Fig. 2: Pseudotemporal analysis of T cell differentiation.

a, b UMAP dimensional reduction for CD8⁺ (left) and CD4⁺ T cells. Colors indicate the enrichment of T cell exhaustion. Cluster-wise enrichment analysis is illustrated by points, which are sized and colored according to their enrichment score for T cell exhaustion. c For CD8⁺ T cells: The two identified terminal states (indicated by colors, names S1-S2) are presented using a two-dimensional subway plot. Terminally exhausted T cells fall under state 1 (S1). d For CD8⁺ T cells: Line plots with pseudotime (from S0 to S1 state) at the x-axis and enrichment scores of different T cell states on the y-axis (upper plot). At the bottom, the RNA-velocity from S0 to S1 state is illustrated (dashed line) with increasing velocity-pseudotime on the y-axis. Additionally, IL-10 and TGFb response is shown (red and blue lines). e Similar visualization (c) from CD4⁺ T cells. These cells reveal a more complex architecture mainly spanning the three major cell states from regulatory T cells (branch S2), TEM/Stress (Branch S1), and Th17 (Branch S3/S4). f Similar representation (d) for CD4+ T cells with enrichment for T cell states (upper plot) and velocity and IL-10/TGFb response (bottom plot).