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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Changes in gene expression of Imr90 cells with age and senescence under 3% and 20% oxygen growth conditions

ABSTRACT: Senescent is an irreversible form of cell cycle arrest initiated by damaged cell constituents and subsequent pro-oncogenic signaling. Replicative senescence in vitro can be considered a model for human aging. When fibroblasts are cultured under atmospheric oxygen conditions of 20%, typical of normal tissue culture procedure, fibroblasts generally reach their replicative capacity at 50-60 population doublings (PDs). When fibroblasts are cultured under normal physiological oxygen conditions of 3%, PDs increase about 30% relative to atmospheric levels. Hence while oxygen is a requirement for normal aerobic respiration, it can contribute to the total amount of oxidative stress to which cells are exposed to, leading to a long-term adverse effect in vitro. Inasmuch, cultures maintained under hyperoxic and hypoxic conditions provide a convenient model system for assessing the relationship between oxygen/oxidative stress and senescence. We used microarrays to profile the changes in global gene expression during aging and senescence of Imr90 cells under growth oxygen conditions of 3% and 20%. Imr90 cells at various population doubling timepoints (young, old, and senescent) grown separately under 3 and 20% oxygen growth conditions were selected for RNA extraction and hybridization on Affymetrix microarrays. Timepoints from cells grown under 3% and 20% oxygen conditions were age matched via population doublings to ensure accurate cross sample comparison.

ORGANISM(S): Homo sapiens

SUBMITTER: Bernd Stab II

PROVIDER: E-GEOD-19018 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Changes in gene expression of Imr90 cells with age and senescence under 3% and 20% oxygen growth conditions

Project description:Senescent is an irreversible form of cell cycle arrest initiated by damaged cell constituents and subsequent pro-oncogenic signaling. Replicative senescence in vitro can be considered a model for human aging. When fibroblasts are cultured under atmospheric oxygen conditions of 20%, typical of normal tissue culture procedure, fibroblasts generally reach their replicative capacity at 50-60 population doublings (PDs). When fibroblasts are cultured under normal physiological oxygen conditions of 3%, PDs increase about 30% relative to atmospheric levels. Hence while oxygen is a requirement for normal aerobic respiration, it can contribute to the total amount of oxidative stress to which cells are exposed to, leading to a long-term adverse effect in vitro. Inasmuch, cultures maintained under hyperoxic and hypoxic conditions provide a convenient model system for assessing the relationship between oxygen/oxidative stress and senescence. We used microarrays to profile the changes in global gene expression during aging and senescence of Imr90 cells under growth oxygen conditions of 3% and 20%.

2010-03-01 | GSE19018 | GEO

Expression data from control infected and H-RASG12V infected IMR90 cells.

Project description:Cellular senescence is a stable proliferation arrest associated with an altered secretory pathway, the Senescence-Associated Secretory Phenotype (SASP). However, cellular senescence is initiated by diverse molecular triggers, such as activated oncogenes and shortened telomeres, and is associated with varied and complex physiological endpoints, such as tumor suppression and tissue aging. The extent to which distinct triggers activate divergent modes of senescence that might be associated with different physiological endpoints is largely unknown. To begin to address this, we performed gene expression profiling to compare the senescence programs associated with two different modes of senescence, oncogene-induced senescence (OIS) and replicative senescence (RS [in part caused by shortened telomeres]). While both OIS and RS are associated with many common changes in gene expression compared to control proliferating cells, they also exhibit substantial differences. These results are discussed in light of potential physiological consequences, tumor suppression and aging. We used microarrays to detail the global programme of gene expression after oncogene induced senescence.

2014-02-28 | E-GEOD-54402 | biostudies-arrayexpress

RNA-seq of human fibroblasts during normal aging and during aging with rotenone perturbation

Project description:Human fibroblasts at different population doublings were treated with low amounts of rotenone (mild stress) and compared to untreated fibroblasts. Two different cell lines were used (MRC-5, HFF). Illumina sequencing (HiSeq2000) was applied to generate 50bp single-end reads. 60 samples: 3 biological replicates for each group: MRC-5 cells at 4 different population doublings (PD) with and without rotenone; HFF cells at 6 different population doublings with and without rotenone

2015-08-26 | E-GEOD-64553 | biostudies-arrayexpress

Effects of hTERT overexpression on gene expression profiles in CD4+ T lymphocytes

Project description:Analysis of gene expression by Affymetrix microarray in a CD4+ T lymphocyte clone transduced with hTERT-GFP vector after after 44 and 80 population doublings (PDs). The untransduced (32 PDs) and GFP-control vector transduced (47 PDs) T cell clone populations served as controls. Keywords: ordered

2005-05-02 | GSE2230 | GEO

Transcription profiling of human CD4+ T lymphocytes overexpressing hTERT

2008-06-12 | E-GEOD-2230 | biostudies-arrayexpress

SerpinB2/TPPII regulates senescence

Project description:Tripeptidyl peptidase II (TPPII) degrades N-terminal tripeptides from proteins and peptides. Studies in both human and mice have shown that TPPII deficiency is linked to cellular immune-senescence, lifespan regulation, and the aging process. However, the mechanism of how TPPII participates in these processes is less clear. In this study, we established a chemical probe-based assay and found that while the mRNA and protein levels of TPPII were not altered during senescence, its enzymatic activity was reduced in senescent human fibroblasts. We also showed that elevation of serine protease inhibitor serpinB2 reduced TPPII activity in senescent cells. Moreover, suppression of TPPII led to elevation of lysosomal contents as well as TPPI and -galactosidase activities, suggesting that the lysosome biogenesis is induced to compensate for the reduction of TPPII activity in senescent cells. Together this study discloses a critical role of the serpinB2/TPPII signaling pathway in proteostasis during senescence. Since serpinB2 level can be increased by a variety of cellular stresses, reduction of TPPII activity through activation of serpinB2 might represent a common pathway for cells to respond to different stress conditions.

2022-05-31 | PXD033808 | Pride

MicroRNA signature of young and replicative senescent human umbilical vein endothelial cells (HUVECs)

Project description:MicroRNAs regulate various cellular processes. While several genes associated with replicative senescence have been described in endothelial cells, miRNAs that regulate these genes remain largely unknown. The present study was designed to identify miRNAs associated with replicative senescence and their target genes in HUVECs. We have employed Agilent Human MicroRNAs microarray platform to evaluate the expressions of 866 human miRNAs and 89 human viral miRNAs, based on Sanger miRNA database release 12.0 miRNA expression profiles were established for young and replicative senescent HUVECs

2013-04-05 | E-GEOD-37092 | biostudies-arrayexpress

Gene signature of young and replicative senescent human umbilical vein endothelial cells (HUVECs)

Project description:MicroRNAs regulate various cellular processes. While several genes associated with replicative senescence have been described in endothelial cells, miRNAs that regulate these genes remain largely unknown. The present study was designed to identify miRNAs associated with replicative senescence and their target genes in HUVECs. Gene profiling was established using the same RNA input as that used for miRNA profiing. We have employed Agilent Whole Human Genome microarray platform to evaluate the expressions of 19,596 human genes . Gene expression profiles were established for young and replicative senescent HUVECs

2013-04-05 | E-GEOD-37091 | biostudies-arrayexpress

Ofd2+/-hypoxia

Project description:Investigation of mRNA expression level changes in S. pombeOfd2 (SPAP8A3.02c) deletion strain compared to wild-type strain at both normal oxygen (normoxia) and low oxygen (hypoxia) growth conditions. Four samples in total consisting of two S. pombeyeast strains, wild type (WT) and a gene deleted strain for Ofd2 (SPAP8A3.02c), analysed for gene expression under two growth conditions, normal oxygen (normoxia) and low oxygen (hypoxia). Five micrograms of total RNA from two independent experiments were pooled and mRNA levels were quantified by Roche NimbleGen using the S. pombe 72K array service

2011-08-05 | E-GEOD-31236 | biostudies-arrayexpress

Myeloma cancer cells can corrupt mesenchymal stromal senescent cells and impair their anti-tumor activity

Project description:Senescent cells secrete many molecules, which contribute to the prevention of cancer progression. We induced MSC senescence by oxidative stress, DNA damage, and replicative exhaustion. The first two are considered inducers of acute senescence while extensive proliferation triggers replicative senescence also named chronic senescence. We cultivated cancer cells in the presence of acute and chronic senescent MSC conditioned media and evaluated proliferation, DNA damage, apoptosis and senescence.

2018-10-25 | PXD003018 | Pride

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