Fig. 2: Single-cell transcriptomic analysis of ‘Treg cell dependencies’ of accessory cell states in mouse lung adenocarcinoma tumor microenvironment.
a,b, t-distributed stochastic neighbor embedding (t-SNE) plots (27,000 cells) representing cell populations from major cell lineages isolated from 48 h DT-treated or PBS-treated (Ctrl) tumor-bearing lungs (three mice per group) colored by cell type (a) and condition (b). c, A density plot showing the distribution of cells between experimental conditions. d,e, t-SNE plots (2,815 cells) representing distribution of the VEC populations colored by subtype (d) and condition (e). f, A density plot of endothelial cells showing the distribution of cells between experimental conditions. g, Graph of neighborhoods of endothelial cells computed using MiloR and t-SNE embedding. Each dot represents a neighborhood and is color coded by the false discovery rate (FDR)-corrected P value (alpha = 1) quantifying the significance of enrichment of DT cells compared to control in each neighborhood. The size of the dot represents the number of cells in the neighborhood. h, Swarm plot depicting the log fold change of differential cell-type abundance in DT-treated versus control samples in each neighborhood across different endothelial cell types. Each dot represents a neighborhood and is color coded by the FDR-corrected P value (alpha = 1) quantifying the significance of enrichment of DT cells compared to control in each neighborhood. A neighborhood is classified as a cell type if it comprises at least 80% of cells in the neighborhood, otherwise it is called ‘mixed’. i, Heat map showing average factor cell score in each cluster for each experimental condition in the VEC population. The scores were row normalized between 0 and 1. Each row represents a factor, and each column represents a cluster in a specific experimental condition. The clusters are grouped based on their phenotype. j, Gene expression heat maps showing the top 200 genes that correlated the most with the imputed activated VEC factor indicated (Methods). Each column represents a cell; cells are ordered based on their factor score (in ascending order from left to right) indicated by the green bar. Select genes of interest are noted on the right. b, e, h and i; Ctrl, PBS, gray; DT, red.
