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Type 1 Diabetes TrialNet

Type 1 Diabetes TrialNet (TrialNet) is an international network of researchers established in 2003 for the purpose of conducting studies designed to evaluate new approaches to prevent, delay and reverse the progression of type 1 diabetes. These include interventions designed to decrease β-cell destruction and/or enhance β-cell survival. TrialNet engages in new onset diabetes trials to assess safety and to determine whether interventions can lead to preservation of C-peptide. Positive results from new onset trials are then evaluated as to whether the intervention can be brought into the prevention space for further evaluation. Other TrialNet goals include characterization of diabetes risk and pathophysiology through genetic, immunologic, and metabolic studies in participants participating in clinical studies.

TN01 Bulk mRNA – RNA Sequencing

The TrialNet “Key Question 1” study investigates immune system alterations associated with Type 1 Diabetes (T1D) progression using a retrospective, longitudinal nested case-control approach. It analyzes immune phenotype and gene expression changes in 178 individuals (89 cases, 89 controls). Cases include islet autoantibody-positive individuals from the TN01 Pathway to Prevention trial who developed T1D within a three year observation period, while controls are non-progressors matched by age, sex, and sampling timepoints.

Serial blood samples were collected over three years, from pre-T1D to clinical diagnosis. Analyses include mass cytometry and transcriptomics. The RNA Sequencing portion of the study examines gene expression in five purified immune cell types: CD4+ T memory cells, CD8+ T memory cells, CD4+ T regulatory (Treg) memory cells, CD19+ B memory cells, and Natural Killer (NK) cells. RNA sequencing, with spike-in control RNA (ERCC), is used to control for batch variation.

Whole Blood Genotyping – ExomeChip

DNA from whole blood samples from TrialNet study participants was obtained and used for genotyping. Individuals included participants from TN01 Pathway to Prevention study and the following interventional trials: TN07 Oral Insulin, TN10 Anti-CD3 Prevention, TN18 Abatacept Prevention, TN20 Immune Effects of Oral Insulin, and TN22 Hydroxychloroquine Prevention. All interventional trial participants originated from TN01 Pathway to Prevention. Genotyping was performed by the University of Virginia using the Illumina TEDDY-T1DExome array. The TEDDY-T1DExome array is a custom chip that contains 550,601 markers from the Infinium CoreExome-24 v1.1 BeadChip and an additional 90,214 tagSNPs specifically selected by the TEDDY investigators based on their associations with nutrients, vitamins, type 2 diabetes, autoimmune diseases, body-mass index, or other exposures and phenotypes measured by TEDDY study. The Illumina GenTrain2 algorithm was used for genotype calling. Sample quality control metrics included sample call rate, heterozygosity rate and concordance of gender between the information reported and genotyped.