VEGFB treated macrophage
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Yvan Devaux
PROVIDER: E-GEOD-27479 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:MicroRNAs (miRs) contribute to both neuronal and immune cell fate, but their involvement in inter-tissue communication remained unexplored. The brain, via vagal secretion of acetylcholine (ACh), suppresses peripheral inflammation by intercepting cytokine production; therefore, we predicted that microRNAs targeting acetylcholinesterase (AChE) can attenuate inflammation. Here, we report that inflammatory stimuli induce leukocyte over-expression of the AChE-targeting miR-132. Injected LNA-modified anti-miR-132 oligonucleotide depleted miR-132 levels while elevating AChE in mouse circulation and tissues. In transfected cells, a mutated 3âUTR miR-132 binding site increased AChE mRNA expression, whereas cells infected with a lentivirus expressing pre-miR-132 showed suppressed AChE. Transgenic mice over-expressing 3'UTR-null AChE showed excessive inflammatory mediators and impaired cholinergic anti-inflammatory regulation, in spite of substantial miR-132 up-regulation in brain and bone marrow. Our findings identify the AChE mRNA-targeting miR-132 as a functional regulator of the brain-to-body resolution of inflammation, opening new avenues for study and therapeutic manipulations of the neuro-immune dialogue. Pathogen-negative leukopacks (Buffy coat) obtained from the Blood Bank at the Hadassah Medical Center, Ein Kerem were transferred into 50 ml conical tubes (~10 ml/tube) and diluted 1:2 with Dulbecco's phosphate buffered saline (PBS, Biological Industries, Beit Haemek, Israel). The diluted blood was gently layered on top of 20 ml of lymphocyte separation medium (LSM)/Ficoll (MP Biomedicals, Solon, OH) without mixing the layers. Following centrifugation (500g, 30 min, 20°C, without brake), three layers were obtained (plasma & platelets, lymphocytes, erythrocytes & granulocytes). The upper phase was drawn with a Pasteur pipette until reaching 2 mm above the interphase cloud, and then 5 to 10 ml interphase lymphocytes were drawn gently with a 1ml pipette, washed once with 45 ml PBS, and centrifuged (400g , 10 min, room temp.). Pellets from all tubes were resuspended in a total of 40 ml PBS. An aliquot of cells was counted in a hemacytometer using 0.5% Trypan Blue Solution (Biological Industries) to determine cell number and viability. Cells were then centrifuged (200g, 5 min, room temp) and resuspended at a concentration of ~ 5 X 106 cells/ml in RPMI-1640 (Sigma, St. Louis, MO) supplemented with 2.5% heat-inactivated (56°C, 30 min) human serum (Sigma). 10 ml of cell suspension were plated in 75 ml flasks and incubated (2 hrs, 37°C, 5% CO¬2). Non-adherent cells were then removed and the adherent monocytes washed 3 times with warm PBS. Cells were incubated for 2hr in 10 ml per dish of RPMI-1640 supplemented with LPS-free 10% foetal bovine serum (FBS), 2 mM L-Glutamine and 0.5% penicillin/streptomycin (GIBCO, Carlsbad, CA) and washed 3 times with warm PBS and 10 ml of complete RPMI supplemented with 10 U/ml granulocyte-monocyte colony stimulating factor (GM-CSF, Sigma, G5035) added every 2-3 days. By ~day 7 monocytes were differentiated to macrophages. Escherichia coli LPS (Sigma) was added to the growth medium to a final concentration of 1μg/ml, which was found optimal to induce innate immune reaction. For comparison, 1 μM of the TLR9 ligand CpG 2006 (type B; Microsynth GmbH) were added for 24 hr. Cells were washed 2-3 times with cold PBS, then incubated in 5 ml of cold filtered PBS + EDTA 2 mM (pH = 7.2) for 10-15 min on ice. Flasks were then tapped firmly to loosen cell attachment, and cells were gently scraped and collected by centrifugation (4°C, 800 rpm, 10 min). Short RNAs isolated from LPS-treated, CpG-treated and control cells were labeled with CyDyes 3 and 5 (each with a dye-swap), and hybridized with slides with spotted miRvana probe set (Ambion) as described for each sample.
2010-05-19 | E-GEOD-19094 | biostudies-arrayexpress
Project description:Aneuploidy and the evolution of aneuploid karyotypes of Candida albicans strains was identified using aCGH. Whole chromosome and segmental aneuploidies, (specifically on the left arm of chromosome 5 - shown to be due to isochromosome formation) are associated with the appearance of resistance to the antifungal drug fluconazole. Keywords: Comparative Genomic Hybridization Hybridization of all strains was compared to the hybridization of SC5314, the sequenced laboratory strain.
2006-06-30 | E-GEOD-4995 | biostudies-arrayexpress
Project description:The existence of two separate lineages of Escherichia coli O157:H7 has previously been reported, and research indicates that one of these lineages (lineage I) might be more pathogenic towards human hosts. We have previously shown that the more pathogenic lineage expresses higher levels of Shiga toxin 2 (Stx2) than the non-pathogenic lineage II. To evaluate why lineage 2 isolates do not express appreciable levels of toxin, two lineage 2 isolates (FRIK966 and FRIK2000) were chosen as representatives of lineage 2 and whole genome microarrays were performed using Agilent microarrays using the E. coli O157:H7 EDL933 lineage I clinical type isolate as a reference. Microarray results were utilized to evaluate what genes and pathways might be missing or differentially expressed. Quantitative RT-PCR was utilized to validate the microarray data. Based upon the transcriptome of Escherichia coli O157:H7 EDL933 an oligonucleotide microarray, made up of 60 mers was designed. A total of 4873 genes in an 8 x 15K Agilent microarray design. Designed using a custom script, specifications for gene specific oligos were based upon various design characteristics such as temperature of melting, 3’ location, specificity, lack of repeat nucleotides, etc. (Charbonnier et al., 2005). Arrays were manufactured using Agilent Sure-print technology. Each array consisted of duplicate elements for each gene randomly distributed with Agilent control elements included. All procedures were performed according to respective manufacturer protocols. Lineage I and lineage II strains were grown overnight as described, a total of 10e7 cells were washed twice in fresh media, normalized based upon optical density, inoculated into fresh media, incubated at 37oC shaking 120 x g for 3 hours and then suspended in RNAprotect bacteria reagent (Qiagen Inc., Valencia, CA.). Total RNA was extracted using RNeasy Bacteria Mini Kit (Qiagen Inc., Valencia, CA.) and trace amounts of DNA were removed using RNase-Free DNase Set (Qiagen Inc., Valencia, CA.). RNA was quantified using Nanodrop system (NanoDrop Technologies, Wilmington, DE) and quality confirmed by electrophoresis on a Bio-rad Experion system (BioRad XXX). For each sample, 10 ug of RNA were labeled with either CyDye3-dCTP or CyDye5-dCTP (Perkin Elmer) using the LabelStar kit (Qiagen Inc., Valencia, CA.) and Random nonamers (Integrated DNA Technologies ). Labeled cDNA were hybridized to the microarray using Agilent Hi-RPM hybridization solution in an Agilent Hybridization chamber (Agilent.). A total of 8 arrays, each with duplicate elements for each gene, alternating dye swap for each replicate (4 biological replicates), were analyzed to obtain genes that were consistently and differentially regulated in comparison to EDL933, while limiting false discover rate (FDR) below a stringent 5% (Benjamini and Hochberg, 1995).
2009-08-31 | E-GEOD-17070 | biostudies-arrayexpress
Project description:The readout of genome information is controlled by transcriptional regulatory elements, but a comprehensive view of the combinatorial control by these DNA sequences, which bind regulatory protein and/or the modified histones in regulating gene transcription, is clearly preliminary. We have developed an experimental strategy for comprehensive determination of such functional elements in human DNA. This strategy involves the application of genome-wide location analysis, also known as ChIP-chip, to a panel of well-characterized regulatory proteins and histones with specific modifications, known to generally associate with transcriptional regulatory elements in vivo. Identification of their genomic binding sites will allow us to determine the sequence features in the human genome that carry out transcriptional regulatory function. We have designed and produced DNA microarrays to represent all the non-repetitive sequences in the 30 million basepair ENCODE regions of the human genome to map various types of transcriptional regulatory elements in three model cell types. We have identified promoters by mapping the genomic sequences associated with RNA polymerase II and the general transcription factor TFIID in cells, enhancer elements by mapping the genomic sequences associated with transcriptional co-activators and enhancer-specific chromatin modifications, and insulators by mapping the genomic sequences associated with the insulator binding protein CTCF. The raw microarray results are released periodically prior to publication. Keywords: ChIP-chip ENCODE ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications. Ren B, Glass CK, Rosenfeld MG, Webster N, Ching KA, Harp L, Ye Z, Stuart RK, Calcar SV, Kim TH, Hawkins RD, Hon G, Barrera LO, Luna R, Wang K
2010-05-15 | E-GEOD-8887 | biostudies-arrayexpress
Project description:The cyclin-dependent kinase inhibitor p16INK4a (CDKN2A) is an important tumor-suppressor gene frequently inactivated in human tumors. p16 suppresses the development of cancer by triggering an irreversible arrest of cell proliferation termed cellular senescence. Here, we describe another anti-oncogenic function of p16 in addition to its ability to halt cell cycle progression. We show that transient expression of p16 stably represses the hTERT gene, encoding the catalytic subunit of telomerase, in both normal and malignant breast epithelial cells. Short-term p16 expression increases the amount of histone H3 trimethylated on lysine 27 (H3K27) bound to the hTERT promoter, resulting in transcriptional silencing, likely mediated by polycomb complexes. Our results indicate that transient p16 exposure may prevent malignant progression in dividing cells by irreversible repression of genes, such as hTERT, whose activity is necessary for extensive self-renewal. 27 samples were analyzed to study three histone modifications (H3K4me3, H3K9me3, H3K27me3) in three different cell lines. Each combination of histone modification and cell line had three biological replicates (A,B,C).
2010-05-19 | E-GEOD-14436 | biostudies-arrayexpress
Project description:Anopheles gambiae mosquitoes exhibit an endophilic, nocturnal blood feeding behavior. Despite the importance of light as a regulator of malaria transmission, our knowledge on the molecular interactions between environmental cues, the circadian oscillators and the host seeking and feeding systems of the Anopheles mosquitoes is limited. In the present study, we show that the blood feeding behavior of mosquitoes is under circadian control and can be modulated by light pulses, both in a clock dependent and in an independent manner. Short light pulses (~2-5 min) in the dark phase can inhibit the blood-feeding propensity of mosquitoes momentarily in a clock independent manner, while longer durations of light stimulation (~1-2 h) can induce a phase advance in blood-feeding propensity in a clock dependent manner. The temporary feeding inhibition after short light pulses may reflect a masking effect of light, an unknown mechanism which is known to superimpose on the true circadian regulation. Nonetheless, the shorter light pulses resulted in the differential regulation of a variety of genes including those implicated in the circadian control, suggesting that light induced masking effects also involve clock components. Light pulses (both short and longer) also regulated genes implicated in feeding as well as different physiological processes like metabolism, transport, immunity and protease digestions. RNAi-mediated gene silencing assays of the light pulse regulated circadian factors timeless, cryptochrome and three takeout homologues significantly up-regulated the mosquito's blood-feeding propensity. In contrast, gene silencing of light pulse regulated olfactory factors down-regulated the mosquito's propensity to Our study suggests that the mosquitoâs feeding behavior is under circadian control. Long and short light pulses can induce inhibition of blood-feeding through circadian and unknown mechanisms, respectively, that involve chemosensory factors. A series of assays were performed to assess transcriptomic changes in mosquitoes upon light stimulation and blood feeding in order to assess relationships between photic stimulation and modulation of feeding behavior.
2010-06-24 | E-GEOD-13560 | biostudies-arrayexpress
Project description:Background: The mosquito Anopheles gambiae is a major vector of human malaria. Increasing evidence indicates that blood cells (hemocytes) comprise an essential arm of the mosquito innate immune response against both bacteria and malaria parasites. To further characterize the role of hemocytes in mosquito immunity, we undertook the first genome-wide transcriptomic analyses of adult female An. gambiae hemocytes following infection by two species of bacteria and a malaria parasite. Results: We identified 4047 genes expressed in hemocytes, using An. gambiae genome-wide microarrays. While 279 transcripts were significantly enriched in hemocytes relative to whole adult female mosquitoes, 959 transcripts exhibited immune challenge-related regulation. The global transcriptomic responses of hemocytes to challenge with different species of bacteria and/or different stages of malaria parasite infection revealed discrete, minimally overlapping, pathogen-specific signatures of infection-responsive gene expression; 105 of these represented putative immunity-related genes including anti-Plasmodium factors. Of particular interest was the specific co-regulation of various members of the Imd and JNK immune signaling pathways during malaria parasite invasion of the mosquito midgut epithelium. Conclusion: Our genome-wide transcriptomic analysis of adult mosquito hemocytes reveals pathogen-specific signatures of gene regulation and identifies several novel candidate genes for future functional studies. In order to identify hemocyte-specific and immune-responsive transcripts, we first compared transcripts expressed in hemocytes from one day old sugar-fed mosquitoes to transcripts detected in whole mosquitoes of the same age and feeding status. This resulted in identification of the hemocyte-enriched transcriptome. We then compared hemocytes from 1 day old mosquitoes, 1 hour after immune challenge with heat-killed Escherichia coli or Micrococcus luteus, to control female mosquitoes injected with sterile PBS to determine the bacteria challenge responsive transcriptomes. We used heat-killed bacteria in these assays, because our primary interest was in identifying the bacterial responsive transcriptome and to avoid the potentially confounding effects of altered gene expression due to the lethal effects of a systemic infection associated with injection of living bacteria. Lastly, we compared hemocytes from mosquitoes at 24 hours and 19 days after ingestion of a blood meal infected with Plasmodium berghei to mosquitoes of the same age fed a non-infected blood meal to determine the ookinete and sporozoite infection responsive transcriptomes, respectively. This design resulted in a total of five experimental treatments. The following samples are not included in this submission: Hemo E coli vs. hemo unchallenged A Hemo E coli vs. hemo unchallenged B Hemo m luteus vs. hemo unchallenged A Hemo m luteus vs. hemo unchallenged B
2011-10-31 | E-GEOD-33269 | biostudies-arrayexpress
Project description:Genome-wide location analysis of transcription factor of c-Myc and Max was conducted using RenLab Hu6K array in Daudi cells. In comparison, the GWLA was also done for general transcription factor RNA polymerase II and TAF1, and sequence specific transcription factor E2F1 in the same cell line. Keywords = GWLA Keywords = RenLab Keywords = Hu6K Keywords = Myc Keywords = Max
2010-06-10 | E-GEOD-2542 | biostudies-arrayexpress
Project description:The local background was subtracted from the fluorescent value of each spot. Feature intensities were extracted from scanned microarray images using GenePix Pro 5.1. (Axon Instruments). The images were visually inspected, and spots from low-quality areas of the array were flagged and excluded from further analysis. Spots were also excluded from analysis if both the combined fluorescent intensity for both channels was less than 1.4 times that of the local background and the pixel-by-pixel correlation coefficient of the spot was less than 0.4. The fluorescence ratios were normalized as previously described (Turton and Gant oncogene 2001website). A hierarchical clustering algorithm (M. Eisen Brown and Botstein PNAS 98 website) was applied to those genes that fulfilled all of the following conditions: they were not flagged; they were differentially expressed (equal or higher than 1.5 fold upregulated or equal or lower than 2 fold downregulated); they had p-values equal or less than 0.02; and they were consistent on at least 4 out of the 5 arrays.
2010-05-27 | E-GEOD-2069 | biostudies-arrayexpress
Project description:The readout of genome information is controlled by transcriptional regulatory elements, but a comprehensive view of the combinatorial control by these DNA sequences, which bind regulatory protein and/or the modified histones in regulating gene transcription, is clearly preliminary. We have developed an experimental strategy for comprehensive determination of such functional elements in human DNA. This strategy involves the application of genome-wide location analysis, also known as ChIP-chip, to a panel of well-characterized regulatory proteins and histones with specific modifications, known to generally associate with transcriptional regulatory elements in vivo. Identification of their genomic binding sites will allow us to determine the sequence features in the human genome that carry out transcriptional regulatory function. We have designed and produced DNA microarrays to represent all the non-repetitive sequences in the 30 million basepair ENCODE regions of the human genome to map various types of transcriptional regulatory elements in three model cell types. We have identified promoters by mapping the genomic sequences associated with RNA polymerase II and the general transcription factor TFIID in cells, enhancer elements by mapping the genomic sequences associated with transcriptional co-activators and enhancer-specific chromatin modifications, and insulators by mapping the genomic sequences associated with the insulator binding protein CTCF. The raw microarray results are released periodically prior to publication. Keywords: ChIP-chip ENCODE ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications. Ren B, Glass CK, Rosenfeld MG, Webster N, Ching KA, Harp L, Ye Z, Stuart RK, Calcar SV, Kim TH, Hawkins RD, Hon G, Barrera LO, Luna R, Wang K
2007-06-01 | E-GEOD-7872 | biostudies-arrayexpress