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Palmisano I, Liu T, Gao W, Zhou L, Merkenschlager M, Müller F, Chadwick J, Rivolta RT, Kong G, King JWD, Al-jibury E, Yan Y, Carlino A, Collison B, De Vitis E, Gongala S, De Virgiliis F, Wang Z, Di Giovanni S. Three-dimensional chromatin mapping of sensory neurons reveals that cohesin-dependent genomic domains are required for axonal regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.09.597974. [PMID: 38895406 PMCID: PMC11185766 DOI: 10.1101/2024.06.09.597974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The in vivo three-dimensional genomic architecture of adult mature neurons at homeostasis and after medically relevant perturbations such as axonal injury remains elusive. Here we address this knowledge gap by mapping the three-dimensional chromatin architecture and gene expression programme at homeostasis and after sciatic nerve injury in wild-type and cohesin-deficient mouse sensory dorsal root ganglia neurons via combinatorial Hi-C and RNA-seq. We find that cohesin is required for the full induction of the regenerative transcriptional program, by organising 3D genomic domains required for the activation of regenerative genes. Importantly, loss of cohesin results in disruption of chromatin architecture at regenerative genes and severely impaired nerve regeneration. Together, these data provide an original three-dimensional chromatin map of adult sensory neurons in vivo and demonstrate a role for cohesin-dependent chromatin interactions in neuronal regeneration.
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Affiliation(s)
- Ilaria Palmisano
- Department of Medicine, Division of Brain Sciences, Centre for Restorative Neuroscience, Imperial College London, London, W12 0NN, UK
- Department of Neuroscience, The Ohio State University, Columbus, 43210, OH, USA
| | - Tong Liu
- Department of Computer Science, University of Miami, 330M Ungar Building, 1365 Memorial Drive, Coral Gables, FL 33124-4245 Miami, FL, USA
| | - Wei Gao
- Department of Medicine, Division of Brain Sciences, Centre for Restorative Neuroscience, Imperial College London, London, W12 0NN, UK
| | - Luming Zhou
- Department of Medicine, Division of Brain Sciences, Centre for Restorative Neuroscience, Imperial College London, London, W12 0NN, UK
| | | | - Franziska Müller
- Department of Medicine, Division of Brain Sciences, Centre for Restorative Neuroscience, Imperial College London, London, W12 0NN, UK
| | - Jessica Chadwick
- Department of Medicine, Division of Brain Sciences, Centre for Restorative Neuroscience, Imperial College London, London, W12 0NN, UK
| | - Rebecca Toscano Rivolta
- Department of Medicine, Division of Brain Sciences, Centre for Restorative Neuroscience, Imperial College London, London, W12 0NN, UK
| | - Guiping Kong
- Department of Medicine, Division of Brain Sciences, Centre for Restorative Neuroscience, Imperial College London, London, W12 0NN, UK
| | - James WD King
- MRC LMS, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Ediem Al-jibury
- MRC LMS, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Yuyang Yan
- Department of Medicine, Division of Brain Sciences, Centre for Restorative Neuroscience, Imperial College London, London, W12 0NN, UK
| | - Alessandro Carlino
- Department of Neuroscience, The Ohio State University, Columbus, 43210, OH, USA
| | - Bryce Collison
- Department of Neuroscience, The Ohio State University, Columbus, 43210, OH, USA
| | - Eleonora De Vitis
- Department of Neuroscience, The Ohio State University, Columbus, 43210, OH, USA
| | - Sree Gongala
- Department of Medicine, Division of Brain Sciences, Centre for Restorative Neuroscience, Imperial College London, London, W12 0NN, UK
| | - Francesco De Virgiliis
- Department of Medicine, Division of Brain Sciences, Centre for Restorative Neuroscience, Imperial College London, London, W12 0NN, UK
| | - Zheng Wang
- Department of Computer Science, University of Miami, 330M Ungar Building, 1365 Memorial Drive, Coral Gables, FL 33124-4245 Miami, FL, USA
| | - Simone Di Giovanni
- Department of Medicine, Division of Brain Sciences, Centre for Restorative Neuroscience, Imperial College London, London, W12 0NN, UK
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2
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Ao X, Parisien M, Fillingim RB, Ohrbach R, Slade GD, Diatchenko L, Smith SB. Whole-genome methylation profiling reveals regions associated with painful temporomandibular disorders and active recovery processes. Pain 2024; 165:1060-1073. [PMID: 38015635 PMCID: PMC11018476 DOI: 10.1097/j.pain.0000000000003104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 08/24/2023] [Indexed: 11/30/2023]
Abstract
ABSTRACT Temporomandibular disorders (TMDs), collectively representing one of the most common chronic pain conditions, have a substantial genetic component, but genetic variation alone has not fully explained the heritability of TMD risk. Reasoning that the unexplained heritability may be because of DNA methylation, an epigenetic phenomenon, we measured genome-wide DNA methylation using the Illumina MethylationEPIC platform with blood samples from participants in the Orofacial Pain: Prospective Evaluation and Risk Assessment (OPPERA) study. Associations with chronic TMD used methylation data from 496 chronic painful TMD cases and 452 TMD-free controls. Changes in methylation between enrollment and a 6-month follow-up visit were determined for a separate sample of 62 people with recent-onset painful TMD. More than 750,000 individual CpG sites were examined for association with chronic painful TMD. Six differentially methylated regions were significantly ( P < 5 × 10 -8 ) associated with chronic painful TMD, including loci near genes involved in the regulation of inflammatory and neuronal response. A majority of loci were similarly differentially methylated in acute TMD consistent with observed transience or persistence of symptoms at follow-up. Functional characterization of the identified regions found relationships between methylation at these loci and nearby genetic variation contributing to chronic painful TMD and with gene expression of proximal genes. These findings reveal epigenetic contributions to chronic painful TMD through methylation of the genes FMOD , PM20D1 , ZNF718 , ZFP57 , and RNF39 , following the development of acute painful TMD. Epigenetic regulation of these genes likely contributes to the trajectory of transcriptional events in affected tissues leading to resolution or chronicity of pain.
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Affiliation(s)
- Xiang Ao
- Faculty of Dental Medicine and Oral Health Sciences; Department of Anesthesia, Faculty of Medicine and Health Sciences; Alan Edwards Centre for Research on Pain; McGill University, Montreal, Canada
| | - Marc Parisien
- Faculty of Dental Medicine and Oral Health Sciences; Department of Anesthesia, Faculty of Medicine and Health Sciences; Alan Edwards Centre for Research on Pain; McGill University, Montreal, Canada
| | - Roger B. Fillingim
- Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, Florida; Pain Research and Intervention Center of Excellence, Department of Community Dentistry and Behavioral Science, College of Dentistry, University of Florida, Gainesville, Florida
| | - Richard Ohrbach
- Department of Oral Diagnostic Sciences, University at Buffalo, Buffalo, New York
| | - Gary D. Slade
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Luda Diatchenko
- Faculty of Dental Medicine and Oral Health Sciences; Department of Anesthesia, Faculty of Medicine and Health Sciences; Alan Edwards Centre for Research on Pain; McGill University, Montreal, Canada
| | - Shad B. Smith
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University, Durham, North Carolina, USA
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3
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Au NPB, Wu T, Chen X, Gao F, Li YTY, Tam WY, Yu KN, Geschwind DH, Coppola G, Wang X, Ma CHE. Genome-wide study reveals novel roles for formin-2 in axon regeneration as a microtubule dynamics regulator and therapeutic target for nerve repair. Neuron 2023; 111:3970-3987.e8. [PMID: 38086376 DOI: 10.1016/j.neuron.2023.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 09/02/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023]
Abstract
Peripheral nerves regenerate successfully; however, clinical outcome after injury is poor. We demonstrated that low-dose ionizing radiation (LDIR) promoted axon regeneration and function recovery after peripheral nerve injury (PNI). Genome-wide CpG methylation profiling identified LDIR-induced hypermethylation of the Fmn2 promoter, exhibiting injury-induced Fmn2 downregulation in dorsal root ganglia (DRGs). Constitutive knockout or neuronal Fmn2 knockdown accelerated nerve repair and function recovery. Mechanistically, increased microtubule dynamics at growth cones was observed in time-lapse imaging of Fmn2-deficient DRG neurons. Increased HDAC5 phosphorylation and rapid tubulin deacetylation were found in regenerating axons of neuronal Fmn2-knockdown mice after injury. Growth-promoting effect of neuronal Fmn2 knockdown was eliminated by pharmaceutical blockade of HDAC5 or neuronal Hdac5 knockdown, suggesting that Fmn2deletion promotes axon regeneration via microtubule post-translational modification. In silico screening of FDA-approved drugs identified metaxalone, administered either immediately or 24-h post-injury, accelerating function recovery. This work uncovers a novel axon regeneration function of Fmn2 and a small-molecule strategy for PNI.
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Affiliation(s)
| | - Tan Wu
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Xinyu Chen
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China
| | - Feng Gao
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | | | - Wing Yip Tam
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China
| | - Kwan Ngok Yu
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Giovanni Coppola
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Chi Him Eddie Ma
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China.
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4
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Rizk E, Madrid A, Koueik J, Sun D, Stewart K, Chen D, Luo S, Hong F, Papale LA, Hariharan N, Alisch RS, Iskandar BJ. Purified regenerating retinal neurons reveal regulatory role of DNA methylation-mediated Na+/K+-ATPase in murine axon regeneration. Commun Biol 2023; 6:120. [PMID: 36717618 PMCID: PMC9886953 DOI: 10.1038/s42003-023-04463-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
While embryonic mammalian central nervous system (CNS) axons readily grow and differentiate, only a minority of fully differentiated mature CNS neurons are able to regenerate injured axons, leading to stunted functional recovery after injury and disease. To delineate DNA methylation changes specifically associated with axon regeneration, we used a Fluorescent-Activated Cell Sorting (FACS)-based methodology in a rat optic nerve transection model to segregate the injured retinal ganglion cells (RGCs) into regenerating and non-regenerating cell populations. Whole-genome DNA methylation profiling of these purified neurons revealed genes and pathways linked to mammalian RGC regeneration. Moreover, whole-methylome sequencing of purified uninjured adult and embryonic RGCs identified embryonic molecular profiles reactivated after injury in mature neurons, and others that correlate specifically with embryonic or adult axon growth, but not both. The results highlight the contribution to both embryonic growth and adult axon regeneration of subunits encoding the Na+/K+-ATPase. In turn, both biochemical and genetic inhibition of the Na+/K+-ATPase pump significantly reduced RGC axon regeneration. These data provide critical molecular insights into mammalian CNS axon regeneration, pinpoint the Na+/K+-ATPase as a key regulator of regeneration of injured mature CNS axons, and suggest that successful regeneration requires, in part, reactivation of embryonic signals.
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Affiliation(s)
- Elias Rizk
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA ,grid.240473.60000 0004 0543 9901Department of Neurological Surgery, Penn State Milton S. Hershey Medical Center, Hershey, PA 17033 USA
| | - Andy Madrid
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Joyce Koueik
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Dandan Sun
- grid.21925.3d0000 0004 1936 9000Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Krista Stewart
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - David Chen
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Susan Luo
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Felissa Hong
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Ligia A. Papale
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Nithya Hariharan
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Reid S. Alisch
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Bermans J. Iskandar
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
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5
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Lee J, Cho Y. Comparative gene expression profiling reveals the mechanisms of axon regeneration. FEBS J 2020; 288:4786-4797. [PMID: 33248003 DOI: 10.1111/febs.15646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/17/2020] [Accepted: 11/25/2020] [Indexed: 01/03/2023]
Abstract
Axons are vulnerable to injury, potentially leading to degeneration or neuronal death. While neurons in the central nervous system fail to regenerate, neurons in the peripheral nervous system are known to regenerate. Since it has been shown that injury-response signal transduction is mediated by gene expression changes, expression profiling is a useful tool to understand the molecular mechanisms of regeneration. Axon regeneration is regulated by injury-responsive genes induced in both neurons and their surrounding non-neuronal cells. Thus, an experimental setup for the comparative analysis between regenerative and nonregenerative conditions is essential to identify ideal targets for the promotion of regeneration-associated genes and to understand the mechanisms of axon regeneration. Here, we review the original research that shows the key factors regulating axon regeneration, in particular by using comparative gene expression profiling in diverse systems.
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Affiliation(s)
- Jinyoung Lee
- Laboratory of Axon Regeneration & Degeneration, Department of Life Sciences, Korea University, Seoul, Korea
| | - Yongcheol Cho
- Laboratory of Axon Regeneration & Degeneration, Department of Life Sciences, Korea University, Seoul, Korea
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6
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Smith TP, Sahoo PK, Kar AN, Twiss JL. Intra-axonal mechanisms driving axon regeneration. Brain Res 2020; 1740:146864. [PMID: 32360100 DOI: 10.1016/j.brainres.2020.146864] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 12/27/2022]
Abstract
Traumatic injury to the peripheral and central nervous systems very often causes axotomy, where an axon loses connections with its target resulting in loss of function. The axon segments distal to the injury site lose connection with the cell body and degenerate. Axotomized neurons in the periphery can spontaneously mount a regenerative response and reconnect to their denervated target tissues, though this is rarely complete in humans. In contrast, spontaneous regeneration rarely occurs after axotomy in the spinal cord and brain. Here, we concentrate on the mechanisms underlying this spontaneous regeneration in the peripheral nervous system, focusing on events initiated from the axon that support regenerative growth. We contrast this with what is known for axonal injury responses in the central nervous system. Considering the neuropathy focus of this special issue, we further draw parallels and distinctions between the injury-response mechanisms that initiate regenerative gene expression programs and those that are known to trigger axon degeneration.
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Affiliation(s)
- Terika P Smith
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Pabitra K Sahoo
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Amar N Kar
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Jeffery L Twiss
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.
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7
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Shin HY, Kim K, Kwon MJ, Oh YJ, Kim EH, Kim HS, Hong CP, Lee JH, Lee K, Kim BG. Alteration in global DNA methylation status following preconditioning injury influences axon growth competence of the sensory neurons. Exp Neurol 2020; 326:113177. [PMID: 31926166 DOI: 10.1016/j.expneurol.2020.113177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/31/2019] [Accepted: 01/07/2020] [Indexed: 12/18/2022]
Abstract
Preconditioning peripheral nerve injury primes the sensory neurons in the dorsal root ganglia (DRGs) to acquire axon regeneration competence. Transcription of a large set of regeneration-associated-genes (RAGs) contributes to the enhanced intrinsic axonal regeneration capacity. However, the mechanism underlying the coordinated upregulation of RAGs orchestrated by preconditioning injury is unclear. We sought to determine potential influence of DNA methylation change on transcriptional activation of RAGs in the L4-L6 DRGs following sciatic nerve injury. Genome-wide sequencing revealed that about 20% of the methylated DNA fragments were differentially methylated, and >3000 genes contained differentially methylated regions. Not only demethylation but also increased methylation was observed to a similar extent. The change in the global DNA methylation did not correlate with the gene expression level of most genes, including the well-documented RAGs. However, pharmacological inhibition or activation of DNA methylation markedly attenuated the axon growth capacity of the preconditioned DRG neurons. Pharmacological perturbation of DNA methylation resulted in simultaneous downregulation of many highly overlapping non-transcription factor RAGs, which was accompanied by a concurrent, robust upregulation of SOCS3 and Serpine1. Overexpression of SOCS3 and Serpine1 in the DRG neurons overrode injury-induced axon growth competence, corroborating their roles as the negative regulators of axon regeneration. We conclude that the injury-induced global alteration of DNA methylome strongly influences the axon growth competence in preconditioned DRG neurons. Our results also suggest a possibility that perturbing DNA methylome changes might lead to the upregulation of negative regulator RAGs thereby attenuating axon growth capacity.
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Affiliation(s)
- Hae Young Shin
- Department of Brain Science, Ajou University Graduate School of Medicine, Suwon, Republic of Korea; Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Kyung Kim
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Min Jung Kwon
- Department of Brain Science, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Young Joo Oh
- Department of Brain Science, Ajou University Graduate School of Medicine, Suwon, Republic of Korea; Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Eun Hye Kim
- Department of Brain Science, Ajou University Graduate School of Medicine, Suwon, Republic of Korea; Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Hyung Soon Kim
- Department of Brain Science, Ajou University Graduate School of Medicine, Suwon, Republic of Korea; Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Chang Pyo Hong
- Theragen Bio Institute, TheragenEtex, Suwon 16229, Republic of Korea
| | - Jae-Hyung Lee
- Department of Life and Nanopharmaceutical Sciences, Department of Maxillofacial Biomedical Engineering, School of Dentistry, Kyung Hee University, Republic of Korea
| | - KiYoung Lee
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Byung Gon Kim
- Department of Brain Science, Ajou University Graduate School of Medicine, Suwon, Republic of Korea; Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea; Department of Neurology, Ajou University School of Medicine, Suwon, Republic of Korea.
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8
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Hervera A, Zhou L, Palmisano I, McLachlan E, Kong G, Hutson TH, Danzi MC, Lemmon VP, Bixby JL, Matamoros‐Angles A, Forsberg K, De Virgiliis F, Matheos DP, Kwapis J, Wood MA, Puttagunta R, del Río JA, Di Giovanni S. PP4-dependent HDAC3 dephosphorylation discriminates between axonal regeneration and regenerative failure. EMBO J 2019; 38:e101032. [PMID: 31268609 PMCID: PMC6600644 DOI: 10.15252/embj.2018101032] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 01/01/2023] Open
Abstract
The molecular mechanisms discriminating between regenerative failure and success remain elusive. While a regeneration-competent peripheral nerve injury mounts a regenerative gene expression response in bipolar dorsal root ganglia (DRG) sensory neurons, a regeneration-incompetent central spinal cord injury does not. This dichotomic response offers a unique opportunity to investigate the fundamental biological mechanisms underpinning regenerative ability. Following a pharmacological screen with small-molecule inhibitors targeting key epigenetic enzymes in DRG neurons, we identified HDAC3 signalling as a novel candidate brake to axonal regenerative growth. In vivo, we determined that only a regenerative peripheral but not a central spinal injury induces an increase in calcium, which activates protein phosphatase 4 that in turn dephosphorylates HDAC3, thus impairing its activity and enhancing histone acetylation. Bioinformatics analysis of ex vivo H3K9ac ChIPseq and RNAseq from DRG followed by promoter acetylation and protein expression studies implicated HDAC3 in the regulation of multiple regenerative pathways. Finally, genetic or pharmacological HDAC3 inhibition overcame regenerative failure of sensory axons following spinal cord injury. Together, these data indicate that PP4-dependent HDAC3 dephosphorylation discriminates between axonal regeneration and regenerative failure.
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Affiliation(s)
- Arnau Hervera
- Department of MedicineDivision of Brain SciencesMolecular NeuroregenerationImperial College LondonLondonUK
- Molecular and Cellular NeurobiotechnologyInstitute for Bioengineering of Catalonia (IBEC)Parc Científic de BarcelonaBarcelonaSpain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)BarcelonaSpain
- Department of Cell Biology, Physiology and ImmunologyUniversitat de BarcelonaBarcelonaSpain
- Institute of NeuroscienceUniversity of BarcelonaBarcelonaSpain
| | - Luming Zhou
- Department of MedicineDivision of Brain SciencesMolecular NeuroregenerationImperial College LondonLondonUK
- Laboratory for NeuroRegeneration and RepairCenter for NeurologyHertie Institute for Clinical Brain ResearchUniversity of TuebingenTuebingenGermany
- Graduate School for Cellular and Molecular NeuroscienceUniversity of TuebingenTuebingenGermany
| | - Ilaria Palmisano
- Department of MedicineDivision of Brain SciencesMolecular NeuroregenerationImperial College LondonLondonUK
| | - Eilidh McLachlan
- Department of MedicineDivision of Brain SciencesMolecular NeuroregenerationImperial College LondonLondonUK
| | - Guiping Kong
- Department of MedicineDivision of Brain SciencesMolecular NeuroregenerationImperial College LondonLondonUK
- Laboratory for NeuroRegeneration and RepairCenter for NeurologyHertie Institute for Clinical Brain ResearchUniversity of TuebingenTuebingenGermany
| | - Thomas H Hutson
- Department of MedicineDivision of Brain SciencesMolecular NeuroregenerationImperial College LondonLondonUK
| | - Matt C Danzi
- The Miami Project to Cure ParalysisDepartment of Neurological SurgeryMiller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Vance P Lemmon
- The Miami Project to Cure ParalysisDepartment of Neurological SurgeryMiller School of MedicineUniversity of MiamiMiamiFLUSA
| | - John L Bixby
- The Miami Project to Cure ParalysisDepartment of Neurological SurgeryMiller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Andreu Matamoros‐Angles
- Molecular and Cellular NeurobiotechnologyInstitute for Bioengineering of Catalonia (IBEC)Parc Científic de BarcelonaBarcelonaSpain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)BarcelonaSpain
- Department of Cell Biology, Physiology and ImmunologyUniversitat de BarcelonaBarcelonaSpain
- Institute of NeuroscienceUniversity of BarcelonaBarcelonaSpain
| | - Kirsi Forsberg
- Laboratory for NeuroRegeneration and RepairCenter for NeurologyHertie Institute for Clinical Brain ResearchUniversity of TuebingenTuebingenGermany
| | - Francesco De Virgiliis
- Department of MedicineDivision of Brain SciencesMolecular NeuroregenerationImperial College LondonLondonUK
- Laboratory for NeuroRegeneration and RepairCenter for NeurologyHertie Institute for Clinical Brain ResearchUniversity of TuebingenTuebingenGermany
- Graduate School for Cellular and Molecular NeuroscienceUniversity of TuebingenTuebingenGermany
| | - Dina P Matheos
- Center for the Neurobiology of Learning & MemoryDepartment of Neurobiology & BehaviorUniversity of CaliforniaIrvineCAUSA
| | - Janine Kwapis
- Center for the Neurobiology of Learning & MemoryDepartment of Neurobiology & BehaviorUniversity of CaliforniaIrvineCAUSA
| | - Marcelo A Wood
- Center for the Neurobiology of Learning & MemoryDepartment of Neurobiology & BehaviorUniversity of CaliforniaIrvineCAUSA
| | - Radhika Puttagunta
- Laboratory for NeuroRegeneration and RepairCenter for NeurologyHertie Institute for Clinical Brain ResearchUniversity of TuebingenTuebingenGermany
- Spinal Cord Injury CenterUniversity Hospital HeidelbergHeidelbergGermany
| | - José Antonio del Río
- Molecular and Cellular NeurobiotechnologyInstitute for Bioengineering of Catalonia (IBEC)Parc Científic de BarcelonaBarcelonaSpain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)BarcelonaSpain
- Department of Cell Biology, Physiology and ImmunologyUniversitat de BarcelonaBarcelonaSpain
- Institute of NeuroscienceUniversity of BarcelonaBarcelonaSpain
| | - Simone Di Giovanni
- Department of MedicineDivision of Brain SciencesMolecular NeuroregenerationImperial College LondonLondonUK
- Laboratory for NeuroRegeneration and RepairCenter for NeurologyHertie Institute for Clinical Brain ResearchUniversity of TuebingenTuebingenGermany
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9
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Stacpoole PW, Martyniuk CJ, James MO, Calcutt NA. Dichloroacetate-induced peripheral neuropathy. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2019; 145:211-238. [PMID: 31208525 DOI: 10.1016/bs.irn.2019.05.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dichloroacetate (DCA) has been the focus of research by both environmental toxicologists and biomedical scientists for over 50 years. As a product of water chlorination and a metabolite of certain industrial chemicals, DCA is ubiquitous in our biosphere at low μg/kg body weight daily exposure levels without obvious adverse effects in humans. As an investigational drug for numerous congenital and acquired diseases, DCA is administered orally or parenterally, usually at doses of 10-50mg/kg per day. As a therapeutic, its principal mechanism of action is to inhibit pyruvate dehydrogenase kinase (PDK). In turn, PDK inhibits the key mitochondrial energy homeostat, pyruvate dehydrogenase complex (PDC), by reversible phosphorylation. By blocking PDK, DCA activates PDC and, consequently, the mitochondrial respiratory chain and ATP synthesis. A reversible sensory/motor peripheral neuropathy is the clinically limiting adverse effect of chronic DCA exposure and experimental data implicate the Schwann cell as a toxicological target. It has been postulated that stimulation of PDC and respiratory chain activity by DCA in normally glycolytic Schwann cells causes uncompensated oxidative stress from increased reactive oxygen species production. Additionally, the metabolism of DCA interferes with the catabolism of the amino acids phenylalanine and tyrosine and with heme synthesis, resulting in accumulation of reactive molecules capable of forming adducts with DNA and proteins and also resulting in oxidative stress. Preliminary evidence in rodent models of peripheral neuropathy suggest that DCA-induced neurotoxicity may be mitigated by naturally occurring antioxidants and by a specific class of muscarinic receptor antagonists. These findings generate a number of testable hypotheses regarding the etiology and treatment of DCA peripheral neuropathy.
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Affiliation(s)
- Peter W Stacpoole
- Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, United States; Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, United States.
| | - Christopher J Martyniuk
- Department of Physiological Sciences, Center for Environmental and Human Toxicology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Margaret O James
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Nigel A Calcutt
- Department of Pathology, University of California San Diego, La Jolla, CA, United States
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10
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Palmisano I, Di Giovanni S. Advances and Limitations of Current Epigenetic Studies Investigating Mammalian Axonal Regeneration. Neurotherapeutics 2018; 15:529-540. [PMID: 29948919 PMCID: PMC6095777 DOI: 10.1007/s13311-018-0636-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Axonal regeneration relies on the expression of regenerative associated genes within a coordinated transcriptional programme, which is finely tuned as a result of the activation of several regenerative signalling pathways. In mammals, this chain of events occurs in neurons following peripheral axonal injury, however it fails upon axonal injury in the central nervous system, such as in the spinal cord and the brain. Accumulating evidence has been suggesting that epigenetic control is a key factor to initiate and sustain the regenerative transcriptional response and that it might contribute to regenerative success versus failure. This review will discuss experimental evidence so far showing a role for epigenetic regulation in models of peripheral and central nervous system axonal injury. It will also propose future directions to fill key knowledge gaps and to test whether epigenetic control might indeed discriminate between regenerative success and failure.
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Affiliation(s)
- Ilaria Palmisano
- Laboratory for Neuroregeneration, Centre for Restorative Neuroscience, Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK.
| | - Simone Di Giovanni
- Laboratory for Neuroregeneration, Centre for Restorative Neuroscience, Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK.
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11
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Nascimento AI, Mar FM, Sousa MM. The intriguing nature of dorsal root ganglion neurons: Linking structure with polarity and function. Prog Neurobiol 2018; 168:86-103. [PMID: 29729299 DOI: 10.1016/j.pneurobio.2018.05.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/26/2018] [Accepted: 05/01/2018] [Indexed: 11/26/2022]
Abstract
Dorsal root ganglion (DRG) neurons are the first neurons of the sensory pathway. They are activated by a variety of sensory stimuli that are then transmitted to the central nervous system. An important feature of DRG neurons is their unique morphology where a single process -the stem axon- bifurcates into a peripheral and a central axonal branch, with different functions and cellular properties. Distinctive structural aspects of the two DRG neuron branches may have important implications for their function in health and disease. However, the link between DRG axonal branch structure, polarity and function has been largely neglected in the field, and relevant information is rather scattered across the literature. In particular, ultrastructural differences between the two axonal branches are likely to account for the higher transport and regenerative ability of the peripheral DRG neuron axon when compared to the central one. Nevertheless, the cell intrinsic factors contributing to this central-peripheral asymmetry are still unknown. Here we critically review the factors that may underlie the functional asymmetry between the peripheral and central DRG axonal branches. Also, we discuss the hypothesis that DRG neurons may assemble a structure resembling the axon initial segment that may be responsible, at least in part, for their polarity and electrophysiological features. Ultimately, we suggest that the clarification of the axonal ultrastructure of DRG neurons using state-of-the-art techniques will be crucial to understand the physiology of this peculiar cell type.
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Affiliation(s)
- Ana Isabel Nascimento
- Nerve Regeneration Group, Instituto de Biologia Molecular e Celular-IBMC and Instituto de Inovação e Investigação em Saúde, University of Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar-ICBAS, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Fernando Milhazes Mar
- Nerve Regeneration Group, Instituto de Biologia Molecular e Celular-IBMC and Instituto de Inovação e Investigação em Saúde, University of Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Mónica Mendes Sousa
- Nerve Regeneration Group, Instituto de Biologia Molecular e Celular-IBMC and Instituto de Inovação e Investigação em Saúde, University of Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.
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12
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Comparison of DNA Methylation in Schwann Cells before and after Peripheral Nerve Injury in Rats. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5393268. [PMID: 28459064 PMCID: PMC5385226 DOI: 10.1155/2017/5393268] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/23/2017] [Accepted: 03/08/2017] [Indexed: 01/13/2023]
Abstract
This study aims to find the difference of genomewide DNA methylation in Schwann cells (SCs) before and after peripheral nerve system (PNS) injury by Methylated DNA Immunoprecipitation Sequencing (MeDIP-Seq) and seek meaningful differentially methylated genes related to repairment of injured PNS. SCs harvested from sciatic nerve were named as activated Schwann cells (ASCs), and the ones harvested from brachial plexus were named as normal Schwann cells (NSCs). Genomic DNA of ASCs and NSCs were isolated and MeDIP-Seq was conducted. Differentially methylated genes and regions were discovered and analyzed by bioinformatic methods. MeDIP-Seq analysis showed methylation differences were identified between ASCs and NSCs. The distribution of differentially methylated regions (DMRs) peaks in different components of genome was mainly located in distal intergenic regions. GO and KEGG analysis of these methylated genes were also conducted. The expression patterns of hypermethylated genes (Dgcr8, Zeb2, Dixdc1, Sox2, and Shh) and hypomethylated genes (Gpr126, Birc2) detected by qRT-PCR were opposite to the MeDIP analysis data with significance (p < 0.05), which proved MeDIP analysis data were real and believable. Our data serve as a basis for understanding the injury-induced epigenetic changes in SCs and the foundation for further studies on repair of PNS injury.
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13
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Shin JE, Cho Y. Epigenetic Regulation of Axon Regeneration after Neural Injury. Mol Cells 2017; 40:10-16. [PMID: 28152303 PMCID: PMC5303884 DOI: 10.14348/molcells.2017.2311] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/16/2017] [Accepted: 01/23/2017] [Indexed: 12/16/2022] Open
Abstract
When peripheral axons are damaged, neuronal injury signaling pathways induce transcriptional changes that support axon regeneration and consequent functional recovery. The recent development of bioinformatics techniques has allowed for the identification of many of the regeneration-associated genes that are regulated by neural injury, yet it remains unclear how global changes in transcriptome are coordinated. In this article, we review recent studies on the epigenetic mechanisms orchestrating changes in gene expression in response to nerve injury. We highlight the importance of epigenetic mechanisms in discriminating efficient axon regeneration in the peripheral nervous system and very limited axon regrowth in the central nervous system and discuss the therapeutic potential of targeting epigenetic regulators to improve neural recovery.
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Affiliation(s)
- Jung Eun Shin
- The Research Institute of Basic Sciences, Seoul National University, Seoul 08826,
Korea
| | - Yongcheol Cho
- Department of Life Sciences, Korea University, Seoul 02841,
Korea
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14
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Al-Ali H, Beckerman SR, Bixby JL, Lemmon VP. In vitro models of axon regeneration. Exp Neurol 2016; 287:423-434. [PMID: 26826447 DOI: 10.1016/j.expneurol.2016.01.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/20/2016] [Accepted: 01/25/2016] [Indexed: 12/31/2022]
Abstract
A variety of in vitro models have been developed to understand the mechanisms underlying the regenerative failure of central nervous system (CNS) axons, and to guide pre-clinical development of regeneration-promoting therapeutics. These range from single-cell based assays that typically focus on molecular mechanisms to organotypic assays that aim to recapitulate in vivo behavior. By utilizing a combination of models, researchers can balance the speed, convenience, and mechanistic resolution of simpler models with the biological relevance of more complex models. This review will discuss a number of models that have been used to build our understanding of the molecular mechanisms of CNS axon regeneration.
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Affiliation(s)
- Hassan Al-Ali
- Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Samuel R Beckerman
- Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - John L Bixby
- Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Center for Computational Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Molecular & Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Vance P Lemmon
- Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Center for Computational Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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