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Title: Gene expression patterns following unilateral traumatic brain injury reveals a local pro-inflammatory and remote anti-inflammatory response      
keywords:
Transcriptome or Gene expression
ID:
PRJNA196846
description:
Abstract Background Traumatic brain injury (TBI) results in irreversible damage at the site of impact and initiates cellular and molecular processes that lead to secondary neural injury in the surrounding tissue. We used microarray analysis to determine which genes, pathways and networks were significantly altered using a rat model of TBI. Adult rats received a unilateral controlled cortical impact (CCI) and were sacrificed 24h post-injury. The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue were used for microarray analysis. Ingenuity Pathway Analysis (IPA) software was used to identify molecular pathways and networks that were associated with the altered gene expression in brain tissues following TBI. Results Inspection of the top fifteen biological functions in IPA associated with TBI in the ipsilateral tissues revealed that all had an inflammatory component. IPA analysis also indicated that inflammatory genes were altered on the contralateral side, but many of the genes were inversely expressed compared to the ipsilateral side. The contralateral gene expression pattern suggests a remote anti-inflammatory molecular response. We created a network of the inversely expressed common (i.e., same gene changed on both sides of the brain) inflammatory response (IR) genes and those IR genes included in pathways and networks identified by IPA that changed on only one side. We ranked the genes by the number of direct connections each had in the network, creating a gene interaction hierarchy (GIH). Two well characterized signaling pathways, toll-like receptor/NF-kappaB signaling and JAK/STAT signaling, were prominent in our GIH. Conclusions Bioinformatic analysis of microarray data following TBI identified key molecular pathways and networks associated with neural injury following TBI. The GIH created here provides a starting point for investigating therapeutic targets in a ranked order that is somewhat different than what has been presented previously. In addition to being a vehicle for identifying potential targets for post-TBI therapeutic strategies, our findings can also provide a context for evaluating the potential of therapeutic agents currently in development. Overall design: The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue (n=3 for each) were used for RNA isolation. The TBI injured animals were Todd 1, 2 Todd, and Todd 3, each yielding an ispilateral and contralateral sample. The naïve animals were Xu 13 control, Xu 2 control, and Xu 6 control.
accesstypes:
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA196846
authentication:
none
authorization:
none
ID:
pmid:23617241
name:
Rattus norvegicus
ncbiID:
ncbitax:10116
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject
  • TL1 RR025010/RR/NCRR NIH HHS/United States

  • T15 LM007056/LM/NLM NIH HHS/United States

  • KL2 TR000455/TR/NCATS NIH HHS/United States

  • KL2 RR025009/RR/NCRR NIH HHS/United States

  • G12 RR003034/RR/NCRR NIH HHS/United States

  • U01 NS 057993/NS/NINDS NIH HHS/United States

  • 52006306/Howard Hughes Medical Institute/United States

  • U54 NS060659/NS/NINDS NIH HHS/United States

  • 5P20M006131-02/PHS HHS/United States

  • U54 RR026137/RR/NCRR NIH HHS/United States

  • S21MD000101/MD/NIMHD NIH HHS/United States

  • TL1 TR000456/TR/NCATS NIH HHS/United States

  • UL1 TR000454/TR/NCATS NIH HHS/United States

  • UL1 RR025008/RR/NCRR NIH HHS/United States

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