Single-cell RNA-seq of CNS T cells derived from Satb1-deficient and Satb1-sufficient animals in EAE model

TH17 cells play an important role in host defense especially in barrier organs. Altered functionality of TH17 cells is associated with dysregulated tissue homeostasis resulting in an increased susceptibility for the development of autoimmune diseases. Thus, it is critical to identify mechanisms governing physiological as well as pathophysiological TH17 cell differentiation and identify strategies targeting TH17 cell differentiation in disease settings. Here, we identified the genome organizer Special AT-rich sequence-binding protein 1 (Satb1) as a pioneering factor for TH17 cell development. Satb1 is highly expressed in TH17 cells and loss of Satb1 prevents the differentiation of TH17 cells. As a consequence, expression of Satb1 in CD4+ T cells is required for the formation of TH17 cell-driven autoimmune diseases. Mechanistically, Satb1 mediates TH17 cell development through regulating accessibility of the Il2 gene locus and thereby preventing IL-2 signaling early during TH17 cell differentiation. Thus, Satb1 is critical by suppressing IL-2 expression during the formation of TH17 cells and may be a novel therapeutic target for the treatment of TH17 cell-driven autoimmune diseases scRNA-seq was performed following BD Rhapsody Express Single-Cell Analysis System. Six Satb1fl/fl x CD4-CreERT2wt/+ mice and two Satb1fl/fl x CD4-CreERT2+/+ control mice received tamoxifen day -7 and day -3 before induction of EAE. Brain and spinal cord were isolated, processed, and CD4+ T cells were sorted (live single CD45+ CD3+ CD4+ cells). CD4+ T cells were multiplexed using oligo-tagged anti-CD45 antibodies before sorting, and cells corresponding to the same genotype were pooled after sort. CD4+ T cells were loaded on a BD Rhapsody cartridge, with cells corresponding to each genotype being loaded on two independent cartridges.