Transcritptomic on Ageing and learning processes (RNA-Seq)
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE246775 | GEO | 2025/06/04
REPOSITORIES: GEO
Similar Datasets
Project description:Transcritptomic on Ageing and learning processes (RNA-Seq)
| PRJNA1034595 | ENA
Project description:This project aims to assess the transcriptomic signature in the dorsal hippocampus of 12 month-old Thy-Tau22 mice in basal conditions and treated with the vehicle CSP (n=4) or CSPTTK21 (n=3), compared to CSP-treated WT (n=4) mice.
2025-06-04 | GSE246774 | GEO
Project description:Background: The risk for dementia increases exponentially from the seventh decade of life. Identifying and understanding the biochemical changes that sensitize the ageing brain to neurodegeneration will provide new opportunities for dementia prevention and treatment. This study aimed to determine how ageing and major genetic risk factors for dementia affect the hippocampal proteome and lipidome of neurologically-normal humans over the age of 65. The hippocampus was chosen as it is highly susceptible to atrophy with ageing and in several neurodegenerative diseases. Methods: Mass spectrometry-based proteomic and lipidomic analysis of CA1 hippocampus samples from 74 neurologically normal human donors, aged 66 – 104, was used in combination with multiple regression models and gene set enrichment analysis to identify age-dependent changes in the proteome and lipidome. ANOVA was used to test the effect of major dementia risk alleles in the TMEM106B and APOE genes on the hippocampal proteome and lipidome, adjusting for age, gender, and post-mortem interval. Fibrillar C-terminal TMEM106B fragments were isolated using sarkosyl fractionation and quantified by immunoblotting. Results: Forty proteins were associated with age at false discovery rate-corrected P<0.05, including proteins that regulate cell adhesion, the cytoskeleton, amino acid and lipid metabolism, and ribosomal subunits. TMEM106B, a regulator of lysosomal and oligodendrocyte function, was regulated with greatest effect size. The increase in TMEM106B levels with ageing was specific to carriers of the rs1990622-A allele in the TMEM106B gene that increases risk for frontotemporal dementia, Alzheimer’s disease, Parkinson’s disease, and hippocampal sclerosis with ageing. Rs1990622-A was also associated with higher TMEM106B fibril content. Hippocampal lipids were not significantly affected by APOE genotype, however levels of myelin-enriched sulfatides and hexosylceramides were significantly lower, and polyunsaturated phospholipids were higher, in rs1990622-A carriers after controlling for APOE genotype. Conclusions: Our study demonstrates that TMEM106B protein abundance is increased with brain ageing in humans, establishes that dementia risk allele rs1990622-A predisposes to TMEM106B fibril formation in the hippocampus, and provides the first evidence that rs1990622-A affects brain lipid homeostasis, particularly myelin lipids. Our data suggests that TMEM106B is one of a growing list of major dementia risk genes that affect glial lipid metabolism.
2023-09-21 | PXD043880 | Pride
Project description:The role of the hippocampus in learning and memory has been widely studied. However, studies of differences along the longitudinal axis indicate that the hippocampus is perhaps not a singular structure, but instead it is thought that the dorsal and ventral poles of the hippocampus have functional differences. An anatomical gradient of hippocampal inputs along the dorsal-ventral axis supports this notion. It has been recently shown that there is transcriptional differentiation along the longitudinal axis of the adult hippocampus, coinciding with functional and anatomical gradients. Understanding the development of the dorsal-ventral hippocampal axis will further our understanding of the different hippocmapal functional contributions along the longitudinal axis. However, analysis of transcriptional gradients along the dorsal ventral axis have not been studied in the neonatal rat during development. We performed an extensive bead-chip based geneome-wide analysis of transcriptional differences in dorsal, intermediate, and ventral hippocampal tissue of rats aged postnatal day 0 (P0), P9, P18 and P60.
2015-05-01 | E-MTAB-2617 | biostudies-arrayexpress
Project description:This project aims to identify epigenetic signatures (histone acetylation-related) associated with Tau pathology in hippocampal region of Thy-Tau22 mice in basal conditions and after treatment with CSP-TTK21. For this we performed ChIP for H3K27ac in whole hippocampus of 12 month-old Tau reated with the vehicle CSP or CSP-TTK21, as well as of CSP-treated 12 month-old WT mice.In total we have 6 IPed samples (Biological duplicates were analyzed) and 3 Inputs. Spike-in from drosophila chromatin was added to the samples.
2025-06-04 | GSE246773 | GEO
Project description:Dorsal and ventral parts of the hippocampus despite similar histological structure are known to be involved in performance of different functions. Previous studies using next generation sequencing showed that these two hippocampal parts differ in the expression of many genes, however, stability of dorsoventral gradient of gene expression remains open question. Here, we analyzed differential expression of genes between the dorsal and ventral hippocampus of rats in polyA-enriched samples and samples subjected to depletion of ribosomal RNA. We present here a detailed analysis of differentially expressed genes between the dorsal and ventral parts of the hippocampus. Intersection of our dataset with data of previous RNAseq studies revealed 544 genes are stably differentially expressed between the hippocampal parts suggesting that, despite strongly variability between the animals and sequencing approaches, there is a subset of genes whose expression stably differs between the dorsal and ventral hippocampus. Analysis of differential splicing showed that the dorsal and ventral parts of the hippocampus express 64 genes whose splice isoforms are different between the hippocampal parts. Furthermore, we show that depletion of ribosomal RNA increases representation of transposable elements in the RNAseq libraries and helps to detect a weak predominance of expression of these elements in the ventral hippocampus.
2022-07-19 | GSE208330 | GEO
Project description:We carried out a global survey of age-related changes in mRNA levels in the C57BL/6NIA mouse hippocampus and found a difference in the hippocampal gene expression profile between 2-month-old young mice and 15-month-old middle-aged mice correlated with an age-related cognitive deficit in hippocampal-based explicit memory formation. Middle-aged mice displayed a mild but specific deficit in spatial memory in the Morris water maze. Experiment Overall Design: No technical replicates; 14 biological replicates for 15-month-old mice, 9 biological replicates for 2-month-old mice. Whole hippocampus.
2007-11-27 | E-GEOD-5078 | biostudies-arrayexpress
Project description:This project aims to assess the transcriptomic signature of FUS∆NLS/+ (FUS) vs FUS+/+ (WT) mice, by identifying differentially expressed genes in basal conditions and also during learning. Cytoplasmic mislocalization of the nuclear Fused in Sarcoma (FUS) protein is associated to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cytoplasmic FUS accumulation is recapitulated in the frontal cortex and spinal cord of heterozygous Fus∆NLS/+ mice. We show that in these mice, the hippocampus, a critical structure involved in learning and memory, paradoxically displays nuclear FUS accumulation. FUS binds to a set of genes characterized by the presence of an ETS/ELK-binding motifs, and involved in RNA metabolism, transcription, ribosome/mitochondria and chromatin organization. Importantly, hippocampal nuclei showed a decompaction of the neuronal chromatin at highly expressed genes and an inappropriate transcriptomic response was observed after spatial training of Fus∆NLS/+ mice. Furthermore, these mice lacked precision in hippocampal-dependent spatial memory task. These studies shows that mutated FUS affects epigenetic regulation of the chromatin landscape in hippocampal neurons, which could participate in FTD/ALS pathogenic events.
2024-11-30 | GSE218226 | GEO
Project description:Aging is associated with a decline in hippocampal mediated learning and memory, a process which can be ameliorated by dietary (caloric) restriction. We used Affymetrix gene expression analysis to monitor changes in three regions of the hippocampus (CA1, CA3, DG) of middle aged (18 months) and old (28 month) rats that were exposed to dietary restriction. Old rats were determined to be good performers (GP) or poor performers (PP) in behavioural tests to assess their hippocampal function. We used Affymetrix gene expression analysis to monitor changes in three regions of the hippocampus (CA1, CA3, DG) of middle aged (18 months) and old (28 month) rats that were exposed to dietary restriction.
2010-06-08 | E-GEOD-21681 | biostudies-arrayexpress
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).
2011-10-21 | E-GEOD-33137 | biostudies-arrayexpress