TEDDY Proteomics Validation Phase Study
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Waters M Class NanoAcquity UPLC, Thermo TSQ Altis mass spectrometer
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Thomas Metz
PROVIDER: MSV000091562 | MassIVE | Mon Mar 27 08:56:00 BST 2023
REPOSITORIES: MassIVE
Similar Datasets
Project description:Type 1 diabetes (T1D) usually has a preclinical phase identified by the presence of circulating autoantibodies to pancreatic islet antigens, and most young children who have multiple autoantibodies progress to diabetes within 10 years. While autoantibodies denote underlying islet autoimmunity, how this process is initiated and then progresses to clinical diabetes on a background of genetic susceptibility is not clearly understood. Only one study has thus far reported changes in gene expression in isolated immune cells associated with progression to islet autoimmunity. We analysed chromatin accessibility by ATAC-seq in CD4+ T cells in four genetically at-risk children with islet autoantibodies who progressed to diabetes in ≤ 3 years (‘progressors’), compared to five at-risk children matched for sex, age and HLA who had not progressed (‘non-progressors). From ATAC-seq data, we generated the first map of chromatin accessibility in T cells of islet autoantibody-positive children. Progression was associated with a subtle reconfiguration of regulatory chromatin regions, and some of the chromatin conformation changes could be linked to progression associated expression changes at cytotoxic genes.
2022-03-09 | GSE185189 | GEO
Project description:Type 1 diabetes (T1D) usually has a preclinical phase identified by the presence of circulating autoantibodies to pancreatic islet antigens, and most young children who have multiple autoantibodies progress to diabetes within 10 years. While autoantibodies denote underlying islet autoimmunity, how this process is initiated and then progresses to clinical diabetes on a background of genetic susceptibility is not clearly understood. We analysed gene expression by RNA-seq in four types of immune cells from five genetically at-risk children with islet autoantibodies who progressed to diabetes in ≤ 3 years (‘progressors’) and in five at-risk children matched for sex, age and HLA who had not progressed to diabetes (‘non-progressors’).
2022-03-09 | GSE185190 | GEO
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.
2010-03-31 | E-TABM-666 | biostudies-arrayexpress
Project description:The gastrointestinal ecosystem is a highly complex environment with a profound influence on human health. Inflammation in the gut, linked to an altered gut microbiome has been associated with the development of multiple human conditions including type 1 diabetes (T1D). Viruses infecting the gastrointestinal tract, especially enteroviruses, are also thought to play an important role in T1D pathogenesis possibly via overlapping mechanisms. Here, we apply an integrative approach to combine comprehensive faecal virome, microbiome and metaproteome data sampled before and at the onset of islet autoimmunity in 40 children. We show strong age and antibody related effects across the datasets. Mastadenovirus infection was associated with profound functional changes in the faecal metaproteome. Multiomic factor analysis modelling revealed proteins associated with carbohydrate transport from the genus Faecalibacterium were associated with islet autoimmunity. These findings demonstrate functional remodelling of the gut microbiota accompanies both islet autoimmunity and viral infection.
2022-08-22 | PXD032997 | Pride
Project description:<h4><strong>AIMS/HYPOTHESIS: </strong>Metabolic dysregulation may precede the onset of type 1 diabetes. However, these metabolic disturbances and their specific role in disease initiation remain poorly understood. In this study, we examined whether children who progress to type 1 diabetes have a circulatory polar metabolite profile distinct from that of children who later progress to islet autoimmunity but not type 1 diabetes and a matched control group.</h4><h4><strong>METHODS: </strong>We analysed polar metabolites from 415 longitudinal plasma samples in a prospective cohort of children in three study groups: those who progressed to type 1 diabetes; those who seroconverted to one islet autoantibody but not to type 1 diabetes; and an antibody-negative control group. Metabolites were measured using two-dimensional GC high-speed time of flight MS.</h4><h4><strong>RESULTS: </strong>In early infancy, progression to type 1 diabetes was associated with downregulated amino acids, sugar derivatives and fatty acids, including catabolites of microbial origin, compared with the control group. Methionine remained persistently upregulated in those progressing to type 1 diabetes compared with the control group and those who seroconverted to one islet autoantibody. The appearance of islet autoantibodies was associated with decreased glutamic and aspartic acids.</h4><h4><strong>CONCLUSIONS/INTERPRETATION: </strong>Our findings suggest that children who progress to type 1 diabetes have a unique metabolic profile, which is, however, altered with the appearance of islet autoantibodies. Our findings may assist with early prediction of the disease.</h4>
2022-01-19 | MTBLS802 | MetaboLights
Project description:Type 1 diabetes (T1D) is one of the most prevalent autoimmune diseases among children in Western countries. Earlier metabolomics studies suggest that T1D is preceded by dysregulation of lipid metabolism. Here we used a lipidomics approach to analyze molecular lipids in a prospective series of 428 plasma samples from 40 children who progressed to T1D (PT1D), 40 children who developed at least a single islet autoantibody but did not progress to T1D during the follow-up (P1Ab) and 40 matched controls (CTR). Sphingomyelins were found to be persistently downregulated in PT1D when compared to the P1Ab and CTR groups. Triacylglycerols and phosphatidylcholines were mainly downregulated in PT1D as compared to P1Ab at the age of 3 months. Our study suggests that children who progressed to islet autoimmunity or overt T1D are characterized by distinct lipidomic signatures, which may be helpful in the identification of at-risk children before the initiation of autoimmunity.
2018-07-16 | MTBLS620 | MetaboLights
Project description:<p>The Environmental Determinants of Diabetes in the Young (TEDDY) Study investigates genetic and genetic-environmental interactions, including gestational events, childhood infections, dietary exposures, and other environmental factors after birth, in relation to the development of islet autoimmunity and type 1 diabetes (T1D). A consortium of six clinical centers assembled to participate in the development and implementation of the study to identify environmental triggers for the development of islet autoimmunity and T1D in genetically susceptible individuals. Beginning in 2004, the TEDDY study screened over 400,000 newborns for high-risk HLA-DR, DQ genotypes from both the general population and families already affected by T1D. The TEDDY study enrolled around 8,676 participants across six clinical centers worldwide (Finland, Germany, Sweden and three in the United States) in the 15-year prospective follow-up.</p> <p>Participants are followed every three months for islet autoantibody (IA) measurements with blood sampling until four years of age and then at least every six months until the age of 15. After the age of four, autoantibody positive participants continue to be followed at three month intervals and autoantibody negative participants are followed at six-month intervals. In addition to the analysis of autoantibodies, additional data and sample collection are performed at each visit. Parents collect monthly stool samples in early childhood. The parents also fill out questionnaires at regular intervals in connection with study visits and record information about diet and health status in the child's TEDDY Book between visits. Continued long-term follow-up of the currently active TEDDY participants will provide important scientific information on early childhood diet, reported and measured infections, vaccinations, and psychosocial stressors that may contribute to the development of type 1 diabetes and islet autoimmunity.</p> <p>Additional information on the TEDDY study is available in the following articles: The Environmental Determinants of Diabetes in the Young (TEDDY) Study. TEDDY Study Group. Annals of the New York Academy of Science, 2008 and TEDDY - The Environmental Determinants of Diabetes in the Young - An Observational Clinical Trial. Annals of the New York Academy of Science, 2006 <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=19120261">Annals of the New York Academy of Science, 2008</a> and TEDDY - The Environmental Determinants of Diabetes in the Young - An Observational Clinical Trial. <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=17130573">Annals of the New York Academy of Science, 2006</a></p> <p> Details of the TEDDY protocol can be found in The Environmental Determinants of Diabetes in the Young (TEDDY): Genetic Criteria and International Diabetes Risk Screening of 421,000 infants. <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=21564455">Pediatric Diabetes, 2011</a></p> <p> There are three substudies associated with the current TEDDY project release in dbGaP: <ul> <li>TEDDY SNP Array - <a href="study.cgi?study_id=phs001037">phs001037</a> with targeted SNP array data.</li> <li>TEDDY Microbiome - <a href="study.cgi?study_id=phs001443">phs001443</a> with metagenomic and 16S rRNA sequencing data.</li> <li>TEDDY Gene Expression - <a href="study.cgi?study_id=phs001562">phs001562</a> with gene expression data.</li> </ul> </p>
| phs001442 | dbGaP
Project description:In this set, we analyzed human plasma samples from The Environmental Determinants of Diabetes in the Young (TEDDY) Study. In total, 2,252 samples from 184 individuals were concatenated into 364 pooled samples from individuals that developed type 1 diabetes or islet autoimmunity and their matched controls. Samples were analyzed from the same individuals pre and post-autoimmunity onset paired against controls. Each pooled sample was depleted with MARS abundant protein depletion column (Agilent), digested with trypsin and labeled with 8-plex iTRAQ reagent. Samples were then multiplexed and fractionated into 24 fractions by high-pH reverse-phase chromatography (DOI: 10.1038/s41596-018-0006-9). Each fraction was analyzed by liquid chromatography tandem mass spectrometry.
2023-03-27 | MSV000091560 | MassIVE
Project description:In type 1 diabetes (T1D), the appearance of multiple islet autoantibodies indicates the onset of islet autoimmunity, often many years before clinical symptoms arise. However, the underlying molecular mechanisms in T cells that can promote aberrant activation thereby triggering autoimmune progression remain poorly understood. Here, we show that during early stages of islet autoimmunity a miRNA142-3p/Tet2 signaling axis in murine and human CD4+T cells interferes with the efficient induction of regulatory T (Treg) cells accompanied by impairments in Treg stability. Specifically, we demonstrate that miR142-3p is induced in islet autoimmunity, while its inhibition enhances Treg induction and stability accompanied by a reduction of islet autoimmunity in non-obese diabetic (NOD) mice. Mechanistically, using HITS-CLIP analyses we identify the methylcytosine dioxygenase Tet2 as a direct target of miR142-3p in CD4+T cells, thereby linking high miR142-3p levels to epigenetic remodeling and impairments in Treg induction and stability. These findings offer a new mechanistic model where during islet-autoimmunity miR142-3p/Tet2-mediated Treg instability can contribute to autoimmune activation and progression.
2019-11-14 | GSE124264 | GEO
Project description:In type 1 diabetes (T1D), the appearance of multiple islet autoantibodies indicates the onset of islet autoimmunity, often many years before clinical symptoms arise. However, the underlying molecular mechanisms in T cells that can promote aberrant activation thereby triggering autoimmune progression remain poorly understood. Here, we show that during early stages of islet autoimmunity a miRNA142-3p/Tet2 signaling axis in murine and human CD4+T cells interferes with the efficient induction of regulatory T (Treg) cells accompanied by impairments in Treg stability. Specifically, we demonstrate that miR142-3p is induced in islet autoimmunity, while its inhibition enhances Treg induction and stability accompanied by a reduction of islet autoimmunity in non-obese diabetic (NOD) mice. Mechanistically, using HITS-CLIP analyses we identify the methylcytosine dioxygenase Tet2 as a direct target of miR142-3p in CD4+T cells, thereby linking high miR142-3p levels to epigenetic remodeling and impairments in Treg induction and stability. These findings offer a new mechanistic model where during islet-autoimmunity miR142-3p/Tet2-mediated Treg instability can contribute to autoimmune activation and progression.
2019-11-14 | GSE140064 | GEO