Stem cell-derived brainstem mouse astrocytes obtain a neurotoxic phenotype in vitro upon neuroinflammation

[1]  B. Barres,et al.  Neurotoxic reactive astrocytes induce cell death via saturated lipids , 2021, Nature.

[2]  S. Liddelow,et al.  Neuroinflammatory astrocyte subtypes in the mouse brain , 2021, Nature Neuroscience.

[3]  R. Franklin,et al.  Diversity of Reactive Astrogliosis in CNS Pathology: Heterogeneity or Plasticity? , 2021, Frontiers in Cellular Neuroscience.

[4]  Igor Dolgalev,et al.  MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format [R package msigdbr version 7.4.1] , 2021 .

[5]  Bin Zhou,et al.  M-CSF, IL-6, and TGF-β promote generation of a new subset of tissue repair macrophage for traumatic brain injury recovery , 2021, Science Advances.

[6]  Kira E. Poskanzer,et al.  Reactive astrocyte nomenclature, definitions, and future directions , 2021, Nature Neuroscience.

[7]  P. Nilsson,et al.  Fluid proteomics of CSF and serum reveal important neuroinflammatory proteins in blood–brain barrier disruption and outcome prediction following severe traumatic brain injury: a prospective, observational study , 2020, Critical Care.

[8]  T. Olsson,et al.  Microglial autophagy–associated phagocytosis is essential for recovery from neuroinflammation , 2020, Science Immunology.

[9]  V. Zachariadis,et al.  A Highly Scalable Method for Joint Whole-Genome Sequencing and Gene-Expression Profiling of Single Cells. , 2020, Molecular cell.

[10]  O. Ziff,et al.  Human stem cell-derived astrocytes exhibit region-specific heterogeneity in their secretory profiles , 2020, Brain : a journal of neurology.

[11]  M. Sofroniew.  Astrocyte Reactivity: Subtypes, States, and Functions in CNS Innate Immunity. , 2020, Trends in immunology.

[12]  Bin Zhang,et al.  CD49f Is a Novel Marker of Functional and Reactive Human iPSC-Derived Astrocytes , 2020, Neuron.

[13]  H. Vogel,et al.  Targeting Aquaporin-4 Subcellular Localization to Treat Central Nervous System Edema , 2020, Cell.

[14]  D. Geschwind,et al.  Conservation and divergence of vulnerability and responses to stressors between human and mouse astrocytes , 2020, Nature Communications.

[15]  V. Zachariadis.  Direct nuclear tagmentation and RNA-sequencing (DNTR-seq) v1 , 2020 .

[16]  B. Deneen,et al.  Regionally Distinct Astrocytes Display Unique Transcription Factor Profiles in the Adult Brain , 2020, Frontiers in Neuroscience.

[17]  David Watson,et al.  M3C: Monte Carlo reference-based consensus clustering , 2020, Scientific Reports.

[18]  J. Rothstein,et al.  Astrocyte Diversity: Current Insights and Future Directions , 2020, Neurochemical Research.

[19]  A. Frostell,et al.  Delineating Astrocytic Cytokine Responses in a Human Stem Cell Model of Neural Trauma , 2019, Journal of neurotrauma.

[20]  Kohske Takahashi,et al.  Welcome to the Tidyverse , 2019, J. Open Source Softw..

[21]  Gennady Korotkevich,et al.  Fast gene set enrichment analysis , 2019, bioRxiv.

[22]  P. Calabresi,et al.  Neurofilament light chain as a biomarker in neurological disorders , 2019, Journal of Neurology, Neurosurgery, and Psychiatry.

[23]  H. Wichterle,et al.  A Stem Cell-Based Screening Platform Identifies Compounds that Desensitize Motor Neurons to Endoplasmic Reticulum Stress. , 2019, Molecular therapy : the journal of the American Society of Gene Therapy.

[24]  N. Déglon,et al.  Human Induced Pluripotent Stem Cell-Derived Astrocytes Are Differentially Activated by Multiple Sclerosis-Associated Cytokines , 2018, Stem cell reports.

[25]  Ludwig Kappos,et al.  Neurofilaments as biomarkers in neurological disorders , 2018, Nature Reviews Neurology.

[26]  I. Allodi,et al.  Modeling Motor Neuron Resilience in ALS Using Stem Cells , 2018, bioRxiv.

[27]  D. Bryder,et al.  Rapid and efficient induction of functional astrocytes from human pluripotent stem cells , 2018, Nature Methods.

[28]  J. Bergquist,et al.  Proteomic differences between focal and diffuse traumatic brain injury in human brain tissue , 2018, Scientific Reports.

[29]  Joseph G Ibrahim,et al.  Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences , 2018, bioRxiv.

[30]  S. Chandran,et al.  Elucidating Pro-Inflammatory Cytokine Responses after Traumatic Brain Injury in a Human Stem Cell Model , 2017, Journal of neurotrauma.

[31]  L. Iyer,et al.  Molecular and Functional Properties of Regional Astrocytes in the Adult Brain , 2017, The Journal of Neuroscience.

[32]  Spyros Darmanis,et al.  Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells , 2017, Neuron.

[33]  Manoj Kumar,et al.  INGE GRUNDKE-IQBAL AWARD FOR ALZHEIMER’S RESEARCH: NEUROTOXIC REACTIVE ASTROCYTES ARE INDUCED BY ACTIVATED MICROGLIA , 2019, Alzheimer's & Dementia.

[34]  N. Marklund,et al.  Extended Anatomical Grading in Diffuse Axonal Injury Using MRI: Hemorrhagic Lesions in the Substantia Nigra and Mesencephalic Tegmentum Indicate Poor Long-Term Outcome , 2017, Journal of neurotrauma.

[35]  A. Reményi,et al.  JNK Signaling: Regulation and Functions Based on Complex Protein-Protein Partnerships , 2016, Microbiology and Molecular Reviews.

[36]  Nathan D. Kingery,et al.  Megf10 Is a Receptor for C1Q That Mediates Clearance of Apoptotic Cells by Astrocytes , 2016, The Journal of Neuroscience.

[37]  Ana P. Teixeira,et al.  Functional and phenotypic differences of pure populations of stem cell‐derived astrocytes and neuronal precursor cells , 2016, Glia.

[38]  Yan Ao,et al.  Astrocyte scar formation aids central nervous system axon regeneration , 2016, Nature.

[39]  M. Sofroniew,et al.  Astrocyte roles in traumatic brain injury , 2016, Experimental Neurology.

[40]  E. Chang,et al.  Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse , 2016, Neuron.

[41]  J. Mesirov,et al.  The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .

[42]  C. Wilke.  Streamlined Plot Theme and Plot Annotations for 'ggplot2' , 2015 .

[43]  J. Zuchero,et al.  Glia in mammalian development and disease , 2015, Development.

[44]  A. Molofsky,et al.  Astrocyte development: A Guide for the Perplexed , 2015, Glia.

[45]  M. Sofroniew.  Astrocyte barriers to neurotoxic inflammation , 2015, Nature Reviews Neuroscience.

[46]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[47]  M. Svensson,et al.  Change of Fate Commitment in Adult Neural Progenitor Cells Subjected to Chronic Inflammation , 2014, The Journal of Neuroscience.

[48]  Milos Pekny,et al.  The dual role of astrocyte activation and reactive gliosis , 2014, Neuroscience Letters.

[49]  Y. Ao,et al.  Heterogeneity of reactive astrocytes , 2014, Neuroscience Letters.

[50]  I. Allodi,et al.  Directed midbrain and spinal cord neurogenesis from pluripotent stem cells to model development and disease in a dish , 2014, Front. Neurosci..

[51]  Åsa K. Björklund,et al.  Full-length RNA-seq from single cells using Smart-seq2 , 2014, Nature Protocols.

[52]  Sung H Yang,et al.  Interleukin 6 Mediates Neuroinflammation and Motor Coordination Deficits After Mild Traumatic Brain Injury and Brief Hypoxia in Mice , 2013, Shock.

[53]  G. Vatcher,et al.  Traumatic scratch injury in astrocytes triggers calcium influx to activate the JNK/c‐Jun/AP‐1 pathway and switch on GFAP expression , 2013, Glia.

[54]  Henning Hermjakob,et al.  The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..

[55]  J. Dasen,et al.  Hox Genes: Choreographers in Neural Development, Architects of Circuit Organization , 2013, Neuron.

[56]  Yoon A. Kim,et al.  Human stem cell-derived spinal cord astrocytes with defined mature or reactive phenotypes. , 2013, Cell reports.

[57]  M. Freeman,et al.  The c-Jun kinase signaling cascade promotes glial engulfment activity through activation of draper and phagocytic function , 2013, Cell Death and Differentiation.

[58]  N. Marklund,et al.  Traumatic axonal injury in the mouse is accompanied by a dynamic inflammatory response, astroglial reactivity and complex behavioral changes , 2013, Journal of Neuroinflammation.

[59]  M. Morganti-Kossmann,et al.  The Role of Markers of Inflammation in Traumatic Brain Injury , 2013, Front. Neurol..

[60]  S. Khan,et al.  Quantification of active and total transforming growth factor-β levels in serum and solid organ tissues by bioassay , 2012, BMC Research Notes.

[61]  D. Loane,et al.  Neuroinflammation after traumatic brain injury: Opportunities for therapeutic intervention , 2012, Brain, Behavior, and Immunity.

[62]  A. Álvarez-Buylla,et al.  Regional Astrocyte Allocation Regulates CNS Synaptogenesis and Repair , 2012, Science.

[63]  R. Sandberg,et al.  Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells , 2012, Nature Biotechnology.

[64]  B. Barres,et al.  Genomic Analysis of Reactive Astrogliosis , 2012, The Journal of Neuroscience.

[65]  David H Rowitch,et al.  Astrocytes and disease: a neurodevelopmental perspective. , 2012, Genes & development.

[66]  A. Helmy,et al.  Cytokines and innate inflammation in the pathogenesis of human traumatic brain injury , 2011, Progress in Neurobiology.

[67]  Mark H. Ellisman,et al.  Development of a Method for the Purification and Culture of Rodent Astrocytes , 2011, Neuron.

[68]  Yan Liu,et al.  Specification of transplantable astroglial subtypes from human pluripotent stem cells , 2011, Nature Biotechnology.

[69]  Helga Thorvaldsdóttir,et al.  Molecular signatures database (MSigDB) 3.0 , 2011, Bioinform..

[70]  M. Al-Rawi,et al.  c-Jun localizes to the nucleus independent of its phosphorylation by and interaction with JNK and vice versa promotes nuclear accumulation of JNK. , 2011, Biochemical and biophysical research communications.

[71]  J. Middeldorp,et al.  GFAP in health and disease , 2011, Progress in Neurobiology.

[72]  Andrew C. Adey,et al.  Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition , 2010, Genome Biology.

[73]  Sanford Weisberg,et al.  An R Companion to Applied Regression , 2010 .

[74]  A. Kriegstein,et al.  Developmental genetics of vertebrate glial–cell specification , 2010, Nature.

[75]  M. Freeman,et al.  Specification and Morphogenesis of Astrocytes , 2010, Science.

[76]  H. Weiner,et al.  Depletion of TGF-β from fetal bovine serum. , 2010, Journal of immunological methods.

[77]  B. Barres,et al.  Astrocyte heterogeneity: an underappreciated topic in neurobiology , 2010, Current Opinion in Neurobiology.

[78]  Axel Weber,et al.  Interleukin-1 (IL-1) Pathway , 2010, Science Signaling.

[79]  E. Birney,et al.  Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.

[80]  G. Raivich.  c‐Jun Expression, activation and function in neural cell death, inflammation and repair , 2008, Journal of neurochemistry.

[81]  David J. Anderson,et al.  Identification of Positionally Distinct Astrocyte Subtypes whose Identities Are Specified by a Homeodomain Code , 2008, Cell.

[82]  Y. Xing,et al.  A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function , 2008, The Journal of Neuroscience.

[83]  C. Werner,et al.  Pathophysiology of traumatic brain injury. , 2007, British journal of anaesthesia.

[84]  J. Rothstein,et al.  Variations in Promoter Activity Reveal a Differential Expression and Physiology of Glutamate Transporters by Glia in the Developing and Mature CNS , 2007, The Journal of Neuroscience.

[85]  Hynek Wichterle,et al.  Astrocytes expressing ALS-linked mutated SOD1 release factors selectively toxic to motor neurons , 2007, Nature Neuroscience.

[86]  M. Svensson,et al.  Nitric Oxide Exposure Diverts Neural Stem Cell Fate from Neurogenesis Towards Astrogliogenesis , 2006, Stem cells.

[87]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[88]  Bart De Moor,et al.  BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis , 2005, Bioinform..

[89]  S. Paek,et al.  Forskolin promotes astroglial differentiation of human central neurocytoma cells , 2004, Experimental & Molecular Medicine.

[90]  M. Esiri,et al.  Axonal damage: a key predictor of outcome in human CNS diseases. , 2003, Brain : a journal of neurology.

[91]  H. Wichterle,et al.  Directed Differentiation of Embryonic Stem Cells into Motor Neurons , 2002, Cell.

[92]  E. Wagner,et al.  AP-1 in mouse development and tumorigenesis , 2001, Oncogene.

[93]  A. Chenchik,et al.  Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. , 2001, BioTechniques.

[94]  L. Eng,et al.  Glial Fibrillary Acidic Protein: GFAP-Thirty-One Years (1969–2000) , 2000, Neurochemical Research.

[95]  V. Hans,et al.  Cell activation and inflammatory response following traumatic axonal injury in the rat , 2000, Neuroreport.

[96]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[97]  M. Vallejo,et al.  Astroglial Differentiation of Cortical Precursor Cells Triggered by Activation of the cAMP-Dependent Signaling Pathway , 1999, The Journal of Neuroscience.

[98]  Daniel A. Lim,et al.  Subventricular Zone Astrocytes Are Neural Stem Cells in the Adult Mammalian Brain , 1999, Cell.

[99]  Clive N Svendsen,et al.  Leukocyte Infiltration, Neuronal Degeneration, and Neurite Outgrowth after Ablation of Scar-Forming, Reactive Astrocytes in Adult Transgenic Mice , 1999, Neuron.

[100]  V. Hans,et al.  Experimental Axonal Injury Triggers Interleukin-6 mRNA, Protein Synthesis and Release into Cerebrospinal Fluid , 1999, Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism.

[101]  Jonas Frisén,et al.  Identification of a Neural Stem Cell in the Adult Mammalian Central Nervous System , 1999, Cell.

[102]  R. McKay,et al.  Multiple Routes to Astrocytic Differentiation in the CNS , 1998, The Journal of Neuroscience.

[103]  H. Sontheimer,et al.  Astrocytes protect neurons from neurotoxic injury by serum glutamate , 1998, Glia.

[104]  M. Greenberg,et al.  Regulation of gliogenesis in the central nervous system by the JAK-STAT signaling pathway. , 1997, Science.

[105]  S. Barnum,et al.  Experimental diffuse axonal injury induces enhanced neuronal C5a receptor mRNA expression in rats. , 1997, Brain research. Molecular brain research.

[106]  S. Rosenzweig,et al.  Activation of C‐jun N‐terminal kinase/stress‐activated protein kinase in primary glial cultures , 1996, Journal of neuroscience research.

[107]  T. Jessell,et al.  Requirement for LIM Homeobox Gene Isl1 in Motor Neuron Generation Reveals a Motor Neuron– Dependent Step in Interneuron Differentiation , 1996, Cell.

[108]  J. Adams,et al.  Diffuse axonal injury in head injury: Definition, diagnosis and grading , 1989, Histopathology.

[109]  Anil Dolgun,et al.  onewaytests: An R Package for One-Way Tests in Independent Groups Designs , 2018, R J..

[110]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[111]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[112]  E. Hansson,et al.  Astrocyte–endothelial interactions at the blood–brain barrier , 2006, Nature Reviews Neuroscience.

[113]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[114]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[115]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[116]  M. Nausch,et al.  [Interleukin 1 (IL 1)]. , 1989, Allergie und Immunologie.

[117]  P. Henson,et al.  Biologial effects of the human complement fragments C5a and C5ades Arg on neutrophil function. , 1980, Immunopharmacology.

[118]  Supplemental Information 2: Kyoto Encyclopedia of genes and genomes. , 2022 .