The microbiota drives circadian entrainment of tryptophan metabolism in the stressed gut
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB58865 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Setaria viridis (A10.1) circadian expression after light or temperature entrainment
2017-07-01 | GSE97739 | GEO
Project description:Mice were fed a normal chow diet or a tryptophan depleted diet for two weeks under normal 12-hr light/dark cycles (LD) or in constant darkness (DD). Mice were sacrificed every 4th hour over the 24-hr circadian cycle. The suprachiasmatic nucleus (SCN) was harvested and RNA was isolated using a standard TRIZOL protocol. The data suggest that dietary tryptophan is an important component of the diet regulating circadian homeostsis.
2023-05-30 | GSE186242 | GEO
Project description:Dietary tryptophan and circadian rhythms
| PRJNA773065 | ENA
Project description:Mice were fed a normal chow diet or a tryptophan depleted diet for two weeks under normal 12-hr light/dark cycles (LD) or in constant darkness (DD). Mice were sacrificed every 4th hour over the 24-hr circadian cycle. The liver was harvested and RNA was isolated using a standard TRIZOL protocol. The data suggest that dietary tryptophan is an important component of the diet regulating circadian homeostsis.
2023-05-30 | GSE190145 | GEO
Project description:Gene expression of yeast fermentor culture after circadian temperature entrainment
| PRJNA503841 | ENA
Project description:In this study we investigate and compare DEGs of K. aerogenes macrocolonies during temperature entrainment (12:12, 35°C:36°C) and subsequent free running conditions (35°C). The goal of this experiment was to identify rhythmically expressed genes in K. aerogenes, the first human gut commensal bacterium with described circadian clock (Paulose et al. 2016). K. aerogenes circadian clock is sensitive to temperature entrainment (Paulose et al. 2019). To further investigate this temperature entrainment of K. aerogenes we performed RNA sequencing experiment. We identified 48 differentially expressed genes when comparing timepoints ZT6 to ZT18, 427 differentially expressed genes when comparing timepoints ZT6 to CT6, 6 differentially expressed genes between timepoints CT6 and CT18, and 2 differentially expressed genes between timepoints ZT18 and CT18.
2023-10-09 | GSE185502 | GEO
Project description:Dietary tryptophan and circadian rhythms in the Liver
| PRJNA785984 | ENA
Project description:DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. We investigated the global changes in mRNA abundance in Escherichia coli elicited by various perturbations of tryptophan metabolism. To do so we printed DNA microarrays containing 95% of all annotated E. coli ORFs. We determined the expression profile that is predominantly dictated by the activity of the tryptophan repressor. Only three operons, trp, mtr, and aroH, exhibited appreciable expression changes consistent with this profile. The quantitative changes we observed in mRNA levels for the five genes of the trp operon were consistent within a factor of 2, with expectations based on established Trp protein levels. Several operons known to be regulated by the TyrR protein, aroF-tyrA, aroL, aroP, and aroG, were down-regulated on addition of tryptophan. TyrR can be activated by any one of the three aromatic amino acids. Only one operon, tnaAB, was significantly activated by the presence of tryptophan in the medium. We uncovered a plethora of likely indirect effects of changes in tryptophan metabolism on intracellular mRNA pools, most prominent of which was the sensitivity of arginine biosynthetic operons to tryptophan starvation. This study is detailed in Khodursky AB et al.(2000) Proc Natl Acad Sci U S A 97:12170-5 Keywords: other
2001-07-30 | GSE7 | GEO
Project description:Circadian rhythms are essential for temporal (~24 h) regulation of molecular processes in diverse species. Dysregulation of circadian gene expression has been implicated in the pathogenesis of various disorders, including hypertension, diabetes, depression, and cancer. Recently, microRNAs (miRNAs) have been identified as critical modulators of gene expression post-transcriptionally, and perhaps involved in circadian clock architecture or their output functions. The aim of the present study is to explore the temporal expression of miRNAs among entrained breast cell lines. For this purpose, we evaluated the temporal (28 h) expression of 2006 miRNAs in MCF-10A, MCF-7, and MDA-MB-231 cells using microarrays after serum shock entrainment. We noted hundreds of miRNAs that exhibit rhythmic fluctuations in each breast cell line, and some of them across two or three cell lines. Afterwards, we validated the rhythmic profiles exhibited by miR-141-5p, miR-1225-5p, miR-17-5p, miR-222-5p, miR-769-3p, and miR-548ay-3p in the above cell lines, as well as in ZR-7530 and HCC-1954 using RT-qPCR. Our results show that serum shock entrainment in breast cells lines induces rhythmic fluctuations of distinct sets of miRNAs, which have the potential to be related to endogenous circadian clock, but extensive investigation is required to elucidate that connection.
2017-07-15 | GSE101461 | GEO
Project description:Intratumoral microglia and MΦ constitute up to 70% of the tumor mass of high-grade gliomas (HGG) with profound impact on hallmarks of malignancy such as angiogenesis and immunosuppression. The dynamics and functional states of intratumoral myeloid cells during tumor progression and the molecular mechanisms controlling them are poorly understood. Here we define homeostatic and antigen-presenting myeloid cellular states in experimental and human HGG by longitudinal single-cell RNA-sequencing and combined transcriptome and proteome profiling. During glioma progression, myeloid cells gradually shift from a homeostatic to a tumor-associated effector state. We show that these dynamics are under strict control by early changes in resident microglia and the tumor genotype: In gliomas with mutations in isocitrate dehydrogenase (IDH), a disease-defining driver mutation, differentiation of invaded myeloid cells was blocked resulting in an immature, immunosuppressive phenotype. In late-stage IDH-mutant gliomas, monocyte-derived MΦ drive a tolerogenic remodeling of the glioma microenvironment thus preventing T-cell response. We define the molecular mechanism responsible for the tumor genotype-dependent education of infiltrating MΦ to be causally related to an enzymatically enhanced tryptophan catabolism via TDO2, resulting in the production of kynurenine, an endogenous ligand of the aryl hydrocarbon receptor (AHR). TDO2 activation further induces an amino acid starvation response triggering the import of exogenous tryptophan by intratumoral MΦ via LAT1-CD98. We here provide evidence that paracrine R-2-HG and tryptophan are critically involved in the differentiation and activation of monocyte-derived MΦ and that the previously observed altered amino acid metabolism in IDHmut gliomas is also responsible for shaping an immunosuppressive tumor microenvironment through maintenance of this complex metabolic axis. We further show that this regulatory metabolic network is particularly active in infiltrating MΦ because of their distinct expression profile that constitutes an immune subset-specific metabolic vulnerability. Consequently, the immunosuppressive phenotype in IDH-mutant glioma models was reversed by pharmacological inhibition of LAT1-CD98 or AHR. Thus, we provide evidence for a tumor genotype-dependent, dynamic network of resident and recruited intratumoral myeloid cells that shape the immune microenvironment of IDH-mutant HGG through pleiotropic interaction with the tumor metabolome and identify tryptophan metabolism as a viable therapeutic target for the immunotherapy of IDH-mutant tumors.
2021-03-04 | GSE166521 | GEO