Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of rats treated with denervation vs. sham treated to identify genes with altered regulation during cortical re-organization

ABSTRACT: The adult somatosensory cortex undergoes reorganization in response to changes in peripheral input, such as limb usage patterns or denervation/amputation. This reorganization underlies important phenomena, such as phantom pain, recovery after stroke, and certain forms of learning. Although cellular processes, such as LTP, receptor regulation, axonal growth and synaptic formation have been theorized and studied in relation to cortical reorganization, conclusive evidence remains elusive. The identification of genes up- and down-regulated during reorganization will provide clues for which processes underlie reorganization. Reorganization is likely to involve forms of signaling between cortical neurons (e.g. release of growth factors), which could be identified through gene chip studies. Identification of genes modulated during reorganization will provide specific direction for further studies in the elucidation of the mechanism(s) underlying cortical reorganization.,To identify those genes with altered regulation during the cortical reorganization process.,We hypothesize that genes regulated during cortical reorganization will be components of the mechanism(s) underlying this important process, and that identification of these genes will provide insight for the design of further studies of cortical plasticity.,Cortical reorganization in rat somatosensory cortex (S1) will be induced at the forepaw/lower jaw border by partially denervating the paw. The animals will be recovered and the reorganization allowed to proceed for 3, 7, 14 and 28 days. Control animals will receive a sham denervation. Following the allotted time, the border between the lower jaw and the now silent forepaw cortex will be mapped in vivo. A 500 um wide strip of cortex surrounding the border area will be excised and stored in RNAlater (Qiagen) at 20oC until processed for RNA extraction. The tissue will be dispersed using a disposable pestle and microcentrifuge tube and then homogenized in Qiashredder (Qiagen) columns. RNA will be extracted using a RNeasy Micro Kit. However, if the UCLA center has a rotor/stator homogenizer with a microcentrifuge tube sized probe, we would like to discuss the possibility of performing the RNA extraction there (we would expect a better yield, and cannot locate this equipment at UCR). An initial portion of this study will done for 3 day experimental and sham control animals, plus non-operated animals, with four animals per group. This will be to determine the variability among our samples and to familiarize our personnel with the process. The number of samples/group necessary for the remaining time points may be modified based on the results of the 3 day study.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Elizabeth Salomon

PROVIDER: E-GEOD-2874 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The adult somatosensory cortex undergoes reorganization in response to changes in peripheral input, such as limb usage patterns or denervation/amputation. This reorganization underlies important phenomena, such as phantom pain, recovery after stroke, and certain forms of learning. Although cellular processes, such as LTP, receptor regulation, axonal growth and synaptic formation have been theorized and studied in relation to cortical reorganization, conclusive evidence remains elusive. The identification of genes up- and down-regulated during reorganization will provide clues for which processes underlie reorganization. Reorganization is likely to involve forms of signaling between cortical neurons (e.g. release of growth factors), which could be identified through gene chip studies. Identification of genes modulated during reorganization will provide specific direction for further studies in the elucidation of the mechanism(s) underlying cortical reorganization. To identify those genes with altered regulation during the cortical reorganization process. We hypothesize that genes regulated during cortical reorganization will be components of the mechanism(s) underlying this important process, and that identification of these genes will provide insight for the design of further studies of cortical plasticity. Cortical reorganization in rat somatosensory cortex (S1) will be induced at the forepaw/lower jaw border by partially denervating the paw. The animals will be recovered and the reorganization allowed to proceed for 3, 7, 14 and 28 days. Control animals will receive a sham denervation. Following the allotted time, the border between the lower jaw and the now silent forepaw cortex will be mapped in vivo. A 500 um wide strip of cortex surrounding the border area will be excised and stored in RNAlater (Qiagen) at 20oC until processed for RNA extraction. The tissue will be dispersed using a disposable pestle and microcentrifuge tube and then homogenized in Qiashredder (Qiagen) columns. RNA will be extracted using a RNeasy Micro Kit. However, if the UCLA center has a rotor/stator homogenizer with a microcentrifuge tube sized probe, we would like to discuss the possibility of performing the RNA extraction there (we would expect a better yield, and cannot locate this equipment at UCR). An initial portion of this study will done for 3 day experimental and sham control animals, plus non-operated animals, with four animals per group. This will be to determine the variability among our samples and to familiarize our personnel with the process. The number of samples/group necessary for the remaining time points may be modified based on the results of the 3 day study. Keywords: time-course

Project description:Genome-wide transcriptional profiling allows characterization of the molecular underpinnings of neocortical organization, including cortical areal specialization, laminar cell type diversity and functional anatomy. Microarray analysis of individual cortical layers across sensorimotor and association cortices in rhesus macaque demonstrated robust and specific laminar and areal molecular signatures driven by differential expression of genes associated with specialized neuronal function. Gene expression corresponding with laminar architecture was generally similar across cortical areas, although genes with robust areal patterning were often highly laminar as well, and these patterns were more highly conserved between macaque and human as compared to mouse. Layer 4 of primate primary visual cortex displayed a distinct molecular signature compared to other cortical regions, a specialization not observed in mouse. Overall, transcriptome-based relationships were strongest between proximal layers in a cortical area, and between neighboring areas along the rostrocaudal axis, reflecting in vivo cortical spatial topography and therefore a developmental imprint. Tissue from male and female monkeys (n = 2-3 animals/gender) was collected from anterior cingulate gyrus (ACG), layers 2, 3, 5, 6; orbitofrontal cortex (OFC), layers 2, 3, 5, 6; dorsolateral prefrontal cortex (DLPFC), layers 2-6; primary motor cortex (M1), layers 2, 3, 5, 6; primary somatosensory cortex (S1), layers 2-6; primary auditory cortex (A1), layers 2-6; primary visual cortex (V1), layers 2-6 including 4A, 4B, 4Calpha (4Ca), 4Cbeta (4Cb); secondary visual cortex (V2), layers 2-6; middle temporal area (MT), layers 2-6; temporal area (TE), layers 2-6; hippocampus, CA1, CA2, CA3, dentate gyrus (DG); and dorsal lateral geniculate nucleus (LGN), magnocellular, parvocellular and koniocellular divisions. Due to the limited number of samples that could be amplified concurrently, amplifications were performed in 3 batches (batches A-C, containing 102, 119 and 10 experimental samples, respectively). To control for batch effects, common RNA pool control samples were amplified and hybridized in each batch. These included LCM extracted hippocampus CA3 samples from the current study and a whole rhesus brain RNA pool (Biochain). These control samples were hybridized in 6 replicates in batch A and B and in 3 replicates in batch C (3 replicates per 96 well plate).

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Transcription profiling of rats treated with denervation vs. sham treated to identify genes with altered regulation during cortical re-organization

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