Eomes regulates mitochondrial function and promotes survival of pathogenic CD4+ T cells during chronic inflammation [ATAC-seq]

The tissue accumulation of T cells expressing the transcription factor Eomesodermin (Eomes) has been reported in several chronic inflammatory diseases, including multiple sclerosis. However, the mechanisms whereby Eomes controls this accumulation and strengthens inflammation remains ill-defined. Here, we show that Eomes deletion in antigen-specific CD4+ T cells is sufficient to protect against central nervous system (CNS) inflammation. We demonstrate that Eomes is dispensable for the initial priming of CD4+ T cells but is required for long-term maintenance of CNS-infiltrating CD4+ T cells. Our transcriptomic studies reveal that the impact Eomes on effector CD4+ T cell longevity is associated with sustained expression of multiple genes involved in mitochondrial organization and function. Accordingly, epigenetic studies demonstrate that Eomes supports mitochondrial function by direct binding to either metabolism-associated genes or mitochondrial transcriptional modulators. Besides, the significance of these findings was confirmed in both healthy donors and multiple sclerosis patients. CD4+ T cells expressing Eomes exhibit enhanced mitochondrial functions, which resulted in their increased capacity to survive upon prolonged in vitro stimulation. Together, our data reveal a new mechanism by which Eomes promotes severity and chronicity of inflammation via the enhancement of CD4+ T cell mitochondrial functions and resistance to stress-induced cell death. Naive CD4+ T cells were isolated from spleen and lymph nodes by negative selection using the « Naive CD4 T Cell Isolation Kit » according to the manufacturer’s instructions (Miltenyi Biotec, Cat: 130-104-453). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 2 mM L-glutamine, 100 U/mL penicillin/streptomycin and 50 μM β-mercaptoethanol in 96 well plates at a seeding concentration of 2x105 cells per well. Polyclonal naïve CD4+ T cells were stimulated with 2 ug/mL anti-CD3 antibody (Biolegend) and 1 ug/mL anti-CD28 (BD Biosciences) under non-polarizing conditions. After 48hrs of stimulation, viable CD4+ T cells (in triplicates, pool of 2 mice for Eomes-GFP+ CD4+ T cells and individual mice for Eomes-TKO) were flow-sorted according to GFP expression