Supplementary Material for: Ageing affects thymopoiesis and EAE development in a strain-dependent manner

Introduction: Considering significance of mechanisms of central tolerance for development of autoimmune diseases, including experimental autoimmune encephalomyelitis (EAE), and suppressive influence of circulating proinflammatory cytokines and alterations in brain-thymus communication characteristic for the central nervous system (CNS) autoimmune diseases, the study was undertaken to identify putative strain-based thymus-related specificities possibly relevant for the opposite effect of ageing on susceptibility of Dark Agouti (DA) and Albino Oxford (AO) rats to EAE. Methods: Quantitative and qualitative changes in thymopoiesis including underlying mechanisms were examined using flow cytometry, and RT-qPCR quantification of mRNAs for molecules relevant for integrity of stroma and T-cell development, respectively. Results: With ageing, differently from DA rats, in AO rats the surface density of CD90, a negative regulator of selection threshold, on thymocytes undergoing lineage commitment was upregulated (consistent with TGF-β expression downregulation), whereas the generation of natural CD4+CD25+Foxp3+ T-regulatory cells (nTregs) was impaired reflecting differences in thymic expression of cytokines supporting their development. Additionally, specifically in old AO rats, in whom EAE development depends on IL-17-producing CD8+ T cells, their thymic differentiation was augmented, reflecting augmented thymic IL-4 expression. In turn, differently from old DA rats developing self-limiting EAE, in age-matched AO rats developing EAE of prolonged duration, EAE development led to impaired generation of nTregs and accumulation of proinflammatory, cytotoxic CD28-CD4+ T cells in the periphery. Discussion: Study indicates that strain-differences in age-related changes in the efficacy of central tolerance, in addition to enhanced thymic generation of CD8+ T cells prone to differentiate into IL-17-producing cells, could partly explain the opposite effect of ageing on DA and AO rat susceptibility to EAE induction. Additionally, it suggested that EAE development leading to a less efficient thymic output of CD4+ cells and nTregs in old AO rats than their DA counterparts could contribute to prolonged EAE duration in AO compared with DA rats. Conclusion: The study warns to caution when designing therapeutic interventions to enhance thymic activity in genetically diverse populations, e.g. humans, and interpreting their outcomes. Furthermore, it indicates that CNS autoimmune patho