Transcriptomic changes assoicated with hepatic AHR or ARNT loss in female mice challenged with high-fat diet
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ABSTRACT:
PROVIDER: PRJNA675758 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13015835_1.fastq.gz | Fastqsanger.gz | |||
| SRR13015835_2.fastq.gz | Fastqsanger.gz | |||
| SRR13015836_1.fastq.gz | Fastqsanger.gz | |||
| SRR13015836_2.fastq.gz | Fastqsanger.gz | |||
| SRR13015837_1.fastq.gz | Fastqsanger.gz |
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Project description:The aryl hydrocarbon receptor (AHR) is an important hepatic transcription factor that appears to have a role in regulating endogenous liver metabolism. Canonical AHR-mediated regulation of transcription requires AHR binding to its DNA-binding partner, the AHR nuclear translocator (ARNT). We previously demonstrated that the AHR can regulate transcription independent of ARNT via “non-canonical” interactions with Kruppel-like factor 6, and that hepatic AHR loss can protect against high-fat diet (HFD) challenge. In this study, we examined the effects of hepatic AHR or ARNT loss in HFD-fed mice to determine whether AHR regulation of liver metabolism might partially occur independent of ARNT. The data show that similar to AHR loss, ARNT loss reduces HFD-driven hepatic lipid deposition, but does not recapitulate the diminished weight gain and adiposity observed in AHR KO animals. Utilizing transcriptomic sequencing analyses, we uncovered specific gene pathways that likely account for these phenotypic differences/similarities associated with AHR or ARNT loss. Together, these data highlight the physiological significance of ARNT-independent AHR activity, and identify discrete aspects of liver metabolism likely regulated via canonical AHR action.
2024-06-08 | GSE161147 | GEO
Project description:The aryl hydrocarbon receptor (AHR) and AHR nuclear translocator (ARNT) activated complex regulates genes in response to the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). AHR has also emerged as a potential therapeutic target for the treatment of human diseases and different cancers, including breast cancer. To better understand AHR and ARNT signaling in breast cancer cells, we used chromatin immunoprecipitation linked to high throughput sequencing to identify AHR- and ARNT-binding sites across the genome in TCDD treated MCF-7 cells. We identified 2,594 AHR-bound, 1,352 ARNT-bound and 882 high confidence AHR/ARNT co-bound regions. No significant differences in the genomic distribution of AHR and ARNT were observed. Approximately 60% of the co-bound regions contained at least one core AHRE, 5'-GCGTG-3'. AHR/ARNT peak density was the highest within 1 kb of transcription start sites (TSS); however, a number of AHR/ARNT co-bound regions were located as far as 100 kb from TSS. De novo motif discovery identified a symmetrical variation of the AHRE (5'-GTGCGTG-3'), as well as FOXA1 and SP1 binding motifs. Microarray analysis identified 104 TCDD responsive genes where 98 genes were up-regulated by TCDD. Of the 104 regulated genes, 69 (66.3%) were associated with an AHR- or ARNT-bound region within 100 kb of their TSS. Overall our study identified AHR/ARNT co-bound regions across the genome, revealed the importance but not absolute requirement for an AHRE in AHR/ARNT interactions with DNA, and identified a modified AHRE motif, thereby increasing our understanding of AHR/ARNT signaling pathway. Examination of genome-wide AHR and ARNT binding pattern in MCF-7
2012-10-24 | E-GEOD-41820 | biostudies-arrayexpress
Project description:The aryl hydrocarbon receptor (AHR) and AHR nuclear translocator (ARNT) activated complex regulates genes in response to the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). AHR has also emerged as a potential therapeutic target for the treatment of human diseases and different cancers, including breast cancer. To better understand AHR and ARNT signaling in breast cancer cells, we used chromatin immunoprecipitation linked to high throughput sequencing to identify AHR- and ARNT-binding sites across the genome in TCDD treated MCF-7 cells. We identified 2,594 AHR-bound, 1,352 ARNT-bound and 882 high confidence AHR/ARNT co-bound regions. No significant differences in the genomic distribution of AHR and ARNT were observed. Approximately 60% of the co-bound regions contained at least one core AHRE, 5'-GCGTG-3'. AHR/ARNT peak density was the highest within 1 kb of transcription start sites (TSS); however, a number of AHR/ARNT co-bound regions were located as far as 100 kb from TSS. De novo motif discovery identified a symmetrical variation of the AHRE (5'-GTGCGTG-3'), as well as FOXA1 and SP1 binding motifs. Microarray analysis identified 104 TCDD responsive genes where 98 genes were up-regulated by TCDD. Of the 104 regulated genes, 69 (66.3%) were associated with an AHR- or ARNT-bound region within 100 kb of their TSS. Overall our study identified AHR/ARNT co-bound regions across the genome, revealed the importance but not absolute requirement for an AHRE in AHR/ARNT interactions with DNA, and identified a modified AHRE motif, thereby increasing our understanding of AHR/ARNT signaling pathway.
2012-10-24 | GSE41820 | GEO
Project description:The aryl hydrocarbon receptor nuclear translocator (ARNT) is a transcription factor present in immune cells as a long and short isoform, referred to as isoform 1 and 3, respectively. However, investigation into potential ARNT isoform-specific immune functions is lacking despite the well-established heterodimerization requirement of ARNT with, and for the activity of, the aryl hydrocarbon receptor (AhR), a critical mediator of immune homeostasis. Here, using global and targeted transcriptomics analyses we show that the relative ARNT isoform 1:3 ratio in human T cell lymphoma cells dictates the amplitude and direction of AhR target gene regulation. Specifically, shifting the ARNT isoform 1:3 ratio lower by suppressing isoform 1 enhances, or higher by suppressing isoform 3 abrogates AhR responsiveness to ligand activation through preprograming a cellular genetic background that directs explicit gene expression patterns. Moreover, the fluctuations in gene expression patterns that accompany a decrease or increase in the ARNT isoform 1:3 ratio are associated with inflammation or immunosuppression, respectively. Molecular studies identified the unique casein kinase 2 (CK2) phosphorylation site within isoform 1 as an essential parameter to the mechanism of ARNT isoform-specific regulation of AhR signaling. Notably, CK2-mediated phosphorylation of ARNT isoform 1 is dependent on ligand-induced AhR nuclear translocation and is required for optimal AhR target gene regulation. These observations reveal ARNT as a central modulator of AhR activity predicated on the status of the ARNT isoform ratio and suggest that ARNT-based therapies are a viable option for tuning the immune system to target immune disorders.
2022-03-31 | GSE184151 | GEO
Project description:BRAF oncogene is mutated in ~50% of human cutaneous melanomas. The BRAF V600E mutation leads to constitutive activation of the mitogen-activated protein kinase (MAPK) pathway fuelling cancer growth. The inhibitors of BRAF V600E (BRAFi), lead to massive and high response rate. However, BRAFi-resistant cells that operate as a cellular reservoir for relapses severely limits the duration of the clinical response. The recent depiction of these resistant cells did not identify druggable targets to ensure long-term survival under BRAFi. Here, we identify the aryl hydrocarbon receptor (AhR) as a target to eradicate resistant cells. We show that BRAFi bind to AhR on a new site, named beta-pocket, and reprogram gene expression independently of its partner ARNT. beta-pocket activation induces a pigmentation signature, which is associated to BRAFi-induced cell death of sensitive BRAF V600E melanoma cells and tumour shrinkage. Intriguingly, in resistant cells, BRAFi does not induced a pigmentation signature since these cells display another AhR program; AhR-ARNT dependant. By this way, AhR directs several key BRAFi-resistant genes. At single cell level, this constitutive activation of AhR-ARNT is identified in rare cells before BRAFi-treatment of melanoma tumours and an enrichment of these alpha-cells is observed under BRAFi. Our data strongly suggest that an endogenous AhR ligand activates AhR-ARNT via the canonical AhR pocket (alpha-pocket), thus favouring BRAFi-resistant gene expression. Importantly, we identify the clinically compatible AhR antagonist, the resveratrol (RSV), able to abrogate the deleterious constitutive activation of AhR and to reduce the cellular reservoir for the relapse. Taken together, this work reveals that constitutive AhR signalling drives BRAFi resistance and constitutes a therapeutic target to achieve long-term patient survival under BRAFi. More broadly, the constitutive activation of AhR by endogenous ligands is in line with the ability of UV radiations to generate potent AhR ligands and to favour melanoma onset.
2018-11-29 | GSE104869 | GEO
Project description:Activation of AhR promotes phosphorylation of ARNT isoform 1 as a switch for optimal AhR activity in human T cell malignancies.
| PRJNA763386 | ENA
Project description:The adaptation of regimented exercise in skeletal muscle including muscular hypertrophy and enhanced strength decline significantly with aging. Transcriptome analysis following RNA sequencing reveals extensive activation of hypoxia-related genes in young exercised mice versus the sedentary, but absent in aged exercised mice. Particularly, less expression of aryl hydrocarbon receptor translocator (ARNT) was observed in response to exercise in aged mice. Young mice underwent skeletal muscle-specific knockout of ARNT (ARNT mKO) obtain deficient benefit from exercise resembling the aged mice. The deletion of ARNT associated with decreased expression of Notch1 intracellular domain(N1ICD) impair muscle hypertrophy and regeneration. Administration of ML228, a systematic agonist of ARNT, rescued skeletal muscle adaptabilities in old mice, which was suppressed by administrating N1ICD inhibitor(DAPT). These results suggest that the loss of skeletal muscle ARNT is partially responsible for diminished response to exercise in aging and activation of hypoxia signaling holds promise for rescuing the adaptability in aged muscle.
2021-12-31 | GSE155937 | GEO
Project description:The aryl hydrocarbon receptor (AHR) mediates most of the toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, TCDD toxicity phenotypes vary widely between species, strains and even between sexes within a strain. While the exact reasons for this variation remain unclear, it is thought to be related to differences in the structure of the AHR. Previous studies comparing the downstream effects of TCDD exposure between animals with different AHR isoforms have been confounded by the genetic differences between these model systems. To address this issue conclusively, we evaluated three transgenic mouse lines, each of which express a different rat AHR isoform (rWT, DEL, and INS) from two strains of rat with highly divergent TCDD-susceptibilities, within identical genetic backgrounds. Here we profile hepatic transcriptomic responses following exposure to TCDD, and use these to identify transcripts associated with toxicity. We have confirmed that the variation in toxicity is inherent to the AHR isoform. Additionally, we note the enhanced activity of the modified transactivation domain of the DEL isoform, relative to the INS isoform, and provide further evidence that the INS isoform is responsible for the high resistance to TCDD observed in H/W rats. We also uncover several candidate genes that were consistently differentially expressed in TCDD-sensitive mice and rats. Adult male transgenic mice were treated by gavage with 0, 125, 250, 500, or 1000 µg/kg TCDD dissolved in corn oil vehicle. Mice were euthanized 4 days following treatment and liver tissue was harvested for analysis. RNA was isolated and the transcriptome for each animal assayed on separate microarrays.
2016-07-03 | E-GEOD-72270 | biostudies-arrayexpress
Project description:The Aryl hydrocarbon Receptor (AhR) is a transcription factor well known in vertebrate to play an essential role as xenobiotic sensor. On the contrary, no ligand has been identified to date for invertebrate AhR. In some model organisms such as D. melanogaster and C. elegans, AhR orthologs have physiological functions and their inability to bind prototypical ligands of vertebrate AhR such as tetrachlorodibenzo-p-dioxin (TCDD) suggests that the detoxification role of the receptor could be an adaptation acquired during evolution. To better understand the physiological roles of AhR, we studied AhR-1, the C. elegans ortholog and performed transcriptomic and metabolomic analysis respectively in neuronal cells expressing AhR-1 and in whole animals. Next, we designed a reporter system in order to investigate if the transcriptional activity of AhR-1 could be modulated. Cos-7 cells were transfected with AhR-1, its dimerization partner AhA-1 (C. elegans ARNT ortholog) and a Firefly luciferase gene under the control of the human cytochrome P450 1A1 promotor. The luciferase bioluminescence measurement allows the identification of C. elegans AhR-1 modulators. Transcriptional profiling in neurons expressing AhR-1 revealed 95 genes down-regulated, and 76 genes up-regulated in AhR-1 KO animals. These genes are associated with nervous system function (depleted) and fatty acid process, oxidative phosphorylation and glycolysis (enriched). Metabolomic profiling results indicate a role for AhR-1 in regulating several endogenous metabolic pathways: amino-acid metabolism, carbohydrate metabolism as well as fatty acid metabolism Then, with the COS-7 in vitro screening model, we identified positive and negative modulators such as bacterial, dietary or environmental compounds. Considering C. elegans environment, these results could be used to highlight the role of invertebrate AhR and identified new features in vertebrate AhR.
2022-06-01 | GSE195728 | GEO