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Zhang Y, Yu Z, Wong KC, Li X. Unraveling Spatial Domain Characterization in Spatially Resolved Transcriptomics with Robust Graph Contrastive Clustering. Bioinformatics 2024; 40:btae451. [PMID: 39012523 PMCID: PMC11272174 DOI: 10.1093/bioinformatics/btae451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 06/12/2024] [Accepted: 07/12/2024] [Indexed: 07/17/2024] Open
Abstract
MOTIVATION Spatial transcriptomics can quantify gene expression and its spatial distribution in tissues, thus revealing molecular mechanisms of cellular interactions underlying tissue heterogeneity, tissue regeneration, and spatially localized disease mechanisms. However, existing spatial clustering methods often fail to exploit the full potential of spatial information, resulting in inaccurate identification of spatial domains. RESULTS In this paper, we develop a deep graph contrastive clustering framework, stDGCC, that accurately uncovers underlying spatial domains via explicitly modeling spatial information and gene expression profiles from spatial transcriptomics data. The stDGCC framework proposes a spatially informed graph node embedding model to preserve the topological information of spots and to learn the informative and discriminative characterization of spatial transcriptomics data through self-supervised contrastive learning. By simultaneously optimizing the contrastive learning loss, reconstruction loss, and Kullback-Leibler (KL) divergence loss, stDGCC achieves joint optimization of feature learning and topology structure preservation in an end-to-end manner. We validate the effectiveness of stDGCC on various spatial transcriptomics datasets acquired from different platforms, each with varying spatial resolutions. Our extensive experiments demonstrate the superiority of stDGCC over various state-of-the-art clustering methods in accurately identifying cellular-level biological structures. AVAILABILITY Code and data are available from https://github.com/TimE9527/stDGCC and https://figshare.com/projects/stDGCC/186525. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yingxi Zhang
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
| | - Zhuohan Yu
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, Hong Kong SAR
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
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2
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Brocato ER, Easter R, Morgan A, Kakani M, Lee G, Wolstenholme JT. Adolescent binge ethanol impacts H3K9me3-occupancy at synaptic genes and the regulation of oligodendrocyte development. Front Mol Neurosci 2024; 17:1389100. [PMID: 38840776 PMCID: PMC11150558 DOI: 10.3389/fnmol.2024.1389100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/06/2024] [Indexed: 06/07/2024] Open
Abstract
Introduction Binge drinking in adolescence can disrupt myelination and cause brain structural changes that persist into adulthood. Alcohol consumption at a younger age increases the susceptibility of these changes. Animal models to understand ethanol's actions on myelin and white matter show that adolescent binge ethanol can alter the developmental trajectory of oligodendrocytes, myelin structure, and myelin fiber density. Oligodendrocyte differentiation is epigenetically regulated by H3K9 trimethylation (H3K9me3). Prior studies have shown that adolescent binge ethanol dysregulates H3K9 methylation and decreases H3K9-related gene expression in the PFC. Methods Here, we assessed ethanol-induced changes to H3K9me3 occupancy at genomic loci in the developing adolescent PFC. We further assessed ethanol-induced changes at the transcription level with qPCR time course approaches in oligodendrocyte-enriched cells to assess changes in oligodendrocyte progenitor and oligodendrocytes specifically. Results Adolescent binge ethanol altered H3K9me3 regulation of synaptic-related genes and genes specific for glutamate and potassium channels in a sex-specific manner. In PFC tissue, we found an early change in gene expression in transcription factors associated with oligodendrocyte differentiation that may lead to the later significant decrease in myelin-related gene expression. This effect appeared stronger in males. Conclusion Further exploration in oligodendrocyte cell enrichment time course and dose response studies could suggest lasting dysregulation of oligodendrocyte maturation at the transcriptional level. Overall, these studies suggest that binge ethanol may impede oligodendrocyte differentiation required for ongoing myelin development in the PFC by altering H3K9me3 occupancy at synaptic-related genes. We identify potential genes that may be contributing to adolescent binge ethanol-related myelin loss.
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Affiliation(s)
- Emily R. Brocato
- Pharmacology and Toxicology Department, Virginia Commonwealth University, Richmond, VA, United States
| | - Rachel Easter
- Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Alanna Morgan
- Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Meenakshi Kakani
- Pharmacology and Toxicology Department, Virginia Commonwealth University, Richmond, VA, United States
| | - Grace Lee
- Pharmacology and Toxicology Department, Virginia Commonwealth University, Richmond, VA, United States
| | - Jennifer T. Wolstenholme
- Pharmacology and Toxicology Department, Virginia Commonwealth University, Richmond, VA, United States
- Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States
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Morrissey ZD, Gao J, Shetti A, Li W, Zhan L, Li W, Fortel I, Saido T, Saito T, Ajilore O, Cologna SM, Lazarov O, Leow AD. Temporal Alterations in White Matter in An App Knock-In Mouse Model of Alzheimer's Disease. eNeuro 2024; 11:ENEURO.0496-23.2024. [PMID: 38290851 PMCID: PMC10897532 DOI: 10.1523/eneuro.0496-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/05/2024] [Accepted: 01/17/2024] [Indexed: 02/01/2024] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia and results in neurodegeneration and cognitive impairment. White matter (WM) is affected in AD and has implications for neural circuitry and cognitive function. The trajectory of these changes across age, however, is still not well understood, especially at earlier stages in life. To address this, we used the AppNL-G-F/NL-G-F knock-in (APPKI) mouse model that harbors a single copy knock-in of the human amyloid precursor protein (APP) gene with three familial AD mutations. We performed in vivo diffusion tensor imaging (DTI) to study how the structural properties of the brain change across age in the context of AD. In late age APPKI mice, we observed reduced fractional anisotropy (FA), a proxy of WM integrity, in multiple brain regions, including the hippocampus, anterior commissure (AC), neocortex, and hypothalamus. At the cellular level, we observed greater numbers of oligodendrocytes in middle age (prior to observations in DTI) in both the AC, a major interhemispheric WM tract, and the hippocampus, which is involved in memory and heavily affected in AD, prior to observations in DTI. Proteomics analysis of the hippocampus also revealed altered expression of oligodendrocyte-related proteins with age and in APPKI mice. Together, these results help to improve our understanding of the development of AD pathology with age, and imply that middle age may be an important temporal window for potential therapeutic intervention.
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Affiliation(s)
- Zachery D Morrissey
- Graduate Program in Neuroscience, University of Illinois Chicago, Chicago, Illinois 60612
- Department of Psychiatry, University of Illinois Chicago, Chicago, Illinois 60612
- Department of Anatomy & Cell Biology, University of Illinois Chicago, Chicago, Illinois 60612
| | - Jin Gao
- Department of Electrical & Computer Engineering, University of Illinois Chicago, Chicago, Illinois 60607
- Preclinical Imaging Core, University of Illinois Chicago, Chicago, Illinois 60612
| | - Aashutosh Shetti
- Department of Anatomy & Cell Biology, University of Illinois Chicago, Chicago, Illinois 60612
| | - Wenping Li
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607
| | - Liang Zhan
- Department of Electrical & Computer Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
| | - Weiguo Li
- Preclinical Imaging Core, University of Illinois Chicago, Chicago, Illinois 60612
- Department of Bioengineering, University of Illinois Chicago, Chicago, Illinois 60607
- Department of Radiology, Northwestern University, Chicago, Illinois 60611
| | - Igor Fortel
- Department of Bioengineering, University of Illinois Chicago, Chicago, Illinois 60607
| | - Takaomi Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako 351-0198, Japan
| | - Takashi Saito
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University, Nagoya 467-8601, Japan
| | - Olusola Ajilore
- Department of Psychiatry, University of Illinois Chicago, Chicago, Illinois 60612
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607
| | - Orly Lazarov
- Department of Anatomy & Cell Biology, University of Illinois Chicago, Chicago, Illinois 60612
| | - Alex D Leow
- Department of Psychiatry, University of Illinois Chicago, Chicago, Illinois 60612
- Department of Bioengineering, University of Illinois Chicago, Chicago, Illinois 60607
- Department of Computer Science, University of Illinois Chicago, Chicago, Illinois 60607
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Fodder K, de Silva R, Warner TT, Bettencourt C. The contribution of DNA methylation to the (dys)function of oligodendroglia in neurodegeneration. Acta Neuropathol Commun 2023; 11:106. [PMID: 37386505 PMCID: PMC10311741 DOI: 10.1186/s40478-023-01607-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023] Open
Abstract
Neurodegenerative diseases encompass a heterogeneous group of conditions characterised by the progressive degeneration of the structure and function of the central or peripheral nervous systems. The pathogenic mechanisms underlying these diseases are not fully understood. However, a central feature consists of regional aggregation of proteins in the brain, such as the accumulation of β-amyloid plaques in Alzheimer's disease (AD), inclusions of hyperphosphorylated microtubule-binding tau in AD and other tauopathies, or inclusions containing α-synuclein in Parkinson's disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). Various pathogenic mechanisms are thought to contribute to disease, and an increasing number of studies implicate dysfunction of oligodendrocytes (the myelin producing cells of the central nervous system) and myelin loss. Aberrant DNA methylation, the most widely studied epigenetic modification, has been associated with many neurodegenerative diseases, including AD, PD, DLB and MSA, and recent findings highlight aberrant DNA methylation in oligodendrocyte/myelin-related genes. Here we briefly review the evidence showing that changes to oligodendrocytes and myelin are key in neurodegeneration, and explore the relevance of DNA methylation in oligodendrocyte (dys)function. As DNA methylation is reversible, elucidating its involvement in pathogenic mechanisms of neurodegenerative diseases and in dysfunction of specific cell-types such as oligodendrocytes may bring opportunities for therapeutic interventions for these diseases.
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Affiliation(s)
- Katherine Fodder
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Rohan de Silva
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Thomas T Warner
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Conceição Bettencourt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.
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Nataf S, Guillen M, Pays L. Irrespective of Plaque Activity, Multiple Sclerosis Brain Periplaques Exhibit Alterations of Myelin Genes and a TGF-Beta Signature. Int J Mol Sci 2022; 23:ijms232314993. [PMID: 36499320 PMCID: PMC9738407 DOI: 10.3390/ijms232314993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
In a substantial share of patients suffering from multiple sclerosis (MS), neurological functions slowly deteriorate despite a lack of radiological activity. Such a silent progression, observed in either relapsing-remitting or progressive forms of MS, is driven by mechanisms that appear to be independent from plaque activity. In this context, we previously reported that, in the spinal cord of MS patients, periplaques cover large surfaces of partial demyelination characterized notably by a transforming growth factor beta (TGF-beta) molecular signature and a decreased expression of the oligodendrocyte gene NDRG1 (N-Myc downstream regulated 1). In the present work, we re-assessed a previously published RNA expression dataset in which brain periplaques were originally used as internal controls. When comparing the mRNA profiles obtained from brain periplaques with those derived from control normal white matter samples, we found that, irrespective of plaque activity, brain periplaques exhibited a TGF-beta molecular signature, an increased expression of TGFB2 (transforming growth factor beta 2) and a decreased expression of the oligodendrocyte genes NDRG1 (N-Myc downstream regulated 1) and MAG (myelin-associated glycoprotein). From these data obtained at the mRNA level, a survey of the human proteome allowed predicting a protein-protein interaction network linking TGFB2 to the down-regulation of both NDRG1 and MAG in brain periplaques. To further elucidate the role of NDRG1 in periplaque-associated partial demyelination, we then extracted the interaction network linking NDRG1 to proteins detected in human central myelin sheaths. We observed that such a network was highly significantly enriched in RNA-binding proteins that notably included several HNRNPs (heterogeneous nuclear ribonucleoproteins) involved in the post-transcriptional regulation of MAG. We conclude that both brain and spinal cord periplaques host a chronic process of tissue remodeling, during which oligodendrocyte myelinating functions are altered. Our findings further suggest that TGFB2 may fuel such a process. Overall, the present work provides additional evidence that periplaque-associated partial demyelination may drive the silent progression observed in a subset of MS patients.
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Affiliation(s)
- Serge Nataf
- Bank of Tissues and Cells, Hospices Civils de Lyon, Hôpital Edouard Herriot, Place d’Arsonval, F-69003 Lyon, France
- Stem-Cell and Brain Research Institute, 18 Avenue de Doyen Lépine, F-69500 Bron, France
- Lyon-Est School of Medicine, University Claude Bernard Lyon 1, 43 Bd du 11 Novembre 1918, F-69100 Villeurbanne, France
- Correspondence:
| | - Marine Guillen
- Bank of Tissues and Cells, Hospices Civils de Lyon, Hôpital Edouard Herriot, Place d’Arsonval, F-69003 Lyon, France
- Stem-Cell and Brain Research Institute, 18 Avenue de Doyen Lépine, F-69500 Bron, France
| | - Laurent Pays
- Bank of Tissues and Cells, Hospices Civils de Lyon, Hôpital Edouard Herriot, Place d’Arsonval, F-69003 Lyon, France
- Stem-Cell and Brain Research Institute, 18 Avenue de Doyen Lépine, F-69500 Bron, France
- Lyon-Est School of Medicine, University Claude Bernard Lyon 1, 43 Bd du 11 Novembre 1918, F-69100 Villeurbanne, France
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Dermitzakis I, Manthou ME, Meditskou S, Miliaras D, Kesidou E, Boziki M, Petratos S, Grigoriadis N, Theotokis P. Developmental Cues and Molecular Drivers in Myelinogenesis: Revisiting Early Life to Re-Evaluate the Integrity of CNS Myelin. Curr Issues Mol Biol 2022; 44:3208-3237. [PMID: 35877446 PMCID: PMC9324160 DOI: 10.3390/cimb44070222] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 02/07/2023] Open
Abstract
The mammalian central nervous system (CNS) coordinates its communication through saltatory conduction, facilitated by myelin-forming oligodendrocytes (OLs). Despite the fact that neurogenesis from stem cell niches has caught the majority of attention in recent years, oligodendrogenesis and, more specifically, the molecular underpinnings behind OL-dependent myelinogenesis, remain largely unknown. In this comprehensive review, we determine the developmental cues and molecular drivers which regulate normal myelination both at the prenatal and postnatal periods. We have indexed the individual stages of myelinogenesis sequentially; from the initiation of oligodendrocyte precursor cells, including migration and proliferation, to first contact with the axon that enlists positive and negative regulators for myelination, until the ultimate maintenance of the axon ensheathment and myelin growth. Here, we highlight multiple developmental pathways that are key to successful myelin formation and define the molecular pathways that can potentially be targets for pharmacological interventions in a variety of neurological disorders that exhibit demyelination.
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Affiliation(s)
- Iasonas Dermitzakis
- Department of Histology-Embryology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.D.); (M.E.M.); (S.M.); (D.M.)
| | - Maria Eleni Manthou
- Department of Histology-Embryology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.D.); (M.E.M.); (S.M.); (D.M.)
| | - Soultana Meditskou
- Department of Histology-Embryology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.D.); (M.E.M.); (S.M.); (D.M.)
| | - Dimosthenis Miliaras
- Department of Histology-Embryology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.D.); (M.E.M.); (S.M.); (D.M.)
| | - Evangelia Kesidou
- Laboratory of Experimental Neurology and Neuroimmunology, Second Department of Neurology, AHEPA University Hospital, 54621 Thessaloniki, Greece; (E.K.); (M.B.); (N.G.)
| | - Marina Boziki
- Laboratory of Experimental Neurology and Neuroimmunology, Second Department of Neurology, AHEPA University Hospital, 54621 Thessaloniki, Greece; (E.K.); (M.B.); (N.G.)
| | - Steven Petratos
- Department of Neuroscience, Central Clinical School, Monash University, Prahran, VIC 3004, Australia;
| | - Nikolaos Grigoriadis
- Laboratory of Experimental Neurology and Neuroimmunology, Second Department of Neurology, AHEPA University Hospital, 54621 Thessaloniki, Greece; (E.K.); (M.B.); (N.G.)
| | - Paschalis Theotokis
- Department of Histology-Embryology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.D.); (M.E.M.); (S.M.); (D.M.)
- Laboratory of Experimental Neurology and Neuroimmunology, Second Department of Neurology, AHEPA University Hospital, 54621 Thessaloniki, Greece; (E.K.); (M.B.); (N.G.)
- Correspondence:
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Iohan LDCC, Lambert JC, Costa MR. Analysis of modular gene co-expression networks reveals molecular pathways underlying Alzheimer’s disease and progressive supranuclear palsy. PLoS One 2022; 17:e0266405. [PMID: 35421130 PMCID: PMC9009680 DOI: 10.1371/journal.pone.0266405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/18/2022] [Indexed: 12/02/2022] Open
Abstract
A comprehensive understanding of the pathological mechanisms involved at different stages of neurodegenerative diseases is key for the advance of preventive and disease-modifying treatments. Gene expression alterations in the diseased brain is a potential source of information about biological processes affected by pathology. In this work, we performed a systematic comparison of gene expression alterations in the brains of human patients diagnosed with Alzheimer’s disease (AD) or Progressive Supranuclear Palsy (PSP) and animal models of amyloidopathy and tauopathy. Using a systems biology approach to uncover biological processes associated with gene expression alterations, we could pinpoint processes more strongly associated with tauopathy/PSP and amyloidopathy/AD. We show that gene expression alterations related to immune-inflammatory responses preponderate in younger, whereas those associated to synaptic transmission are mainly observed in older AD patients. In PSP, however, changes associated with immune-inflammatory responses and synaptic transmission overlap. These two different patterns observed in AD and PSP brains are fairly recapitulated in animal models of amyloidopathy and tauopathy, respectively. Moreover, in AD, but not PSP or animal models, gene expression alterations related to RNA splicing are highly prevalent, whereas those associated with myelination are enriched both in AD and PSP, but not in animal models. Finally, we identify 12 AD and 4 PSP genetic risk factors in cell-type specific co-expression modules, thus contributing to unveil the possible role of these genes to pathogenesis. Altogether, this work contributes to unravel the potential biological processes affected by amyloid versus tau pathology and how they could contribute to the pathogenesis of AD and PSP.
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Affiliation(s)
- Lukas da Cruz Carvalho Iohan
- Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Jean-Charles Lambert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, DISTALZ, Lille, France
| | - Marcos R. Costa
- Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, DISTALZ, Lille, France
- * E-mail:
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Dong K, Zhang S. Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder. Nat Commun 2022; 13:1739. [PMID: 35365632 PMCID: PMC8976049 DOI: 10.1038/s41467-022-29439-6] [Citation(s) in RCA: 142] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/16/2022] [Indexed: 11/29/2022] Open
Abstract
Recent advances in spatially resolved transcriptomics have enabled comprehensive measurements of gene expression patterns while retaining the spatial context of the tissue microenvironment. Deciphering the spatial context of spots in a tissue needs to use their spatial information carefully. To this end, we develop a graph attention auto-encoder framework STAGATE to accurately identify spatial domains by learning low-dimensional latent embeddings via integrating spatial information and gene expression profiles. To better characterize the spatial similarity at the boundary of spatial domains, STAGATE adopts an attention mechanism to adaptively learn the similarity of neighboring spots, and an optional cell type-aware module through integrating the pre-clustering of gene expressions. We validate STAGATE on diverse spatial transcriptomics datasets generated by different platforms with different spatial resolutions. STAGATE could substantially improve the identification accuracy of spatial domains, and denoise the data while preserving spatial expression patterns. Importantly, STAGATE could be extended to multiple consecutive sections to reduce batch effects between sections and extracting three-dimensional (3D) expression domains from the reconstructed 3D tissue effectively.
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Affiliation(s)
- Kangning Dong
- NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shihua Zhang
- NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 310024, China.
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Kang M, Yao Y. Laminin regulates oligodendrocyte development and myelination. Glia 2021; 70:414-429. [PMID: 34773273 DOI: 10.1002/glia.24117] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 11/08/2022]
Abstract
Oligodendrocytes are the cells that myelinate axons and provide trophic support to neurons in the CNS. Their dysfunction has been associated with a group of disorders known as demyelinating diseases, such as multiple sclerosis. Oligodendrocytes are derived from oligodendrocyte precursor cells, which differentiate into premyelinating oligodendrocytes and eventually mature oligodendrocytes. The development and function of oligodendrocytes are tightly regulated by a variety of molecules, including laminin, a major protein of the extracellular matrix. Accumulating evidence suggests that laminin actively regulates every aspect of oligodendrocyte biology, including survival, migration, proliferation, differentiation, and myelination. How can laminin exert such diverse functions in oligodendrocytes? It is speculated that the distinct laminin isoforms, laminin receptors, and/or key signaling molecules expressed in oligodendrocytes at different developmental stages are the reasons. Understanding molecular targets and signaling pathways unique to each aspect of oligodendrocyte biology will enable more accurate manipulation of oligodendrocyte development and function, which may have implications in the therapies of demyelinating diseases. Here in this review, we first introduce oligodendrocyte biology, followed by the expression of laminin and laminin receptors in oligodendrocytes and other CNS cells. Next, the functions of laminin in oligodendrocyte biology, including survival, migration, proliferation, differentiation, and myelination, are discussed in detail. Last, key questions and challenges in the field are discussed. By providing a comprehensive review on laminin's roles in OL lineage cells, we hope to stimulate novel hypotheses and encourage new research in the field.
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Affiliation(s)
- Minkyung Kang
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Yao Yao
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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Mühlebner A, van Scheppingen J, de Neef A, Bongaarts A, Zimmer TS, Mills JD, Jansen FE, Spliet WGM, Krsek P, Zamecnik J, Coras R, Blumcke I, Feucht M, Scholl T, Gruber VE, Hainfellner JA, Söylemezoğlu F, Kotulska K, Lagae L, Jansen AC, Kwiatkowski DJ, Jozwiak S, Curatolo P, Aronica E. Myelin Pathology Beyond White Matter in Tuberous Sclerosis Complex (TSC) Cortical Tubers. J Neuropathol Exp Neurol 2021; 79:1054-1064. [PMID: 32954437 PMCID: PMC7559237 DOI: 10.1093/jnen/nlaa090] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Tuberous sclerosis complex (TSC) is a monogenetic disease that arises due to mutations in either the TSC1 or TSC2 gene and affects multiple organ systems. One of the hallmark manifestations of TSC are cortical malformations referred to as cortical tubers. These tubers are frequently associated with treatment-resistant epilepsy. Some of these patients are candidates for epilepsy surgery. White matter abnormalities, such as loss of myelin and oligodendroglia, have been described in a small subset of resected tubers but mechanisms underlying this phenomenon are unclear. Herein, we analyzed a variety of neuropathologic and immunohistochemical features in gray and white matter areas of resected cortical tubers from 46 TSC patients using semi-automated quantitative image analysis. We observed divergent amounts of myelin basic protein as well as numbers of oligodendroglia in both gray and white matter when compared with matched controls. Analyses of clinical data indicated that reduced numbers of oligodendroglia were associated with lower numbers on the intelligence quotient scale and that lower amounts of myelin-associated oligodendrocyte basic protein were associated with the presence of autism-spectrum disorder. In conclusion, myelin pathology in cortical tubers extends beyond the white matter and may be linked to cognitive dysfunction in TSC patients.
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Affiliation(s)
- Angelika Mühlebner
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jackelien van Scheppingen
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Andrew de Neef
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anika Bongaarts
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Till S Zimmer
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - James D Mills
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Floor E Jansen
- Department of Pediatric Neurology, Brain Center University Medical Center
| | - Wim G M Spliet
- Department of Pathology, University Medical Center Utrecht (WGMS) Utrecht, The Netherlands
| | | | | | - Roland Coras
- Second Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic; Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Ingmar Blumcke
- Second Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic; Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | | | | | | | | | - Figen Söylemezoğlu
- Medical University of Vienna, Vienna, Austria; Department of Pathology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Lieven Lagae
- Department of Development and Regeneration-Section Pediatric Neurology, University Hospitals KU Leuven, Leuven
| | - Anna C Jansen
- Pediatric Neurology Unit-UZ Brussel, Brussels Belgium
| | | | - Sergiusz Jozwiak
- Department of Neurology and Epileptology, The Children's Memorial Health Institute.,Department of Child Neurology, Medical University of Warsaw Warsaw, Poland
| | - Paolo Curatolo
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, Rome, Italy
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, The Netherlands
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11
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Raasakka A, Kursula P. Flexible Players within the Sheaths: The Intrinsically Disordered Proteins of Myelin in Health and Disease. Cells 2020; 9:cells9020470. [PMID: 32085570 PMCID: PMC7072810 DOI: 10.3390/cells9020470] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/16/2020] [Accepted: 02/16/2020] [Indexed: 02/07/2023] Open
Abstract
Myelin ensheathes selected axonal segments within the nervous system, resulting primarily in nerve impulse acceleration, as well as mechanical and trophic support for neurons. In the central and peripheral nervous systems, various proteins that contribute to the formation and stability of myelin are present, which also harbor pathophysiological roles in myelin disease. Many myelin proteins have common attributes, including small size, hydrophobic segments, multifunctionality, longevity, and regions of intrinsic disorder. With recent advances in protein biophysical characterization and bioinformatics, it has become evident that intrinsically disordered proteins (IDPs) are abundant in myelin, and their flexible nature enables multifunctionality. Here, we review known myelin IDPs, their conservation, molecular characteristics and functions, and their disease relevance, along with open questions and speculations. We place emphasis on classifying the molecular details of IDPs in myelin, and we correlate these with their various functions, including susceptibility to post-translational modifications, function in protein–protein and protein–membrane interactions, as well as their role as extended entropic chains. We discuss how myelin pathology can relate to IDPs and which molecular factors are potentially involved.
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Affiliation(s)
- Arne Raasakka
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5009 Bergen, Norway;
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5009 Bergen, Norway;
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Aapistie 7A, FI-90220 Oulu, Finland
- Correspondence:
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12
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Mukherjee A, Singh R, Udayan S, Biswas S, Reddy PP, Manmadhan S, George G, Kumar S, Das R, Rao BM, Gulyani A. A Fyn biosensor reveals pulsatile, spatially localized kinase activity and signaling crosstalk in live mammalian cells. eLife 2020; 9:50571. [PMID: 32017701 PMCID: PMC7000222 DOI: 10.7554/elife.50571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
Cell behavior is controlled through spatio-temporally localized protein activity. Despite unique and often contradictory roles played by Src-family-kinases (SFKs) in regulating cell physiology, activity patterns of individual SFKs have remained elusive. Here, we report a biosensor for specifically visualizing active conformation of SFK-Fyn in live cells. We deployed combinatorial library screening to isolate a binding-protein (F29) targeting activated Fyn. Nuclear-magnetic-resonance (NMR) analysis provides the structural basis of F29 specificity for Fyn over homologous SFKs. Using F29, we engineered a sensitive, minimally-perturbing fluorescence-resonance-energy-transfer (FRET) biosensor (FynSensor) that reveals cellular Fyn activity to be spatially localized, pulsatile and sensitive to adhesion/integrin signaling. Strikingly, growth factor stimulation further enhanced Fyn activity in pre-activated intracellular zones. However, inhibition of focal-adhesion-kinase activity not only attenuates Fyn activity, but abolishes growth-factor modulation. FynSensor imaging uncovers spatially organized, sensitized signaling clusters, direct crosstalk between integrin and growth-factor-signaling, and clarifies how compartmentalized Src-kinase activity may drive cell fate.
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Affiliation(s)
- Ananya Mukherjee
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.,SASTRA University, Thanjavur, India
| | - Randhir Singh
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Sreeram Udayan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Sayan Biswas
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | | | - Saumya Manmadhan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Geen George
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Shilpa Kumar
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Ranabir Das
- National Centre for Biological Sciences, Bangalore, India
| | - Balaji M Rao
- North Carolina State University, Raleigh, United States
| | - Akash Gulyani
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
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13
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White matter DNA methylation profiling reveals deregulation of HIP1, LMAN2, MOBP, and other loci in multiple system atrophy. Acta Neuropathol 2020; 139:135-156. [PMID: 31535203 PMCID: PMC6942018 DOI: 10.1007/s00401-019-02074-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/29/2019] [Accepted: 09/09/2019] [Indexed: 12/14/2022]
Abstract
Multiple system atrophy (MSA) is a fatal late-onset neurodegenerative disease. Although presenting with distinct pathological hallmarks, which in MSA consist of glial cytoplasmic inclusions (GCIs) containing fibrillar α-synuclein in oligodendrocytes, both MSA and Parkinson’s disease are α-synucleinopathies. Pathologically, MSA can be categorized into striatonigral degeneration (SND), olivopontocerebellar atrophy (OPCA) or mixed subtypes. Despite extensive research, the regional vulnerability of the brain to MSA pathology remains poorly understood. Genetic, epigenetic and environmental factors have been proposed to explain which brain regions are affected by MSA, and to what extent. Here, we explored for the first time epigenetic changes in post-mortem brain tissue from MSA cases. We conducted a case–control study, and profiled DNA methylation in white mater from three brain regions characterized by severe-to-mild GCIs burden in the MSA mixed subtype (cerebellum, frontal lobe and occipital lobe). Our genome-wide approach using Illumina MethylationEPIC arrays and a powerful cross-region analysis identified 157 CpG sites and 79 genomic regions where DNA methylation was significantly altered in the MSA mixed-subtype cases. HIP1, LMAN2 and MOBP were amongst the most differentially methylated loci. We replicated these findings in an independent cohort and further demonstrated that DNA methylation profiles were perturbed in MSA mixed subtype, and also to variable degrees in the other pathological subtypes (OPCA and SND). Finally, our co-methylation network analysis revealed several molecular signatures (modules) significantly associated with MSA (disease status and pathological subtypes), and with neurodegeneration in the cerebellum. Importantly, the co-methylation module having the strongest association with MSA included a CpG in SNCA, the gene encoding α-synuclein. Altogether, our results provide the first evidence for DNA methylation changes contributing to the molecular processes altered in MSA, some of which are shared with other neurodegenerative diseases, and highlight potential novel routes for diagnosis and therapeutic interventions.
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14
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Thomason EJ, Escalante M, Osterhout DJ, Fuss B. The oligodendrocyte growth cone and its actin cytoskeleton: A fundamental element for progenitor cell migration and CNS myelination. Glia 2019; 68:1329-1346. [PMID: 31696982 DOI: 10.1002/glia.23735] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/26/2019] [Accepted: 10/01/2019] [Indexed: 01/06/2023]
Abstract
Cells of the oligodendrocyte (OLG) lineage engage in highly motile behaviors that are crucial for effective central nervous system (CNS) myelination. These behaviors include the guided migration of OLG progenitor cells (OPCs), the surveying of local environments by cellular processes extending from differentiating and pre-myelinating OLGs, and during the process of active myelin wrapping, the forward movement of the leading edge of the myelin sheath's inner tongue along the axon. Almost all of these motile behaviors are driven by actin cytoskeletal dynamics initiated within a lamellipodial structure that is located at the tip of cellular OLG/OPC processes and is structurally as well as functionally similar to the neuronal growth cone. Accordingly, coordinated stoichiometries of actin filament (F-actin) assembly and disassembly at these OLG/OPC growth cones have been implicated in directing process outgrowth and guidance, and the initiation of myelination. Nonetheless, the functional importance of the OLG/OPC growth cone still remains to be fully understood, and, as a unique aspect of actin cytoskeletal dynamics, F-actin depolymerization and disassembly start to predominate at the transition from myelination initiation to myelin wrapping. This review provides an overview of the current knowledge about OLG/OPC growth cones, and it proposes a model in which actin cytoskeletal dynamics in OLG/OPC growth cones are a main driver for morphological transformations and motile behaviors. Remarkably, these activities, at least at the later stages of OLG maturation, may be regulated independently from the transcriptional gene expression changes typically associated with CNS myelination.
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Affiliation(s)
- Elizabeth J Thomason
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Miguel Escalante
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, Virginia.,Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Donna J Osterhout
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York
| | - Babette Fuss
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, Virginia
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15
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Lien YC, Condon DE, Georgieff MK, Simmons RA, Tran PV. Dysregulation of Neuronal Genes by Fetal-Neonatal Iron Deficiency Anemia Is Associated with Altered DNA Methylation in the Rat Hippocampus. Nutrients 2019; 11:nu11051191. [PMID: 31137889 PMCID: PMC6566599 DOI: 10.3390/nu11051191] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 02/06/2023] Open
Abstract
Early-life iron deficiency results in long-term abnormalities in cognitive function and affective behavior in adulthood. In preclinical models, these effects have been associated with long-term dysregulation of key neuronal genes. While limited evidence suggests histone methylation as an epigenetic mechanism underlying gene dysregulation, the role of DNA methylation remains unknown. To determine whether DNA methylation is a potential mechanism by which early-life iron deficiency induces gene dysregulation, we performed whole genome bisulfite sequencing to identify loci with altered DNA methylation in the postnatal day (P) 15 iron-deficient (ID) rat hippocampus, a time point at which the highest level of hippocampal iron deficiency is concurrent with peak iron demand for axonal and dendritic growth. We identified 229 differentially methylated loci and they were mapped within 108 genes. Among them, 63 and 45 genes showed significantly increased and decreased DNA methylation in the P15 ID hippocampus, respectively. To establish a correlation between differentially methylated loci and gene dysregulation, the methylome data were compared to our published P15 hippocampal transcriptome. Both datasets showed alteration of similar functional networks regulating nervous system development and cell-to-cell signaling that are critical for learning and behavior. Collectively, the present findings support a role for DNA methylation in neural gene dysregulation following early-life iron deficiency.
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Affiliation(s)
- Yu-Chin Lien
- Center for Research on Reproduction and Women's Health, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - David E Condon
- Center for Research on Reproduction and Women's Health, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Michael K Georgieff
- Department of Pediatrics, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA.
| | - Rebecca A Simmons
- Center for Research on Reproduction and Women's Health, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA.
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Phu V Tran
- Department of Pediatrics, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA.
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16
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Abe T, Kutsuna N, Kiyonari H, Furuta Y, Fujimori T. ROSA26 reporter mouse lines and image analyses reveal distinct region-specific cell behaviors in the visceral endoderm. Development 2018; 145:dev.165852. [PMID: 30327323 DOI: 10.1242/dev.165852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 10/08/2018] [Indexed: 11/20/2022]
Abstract
The early post-implantation mouse embryo changes dramatically in both size and shape. These morphological changes are based on characteristic cellular behaviors, including cell growth and allocation. To perform clonal analysis, we established a Cre/loxP-based reporter mouse line, R26R-ManGeKyou, that enables clonal labeling with multiple colors. We also developed a novel ImageJ plugin, LP-Clonal, for quantitative measurement of the tilt angle of clonal cluster shape, enabling identification of the direction of cluster expansion. We carried out long-term and short-term lineage tracking. We also performed time-lapse imaging to characterize cellular behaviors using R26-PHA7-EGFP and R26R-EGFP These images were subjected to quantitative image analyses. We found that the proximal visceral endoderm overlying the extra-embryonic ectoderm shows coherent cell growth in a proximal-anterior to distal-posterior direction. We also observed that directional cell migration is coupled with cell elongation in the anterior region. Our observations suggest that the behaviors of visceral endoderm cells vary between regions during peri-implantation stages.
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Affiliation(s)
- Takaya Abe
- Animal Resource Development, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan .,Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan.,Animal Resource Development Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan.,Genetic Engineering Team, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan
| | - Natsumaro Kutsuna
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa 277-8562, Japan.,Research & Development Department, LPixel Inc., TechLab 6F, Otemachi Building, 1-6-1, Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Hiroshi Kiyonari
- Animal Resource Development, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan.,Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan.,Animal Resource Development Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan.,Genetic Engineering Team, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan
| | - Yasuhide Furuta
- Animal Resource Development, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan.,Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan.,Animal Resource Development Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan.,Genetic Engineering Team, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan
| | - Toshihiko Fujimori
- Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan.,Genetic Engineering Team, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan.,Division of Embryology, National Institute for Basic Biology (NIBB), Okazaki 444-8787, Japan.,Department of Basic Biology, School of Life Science, Sokendai 444-8787, Japan
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17
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Inamura N, Kito M, Go S, Kishi S, Hosokawa M, Asai K, Takakura N, Takebayashi H, Matsuda J, Enokido Y. Developmental defects and aberrant accumulation of endogenous psychosine in oligodendrocytes in a murine model of Krabbe disease. Neurobiol Dis 2018; 120:51-62. [PMID: 30176352 DOI: 10.1016/j.nbd.2018.08.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/19/2018] [Accepted: 08/30/2018] [Indexed: 12/16/2022] Open
Abstract
Krabbe disease (KD), or globoid cell leukodystrophy, is an inherited lysosomal storage disease with leukodystrophy caused by a mutation in the galactosylceramidase (GALC) gene. The majority of patients show the early onset form of KD dominated by cerebral demyelination with apoptotic oligodendrocyte (OL) death. However, the initial pathophysiological changes in developing OLs remain poorly understood. Here, we show that OLs of twitcher mice, an authentic mouse model of KD, exhibited developmental defects and impaired myelin formation in vivo and in vitro. In twitcher mouse brain, abnormal myelination and reduced expression of myelin genes during the period of most active OL differentiation and myelination preceded subsequent progressive OL death and demyelination. Importantly, twitcher mouse OL precursor cells proliferated normally, but their differentiation and survival were intrinsically defective. These defects were associated with aberrant accumulation of endogenous psychosine (galactosylsphingosine) and reduced activation of the Erk1/2 and Akt/mTOR pathways before apoptotic cell death. Collectively, our results demonstrate that GALC deficiency in developing KD OLs profoundly affects their differentiation and maturation, indicating the critical contribution of OL dysfunction to KD pathogenesis.
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Affiliation(s)
- Naoko Inamura
- Department of Pathology, Institute for Developmental Research, Aichi Human Service Center, 713-8 Kamiya-cho, Kasugai, Aichi 480-0392, Japan
| | - Momoko Kito
- Department of Pathology, Institute for Developmental Research, Aichi Human Service Center, 713-8 Kamiya-cho, Kasugai, Aichi 480-0392, Japan; Department of Molecular Neurobiology, Nagoya City University School of Medicine, 1 Kawasumi, Mizuho-cho, Mizuho-ku Nagoya, Aichi 467-8601, Japan
| | - Shinji Go
- Department of Pathophysiology and Metabolism, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Soichiro Kishi
- Department of Pathology, Institute for Developmental Research, Aichi Human Service Center, 713-8 Kamiya-cho, Kasugai, Aichi 480-0392, Japan
| | - Masanori Hosokawa
- Department of Pathology, Institute for Developmental Research, Aichi Human Service Center, 713-8 Kamiya-cho, Kasugai, Aichi 480-0392, Japan
| | - Kiyofumi Asai
- Department of Molecular Neurobiology, Nagoya City University School of Medicine, 1 Kawasumi, Mizuho-cho, Mizuho-ku Nagoya, Aichi 467-8601, Japan
| | - Nobuyuki Takakura
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirohide Takebayashi
- Division of Neurobiology and Anatomy, Graduate School of Medicine and Dental Science, Niigata University, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Junko Matsuda
- Department of Pathophysiology and Metabolism, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Yasushi Enokido
- Department of Pathology, Institute for Developmental Research, Aichi Human Service Center, 713-8 Kamiya-cho, Kasugai, Aichi 480-0392, Japan.
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18
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Poli G, Lapillo M, Granchi C, Caciolla J, Mouawad N, Caligiuri I, Rizzolio F, Langer T, Minutolo F, Tuccinardi T. Binding investigation and preliminary optimisation of the 3-amino-1,2,4-triazin-5(2H)-one core for the development of new Fyn inhibitors. J Enzyme Inhib Med Chem 2018; 33:956-961. [PMID: 29747534 PMCID: PMC6009924 DOI: 10.1080/14756366.2018.1469017] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Fyn tyrosine kinase inhibitors are considered potential therapeutic agents for a variety of human cancers. Furthermore, the involvement of Fyn kinase in signalling pathways that lead to severe pathologies, such as Alzheimer's and Parkinson's diseases, has also been demonstrated. In this study, starting from 3-(benzo[d][1,3]dioxol-5-ylamino)-6-methyl-1,2,4-triazin-5(2H)-one (VS6), a hit compound that showed a micromolar inhibition of Fyn (IC50 = 4.8 μM), we computationally investigated the binding interactions of the 3-amino-1,2,4-triazin-5(2H)-one scaffold and started a preliminary hit to lead optimisation. This analysis led us to confirm the hypothesised binding mode of VS6 and to identify a new derivative that is about 6-fold more active than VS6 (compound 3, IC50 = 0.76 μM).
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Affiliation(s)
- Giulio Poli
- a Department of Pharmacy , University of Pisa , Pisa , Italy
| | | | | | | | - Nayla Mouawad
- a Department of Pharmacy , University of Pisa , Pisa , Italy.,b Pathology Unit, Department of Molecular Biology and Translational Research , National Cancer Institute and Center for Molecular Biomedicine , Aviano (PN) , Italy
| | - Isabella Caligiuri
- b Pathology Unit, Department of Molecular Biology and Translational Research , National Cancer Institute and Center for Molecular Biomedicine , Aviano (PN) , Italy
| | - Flavio Rizzolio
- b Pathology Unit, Department of Molecular Biology and Translational Research , National Cancer Institute and Center for Molecular Biomedicine , Aviano (PN) , Italy.,c Department of Molecular Science and Nanosystems , Ca' Foscari Università di Venezia , Venezia-Mestre , Italy
| | - Thierry Langer
- d Department of Pharmaceutical Chemistry, Faculty of Life Sciences , University of Vienna , Vienna , Austria
| | | | - Tiziano Tuccinardi
- a Department of Pharmacy , University of Pisa , Pisa , Italy.,e Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University , Philadelphia , PA , USA
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19
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Azevedo MM, Domingues HS, Cordelières FP, Sampaio P, Seixas AI, Relvas JB. Jmy regulates oligodendrocyte differentiation via modulation of actin cytoskeleton dynamics. Glia 2018; 66:1826-1844. [DOI: 10.1002/glia.23342] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/26/2018] [Accepted: 04/05/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Maria M. Azevedo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- IBMC - Instituto de Biologia Molecular e Celular; Porto Portugal
| | - Helena S. Domingues
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- IBMC - Instituto de Biologia Molecular e Celular; Porto Portugal
| | - Fabrice P. Cordelières
- Bordeaux Imaging Centre, UMS 3420 CNRS, CNRS-INSERM, University of Bordeaux; Bordeaux France
| | - Paula Sampaio
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- IBMC - Instituto de Biologia Molecular e Celular; Porto Portugal
| | - Ana I. Seixas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- IBMC - Instituto de Biologia Molecular e Celular; Porto Portugal
| | - João B. Relvas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- IBMC - Instituto de Biologia Molecular e Celular; Porto Portugal
- The Discoveries Centre for Regeneration and Precision Medicine, Porto campus; Porto Portugal
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20
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Mattugini N, Merl-Pham J, Petrozziello E, Schindler L, Bernhagen J, Hauck SM, Götz M. Influence of white matter injury on gray matter reactive gliosis upon stab wound in the adult murine cerebral cortex. Glia 2018; 66:1644-1662. [PMID: 29573353 DOI: 10.1002/glia.23329] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 02/13/2018] [Accepted: 03/02/2018] [Indexed: 01/01/2023]
Abstract
Traumatic brain injury frequently affects the cerebral cortex, yet little is known about the differential effects that occur if only the gray matter (GM) is damaged or if the injury also involves the white matter (WM). To tackle this important question and directly compare similarities and differences in reactive gliosis, we performed stab wound injury affecting GM and WM (GM+) and one restricted to the GM (GM-) in the adult murine cerebral cortex. First, we examined glial reactivity in the regions affected (WM and GM) and determined the influence of WM injury on reactive gliosis in the GM comparing the same area in the two injury paradigms. In the GM+ injury microglia proliferation is increased in the WM compared with GM, while proliferating astrocytes are more abundant in the GM than in the WM. Interestingly, WM lesion exerted a strong influence on the proliferation of the GM glial cells that was most pronounced at early stages, 3 days post lesion. While astrocyte proliferation was increased, NG2 glia proliferation was decreased in the GM+ compared with GM- lesion condition. Importantly, these differences were not observed when a lesion of the same size affected only the GM. Unbiased proteomic analyses further corroborate our findings in support of a profound difference in GM reactivity when WM is also injured and revealed MIF as a key regulator of NG2 glia proliferation.
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Affiliation(s)
- Nicola Mattugini
- Physiological Genomics, Biomedical center (BMC), Ludwig-Maximilians-University (LMU), Großhaderner Str. 9, Planegg/Martinsried, 82152, Germany.,Institute of Stem Cell Research, Helmholtz Center Munich, Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University (LMU), Großhaderner Str. 9, Planegg/Martinsried, 82152, Germany.,Graduate School of Systemic Neurosciences Ludwig-Maximilians University (LMU), Großhaderner Str. 2, Planegg/Martinsried, 82152, Germany
| | - Juliane Merl-Pham
- Research Unit Protein Science, Helmholtz Center Munich, Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany
| | - Elisabetta Petrozziello
- Institute for Immunology, Biomedical Center (BMC), Ludwig-Maximilians-University (LMU), Großhadernerstr. 9, Planegg/Martinsried, 82152, Germany
| | - Lisa Schindler
- Vascular Biology, Institute for Stroke and Dementia Research (ISD), Ludwig-Maximilians-University (LMU) Munich, Munich, 81377, Germany
| | - Jürgen Bernhagen
- Vascular Biology, Institute for Stroke and Dementia Research (ISD), Ludwig-Maximilians-University (LMU) Munich, Munich, 81377, Germany.,SyNergy Excellence Cluster, Munich, 81377, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Center Munich, Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany
| | - Magdalena Götz
- Physiological Genomics, Biomedical center (BMC), Ludwig-Maximilians-University (LMU), Großhaderner Str. 9, Planegg/Martinsried, 82152, Germany.,Institute of Stem Cell Research, Helmholtz Center Munich, Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University (LMU), Großhaderner Str. 9, Planegg/Martinsried, 82152, Germany.,SyNergy Excellence Cluster, Munich, 81377, Germany
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Hoch-Kraft P, White R, Tenzer S, Krämer-Albers EM, Trotter J, Gonsior C. Dual role of the RNA helicase DDX5 in post-transcriptional regulation of Myelin Basic Protein in oligodendrocytes. J Cell Sci 2018; 131:jcs.204750. [DOI: 10.1242/jcs.204750] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 03/28/2018] [Indexed: 01/11/2023] Open
Abstract
In the central nervous system, oligodendroglial expression of Myelin Basic Protein (MBP) is crucial for the assembly and structure of the myelin sheath. MBP synthesis is tightly regulated in space and time, particularly on the post-transcriptional level. We have identified the DEAD-box RNA helicase DDX5 (alias p68) in a complex with Mbp mRNA in oligodendroglial cells. Expression of DDX5 is highest in progenitor cells and immature oligodendrocytes, where it localizes to heterogeneous populations of cytoplasmic ribonucleoprotein (RNP) complexes associated with Mbp mRNA in the cell body and processes. Manipulation of DDX5 protein amounts inversely affects levels of MBP protein. We present evidence that DDX5 is involved in post-transcriptional regulation of MBP protein synthesis, with implications for oligodendroglial development. In addition, DDX5 knockdown results in an increased abundance of MBP exon 2-positive isoforms in immature oligodendrocytes, most likely by regulating alternative splicing of Mbp. Our findings contribute to the understanding of the complex nature of MBP post-transcriptional control in immature oligodendrocytes where DDX5 appears to affect the abundance of MBP proteins via distinct but converging mechanisms.
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Affiliation(s)
- Peter Hoch-Kraft
- Molecular Cell Biology, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-University of Mainz, Anselm-Franz-von-Bentzelweg 3, 55128 Mainz, Germany
| | - Robin White
- Molecular Cell Biology, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-University of Mainz, Anselm-Franz-von-Bentzelweg 3, 55128 Mainz, Germany
- Institute of Physiology and Pathophysiology, University Medical Center of the Johannes Gutenberg-University, Duesbergweg 6, 55128 Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Eva-Maria Krämer-Albers
- Molecular Cell Biology, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-University of Mainz, Anselm-Franz-von-Bentzelweg 3, 55128 Mainz, Germany
| | - Jacqueline Trotter
- Molecular Cell Biology, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-University of Mainz, Anselm-Franz-von-Bentzelweg 3, 55128 Mainz, Germany
| | - Constantin Gonsior
- Molecular Cell Biology, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-University of Mainz, Anselm-Franz-von-Bentzelweg 3, 55128 Mainz, Germany
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