Characterization of iNKT cells in healthy individuals, in patients after receiving allogeneic HSCT, and in T1D patients. (A) iNKT cell phenotypes in peripheral blood were assessed using multiparametric flow cytometry in healthy individuals and in patients after allogeneic HSCT. The markers used for flow cytometry were derived from our scRNA-seq data and from those previously reported in the literature. Subpopulations were manually gated, and principal component analysis (PCA) was performed on the data set. Each dot represents 1 patient and is colored according to that patient’s clinical status. (B) Representative tSNE contour plots in 3 flow cytometric data sets consisting of 3 healthy individuals, 11 patients after HSCT without GVHD, and 3 patients at GVHD diagnosis (Dx). (C) Four parameters were identified from PCA that accounted for most of the variation among the 3 groups, and these parameters were manually assessed and presented in 2D dot plots showing the frequency of expression of each marker in each patient. (D) Representative tSNE contour plots in 1 flow cytometric data set consisting of 3 T1D patients. The parameters here are the same as in panel B. (E) Phenotypic expression of iNKT cells in T1D (n = 11) vs healthy individuals (n = 16). Means ± standard error of the mean (C,E). *P = .05-.01; **P = .009-.001; ***P < .001; ****P < .0001. ns, not significant.