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Epigenetic profiling of children with respiratory allergy

ABSTRACT: Epigenetic profiling of children with respiratory allergy

PROVIDER: PRJNA432925 | ENA |

REPOSITORIES: ENA

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Epigenetic profiling of children with respiratory allergy

Project description:The prevalence of respiratory allergy in children is increasing. Epigenetic changes (e.g. DNA methylation) are plausible underlying molecular mechanisms. Longitudinal birth cohorts are instrumental to study the relation between early-life environmental factors and the development of complex diseases. Our AXA Research Fund and Cefic-LRI supported project explores the hypothesis that chemical exposures during pregnancy can influence the immune system and development of allergy in children. Questionnaire data, as well as cord blood, plus blood and saliva samples at age 11 years, were collected in substudies of two longitudinal birth cohorts in Belgium (FLEHS1 & FLEHS2) and analyzed with Illumina Methylation 450K BeadChips as well as gene targeted iPLEX MassArrays analysis. The project aims to answer the following questions: 1) can we identify specific changes in epigenetic modifications on DNA from allergic compared to not-allergic children; 2) are these allergy-related epigenetic changes a result of chemical exposure during pregnancy; and 3) did the early life exposures leave an epigenetic “mark” that is maintained through childhood. If chemicals exposures and resulting predictive markers of allergic diseases can be detected early, prevention strategies, particularly in children or before pregnancy, could be developed.

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Methylomes from naïve CD4+ T-cells from infants and children with and without food allergy [methylation]

Project description:Here we studied the epigenetic regulation of the naïve CD4+ T-cell activation response among children with IgE-mediated food allergy. Using integrated DNA methylation and transcriptomic profiling, we found that food allergy in infancy is associated with dysregulation of T-cell activation genes. Reduced expression of cell cycle related targets of the E2F and MYC transcription factor networks, and remodeling of DNA methylation at metabolic (RPTOR, PIK3D, MAPK1, FOXO1) and inflammatory genes (IL1R, IL18RAP, CD82) were associated with poorer T-lymphoproliferative responses in infancy after polyclonal activation of the T-cell receptor.

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Transcriptomes from naïve CD4+ T-cells from infants and children with and without food allergy [RNA-seq]

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Obesity and oral tolerance in respiratory allergy

Project description:Obesity and oral tolerance in respiratory allergy

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Host transcriptome profile of children with respiratory virus infection

Project description:Purpose: The aim of this study is to determine the expression profile in whole blood samples of children infected with respiratory syncytial virus and other respiratory viruses. Method: Host mRNA profiles in whole blood samples of children were generated by next-generation sequencing using Illumina Hiseq. Sequence reads were trimmed for adapter using skewer, mapped to reference human genome using STAR, and quantified using RSEM. Differential expression analysis was performed using DESeq2. Results: Transcriptional module analysis revealed dysregulation of genes related to inflammatory response, neutrophils, monocytes, B-cell and T-cell response. Conclusion: This study showed an imbalance in innate and adaptive immune responses in children with respiratory virus infections. This study also showed that NGS provides a comprehensive assessment of transcripts in whole blood samples.

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Specific Gut Microbiome Signatures in Children with Cow’s Milk Allergy

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Low Vaccine Responder, Infection- and Asthma-prone Children Demonstrate Distinct Mononuclear Cell DNA methylation Pathways

Project description:In this proof-of-concept study, we piloted a precision endotyping approach focused on DNA methylation biomarkers (CpG methylation) which are regulatory base modifications to DNA that influence cellular immune responses across the life course. The aims of this study were to (a) pilot a precision endotyping approach in a selected group of children from the Rochester prospective cohort who exhibited characteristics of high respiratory infection allergy/asthma prone (IAP) and low vaccine responsiveness (LVR) in early childhood, compared to non-respiratory infection allergy/asthma prone (NIAP) children and (b) assess whether stimulation of PBMCs with stimuli a vaccine adjuvant that activating activates a pattern recognition receptors (PRRs) could re-shape the epigenome.

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Distinct epithelial gene expression phenotypes in childhood respiratory allergy

Project description:Distinct epithelial gene expression phenotypes in childhood respiratory allergy

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Project description:The objective of the study was to investigate how oral immunotherapy (OIT) for food allergy modulates inflammation and immune cell responses. The blood cell transcriptome of 50 children receiving egg OIT was profiled using peripheral blood mononuclear cell (PBMC) samples obtained at baseline and after 3 and 8 months of OIT.

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Distinct epithelial gene expression phenotypes in childhood respiratory allergy

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