Abstract: Autoimmune thyroid diseases (AITD) such as Graves’ disease (GD) or Hashimoto’s thyroiditis (HT) are organ-specific diseases that involve complex interactions between distinct components of thyroid tissue. Here, we use spatial transcriptomics to explore the molecular architecture, heterogeneity and location of different cells present in the thyroid tissue, including thyroid follicular cells (TFCs), stromal cells such as fibroblasts, endothelial cells, and thyroid infiltrating lymphocytes. We identify damaged antigen-presenting TFCs with upregulated CD74 and MIF expression in thyroid samples from AITD patients. Furthermore, we discern two main fibroblast subpopulations in the connective tissue including ADIRF+ myofibroblasts, mainly enriched in GD, and inflammatory fibroblasts, enriched in HT patients. We also demonstrate an increase of fenestrated PLVAP+ vessels in AITD, especially in GD. Our data unveil stromal and thyroid epithelial cell subpopulations that could play a role in the pathogenesis of AITD ; This workwas supported by the following grants: Proyectos de Investigación en Salud PI19/00584, PI22/01404, and PMP22/00021 (funded by Instituto de Salud Carlos III), iTIRONET- P2022/BMD7379 (funded by Comunidad de Madrid), Research project IPI/2022/N5 (funded by Sociedad de Endocrinología, Nutrición y Diabetes de la Comunidad de Madrid-SENDIMAD) and co-financed by FEDER funds to M.M. and R.M.H., as well as Contratos Predoctorales de Formación en Investigación en Salud (FI20/00035 and FI23/00052) grants to P.S.G. and N.S.B. The funders had no role in study design, data collection, data analysis, interpretation or writing of the report
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