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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse dendritic cells reveals stimulatory effect of Echinacea purpurea extract on trafficking activity

ABSTRACT: To seek scientific evidence supporting therapeutic use of Echinacea, the transcriptomic effects of Echinacea purpurea extract on mouse bone marrow-derived dendritic cells (BMDCs) were analyzed using primary cultures. Affymetrix DNA microarray and bioinformatics analyses of genes differentially expressed in DCs treated with [BF/S+L/Ep] for 4 or 12 h revealed that the majority of responsive genes were related to cell adhesion or motility (Cdh10, Itga6, Cdh1, Gja1 and Mmp8), or were chemokines (Cxcl2, Cxcl7) or signaling molecules (Nrxn1, Pkce and Acss1). Experiment Overall Design: BMDCs from mice were treated with [BF/S+L/Ep] or DMSO for 4 h or 12 h in duplicates.

ORGANISM(S): Mus musculus

SUBMITTER: Ning-Sun Yang

PROVIDER: E-GEOD-19369 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Stimulatory effect of Echinacea purpurea extract on trafficking activity in mouse dendritic cells

Project description:To seek scientific evidence supporting therapeutic use of Echinacea, the transcriptomic effects of Echinacea purpurea extract on mouse bone marrow-derived dendritic cells (BMDCs) were analyzed using primary cultures. Affymetrix DNA microarray and bioinformatics analyses of genes differentially expressed in DCs treated with [BF/S+L/Ep] for 4 or 12 h revealed that the majority of responsive genes were related to cell adhesion or motility (Cdh10, Itga6, Cdh1, Gja1 and Mmp8), or were chemokines (Cxcl2, Cxcl7) or signaling molecules (Nrxn1, Pkce and Acss1).

2010-09-13 | GSE19369 | GEO

STING mediates lupus via the activation of conventional dendritic cell maturation and plasmacytoid dendritic cell differentiation

Project description:BMDCs from WT, Fcgr2b-/- and Stinggt/gt were cultured, then stimulated with DMXAA for 3 and 6 hr. Cells were collected and lysed with 1 % IGEPAL CA-630, 0.5% TritonX-100, 150 mM NaCl, 50 mM Tris pH 7.4, 5% glycerol, 100 mM beta-Glycerophosphate, 2 mM Na3VO4 and 1X proteases inhibitor cocktail (Roche). First, antibody were mixed with the magnetic beads by adding 10 µg of STING antibody with 400 ug of SureBeads™ Protein A magnetic beads (Biorad, California, USA) and incubated for 1 hour at room temperature. Then, Protein lysates were added and incubated with antibody-conjugated beads for overnight at 4oC. After incubation, the beads were washed 3 times with wash buffer (150 mM NaCl and 50 mM Tris-HCL pH 7.4). Samples were eluted by adding 5X laemmli buffer and, boiled 950C for 10 minutes. The eluted protein samples were separated by 10 % SDS-PAGE gel. The STING interacting proteins from co-IP were analyzed by in-gel digestion followed by LC-MS/MS analysis.

2020-09-14 | PXD019239 | Pride

PDL2+, PDL2- and LPS treated PDL2- WT bone-marrow derived murine DCs

Project description:Cultured BMDCs were purified by FACS sorting for PDL2 surface expression and stimulated with LPS at 100 ng/mL or left unstimulated. Microarray data was used to demonstrate gene expression differences between PDL2- and PDL2+ DC populations. Microarray data was also used to show that PDL2+ mature DCs were distinct from LPS treated DCs. Two populations of murine DCs derived from ex vivo culture were compared.

2013-09-17 | E-GEOD-50898 | biostudies-arrayexpress

Membrane Vesicles of a Bacterial Mutualist Mediate Immune Regulation via Dendritic Cells

Project description:Microbial molecules have evolved to promote transient and/or permanent associations with mammals. Although numerous examples of secretion systems employed by pathogens have been described, mechanisms by which commensal bacteria export molecules during symbiosis remain unknown. The human gut mutualist Bacteroides fragilis produces a capsular polysaccharide (PSA) that directs host immune development. We reveal herein that outer membrane vesicles (OMVs) deliver PSA to dendritic cells (DCs), promoting regulatory T cells and inducing anti-inflammatory cytokines during protection from intestinal disease. In addition, we found that TLR2 signaling by DCs is required for OMV sensing. Following internalization into DCs and engagement of TLR2, OMVs initiate a gene expression program that results in IL-10 production by DCs. Although it is known that the outcome of PSA sensing by the immune system is Treg induction, nothing is known about the intracellular signaling pathway(s) activated by PSA within DCs. We analyzed the gene expression profile of DCs treated with OMVs to uncover factors that are expressed in a PSA-dependent, TLR2-dependent manner. Our findings demonstrate DC-induced protection from disease via OMV-delivery of a beneficial microbial molecule, uncovering a novel paradigm for inter-kingdom communication between the microbiota and mammals. RNA samples (1ug total RNA) from BMDCs were labeled with fluorescent dyes using the Quick Amp Labeling Kit (Agilent). Microarray (AgilentWhole Mouse Genome chip) hybridizations (65M-BM-0C for 16 hours) and washes were performed with Agilent reagents following standard protocols. Microarrays were analyzed using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 10.1.1.1. Significant genes were selected based on p< 0.01 and fold change >2.0.

2012-07-22 | E-GEOD-39563 | biostudies-arrayexpress

Transcription profiling of human dendritic cells treated with Echinacea purpurea phytocompounds

Project description:This study investigated the specific and differential gene expression in human immature DCs (iDCs) in response to treatment with a butanol fraction containing defined bioactive phytocompounds extracted from stems and leaves of Echinacea purpurea Experiment Overall Design: Human immature DCs (iDCs) differentiated from primary monocytes in vitro were incubated with [BF/S+L/Ep] or cichoric acid for 4 or 24 h to characterize early- or late-responsive genes. A total of nine Affymetrix HU-133A chips were hybridized to determine the transcriptome profiles in human iDCs.

2008-10-25 | E-GEOD-12259 | biostudies-arrayexpress

Gene expression signature of Gata6 positive epidermal cells.

Project description:To characterize gene expression in Gata6 positive epidermal cells we analyzed a Gata6 reporter mouse in which the endogenous Gata6 promoter drives expression of mTomato. We performed flow cytometry followed by transcriptome analysis. We compared four subpopulations of telogen epidermal cells: Gata6+/Itga6+ cells, Gata6+/itga6- cells, CD34+/Itga6+ cells (which are Gata6-) and all remaining Itga6+ cells (Gata6-/CD34-). The RNA was isolated from age and sex matched mice. We compared four subpopulations of telogen epidermal cells: Gata6+/Itga6+ cells, Gata6+/itga6- cells, CD34+/Itga6+ cells (which are Gata6-) and all remaining Itga6+ cells (Gata6-/CD34-). The RNA was isolated from age and sex matched mice. Three biological replicates for each cell population were analyzed

2017-05-16 | E-GEOD-62606 | biostudies-arrayexpress

Quantitative proteomic analysis of gastric cancer cells treated by bifidobacterium infantis-mediated herpes simplex virus-TK/ganciclovir.

Project description:MKN-45 cells were treated with PBS, BF-TK, BF/GCV or BF-TK/GCV for 48 h (GCV, 167 µg/ml), respectively. BF-TK (n = 3), BF/GCV (n = 3) or BF-TK/GCV (n = 3) groups were analyzed in triplicate.

2023-10-24 | PXD042044 | Pride

Cross-Platform Validation of Neurotransmitter Release Impairments in Schizophrenia Patient-Derived NRXN1-Mutant Neurons

Project description:Heterozygous NRXN1 deletions constitute the most prevalent currently known single-gene mutation associated with schizophrenia, and predispose to multiple other neurodevelopmental disorders. Previous studies showed that engineered heterozygous NRXN1 deletions impaired neurotransmitter release in human neurons, suggesting a synaptic pathophysiological mechanism. Utilizing this observation for drug discovery, however, requires confidence in its robustness and validity. Here, we describe a multi-center effort to test the generality of this pivotal observation, using independent analyses at two laboratories of patient-derived and newly engineered human neurons with heterozygous NRXN1 deletions. We show that in neurons that were trans-differentiated from induced pluripotent stem cells derived from three NRXN1-deletion patients, the same impairment in neurotransmitter release was observed as in engineered NRXN1-deficient neurons. This impairment manifested as a decrease in spontaneous synaptic events and in evoked synaptic responses, and an alteration in synaptic paired-pulse depression. Nrxn1-deficient mouse neurons generated from embryonic stem cells by the same method as human neurons did not exhibit impaired neurotransmitter release, suggesting a human-specific phenotype. NRXN1 deletions produced a reproducible increase in the levels of CASK, an intracellular NRXN1-binding protein, and were associated with characteristic gene expression changes. Thus, heterozygous NRXN1 deletions robustly impair synaptic function in human neurons regardless of genetic background, enabling future drug discovery efforts.

2021-03-12 | GSE168762 | GEO

Intellectual disability and mood disorder associated with partial deletion of the Neurexin 1 Gene

Project description:Abstract Background Neurexins are proteins located in the presynaptic membrane that bind postsynaptic ligands, neuroligins, neurexophilins, and dystrophoglycan. They exert profound effects on neurological function by mediating signalling across synapses and determining synaptic characteristics through the recruitment of additional proteins for synapse formation. Alterations in neurexin-encoding genes cause cognitive disorders such as autism, developmental delay and schizophrenia. The three neurexin genes in the human genome (NRXN1, NRXN2, and NRXN3) each have two different functional promoters, producing a large (alpha) and small (beta) transcript with corresponding proteins. NRXN1 produces hundreds, perhaps thousands, of different transcripts with differential localization in the CNS. Results We report here the identification of an individual (53825) with mild dysmorphia, severe language disorder, mild intellectual disability, attention deficit hyperactivity disorder (ADHD), and a mood disorder. Genomic analysis by Affymetrix 6.0 Gene Chip and FISH (fluorescence in situ hybridization) using probes specific for NRXN1 revealed a hemizygous deletion of approximately 190 Kb, which includes exons 3-5 of NRXN1. This deletion should result in the absence of the vast majority of different NRXN1 alpha transcripts from one of the NRXN1 gene copies, without effecting NRXN1 beta transcription. Copy number analysis of Affymetrix 6.0 SNP arrays was performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples for pediatric patients. One sample showed partial deletion of NRXN1 alpha; data presented in this Series.

2011-06-24 | E-GEOD-23358 | biostudies-arrayexpress

Neuronal impact of patient-specific aberrant NRXN1α splicing [whole]

Project description:We performed targeted long-read and short-read RNA sequencing to identify and quantify NRXN1 isoforms in human post-mortem dlPFC and hiPSC-neurons derived from controls and NRXN1+/- individuals. We also performed whole transcriptome RNA seuqencing and 10x genomics single cell sequencing to determine transcriptional changes in NRXN1+/- hiPSC-neurons compared to controls.

2019-09-10 | GSE137101 | GEO

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