CBir1 T cells acquire an effector phenotype during inflammation (ATAC-seq)

CD4+ T cells specific for commensal bacterial antigens are expanded in inflammatory bowel disease (IBD) patients compared to healthy individuals. How and where commensal-specific CD4+ T cells get activated is yet to be fully understood. We used TCR-transgenic CD4+ T cells specific to a commensal bacterial antigen (CBir1 T cells) and the dextran sulfate sodium (DSS) model of IBD to characterize how and where the activation of commensal-specific CD4+ T cells occurs. We found that CBir1 T cells proliferate following intestinal damage and cognate antigen presentation is mediated by CD11c+ cells in the colon-draining mesenteric lymph nodes (cMLNs). Using assay for transposase-accessible chromatin sequencing (ATAC-seq) and flow cytometry, we showed that activated CBir1 T cells preferentially acquire an effector rather than regulatory phenotype, which is plastic over time. To understand the functional polarization of CBir1 cells during intestinal inflammation, we analyzed the chromatin landscape of CBir1 T cells following DSS-mediated activation. Naïve CD4+ CBir1 T cells were enriched from the spleen of CBir1 transgenic mice, using Miltenyi kit 130-104-453, stained with CellTraceTM Violet and injected into four WT C57BL/6J recipient mice. Starting on the following day, recipient mice were treated with 2% dextran sulfate sodium (DSS) in drinking water for 7 days, followed by normal drinking water, to induce intestinal barrier disruption. Recipient mice received 1 mg/kg of body weight FTY720 on days 7, 10 and 13 after the beginning of DSS administration, to retain cells in the lymph nodes. On day 14 after the beginning of DSS treatment, we isolated cells from the colon-draining mesenteric lymph nodes (cMLNs) of recipient mice, and sorted them into 3 fractions: 1) undivided (CTVhi) CBir1 T cells, 2) divided (CTVdim) CBir1 T cells, and 3) total non-CBir1 endogenous CD4+ T cells (polyclonal Th cells). Analogous fractions from two mice were pooled, to guarantee a sufficient number of cells for library construction, in duplicate. Libraries were prepared using the method described in Buenrostro et al. (Nature Methods 2013).