Fig. 1: Landscape of the TME in pan-cancer illustrated using scRNA-seq analysis.
a The cancer types included in this pan-cancer study. b The sample size histography of the selected normal/adjacent/tumor tissues. The sample size of replicates is shown when applicable. c Uniform Manifold Approximation and Projection (UMAP) plots of pan-cancer with 34 TME clusters, which are grouped into 4 main parts (i.e., endothelial cells, fibroblasts, lymphocytes/plasma cells, and myeloid cells). d Histography of the composition proportion of different tissue types in each TME cluster. e Clustering of TME components and their composition proportions in normal, adjacent, and tumor tissues. The proportion was normalized to the total cell number in each cancer. f Cancer type composition histography of tissue-enriched clusters according to cellular origin (c4-6, c16 and c20). g Significantly decreased proportions of FABP4+ macrophages along adjacent normal lung (Lung_N, n = 11), lung tumor (Lung_T, n = 11), advanced stage of tumor (tLB, n = 4), and brain metastasized (mBrain, n = 10) tissues, The box is bounded by the first and third quartile with a horizontal line at the median and whiskers extend to the maximum and minimum value. Dunnett-t two-sided test is used to test the significance of FABP4 + macrophages proportion between different tumor and normal tissue categories, Lung_N vs Lung_T p-value is 5.87 × 10−7, Lung_N vs tLB, p-value is 1.26 × 10−5, Lung_N vs mBrain, p-value is 2.97 × 10−8; ***: p < 0.001. h Feature plot of SPP1 and C1QC expression in the tumor-associated macrophage cluster. i Comparison of C1QC+ TAMs, SPP1+ TAMs, C1QC+/SPP1+ TAMs and C1QC-/SPP1- TAMs in normal and adjacent/tumor tissues, normal tissue n = 43, adjacent/tumor tissue n = 159. The box is bounded by the first and third quartile with a horizontal line at the median and whiskers extend to the maximum and minimum value. Mann–Whitney two-sided test is used to test the significance of proportion between different cell types. ***p < 0.001. j Differentially expressed genes clustering and specifically altered genes between tumor endothelial cells (TECs) and normal endothelial cells (NECs). Mann–Whitney two-sided test is used to test the significance of gene expression level between NEC and TEC categories. Source data are provided as a Source Data file.
