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Genomic transcriptional profiling identifies candidates genes for successful aging

ABSTRACT: The inbred LOU/C/Jall rat is currently described as a model of successful aging. These rats have a longer healthy median lifespan than other strains, do not develop obesity, diabetes, or tumor and more importantly they do not show cognitive decline with aging. This is the first study to examine gene expression changes in the inbred LOU/C/Jall rat hippocampus and frontal cortex. Microarray data from LOU/C/Jall rats aged of 5 months were compared to the one measured in rats aged of 26 month. We have identified a set of 15 genes in the hippocampus and 70 genes in the frontal cortex that could be grouped into several clusters of similar expression profiles and that are involved in biological functions, namely regulation of plasticity, inflammatory response, metabolic, catabolic and homeostatic processes, and transcription. Genes were mainly up-regulated in aged brain.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE36722 | GEO | 2012/10/01

SECONDARY ACCESSION(S): PRJNA153797

REPOSITORIES: GEO

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Genomic transcriptional profiling identifies candidates genes for successful aging

Project description:The inbred LOU/C/Jall rat is currently described as a model of successful aging. These rats have a longer healthy median lifespan than other strains, do not develop obesity, diabetes, or tumor and more importantly they do not show cognitive decline with aging. This is the first study to examine gene expression changes in the inbred LOU/C/Jall rat hippocampus and frontal cortex. Microarray data from LOU/C/Jall rats aged of 5 months were compared to the one measured in rats aged of 26 month. We have identified a set of 15 genes in the hippocampus and 70 genes in the frontal cortex that could be grouped into several clusters of similar expression profiles and that are involved in biological functions, namely regulation of plasticity, inflammatory response, metabolic, catabolic and homeostatic processes, and transcription. Genes were mainly up-regulated in aged brain. Gene expression profil in hippocampus and cortex frontal of LOU/C/Jall rats strain. Rats were 3 and 26 months old.

2012-10-01 | E-GEOD-36722 | biostudies-arrayexpress

Transcription profiling of rats from inbred alcohol-preferring and -non-preferring strains in five brain regions

Project description:The objective of this study was to test the hypothesis that innate differences in gene expression in the brain could; contribute to the differences in alcohol drinking or response to alcohol between adult male inbred alcohol-preferring (iP) and -non-preferring; (iNP) rats. Gene expression was determined in the nucleus accumbens (ACB), amygdala (AMYG), frontal cortex (FC), caudate-putamen (CPU) and; hippocampus (HIP) of alcohol-na√É¬Øve adult male iP and iNP rats, using Affymetrix Rat Genome U34A microarrays (n = 6/strain). Significant differences between the two strains for each region were determined using Statistical Analysis of Microarrays (SAM). Using a false discovery rate threshold of 0.2, there were 46 genes with higher expression in iP rats and 61 genes with lower expression in; the ACB, 111 genes with higher and 56 genes with lower expression in the AMYG, 61 genes with higher and 25 genes with lower expression in the FC,; 39 genes with higher and 42 genes with lower expression in the CPU, and 35 genes with higher and 51 genes with lower expression in the HIP. In the AMYG, iP rats had higher expression of genes that are involved in neuronal growth and neurogenesis, e.g., brain derived neurotrophic factor,; neuritin, etc. In contrast, in the ACB, iP rats had lower expression of genes involved in neurogenesis or cellular plasticity,; e.g. cyclin E, vascular endothelial growth factor A. Many of the differences were in genes involved in intracellular signaling,; cell membranes, extracellular matrix, and metabolism. These regional gene differences between the iP and iNP rat lines may contribute to; the divergent alcohol drinking phenotypes of these rats. Experiment Overall Design: Brain regions (accumbens, amygdala, frontal cortex, hippocampus, and striatum) from 6 biologic replicates of the selected inbred alcohol preferring and non-preferring lines iP5C and iNP1 were dissected and subjected to microarray analysis for comparison.

2008-11-22 | E-GEOD-4494 | biostudies-arrayexpress

Functional Gene Expression Differences between Inbred Alcohol-Preferring (iP) and non-preferring (iNP) Rats

Project description:The objective of this study was to test the hypothesis that innate differences in gene expression in the brain could contribute to the differences in alcohol drinking or response to alcohol between adult male inbred alcohol-preferring (iP) and -non-preferring (iNP) rats. Gene expression was determined in the nucleus accumbens (ACB), amygdala (AMYG), frontal cortex (FC), caudate-putamen (CPU) and hippocampus (HIP) of alcohol-naïve adult male iP and iNP rats, using Affymetrix Rat Genome U34A microarrays (n = 6/strain). Significant differences between the two strains for each region were determined using Statistical Analysis of Microarrays (SAM). Using a false discovery rate threshold of 0.2, there were 46 genes with higher expression in iP rats and 61 genes with lower expression in the ACB, 111 genes with higher and 56 genes with lower expression in the AMYG, 61 genes with higher and 25 genes with lower expression in the FC, 39 genes with higher and 42 genes with lower expression in the CPU, and 35 genes with higher and 51 genes with lower expression in the HIP. In the AMYG, iP rats had higher expression of genes that are involved in neuronal growth and neurogenesis, e.g., brain derived neurotrophic factor, neuritin, etc. In contrast, in the ACB, iP rats had lower expression of genes involved in neurogenesis or cellular plasticity, e.g. cyclin E, vascular endothelial growth factor A. Many of the differences were in genes involved in intracellular signaling, cell membranes, extracellular matrix, and metabolism. These regional gene differences between the iP and iNP rat lines may contribute to the divergent alcohol drinking phenotypes of these rats. Keywords: alcohol, inbred, rat, gene expression, brain, nucleus accumbens, amygdala, frontal cortex, hippocampus, caudate-putamen

2007-07-28 | GSE4494 | GEO

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2014-04-01 | E-GEOD-55352 | biostudies-arrayexpress

Regional Differences in gene expression and promoter usage in aged human brains

Project description:Cap analysis of gene expression (CAGE) and massive parallel sequencing were used to profile the promoterome of aged human brains from five regions, namely: caudate, frontal cortex, hippocampus, putamen and temporal cortex. 25 RNA libraries from post-mortem brain tissue (five caudate, five frontal, 5 hippocampus, 5 putamen, five temporal RNA libraries from seven individuals) were processed using CAGE protocol and CAGE tags derived from the 25 libraries were sequenced with Illumina.

2013-01-15 | E-GEOD-43472 | biostudies-arrayexpress

Gene expression analysis of mouse brain.

Project description:Inbred mouse strains differ in their innate anxiety levels. We used RNA-sequencing to identify gene expression differences in hippocampus and frontal cortex of six mouse strains.

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Proteome profiling in aging rat brain by LC-MS/MS

Project description:This study investigated proteome profile in the hippocampus, medial prefrontal cortex (mPFC), and striatum of 14, 18, 23, and 27 months old rats in order to see the effect of aging on proteins in these regions. Using ultrahigh performance liquid chromatography coupled with Q Exactive HF Orbitrap mass spectrometry, we identified 1074 proteins in the hippocampus, 871 proteins in the mPFC, and 241 proteins the striatum. Ninety-seven, 25, and 5 of these proteins were differentially expressed with age in the hippocampus, mPFC, and striatum, respectively. Overall, aging causes divergent protein changes in specific brain regions, with the most prominent changes observed in the late-aged.

2018-07-12 | PXD009212 | Pride

Regional Differences in gene expression and promoter usage in aged human brains

2013-01-15 | GSE43472 | GEO

Transcription profiling of rat dentate gyrus of the hippocampus from young and aged rats to identification of putative learning and memory genes following the Morris Water Maze

Project description:The aim of this study was to investigate whether the differences in memory decline associated with aging are a result of differences in gene expression. We first categorized age-unimpaired and age-impaired rats based on their performance in the Morris water maze, when compared to young rats. Then we isolated messenger RNA from the dentate gyrus of the hippocampus of each animal to interrogate Affymetrix RAE 230A rat genome microarrays. Supervised statistical analysis of the different groups of aged animals recognized 85 genes (p<0.005) that were significantly different in the dentate gyrus of aged rats that had learned the Morris water maze (MWM) paradigm when compared to learning impaired and a number of controls for stress, exercise and non-spatial learning. In addition, statistical analysis of the microarray data that included young and aged rats identified 1129 genes (p<0.005) that were differentially expressed between aged and young rats independent of behavior, but due to aging alone. Experiment Overall Design: a total of 80 samples were analyzed including aged and young rats for aged versus young comparisons. One chip was interrogated per animal. Supervised analysis of aged rat data (aged unimpaired (HID U) versus controls : HID I, VIS, YOKE, SIT includes 39 samples (intermediate learners were not included in the analysis). Controls include cage controls, yoke controls (no platform), visible platform controls.

2008-06-13 | E-GEOD-4821 | biostudies-arrayexpress

Expression data from hippocampus and cortex of 6- and 12-week curcumin-treated 15-month-old rats

Project description:Curcumin has been demonstrated to have many neuroprotective properties, including improvement of cognition in humans and neurogenesis in animals, yet the mechanism of such effects remains unclear. Here, we assessed behavioural performance and hippocampal cell proliferation in aged rats after 6- and 12-week curcumin-fortified diets. Curcumin enhanced non-spatial and spatial memory, as well as dentate gyrate cell proliferation as compared to control diet rats. We also investigated underlying mechanistic pathways that might link curcumin treatment to increased cognition and neurogenesis via microarray analysis of cortical and hippocampal mRNA transcription. We used microarrays to investigate the effects of short-term (6-week) and long-term (12-week) curcumin-supplemented diet on gene expression of hippocampus and cortex in aged rats. The hippocampus and cortex of every three rats from one group were pooled together, respectively and used for RNA extraction and hybridization on Affymetrix microarrays. To ensure the reliability of the data, we conducted hybridization experiments in duplicate microarrays from each RNA sample. The tissues examined by microarray are as follows: the hippocampus and cortex of 6-week curcumin-treated 15-month-old rats, the hippocampus and cortex of 6-week no curcumin-treated 15-month-old rats (control rats), the hippocampus and cortex of 12-week curcumin-treated 15-month-old rats, the hippocampus and cortex of 12-week no curcumin-treated 15-month-old rats (control rats).

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