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Profiling of peripheral blood B-cell transcriptome in children who developed coeliac disease in a prospective study

ABSTRACT: Profiling of peripheral blood B-cell transcriptome in children who developed coeliac disease in a prospective study

PROVIDER: PRJNA769305 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16230621.fastq.gz	Fastqsanger.gz
	SRR16230622.fastq.gz	Fastqsanger.gz
	SRR16230623.fastq.gz	Fastqsanger.gz
	SRR16230624.fastq.gz	Fastqsanger.gz
	SRR16230625.fastq.gz	Fastqsanger.gz

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Profiling of peripheral blood B-cell transcriptome in children who developed coeliac disease in a prospective study

Project description:Background: In coeliac disease (CoD), the role of B cells has mainly been considered to be production of antibodies. The functional role of B cells has not been analysed extensively in CoD. Methods: We conducted a study to characterize gene expression in B cells from children developing CoD early in life using samples collected before and at the diagnosis of the disease. Blood samples were collected from children at risk at 12, 18, 24 and 36 months of age. RNA from peripheral blood CD19+ cells was sequenced and differential gene expression was analysed using R package Limma. Findings: Overall, we found one gene, HNRNPL, modestly downregulated in all patients (logFC -0·7; q=0·09), and several others downregulated in those diagnosed with CoD already by the age of 2 years. Interpretation: The data highlight the role of B-cells in CoD development. The role of HNRPL in suppressing enteroviral replication suggests that the predisposing factor for both CoD and enteroviral infections is the low level of HNRNPL expression.

2023-02-01 | GSE185503 | GEO

Profiling of peripheral blood B-cell transcriptome in children who developed coeliac disease in a prospective study.

Project description:BackgroundIn coeliac disease (CoD), the role of B-cells has mainly been considered to be production of antibodies. The functional role of B-cells has not been analysed extensively in CoD.MethodsWe conducted a study to characterize gene expression in B-cells from children developing CoD early in life using samples collected before and at the diagnosis of the disease. Blood samples were collected from children at risk at 12, 18, 24 and 36 months of age. RNA from peripheral blood CD19+ cells was sequenced and differential gene expression was analysed using R package Limma.FindingsOverall, we found one gene, HNRNPL, modestly downregulated in all patients (logFC -0·7; q = 0·09), and several others downregulated in those diagnosed with CoD already by the age of 2 years.InterpretationThe data highlight the role of B-cells in CoD development. The role of HNRPL in suppressing enteroviral replication suggests that the predisposing factor for both CoD and enteroviral infections is the low level of HNRNPL expression.FundingEU FP7 grant no. 202063, EU Regional Developmental Fund and research grant PRG712, The Academy of Finland Centre of Excellence in Molecular Systems Immunology and Physiology Research (SyMMyS) 2012-2017, grant no. 250114) and, AoF Personalized Medicine Program (grant no. 292482), AoF grants 292335, 294337, 319280, 31444, 319280, 329277, 331790) and grants from the Sigrid Jusélius Foundation (SJF).

| S-EPMC9883278 | biostudies-literature

Transcription profiling human whole blood from children with pre-type1diabetes

Project description:Type 1 diabetes (T1D) is an autoimmune disease caused by selective destruction of insulin producing pancreatic beta-cells in the islets of the Langerhans. The progression to clinical diabetes is characterized by the appearance of autoantibodies against islet cells (ICA) and beta-cell-specific antigens (IAA, IA-2 and GADA), which are considered the first markers signifying onset of autoimmunity. The mechanisms initiating or enhancing the autoimmune process remain poorly understood. Transcriptomic profiling on whole blood samples provides an approach for monitoring T1D disease process. In these investigations of pathways that are changed during the disease process, we have analyzed RNA from longitudinal peripheral blood samples of children who have developed T1D associated autoantibodies and eventually clinical type 1 diabetes . All study subjects were participants of the Type 1 Diabetes Prediction and Prevention (DIPP) study in Finland (38). Whole-blood RNA samples were collected during periodic clinic visits, typically at 3 to 12 month intervals. 2.5 ml venous blood was drawn into PAXgene Blood RNA tubes (Becton-Dickinson) and stored at -70°C. T1D-associated autoantibodies were measured from blood samples taken at each visit. Prospective samples from 3 children who developed T1D (subjects T1D_1 - T1D_3) and 2 children who developed ICA (subjects ICA_1 and ICA_2) during the DIPP follow-up were selected to the present study. Control children for the T1D cases (subjects T1D_C1 - T1D_C2) were matched for age, gender, birth place and HLA-genotype, from families who have no first-degree relatives with T1D. All samples (n=60) were processed and hybridized on Affymetrix Human Genome U133 Plus 2.0 arrays.

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Project description:Asthma is the most common chronic pulmonary disease in children. The pathogenesis of asthma is not fully understood,and existing treatments have little effect on some children.MicroRNAs(miRNAs) play a regulatory role in the occurrence and development of asthma,and miRNA therapy is a promising treatment for asthma.The purpose of this study was to explore the differential expression of miRNAs in peripheral blood of children with asthma and to find a miRNA that can alleviate asthma inflammation.We used high-throughput sequencing to analyze miRNA differences in peripheral blood between children with acute asthma attacks and healthy children,target gene prediction and functional enrichment analysis were performed for them..Overall,51 differentially expressed miRNAs were identified,with 9 being upregulated and 42 downregulated.

2024-10-07 | GSE263408 | GEO

Genome-wide methylation profiles in coeliac disease and healthy controls

Project description:Genome wide DNA methylation profiling in saliva samples from individuals with and without coeliac disease. The Illumina Infinium 450k Human DNA methylation BeadChip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. The study investigated DNA methylation profiles associated with CD.

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Gene expression of immune-related genes in peripheral blood of children with Down syndrome

Project description:To identify differentially expressed genes that might be of pathogenetic importance for the development of the immunological alterations observed in individuals with Down syndrome (DS) we profiled the expression pattern of 92 immune-related genes in peripheral blood mononuclear cells (PBMC) of two different groups, children with DS and control children.

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Alterations of DNA Methylation Profile in Peripheral Blood of Children with Simple Obesity

Project description:Genome wide DNA methylation profiling of peripheral blood samples from 41 children with simple obesity and 31 normal controls. The Illumina Infinium MethylationEPIC BeadChip (Illumina 850k, San Diego, CA) was used to obtain DNA methylation profiles across greater than 850,000 CpG sites across the genome. Samples included 31 normal and 41 obesity peripheral blood.

2023-01-03 | GSE221864 | GEO

Transcriptome profile of peripheral blood mononuclear cells in children with acute otitis media caused by Streptococcus pneumoniae

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