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Innate immune responses are increased in children with acute asthma exacerbation

ABSTRACT: Innate immune responses are increased in children with acute asthma exacerbation

PROVIDER: PRJNA1080008 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28083126_1.fastq.gz	Fastqsanger.gz
	SRR28083126_2.fastq.gz	Fastqsanger.gz
	SRR28083127_1.fastq.gz	Fastqsanger.gz
	SRR28083127_2.fastq.gz	Fastqsanger.gz
	SRR28083128_1.fastq.gz	Fastqsanger.gz

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Innate immune responses are increased in children with acute asthma exacerbation

Project description:Our study aimed to better understand the immune responses during an acute asthma exacerbation in children. Gene expression profiles were examined by RNA-sequencing in blood samples. Samples were collected on average 2.5 day after systemic corticosteroid treatment. Our findings show that pro-inflammatory genes and pathways related to innate responses and signaling remained increased in children hospitalized for acute asthma exacerbation. Genes and pathways involved in adaptive immune respones, particularly T lymphocyte activation, were decreased in children hospitalized for acute asthma exacerbation. These studies suggest that innate immune responses may remain activated following hospitalization for asthma exacerbation.

2024-06-17 | GSE256534 | GEO

Untargeted metabolomics on plasma from children with asthma, comparing exacerbation-prone to non-exacerbation-prone

Project description:Background: Some children with asthma remain poorly controlled and have recurrent exacerbations despite treatment with inhaled corticosteroids. Aside from prior exacerbations, there are currently no reliable predictors of exacerbation-prone asthma in these children and limited understanding of potential underlying mechanisms. Objective: We sought to quantify small molecules in the plasma of children with exacerbation- prone asthma through mass spectrometry-based metabolomics. We hypothesized that the plasma metabolome of these children would differ from that of children with non-exacerbation- prone asthma. Methods: Plasma metabolites were extracted from four pediatric asthma cohorts (n=215 total, n=41 with exacerbation-prone asthma) and detected using a ZIC-HILIC column coupled to a Q Exactive HF mass spectrometer. High-confidence annotations were retained for univariate analysis and were confirmed by a sensitivity analysis in subjects on high-dose inhaled corticosteroids. Metabolites that varied by cohort were excluded. Metaboanalyst was used to identify pathways of interest. Concentrations were calculated by reference standardization to NIST SRM 1950. Results: We identified 32 unique, cohort-independent metabolites that differed in children with exacerbation-prone asthma compared to children with non-exacerbation-prone asthma. Comparison of metabolite concentrations to literature-reported values for healthy children revealed that most metabolites were decreased in both asthma groups, but more so in exacerbation-prone asthma. Pathway analysis identified arginine, lysine, and methionine pathways as most impacted. Conclusions: Several plasma metabolites are perturbed in children with exacerbation-prone asthma and are largely related to arginine, lysine, and methionine pathways. While validation is needed, plasma metabolites may be potential biomarkers for exacerbation-prone asthma in children.

2022-07-25 | ST002251 | MetabolomicsWorkbench

Gene expression profiling of nasal swabs samples from children with asthma or wheezing exacerbations.

Project description:Nasal swab specimens were collected from children who presented to the emergency department with an acute exacerbation of asthma or wheeze. Samples were also collected from control subjects. Convalescent/quiescent samples were collected from children who were followed-up at least 6 weeks after an acute exacerbation of asthma or wheeze. Gene expression was profiled on microarrays.

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Gene Expression Patterns in Peripheral Blood Mononuclear Cells Associated with Asthma Exacerbation Attack

Project description:A large, prospective, non-interventional study was designed to study gene expression changes in peripheral blood mononuclear cells (PBMCs) associated with asthma exacerbations over the course of a year. PBMC samples were collected from subjects at the time of the study visits defined as 1) Quiet: during stable disease at 3 month intervals, 2) Exacerbation: during a 14 day period of deteriorating asthma and 3) Follow-up: within 14 days after cessation of an exacerbation. Gene expression levels during stable asthma, exacerbation, and two weeks after an exacerbation were compared. This series of samples comprises of peripheral blood mononuclear cells (PBMCs) collected during the following study visits (a) quiet (N=394 samples from 118 subjects), (b) exacerbation (N=166 samples from 118 subjects) and (c) follow-up (N=125 samples from 102 subjects)

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Gene Expression Patterns in Peripheral Blood Mononuclear Cells Associated with Asthma Exacerbation Attack

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Virograms for prediction of predisposition to asthma exacerbation

Project description:Background: Clinical transcriptomics of peripheral blood mononuclear cells (PBMC) are coming into focus as a surrogate approach for prognosis, diagnosis, biomarker discovery and examination disease mechanisms. However, bioassays paired with transcriptomic analytic tools are yet to be developed and made available at point of care. Harnessing personal dynamic genomic responses to tailor patient asthma treatment or prevent disease exacerbations remain unmet medical needs. Method: We developed a rhinovirus-stimulated peripheral blood based-assay (virogram assay) coupled with single-subject analytics (N-of-1-patwhays) to capture dynamic genome-wide expression and dysregulated pathways to retrospectively predict childhood asthma exacerbation. We hypothesized that some genomic factors might predispose any given individual, healthy or asthmatic, to a set of similar transcriptional responses to rhinovirus stimulation. We first generated a classifier from paired sample microarrays, control and stimulated PBMC from healthy subjects and applied this classifier on the transcriptomic analysis of control and HRV-stimulated PBMC samples (virogram assay) from children with asthma. Results: The analysis of the different genomic responses of single-subject paired PBMC samples (HRV-stimulated and control) derived from healthy individuals (external dataset) enabled the discovery of dysregulated pathways related to acquired immunity, epigenetics and morphogenesis. The classifier built on these results and applied on the transcriptional analysis derived from the virogram assay predicted that the risk of asthma exacerbation among asthmatic subjects with an accuracy of 70%. Conclusion: We provide evidence that clinical prognosis can be predicted with a PBMC based-bioassay aligned with adequate single-subject analytics to assess dynamic transcriptomic response to specific disease-associated stimuli.

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Project description:To investigate the role of γ-glutamyltranspeptidase in severe asthma, we established an OVA/ LPS-induced asthma model. Inflammation analysis and second-generation sequencing revealed the mechanism by which inhibition of γ-glutamyltranspeptidase inhibited LPS-induced asthma exacerbation in mice.

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Gene expression data from severe asthmatic children: PBMC profiles during acute exacerbation versus convalescence

Project description:Severe asthma exacerbations in children requiring hospitalisation are typically associated with viral infection, and occur almost exclusively amongst atopics, but the significance of these comorbidities is unknown. We hypothesised that underlying interactions between immunoinflammatory pathways related to responses to aeroallergen and virus are involved, and that evidence of these interactions is detectable in circulating cells during exacerbations. To address this hypothesis we used a genomics-based approach involving profiling of PBMC subpopulations collected during acute exacerbation versus convalescence by microarray and flow cytometry.

2009-05-09 | GSE16032 | GEO

Proteome analysis of lung tissue from mice with allergic asthma, influenza-induced exacerbation of asthma (or treated with dexamethasone) vs. healthy mice

Project description:We have run shotgun proteomic analysis of lung proteome from mice with allergic asthma, influenza-induced exacerbation of asthma (or treated with dexamethasone) vs. healthy mice using LC-MS/MS. PRM proteomic analysis coupled with stable isotopic labelling was performed for quantification of protein STAT1. Protein digestion was done with Trypsin/Lys-C mix endoproteinase.

2021-10-01 | MSV000088182 | MassIVE

Transcriptomic evaluation of skin tape-strips in children with allergic asthma uncovers epidermal barrier dysfunction and asthma-associated biomarkers abnormalities

Project description:Tape-strips were obtained from skin of 18 pediatric patients with moderate allergic asthma (MAA) (n=11), severe allergic asthma (SAA) (n=9), and from healthy children (n=12) and analyzed with bulk RNA-sequencing (RNA-seq). Differential expression was defined as |fold change|≥2 and false discovery rate<0.05. MAA and SAA shared downregulation of G-protein-coupled receptor- (GPCR), mitochondria-, and Wnt-signaling-related genes. Terminal differentiation (FLG/filaggrin), cell adhesion (CDH19, JAM2), lipid biosynthesis/metabolism (ACOT2, LOXL2) markers were significantly downregulated in MAA and SAA (FDR<0.05). Many of these markers additionally correlated with metrics of asthma severity (e.g. exacerbation rate per year, forced expiratory volume in 1 second [FEV1] [% predicted], impulse oscillometry [IOS] R5-20 Hz, fractional excretion of nitric oxide [FeNO]).

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