Bulk RNA sequencing of Vegfr3 fl/fl (Ctrl) and Vegfr3 fl/fl;prox1creERT2 (Vegfr3iLKCko) mouse conjunctival tissue with or without allergic eye disease
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE206645 | GEO | 2022/06/30
REPOSITORIES: GEO
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Project description:Bulk RNA sequencing of Vegfr3 fl/fl (Ctrl) and Vegfr3 fl/fl;prox1creERT2 (Vegfr3iLKCko) mouse conjunctival tissue with or without allergic eye disease
| PRJNA851711 | ENA
Project description:To determine the differential expression of miRNAs in the lungs of mice subjected to a model of allergic airways disease and non-allergic and steroid-treated control animals. Total lung RNA was collected from mice sensitised and challenged with PBS or OVA with or without DEX treatment at day 16 and miRNA microarrays performed.
2015-12-31 | E-GEOD-72793 | biostudies-arrayexpress
Project description:Background: Inhalation exposure to biological particulate matter (BioPM) from livestock farms may provoke exacerbations in subjects suffering from allergy and asthma. The aim of this study was to use a murine model of allergic asthma to determine the effect of BioPM derived from goat farm on airway allergic responses Methods: Fine (< 2.5 μm) BioPM was collected from an indoor goat stable. Female BALB/c mice were ovalbumin (OVA) sensitized and challenged with OVA or saline as control. The OVA and saline groups were divided in sub-groups and exposed intranasally to different concentrations (0, 0.9, 3, or 9 μg) of goat farm BioPM. Bronchoalveolar lavage fluid (BALF), blood and lung tissues were collected. Results: In saline-challenged mice, goat farm BioPM alone induced a dose-dependent increase in neutrophils in BALF and induced production of macrophage inflammatory protein-3a). In OVA-challenged mice, BioPM significantly enhanced 1) inflammatory cells in BALF, 2) OVA-specific Immunoglobulin (Ig)G1, 3) interleukin-23 production, 4) airway mucus secretion-specific gene expression. RNAseq analysis of lungs indicates that neutrophil chemotaxis and oxidation-reduction processes were the representative genomic pathways in saline and OVA-challenged mice, respectively. Conclusions: A single exposure to goat farm BioPM enhanced airway inflammation in both saline and OVA-challenged allergic mice, with neutrophilic response as Th17 disorder and eosinophilic response as Th2 disorder indicative of the severity of allergic responses. Identification of the mode of action by which farm PM interacts with airway allergic pathways will be useful to design potential therapeutic approaches.
2020-08-01 | GSE148240 | GEO
Project description:Allergen challenge induced mucus metaplasia modify the expression of two transcription factors belonging to the FOXA family: FOXA2 and FOXA3. Foxa2 expression is decreased during allergic airway disease whereas, Foxa3 expression is increased by allergen. Therefore, we asked whether persistent expression of Foxa2 prevents mucus and whether absence of Foxa3 affects mucus or other features asociated with allergic airway disease. We analyzed the effects of these changes in FOXA transcription factor expression using Foxa2 transgenic mice and Foxa3-/- mice. We found that persistent expression of FOXA2 reduced mucus but the absence of FOXA3 had no effect on mucus production induced by allergen challenge. However, the absence of FOXA3 decreased airway hyperreactivity and increased IgE production and eosinophilic inflammation but none of these features were affected by persistent expression of FOXA2. These results indicate that FOXA3 has functions distinct from those of FOXA2 in the allergic response. Keywords: gene expression comparison between Foxa3-/- and littermate control mice both challenged with OVA DNA miocroarrays were used to analyze lung mRNA expression of Foxa3 KO and littermate control mice challenged with saline or OVA. The experiment incorporated a 1 color design and used Agilent arrays that contained roughly 44,000 60mer probes that provide complete coverage of the mouse genome. 11 arrays were hybridized and represent 3 lung samples for groups WT saline, WT OVA and KO OVA. There are 2 lung samples for the KO saline group.
2010-04-03 | E-GEOD-13382 | biostudies-arrayexpress
Project description:Neural stem cells (NSCs) continuously produce new neurons within the adult mammalian hippocampus. However, this process declines with age and this decline correlates with defects in cognitive function and mood. Molecular mechanisms that activate quiescent NSCs to generate progenitor cells in vivo remain poorly understood. Here we show that adult hippocampal NSCs express VEGFR3, a key regulator of vascular and neural development, and are activated by the VEGFR3 ligand VEGF-C to enter the cell cycle and convert into progenitor cells. Conditional deletion of Vegfr3 in NSCs leads to a decline in hippocampal neurogenesis. Functionally, this is associated with increased anxiety behavior and compromised NSC activation in response to VEGF-C and physical activity. These findings establish VEGFR3 expression as a hallmark of adult mouse NSCs and demonstrate a specific requirement for VEGF-C/VEGFR signaling in NSC activation. Enhancing VEGFR3 signaling by VEGF-C may improve neurogenesis and mood during aging. Vegfr3 YFP and Vegfr3 YFP-negative cells were FACS-sorted from two separated groups of Vegfr3::YFP mice (16 mice/ each group; 12-30.10^5 Vegfr3YFP cells/group). Vegfr3 YFP and Vegfr3 YFP-negative cells were suspended in CCMM-BM- were seeded in 24-well plates with or without VEGF-C (50ng/ml). After an 18h-culture period,M-BM- the cells were collected in eppendorf tubes, washed in PBS, and the total RNAs were extracted by Qiagen RNA Micro kit (QIAGEN, Valencia, CA). For each culture condition, the pellets from the two groups of Vegfr3 YFP or Vegfr3 YFP-negative cells were pooled. The RNA integrity number (RIN) of each RNA sample was checked by 2100 Bioanalyzer of Agilent Technologies (Santa Clara, CA). The mRNA library construction were performed by SMARTer Ultra Low RNA Kit for Illumina Sequencing pherchased from Clontech Laboratory (Mountain View, CA) using manufacturer's protocol. And then, the validated libraries were applied to the 75 bp, paired end sequencing process of HiSeq 2500 (Illumina) to generate raw sequencing FASTQ data files. All sequencing procedures from RNA extraction to FASTQ generation were carried out by YCGA (Yale Center for Genome Analysis, West Haven, CT). The quality control check of FASTQ files was carried out by FastQC:ReadQC (version 0.52) analysis in Galaxy web-based platform and the sequences passed on M-bM-^@M-^Xper base sequence qualityM-bM-^@M-^Y were mapped on the UCSC mm10 mouse genome (Dec. 2011 Mus musculus assembly (Genome Reference Consortium Mouse Build 38)) using Tophat-2.0.9 including Bowtie-2-2.1.0 and Samtools-0.1.18. As the option of library type in Tophat, M-bM-^@M-^Xfr-unstrandedM-bM-^@M-^Y for Illumina TruSeq protocol was set as the default and the option of M-bM-^@M-^Xno-novel-juncsM-bM-^@M-^Y was chosen to quantify the reference annotation only. Cuffdiff, a separate program of Cufflinks-2.1.1, analyzed the differentially regulated transcriptional level among the reference transcriptoms of our samples and the results were visualized and further manipulated by CummeRbund-2.12.
2014-03-06 | E-GEOD-55621 | biostudies-arrayexpress
Project description:Neural stem cells (NSCs) continuously produce new neurons within the adult mammalian hippocampus. However, this process declines with age and this decline correlates with defects in cognitive function and mood. Molecular mechanisms that activate quiescent NSCs to generate progenitor cells in vivo remain poorly understood. Here we show that adult hippocampal NSCs express VEGFR3, a key regulator of vascular and neural development, and are activated by the VEGFR3 ligand VEGF-C to enter the cell cycle and convert into progenitor cells. Conditional deletion of Vegfr3 in NSCs leads to a decline in hippocampal neurogenesis. Functionally, this is associated with increased anxiety behavior and compromised NSC activation in response to VEGF-C and physical activity. These findings establish VEGFR3 expression as a hallmark of adult mouse NSCs and demonstrate a specific requirement for VEGF-C/VEGFR signaling in NSC activation. Enhancing VEGFR3 signaling by VEGF-C may improve neurogenesis and mood during aging.
2014-03-06 | GSE55621 | GEO
Project description:Allergen exposure was thought to play a critical role in the etiology of AR. And allergen avoidance, the practice of avoiding exposure to allergens, has been generally advised as the management of AR. However, the effect is uncertain and the underlying mechanism is far from known. We used gene expression microarrays to identify genes differentially regulated by allergen avoidance in allergic rhinitis mouse model. Affymetrix Mouse Gene 1.0 ST arrays were used to identify the expression profiling of nasal mucosa in three groups of mice: (1) mice sensitized and challenged with saline (control group); (2) mice sensitized and challenged with ovalbumin (OVA) and sacrificed 2 hours after the last challenge (OVA group); (3) mice sensitized and challenged with OVA and sacrificed 4 weeks after the last challenge (4w-after group).
2013-11-28 | E-GEOD-52804 | biostudies-arrayexpress
Project description:Colorectal cancer (CRC) is one of the major causes of cancer-related death in Western countries and is associated with increased numbers of lymphatic vessels (LVs) and tumor-associated macrophages (TAMs). The VEGFC/VEGFR3 pathway is regarded as the principal inducer of lymphangiogenesis and it contributes to metastases; however, no data are available on its role during CRC development. We found that both VEGFC and VEGFR3 were upregulated in human non-metastatic CRC, with VEGFR3 localising on both LVs and TAMs. We further proved in different preclinical models of CRC, that VEGFC/VEGFR3 axis can shape both LECs and TAMs to synergically inhibit anti-tumor immunity and promote primary CRC growth. VEGFR3-directed therapy could be envisioned for the treatment of non-metastatic CRC.
2020-03-17 | GSE110990 | GEO
Project description:Studying the proteomes of tissue-derived extracellular vesicles (EVs) can lead to the identifica-tion of biomarkers of disease and can provide a better understanding of cell-to-cell communica-tion in both healthy and diseased tissue. The aim of this study was to apply our previously es-tablished tissue-derived EV isolation protocol to mouse lungs in order to determine the changes in the proteomes of lung tissue-derived EVs during allergen-induced eosinophilic airway in-flammation. A mouse model for allergic airway inflammation was used by sensitizing the mice intraperitoneal with ovalbumin (OVA), and one week after the final sensitization, the mice were challenged intranasal with OVA or PBS. The animals were sacrificed 24 h after the final chal-lenge, and their lungs were removed and sliced into smaller pieces that were incubated in cul-ture media with DNase I and Collagenase D for 30 min at 37 °C. Vesicles were isolated from the medium by ultracentrifugation and bottom-loaded iodixanol density cushions, and the proteo-mes were determined using quantitative mass spectrometry. More EVs were present in the lungs of the OVA-challenged mice compared to the PBS-challenged control mice. In total, 4510 proteins were quantified in all samples. Among them, over 1000 proteins were significantly altered (fold change >2), with 614 proteins being increased and 425 proteins being decreased in the EVs from OVA-challenged mice compared to EVs from PBS-challenged animals. The associated cellular components and biological processes were analyzed for the altered EV proteins, and the proteins enriched during allergen-induced airway inflammation were mainly associated with gene on-tology (GO) terms related to immune responses. In conclusion, EVs can be isolated from mouse lung tissue, and the EVs’ proteomes undergo changes in response to allergen-induced airway in-flammation. This suggests that the composition of lung-derived EVs is altered in diseases asso-ciated with inflammation of the lung, which may have implications in type-2 driven eosino-philic asthma pathogenesis.
2022-02-17 | PXD025688 | Pride
Project description:The crosstalk between cancer cells and the lymphatic vasculature has long been proposed to define competency for metastasis. Nevertheless, the discovery of selective blockers of lymphovascular niches has been compromised by the paucity of experimental systems for whole-body analyses of tumor progression. Spatio-temporal analyses in autochthonous melanomas and patient-derived xenografts identified double stranded RNA mimics (dsRNA nanoplexes) as potent repressors of lymphangiogenesis and metastasis. Mechanistically, dsRNA nanoplexes were found to suppress lymphangiogenic drivers in both tumor cells and their associated lymphatic vasculature (via MIDKINE and Vegfr3, respectively). This dual inhibitory action, driven by type I interferon, was not shared by FDA-approved antimelanoma treatments or by lymphangiogenic blockers in clinical testing. These results underscore the power of Vegfr3-lymphoreporters for pharmacological testing in otherwise aggressive cancers
2021-10-13 | GSE180629 | GEO