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Gene expression analysis of human lymphoblastoid cell lines

ABSTRACT: Human lymphoblastoid cell lines (EBV-immortalised B cells, LcL) obtained from subjects of different age (young 28-40 years, centenarians >95 years) were analysed for gene expression at basal culture conditions and after 48 hours of serum starvation. Lymphoid B cells from centenarians were more resistant to apoptosis induction and displayed a more developed lysosomal compartment, the most critical component of phagic machinery. In addition, cells from centenarians were capable of engulfing and digesting other cells, i.e. their siblings (even entire cells). This behavior was improved by nutrient deprivation but, strikingly, it was unaffected by the autophagy modulating drugs rapamycin, an autophagy inducer, and 3-methyladenine, an autophagy inhibitor. 12 samples, divided into 4 groups: young basal, young starved, centenarians basal and centenarians starved.

ORGANISM(S): Homo sapiens

SUBMITTER: Daniel Remondini

PROVIDER: E-GEOD-31040 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression analysis of human lymphoblastoid cell lines

Project description:Human lymphoblastoid cell lines (EBV-immortalised B cells, LcL) obtained from subjects of different age (young 28-40 years, centenarians >95 years) were analysed for gene expression at basal culture conditions and after 48 hours of serum starvation. Lymphoid B cells from centenarians were more resistant to apoptosis induction and displayed a more developed lysosomal compartment, the most critical component of phagic machinery. In addition, cells from centenarians were capable of engulfing and digesting other cells, i.e. their siblings (even entire cells). This behavior was improved by nutrient deprivation, but strikingly, it was unaffected by the autophagy-modulating drugs rapamycin, an autophagy inducer, and 3-methyladenine, an autophagy inhibitor.

2011-07-30 | GSE31040 | GEO

Epigenetic and transcriptional regulation of starvation-induced atrophy and autophagy programs by Foxk1 and Sin3A

Project description:Autophagy is the primary catabolic process triggered in response to starvation. Although autophagic regulation within the cytosolic compartment is well established, it is becoming clear that nuclear events also regulate the induction or repression of autophagy. Nevertheless, a thorough understanding of the mechanisms by which sequence-specific transcription factors modulate expression of genes required for autophagy is lacking. Here, we identify Foxk proteins (Foxk1 and Foxk2) as transcriptional repressors of autophagy in muscle cells and fibroblasts. Interestingly, Foxk1/2 serve to counter-balance another forkhead transcription factor, Foxo3, which induces an overlapping set of autophagic and atrophic targets in muscle. Foxk1/2 specifically recruits Sin3A-HDAC complexes to restrict acetylation of histone H4 and expression of critical autophagy genes. Remarkably, mTOR promotes the transcriptional activity of Foxk1 by facilitating nuclear entry to specifically limit basal levels of autophagy in nutrient-rich conditions. Our study highlights an ancient, conserved mechanism whereby nutritional status is interpreted by mTOR to restrict autophagy by repressing essential autophagy genes via Foxk-Sin3-mediated transcriptional control. Examination of (1) chromatin binding of Foxk1 and Sin3A in non-starved myoblasts and (2) gene expression profiling upon either starvation or siRNA-mediated depletion of Foxk1 relative to a non-starved control.

2014-11-17 | E-GEOD-56932 | biostudies-arrayexpress

Gene Expression Data in Human Monocyte-derived Dendritic Cell (MoDC) from Young and Aged Donors

Project description:Dendritic cells (DCs) are major antigen-presenting cells that play a key role in initiating and regulating innate and adaptive immune responses. DCs are critical mediators of tolerance and immunity. The functional properties of DCs changes with age. The purpose of this study was to define the age-associated molecular changes in DCs by gene array analysis using Affymatrix GeneChips. We identified up and down-regulated gene expression changes in DC from aged donors compared to young donors. Total 9 MoDC RNA samples from four young donors (20-27 years) and five aged donors (77-84 years) were analyzed using Affymetrix HG-U133A_2 Gene Arrays to compare differential gene expression changes in MoDC between aged and young groups

2014-05-28 | E-GEOD-58015 | biostudies-arrayexpress

Expression profile of miR-101 transfection in MCF-7 cells compared with scramble control

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2011-08-19 | E-GEOD-31397 | biostudies-arrayexpress

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2021-06-03 | E-MTAB-10413 | biostudies-arrayexpress

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2009-10-22 | E-MEXP-2379 | biostudies-arrayexpress

RNA expression in squamous cell carcinoma of the tongue and normal tissue adjacent to squamous cell carcinoma of the tongue

Project description:Increasing incidence of squamous cell carcinoma of the tongue (SCCT) in young patients has been reported. In this study, we aimed to investigate the transcriptional profiles in tumour and matched tumour-free tissue from patients with SCCT. Particularly, transcriptional profiles of young patients (< 40 years) were compared with those of old patients (> 50 years), in order to know whether young patients are transcriptionally different to old patients. A total of 12 patients with SCCT treated at The University hospital of Umeå (NUS) were recruited. Three patients were younger than 40 years old at diagnosis (young patient), and the other 9 patients were older than 50 years old (old patient). Biopsies of tumour and tumour-free tissues were fresh-frozen in liquid nitrogen and stored at -80°C until nuclear acid extraction.

2019-03-30 | E-MTAB-5534 | biostudies-arrayexpress

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2013-10-01 | E-MEXP-3878 | biostudies-arrayexpress

CG14435 (detour), the Drosophila ZNRF1 and 2 homologue, regulates autophagosome biogenesis critical for healthy aging

Project description:Autophagy is essential for animal development and homeostasis, and its deregulation is associated with numerous human pathologies. Here we identify a novel regulator of autophagy, the RING domain containing ubiquitin ligase CG14435 (detour). Depletion of CG14435 resulted in increased early-stage autophagic puncta, premature tissue contraction, and an accumulation of autophagy related proteins in young adults. Overexpression of CG14435 or the mammalian homologues, Zinc and RING finger (ZNRF) 1 and ZNRF2, increased late-stage autophagy puncta size. The ablation of ZNRF1 or ZNRF2 in mammalian cells increased basal autophagy. We identified CG14435 interacting proteins including HOPS complex subunits, deep orange (Vps18), Vps16A, and light (Vps41). Furthermore, in the presence of CG14435, dor ubiquitination was increased. The CG14435 mutant adults displayed premature aging, impaired motor function (neurodegeneration), and activation of innate immunity. Our findings reveal a novel role for CG14435 in autophagy, likely through regulation of HOPS complex, required for healthy aging.

2024-05-21 | PXD036857 | Pride

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