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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of liver from wild type mice of different ages to determine whether gene expression changes in naturally aged mice overlap with those from DNA repair deficient mice

ABSTRACT: To investigate whether and to which extent the gene expression changes in DNA repair deficient mice (i.e. Csbm/m/Xpa-/- and Ercc1-/-) overlap with those observed in a natural aged liver, we sought to compare the full mouse liver transcriptome of adult 16-, 96- and 130-week old wt C57Bl/6J mice (n=4) with that of adult 8-week old wt C57Bl/6J mice

ORGANISM(S): Mus musculus

SUBMITTER: Gijsbertus van der Horst

PROVIDER: E-MEXP-839 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A new progeroid syndrome reveals that genotoxic stress suppresses the somatotroph axis.

Niedernhofer Laura J LJ Garinis George A GA Raams Anja A Lalai Astrid S AS Robinson Andria Rasile AR Appeldoorn Esther E Odijk Hanny H Oostendorp Roos R Ahmad Anwaar A van Leeuwen Wibeke W Theil Arjan F AF Vermeulen Wim W van der Horst Gijsbertus T J GT Meinecke Peter P Kleijer Wim J WJ Vijg Jan J Jaspers Nicolaas G J NG Hoeijmakers Jan H J JH

Nature 20061201 7122

XPF-ERCC1 endonuclease is required for repair of helix-distorting DNA lesions and cytotoxic DNA interstrand crosslinks. Mild mutations in XPF cause the cancer-prone syndrome xeroderma pigmentosum. A patient presented with a severe XPF mutation leading to profound crosslink sensitivity and dramatic progeroid symptoms. It is not known how unrepaired DNA damage accelerates ageing or its relevance to natural ageing. Here we show a highly significant correlation between the liver transcriptome of old ...[more]

PMID: 17183314

Similar Datasets

Transcription profiling of liver from wild type or Ercc1 mutant mice

Project description:The XPF-ERCC1 endonuclease is required for repair of helix-distorting DNA damage and interstrand crosslinks. Here we have engineered a severe mutation in Ercc1 gene (in which the last 7 amino acids are missing; named as "Ercc1-delta") leading to extreme sensitivity to DNA crosslinks and progeria.To investigate whether a disturbance in growth and metabolism could explain the pronounced accelerated organismal deterioration seen in Ercc1 delta mice, we evaluated the liver transcriptome of 16-week-old wt and mutant mice (n=6). At this age, the Ercc1-delta mice have not yet become cachectic.

2008-06-01 | E-MEXP-1503 | biostudies-arrayexpress

Transcription profiling of liver from Ercc1-/- mice and wild type littermates to investigate features of premature aging

Project description:To investigate the cause of the premature aging features in the Ercc1-/- mouse, we compared the entire transcriptome of the Ercc1-/- mouse liver to that of wildtype littermates at the age of 15 days, when the Ercc1-/- mice reached their maximal weight and had symptoms of progeria, yet overall pathology was still limited. The liver was selected because the tissue showed several well-defined histological changes associated with aging (polyploidy and intranuclear inclusions) as well as evidence that it is responding to endogenous genotoxic stress (stabilized p53).

2006-12-21 | E-MEXP-834 | biostudies-arrayexpress

Transcription profiling of liver from Csbm/m/Xpa-/- knockout mice to investigate the effect of nucleotide excision repair pathway inactivation

Project description:Cockayne syndrome (CS) is a photosensitive, DNA repair disorder associated with progeria caused by a defect in the transcription-coupled repair (TCR) subpathway of nucleotide excision repair (NER). Here, complete inactivation of NER in Csbm/m/Xpa-/- mutants causes a phenotype that reliably mimics the human progeroid CS syndrome. Newborn Csbm/m/Xpa-/- mice display attenuated growth, progressive neurological dysfunction, retinal degeneration, cachexia, kyphosis and die before weaning. To investigate whether a disturbance in growth and metabolism could explain the pronounced accelerated organismal deterioration seen in Csbm/m/Xpa-/- mice, we evaluated the liver transcriptome of 15-day old wt, single and double mutant mice (n=4). At this age, the Csbm/m/Xpa-/- pups have not yet become cachectic. Mouse liver transcriptome analysis and several physiological endpoints revealed systemic suppression of the GH/IGF1 somatotroph axis and oxidative metabolism, increased antioxidant responses, hypoglycemia together with hepatic glycogen and fat accumulation. Broad genome-wide parallels between Csbm/m/Xpa-/- and naturally aged mouse liver transcriptomes suggested that these changes are intrinsic to natural aging and the DNA repair-deficient mice. Importantly, wild type (wt) mice exposed to a low dose of chronic genotoxic stress and adult Csbm/m mutant mice recapitulated this response, thereby pointing to a novel link between genome instability and the age-related decline of the somatotroph axis.

2007-01-01 | E-MEXP-835 | biostudies-arrayexpress

Transcription profiling of liver, lung, spleen and kidney from young (13 week) and aged (130 week) wild type mice

Project description:We compared the complete mouse liver, spleen, lung and kidney transcriptome of adult 13- and 130-wk old wt C57Bl/6J mice (n=3) to develop gene sets for young adult and aged wt mice, respectively

2008-06-01 | E-MEXP-1504 | biostudies-arrayexpress

Transcription profiling of aorta from mice underexpressing Fibulin-4 to investigate its role in elastic fibre assembly and cardio-vasuclar disease

Project description:Extracellular elastic fibres apply structure and mechanical elasticity to organs such as large arteries, lungs and skin 1. Elastic fibres are assembled through polymerization of tropoelastin monomers and loss of elastin is associated with aneurysmal degeneration of the aorta 2. The Fibulins are a six-member protein family hypothesized to function as intermolecular bridges that stabilize the organization of extracellular matrix structures such as elastic fibres and basement membranes 3. Fibulin-4 is found in the medial layers of arteries and moderately expressed in heart valves 4. To examine a potential role of Fibulin-4 in elastic fibre assembly and cardio-vascular disease we generated a mouse model underexpressing Fibulin-4. To get insight into the underlying molecular pathways involved in aneurysm formation, we determined the aorta transcriptome of Fibulin-4R/R animals and identified biological processes that were significantly overrepresented including apoptosis and cell death as well as several novel gene targets implicated in the response to aortic failure. We conclude that decreased Fibulin-4 expression causes aberrant composition of the elastin layers in the aorta and valvular leaflets, resulting in aortic aneurysms and heart abnormalities.

2007-01-01 | E-MEXP-840 | biostudies-arrayexpress

Gene expression profiling of Ercc1-/- and age-matched wt pancreata

Project description:Total RNA was isolated from wt and Ercc1-/- pancreata from 15 days old C57BL/6J wt and Ercc1-/- mice

2021-05-15 | E-MTAB-10393 | biostudies-arrayexpress

Two siblings with strong NER inactivation due to inherited ERCC1 deficiency display mild clinical features of XP and CS with severe liver impairment

Project description:The ERCC1-XPF heterodimer is a multifunctional endonuclease involved in nucleotide excision repair (NER), inter-strand crosslink (ICL) repair, and DNA double-strand break (DSB) repair. Only two patients with inherited ERCC1 defects have been reported who both died at an early age. Here, we describe a new case of ERCC1 deficiency in two siblings (11 and 13 years) who show mild features of Xeroderma Pigmentosum and Cockayne Syndrome. Both patients displayed microcephaly, mild developmental delay, mild photosensitivity, and severe cholestatic liver problems. Genetic analysis revealed a maternal deletion and a paternal missense variant in ERCC1 (R156W) that affect a salt bridge just below the XPA-binding pocket. Studies in patient-derived fibroblasts and reconstituted knockout cells confirmed that mutant ERCC1 is not efficiently recruited to the NER complex due to a decreased interaction with XPA. Consequently, patient cells show a strong NER defect, although residual repair could be detected. The steady-state protein levels of ERCC1 and XPF were severely reduced in patient cells, but this only led to a mild defect in ICL repair, and no impact on DSB repair. We report a new case of ERCC1 deficiency that particularly affect NER and has only a mild impact on other ERCC1-dependent repair pathways.

2021-01-26 | PXD017940 | Pride

Transcription profiling of mouse wild type and DNA repair-deficient primary dermal fibroblasts upon exposure to ultraviolet irradiation

Project description:Transcription profiling of wild type and DNA repair-deficient cells upon exposure to ultraviolet irradiation.

2009-04-01 | E-MEXP-1968 | biostudies-arrayexpress

Transcription profiling of mouse dermal fibroblasts exposed to hydrogen peroxide

Project description:Mouse dermal fibroblasts exposed to 0, 10 and 50mM of Hydrogen peroxide

2009-03-01 | E-MEXP-1975 | biostudies-arrayexpress

R_HAN_01.05 Mice sera fed with prebiotic or antibiotics

Project description:Control diet for C57Bl/6j Mice and effect on microbiota and immunity. Metabolome content of blood of these mice. LC-HRMS/MS C18+.

2019-07-05 | MSV000084062 | MassIVE

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