Extended Data Fig. 7: Myeloid depletion reduces T cell recruitment and transition towards inflamed phenotype.
From: In situ tumour arrays reveal early environmental control of cancer immunity
a, STAMP scRNA-seq atlas UMAP embedding of innate, myeloid, and stromal cell clusters from STAMP single tumour biopsies pooled per immune phenotype. b, UMAP embedding for the myeloid compartment of the scRNA from single tumour biopsies pooled per immune phenotypes. c, Dot plot for expression of Cxcl9 and Cxcl10 across all cell clusters of the scRNA sequencing STAMP tumour atlas described in a. d, Flow cytometry-based myeloid cell profiling of 5 pooled tumour biopsies per immune phenotype at 10 days post tumour implantation. n = 6 animals. Data are mean +/− s.e.m. Statistical analysis was performed using a two-tailed Mann-Whitney U-test. P values are shown at the top of the graphs. e, Scores of myeloid signatures in bulk RNA-seq of tumours at 8 days post-implantation. n = 7 tumours per group (gene signatures for each myeloid population have been derived from the scRNA-seq myeloid STAMP Atlas). Box plots show quartiles of the dataset and whiskers show the rest of the distribution. Statistical analysis was performed using a two-tailed t-test with unequal variances, adjusted for false discovery rate. P values are at the top of the graphs. f. Total T cell abundance in individual tumours over time in control, Ly6C- and Gr1-depleted animals as described in Fig. 3b, n = 6 Isotype control-treated animals, n = 5 Ly6c- and n = 5 Gr1-depleted animals, n = 319 Isotype control-treated, n = 301 Ly6c- and n = 187 Gr1-depleted tumours. Box plots show quartiles of the dataset and whiskers show the rest of the distribution, excluding points determined to be outliers by exceeding 1.5x the interquartile range. Statistical analysis was performed using a two-tailed t-test (referenced to Isotype control treated tumours). P values are shown in the graph. g, Analysis of immune phenotype transition dynamics of tumours in Isotype control-treated, Ly6C- and Gr1-depleted animals related to f. Arrows represent fold changes in transition likelihood between control and depleted animals. Black = increased transition, blue = decreased transition.
