Extended Data Fig. 5: Characterization of TIE in PBMC.
From: Immune awakening revealed by peripheral T cell dynamics after one cycle of immunotherapy
Analysis of published cohort of PBMC single cell data from reference #27. a Violin plots of the expression level of selected phenotypic and transcriptomic features of the clusters identifying peripheral T cell subsets (n=7488 single cells), the cluster with TIE phenotype is indicated in red; the plots represent the density probability, the area shapes reflect the data distribution; horizontal lines represent the minima and maxima values; central dots represent the medians. Overall minima, mean and maxima values: surface CD3=0, 0.3785, 4.1396; surface CD8a=0, 0.96327, 6.21476; surface CD45RA=0, 0.8161, 4.8508; surface CD45RO=0, 0.6628, 4.6468; surface CD197/CCR7=0, 0.8961, 5.7975; surface CD69=0, 0.5219, 4.2200; surface CD279=0, 0.09787, 3.84886; surface CD25=0, 0.08653, 4.00428; surface TIGIT=0, 0.4663, 4.2381; surface CD155=0, 0.4850, 4.6679; surface CD40=0, 0.6003, 5.5083; surface CD154=0, 0.4062, 3.8159; surface CD357=0, 0.1193, 4.0316; LGALS2=0, 0.561, 6.089; TYROBP=0, 1.337, 6.662; FCN1=0, 1.290, 6.789; CST3=0, 1.404, 6.504; LST1=0, 1.042, 6.097; LYZ=0, 1.775, 6.859. b T-SNE plot showing the clusters identified by means of the antibody derived tags (ADT) targeted to surface markers (n=7488 single cells); the black arrow indicates the cluster with TIE phenotype. c Plot showing the proportion of cells with the TIE phenotype from the same published cohort after standard in vitro culture (CTRL, n=3 sorted healthy donor peripheral blood CD8+ naĂŻve T cell samples in standard culture) or following stimulation with anti-CD3/anti-CD27 Dynabeads23 (STIM, n=3 sorted healthy donor peripheral blood CD8+ naĂŻve T cell samples after stimulation) (P=0.0267, two-sided paired t test, two degrees of freedom) and d Volcano plot representing the transcriptomic differential expression of the cells with the TIE phenotype in PBMC presented in a (n=7488 single cells) or expanded from naive CD8+ T cells from the experiment presented in c22 (n=12217 single cells; two-sided Wilcoxon test with Bonferroni correction for multiple comparisons).
