Extended Data Fig. 4: Profiling neoantigen-specific CD8+ T-cells using LLC tumor model. Related to Fig. 3g.
(a) Schematics of the experimental design using LLC tumor-bearing mice, without treatment or treated with aPD1. Time points of tumor dissection were on day 9 and day 13 after tumor injection. Cells were taken for FACS analysis and scRNA sequencing. (b) Scatter plots of log2 down-sampled UMIs pooled across neoantigen-specific 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 control (X-axis) and aPD1 (Y-axis) treated mice. (c) Boxplots showing the tumor fraction of Tendo cells active for the functional programs not included in Fig. 3g, with each dot representing an individual mouse, comparing control (yellow, N = 7 for Neoantigen-specific, N = 8 for Neoantigen Non-specific) to aPD1 treated (blue, N = 5 for Neoantigen-specific, N = 7 for Neoantigen Non-specific) mice divided into neoantigen-specific and non-specific cells in each treatment condition. Data in c was 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.
