Regulatory Mechanisms of T cell differentiation in inflammation: Modulation of Th subset differentiation in low oxygen condition.

T helper cells (Th) are key mediators of adaptive immunity. Distinct Th cell subsets differentiate from CD4+ naïve cells in response to lineage-specific cytokines. Each subset has specific functions, including pro-inflammatory (Th1, Th2, Th17) and anti-inflammatory (Treg) functions. Th17 and Treg cells play a role in inflammatory disease. In healthy individuals, there is a balance between the Th17 and Treg cells and the Treg cells suppress inflammation. Importantly, Th17 differentiation at the expense of Treg cells can tilt the balance and lead to chronic inflammation. The Th17/Treg balance can shift in response to microenvironment cues such as low oxygen concentrations, known as hypoxia, observed in an inflamed tissue. Although the functions and cytokine profiles of different Th subsets have been identified, the mechanisms of the Th cell differentiation in inflammation and immune-related disease are still poorly understood. In this thesis, different factors that can affect the Th subset differentiation were explored using three different approaches. First, the effect of hygiene conditions in Th subsets and in the development of colitis was studied in mice. Using a T cell transfer model of colitis, we showed that housing conditions impact the development of colitis as observed by changes in the Th cell differentiation. Second, the effects of hypoxia, HIF-P4H inhibition and HIF stabilization in the Th17/Treg balance were investigated. We showed that in mouse cells, HIF-P4H inhibitors (DMOG, Roxadustat) and hypoxia affect the Th17/Treg balance differently. RNA- and ATAC-sequencing allowed the identification of potential epigenetic modulators suppressing the Treg differentiation in hypoxia. Interestingly, the regulation of the Treg differentiation in hypoxia appears to differ between mouse and human cells. Third, the role for the estrogen receptor alpha in the modulation of the Th cell differentiation in hypoxia was explored. We showed that the estrogen receptor might be involved in Th17, but not Treg differentiation, based on changes observed in HIF-1α levels. These results contribute to a better understanding of the inflammatory disease by identifying factors that shift the balance to a pro-inflammatory or anti-inflammatory phenotype, thus helping define targets that could be used to modulate T cells in the immune response in various human diseases.