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Microarray data for rejuvenation experiments through reprogramming

ABSTRACT: Proliferative and replicative senescent fibroblasts from aged human donors were reprogrammed towards pluripotency and re-differentiated in fibroblasts and then further analyzed for rejuvenation assessment.

ORGANISM(S): Homo sapiens

PROVIDER: GSE27924 | GEO | 2011/12/14

SECONDARY ACCESSION(S): PRJNA137839

REPOSITORIES: GEO

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Microarray data for rejuvenation experiments through reprogramming

Project description:Proliferative and replicative senescent fibroblasts from aged human donors were reprogrammed towards pluripotency and re-differentiated in fibroblasts and then further analyzed for rejuvenation assessment. Comparison of microarrays were performed by non hierarchical clustering visualized in with Treeview software

2011-12-14 | E-GEOD-27924 | biostudies-arrayexpress

Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (RNA-Seq)

2024-03-20 | GSE237269 | GEO

Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (Hi-C)

Project description:Aging is associated with a progressive decline in cellular function. To reset the aged cellular phenotype, various reprogramming approaches, including mechanical routes, have been proposed. However, the epigenetic mechanisms underlying cellular rejuvenation are poorly understood. We studied the transcriptional and genome-wide chromatin organization changes in young, aged and mechanically rejuvenated fibroblasts using RNA-seq and Hi-C experiments. The mechanically rejuvenated aged fibroblasts, that had reset their transcription to a younger cell state, showed a reorganization of the inter-chromosomal contacts and lamina-associated domains. Interestingly, the observed chromatin reorganization correlated with the transcriptional changes. Immunofluorescence experiments in the rejuvenated state confirmed increased contractility and reduced chromosome copy number variations, similar to younger fibroblasts. In addition, the rejuvenated contractile properties were maintained over multiple cell passages. Taken together, our results provide a multi-scale characterization of the chromatin reorganization that accompanies cellular aging and rejuvenation.

2024-03-20 | GSE237268 | GEO

Development of gene expression signatures for identifying novel factors that can overcome age-associated reprogramming barriers

Project description:To investigate the molecular features underlying senescence and rejuvenation during aged cell reprogramming and identify novel factors that can overcome age-associated barriers, we compared gene expression for reprogramming intermediates on D8 of tail-tip fibroblasts (TTFs) from young Wild Type (WT), old WT, and old p16 knockout (KO) mice. We collected TTFs from young WT, old WT, and old p16 KO mice and reprogrammed the cells by introducing four reprogramming factors, including Oct4, Sox2, Klf4, and c-Myc. Gene expression of reprogramming intermediates on D8 were compared. Two independent experiments were performed using different mice donors for each experiment.

2016-03-31 | E-GEOD-79747 | biostudies-arrayexpress

Combining Stem Cell Rejuvenation and Senescence Targeting to Synergistically Extend Lifespan

Project description:We combine transient stem cell rejuvenation with targeted removal of senescent cells to test the hypothesis that simultaneously targeting both cell-fate based aging mechanisms will maximize life and health span benefits.

2022-04-24 | GSE201338 | GEO

RNAseq Replicate experiments from PD38 and PD79 IMR90s

Project description:RNAseq replicate in Proliferating and Senescent IMR90s We used RNAseq to examine RNA levels in human IMR90 replicative senescence (RS)

2014-12-15 | E-GEOD-53330 | biostudies-arrayexpress

H3K9me3 ChIPseq experiments from PD IMR90s

Project description:H3K9me3 ChIPseq in Proliferating and Senescent IMR90s We used ChIP-seq to examine the global binding of H3K9me3 in human IMR90 replicative senescence (RS) and oncogene-induced (OIS)

2014-12-15 | E-GEOD-53329 | biostudies-arrayexpress

Paracrine-Mediated Rejuvenation of Aged Mesenchymal Stem Cells

Project description:Paracrine-Mediated Rejuvenation of Aged Mesenchymal Stem Cells

| PRJNA844080 | ENA

NF-κB activation impairs somatic cell reprogramming in ageing [NGPS_iPSCs]

Project description:Transcriptional profiling of human control and Néstor-Guillermo Progeria Syndrome (NGPS) fibroblasts and induced pluripotent stem cells (iPSCs). Somatic cell reprogramming involves rejuvenation of adult cells and relies on the ability to erase age-associated molecular marks. Accordingly, reprogramming efficiency declines with ageing, and age-associated features such as genetic instability, cell senescence or telomere shortening negatively affect this process. However, the regulatory mechanisms that constitute age-associated barriers for cell reprogramming remain largely unknown. Here, by using cells from patients with premature ageing, we demonstrate that NF-κB activation is a critical barrier for the generation of induced pluripotent stem cells (iPSCs) in ageing. We show that NF-κB repression occurs during cell reprogramming towards a pluripotent state. Conversely, ageing-associated NF-κB hyperactivation impairs generation of iPSCs by eliciting reprogramming repressors DOT1L and YY1, reinforcing cell senescence signals and down-regulating pluripotency genes. We also show that genetic and pharmacological NF-κB inhibitory strategies significantly increase the reprogramming efficiency of fibroblasts from Néstor-Guillermo Progeria Syndrome (NGPS) and Hutchinson-Gilford Progeria Syndrome (HGPS) patients, as well as from normal aged donors. Finally, we demonstrate that DOT1L inhibition in vivo ameliorates the accelerated ageing phenotype and extends lifespan in a progeroid animal model. Collectively, our results provide evidence for a novel role of NF-κB in the control of cell fate transitions and reinforce the interest of studying age-associated molecular impairments to implement cell reprogramming methodologies, and to identify new targets of rejuvenation strategies. Control and NGPS fibroblasts were reprogrammed. RNA was extracted and transcriptional profiling was obtained with GeneChip Human Exon 1.0 ST Arrays.

2015-07-01 | E-GEOD-65170 | biostudies-arrayexpress

Induced Mesenchymal stromal cells derived from iPS cells from aged individuals acquire a rejuvenation signature and a MSC-specific secretome

Project description:Human induced pluripotent stem cells (iPSCs) - derived mesenchymal stromal cells (iMSCs) are a potentially useful cell type for circumventing ageing-related shortfalls associated with primary mesenchymal or skeletal stromal cells (MSCs/SSCs). To date, the extent of the reflection of ageing-hallmarks in iMSCs differentiated from iPSCs derived from elderly donors remains unclear. In this study, we show that fetal (55 days post conception) femur-derived MSCs and MSCs isolated from aged (60 – 74 years) donors differ in their transcriptome and secretome profile. Yet, iMSCs irrespective of donor age and cell type acquired a rejuvenation gene signature, specifically, INHBE, DNMT3B, POU5F1P1, CDKN1C, GCNT2; also present in pluripotent stem cells but not observed in the parental MSCs. Furthermore, dendrograms generated from the transcriptomes of iMSCs derived from the human embryonic stem cell line H1, fetal and aged MSCs always clustered together with the parental fetal femur-derived MSCs. In addition, these were distinct from MSCs isolated from aged donors when comparing gene ontologies (GOs) related to ageing processes. Critically, in terms of regenerative medicine applications, iMSCs re-acquired a similar secretome (e.g. SERPINE1, SDF-1a, HGF, IL6, IL10, THBS1) to that of the parental fetal MSCs, thus re-enforcing their capabilities of imparting context dependent paracrine signaling.

2019-03-13 | GSE97311 | GEO

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