Fig. 2.

Expression programs of tumor cells correlated with neoCRT responses. (a) UMAP plot showing the inferred CNV score and classification of 2970 epithelial cells. (b) UMAP plot of 2403 tumor cells in 8 pre- and 1 post-neoCRT ESCC samples. (c) UMAP plot of 5 clusters of tumor cells. (d) Heatmap depicting pairwise correlation of 60 intra-tumoral expression programs, and clustering identifying 5 coherent meta-programs across tumor cells from 8 pre-neoCRT samples. (e) Differences in the top 30-gene cell scores of the 4 major meta-programs between pre-neoCRT malignant cells from major or minor responders. Major, major responders; minor, minor responders. ∗∗∗, P < 0.001 by Mann–Whitney U test with Benjamini-Hochberg correction.