Acute effects of caffeine on iPSC-derived neuronal cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB20092 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1904240.fastq.gz | Fastqsanger.gz | |||
| ERR1904250.fastq.gz | Fastqsanger.gz | |||
| ERR1904260.fastq.gz | Fastqsanger.gz | |||
| ERR1904270.fastq.gz | Fastqsanger.gz | |||
| ERR1904241.fastq.gz | Fastqsanger.gz |
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Project description:Caffeine is the most widely consumed psychoactive substance worldwide. Strikingly, molecular pathways engaged by its regular consumption remain unclear. We herein addressed the mechanisms associated with habitual (chronic) caffeine consumption in the mouse hippocampus using untargeted orthogonal-omics techniques. Our results revealed that chronic caffeine exerts concerted pleiotropic effects in the hippocampus, at the epigenomic, proteomic and metabolomic levels, lowered metabolic-related processes in bulk tissue, while inducing neuronal-specific epigenetic changes at synaptic transmission/neuronal activity-related genes. Altogether, these findings suggest that regular intake of caffeine improves the signal-to-noise ratio during information encoding in learning in part through a re-setting of metabolic genes helping to bolster the salience of information processing in neuronal circuits.
2022-06-22 | GSE200156 | GEO
Project description:Caffeine is the most widely consumed psychoactive substance worldwide. Strikingly, molecular pathways engaged by its regular consumption remain unclear. We herein addressed the mechanisms associated with habitual (chronic) caffeine consumption in the mouse hippocampus using untargeted orthogonal-omics techniques. Our results revealed that caffeine exerts concerted pleiotropic effects in the hippocampus, at the epigenomic, proteomic and metabolomic levels, aimed at lowering metabolic-related processes while re-setting learning-associated transcriptome associated with neuronal activity. These processes involve BDNF, CREB and adenosine A2A receptors-related mechanisms. Altogether, these findings suggest that regular intake of caffeine improves the signal-to-noise ratio during information encoding in learning and bolsters the salience of information encoding in brain circuits.
2022-06-22 | GSE167122 | GEO
Project description:Caffeine is the most widely consumed psychoactive substance worldwide. Strikingly, molecular pathways engaged by its regular consumption remain unclear. We herein addressed the mechanisms associated with habitual (chronic) caffeine consumption in the mouse hippocampus using untargeted orthogonal-omics techniques. Our results revealed that caffeine exerts concerted pleiotropic effects in the hippocampus, at the epigenomic, proteomic and metabolomic levels, aimed at lowering metabolic-related processes while re-setting learning-associated transcriptome associated with neuronal activity. These processes involve BDNF, CREB and adenosine A2A receptors-related mechanisms. Altogether, these findings suggest that regular intake of caffeine improves the signal-to-noise ratio during information encoding in learning and bolsters the salience of information encoding in brain circuits.
2022-06-22 | GSE167121 | GEO
Project description:Genetic variants in gene regulatory sequences can modify gene expression and mediate the molecular response to environmental stimuli. In addition, genotype–environment interactions (GxE) contribute to complex traits such as cardiovascular disease. Caffeine is the most widely consumed stimulant and is known to produce a vascular response. To investigate GxE for caffeine, we treated vascular endothelial cells with caffeine and used a massively parallel reporter assay to measure allelic effects on gene regulation for over 43,000 genetic variants. We identified 665 variants with allelic effects on gene regulation and 6 variants that regulate the gene expression response to caffeine (GxE, false discovery rate [FDR] < 5%). When overlapping our GxE results with expression quantitative trait loci colocalized with coronary artery disease and hypertension, we dissected their regulatory mechanisms and showed a modulatory role for caffeine. Our results demonstrate that massively parallel reporter assay is a powerful approach to identify and molecularly characterize GxE in the specific context of caffeine consumption.
2024-02-26 | GSE221514 | GEO
Project description:Induced pluripotent stem cells (iPSCs) are a valuable resource for neurological disease-modeling and drug discovery, due to their ability to differentiate into neurons reflecting the genetics of the patient from which they are derived. iPSC-derived cultures, however, are highly variable due to differences in culture conditions. We investigated the effect of iPSC passage number on differentiation to optimize the generation of functional, mature sensory neurons (iPSC-dSNs). Three iPSC lines were differentiated into iPSC-dSNs at passage numbers within each of the following ranges: low (LP; 5-10), middle (MP; 20-26), and high (HP; 30-38). Morphology and pluripotency of the parent iPSCs were assessed prior to differentiation at each passage number. iPSC-dSNs were evaluated based on electrophysiological properties and expression of key neuronal markers. All iPSC lines displayed the same morphology and were similarly pluripotent across passage numbers. iPSC-dSNs were also morphologically comparable across passage numbers. However, the expression levels of neuronal markers and an analysis of sodium channel function indicated greater maturity in LP iPSC-dSNs. Our results demonstrate that lower passage numbers may be better suited for differentiation into peripheral sensory neurons. Further studies are warranted to elucidate factors that may contribute to the variability associated with iPSC passage number.
2022-07-19 | GSE193571 | GEO
Project description:Purpose: This study aimed to identify differentially expressed genes including alternative splice variants in embryonic ventricles following in utero caffeine treatment. Methods: Pregnant CD-1 mice were injected with 20 mg/kg of caffeine or vehicle control daily from embryonic day (E) 6.5-9.5. On E10.5, total RNA was isolated from embryonic ventricles and used for transcriptomic RNA sequencing with Illumina HiSeq 2000 (1X75bp). RNA-seq reads were aligned to the mouse genome (build mm10) with the Tophat for Illumina tool in the PSU galaxy platform. Counting and annotation of RNA-seq reads as well as alternative splicing analysis were performed with Partek Genomics Suite version 6.11. Differential expression of gene and transcript reads between treatments was analyzed with R package EdgeR. Genes/transcripts with false discovery rate (FDR) less than 0.05 and absolute fold change greater than 1.5 were considered as significant. Differentially expressed genes were defined as genes with altered expression at either gene or transcript level. Unique differentially expressed genes were identified by combining the results from annotations with the RefSeq Transcripts (2013-05-10) or Ensembl Transcripts release 71 databases. Results: Differential expression analysis revealed that 59 genes and 451 transcripts were significantly up-regulated, and 65 genes and 398 transcripts were down-regulated by prenatal caffeine treatment (fold change >1.5 or <-1.5; p-value with FDR<0.05). In total, 900 unique genes were identified to have altered expression either at the gene or transcription level. Further analysis with Partek GS revealed that 183 genes had abnormal alternative splicing at the exon level after in utero caffeine treatment. Conclusions: In utero caffeine exposure caused gene expression changes in embryonic ventricles and these changes may lead to long-term effects on cardiac morphology and function. mRNA profiles in E10.5 heart ventricles treated with caffeine were generated by deep sequencing (n=2 for vehicle, n=3 for caffeine), using Illumina HiSeq 2000.
2015-01-07 | E-GEOD-56902 | biostudies-arrayexpress
Project description:Postoperative bowel paralysis is common after abdominal operations, including colectomy. As a result, hospitalization may be prolonged leading to increased cost. A recent randomized controlled trial from the University of Heidelberg showed that consumption of regular black coffee after colectomy is safe and associated with a significantly faster resumption of intestinal motility (Müller 2012). The mechanism how coffee stimulates intestinal motility is unknown but caffeine seems to be the most likely stimulating agent.
Thus, this trial addresses the question: Does caffeine reduce postoperative bowel paralysis after elective laparoscopic colectomy?
Patients after laparoscopic colectomy will receive either 100 mg caffeine, 200 mg caffeine, or 250mg corn starch (placebo) 3 times daily in identically looking gelatin capsules.
The study is a randomized, controlled trial, with blinding of physicians, patients and nursing stuff (evaluating the endpoints).
Primary endpoint will be the time to first bowel movement.
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Project description:To explore the mechanistic basis of ApoE Ɛ4 vs ApoE Ɛ3 protein expression on endocytic pathways responsible for tau uptake in neurons and astrocytes and the maturation of neuronal networks, we have developed genotype matched co-cultures of iPSC derived astrocytes and neurons derived from isogenic triads of iPSC lines generated by the ADAPTED consortium (Schmid et al., 2019, 2020) . We show that isogenic iPSC derived APOE-E4 expressing astrocytes take up less extracellular tau than APOE-E3 or APOE null astrocytes, while isogenic neurons in monoculture take up equivalent amounts of tau primarily through macropinocytosis. Co-culture of neurons with genotype matched astrocytes increases the general uptake capacity of neurons by increasing the dependence of neuronal endocytosis on dynamin mediated pathways. Co-culture also enhances the emergence of spontaneous neuronal activity; however, the emergence of synchronous network activity is impaired by the expression of APOE-E4 genotype. We performed RNA-Seq on the astrocytes, neurons and co-cultures to understand the molecular pathway changes associated with different ApoE genotypes.
2024-04-08 | GSE171700 | GEO
Project description:Affect of iPSC Passage Number on Neuronal Differentiation
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Project description:Neuronal or glial cell fates related gene expression from single cells with variety of sAPPa or total Aβ secretion profiles were presented here. Single living human iPSC-derived forebrain neuronal cells with variety of sAPPa or total Aβ secretion profiles were selected and examined for gene expression.
2016-01-06 | E-GEOD-76547 | biostudies-arrayexpress