Figure 1 Comparison of natural killer T (NKT) type II and Crohn's-associated invariant T (CAIT) cells. (A) Sequence similarity analysis of NKT type II 2 3 and CAIT T cell receptors (TCRs). Each node corresponds to the unique alpha/beta TCR sequence and edges connect highly similar TCRs (tcrdist metric<150). Larger nodes indicate TCRs used for cloning. TCRdist sequence logos for TCRalpha and TCRbeta chains of TCRs from the cluster are shown at the bottom. (B). Genomic segments and amino acid CDR3 sequences of TCRs picked for experimental validation. Red font indicates differences in CDR3 regions. (C). Chemical structures of phenyl-pentamethyldihydrobenzofuransulfonate (PPBF) and chlorophenyil-pentamethyld ihydrobenzofuransulfonate (ClPPBF). (D.) Gating strategy and representative flow plots for pentamethylbenzofuransulfonates (PBFs) stimulation experiment. (E). Frequency of activated cells reactive to PPBF (top) and ClPPBF (bottom). Only significant p values from a T-test with Holm method for multiple testing correction are shown (*<0.05, **<0.01, ***<0.001, ****<0.0001). (F). Anti-CD1d antibody prevents activation of all four cell lines with PPBF (top) and ClPPBF (bottom). Only significant p values from a t-test with Holm method for multiple testing correction are shown (*<0.05, **<0.01, ***<0.001, ****<0.0001). (G.) Frequency of CAITlike NKT type II TCRs from Almeida et al (attached to a large cluster on figure 1A) and non-CAIT like NKT type II TCRs in Crohn's disease and healthy cohorts from Rosati et al . 1 Only significant p value (****<0.0001) from a Mann-Whitney U-test is shown.