title: Network Reconstruction Reveals that Valproic Acid Activates Neurogenic Transcriptional Programs in Adult Brain Following Traumatic Injury.
abstract: OBJECTIVE
  To determine the mechanism of action of valproic acid (VPA) in the adult central nervous system (CNS) following traumatic brain injury (TBI) and hemorrhagic shock (HS).
  
  
  METHODS
  Data were analyzed from different sources, including experiments in a porcine model, data from postmortem human brain, published studies, public and commercial databases.
  
  
  RESULTS
  The transcriptional program in the CNS following TBI, HS, and VPA treatment includes activation of regulatory pathways that enhance neurogenesis and suppress gliogenesis. Genes which encode the transcription factors (TFs) that specify neuronal cell fate, including MEF2D, MYT1L, NEUROD1, PAX6 and TBR1, and their target genes, are induced by VPA. VPA represses genes responsible for oligodendrogenesis, maintenance of white matter, T-cell activation, angiogenesis, and endothelial cell proliferation, adhesion and chemotaxis. NEUROD1 has regulatory interactions with 38% of the genes regulated by VPA in a swine model of TBI and HS in adult brain. Hi-C spatial mapping of a VPA pharmacogenomic SNP in the GRIN2B gene shows it is part of a transcriptional hub that contacts 12 genes that mediate chromatin-mediated neurogenesis and neuroplasticity.
  
  
  CONCLUSIONS
  Following TBI and HS, this study shows that VPA administration acts in the adult brain through differential activation of TFs responsible for neurogenesis, genes responsible for neuroplasticity, and repression of TFs that specify oligodendrocyte cell fate, endothelial cell chemotaxis and angiogenesis. Short title: Mechanism of action of valproic acid in traumatic brain injury.
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA. gehiggin@med.umich.edu.
authors.forename: Gerald A
authors.initials: GA
authors.lastname: Higgins
authors.affiliation: Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Georgoff
authors.affiliation: Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA.
authors.forename: Vahagn
authors.initials: V
authors.lastname: Nikolian
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
authors.forename: Ari
authors.initials: A
authors.lastname: Allyn-Feuer
authors.affiliation: College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Pauls
authors.affiliation: Department of Computer Science, University of Maryland, College Park, Maryland, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Higgins
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA.|Michigan Institute for Data Science (MIDAS), Ann Arbor, Michigan, USA.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Athey
authors.affiliation: Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA.
authors.forename: Hasan E
authors.initials: HE
authors.lastname: Alam
mesh_terms: D000328:Adult; D000818:Animals; D000927:Anticonvulsants / Q000494:pharmacology*; D001921:Brain / Q000187:drug effects* / Q000378:metabolism / Q000473:pathology; D000070642:Brain Injuries, Traumatic / Q000378:metabolism* / Q000473:pathology; D045744:Cell Line, Tumor; D015870:Gene Expression; D053263:Gene Regulatory Networks; D006801:Humans; D055495:Neurogenesis / Q000235:genetics; D009473:Neuronal Plasticity / Q000235:genetics; D009474:Neurons / Q000473:pathology; D009836:Oligodendroglia / Q000473:pathology; D010597:Pharmacogenetics; D012377:Rodentia; D012771:Shock, Hemorrhagic / Q000378:metabolism* / Q000473:pathology; D013552:Swine; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D015533:Transcriptional Activation; D014635:Valproic Acid / Q000494:pharmacology*
chemical_list: D000927:Anticonvulsants; D014157:Transcription Factors; D014635:Valproic Acid
keywords: bioinformatics; network modeling; pharmacoepigenomics