Lucas Nygård

To study the genotype-to-phenotype effects caused by T1D-associated SNPs, we have generated a novel study cohort from subjects participating in the Finnish Diabetes Prediction and Prevention (DIPP) study. Since 1994, the DIPP study has screened newborns for the presence of HLA genes predisposing to T1D, and conducted a longitudinal follow-up. The follow-up includes a periodical blood sampling that allows for the screening for autoantibodies (AAb), in tandem with the extraction and cryopreservation of peripheral blood mononuclear cells (PBMCs). The novel DIPP subcohort, named GenoPheno, consists of 694 healthy, AAb-negative children genotyped for autoimmunity-associated polymorphisms thought to modify the immunophenotype. The GenoPheno project’s goals, structure and methodologies have previously been thoroughly presented in the applicant’s MSc thesis. The core aim of the GenoPheno project, and of the doctoral thesis, is to isolate and determine the causal effects of T1D-associated SNPs on immune cells

The GenoPheno cohort was established to phenotype young children (≤5 years of age) who should have a less heterogeneous immunophenotype due to a restricted immunization history and limited exposure to environmental risk factors. This approach is postulated to reduce cohort heterogeneity and improve our chances of detecting subtle SNP-mediated alterations in the immunophenotype, thus enabling us to use smaller sample sizes.

Various ex vivo immune assays, such as multiparameter flow cytometry, single cell transcriptomics with the BD Rhapsody platform, as well as cytokine secretion, proliferation and suppression assays, have already been implemented by the research group in previous studies of immune-cell function. The GenoPheno project will now also utilize these assays to compare immune cells from individuals carrying T1D-associated or protective alleles in each locus of interest. By genotyping multiple SNPs within one locus, it is possible to enrich for genotypes that isolate specific variants, or completely lack the risk variants. Moreover, when SNP-mediated alterations in the non-diabetic immunophenotypes are identified, our intention is to evaluate the alterations’ relevance for autoimmunity by analyzing additional samples from individuals with established autoimmunity, i.e., in AAb-positive and diabetic children.

We expect our translational approach to generate important new insights into the pathogenesis of T1D, and, potentially, elucidate the common mechanisms behind the genetic predisposition to autoimmunity. This information can, in turn, potentially be translated into novel immunotherapeutic approaches or prognostic biomarkers for T1D risk stratification. Since T1D is a common pediatric autoimmune disease, scientific progress in understanding the disease mechanisms better may have considerable societal impact. Even though our thesis project focuses on the effects of gene variants associated with T1D, the same polymorphisms increase susceptibility to a spectrum of autoimmune and non-autoimmune diseases. Our results have, therefore, a direct translational impact by explaining the genetic etiology of multiple pathologies.