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| Status |
Public on Oct 31, 2014 |
| Title |
Unraveling the Specific Ischemic Core and Penumbra Transcriptome in Permanent Middle Cerebral Artery Occlusion Model Mice Brain Treated with Neuropeptide PACAP38 |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
Our group has been systematically investigating effects of the neuropeptide pituitary adenylate-cyclase activating polypeptide (PACAP) on the ischemic brain. To do so, we have established and utilizing the permanent middle cerebral artery occlusion (PMCAO) mouse model, where PACAP38 (1 pmol) injection is given intracerebroventrically in comparison to a control saline (0.9% NaCl) injection, in conjunction with high-throughput DNA microarray analysis. In previous studies, we have accumulated a large volume of data (gene inventory) from the whole brain (ipsilateral and contralateral hemispheres) by this approach. In our latest research, we have targeted specifically infract/ischemic core (hereafter IC) and the penumbra (hereafter P) post-PACA38 injection, for re-examining the transcriptome at 6 and 24 h post-treatment. The aim of the current study is simple – to delineate the specificity of expression and localization of differentially expressed molecular factors influenced by PACAP38. Prior to this highly expensive and time-consuming omic analysis, we checked the validity of our hypothesis and experimental strategy wherein, ischemic core and penumbra were carefully sampled and compared to the corresponding contralateral (healthy) IC and P regions at 6 and 24 h, post PACAP38 or saline injections to reveal expected differences in gene and protein expression by traditional reverse transcriptase-polymerase chain reaction (RT-PCR) and Western blot analyses, respectively (Hori et al., 2014). Our present results using the mouse 4x44K whole genome DNA chip reveal numerous changes (≧/≦ 1.5/0.75-fold) at both 6 h (654 and 456, and 522 and 449 up- and down-regulated genes for IC and P, respectively; and 24 h (2568 and 2684, and 1947 and 1592 up- and down-regulated genes for IC and P, respectively) after PACAP38 treatment. Using bioinformatics analysis by pathway- or specific-disease-state focused gene classifications and Ingenuity Pathway Analysis (IPA), these genes were functionally classified and discussed. Taken together, the DNA microarray analysis provides not only a great resource for further study, but also reinforces the importance of region-specific analyses in genome-wide identification of target molecular factors that might play a role in the neuroprotective function of PACAP38.
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| Overall design |
In the present study, we used three mice each in PMCAO groups for PACAP38 and saline injections, respectively, that exhibited neurological grades G1 and G2 for the subsequent downstream analysis. Six or 24 h post-injection of PACAP38 or saline, the mice were removed from their cages, decapitated, and their brains carefully removed on ice. The right (ipsilateral; ischemic) and left (contralateral) hemispheres were dissected, and from each hemisphere the ischemic core and penumbra regions and corresponding healthy core and penumbra were carefully removed with a sterile scalpel, and placed in 2 ml Eppendorf tubes. The samples were then quickly immersed in liquid nitrogen and stored in -80 ºC prior to further analysis. Effect of the intracerebroventricular PACAP38 administration into ischemic mouse brain was evaluated at the molecular level in the ischemic core and penumbra of ipsilateral (right) hemisphere over the saline injection by whole genome DNA microarray analysis (4x44K, Agilent).
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| Contributor(s) |
Hori M, Nakamachi T, Shibato J, Rakwal R, Shioda S, Numazawa S |
| Citation(s) |
25257527 |
| Submission date |
Oct 31, 2014 |
| Last update date |
May 10, 2018 |
| Contact name |
RANDEEP RAKWAL |
| E-mail(s) |
plantproteomics@gmail.com
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| Phone |
+81-(0)90-1853-7875
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| Organization name |
University of Tsukuba
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| Department |
Institute of Health and Sport Sciences
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| Lab |
GSI 403
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| Street address |
1-1-1 Tennodai
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| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8574 |
| Country |
Japan |
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| Platforms (1) |
| GPL4134 |
Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Feature Number version) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA265929 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE62884_RAW.tar |
41.6 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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