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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression analysis of aging cardiac tubes in Drosophila

ABSTRACT: Investigation of the whole genome expression levels from dissected adult cardiac tubes at 10 days and 40 day. We describe a functional genomic investigation of the genetic control of cardiac senescence in Drosophila. Molecular signatures of heart aging were identified by differential transcriptome analysis followed by a detailed bio-informatic analysis. This approach implicated the JNK/dJun pathway and the transcription factor Vri/dNFIL3 in the transcription regulatory network involved in cardiac senescence and suggested the possible involvement of oxidative stress (OS) in the aging process. 4 biological replicates for each time point (10 days and 40 days) were used. Dye-swap replications, in which each hybridization is done twice, with dye assignments reversed in the second hybridization, were used with a design which allows direct comparison between time points . This method allows technical replicates and eliminates variation that might result from differences in fluorescence dye intensities.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Laurent Perrin

PROVIDER: E-GEOD-40253 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression analysis of aging cardiac tubes in Drosophila

Project description:Investigation of the whole genome expression levels from dissected adult cardiac tubes at 10 days and 40 day. We describe a functional genomic investigation of the genetic control of cardiac senescence in Drosophila. Molecular signatures of heart aging were identified by differential transcriptome analysis followed by a detailed bio-informatic analysis. This approach implicated the JNK/dJun pathway and the transcription factor Vri/dNFIL3 in the transcription regulatory network involved in cardiac senescence and suggested the possible involvement of oxidative stress (OS) in the aging process.

2012-12-01 | GSE40253 | GEO

Gene Expression Profiling Data of African Malaria Vector Anopheles gambiae Aging

Project description:Senescence is a biological phenomenon experienced by all living eukaryote organisms. Genome-wide gene expression associated with aging has been explored in model organisms such as Drosophila melanogaster and Caenorhabditis elegans, but this has not been well understood in African malaria vector, Anopheles gambiae. Gene expression profiling using DNA microarray allows for simultaneous study of changes in mRNA levels for thousands of genes. This study examined genome-wide gene expression during aging process in An. gambiae. The influence of blood feeding on gene expression was also examined. The data can be used to further our understanding of mosquito senescence and identify biomarkers for mosquito age grading. Transcriptional profiles of Anopheles gambiae female mosquitoes were determined at 1, 4, 10, 19 and 28 days post adult eclosion. Additionally mosquitoes that had access to blood meals were compared to those that were maintained with access to only water and sugar.

2010-12-31 | E-GEOD-19756 | biostudies-arrayexpress

Introducing cellular senescence in human induced pluripotent stem cells and differentiated neural lineage for modeling of age-associated diseases

Project description:Reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) resets the epigenetic landscapes that mark the aging clock, and consequently cells differentiated from iPSCs resemble fetal cells rather than adult or aged cells. The lack of proper cellular aging in cells differentiated from iPSCs presents a significant problem in iPSC-based disease models to investigate the pathological progression of age-associated diseases such as neurodegeneration. To address this caveat, we introduced cellular senescence into iPSC-based cell models in this study, as senescence has been shown to play a critical role not only in aging but also in neurodegeneration. We created an inducible CRISPR interference (CRISPRi) targeting TERF2, a major component of the telomere protecting Shelterin complex. We demonstrated that suppression of TERF2 robustly activated DNA damage response, the p53/p21 signaling, cellular senescence and inflammatory response in iPSCs. The inducible approach allows the temporal control of senescence activation over the course of differentiation of iPSCs to desired cell types. We applied the CRISPRi-TERF2 system to differentiation of iPSCs into neural progenitor cells (NPCs) and showed that suppression of TERF2 efficiently activated DNA damage response, the p53/p21 signaling and senescence in differentiated NPCs. The inducible cell model of cellular senescence generated in this study has broad application in investigation of cellular senescence in the progression of age-related diseases and improvement of disease modeling with a proper cellular aging context to facilitate drug discovery.

2023-12-25 | GSE251814 | GEO

Single Nuclei Sequencing of old and young mice hearts under senolytica (Ageing impairs the neuro-vascular interface in the heart)

Project description:Aging is a major risk factor for impaired cardiovascular health. The aging myocardium is characterized by microcirculatory and diastolic dysfunction and increased susceptibility to arrhythmias. Nerves align with vessels during development. However, the impact of aging on the cardiac neuro-vascular interface is entirely unknown. Here, we report that aging reduces nerve density specifically in the left ventricle and dysregulates vascular-derived neuro-regulatory genes. Aging leads to a down-regulation of miR-145 and de-repression of the neuro-repulsive factor Semaphorin-3A. miR-145 deletion, which increased Sema3a expression, or endothelial Sema3a overexpression reduced axon density, thus mimicking the observed aged heart phenotype. Removal of senescent cells, which accumulated with chronological age in parallel to the decline in nerve density, rescued age-induced denervation, reduced Sema3a expression, preserved heart rate variability and reduced electrical instability. These data suggest that senescence-associated regulation of neuro-regulatory genes is associated with reduced nerve density and, thereby, contributes to age-associated cardiac dysfunction.

2023-07-05 | E-MTAB-13093 | biostudies-arrayexpress

Deep sequencing and functional annotation reveal miRNAs implicated in the cell senescence phenotype

Project description:In cell senescence, cultured cells cease proliferating and acquire aberrant gene expression patterns. MicroRNAs (miRNAs) modulate gene expression through translational repression or mRNA degradation, and have been implicated in senescence. We have used deep sequencing to carry out a comprehensive survey of miRNA expression and its involvement in cell senescence. Informatic analysis of small RNA sequence datasets from young and senescent IMR90 human fibroblasts identifies many known miRNAs, and a small number of novel miRNAs, that are regulated (either up or down) with cell senescence. Comparison with mRNA expression profiles revealed potential mRNA targets of the senescence-regulated miRNAs. The target mRNAs are enriched for genes involved in biological processes associated with cell senescence. This result greatly extends existing information on the role of miRNAs in cell senescence, and is consistent with miRNAs having a causal role in the process. Comprehensive survey of miRNA from young and senescent IMR90 fibroblasts using deep sequencing

2011-08-09 | E-GEOD-27404 | biostudies-arrayexpress

Gene Expression Profiling Data of African Malaria Vector Anopheles gambiae Aging

2010-12-31 | GSE19756 | GEO

Deep sequencing and functional annotation reveal miRNAs implicated in the cell senescence phenotype

2011-08-09 | GSE27404 | GEO

Global profiling of gene expression during glycerol-induced spore formation in Myxococcus xanthus

Project description:Myxococcus xanthus is a gram negative rod-shaped delta proteobacterium that differentiates into environmentally resistant spores in response to starvation. Little is known about the sporulation mechanism in part because sporulation occurs in a subpopulation of cells undergoing a lenghtly complex multicellular developmental program. This developmental program requires a solid surface, motility, a minimum population density and a sophisticated network of inter and intra-cellular signals which direct some cells first to aggregate into multicellular fruiting bodies and then to sporulate exclusively within these fruiting bodies. However, it has previously been demonstrated that synchronous conversion of vegetative cells into myxospores can also be triggered in nutrient-rich liquid medium by addition of glycerol to 0.5 M. Here, we took advantage of the glycerol-induced sporulation process to gain information about the core M. xanthus sprorulation mechanism. We determined changes in the global gene expression at 0.5, 1, 2, and 4 hours after glycerol induction compared to vegetative cells (wild-type DK1622). The expression of nearly 1,500 genes was found to be significantly altered at least two-fold within four hours of glycerol-induced development. Most of the known core sporulation marker genes were up-regulated, whereas most genes required for proper aggregation and fruiting body formation were not significantly regulated. Keywords: Time course of glycerol-induced (0.5 M final conc.) development with 4 time points referenced to vegetative cells 3 biological replicates each; normalized ratios to vegetative cells of DK1622 (wt) Cy3

2010-05-06 | E-GEOD-17912 | biostudies-arrayexpress

Transcriptome Signature of Cellular Senescence

Project description:Abstract: Cellular senescence, an integral component of aging and cancer, arises in response to diverse triggers, including telomere attrition, macromolecular damage, and signaling from activated oncogenes. At present, senescent cells are identified by the combined presence of multiple traits, such as senescence-associated protein expression and secretion, DNA damage, and β-galactosidase activity; unfortunately, these traits are neither exclusively nor universally present in senescent cells. To identify robust shared markers of senescence, we have performed RNA-sequencing analysis across 8 diverse models of senescence triggered in human diploid fibroblasts (WI-38, IMR-90) and endothelial cells (HUVEC, HAEC) by replicative exhaustion, exposure to ionizing radiation or doxorubicin, and expression of the oncogene HRASG12V. The intersection of the altered transcriptomes revealed 47 RNAs consistently elevated and 26 RNAs consistently reduced across all senescence models, including many protein-coding mRNAs and some long noncoding RNAs. We propose that these shared transcriptome profiles will enable the identification of senescent cells in vivo, the investigation of their roles in aging and malignancy, and the development of strategies to target senescent cells therapeutically.

2019-06-12 | GSE130727 | GEO

Global profiling of gene expression in A signal mutants of Myxococcus xanthus

Project description:In response to starvation Myxococcus xanthus initiates a developmental program that culminates in the formation of fruiting bodies inside which the rod-shaped cells differentiate to spores. Fruiting body formation depends on intercellular communication and two intercellular signals are known, the A-signal and the C-signal. Five genes have been identified which are required for A-signal synthesis. To begin to understand the function of the genes required for A-signal synthesis, we have analysed gene expression in the asgA and the asgB mutant. Keywords: Vegetative cells of WT (DK1622) and AsgA mutant (DK5057) and AsgB mutant (DK4398) 3 biological replicates each; normalized ratios to vegetative cells of DK1622 (wt) Cy5

2012-05-17 | E-GEOD-18029 | biostudies-arrayexpress

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