Extended Data Fig. 6: Modeling T cell dynamics following cDC1 perturbation. Related to Fig. 4.
(a) Boxplot showing the tdLN percentage of Tot1 out of total CD8 cells, with each dot representing an individual mouse, compared between treatment naïve (yellow, N = 11), aPD1 (blue, N = 14), DT (purple, N = 11) and DT+aPD1 (pink, N = 15) treated mice, at day 6 post transfer. *P = 0.02638. (b) Metacells 2D projection of the Tot1 and Tendo transcriptional profiles from the XCR1-DTR experiments, with colors showing annotations transferred from the CD8 atlas (top). Median normalized protein values per metacell are shown as color (blue low, red high) for CD62L, TIM3 and PDCD1 (bottom). (c) Boxplots showing the tumor FACS mean protein values for the Tot1 cells with transcriptional profiles from the XCR1-DTR mice, with each dot representing an individual mouse, compared between treatment naïve (yellow, N = 4), aPD1 (blue, N = 5), DT (purple, N = 3) and DT+aPD1 (pink, N = 5) treated mice, at day 6 post transfer. Statistics by Wilcoxon rank sum test. (d) Scatter plots of log2 down-sampled UMIs pooled across Tot1 cells active for the Naïve/Memory-Like (left) or Effector/Dysfunction programs (right), with each dot representing a gene, and red dot with names are > 2 log fold change difference in expression between aPD1 treated + PBS (X-axis) and aPD1 treated + DT (Y-axis) mice. (e) Boxplots showing the tumor fraction of Tot1 active for functional programs not shown in Fig. 4d, with each dot representing an individual mouse, compared between treatment naïve (yellow, N = 9), aPD1 (blue, N = 7), DT (purple, N = 8) and DT+aPD1 (pink, N = 9) treated mice, at day 6 post transfer. (f) Boxplots showing the fraction of Tot1 active for the functional programs for the in-vitro B16-OVA and Tot1 co-culture experiments, with each dot representing a different plate, compared between treatment naïve (yellow, N = 4) and aPD1 (blue, N = 7) treatment plates (left). Scatter plots show a comparison between the fractions of active cells for a program (X) and CFSE, PD1, CD62L or TIM3 protein levels per plate. Data in a,c,e and f were analyzed by Wilcoxon rank-sum exact test (two sided). In box plots central mark is median, with 5th and 95th percentiles at the whiskers, 25th and 75th percentiles at the box and minima and maxima marked by dots.
