vincent Tano
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| | - Kagistia Hana Utami
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore; Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Nur Amirah Binte Mohammad Yusof
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Jocelyn Bégin
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Willy Wei Li Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| | - Mahmoud A Pouladi
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore; Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore.
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3
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Zsindely N, Nagy G, Siági F, Farkas A, Bodai L. Dysregulated miRNA and mRNA Expression Affect Overlapping Pathways in a Huntington's Disease Model. Int J Mol Sci 2023; 24:11942. [PMID: 37569316 PMCID: PMC10419151 DOI: 10.3390/ijms241511942] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
Huntington's disease (HD) is a fatal neurodegenerative disorder caused by the expansion of a CAG trinucleotide repeat in the Huntingtin gene. Transcriptional dysregulation is one of the main cellular processes affected by mutant Huntingtin (mHtt). In this study, we investigate the alterations in miRNA and mRNA expression levels in a Drosophila model of HD by RNA sequencing and assess the functional effects of misregulated miRNAs in vivo. We found that in head samples of HD flies, the level of 32 miRNAs changed significantly; half of these were upregulated, while the other half were downregulated. After comparing miRNA and mRNA expression data, we discovered similarities in the impacted molecular pathways. Additionally, we observed that the putative targets of almost all dysregulated miRNAs were overrepresented among the upregulated mRNAs. We tested the effects of overexpression of five misregulated miRNAs in the HD model and found that while mir-10 and mir-219 enhanced, mir-137, mir-305, and mir-1010 ameliorated mHtt-induced phenotypes. Based on our results, we propose that while altered expression of mir-10, mir-137, and mir-1010 might be part of HD pathology, the upregulation of mir-305 might serve as a compensatory mechanism as a response to mHtt-induced transcriptional dysregulation.
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Affiliation(s)
- Nóra Zsindely
- Department of Genetics, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary;
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Gábor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Fruzsina Siági
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Anita Farkas
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
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4
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Arancibia-Opazo S, Contreras-Riquelme JS, Sánchez M, Cisternas-Olmedo M, Vidal RL, Martin AJM, Sáez MA. Transcriptional and Histone Acetylation Changes Associated with CRE Elements Expose Key Factors Governing the Regulatory Circuit in the Early Stage of Huntington's Disease Models. Int J Mol Sci 2023; 24:10848. [PMID: 37446028 DOI: 10.3390/ijms241310848] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Huntington's disease (HD) is a disorder caused by an abnormal expansion of trinucleotide CAG repeats within the huntingtin (Htt) gene. Under normal conditions, the CREB Binding Protein interacts with CREB elements and acetylates Lysine 27 of Histone 3 to direct the expression of several genes. However, mutant Htt causes depletion of CBP, which in turn induces altered histone acetylation patterns and transcriptional deregulation. Here, we have studied a differential expression analysis and H3K27ac variation in 4- and 6-week-old R6/2 mice as a model of juvenile HD. The analysis of differential gene expression and acetylation levels were integrated into Gene Regulatory Networks revealing key regulators involved in the altered transcription cascade. Our results show changes in acetylation and gene expression levels that are related to impaired neuronal development, and key regulators clearly defined in 6-week-old mice are proposed to drive the downstream regulatory cascade in HD. Here, we describe the first approach to determine the relationship among epigenetic changes in the early stages of HD. We determined the existence of changes in pre-symptomatic stages of HD as a starting point for early onset indicators of the progression of this disease.
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Affiliation(s)
- Sandra Arancibia-Opazo
- Chromatin, Epigenetic, and Neuroscience Laboratory, Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago 8580745, Chile
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Universidad San Sebastián, Santiago 8580704, Chile
| | - J Sebastián Contreras-Riquelme
- Plant Genome Regulation Lab, Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
| | - Mario Sánchez
- Chromatin, Epigenetic, and Neuroscience Laboratory, Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
| | - Marisol Cisternas-Olmedo
- Centro de Biología Integrativa, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Biomedical Neuroscience Institute, University of Chile, Santiago 8380455, Chile
- Center for Geroscience, Brain Health, and Metabolism, Santiago 8380453, Chile
| | - René L Vidal
- Centro de Biología Integrativa, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Biomedical Neuroscience Institute, University of Chile, Santiago 8380455, Chile
- Center for Geroscience, Brain Health, and Metabolism, Santiago 8380453, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - Alberto J M Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Universidad San Sebastián, Santiago 8580704, Chile
- Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago 7500000, Chile
| | - Mauricio A Sáez
- Chromatin, Epigenetic, and Neuroscience Laboratory, Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
- Centro de Oncología de Precisión, Facultad de Medicina Universidad Mayor, Santiago 7560908, Chile
- Laboratorio de Investigación en Salud de Precisión, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Temuco 4813302, Chile
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5
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Ducker C, Ratnam M, Shaw PE, Layfield R. Comparative analysis of protein expression systems and PTM landscape in the study of transcription factor ELK-1. Protein Expr Purif 2023; 203:106216. [PMID: 36528218 DOI: 10.1016/j.pep.2022.106216] [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: 10/11/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Post-translational modifications (PTMs) are important for protein folding and activity, and the ability to recreate physiologically relevant PTM profiles on recombinantly-expressed proteins is vital for meaningful functional analysis. The ETS transcription factor ELK-1 serves as a paradigm for cellular responses to mitogens and can synergise with androgen receptor to promote prostate cancer progression, although in vitro protein function analyses to date have largely overlooked its complex PTM landscapes. We expressed and purified human ELK-1 using mammalian (HEK293T), insect (Sf9) and bacterial (E. coli) systems in parallel and compared PTMs imparted upon purified proteins, along with their performance in DNA and protein interaction assays. Phosphorylation of ELK-1 within its transactivation domain, known to promote DNA binding, was most apparent in protein isolated from human cells and accordingly conferred the strongest DNA binding in vitro, while protein expressed in insect cells bound most efficiently to the androgen receptor. We observed lysine acetylation, a hitherto unreported PTM of ELK-1, which appeared highest in insect cell-derived ELK-1 but was also present in HEK293T-derived ELK-1. Acetylation of ELK-1 was enhanced in HEK293T cells following starvation and mitogen stimulation, and modified lysines showed overlap with previously identified regulatory SUMOylation and ubiquitination sites. Our data demonstrate that the choice of recombinant expression system can be tailored to suit biochemical application rather than to maximise soluble protein production and suggest the potential for crosstalk and antagonism between different PTMs of ELK-1.
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Affiliation(s)
- Charles Ducker
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom.
| | - Manohar Ratnam
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA
| | - Peter E Shaw
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Robert Layfield
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
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6
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Ahamad S, Bhat SA. The Emerging Landscape of Small-Molecule Therapeutics for the Treatment of Huntington's Disease. J Med Chem 2022; 65:15993-16032. [PMID: 36490325 DOI: 10.1021/acs.jmedchem.2c00799] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin gene (HTT). The new insights into HD's cellular and molecular pathways have led to the identification of numerous potent small-molecule therapeutics for HD therapy. The field of HD-targeting small-molecule therapeutics is accelerating, and the approval of these therapeutics to combat HD may be expected in the near future. For instance, preclinical candidates such as naphthyridine-azaquinolone, AN1, AN2, CHDI-00484077, PRE084, EVP4593, and LOC14 have shown promise for further optimization to enter into HD clinical trials. This perspective aims to summarize the advent of small-molecule therapeutics at various stages of clinical development for HD therapy, emphasizing their structure and design, therapeutic effects, and specific mechanisms of action. Further, we have highlighted the key drivers involved in HD pathogenesis to provide insights into the basic principle for designing promising anti-HD therapeutic leads.
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Affiliation(s)
- Shakir Ahamad
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh202002, India
| | - Shahnawaz A Bhat
- Department of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh202002, India
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7
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Lim RG, Al-Dalahmah O, Wu J, Gold MP, Reidling JC, Tang G, Adam M, Dansu DK, Park HJ, Casaccia P, Miramontes R, Reyes-Ortiz AM, Lau A, Hickman RA, Khan F, Paryani F, Tang A, Ofori K, Miyoshi E, Michael N, McClure N, Flowers XE, Vonsattel JP, Davidson S, Menon V, Swarup V, Fraenkel E, Goldman JE, Thompson LM. Huntington disease oligodendrocyte maturation deficits revealed by single-nucleus RNAseq are rescued by thiamine-biotin supplementation. Nat Commun 2022; 13:7791. [PMID: 36543778 PMCID: PMC9772349 DOI: 10.1038/s41467-022-35388-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
The complexity of affected brain regions and cell types is a challenge for Huntington's disease (HD) treatment. Here we use single nucleus RNA sequencing to investigate molecular pathology in the cortex and striatum from R6/2 mice and human HD post-mortem tissue. We identify cell type-specific and -agnostic signatures suggesting oligodendrocytes (OLs) and oligodendrocyte precursors (OPCs) are arrested in intermediate maturation states. OL-lineage regulators OLIG1 and OLIG2 are negatively correlated with CAG length in human OPCs, and ATACseq analysis of HD mouse NeuN-negative cells shows decreased accessibility regulated by OL maturation genes. The data implicates glucose and lipid metabolism in abnormal cell maturation and identify PRKCE and Thiamine Pyrophosphokinase 1 (TPK1) as central genes. Thiamine/biotin treatment of R6/1 HD mice to compensate for TPK1 dysregulation restores OL maturation and rescues neuronal pathology. Our insights into HD OL pathology spans multiple brain regions and link OL maturation deficits to abnormal thiamine metabolism.
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Affiliation(s)
- Ryan G Lim
- UCI MIND, University of California Irvine, Irvine, CA, USA
| | - Osama Al-Dalahmah
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Maxwell P Gold
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Guomei Tang
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Miriam Adam
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David K Dansu
- Advanced Science Research Center at the City University of New York, New York, NY, USA
| | - Hye-Jin Park
- Advanced Science Research Center at the City University of New York, New York, NY, USA
| | - Patrizia Casaccia
- Advanced Science Research Center at the City University of New York, New York, NY, USA
| | | | - Andrea M Reyes-Ortiz
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Alice Lau
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA
| | - Richard A Hickman
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Fatima Khan
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Fahad Paryani
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Alice Tang
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Kenneth Ofori
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Emily Miyoshi
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Neethu Michael
- Department of Pathology, University of California Irvine, Irvine, CA, USA
| | - Nicolette McClure
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Xena E Flowers
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, New York, NY, USA
| | - Jean Paul Vonsattel
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, New York, NY, USA
| | - Shawn Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ, USA
| | - Vilas Menon
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Vivek Swarup
- UCI MIND, University of California Irvine, Irvine, CA, USA
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - James E Goldman
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, New York, NY, USA.
| | - Leslie M Thompson
- UCI MIND, University of California Irvine, Irvine, CA, USA.
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA.
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA.
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA.
- Sue and Bill Gross Stem Cell Center University of California Irvine, Irvine, CA, USA.
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Integrative Meta-Analysis of Huntington's Disease Transcriptome Landscape. Genes (Basel) 2022; 13:genes13122385. [PMID: 36553652 PMCID: PMC9777612 DOI: 10.3390/genes13122385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/24/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder with autosomal dominant inheritance caused by glutamine expansion in the Huntingtin gene (HTT). Striatal projection neurons (SPNs) in HD are more vulnerable to cell death. The executive striatal population is directly connected with the Brodmann Area (BA9), which is mainly involved in motor functions. Analyzing the disease samples from BA9 from the SRA database provides insights related to neuron degeneration, which helps to identify a promising therapeutic strategy. Most gene expression studies examine the changes in expression and associated biological functions. In this study, we elucidate the relationship between variants and their effect on gene/downstream transcript expression. We computed gene and transcript abundance and identified variants from RNA-seq data using various pipelines. We predicted the effect of genome-wide association studies (GWAS)/novel variants on regulatory functions. We found that many variants affect the histone acetylation pattern in HD, thereby perturbing the transcription factor networks. Interestingly, some variants affect miRNA binding as well as their downstream gene expression. Tissue-specific network analysis showed that mitochondrial, neuroinflammation, vasculature, and angiogenesis-related genes are disrupted in HD. From this integrative omics analysis, we propose that abnormal neuroinflammation acts as a two-edged sword that indirectly affects the vasculature and associated energy metabolism. Rehabilitation of blood-brain barrier functionality and energy metabolism may secure the neuron from cell death.
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Faragó A, Zsindely N, Farkas A, Neller A, Siági F, Szabó MR, Csont T, Bodai L. Acetylation State of Lysine 14 of Histone H3.3 Affects Mutant Huntingtin Induced Pathogenesis. Int J Mol Sci 2022; 23:15173. [PMID: 36499499 PMCID: PMC9738228 DOI: 10.3390/ijms232315173] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Huntington's Disease (HD) is a fatal neurodegenerative disorder caused by the expansion of a polyglutamine-coding CAG repeat in the Huntingtin gene. One of the main causes of neurodegeneration in HD is transcriptional dysregulation that, in part, is caused by the inhibition of histone acetyltransferase (HAT) enzymes. HD pathology can be alleviated by increasing the activity of specific HATs or by inhibiting histone deacetylase (HDAC) enzymes. To determine which histone's post-translational modifications (PTMs) might play crucial roles in HD pathology, we investigated the phenotype-modifying effects of PTM mimetic mutations of variant histone H3.3 in a Drosophila model of HD. Specifically, we studied the mutations (K→Q: acetylated; K→R: non-modified; and K→M: methylated) of lysine residues K9, K14, and K27 of transgenic H3.3. In the case of H3.3K14Q modification, we observed the amelioration of all tested phenotypes (viability, longevity, neurodegeneration, motor activity, and circadian rhythm defects), while H3.3K14R had the opposite effect. H3.3K14Q expression prevented the negative effects of reduced Gcn5 (a HAT acting on H3K14) on HD pathology, while it only partially hindered the positive effects of heterozygous Sirt1 (an HDAC acting on H3K14). Thus, we conclude that the Gcn5-dependent acetylation of H3.3K14 might be an important epigenetic contributor to HD pathology.
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Affiliation(s)
- Anikó Faragó
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Nóra Zsindely
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Anita Farkas
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Alexandra Neller
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Fruzsina Siági
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Márton Richárd Szabó
- Department of Biochemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- Interdisciplinary Centre of Excellence, University of Szeged, H-6720 Szeged, Hungary
| | - Tamás Csont
- Department of Biochemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- Interdisciplinary Centre of Excellence, University of Szeged, H-6720 Szeged, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
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10
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Zhang L, Liu Y, Lu Y, Wang G. Targeting epigenetics as a promising therapeutic strategy for treatment of neurodegenerative diseases. Biochem Pharmacol 2022; 206:115295. [DOI: 10.1016/j.bcp.2022.115295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022]
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11
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Angelopoulos I, Gakis G, Birmpas K, Kyrousi C, Habeos EE, Kaplani K, Lygerou Z, Habeos I, Taraviras S. Metabolic regulation of the neural stem cell fate: Unraveling new connections, establishing new concepts. Front Neurosci 2022; 16:1009125. [PMID: 36340763 PMCID: PMC9634649 DOI: 10.3389/fnins.2022.1009125] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/03/2022] [Indexed: 11/30/2022] Open
Abstract
The neural stem cell niche is a key regulator participating in the maintenance, regeneration, and repair of the brain. Within the niche neural stem cells (NSC) generate new neurons throughout life, which is important for tissue homeostasis and brain function. NSCs are regulated by intrinsic and extrinsic factors with cellular metabolism being lately recognized as one of the most important ones, with evidence suggesting that it may serve as a common signal integrator to ensure mammalian brain homeostasis. The aim of this review is to summarize recent insights into how metabolism affects NSC fate decisions in adult neural stem cell niches, with occasional referencing of embryonic neural stem cells when it is deemed necessary. Specifically, we will highlight the implication of mitochondria as crucial regulators of NSC fate decisions and the relationship between metabolism and ependymal cells. The link between primary cilia dysfunction in the region of hypothalamus and metabolic diseases will be examined as well. Lastly, the involvement of metabolic pathways in ependymal cell ciliogenesis and physiology regulation will be discussed.
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Affiliation(s)
| | - Georgios Gakis
- Department of Physiology, Medical School, University of Patras, Patras, Greece
| | - Kyriakos Birmpas
- Department of Physiology, Medical School, University of Patras, Patras, Greece
| | - Christina Kyrousi
- First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, Eginition Hospital, Athens, Greece
- University Mental Health, Neurosciences and Precision Medicine Research Institute “Costas Stefanis”, Athens, Greece
| | - Evagelia Eva Habeos
- Department of Physiology, Medical School, University of Patras, Patras, Greece
| | - Konstantina Kaplani
- Department of Physiology, Medical School, University of Patras, Patras, Greece
| | - Zoi Lygerou
- Department of General Biology, School of Medicine, University of Patras, Patras, Greece
| | - Ioannis Habeos
- Division of Endocrinology, Department of Internal Medicine, University of Patras, Patras, Greece
| | - Stavros Taraviras
- Department of Physiology, Medical School, University of Patras, Patras, Greece
- *Correspondence: Stavros Taraviras,
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12
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Thudium S, Palozola K, L'Her É, Korb E. Identification of a transcriptional signature found in multiple models of ASD and related disorders. Genome Res 2022; 32:gr.276591.122. [PMID: 36104286 PMCID: PMC9528985 DOI: 10.1101/gr.276591.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 07/22/2022] [Indexed: 11/25/2022]
Abstract
Epigenetic regulation plays a critical role in many neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD). In particular, many such disorders are the result of mutations in genes that encode chromatin-modifying proteins. However, although these disorders share many features, it is unclear whether they also share gene expression disruptions resulting from the aberrant regulation of chromatin. We examined five chromatin modifiers that are all linked to ASD despite their different roles in regulating chromatin. Specifically, we depleted ASH1L, CHD8, CREBBP, EHMT1, and NSD1 in parallel in a highly controlled neuronal culture system. We then identified sets of shared genes, or transcriptional signatures, that are differentially expressed following loss of multiple ASD-linked chromatin modifiers. We examined the functions of genes within the transcriptional signatures and found an enrichment in many neurotransmitter transport genes and activity-dependent genes. In addition, these genes are enriched for specific chromatin features such as bivalent domains that allow for highly dynamic regulation of gene expression. The down-regulated transcriptional signature is also observed within multiple mouse models of NDDs that result in ASD, but not those only associated with intellectual disability. Finally, the down-regulated transcriptional signature can distinguish between control and idiopathic ASD patient iPSC-derived neurons as well as postmortem tissue, demonstrating that this gene set is relevant to the human disorder. This work identifies a transcriptional signature that is found within many neurodevelopmental syndromes, helping to elucidate the link between epigenetic regulation and the underlying cellular mechanisms that result in ASD.
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Affiliation(s)
- Samuel Thudium
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Katherine Palozola
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Éloïse L'Her
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Erica Korb
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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13
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Li X, Liu J, Lu L, Huang T, Hou W, Wang F, Yu L, Wu F, Qi J, Chen X, Meng Z, Zhu M. Sirt7 associates with ELK1 to participate in hyperglycemia memory and diabetic nephropathy via modulation of DAPK3 expression and endothelial inflammation. Transl Res 2022; 247:99-116. [PMID: 35470010 DOI: 10.1016/j.trsl.2022.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 04/01/2022] [Accepted: 04/18/2022] [Indexed: 02/08/2023]
Abstract
Diabetic nephropathy (DN) is one of the most serious complications of advanced diabetes, and increases patient mortality. Recently, epigenetics-mediated hyperglycemic memory in pathological process of DN has received attention. The purpose of this study was to determine the underlying mechanism by which sirt7 modulates hyperglycemic memory in DN. In glomerular endothelial cells (GECs) cultured in high glucose and glomeruli of DN patients and rats, an increase in p65 phosphorylation and endothelial adhesion molecule levels persisted after glucose normalization but was reversed by glucose normalization associated with death-associated protein kinase-3 (DAPK3) knockout or DAPK3 inhibitor. High glucose-mediated decrease in sirt7, the deacetylase modulating H3K18-acetylation (H3K18ac), was sustained after normoglycemia. Sirt7 overexpression accompanied by glucose normalization suppressed DAPK3 expression and inflammation in GECs. Moreover, sh-sirt7-induced inflammation was inhibited by si-DAPK3. Furthermore, sirt7 and H3K18ac were located at the DAPK3 promoter region. ELK1 was found to combine with sirt7. si-ELK1 supplemented with normoglycemia inhibited high glucose-induced DAPK3 expression and inflammation in GECs. ELK1 overexpression-mediated inflammation was inhibited by si-DAPK3. In addition, ELK1 and sirt7 were located at the same promoter region of DAPK3. ELK1 overexpression enhanced DAPK3 promoter activity, which disappeared after specific binding site mutation. In vivo, sirt7 overexpression decreased inflammation and improved renal function during insulin treatment of DN rats, whereas insulin alone did not work. Our data demonstrated high glucose-mediated mutual inhibition between sirt7 and ELK1 induced DAPK3 transcription and inflammation despite normoglycemia in GECs, thus forming a vicious cycle and participating in the occurrence of hyperglycemic memory in DN.
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Affiliation(s)
- Xue Li
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jing Liu
- Department of Anaesthesiology, Huzhou Maternal & Child Health Care Hospital, Huzhou, Zhejiang, China
| | - Lihong Lu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ting Huang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenting Hou
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fei Wang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lang Yu
- Department of Anaesthesiology, Huzhou Central Hospital, Affiliated Central Hospital of HuZhou University, No.1558 Sanhuan North Road, Huzhou, Zhejiang, China
| | - Fengfeng Wu
- Department of Orthopedics and Rehabilitation, Huzhou Central Hospital, Affiliated Central Hospital of HuZhou University, No.1558 Sanhuan North Road, Huzhou, Zhejiang, China
| | - Jie Qi
- Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangyuan Chen
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhipeng Meng
- Department of Anaesthesiology, Huzhou Central Hospital, Affiliated Central Hospital of HuZhou University, No.1558 Sanhuan North Road, Huzhou, Zhejiang, China.
| | - Minmin Zhu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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14
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Pupak A, Singh A, Sancho-Balsells A, Alcalá-Vida R, Espina M, Giralt A, Martí E, Ørom UAV, Ginés S, Brito V. Altered m6A RNA methylation contributes to hippocampal memory deficits in Huntington's disease mice. Cell Mol Life Sci 2022; 79:416. [PMID: 35819730 PMCID: PMC9276730 DOI: 10.1007/s00018-022-04444-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/07/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022]
Abstract
N6-methyladenosine (m6A) regulates many aspects of RNA metabolism and is involved in learning and memory processes. Yet, the impact of a dysregulation of post-transcriptional m6A editing on synaptic impairments in neurodegenerative disorders remains unknown. Here we investigated the m6A methylation pattern in the hippocampus of Huntington’s disease (HD) mice and the potential role of the m6A RNA modification in HD cognitive symptomatology. m6A modifications were evaluated in HD mice subjected to a hippocampal cognitive training task through m6A immunoprecipitation sequencing (MeRIP-seq) and the relative levels of m6A-modifying proteins (FTO and METTL14) by subcellular fractionation and Western blot analysis. Stereotaxic CA1 hippocampal delivery of AAV-shFTO was performed to investigate the effect of RNA m6A dysregulation in HD memory deficits. Our results reveal a m6A hypermethylation in relevant HD and synaptic related genes in the hippocampal transcriptome of Hdh+/Q111 mice. Conversely, m6A is aberrantly regulated in an experience-dependent manner in the HD hippocampus leading to demethylation of important components of synapse organization. Notably, the levels of RNA demethylase (FTO) and methyltransferase (METTL14) were modulated after training in the hippocampus of WT mice but not in Hdh+/Q111 mice. Finally, inhibition of FTO expression in the hippocampal CA1 region restored memory disturbances in symptomatic Hdh+/Q111 mice. Altogether, our results suggest that a differential RNA methylation landscape contributes to HD cognitive symptoms and uncover a role of m6A as a novel hallmark of HD.
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Affiliation(s)
- Anika Pupak
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Ankita Singh
- Department for Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Anna Sancho-Balsells
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Rafael Alcalá-Vida
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, Strasbourg, France
| | - Marc Espina
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Albert Giralt
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Eulàlia Martí
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | | | - Silvia Ginés
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain. .,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
| | - Verónica Brito
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurosciències, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain. .,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
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15
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Environmental stimulation in Huntington disease patients and animal models. Neurobiol Dis 2022; 171:105725. [DOI: 10.1016/j.nbd.2022.105725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
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16
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Li X, Lu L, Hou W, Wang F, Huang T, Meng Z, Zhu M. The SETD8/ELK1/bach1 complex regulates hyperglycaemia-mediated EndMT in diabetic nephropathy. J Transl Med 2022; 20:147. [PMID: 35351142 PMCID: PMC8961497 DOI: 10.1186/s12967-022-03352-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/16/2022] [Indexed: 12/18/2022] Open
Abstract
Background Diabetic nephropathy (DN), the most common microvascular complication in patients with diabetes, induces kidney failure. Previous research showed that endothelial-to-mesenchymal transition (EndMT) of human glomerular endothelial cells (HGECs) is involved in the progression of DN. Moreover, SET domain-containing protein 8 (SETD8), ETS-domain containing protein (ELK1) and BTB and CNC homology 1 (bach1) all participate in endothelial injury. In this study, we hypothesize that the SETD8/ELK1/bach1 functional axis is involved in mediating EndMT in diabetic nephropathy. Methods Immunohistochemistry, Western blotting and qPCR were performed to determine the protein and mRNA levels of genes in HGECs and the kidney tissues of participants and rats. Immunofluorescence, Co-IP and GST pulldown assays were performed to verify the direct interaction between SETD8 and ELK1. ChIP and dual-luciferase assays were performed to determine the transcriptional regulation of bach1 and Snail. AVV-SETD8 injection in rat kidney was used to verify the potential protective effect of SETD8 on DN. Results Our current study showed that hyperglycaemia triggered EndMT by increasing Snail expression both in vitro and in vivo. Moreover, high glucose increased bach1 expression in HGECs, positively regulating Snail and EndMT. As a transcription factor, ELK1 was augmented and participated in hyperglycaemia-induced EndMT via modulation of bach1 expression. Moreover, ELK1 was found to associate with SETD8. Furthermore, SETD8 negatively regulated EndMT by cooperating with bach1 to regulate Snail transcription. Furthermore, histone H4-Lys-20 monomethylation (H4K20me1), which is downstream of SETD8, was accompanied by ELK1 localization at the same promoter region of bach1. ELK1 overexpression enhanced bach1 promoter activity, which disappeared after specific binding site deletion. Mutual inhibition between ELK1 and SETD8 was found in HGECs. In vivo, SETD8 overexpression decreased ELK1 and bach1 expression, as well as EndMT. Moreover, SETD8 overexpression improved the renal function of rats with DN. Conclusions SETD8 cooperates with ELK1 to regulate bach1 transcription, thus participating in the progression of DN. In addition, SETD8 interacts with bach1 to modulate Snail transcription, thus inducing EndMT in DN. SETD8 plays a core role in the SETD8/ELK1/bach1 functional axis, which participates in hyperglycaemia-mediated EndMT in DN, and SETD8 may be a potential therapeutic target for DN. Trial registration ChiCTR, ChiCTR2000029425. 2020/1/31, http://www.chictr.org.cn/showproj.aspx?proj=48548 Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03352-4.
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Affiliation(s)
- Xue Li
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Lihong Lu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wenting Hou
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Fei Wang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ting Huang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhipeng Meng
- Department of Anaesthesiology, Huzhou Hospital Affiliated to Zhejiang University, Affiliated Central Hospital of HuZhou University, Huzhou, 313000, Zhejiang, China.
| | - Minmin Zhu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China. .,Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, People's Republic of China.
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17
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Bottero V, Santiago JA, Quinn JP, Potashkin JA. Key Disease Mechanisms Linked to Amyotrophic Lateral Sclerosis in Spinal Cord Motor Neurons. Front Mol Neurosci 2022; 15:825031. [PMID: 35370543 PMCID: PMC8965442 DOI: 10.3389/fnmol.2022.825031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/15/2022] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with no modifying treatments available. The molecular mechanisms underpinning disease pathogenesis are not fully understood. Recent studies have employed co-expression networks to identify key genes, known as “switch genes”, responsible for dramatic transcriptional changes in the blood of ALS patients. In this study, we directly investigate the root cause of ALS by examining the changes in gene expression in motor neurons that degenerate in patients. Co-expression networks identified in ALS patients’ spinal cord motor neurons revealed 610 switch genes in seven independent microarrays. Switch genes were enriched in several pathways, including viral carcinogenesis, PI3K-Akt, focal adhesion, proteoglycans in cancer, colorectal cancer, and thyroid hormone signaling. Transcription factors ELK1 and GATA2 were identified as key master regulators of the switch genes. Protein-chemical network analysis identified valproic acid, cyclosporine, estradiol, acetaminophen, quercetin, and carbamazepine as potential therapeutics for ALS. Furthermore, the chemical analysis identified metals and organic compounds including, arsenic, copper, nickel, and benzo(a)pyrene as possible mediators of neurodegeneration. The identification of switch genes provides insights into previously unknown biological pathways associated with ALS.
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Affiliation(s)
- Virginie Bottero
- Chicago Medical School, Rosalind Franklin University of Medicine and Science, Center for Neurodegenerative Diseases and Therapeutics, Discipline of Cellular and Molecular Pharmacology, North Chicago, IL, United States
| | | | | | - Judith A. Potashkin
- Chicago Medical School, Rosalind Franklin University of Medicine and Science, Center for Neurodegenerative Diseases and Therapeutics, Discipline of Cellular and Molecular Pharmacology, North Chicago, IL, United States
- *Correspondence: Judy A. Potashkin
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18
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DNA Methylation in Huntington's Disease. Int J Mol Sci 2021; 22:ijms222312736. [PMID: 34884540 PMCID: PMC8657460 DOI: 10.3390/ijms222312736] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
Methylation of cytosine in CpG dinucleotides is the major DNA modification in mammalian cells that is a key component of stable epigenetic marks. This modification, which on the one hand is reversible, while on the other hand, can be maintained through successive rounds of replication plays roles in gene regulation, genome maintenance, transgenerational epigenetic inheritance, and imprinting. Disturbed DNA methylation contributes to a wide array of human diseases from single-gene disorders to sporadic metabolic diseases or cancer. DNA methylation was also shown to affect several neurodegenerative disorders, including Huntington's disease (HD), a fatal, monogenic inherited disease. HD is caused by a polyglutamine repeat expansion in the Huntingtin protein that brings about a multifaceted pathogenesis affecting several cellular processes. Research of the last decade found complex, genome-wide DNA methylation changes in HD pathogenesis that modulate transcriptional activity and genome stability. This article reviews current evidence that sheds light on the role of DNA methylation in HD.
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19
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Qu W, Zhuang Y, Li X. The roles of epigenetic modifications in neurodegenerative diseases. Zhejiang Da Xue Xue Bao Yi Xue Ban 2021; 50:642-650. [PMID: 34986527 PMCID: PMC8732261 DOI: 10.3724/zdxbyxb-2021-0160] [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: 06/04/2021] [Accepted: 08/30/2021] [Indexed: 06/14/2023]
Abstract
In neuronal system, epigenetic modifications are essential for neuronal development, the fate determination of neural stem cells and neuronal function. The dysfunction of epigenetic regulation is closely related to occurrence and development of neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington's disease. Abnormally elevated DNA methylation inhibits the expression of some DNA repair-related genes and affects the progression of Huntington's disease. In the brain of Alzheimer's disease patients, the levels of H3K27ac and H3K9ac histone modifications increased. In addition, the alteration of RNA methylation in animal models of Alzheimer's disease and Parkinson's disease showed discrepancy trends. Therefore, epigenetic modifications may serve as potential therapeutic targets for neurodegenerative diseases. Here, we summarize the recent progress of the roles of epigenetic modifications in neurodegenerative diseases.
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Affiliation(s)
- Wenzheng Qu
- of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Yingliang Zhuang
- of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Xuekun Li
- of Translational Medicine, Zhejiang University, Hangzhou 310029, China
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20
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Malla B, Guo X, Senger G, Chasapopoulou Z, Yildirim F. A Systematic Review of Transcriptional Dysregulation in Huntington's Disease Studied by RNA Sequencing. Front Genet 2021; 12:751033. [PMID: 34721539 PMCID: PMC8554124 DOI: 10.3389/fgene.2021.751033] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/15/2021] [Indexed: 12/21/2022] Open
Abstract
Huntington's disease (HD) is a chronic neurodegenerative disorder caused by an expansion of polyglutamine repeats in exon 1 of the Huntingtin gene. Transcriptional dysregulation accompanied by epigenetic alterations is an early and central disease mechanism in HD yet, the exact mechanisms and regulators, and their associated gene expression programs remain incompletely understood. This systematic review investigates genome-wide transcriptional studies that were conducted using RNA sequencing (RNA-seq) technology in HD patients and models. The review protocol was registered at the Open Science Framework (OSF). The biomedical literature and gene expression databases, PubMed and NCBI BioProject, Array Express, European Nucleotide Archive (ENA), European Genome-Phenome Archive (EGA), respectively, were searched using the defined terms specified in the protocol following the PRISMA guidelines. We conducted a complete literature and database search to retrieve all RNA-seq-based gene expression studies in HD published until August 2020, retrieving 288 articles and 237 datasets from PubMed and the databases, respectively. A total of 27 studies meeting the eligibility criteria were included in this review. Collectively, comparative analysis of the datasets revealed frequent genes that are consistently dysregulated in HD. In postmortem brains from HD patients, DNAJB1, HSPA1B and HSPB1 genes were commonly upregulated across all brain regions and cell types except for medium spiny neurons (MSNs) at symptomatic disease stage, and HSPH1 and SAT1 genes were altered in expression in all symptomatic brain datasets, indicating early and sustained changes in the expression of genes related to heat shock response as well as response to misfolded proteins. Specifically in indirect pathway medium spiny neurons (iMSNs), mitochondria related genes were among the top uniquely dysregulated genes. Interestingly, blood from HD patients showed commonly differentially expressed genes with a number of brain regions and cells, with the highest number of overlapping genes with MSNs and BA9 region at symptomatic stage. We also found the differential expression and predicted altered activity of a set of transcription factors and epigenetic regulators, including BCL6, EGR1, FOSL2 and CREBBP, HDAC1, KDM4C, respectively, which may underlie the observed transcriptional changes in HD. Altogether, our work provides a complete overview of the transcriptional studies in HD, and by data synthesis, reveals a number of common and unique gene expression and regulatory changes across different cell and tissue types in HD. These changes could elucidate new insights into molecular mechanisms of differential vulnerability in HD. Systematic Review Registration: https://osf.io/pm3wq.
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Affiliation(s)
- Bimala Malla
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Xuanzong Guo
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Gökçe Senger
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Zoi Chasapopoulou
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ferah Yildirim
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
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21
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Li L, Sun Y, Zhang Y, Wang W, Ye C. Mutant Huntingtin Impairs Pancreatic β-cells by Recruiting IRS-2 and Disturbing the PI3K/AKT/FoxO1 Signaling Pathway in Huntington's Disease. J Mol Neurosci 2021; 71:2646-2658. [PMID: 34331233 DOI: 10.1007/s12031-021-01869-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/09/2021] [Indexed: 10/20/2022]
Abstract
Patients with Huntington's disease (HD) have an increased incidence of diabetes. However, the molecular mechanisms of pancreatic β-cell dysfunction have not been entirely clarified. Revealing the pathogenesis of diabetes can provide a novel understanding of the onset and progression of HD, as well as potential clues for the development of new therapeutics. Here, we demonstrated that the mouse pancreatic insulinoma cell line NIT-1 expressing N-terminal mutant huntingtin (mHTT) containing 160 polyglutamine (160Q cells) displayed lower cell proliferative ability than the cells expressing N-terminal wild-type HTT containing 20 polyglutamine (20Q cells). In addition, 160Q cells were more prone to apoptosis and exhibited deficient glucose-stimulated insulin expression and secretion. Furthermore, insulin signaling molecule insulin receptor substrate 2 (IRS-2) expression decreased and was recruited into mHTT aggregates. Consequently, glucose stimulation failed to activate the downstream molecule phosphatidylinositol-3 kinase (PI3K) in 160Q cells, leading to reduced phosphorylation levels of serine-threonine protein kinase AKT and forkhead box protein O1 (FoxO1). These data indicate that activation of the glucose-stimulated PI3K/AKT/FoxO1 signaling pathway is significantly blocked in pancreatic β-cells in HD. Importantly, insulin treatment inhibited the aggregation of mHTT and significantly improved the activation of PI3K/AKT/FoxO1 signaling in 160Q cells. These results suggest that the inhibition of the PI3K/AKT/FoxO1 pathway might be due to the recruitment of IRS-2 into mHTT aggregates in HD β-cells, ultimately contributing to the impairment of pancreatic β-cells. In conclusion, our work provides new insight into the underlying mechanisms of the high incidence of diabetes and abnormal glucose homeostasis in HD.
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Affiliation(s)
- Li Li
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Hong Kong S.A.R., P.R. of China
| | - Yun Sun
- Department of Histology and Embryology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. of China
| | - Yinong Zhang
- Department of Histology and Embryology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. of China
| | - Weixi Wang
- Department of Histology and Embryology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. of China
| | - Cuifang Ye
- Department of Histology and Embryology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. of China.
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22
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Hyeon JW, Kim AH, Yano H. Epigenetic regulation in Huntington's disease. Neurochem Int 2021; 148:105074. [PMID: 34038804 DOI: 10.1016/j.neuint.2021.105074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/23/2021] [Accepted: 05/17/2021] [Indexed: 12/25/2022]
Abstract
Huntington's disease (HD) is a devastating and fatal monogenic neurodegenerative disorder characterized by progressive loss of selective neurons in the brain and is caused by an abnormal expansion of CAG trinucleotide repeats in a coding exon of the huntingtin (HTT) gene. Progressive gene expression changes that begin at premanifest stages are a prominent feature of HD and are thought to contribute to disease progression. Increasing evidence suggests the critical involvement of epigenetic mechanisms in abnormal transcription in HD. Genome-wide alterations of a number of epigenetic modifications, including DNA methylation and multiple histone modifications, are associated with HD, suggesting that mutant HTT causes complex epigenetic abnormalities and chromatin structural changes, which may represent an underlying pathogenic mechanism. The causal relationship of specific epigenetic changes to early transcriptional alterations and to disease pathogenesis require further investigation. In this article, we review recent studies on epigenetic regulation in HD with a focus on DNA and histone modifications. We also discuss the contribution of epigenetic modifications to HD pathogenesis as well as potential mechanisms linking mutant HTT and epigenetic alterations. Finally, we discuss the therapeutic potential of epigenetic-based treatments.
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Affiliation(s)
- Jae Wook Hyeon
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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23
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Impaired inhibitory GABAergic synaptic transmission and transcription studied in single neurons by Patch-seq in Huntington's disease. Proc Natl Acad Sci U S A 2021; 118:2020293118. [PMID: 33952696 DOI: 10.1073/pnas.2020293118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Transcriptional dysregulation in Huntington's disease (HD) causes functional deficits in striatal neurons. Here, we performed Patch-sequencing (Patch-seq) in an in vitro HD model to investigate the effects of mutant Huntingtin (Htt) on synaptic transmission and gene transcription in single striatal neurons. We found that expression of mutant Htt decreased the synaptic output of striatal neurons in a cell autonomous fashion and identified a number of genes whose dysregulation was correlated with physiological deficiencies in mutant Htt neurons. In support of a pivotal role for epigenetic mechanisms in HD pathophysiology, we found that inhibiting histone deacetylase 1/3 activities rectified several functional and morphological deficits and alleviated the aberrant transcriptional profiles in mutant Htt neurons. With this study, we demonstrate that Patch-seq technology can be applied both to better understand molecular mechanisms underlying a complex neurological disease at the single-cell level and to provide a platform for screening for therapeutics for the disease.
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24
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Ma SP, Xi HR, Gao XX, Yang JM, Kurita R, Nakamura Y, Song XM, Chen HY, Lu DR. Long noncoding RNA HBBP1 enhances γ-globin expression through the ETS transcription factor ELK1. Biochem Biophys Res Commun 2021; 552:157-163. [PMID: 33744764 DOI: 10.1016/j.bbrc.2021.03.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/10/2021] [Indexed: 11/26/2022]
Abstract
β-Thalassemia is an autosomal recessive genetic disease caused by defects in the production of adult hemoglobin (HbA, α2β2), which leads to an imbalance between α- and non-α-globin chains. Reactivation of γ-globin expression is an effective strategy to treat β-thalassemia patients. Previously, it was demonstrated that hemoglobin subunit beta pseudogene 1 (HBBP1) is associated with elevated fetal hemoglobin (HbF, α2γ2) in β-thalassemia patients. However, the mechanism underlying HBBP1-mediated HbF production is unknown. In this study, using bioinformatics analysis, we found that HBBP1 is involved in γ-globin production, and then preliminarily confirmed this finding in K562 cells. When HBBP1 was overexpressed, γ-globin expression was increased at the transcript and protein levels in HUDEP-2 cells. Next, we found that ETS transcription factor ELK1 (ELK1) binds to the HBBP1 proximal promoter and significantly promotes its activity. Moreover, the synthesis of γ-globin was enhanced when ELK1 was overexpressed in HUDEP-2 cells. Surprisingly, ELK1 also directly bound to and activated the γ-globin proximal promoter. Furthermore, we found that HBBP1 and ELK1 can interact with each other in HUDEP-2 cells. Collectively, these findings suggest that HBBP1 can induce γ-globin by enhancing ELK1 expression, providing some clues for γ-globin reactivation in β-thalassemia.
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Affiliation(s)
- Shuang-Ping Ma
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hai-Rui Xi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xu-Xia Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jing-Min Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ryo Kurita
- Japanese Red Cross Society, Department of Research and Development, Central Blood Institute, Tokyo, 105-8521, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Xian-Min Song
- Department of Hematology, Shanghai General Hospital (affiliated to Shanghai Jiao Tong University), No. 100 Haining Road, 200080, Shanghai, China
| | - Hong-Yan Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Da-Ru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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25
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Elorza A, Márquez Y, Cabrera JR, Sánchez-Trincado JL, Santos-Galindo M, Hernández IH, Picó S, Díaz-Hernández JI, García-Escudero R, Irimia M, Lucas JJ. Huntington's disease-specific mis-splicing unveils key effector genes and altered splicing factors. Brain 2021; 144:2009-2023. [PMID: 33725094 PMCID: PMC8370404 DOI: 10.1093/brain/awab087] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 12/31/2022] Open
Abstract
Correction of mis-splicing events is a growing therapeutic approach for neurological diseases such as spinal muscular atrophy or neuronal ceroid lipofuscinosis 7, which are caused by splicing-affecting mutations. Mis-spliced effector genes that do not harbour mutations are also good candidate therapeutic targets in diseases with more complex aetiologies such as cancer, autism, muscular dystrophies or neurodegenerative diseases. Next-generation RNA sequencing (RNA-seq) has boosted investigation of global mis-splicing in diseased tissue to identify such key pathogenic mis-spliced genes. Nevertheless, while analysis of tumour or dystrophic muscle biopsies can be informative on early stage pathogenic mis-splicing, for neurodegenerative diseases, these analyses are intrinsically hampered by neuronal loss and neuroinflammation in post-mortem brains. To infer splicing alterations relevant to Huntington’s disease pathogenesis, here we performed intersect-RNA-seq analyses of human post-mortem striatal tissue and of an early symptomatic mouse model in which neuronal loss and gliosis are not yet present. Together with a human/mouse parallel motif scan analysis, this approach allowed us to identify the shared mis-splicing signature triggered by the Huntington’s disease-causing mutation in both species and to infer upstream deregulated splicing factors. Moreover, we identified a plethora of downstream neurodegeneration-linked mis-spliced effector genes that—together with the deregulated splicing factors—become new possible therapeutic targets. In summary, here we report pathogenic global mis-splicing in Huntington’s disease striatum captured by our new intersect-RNA-seq approach that can be readily applied to other neurodegenerative diseases for which bona fide animal models are available.
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Affiliation(s)
- Ainara Elorza
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Yamile Márquez
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
| | - Jorge R Cabrera
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - José Luis Sánchez-Trincado
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - María Santos-Galindo
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Ivó H Hernández
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain.,Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Sara Picó
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Juan I Díaz-Hernández
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Ramón García-Escudero
- Molecular Oncology Unit, CIEMAT, Madrid 28040, Spain.,Biomedical Research Institute i+12, Hospital 12 de Octubre, Madrid 28041, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology, 08003 Barcelona, Spain.,Universitat Pompeu Fabra, 08003, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - José J Lucas
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
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26
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Hecklau K, Mueller S, Koch SP, Mehkary MH, Kilic B, Harms C, Boehm-Sturm P, Yildirim F. The Effects of Selective Inhibition of Histone Deacetylase 1 and 3 in Huntington's Disease Mice. Front Mol Neurosci 2021; 14:616886. [PMID: 33679321 PMCID: PMC7925995 DOI: 10.3389/fnmol.2021.616886] [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: 10/13/2020] [Accepted: 01/27/2021] [Indexed: 01/15/2023] Open
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disease characterized by a late clinical onset of psychiatric, cognitive, and motor symptoms. Transcriptional dysregulation is an early and central disease mechanism which is accompanied by epigenetic alterations in HD. Previous studies demonstrated that targeting transcriptional changes by inhibition of histone deacetylases (HDACs), especially the class I HDACs, provides therapeutic effects. Yet, their exact mechanisms of action and the features of HD pathology, on which these inhibitors act remain to be elucidated. Here, using transcriptional profiling, we found that selective inhibition of HDAC1 and HDAC3 by RGFP109 alleviated transcriptional dysregulation of a number of genes, including the transcription factor genes Neurod2 and Nr4a2, and gene sets and programs, especially those that are associated to insulin-like growth factor pathway, in the striatum of R6/1 mice. RGFP109 treatment led to a modest improvement of the motor skill learning and coordination deficit on the RotaRod test, while it did not alter the locomotor and anxiety-like phenotypes in R6/1 animals. We also found, by volumetric MRI, a widespread brain atrophy in the R6/1 mice at the symptomatic disease stage, on which RGFP109 showed no significant effects. Collectively, our combined work suggests that specific HDAC1 and HDAC3 inhibition may offer benefits for alleviating the motor phenotypic deficits and transcriptional dysregulation in HD.
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Affiliation(s)
- Katharina Hecklau
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Susanne Mueller
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité Core Facility 7T Experimental MRIs, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Paul Koch
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité Core Facility 7T Experimental MRIs, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Mustafa Hussain Mehkary
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Busra Kilic
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Harms
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité – Universitätsmedizin Berlin, Berlin, Germany
- Einstein Center for Neurosciences Berlin, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Philipp Boehm-Sturm
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité Core Facility 7T Experimental MRIs, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Ferah Yildirim
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Einstein Center for Neurosciences Berlin, Charité – Universitätsmedizin Berlin, Berlin, Germany
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27
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Ulrich M, Wissenbach U, Thiel G. The super-cooling compound icilin stimulates c-Fos and Egr-1 expression and activity involving TRPM8 channel activation, Ca2+ ion influx and activation of the ternary complex factor Elk-1. Biochem Pharmacol 2020; 177:113936. [DOI: 10.1016/j.bcp.2020.113936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/23/2020] [Indexed: 12/12/2022]
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28
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Early epigenomic and transcriptional changes reveal Elk-1 transcription factor as a therapeutic target in Huntington's disease. Proc Natl Acad Sci U S A 2019; 116:24840-24851. [PMID: 31744868 DOI: 10.1073/pnas.1908113116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Huntington's disease (HD) is a chronic neurodegenerative disorder characterized by a late clinical onset despite ubiquitous expression of the mutant Huntingtin gene (HTT) from birth. Transcriptional dysregulation is a pivotal feature of HD. Yet, the genes that are altered in the prodromal period and their regulators, which present opportunities for therapeutic intervention, remain to be elucidated. Using transcriptional and chromatin profiling, we found aberrant transcription and changes in histone H3K27acetylation in the striatum of R6/1 mice during the presymptomatic disease stages. Integrating these data, we identified the Elk-1 transcription factor as a candidate regulator of prodromal changes in HD. Exogenous expression of Elk-1 exerted beneficial effects in a primary striatal cell culture model of HD, and adeno-associated virus-mediated Elk-1 overexpression alleviated transcriptional dysregulation in R6/1 mice. Collectively, our work demonstrates that aberrant gene expression precedes overt disease onset in HD, identifies the Elk-1 transcription factor as a key regulator linked to early epigenetic and transcriptional changes in HD, and presents evidence for Elk-1 as a target for alleviating molecular pathology in HD.
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