Fig. 7: Factor analysis of Treg cell ‘dependencies’ of accessory cell transcriptional states in human and mouse lung adenocarcinomas.
a, Schematic of the experimental design. b, t-SNE plot of all cells (82,991 total cells) from 25 primary human LuAd or local metastases labeled by lineage. c, t-SNE of T/NK cell lineage colored by unique molecular identifier (UMI) counts of Treg cell marker genes (maximum of two). d, Jaccard similarity between genes associated with mouse and human factors in tumor endothelial cells. Factors of interest with high correlation are highlighted by a green box. e, Conservation of activated VEC signature genes. Normalized gene loading (fraction of gene score across all factors) of genes within the mouse activated VEC signature across all human endothelial factors. Upper and lower notches of the box plot correspond to the 75th and 25th quartiles, respectively, and the middle notch corresponds to the median. Whiskers extend to the farthest data point no more than 1.5 times the interquartile range from the hinge, with outliers beyond that displayed as individual points. Select genes with high loadings of factors 3 and 5 are highlighted (N = 45 genes). f, Mean log2 sum of inflammation/angiogenesis associated human endothelial factor (3, 4 and 5) cell loadings plotted against log2 Treg cell proportion in each human sample. Spearman correlation estimate (R) and P value are listed. Trend line represents a linear model fit between the two and shading indicating the 95% confidence interval (N = 19 human samples). g, Normalized gene scores (fraction of gene scores across all factors) in orthologous genes between mouse and human inflammation/hypoxia factors. Genes significantly attributed to both human factors and mouse factors are highlighted as conserved. VEGF-induced genes in endothelial cells were derived from the CytoSig database.
