Extended Data Fig. 3: Transcriptionally distinct lesions with inflamed, excluded, and desert immune phenotypes coexist in tumour arrays.
From: In situ tumour arrays reveal early environmental control of cancer immunity
a, PCA of the top 1000 most variable genes of the bulk RNA-seq data of individually biopsied tumours with differential immune phenotype inflamed, desert, excluded. Ellipses at 95% confidence level are shown for each group. The percentage of explained variance for each principal component is annotated on the principal component axes. b, Detailed GSEA for selected pathways that are significantly enriched between three different immune phenotypes (inflamed, desert, excluded) from STAMP tumours. c, Representative STAMP tumour array of KPP-EGFP in Foxn1-Nude mice reconstituted with tdTomato + T cells at 8 days post tumour implantation. Magenta = T cells, cyan = KPP-EGFP. n = 5 animals. d, Proportion of immune phenotypes present in STAMP arrays of three murine tumour models. NSCLC = non-small cell lung cancer (n = 175 tumours, n = 2 animals), KPP = pancreatic ductal adenocarcinoma (n = 240 tumours, n = 4 animals), and B16F10 = melanoma (n = 229 tumours, n = 4 animals). e, Representative images of STAMP tumour arrays of KPP-EGFP on abdominal skin of Rag-2-deficient mice reconstituted with tdTomato T cells, 8 days post tumour implantation, Red = T cells, green = KPP-EGFP. Overview of the entire abdominal tumour array (left panel), enlarged images of neighbouring tumours with inflamed, excluded, and desert immune phenotypes (right panels). n = 3 animals. f, Representative images of experimental lung metastases of KPP-EGFP in Rag-2-deficient mice reconstituted with tdTomato T cells, 8 days post tumour implantation. Red = T cells, green = KPP-EGFP. Overview of the entire lung lobe (left panel), enlarged images of metastatic lesions with inflamed, excluded, and desert immune phenotypes (right panel). n = 3 animals.
