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Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats

ABSTRACT: Aging is associated with the decline of protein, cell, and organ function. Here, we use an integrated approach to characterize gene expression, bulk translation, and cell biology in the brains and livers of young and old rats. We identify 468 differences in protein abundance between young and old animals. The majority are a consequence of altered translation output, that is, the combined effect of changes in transcript abundance and translation efficiency. In addition, we identify 130 proteins whose overall abundance remains unchanged but whose sub-cellular localization, phosphorylation state, or splice-form varies. While some protein-level differences appear to be a generic property of the rats’ chronological age, the majority are specific to one organ. These may be a consequence of the organ’s physiology or the chronological age of the cells within the tissue. Taken together, our study provides an initial view of the proteome at the molecular, sub-cellular, and organ level in young and old rats.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE66715 | GEO | 2015/09/22

SECONDARY ACCESSION(S): PRJNA277771

REPOSITORIES: GEO

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Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats

Project description:Aging is associated with the decline of protein, cell, and organ function. Here, we use an integrated approach to characterize gene expression, bulk translation, and cell biology in the brains and livers of young and old rats. We identify 468 differences in protein abundance between young and old animals. The majority are a consequence of altered translation output, that is, the combined effect of changes in transcript abundance and translation efficiency. In addition, we identify 130 proteins whose overall abundance remains unchanged but whose sub-cellular localization, phosphorylation state, or splice-form varies. While some protein-level differences appear to be a generic property of the rats’ chronological age, the majority are specific to one organ. These may be a consequence of the organ’s physiology or the chronological age of the cells within the tissue. Taken together, our study provides an initial view of the proteome at the molecular, sub-cellular, and organ level in young and old rats. The corresponding dataset in Gene Expression Omnibus is <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66715">GSE66715</a>.

2015-10-05 | PXD002467 | Pride

Integrated genome and proteome-wide analysis reveals organ-specific proteome deterioration during aging in rat

Project description:RNA-Seq and ribosome profiling describes changes in gene expression during aging RNA-Seq and ribosome profiling from matched young and old rat liver and brain

2015-09-22 | E-GEOD-66715 | biostudies-arrayexpress

miRNA expression data from sun-exposed and sun- protected skin of young (18-25 years) and old (>70 years) females

Project description:In this study we explored the effects of chronological and photoageing on the miRNome of human skin. To this end, miRNA expression was analysed in biopsies collected from sun-exposed (outer arm) and sun-protected (inner arm) skin from fair-skinned (phototype II/III) healthy female volunteers of two age groups: young, 18-25 years and aged, >70 years. Strict inclusion criteria were used for photoageing scoring and for chronological ageing. Microarray analysis revealed that chronological ageing had minor effect on the human skin miRNome. In contrast, photoageing had a robust impact on miRNAs, and a set of miRNAs differentially expressed between sun-protected and sun-exposed skin of the young and aged groups was identified. We have performed miRNome analysis (using microarray) on RNA isolated from sun-exposed and sun-protected skin of young and old females

2018-08-31 | GSE114006 | GEO

Epigenetic determinants of muscle stem cell quiescence and chronological aging (ChIP-seq)

Project description:Skeletal muscle is a post-mitotic tissue that exhibits an extremely low turnover in the absence of disease or injury. At the same time, muscle possesses remarkable regenerative capacity mediated by satellite cells (SCs) that reside in close association with individual myofibers, underneath the fiberM-bM-^@M-^Ys basal lamina. Consistent with the low turnover of the muscle, SCs in adult animals are mitotically quiescent and therefore provide an excellent model to study stem cell quiescence. As an organism grows older, the resident stem cells are exposed to a deteriorating environment and experience chronological aging. In stem cells with high turnover, the effects of chronological aging are superimposed upon the effects of the replicative aging that results from DNA replication and cell division. On the contrary, SCs experience minimal replicative aging due to their low turnover. They are thus a good model to study the consequence of chronological aging of quiescent stem cells. We have developed an isolation protocol to selectively enrich SCs by FACS from adult mice and applied the ChIP-seq technology to obtain H3K4me3, H3K27me3 and H3K36me3 from quiescent and activated SCs from young mice and from quiescent SCs from old mice. Our analysis aims to understand the chromatin features underlying stem cell properties such as quiecence and lineage-potency, and to understand how the chromatin structure of a quiescent stem cell pouplation changes with age. VCAM+/CD31-/CD45-/Sca1- quiescent satellite cells (QSCs) were isolated by FACS from hindlimb muscle of uninjured 2-3- or 22-24-month old mice and processed for ChIP-seq.

2013-08-13 | E-GEOD-47362 | biostudies-arrayexpress

Metabolomics Workbench ST000759 - GNPS - Age and exercise effect on metabolomics in rats

Project description:N/NIH rats were selected for either low (LRT) or high (HRT) response to training. Rats at 2 year of age were trained for 8 weeks with an improvement in oxidative capacity. Selection was also performed for high (HCR) or low (LCR) intrinsic running capacity. Young and old animals are compared to 12 week old animals.

2018-08-02 | MSV000082734 | GNPS

Genome-wide maps of small RNA transcription in young and old mouse oocytes

Project description:We report the abundance of different small RNAs in oocytes of young (8 weeks old) and older (9 months old) mouse females

2020-11-05 | GSE159789 | GEO

Expression data from rat skeletal muscle

Project description:We used old (~96-102 weeks of age) and young (~28-34 weeks of age) rats from HCR and LCR generations 29 and 32, respectively. The study included eight groups; HCR-Old-Exhausted (H-O-E, n=6), HCR-Old-Rest (H-O-R, n=6), HCR-Young-Exhausted (H-Y-E, n=6), HCR- Young -Rest (H-Y-R, n=6), LCR-Old-Exhausted (L-O-E, n=6), LCR-Old-Rest (L-O-R, n=6), LCR-Young-Exhausted (L-Y-E, n=6), and LCR- Young -Rest (L-Y-R, n=6). For the exhausted rats, dissections were performed within 10 min after the maximal running distance was reached. We extracted skeletal muscle RNA from a total of 48 female animals (n=6 in each of the 8 group). Skeletal muscle tissue was obtained from the Extensor digitorum longus (EDL). All rats were dissected immediately after sacrificing, and all tissue samples were immediately weighed and snap frozen in liquid nitrogen, and stored at -80 ºC. Total RNA was extracted from frozen tissue with Trizol reagent (Invitrogen, Carlsbad, CA), treated with DNase-free (Invitrogen, Carlsbad, CA) and cleaned up with RNeasy columns (Qiagen, Hilden, Germany)

2015-12-03 | GSE75629 | GEO

Effect of Age on Fracture Healing in the Rat: Series 2

Project description:Study of rat femur fracture healing in young (6 weeks old), adult (26 weeks old), and older (52 weeks old) rats with samples collected at 0 time (no fracture) and at 0.4, 1, 2, 4, and 6 weeks after fracture. RNA from two rats were pooled for each array. Keywords = rat, femur, fracture, age, time Keywords: time-course

2004-02-01 | GSE592 | GEO

Epigenetic determinants of muscle stem cell quiescence and chronological aging

Project description:Skeletal muscle is a post-mitotic tissue that exhibits an extremely low turnover in the absence of disease or injury. At the same time, muscle possesses remarkable regenerative capacity mediated by satellite cells (SCs) that reside in close association with individual myofibers, underneath the fiber’s basal lamina. Consistent with the low turnover of the muscle, SCs in adult animals are mitotically quiescent and therefore provide an excellent model to study stem cell quiescence. As an organism grows older, the resident stem cells are exposed to a deteriorating environment and experience chronological aging. In stem cells with high turnover, the effects of chronological aging are superimposed upon the effects of the replicative aging that results from DNA replication and cell division. On the contrary, SCs experience minimal replicative aging due to their low turnover. They are thus a good model to study the consequence of chronological aging of quiescent stem cells. We performed microarray analysis of quiescent and activated SCs from both young and aged mice to understand the global gene expression profile underlying stem cell properties such as quiecence and self-renewal, and to understand how the transcriptome of a quiescent stem cell pouplation changes with age. VCAM+/CD31-/CD45-/Sca1- quiescent satellite cells (QSCs) were isolated by FACS from hindlimb muscle of uninjured 2-3- or 22-24-month old mice. Activated satellite cells (ASCs) were isolated from hindlimb muscles of BaCl2-injured mice of the same age 36, 60 and 84 hours after injury using the same cell surface marker combination. YFP-expressing cells were isolated from 2-3-month old Pax7CreER/+; ROSA26eYFP/+ mice in which satellite cells are labeled geneticall by YFP expression. Total RNA was extracted from cells with the Trizol reagent according to manufacturer's instructions. RNA was then processed and assayed with Affymetrix Mouse Gene 1.0 ST arrays.

2013-05-23 | E-GEOD-47177 | biostudies-arrayexpress

MicroRNA profiling of human CD8 T cells - miR-17 and miR-19b to investigate down-regulatation in human aging

Project description:T cells from several blood donors were separated in populations corresponding to CD8+ CD28+ and CD8+ CD28- surface markers. Total RNA extracts from cells were hybridized to MRC LNA microarray. Contrasts of interest were CD8CD28- minus CD8CD28+ (replicative aging) and CD8CD28+ (old donors) minus CD8CD28+ (young donors), which corresponds to chronological aging.

2010-04-19 | E-MEXP-2398 | biostudies-arrayexpress

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