1
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Yaqubi M, Luo JXX, Baig S, Cui QL, Petrecca K, Desu H, Larochelle C, Afanasiev E, Hall JA, Dudley R, Srour M, Haglund L, Ouellet J, Georgiopoulos M, Santaguida C, Sonnen JA, Healy LM, Stratton JA, Kennedy TE, Antel JP. Regional and age-related diversity of human mature oligodendrocytes. Glia 2022; 70:1938-1949. [PMID: 35735919 DOI: 10.1002/glia.24230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/03/2022] [Accepted: 06/05/2022] [Indexed: 11/07/2022]
Abstract
Morphological and emerging molecular studies have provided evidence for heterogeneity within the oligodendrocyte population. To address the regional and age-related heterogeneity of human mature oligodendrocytes (MOLs) we applied single-cell RNA sequencing to cells isolated from cortical/subcortical, subventricular zone brain tissue samples, and thoracolumbar spinal cord samples. Unsupervised clustering of cells identified transcriptionally distinct MOL subpopulations across regions. Spinal cord MOLs, but not microglia, exhibited cell-type-specific upregulation of immune-related markers compared to the other adult regions. SVZ MOLs showed an upregulation of select number of development-linked transcription factors compared to other regions; however, pseudotime trajectory analyses did not identify a global developmental difference. Age-related analysis of cortical/subcortical samples indicated that pediatric MOLs, especially from under age 5, retain higher expression of genes linked to development and to immune activity with pseudotime analysis favoring a distinct developmental stage. Our regional and age-related studies indicate heterogeneity of MOL populations in the human CNS that may reflect developmental and environmental influences.
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Affiliation(s)
- Moein Yaqubi
- Neuro-immunology Unit, Montreal Neurological Institute and Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Julia Xiao Xuan Luo
- Neuro-immunology Unit, Montreal Neurological Institute and Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Salma Baig
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Qiao-Ling Cui
- Neuro-immunology Unit, Montreal Neurological Institute and Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Haritha Desu
- Department of Neurosciences, Centre de Recherche du Centre Hospitalier de l'Université deMontréal, Montreal, QC, Canada
| | - Catherine Larochelle
- Department of Neurosciences, Centre de Recherche du Centre Hospitalier de l'Université deMontréal, Montreal, QC, Canada
| | - Elia Afanasiev
- Neuro-immunology Unit, Montreal Neurological Institute and Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Jeffery A Hall
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Roy Dudley
- Department of Pediatric Neurosurgery, Montreal Children's Hospital, Montreal, Canada
| | - Myriam Srour
- Division of Pediatric Neurology, Montreal Children's Hospital, Montreal, Canada
| | - Lisbet Haglund
- The Orthopedic Research Laboratory, Department of Surgery, McGill University, Montreal, Canada
| | - Jean Ouellet
- The Orthopedic Research Laboratory, Department of Surgery, McGill University, Montreal, Canada.,McGill Scoliosis and Spine Group, Department of Surgery, McGill University, Montreal, Canada
| | - Miltiadis Georgiopoulos
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Canada.,The Orthopedic Research Laboratory, Department of Surgery, McGill University, Montreal, Canada
| | - Carlo Santaguida
- McGill Scoliosis and Spine Group, Department of Surgery, McGill University, Montreal, Canada
| | - Joshua A Sonnen
- Departments of Pathology, Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Luke M Healy
- Neuro-immunology Unit, Montreal Neurological Institute and Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Jo Anne Stratton
- Neuro-immunology Unit, Montreal Neurological Institute and Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Timothy E Kennedy
- Neuro-immunology Unit, Montreal Neurological Institute and Department of Neurology and Neurosurgery, McGill University, Montreal, Canada.,Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Jack P Antel
- Neuro-immunology Unit, Montreal Neurological Institute and Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
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2
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Leveraging interindividual variability of regulatory activity for refining genetic regulation of gene expression in schizophrenia. Mol Psychiatry 2022; 27:5177-5185. [PMID: 36114277 PMCID: PMC9763101 DOI: 10.1038/s41380-022-01768-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 01/14/2023]
Abstract
Schizophrenia is a polygenic psychiatric disorder with limited understanding about the mechanistic changes in gene expression regulation. To elucidate on this, we integrate interindividual variability of regulatory activity (ChIP-sequencing for H3K27ac histone mark) with gene expression and genotype data captured from the prefrontal cortex of 272 cases and controls. By measuring interindividual correlation among proximal chromatin peaks, we show that regulatory element activity is structured into 10,936 and 10,376 cis-regulatory domains in cases and controls, respectively. The schizophrenia-specific cis-regulatory domains are enriched for fetal-specific (p = 0.0014, OR = 1.52) and depleted of adult-specific regulatory activity (p = 3.04 × 10-50, OR = 0.57) and are enriched for SCZ heritability (p = 0.001). By studying the interplay among genetic variants, gene expression, and cis-regulatory domains, we ascertain that changes in coordinated regulatory activity tag alterations in gene expression levels (p = 3.43 × 10-5, OR = 1.65), unveil case-specific QTL effects, and identify regulatory machinery changes for genes affecting synaptic function and dendritic spine morphology in schizophrenia. Altogether, we show that accounting for coordinated regulatory activity provides a novel mechanistic approach to reduce the search space for unveiling genetically perturbed regulation of gene expression in schizophrenia.
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3
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Genetic Variation in CNS Myelination and Functional Brain Connectivity in Recombinant Inbred Mice. Cells 2020; 9:cells9092119. [PMID: 32961889 PMCID: PMC7564997 DOI: 10.3390/cells9092119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 01/29/2023] Open
Abstract
Myelination greatly increases the speed of action potential propagation of neurons, thereby enhancing the efficacy of inter-neuronal communication and hence, potentially, optimizing the brain’s signal processing capability. The impact of genetic variation on the extent of axonal myelination and its consequences for brain functioning remain to be determined. Here we investigated this question using a genetic reference panel (GRP) of mouse BXD recombinant inbred (RI) strains, which partly model genetic diversity as observed in human populations, and which show substantial genetic differences in a variety of behaviors, including learning, memory and anxiety. We found coherent differences in the expression of myelin genes in brain tissue of RI strains of the BXD panel, with the largest differences in the hippocampus. The parental C57BL/6J (C57) and DBA/2J (DBA) strains were on opposite ends of the expression spectrum, with C57 showing higher myelin transcript expression compared with DBA. Our experiments showed accompanying differences between C57 and DBA in myelin protein composition, total myelin content, and white matter conduction velocity. Finally, the hippocampal myelin gene expression of the BXD strains correlated significantly with behavioral traits involving anxiety and/or activity. Taken together, our data indicate that genetic variation in myelin gene expression translates to differences observed in myelination, axonal conduction speed, and possibly in anxiety/activity related behaviors.
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4
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Bagheri H, Friedman H, Siminovitch KA, Peterson AC. Transcriptional regulators of the Golli/myelin basic protein locus integrate additive and stealth activities. PLoS Genet 2020; 16:e1008752. [PMID: 32790717 PMCID: PMC7446974 DOI: 10.1371/journal.pgen.1008752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/25/2020] [Accepted: 07/01/2020] [Indexed: 11/19/2022] Open
Abstract
Myelin is composed of plasma membrane spirally wrapped around axons and compacted into dense sheaths by myelin-associated proteins. Myelin is elaborated by neuroepithelial derived oligodendrocytes in the central nervous system (CNS) and by neural crest derived Schwann cells in the peripheral nervous system (PNS). While some myelin proteins accumulate in only one lineage, myelin basic protein (Mbp) is expressed in both. Overlapping the Mbp gene is Golli, a transcriptional unit that is expressed widely both within and beyond the nervous system. A super-enhancer domain within the Golli/Mbp locus contains multiple enhancers shown previously to drive reporter construct expression specifically in oligodendrocytes or Schwann cells. In order to determine the contribution of each enhancer to the Golli/Mbp expression program, and to reveal if functional interactions occur among them, we derived mouse lines in which they were deleted, either singly or in different combinations, and relative mRNA accumulation was measured at key stages of early development and at maturity. Although super-enhancers have been shown previously to facilitate interaction among their component enhancers, the enhancers investigated here demonstrated largely additive relationships. However, enhancers demonstrating autonomous activity strictly in one lineage, when missing, were found to significantly reduce output in the other, thus revealing cryptic "stealth" activity. Further, in the absence of a key oligodendrocyte enhancer, Golli accumulation was markedly and uniformly attenuated in all cell types investigated. Our observations suggest a model in which enhancer-mediated DNA-looping and potential super-enhancer properties underlie Golli/Mbp regulatory organization.
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Affiliation(s)
- Hooman Bagheri
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Hana Friedman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Katherine A. Siminovitch
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Lunenfeld-Tanenbaum and Toronto General Hospital Research Institutes, Toronto, Ontario, Canada
| | - Alan C. Peterson
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
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5
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Sophie B, Jacob H, Jordan VJS, Yungki P, Laura FM, Yannick P. YAP and TAZ Regulate Cc2d1b and Purβ in Schwann Cells. Front Mol Neurosci 2019; 12:177. [PMID: 31379499 PMCID: PMC6650784 DOI: 10.3389/fnmol.2019.00177] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 07/04/2019] [Indexed: 12/31/2022] Open
Abstract
Schwann cells (SCs) are exquisitely sensitive to the elasticity of their environment and their differentiation and capacity to myelinate depend on the transduction of mechanical stimuli by YAP and TAZ. YAP/TAZ, in concert with other transcription factors, regulate several pathways including lipid and sterol biosynthesis as well as extracellular matrix receptor expressions such as integrins and G-proteins. Yet, the characterization of the signaling downstream YAP/TAZ in SCs is incomplete. Myelin sheath production by SC coincides with rapid up-regulation of numerous transcription factors. Here, we show that ablation of YAP/TAZ alters the expression of transcription regulators known to regulate SC myelin gene transcription and differentiation. Furthermore, we link YAP/TAZ to two DNA binding proteins, Cc2d1b and Purβ, which have no described roles in myelinating glial cells. We demonstrate that silencing of either Cc2d1b or Purβ limits the formation of myelin segments. These data provide a deeper insight into the myelin gene transcriptional network and the role of YAP/TAZ in myelinating glial cells.
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Affiliation(s)
- Belin Sophie
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY, United States
| | - Herron Jacob
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY, United States
| | - VerPlank J S Jordan
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Park Yungki
- Department of Biochemistry, Hunter James Kelly Research Institute, University at Buffalo, Buffalo, NY, United States
| | - Feltri M Laura
- Department of Biochemistry, Hunter James Kelly Research Institute, University at Buffalo, Buffalo, NY, United States.,Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Poitelon Yannick
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY, United States
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6
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Lamont H, Ille A, Amico-Ruvio SA. Identification of a novel variant of Golli myelin basic protein BG21 in the uniquely neuroprotective white-footed mouse. Neurosci Lett 2019; 701:8-13. [PMID: 30742937 DOI: 10.1016/j.neulet.2019.02.006] [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: 10/17/2018] [Revised: 01/12/2019] [Accepted: 02/05/2019] [Indexed: 11/26/2022]
Abstract
The myelin basic protein (MBP) gene is a complex gene which codes for several distinct forms of MBP. The various forms of MBP are functionally involved in the development of the nervous system, T-cell regulation, and myelination. Several neurological disorders have been linked to MBP abnormality, further demonstrating its functional significance in the nervous system. The white-footed mouse (Peromyscus leucopus) exhibits profound neuroprotective characteristics, is asymptomatic to various disease-states, and has a lifespan twice that of the house mouse (Mus musculus). We used M. musculus mouse MBP as a reference to explore MBP in P. leucopus mice. Through genetic and downstream proteomic data analysis, we identified a novel variant of the BG21 isoform of MBP in P. leucopus mice. Variation in this isoform is present at the genetic level between the two species of mice. Our results show differences within the open reading frame of the transcripts accompanied by corresponding differences in protein structure prediction. These data introduce the potential of MBP variation as one of many causal variables contributing to the unique presentation of enhanced neuroprotection and longevity in P. leucopus mice.
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Affiliation(s)
- Hannah Lamont
- D'Youville College, 320 Porter Ave, Buffalo, NY, 14201, USA.
| | - Alexander Ille
- D'Youville College, 320 Porter Ave, Buffalo, NY, 14201, USA.
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Maheras KJ, Peppi M, Ghoddoussi F, Galloway MP, Perrine SA, Gow A. Absence of Claudin 11 in CNS Myelin Perturbs Behavior and Neurotransmitter Levels in Mice. Sci Rep 2018; 8:3798. [PMID: 29491447 PMCID: PMC5830493 DOI: 10.1038/s41598-018-22047-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/15/2018] [Indexed: 12/20/2022] Open
Abstract
Neuronal origins of behavioral disorders have been examined for decades to construct frameworks for understanding psychiatric diseases and developing useful therapeutic strategies with clinical application. Despite abundant anecdotal evidence for white matter etiologies, including altered tractography in neuroimaging and diminished oligodendrocyte-specific gene expression in autopsy studies, mechanistic data demonstrating that dysfunctional myelin sheaths can cause behavioral deficits and perturb neurotransmitter biochemistry have not been forthcoming. At least in part, this impasse stems from difficulties in identifying model systems free of degenerative pathology to enable unambiguous assessment of neuron biology and behavior in a background of myelin dysfunction. Herein we examine myelin mutant mice lacking expression of the Claudin11 gene in oligodendrocytes and characterize two behavioral endophenotypes: perturbed auditory processing and reduced anxiety/avoidance. Importantly, these behaviors are associated with increased transmission time along myelinated fibers as well as glutamate and GABA neurotransmitter imbalances in auditory brainstem and amygdala, in the absence of neurodegeneration. Thus, our findings broaden the etiology of neuropsychiatric disease to include dysfunctional myelin, and identify a preclinical model for the development of novel disease-modifying therapies.
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Affiliation(s)
- Kathleen J Maheras
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Marcello Peppi
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Farhad Ghoddoussi
- Department of Anesthesiology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Matthew P Galloway
- Department of Anesthesiology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Shane A Perrine
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Alexander Gow
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
- Carman and Ann Adams Dept of Pediatrics, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
- Dept of Neurology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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8
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Davidson NL, Yu F, Kijpaisalratana N, Le TQ, Beer LA, Radomski KL, Armstrong RC. Leukemia/lymphoma-related factor (LRF) exhibits stage- and context-dependent transcriptional controls in the oligodendrocyte lineage and modulates remyelination. J Neurosci Res 2017; 95:2391-2408. [PMID: 28556945 PMCID: PMC5655903 DOI: 10.1002/jnr.24083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 02/03/2023]
Abstract
Leukemia/lymphoma‐related factor (LRF), a zinc‐finger transcription factor encoded by Zbtb7a, is a protooncogene that regulates differentiation in diverse cell lineages, and in the CNS, its function is relatively unexplored. This study is the first to examine the role of LRF in CNS pathology. We first examined LRF expression in a murine viral model of spinal cord demyelination with clinically relevant lesion characteristics. LRF was rarely expressed in oligodendrocyte progenitors (OP) yet, was detected in nuclei of the majority of oligodendrocytes in healthy adult CNS and during remyelination. Plp/CreERT:Zbtb7afl/fl mice were then used with cuprizone demyelination to determine the effect of LRF knockdown on oligodendrocyte repopulation and remyelination. Cuprizone was given for 6 weeks to demyelinate the corpus callosum. Tamoxifen was administered at 4, 5, or 6 weeks after the start of cuprizone. Tamoxifen‐induced knockdown of LRF impaired remyelination during 3 or 6‐week recovery periods after cuprizone. LRF knockdown earlier within the oligodendrocyte lineage using NG2CreERT:Zbtb7afl/fl mice reduced myelination after 6 weeks of cuprizone. LRF knockdown from either the Plp/CreERT line or the NG2CreERT line did not significantly change OP or oligodendrocyte populations. In vitro promoter assays demonstrated the potential for LRF to regulate transcription of myelin‐related genes and the notch target Hes5, which has been implicated in control of myelin formation and repair. In summary, in the oligodendrocyte lineage, LRF is expressed mainly in oligodendrocytes but is not required for oligodendrocyte repopulation of demyelinated lesions. Furthermore, LRF can modulate the extent of remyelination, potentially by contributing to interactions regulating transcription.
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Affiliation(s)
| | - Fengshan Yu
- Department of Anatomy, Physiology, and Genetics, Uniformed Services, University of the Health Sciences, Bethesda, Maryland, USA
| | | | - Tuan Q Le
- Department of Anatomy, Physiology, and Genetics, Uniformed Services, University of the Health Sciences, Bethesda, Maryland, USA
| | - Laurel A Beer
- Department of Anatomy, Physiology, and Genetics, Uniformed Services, University of the Health Sciences, Bethesda, Maryland, USA
| | - Kryslaine L Radomski
- Department of Anatomy, Physiology, and Genetics, Uniformed Services, University of the Health Sciences, Bethesda, Maryland, USA
| | - Regina C Armstrong
- Program in Neuroscience, Bethesda, Maryland, USA.,Department of Anatomy, Physiology, and Genetics, Uniformed Services, University of the Health Sciences, Bethesda, Maryland, USA
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Qi B, Hu L, Zhu L, Shang L, Sheng L, Wang X, Liu N, Wen N, Yu X, Wang Q, Yang Y. Metformin Attenuates Cognitive Impairments in Hypoxia–Ischemia Neonatal Rats via Improving Remyelination. Cell Mol Neurobiol 2016; 37:1269-1278. [DOI: 10.1007/s10571-016-0459-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/22/2016] [Indexed: 02/06/2023]
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10
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Aaker JD, Elbaz B, Wu Y, Looney TJ, Zhang L, Lahn BT, Popko B. Transcriptional Fingerprint of Hypomyelination in Zfp191null and Shiverer (Mbpshi) Mice. ASN Neuro 2016; 8:8/5/1759091416670749. [PMID: 27683878 PMCID: PMC5046175 DOI: 10.1177/1759091416670749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/22/2016] [Indexed: 12/20/2022] Open
Abstract
The transcriptional program that controls oligodendrocyte maturation and central nervous system (CNS) myelination has not been fully characterized. In this study, we use high-throughput RNA sequencing to analyze how the loss of a key transcription factor, zinc finger protein 191 (ZFP191), results in oligodendrocyte development abnormalities and CNS hypomyelination. Using a previously described mutant mouse that is deficient in ZFP191 protein expression (Zfp191null), we demonstrate that key transcripts are reduced in the whole brain as well as within oligodendrocyte lineage cells cultured in vitro. To determine whether the loss of myelin seen in Zfp191null mice contributes indirectly to these perturbations, we also examined the transcriptome of a well-characterized mouse model of hypomyelination, in which the myelin structural protein myelin basic protein (MBP) is deficient. Interestingly, Mbpshi (shiverer) mice had far fewer transcripts perturbed with the loss of myelin alone. This study demonstrates that the loss of ZFP191 disrupts expression of genes involved in oligodendrocyte maturation and myelination, largely independent from the loss of myelin. Nevertheless, hypomyelination in both mouse mutants results in the perturbation of lipid synthesis pathways, suggesting that oligodendrocytes have a feedback system that allows them to regulate myelin lipid synthesis depending on their myelinating state. The data presented are of potential clinical relevance as the human orthologs of the Zfp191 and MBP genes reside on a region of Chromosome 18 that is deleted in childhood leukodystrophies.
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Affiliation(s)
- Joshua D Aaker
- Department of Neurology, The University of Chicago Center for Peripheral Neuropathy, The University of Chicago, IL, USA
| | - Benayahu Elbaz
- Department of Neurology, The University of Chicago Center for Peripheral Neuropathy, The University of Chicago, IL, USA
| | - Yuwen Wu
- Department of Neurology, The University of Chicago Center for Peripheral Neuropathy, The University of Chicago, IL, USA
| | - Timothy J Looney
- Department of Human Genetics, The University of Chicago, IL, USA
| | - Li Zhang
- Department of Human Genetics, The University of Chicago, IL, USA
| | - Bruce T Lahn
- Department of Human Genetics, The University of Chicago, IL, USA
| | - Brian Popko
- Department of Neurology, The University of Chicago Center for Peripheral Neuropathy, The University of Chicago, IL, USA
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11
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Porcu G, Serone E, De Nardis V, Di Giandomenico D, Lucisano G, Scardapane M, Poma A, Ragnini-Wilson A. Clobetasol and Halcinonide Act as Smoothened Agonists to Promote Myelin Gene Expression and RxRγ Receptor Activation. PLoS One 2015; 10:e0144550. [PMID: 26658258 PMCID: PMC4689554 DOI: 10.1371/journal.pone.0144550] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 11/19/2015] [Indexed: 12/14/2022] Open
Abstract
One of the causes of permanent disability in chronic multiple sclerosis patients is the inability of oligodendrocyte progenitor cells (OPCs) to terminate their maturation program at lesions. To identify key regulators of myelin gene expression acting at the last stages of OPC maturation we developed a drug repositioning strategy based on the mouse immortalized oligodendrocyte (OL) cell line Oli-neu brought to the premyelination stage by stably expressing a key factor regulating the last stages of OL maturation. The Prestwick Chemical Library® of 1,200 FDA-approved compound(s) was repositioned at three dosages based on the induction of Myelin Basic Protein (MBP) expression. Drug hits were further validated using dosage-dependent reproducibility tests and biochemical assays. The glucocorticoid class of compounds was the most highly represented and we found that they can be divided in three groups according to their efficacy on MBP up-regulation. Since target identification is crucial before bringing compounds to the clinic, we searched for common targets of the primary screen hits based on their known chemical-target interactomes, and the pathways predicted by top ranking compounds were validated using specific inhibitors. Two of the top ranking compounds, Halcinonide and Clobetasol, act as Smoothened (Smo) agonists to up-regulate myelin gene expression in the Oli-neuM cell line. Further, RxRγ activation is required for MBP expression upon Halcinonide and Clobetasol treatment. These data indicate Clobetasol and Halcinonide as potential promyelinating drugs and also provide a mechanistic understanding of their mode of action in the pathway leading to myelination in OPCs. Furthermore, our classification of glucocorticoids with respect to MBP expression provides important novel insights into their effects in the CNS and a rational criteria for their choice in combinatorial therapies in de-myelinating diseases.
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Affiliation(s)
- Giampiero Porcu
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
- Department of Translational Pharmacology, Fondazione Mario Negri Sud, S. Maria Imbaro (CH), Italy
| | - Eliseo Serone
- Department of Translational Pharmacology, Fondazione Mario Negri Sud, S. Maria Imbaro (CH), Italy
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L’Aquila, Italy
| | - Velia De Nardis
- Department of Translational Pharmacology, Fondazione Mario Negri Sud, S. Maria Imbaro (CH), Italy
| | - Daniele Di Giandomenico
- Department of Translational Pharmacology, Fondazione Mario Negri Sud, S. Maria Imbaro (CH), Italy
| | - Giuseppe Lucisano
- Department of Translational Pharmacology, Fondazione Mario Negri Sud, S. Maria Imbaro (CH), Italy
- Center for Outcomes Research and Clinical Epidemiology, Pescara, Italy
- Dipartimento di Scienze Mediche di Base, Neuroscienze ed Organi di Senso, Università di Bari Aldo Moro, Bari, Italy
| | - Marco Scardapane
- Department of Translational Pharmacology, Fondazione Mario Negri Sud, S. Maria Imbaro (CH), Italy
- Center for Outcomes Research and Clinical Epidemiology, Pescara, Italy
| | - Anna Poma
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L’Aquila, Italy
| | - Antonella Ragnini-Wilson
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
- Department of Translational Pharmacology, Fondazione Mario Negri Sud, S. Maria Imbaro (CH), Italy
- * E-mail:
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12
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Eising E, de Leeuw C, Min JL, Anttila V, Verheijen MHG, Terwindt GM, Dichgans M, Freilinger T, Kubisch C, Ferrari MD, Smit AB, de Vries B, Palotie A, van den Maagdenberg AMJM, Posthuma D. Involvement of astrocyte and oligodendrocyte gene sets in migraine. Cephalalgia 2015; 36:640-7. [DOI: 10.1177/0333102415618614] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 10/26/2015] [Indexed: 01/13/2023]
Abstract
Background Migraine is a common episodic brain disorder characterized by recurrent attacks of severe unilateral headache and additional neurological symptoms. Two main migraine types can be distinguished based on the presence of aura symptoms that can accompany the headache: migraine with aura and migraine without aura. Multiple genetic and environmental factors confer disease susceptibility. Recent genome-wide association studies (GWAS) indicate that migraine susceptibility genes are involved in various pathways, including neurotransmission, which have already been implicated in genetic studies of monogenic familial hemiplegic migraine, a subtype of migraine with aura. Methods To further explore the genetic background of migraine, we performed a gene set analysis of migraine GWAS data of 4954 clinic-based patients with migraine, as well as 13,390 controls. Curated sets of synaptic genes and sets of genes predominantly expressed in three glial cell types (astrocytes, microglia and oligodendrocytes) were investigated. Discussion Our results show that gene sets containing astrocyte- and oligodendrocyte-related genes are associated with migraine, which is especially true for gene sets involved in protein modification and signal transduction. Observed differences between migraine with aura and migraine without aura indicate that both migraine types, at least in part, seem to have a different genetic background.
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Affiliation(s)
- Else Eising
- Department of Human Genetics, Leiden University Medical Centre, The Netherlands
| | - Christiaan de Leeuw
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
- Institute for Computing and Information Sciences, Radboud University, The Netherlands
| | - Josine L Min
- MRC Integrative Epidemiology Unit, University of Bristol, UK
| | - Verneri Anttila
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, USA
| | - Mark HG Verheijen
- Department of Molecular and Cellular Neurobiology, Centre for Neurogenomics and Cognitive Research, Neuroscience, Campus Amsterdam, VU University, The Netherlands
| | - Gisela M Terwindt
- Department of Neurology, Leiden University Medical Centre, The Netherlands
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität, Germany
- Munich Cluster for Systems Neurology (SyNergy), Germany
| | - Tobias Freilinger
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität, Germany
- Department of Neurology and Epileptology and Hertie-Institute for Clinical Brain Research, University of Tübingen, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Germany
| | - Michel D Ferrari
- Department of Neurology, Leiden University Medical Centre, The Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Centre for Neurogenomics and Cognitive Research, Neuroscience, Campus Amsterdam, VU University, The Netherlands
| | - Boukje de Vries
- Department of Human Genetics, Leiden University Medical Centre, The Netherlands
| | - Aarno Palotie
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, USA
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, UK
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
| | - Arn MJM van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Centre, The Netherlands
- Department of Neurology, Leiden University Medical Centre, The Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
- Department of Clinical Genetics, VU University Medical Centre, The Netherlands
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13
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Lopez-Anido C, Sun G, Koenning M, Srinivasan R, Hung HA, Emery B, Keles S, Svaren J. Differential Sox10 genomic occupancy in myelinating glia. Glia 2015; 63:1897-1914. [PMID: 25974668 PMCID: PMC4644515 DOI: 10.1002/glia.22855] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/22/2015] [Indexed: 11/11/2022]
Abstract
Myelin is formed by specialized myelinating glia: oligodendrocytes and Schwann cells in the central and peripheral nervous systems, respectively. While there are distinct developmental aspects and regulatory pathways in these two cell types, myelination in both systems requires the transcriptional activator Sox10. Sox10 interacts with cell type-specific transcription factors at some loci to induce myelin gene expression, but it is largely unknown how Sox10 transcriptional networks globally compare between oligodendrocytes and Schwann cells. We used in vivo ChIP-Seq analysis of spinal cord and peripheral nerve (sciatic nerve) to identify unique and shared Sox10 binding sites and assess their correlation with active enhancers and transcriptional profiles in oligodendrocytes and Schwann cells. Sox10 binding sites overlap with active enhancers and critical cell type-specific regulators of myelination, such as Olig2 and Myrf in oligodendrocytes, and Egr2/Krox20 in Schwann cells. Sox10 sites also associate with genes critical for myelination in both oligodendrocytes and Schwann cells and are found within super-enhancers previously defined in brain. In Schwann cells, Sox10 sites contain binding motifs of putative partners in the Sp/Klf, Tead, and nuclear receptor protein families. Specifically, siRNA analysis of nuclear receptors Nr2f1 and Nr2f2 revealed downregulation of myelin genes Mbp and Ndrg1 in primary Schwann cells. Our analysis highlights different mechanisms that establish cell type-specific genomic occupancy of Sox10, which reflects the unique characteristics of oligodendrocyte and Schwann cell differentiation. GLIA 2015;63:1897-1914.
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Affiliation(s)
- Camila Lopez-Anido
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Comparative Biomedical Sciences Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Guannan Sun
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Matthias Koenning
- Department of Anatomy and Neuroscience and the Centre for Neuroscience Research, University of Melbourne, Melbourne, Australia
| | - Rajini Srinivasan
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Holly A. Hung
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ben Emery
- Department of Anatomy and Neuroscience and the Centre for Neuroscience Research, University of Melbourne, Melbourne, Australia
| | - Sunduz Keles
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - John Svaren
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53705, USA
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14
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Dionne N, Dib S, Finsen B, Denarier E, Kuhlmann T, Drouin R, Kokoeva M, Hudson TJ, Siminovitch K, Friedman HC, Peterson AC. Functional organization of anMbpenhancer exposes striking transcriptional regulatory diversity within myelinating glia. Glia 2015; 64:175-94. [DOI: 10.1002/glia.22923] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/04/2015] [Accepted: 09/09/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Nancy Dionne
- Laboratory of Developmental Biology; Ludmer Research and Training Building, McGill University; Montreal Quebec Canada
| | - Samar Dib
- Laboratory of Developmental Biology; Ludmer Research and Training Building, McGill University; Montreal Quebec Canada
| | - Bente Finsen
- Department of Neurobiology Research; Institute of Molecular Medicine, University of Southern Denmark; Odense Denmark
| | - Eric Denarier
- Institut National De La Santé Et De La Recherche Médicale, U836-GIN iRTSV-GPC; Site Santé La Tronche, BP170 Grenoble Cedex 9 France
| | - Tanja Kuhlmann
- Institute of Neuropathology, University Hospital, Münster; Pottkamp 2 Münster Germany
| | - Régen Drouin
- Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences; Université De Sherbrooke; Sherbrooke Quebec Canada
| | - Maia Kokoeva
- Department of Medicine; McGill University/MUHC Research Institute; Montreal Quebec Canada
| | - Thomas J. Hudson
- Ontario Institute for Cancer Research, MaRS Centre; South Tower Toronto Ontario Canada
| | - Kathy Siminovitch
- Department of Medicine; University of Toronto, Samuel Lunenfeld and Toronto General Research Institutes; Toronto Ontario Canada
- Department of Immunology and Molecular Genetics; University of Toronto; Toronto Ontario Canada
| | - Hana C Friedman
- Laboratory of Developmental Biology; Ludmer Research and Training Building, McGill University; Montreal Quebec Canada
| | - Alan C. Peterson
- Laboratory of Developmental Biology; Ludmer Research and Training Building, McGill University; Montreal Quebec Canada
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15
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Hung HA, Sun G, Keles S, Svaren J. Dynamic regulation of Schwann cell enhancers after peripheral nerve injury. J Biol Chem 2015; 290:6937-50. [PMID: 25614629 PMCID: PMC4358118 DOI: 10.1074/jbc.m114.622878] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/31/2014] [Indexed: 12/20/2022] Open
Abstract
Myelination of the peripheral nervous system is required for axonal function and long term stability. After peripheral nerve injury, Schwann cells transition from axon myelination to a demyelinated state that supports neuronal survival and ultimately remyelination of axons. Reprogramming of gene expression patterns during development and injury responses is shaped by the actions of distal regulatory elements that integrate the actions of multiple transcription factors. We used ChIP-seq to measure changes in histone H3K27 acetylation, a mark of active enhancers, to identify enhancers in myelinating rat peripheral nerve and their dynamics after demyelinating nerve injury. Analysis of injury-induced enhancers identified enriched motifs for c-Jun, a transcription factor required for Schwann cells to support nerve regeneration. We identify a c-Jun-bound enhancer in the gene for Runx2, a transcription factor induced after nerve injury, and we show that Runx2 is required for activation of other induced genes. In contrast, enhancers that lose H3K27ac after nerve injury are enriched for binding sites of the Sox10 and early growth response 2 (Egr2/Krox20) transcription factors, which are critical determinants of Schwann cell differentiation. Egr2 expression is lost after nerve injury, and many Egr2-binding sites lose H3K27ac after nerve injury. However, the majority of Egr2-bound enhancers retain H3K27ac, indicating that other transcription factors maintain active enhancer status after nerve injury. The global epigenomic changes in H3K27ac deposition pinpoint dynamic changes in enhancers that mediate the effects of transcription factors that control Schwann cell myelination and peripheral nervous system responses to nerve injury.
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Affiliation(s)
- Holly A Hung
- From the Waisman Center, Cellular and Molecular Pathology Graduate Program, and
| | - Guannan Sun
- Departments of Biostatistics and Medical Informatics and
| | - Sunduz Keles
- Departments of Biostatistics and Medical Informatics and
| | - John Svaren
- From the Waisman Center, Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin 53705
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16
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Goudriaan A, de Leeuw C, Ripke S, Hultman CM, Sklar P, Sullivan PF, Smit AB, Posthuma D, Verheijen MHG. Specific glial functions contribute to schizophrenia susceptibility. Schizophr Bull 2014; 40:925-35. [PMID: 23956119 PMCID: PMC4059439 DOI: 10.1093/schbul/sbt109] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Schizophrenia is a highly polygenic brain disorder. The main hypothesis for disease etiology in schizophrenia primarily focuses on the role of dysfunctional synaptic transmission. Previous studies have therefore directed their investigations toward the role of neuronal dysfunction. However, recent studies have shown that apart from neurons, glial cells also play a major role in synaptic transmission. Therefore, we investigated the potential causal involvement of the 3 principle glial cell lineages in risk to schizophrenia. We performed a functional gene set analysis to test for the combined effects of genetic variants in glial type-specific genes for association with schizophrenia. We used genome-wide association data from the largest schizophrenia sample to date, including 13 689 cases and 18 226 healthy controls. Our results show that astrocyte and oligodendrocyte gene sets, but not microglia gene sets, are associated with an increased risk for schizophrenia. The astrocyte and oligodendrocyte findings are related to astrocyte signaling at the synapse, myelin membrane integrity, glial development, and epigenetic control. Together, these results show that genetic alterations underlying specific glial cell type functions increase susceptibility to schizophrenia and provide evidence that the neuronal hypothesis of schizophrenia should be extended to include the role of glia.
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Affiliation(s)
- Andrea Goudriaan
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, the Netherlands;
| | - Christiaan de Leeuw
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, the Netherlands; Institute for Computing and Information Sciences, Radboud University, Nijmegen, the Netherlands
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Pamela Sklar
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Center for Psychiatric Genomics, Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, the Netherlands
| | - Danielle Posthuma
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, the Netherlands;
| | - Mark H G Verheijen
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, the Netherlands
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17
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Qu X, Qi D, Dong F, Wang B, Guo R, Luo M, Yao R. Quercetin improves hypoxia-ischemia induced cognitive deficits via promoting remyelination in neonatal rat. Brain Res 2014; 1553:31-40. [PMID: 24480472 DOI: 10.1016/j.brainres.2014.01.035] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/07/2014] [Accepted: 01/20/2014] [Indexed: 12/26/2022]
Abstract
Myelination failure is associated with perinatal cerebral hypoxia-ischemia (PHI) induced brain injury in premature infants. How to efficiently promote remyelination is crucial for improving cognitive deficits caused by brain injury. Here, we demonstrated that quercetin (Que), a kind of flavonoids, significantly improved cognitive deficits and the behavior of PHI-rat in Morris water maze and open field tasks. After administration of Que to PHI-rat, the number of neogenetic Olig2⁺ oligodendrocyte progenitor cells (OPCs) was evidently increased in the subventricular zone. Additionally, in corpus callosum (CC), the expression of MBP (myelin basic protein) was increased, and the myelin sheaths reached normal level at 30 days with more compact while less damaged myelin sheaths and more mature oligodendrocytes (OLs) repopulating the CC compared with PHI groups. In a word, our findings indicated that Que could remarkably improve both cognition performance and myelination in the context of PHI-induced brain injury by promoting the proliferation of OPCs and strengthening survival of OLs in vivo.
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Affiliation(s)
- Xuebin Qu
- Department of Neurobiology, Xuzhou Medical College, Xuzhou 221009, Jiangsu, PR China
| | - Dashi Qi
- Department of Neurobiology, Xuzhou Medical College, Xuzhou 221009, Jiangsu, PR China
| | - Fuxing Dong
- Department of Neurobiology, Xuzhou Medical College, Xuzhou 221009, Jiangsu, PR China
| | - Bei Wang
- Department of Neurobiology, Xuzhou Medical College, Xuzhou 221009, Jiangsu, PR China
| | - Rui Guo
- Department of Neurobiology, Xuzhou Medical College, Xuzhou 221009, Jiangsu, PR China
| | - Mengjiao Luo
- Department of Neurobiology, Xuzhou Medical College, Xuzhou 221009, Jiangsu, PR China
| | - Ruiqin Yao
- Department of Neurobiology, Xuzhou Medical College, Xuzhou 221009, Jiangsu, PR China.
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18
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Laulederkind SJF, Hayman GT, Wang SJ, Smith JR, Lowry TF, Nigam R, Petri V, de Pons J, Dwinell MR, Shimoyama M, Munzenmaier DH, Worthey EA, Jacob HJ. The Rat Genome Database 2013--data, tools and users. Brief Bioinform 2013; 14:520-6. [PMID: 23434633 PMCID: PMC3713714 DOI: 10.1093/bib/bbt007] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The Rat Genome Database (RGD) was started >10 years ago to provide a core genomic resource for rat researchers. Currently, RGD combines genetic, genomic, pathway, phenotype and strain information with a focus on disease. RGD users are provided with access to structured and curated data from the molecular level through the organismal level. Those users access RGD from all over the world. End users are not only rat researchers but also researchers working with mouse and human data. Translational research is supported by RGD’s comparative genetics/genomics data in disease portals, in GBrowse, in VCMap and on gene report pages. The impact of RGD also goes beyond the traditional biomedical researcher, as the influence of RGD reaches bioinformaticians, tool developers and curators. Import of RGD data into other publicly available databases expands the influence of RGD to a larger set of end users than those who avail themselves of the RGD website. The value of RGD continues to grow as more types of data and more tools are added, while reaching more types of end users.
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Affiliation(s)
- Stanley J F Laulederkind
- Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA.
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19
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Extensive transcriptional regulation of chromatin modifiers during human neurodevelopment. PLoS One 2012; 7:e36708. [PMID: 22590590 PMCID: PMC3348879 DOI: 10.1371/journal.pone.0036708] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 04/05/2012] [Indexed: 11/19/2022] Open
Abstract
Epigenetic changes, including histone modifications or chromatin remodeling are regulated by a large number of human genes. We developed a strategy to study the coordinate regulation of such genes, and to compare different cell populations or tissues. A set of 150 genes, comprising different classes of epigenetic modifiers was compiled. This new tool was used initially to characterize changes during the differentiation of human embryonic stem cells (hESC) to central nervous system neuroectoderm progenitors (NEP). qPCR analysis showed that more than 60% of the examined transcripts were regulated, and >10% of them had a >5-fold increased expression. For comparison, we differentiated hESC to neural crest progenitors (NCP), a distinct peripheral nervous system progenitor population. Some epigenetic modifiers were regulated into the same direction in NEP and NCP, but also distinct differences were observed. For instance, the remodeling ATPase SMARCA2 was up-regulated >30-fold in NCP, while it remained unchanged in NEP; up-regulation of the ATP-dependent chromatin remodeler CHD7 was increased in NEP, while it was down-regulated in NCP. To compare the neural precursor profiles with those of mature neurons, we analyzed the epigenetic modifiers in human cortical tissue. This resulted in the identification of 30 regulations shared between all cell types, such as the histone methyltransferase SETD7. We also identified new markers for post-mitotic neurons, like the arginine methyl transferase PRMT8 and the methyl transferase EZH1. Our findings suggest a hitherto unexpected extent of regulation, and a cell type-dependent specificity of epigenetic modifiers in neurodifferentiation.
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