Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of rat spinal cord and oculomotor nucleus samples from animals aged 6, 18 and 30 months

ABSTRACT: Some of the most common neurodegenerative disorders have a strong association with aging. Curiously, these conditions tend to involve specific areas of the central and peripheral nervous system, at least initially. For example, amyotrophic lateral sclerosis preferentially targets spinal motor neurons and spares oculomotor neurons. This suggests that aging has divergent effects on brain stem and spinal cord, a factor that may explain differential susceptibility to certain neurodegenerative disorders. Therefore, for this study we asked whether aging induces a change in the evolution of the transcriptome of oculomotor nucleus (OMN) throughout the lifespan which would be different than that of the spinal cord aging. Age induced a transcriptome shift to a pattern consistent with inflammation/immune response in both OMN and spinal cord. However, the response was more dramatic in the spinal cord. On the other hand, age repressed genes coding ion channels and transporters in OMN and cytoskeletal proteins in the spinal cord. The results indicate that OMN and spinal cord transcriptomes change differently with age. The results give an initial glimpse of how tissue-specific gene expression patterns may underlie the differential susceptibility to age-related neuromuscular dysfunction. Experiment Overall Design: Total RNA was obtained with TRIzol (Invitrogen Carlsbad, CA) following the manufacturers recommended protocol. Tissues from 4 animals were combined into each RNA sample to decrease inter-subject variability. Biotinylated cRNA samples were hybridized to Affymetrix Rat Genome RA230 gene chips (n=18 chips) described previously [McMullen et al. 2004]. Microarrays were washed and stained with a streptavidin-bound marker and scanned. Data were analyzed with Affymetrix Microarray Suite 5.0 software. Only genes with consistent absent/present calls in all four independent replicates per group were considered for further analysis. Comparisons used the 6-mo transcriptome as the baseline and the one-sided Wilcoxonâ??s signed rank test to estimate â??increase/no change/ decreaseâ?? difference calls for each pair-wise comparison. Only difference calls consistent in all pair-wise comparisons and with average changes > 1.70 were considered significant, resulting in a conservative list of genes with changed expression levels. Functional classification of genes was based on an extensive literature review.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Colleen McMullen

PROVIDER: E-GEOD-3305 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Amyotrophic lateral sclerosis (ALS) spares the ocular motor system. In this study, we tested the hypothesis that the oculomotor neurons are intrinsically protected in ALS. Using high-density cDNA microarrays, we examined the transcriptome of oculomotor nuclei and spinal cords in mice expressing a human mutant SOD1, the SOD1(G93A) ALS model, at 6 and 10 weeks of age. Comparison of gene expression profiles of these pre-symptomatic SOD1(G93A) mice showed a shift to a proapoptotic state in spinal cords, while the opposite was true in oculomotor nuclei. Seventeen members of the A, B, C and D Hox clusters increased in oculomotor nuclei from 6 to 10 weeks of age; 15 were downregulated in spinal cord. Although only the first 4 classes of a given Hox cluster (e.g., Hoxa1-4) are normally expressed in the developing hindbrain, we found differential expression of mostly the latter classes in both oculomotor nuclei and spinal cords. Also, semaphorin 3B was expressed at 28-fold greater levels in oculomotor nuclei and 61-fold less in spinal cords in 10-week old SOD1(G93A) mice compared to 6-week old mice. Semaphorins 3A and 3E were also differentially regulated. Comparison of gene expression profiles of control SOD1 mice of 6 and 10 weeks of age did not show these changes. Based on these results, we rejected our hypothesis and conclude that the oculomotor nuclei actively adapt to the ALS-inducing mutation.,Supported by NEI and ALSA. <br>Overall design<br>Oligonucleotide microarray studies using the Affymetrix system were conducted as described earlier (McMullen et al., 2004). Biotinylated cRNA was hybridized to Affymetrix Mouse Expression Set 430A GeneChips. Then, the microarrays were washed and stained with a streptavidin-bound marker, and scanned with a laser scanner. Resulting microarray data were analyzed with Affymetrix Microarray Suite 5.0 software. Only those genes with consistent absent/present calls in the three independent replicates per group were considered for further analyses. Comparisons were crossed such that each oculomotor nuclei sample was compared with each spinal cord sample at the corresponding age. The Affymetrix software uses the one-sided Wilcoxons signed rank test to estimate increase/no change/decrease difference calls and fold-changes for each pair-wise comparison. Only difference calls consistent in all pair-wise comparisons and with average changes greater than 2-fold were considered significant, resulting in a conservative list of genes with changed expression levels.

Project description:ALS is a uniformly fatal neurodegenerative disease in which motor neurons in the spinal cord and brain stem are selectively lost. Individual motor - groups of motor neurons innervating single muscles - show widely varying degrees of disease resistance: in the final stages of ALS, nearly all voluntary movement is lost but eye movement and eliminative and sexual functions remain relatively unimpaired. These functions are controlled by motor neurons of the oculomotor (III), trochlear (IV) and abducens (VI) nuclei in the midbrain and brainstem, and by Onuf's nucleus in the lumbosacral spinal cord, respectively. Correspondingly, in ALS autopsies the oculomotor and Onuf's nuclei are almost completely preserved. We used microarray profiling of isolated wildtype mouse motor neurons to identify genes whose expression was characteristic of both oculomotor and Onuf's nuclei but not of vulnerable lumbar spinal neurons, or vice versa. Three wild-type C57BL/6J P7 male animals were perfused with 30% sucrose, lumbosacral spinal cord and midbrain regions were rapidly recovered, embedded in OCT compound, and frozen in liquid nitrogen. 12 um-thick cryosections were mounted on RNAse-free, PEN-foil covered glass slides (Zeiss), fixed for 2 min in 100% EtOH, rinsed in 50% EtOH, stained with 1% cresyl violet for 2 min, rinsed with 50% EtOH, dehydrated in graded solutions of ethanol and air dried prior to LCM using PALM Microbeam system (Zeiss). From each animal, ~200 DL, L5, and oculomotor motor neurons were collected directly in lysis buffer. RNA was purified using Absolutely RNA, NanoPrep kit (Stratagene, La Jolla, CA). RNA integrity was assessed on the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). At least 1.5 ng of purified RNA was the starting material used in the WT-Ovation Pico RNA Amplification System (Nugen, San Carlos,CA) with the FL-Ovation cDNA Biotin Module V2 (Nugen) to generate labeled probe. 10 ug of biotinylated cRNA from three independent samples for each motor neuron group isolated by LCM was hybridized to on Affymetrix (Santa Clara, CA) Mouse Genome 430 2.0 Arrays. Gene ontology and pathway analysis was performed using DAVID Bioinformatics Resources 6.7 (National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD).

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Transcription profiling of rat spinal cord and oculomotor nucleus samples from animals aged 6, 18 and 30 months

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