Cytokine Signaling Co-opts the CREB/CRTC Pathway in Obesity
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ABSTRACT:
PROVIDER: PRJNA673713 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12962100.fastq.gz | Fastqsanger.gz | |||
| SRR12962101.fastq.gz | Fastqsanger.gz | |||
| SRR12962102.fastq.gz | Fastqsanger.gz | |||
| SRR12962103.fastq.gz | Fastqsanger.gz | |||
| SRR12962104.fastq.gz | Fastqsanger.gz |
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Project description:Cytokine Signaling Co-opts the CREB/CRTC Pathway in Obesity
| PRJNA673925 | ENA
Project description:Obesity stimulates the infiltration of adipose tissue by innate immune cells, which in turn promote insulin resistance via the NFkB mediated induction of pro-inflammatory cytokines, which interfere with triglyceride metabolism. The cAMP responsive factor CREB has also been implicated in adipose tissue inflammation and insulin resistance, although the underlying mechanism is unclear. Here, we show that high fat diet (HFD) feeding triggers activation of the CREB cofactors CRTC2 and CRTC3, which bind to CREB and mediate induction of CXCL1 and other cytokine genes in cooperation with NFkB. HFD feeding reduced adipocyte C/EBPa expression in adipose, leading to decreases in the expression of Salt Inducible Kinase 2 (SIK2), which otherwise phosphorylates and sequesters CRTCs in the cytoplasm. Depletion of SIK2 in adipose led to dephosphorylation of CRTC2 and CRTC3 (CRTC2/3) and to the induction of CXCL1 and other cytokine genes in adipocytes. Indeed, CRTC2/3 were found to stimulate the expression of a subset of cellular genes cooperatively with NF-kB in adipocytes. Knockout of both CRTC2 and CRTC3 in adipose decreased the expression of CXCL1/2 and thereby reduced neutrophil and macrophage infiltration. As depletion of CXCL1/2, with neutralizing antiserum or by KO of the CXCL1 gene restored glucose tolerance and insulin sensitivity in the setting of diet induced obesity, our results demonstrate that NF-kB and CREB/CRTC pathways modulate adipose tissue function in part via cooperative effects on target gene expression.
2021-10-27 | GSE160597 | GEO
Project description:Cooperative effects of CREB and NF-kB Pathways on Adipose Tissue Inflammation in Obesity
2021-10-27 | GSE160684 | GEO
Project description:Purpose: Exploring the alteration in CREB/CRTC binding related to long-term memory Methods: The nuclei of Drosophila mushroom bodies were purified and the histone acetylation and CREB/CRTC binding were examined by ChIP-seq using specific antibodies. The sequencing was performed using Miseq, and aligned to dm3 using CLCbio. The sequence reads that passed quality filters were analyzed by peak calling using PICS and ERD equipped on Strand NGS software. This method using two algorisms excludes false-positive calling of peaks. The PICS and ERD were run using a default setting except for the following parameters; for PICS, 120 bp as an average fragment length, 10 bp as a minimum distance between forward and reverse reads, 200 bp as a minimum distance between forward and reverse reads, 100 bp as a window width, with 5% false discovery rate; for ERD, 1.5 as an enrichment factor, 100 bp as a window size, 10 bp as a window slide size, 100 bp as a minimum region size. The peaks obtained by ERD analysis were filtered by an enrichment factor of 2, and a density of reads at 0.12 for CREB and 0.2 for CRTC. The CREB and the CRTC binding sites were determined as the peak-called region in at least 2 samples out of the three replicates. The CREB and the CRTC binding sites located 200 bp vicinity to each other were defined as the CREB/CRTC binding sites. In parallel, the read counts were obtained in the 1 kb window covering entire genome and analyzed by DESeq2, to determine the region enriched with CREB/CRTC in a specific group of samples. The region with increased or decreased CREB/CRTC binding were determined if the region were defined by the CREB/CRTC binding sites in the above criteria. Results: Using an optimized data analysis workflow, the filtered reads amounted to 8-11million reads for CREB in each of 3 replicates, 8-17 million reads for CRTC in each of 3 replicates, and 4.4 million reads for input. Using anti-CREB antibody, we found 239 significant increases in CREB binding out of 4995 CREB/CRTC binding sites 1 day after training. Using anti-CRTC antibody, we found 4989 significant increases in CRTC binding out of 4995 CREB/CRTC binding sites 1 day after spaced training. Conclusions: Our study shows that, although CREB binding is mostly unchanged, CRTC binding is significantly increased after long-term memory formation in Drosophila mushroom bodies.
2017-02-09 | GSE81456 | GEO
Project description:AMPK (AAK-2) and calcineurin (TAX-6) mediate longevity exclusively through post-translational modification of CRTC-1, the sole C. elegans CRTC (CREB regulated transcriptional coactivator). We performed microarrays to examine the transcriptional responses elicited by the pro-longevity: activation of AMPK, deactivation of calcineurin, and decrease of CREB (CRH-1) activity.
2010-11-20 | GSE25513 | GEO
Project description:AMPK (AAK-2) and calcineurin (TAX-6) mediate longevity exclusively through post-translational modification of CRTC-1, the sole C. elegans CRTC (CREB regulated transcriptional coactivator). We performed microarrays to examine the transcriptional responses elicited by the pro-longevity: activation of AMPK, deactivation of calcineurin, and decrease of CREB (CRH-1) activity. Gene expression profiles for crh1 (nn3315) and tax-6 (ok2065) mutants, aak-2c (aa1-321) overexpressers and WT (N2) controls were obtained by measuring RNA levels in replicate pools of 3000 synchronized L4 worms. Three replicate pools of each strain were prepared on separate days.
2010-11-20 | E-GEOD-25513 | biostudies-arrayexpress
Project description:Purpose: Exploring the alteration in histone acetylation colocalized with CREB/CRTC binding, which are important for long-term memory maintenance Methods: The nuclei of Drosophila mushroom bodies were purified and the histone acetylation and CREB/CRTC binding were examined by ChIP-seq using specific antibodies. The sequencing was performed using SOLiD, and aligned to dm3 using Lifescope..The sequence reads that passed quality filters were analyzed by peak calling using PICS and ERD equipped on Strand NGS software. This method using two algorisms excludes false-positive calling of peaks. The PICS and ERD were run using a default setting except for the following parameters; for PICS, 120 bp as an average fragment length, 10 bp as a minimum distance between forward and reverse reads, 200 bp as a minimum distance between forward and reverse reads, 100 bp as a window width, with 5% false discovery rate; for ERD, 2 as an enrichment factor, 100 bp as a window size, 10 bp as a window slide size, 100 bp as a minimum region size. The peaks obtained by ERD analysis were filtered by an enrichment factor of 1.5, and a density of reads at 0.3 for H3K9Ac, 0.15 for H4K16Ac, 0.18 for CREB and 0.15 for CRTC. To determine the histone acetylation-increased sites, the peaks determined from 3 replicates of the trained samples were summed to analyze all peaks. Then the centers of the H3K9Ac and H4K16Ac peaks were extracted, and then used to create neighboring 400 bp windows. The mapped reads were counted in these 400 bp windows for each biological replicate of ChIP-seq analysis. The counted read numbers in individual regions were normalized by elav for H3K9Ac ChIP-seq, and gapdh2 for H4K16Ac ChIP. The normalized read numbers in individual windows obtained from the spaced trained flies and the naïve flies were analyzed by Student’s t test (p < 0.05). Standard deviations of the normalized read numbers in individual windows from 3 replicates of naïve flies were 0.07 in H3K9Ac-ChIP-seq and 0.10 in H4K16Ac-ChIP-seq. Significantly increased peaks showing a more than 1.2-fold increase (>2SD) were determined as sites with an increase in H3K9Ac or H4K16Ac. Results: Using an optimized data analysis workflow, the filtered reads amounted to 12-15 million reads for H3K9Ac in each of 3 replicates, 5-7 million reads for H4K16 in each of 3 replicates, 2.4 million reads for CREB, 2 million reads for CRTC, and 2.9 million reads for input. Using anti-H3K9Ac antibody, we found significant increases in H3K9Ac 1 day after training, and 75.0% of these mapped within 500bps of the transcriptional start sites (TSSs) of 1766 genes. Using anti-H4K16Ac antibody, we found significant increases in H4K16Ac 1 day after spaced training, and 61.6% of these mapped within 500bps of the TSSs of 1320 genes. Epigenetic changes in the vicinity of TSSs suggests that expression of these genes may be increased in LTM maintenance. We also examined CRTC and CREB binding 1 day after training. We identified 2390 CRTC binding sites, of which 79.6% of these were close to CREB binding sites. These CREB/CRTC binding sites mapped to 1394 genes, and were predominately located within 500bp from TSSs (55.4%). Of the 1394 CREB/CRTC target genes, 346 genes showed increases in H3K9Ac, 319 showed increases in H4K16Ac, and 135 showed increases in both. Conclusions: Our study represents the first detailed analysis of chromatin state related to memory in Drosophila mushroom bodied. The optimized data analysis workflows reported here should provide a framework for comparative investigations of tissue-specific epigenetic alterations.
2017-02-09 | GSE73386 | GEO
Project description:CREB-Regulated Transcription Co-activator (CRTC) regulates metabolism in liver where activation by calcineurin regulates gluconeogenic genes. CaN also has roles in pathological cardiac hypertrophy, however cardiac roles for CRTC have not been identified. In Drosophila, CRTC null mutants exhibit severe cardiac restriction, myofibrillar disorganization, cardiac fibrosis, and tachycardia. Cardiac-specific knockdown (KD) of CRTC mimicked the heart defects of CRTC mutants and cardiac-overexpression (OE) of CRTC or calcineurin caused hypertrophy that was reduced in CRTC mutants, suggesting CRTC mediates calcineurin’s effects. RNAseq of CRTC KD or OE hearts revealed contra-regulated genes involved in glucose, fatty acid, and amino acid metabolism. Genes with conserved CREB binding sites included the fly ortholog of Sarcalumenin, a Ca2+-binding protein. Cardiac KD of this gene recapitulated CRTC KD restriction and fibrotic phenotypes. KD in zebrafish also caused restriction, indicating a conserved role in cardiomyocyte maintenance, and suggesting CaN-CRTC-Sarcalumenin signaling represents a novel pathway underlying cardiac hypertrophy.
2024-07-29 | GSE271481 | GEO
Project description:Populations of circulating immune cells are maintained in equilibrium through signals that enhance the retention or egress of hematopoietic stem cells (HSCs) from bone marrow (BM). Prostaglandin E2 (PGE2) stimulates HSC renewal and engraftment, for example, via induction of the cAMP pathway. Triggering of PGE2 receptors increases HSC survival in part via the PKA-mediated induction of the CREB signaling pathway. PKA stimulates cellular gene expression by phosphorylating CREB at Ser133 and by promoting the dephosphorylation of the cAMP Responsive Transcriptional Coactivators (CRTCs). We show here that disruption of both CRTC2 and CRTC3 causes embryonic lethality, and that a single allele of either CRTC2 or CRTC3 is sufficient for viability. CRTC2 knockout mice that express one CRTC3 allele (CRTC2/3m mice) develop neutrophilia and splenomegaly in adulthood due to the up-regulation of Granulocyte-Colony Stimulating Factor (G-CSF); these effects are reversed following administration of neutralizing anti-G-CSF antiserum. Adoptive transfer of CRTC2/3m BM conferred the splenomegaly/neutrophilia phenotype on WT recipients. Indeed, targeted disruption of both CRTC2 and CRTC3 in stromal cells with a mesenchymal Prx1-Cre transgene also promoted this phenotype. Depletion of CRTC2/3 was found to decrease the expression of Suppressor of Cytokine Signaling 3 (SOCS3), leading to increases in STAT3 phosphorylation and to the induction of CEBPb, a key regulator of the G-CSF gene. As small molecule inhibition of JAK activity disrupted CEBPb induction and reduced G-CSF expression in CRTC2/3m stromal cells, our results demonstrate how cross-coupling between the CREB/CRTC and JAK/STAT pathways contributes to BM homeostasis.
2018-02-01 | GSE103999 | GEO
Project description:High- and low-grade inflammatory responses represent a hallmark of numerous pathologies such as sepsis and bacterial infection or insulin resistance and obesity, respectively. Here we describe an unexpected co-activator function of receptor interacting protein (RIP) 140 for nuclear factor (NF) kB, a master transcriptional regulator of inflammation in multiple tissues. Genetic as well as acute deficiency of RIP140, which has been characterized as a co-repressor of various nuclear receptors on metabolic target genes, led to the inhibition of the proinflammatory program in macrophages, mediated by RIP140’s direct impact on cytokine gene promoter activity. Intriguingly, RIP140’s co-activator function in this setting was found to rely on direct protein-protein interactions with the NFκB subunit p65 and histone acetylase CREB-binding protein (CBP). RIP140-dependent control of proinflammatory gene expression via p65/CBP may, therefore, represent a molecular rational for the cellular integration of metabolic and inflammatory pathways. Keywords: expression profiling
2008-03-31 | GSE10386 | GEO