Effect of dietary abscisic acid (ABA) supplementation on spleen transcriptome in LPS-challenged mice
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ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Saroj Mohapatra
PROVIDER: E-GEOD-21013 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Inflammatory bowel disease (IBD) is a condition characterized by severe intestinal inflammation and immune cell activation. The severity of the disease can be mitigated by compounds which activate peroxisome proliferator-activated receptor gamma (PPAR gamma), a receptor present widely in tissues involved in IBD pathogenesis. Our objective was to assess the affect of macrophage-specific deficiency of PPAR gamma on peripheral and colonic immune populations and colonic gene expression in experimental IBD. Macrophage-specific PPAR gamma-deficient mice (PPAR gamma flfl Lysozyme M Cre+) and control (PPAR gamma flfl Lysozyme M Cre-) littermates were treated with 2.5% dextran sodium sulfate (DSS) for 7 days. Disease activity was recorded daily and immune cell populations in the blood, spleen, mesenteric lymph nodes (MLN), and lamina propria were examined by flow cytometry. Colonic gene expression was assessed by real time PCR and microarray analyses. Our findings show that macrophage PPAR r-deficiency significantly exacerbates DSS inflammation. CD4+CD25+FoxP3+ regulatory T cells (T-regs) were significantly reduced in Cre+ mice, and MLN macrophages and CD40 expression were enhanced. There were significant differences in the number colonic macrophages between Cre+ and Cre- mice, but those from Cre+ mice expressed more CD40, Ly6C, and TLR-4. PPAR r-deficiency also increased the percent of CD8+ T cells in the lamina propria and enhanced colonic interferon gamma expression. Our findings indicate that macrophage PPAR gamma deficiency augments the severity of DSS colitis by reducing peripheral T-regs and increasing colonic macrophage activation and T cell inflammation. RNA from 3 PPAR gamma-deficient mice (PPAR gamma flfl; Lysozyme M Cre+) and 3 control (PPAR gamma flfl; Lysozyme M Cre-) littermates was processed and labeled according to the standard target labeling protocols. The samples were hybridized, stained, and scanned per standard Affymetrix protocols at the Virginia Bioinformatics Institute (VBI) core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).
2011-11-12 | E-GEOD-23421 | biostudies-arrayexpress
Project description:BACKGROUND: Peroxisome proliferator-activated receptor g (PPAR g) is a nuclear receptor whose activation has been shown to modulate macrophage and epithelial cell-mediated inflammation. The objective of this study was to use a systems approach for investigating the mechanism by which the deletion of PPAR g in T cells modulates the severity of dextran-sodium sulfate (DSS)-induced colitis, immune cell distribution and global gene expression. METHODS: Wild-type (WT) or PPAR g flfl; CD4 Cre+ (CD4cre) mice in a C57BL/6 background were challenged with 2.5% DSS in their drinking water for 0, 2, or 7 days. Mice were scored on disease severity both clinically and histopathologically. Flow cytometry was used to assess lymphocyte and macrophage populations in the blood, spleen, and mesenteric lymph nodes (MLN). Global gene expression in colonic mucosa was profiled using Affymetrix microarrays. RESULTS: Both disease severity and inflammation-related body weight loss were accelerated by the deficiency of PPAR g in T cells. Examination of colon histopathology revealed significantly greater epithelial erosion, leukocyte infiltration, and mucosal thickening in the CD4cre mice on day 7. CD4cre mice had more CD8+ T cells than wt mice and fewer CD4+FoxP3+ regulatory T cells (Treg) and IL10+CD4+ T cells in blood and MLN, respectively. Transcriptomic profiling revealed around 3000 genes being transcriptionally altered as a result of DSS challenge in CD4cre mice. These included up-regulated adhesion molecules on day 7 and proinflammatory cytokines interleukin-6 (IL-6) and IL-1b, and suppressor of cytokine signaling 3 (SOCS-3) mRNA expression. CONCLUSIONS: These findings suggest that T cell PPAR g down-regulates inflammation during DSS colitis by inhibiting colonic expression of inflammatory mediators and increasing MLN Treg. Colonic mucosa from wt and CD4cre mice were sampled at 0 (no DSS), 2, and 7 days of DSS-induced experimental colitis
2010-07-08 | E-GEOD-20523 | biostudies-arrayexpress
Project description:BACKGROUND: Peroxisome proliferator-activated receptor g (PPAR g) is a nuclear receptor whose activation has been shown to modulate macrophage and epithelial cell-mediated inflammation. The objective of this study was to use a systems approach for investigating the mechanism by which the deletion of PPAR g in epithelial cells modulates the severity of dextran-sodium sulfate (DSS)-induced colitis, immune cell distribution and global gene expression. RESULTS: The deficiency of PPAR g in epithelial cells does not significantly affect disease activity or body weight but worsens colon histopathlogy. WT mice have greater CD4+IL10+ T cells and fewer MHC II+ macrophages in mesenteric lymph nodes. Global gene expression analysis reveals greater changes after 7 days of DSS challenge (compared to 2 days). Colonic mucosa from VC- (WT) and VC+ (PPARg knock-out in epithelial cells) mice were sampled at 0 (no DSS), 2, and 7 days of DSS-induced experimental colitis
2010-07-08 | E-GEOD-20621 | biostudies-arrayexpress
Project description:BACKGROUND: Dietary ABA-supplementation modulates immune and inflammatory responses in mouse models of chronic and infectious disease. However, the underlying mechanisms by which ABA elicits its immune modulatory effects are not well understood. This project used a systems approach in combination with functional and in vivo studies to investigate the target gene pathways modulated by ABA in the context of an inflammatory LPS challenge. RESULTS: Dietary ABA-supplementation regulates the expression of gene pathways associated with peroxisome proliferator-activated receptor gamma (PPAR g), cAMP signaling and lipid metabolism in PPAR g-expressing mice. However, the pattern of differentially expressed genes is significantly reduced in the spleens of tissue-specific PPAR g null mice fed ABA. These differences in gene expression coincided with enhanced PPAR g-reporter activity of macrophages treated with ABA and enhanced intracellular cAMP accumulation in ABA-treated splenocytes.
2010-09-01 | GSE21013 | GEO
Project description:4 weeks old rooted plantlets of P. × canescens (Clone INRA717 1-B4) were cultivated in hydroponics in 2 l pots in Long Ashton nutrient solution in a culture room for 8 weeks before treatments started. Three treatments were applied to the plants: control treatment (-ABA), continuous 100 µM ABA treatment (+ABA) and discontinuous 100 µM ABA treatment (±ABA). ABA was fed to +ABA plants during the whole treatment period of 30 days. ABA was fed to ±ABA plants for three days in two weeks. Developing xylem and mature xylem were collected separately during the harvest and shortly frozen in liquid nitrogen. RNA was extracted from these samples and followed by RNA-sequencing.
2019-01-20 | E-MTAB-7587 | biostudies-arrayexpress
Project description:Peroxisome proliferator-activated receptor beta/delta protects against obesity by reducing dyslipidemia and insulin resistance via effects in various organs, including muscle, adipose tissue, liver, and heart. However, nothing is known about the function of PPAR-beta in pancreas, a prime organ in the control of glucose metabolism. To gain insight into so far hypothetical functions of this PPAR isotype in insulin production, we specifically ablated Ppar-beta in pancreas. The mutated mice developed a chronic hyperinsulinemia, due to an increase in both beta-cell mass and insulin secretion. Gene expression profiling indicated a broad repressive function of PPAR-beta impacting the vesicular compartment, actin cytoskeleton, and metabolism of glucose and fatty acids. Analyses of insulin release from the islets revealed an increased second-phase glucose-stimulated insulin secretion. Higher levels of PKD, PKC-delta and diacyglycerol in mutated animals lead to an enhanced formation of trans-Golgi network (TGN)-to-plasma-membrane transport carriers in concert with F-actin disassembly, which resulted in increased insulin secretion and its associated systemic effects. Taken together, these results provide evidence for PPAR-beta playing a repressive role on beta-cell growth and insulin exocytosis, which shed new light on its anti-obesity action. Pancreas-specific knock-out animals were generated by breeding mice harbouring a floxed Ppar-beta (PPARbetafl/fl) to mice expressing the Cre transgene under the control of the Pdx1 promoter (Pdx1Cre). Islets from 3 different animals from the knock-out group Pdx1Cre;PPARbetafl/fl and the control littermates group PPARbetafl/fl were compared.
2012-08-30 | E-GEOD-16048 | biostudies-arrayexpress
Project description:Plant hormones involved in environmental stresses, namely abscisic acid (ABA), salicylic acid (SA), and jasmonic acid (JA), have been shown to interact with each other in a complex manner. To address the network of the hormone interactions, we have investigated the changes in expression under multiple hormone treatments, ABA+SA and ABA+JA. We chose cultured cells to remove the difference in the response to hormones among developmental cells or tissues. The cells were treated for 3hr and 24hr to see the rapid or transient response and steady-state response. The obtained data indicate that ABA and SA affect antagonistically, but these hormones affected many genes collaboratively. Indeed, according to the microarray data, there are many genes that responded only to ABA+SA. In addition, the ABA+SA responsive genes also responded to ABA+JA. These data suggest that hormone crosstalk is more complicated than expected and that more systematic analysis is required to untangle the hormone crosstalk network. To investigate the hormonal interactions, Arabidopsis T87 cultured cells were exposed to ABA, SA, or JA alone, or two hormones simultaneously, ABA+SA or ABA+JA, for 3hr and 24 hr. Comparing the data among those treatments, the relationships among these hormones were deduced.
2011-12-01 | E-GEOD-28600 | biostudies-arrayexpress
Project description:Purpose: to screen the candidate genes involved in the peanut drought stress response, we conducted global transcriptome analysis of peanut plants challenged with water deficit and ABA, using the Illumina HiSeq2000 sequencing platform. Methods: a sequences library of Yueyou7 were constructed at first. Then the profile of diffentialy expressed genes (DEGs) under three different treatments (control, water deficit without ABA, and water deficit with ABA) were conducted based on above sequence library. For sequencing library construction, plants were grown under normal conditions, as described previously , Seeds were planted in soil and kep in the greenhouse at temperature of 25-30M-bM-^DM-^C and water well. Three tissues (leaves, roots, and stems) were collected at three development stages (four-leaf, flowering and podding stages), respectively. Then all of these tissues were mixed to extract the total RNA for sequence library construction. For DEGs study, two-week-old plants were divided into three groups with three independent replication: (1). Water deficit without ABA groups. Plants directly steeped in water containing 30% PEG600 for 30 min in this groups. (2) Water deficit with ABA groups. Plant was subjected to 100 M-BM-5mol/L ABA for 30 min and then steeped in water containing 30% PEG6000 for 30 min in this groups, (3) Control. Plants steeped in H2O. All treatments were conducted in parallel. After treatments, Total RNA was extracted from 100 mg of plant material, and RNA integrity was checked by gel electrophoresis. Also RNA quality was checked and RNA was quantified using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA) and Nanodrop ND-1000 (Thermo Scientific, Waltham, USA). Results: we generated 4.96M-CM-^W107 raw sequence reads and assembled the high quality reads into 92,390 unique genes. Compared with the control, we found that 621 genes (M-bM-^IM-%1.5 fold change) responded rapidly to water deficit and 2665 genes (M-bM-^IM-%1.5 fold change) responded rapidly to ABA. We found 279 genes that overlapped between water deficit and ABA responses, 264 genes that showed the same trend in expression while 15 genes expression that showed opposite trend. Among the identified genes, 257 showed high induction by ABA (>5 fold), and 19 showed high induction by drought (>5 fold). In addition, we identified 100 transcription factor genes among the ABA-inducible genes but only 22 transcription factor genes among the water deficit-inducible genes. Conclusions: we identified genes differentially expressed in the early response to water deficit or ABA. These genes were annotated with GO functional categories for water deficit (33 categories) or ABA (31 categories). We found that only 19 genes were highly induced by water deficit, but 257 genes were highly induced by ABA. Our previous work has examined many of these genes and our future work will reveal their functions and relationships. These data will facilitate functional genomic studies and have established a biotechnological platform for examination of the early drought- and ABA-responsive transcriptome regulatory network in peanut. Two-week-old plants were divided into three groups with three independent replication: (1). Water deficit without ABA groups. Plants directly steeped in water containing 30% PEG600 for 30 min in this groups. (2) Water deficit with ABA groups. Plant was subjected to 100 M-BM-5mol/L ABA for 30 min and then steeped in water containing 30% PEG6000 for 30 min in this groups, (3) Control. Plants steeped in H2O. All treatments were conducted in parallel.
2014-05-13 | E-GEOD-56439 | biostudies-arrayexpress
Project description:Microarray experiments were performed using Arabidopsis wild type plants (Col-0) and srk2dei triple knockout mutant to investigate the functions of ABA-activated protein kinases, SRK2D/SnRK2.2, SRK2E/OST1 and SRK2I/SnRK2.3. Transcription profiles of wild type and mutants were compared under ABA treatment or dehydration stress for 0 and 90 min. The srk2dei mutant was established by crossing T-DNA insertion mutants provided from Arabidopsis Biological Resource Center.
2013-03-31 | E-MEXP-3713 | biostudies-arrayexpress
Project description:Background: Abscisic acid (ABA) regulates various developmental processes and stress responses over both short (i.e. hours or days) and longer (i.e. months or seasons) time frames. To elucidate the transcriptional regulation of early responses of grapevine (Vitis vinifera) responding to ABA, different organs of grape (berries, shoot tips, leaves, roots and cell cultures) were treated with 10 μM (S)-(+)-ABA for 2 h. NimbleGen whole genome microarrays of Vitis vinifera were used to determine the effects of ABA on organ-specific mRNA expression patterns. Results: Transcriptomic analysis revealed 839 genes whose transcript abundances varied significantly in a specific organ in response to ABA treatment. No single gene exhibited the same changes in transcript abundance across all organs in response to ABA. The biochemical pathways affected by ABA were identified using the Cytoscape program with the BiNGO plug-in software. The results indicated that these 839 genes were involved in several biological processes such as flavonoid metabolism, response to reactive oxygen species, response to light, and response to temperature stimulus. ABA affected ion and water transporters, particularly in the root. The protein amino acid phosphorylation process was significantly overrepresented in shoot tips and roots treated with ABA. ABA affected mRNA abundance of genes (CYP707As, UGTs, and PP2Cs) associated with ABA degradation, conjugation, and the ABA signaling pathway. ABA also significantly affected the expression of several transcription factors (e.g. AP2/ERF, MYC/MYB, and bZIP/AREB). The greatest number of significantly differentially expressed genes was observed in the roots followed by cell cultures, leaves, berries, and shoot tips, respectively. Each organ had a unique set of gene responses to ABA. Conclusions: This study examined the short-term effects of ABA on different organs of grapevine. The responses of each organ were unique indicating that ABA signaling varies with the organ. Understanding the ABA responses in an organ-specific manner is crucial to fully understand hormone action and plant responses to water deficit. Shoot tips and berries samples were collected at the University of California, Davis, CA, USA (2010); cell culture samples were sampled at Oregon State University, OR, USA (2010); roots and leaf samples were collected at the University of Nevada, Reno, Reno, NV, USA (2011). Three independent experimental (and biological) replicates were harvested to compare between ABA-treated and untreated samples. Tissue was derived from Vitis vinifera L. cv. Cabernet Sauvignon.
2016-03-01 | E-GEOD-78798 | biostudies-arrayexpress