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. 2023 Jan 30;8:44. doi: 10.1038/s41392-022-01264-9

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — RCT activates the expression of immune response genes in epithelial cells. a Volcano plot showing the changes in gene expression in epithelial cells pre- and post-RCT. The colored dots represent the top most variable genes. b Violin plots showing the expression level of the indicated genes in epithelial cells pre- and post-RCT (two-sided Wilcoxon test). c The enriched GO terms for epithelial cells in pre- versus post-RCT samples. d Violin plots showing the indicated pathway enrichment of each Epi subcluster pre- and post-RCT (two-sided Wilcoxon test). e Heatmap showing the relative changes in MHC class I and II gene expression in all epithelial cells and each Epi subcluster in pre- and post-RCT groups. The intensity of the color indicates the extent of upregulation post-RCT (red) or pre-RCT (blue). f Representative images of IHC staining of MHC-II (HLA-DR + DP + DQ) in epithelial cells in paired pre-RCT and post-RCT FFPE tissues. Scale bar, 50 μm. g Box plot showing the fraction of MHC-II positive Epi cells among all Epi cells in pre-RCT and post-RCT samples based on IHC results in f. The p value corresponds to the paired t test. h Bar plots showing the proportion of cells in each cell cycle phase within each Epi subcluster normal, pre-RCT, and post-RCT samples. i Bar plots showing the percentage of aneuploid cells (tumor cells) within each Epi subcluster in normal, pre-RCT, and post-RCT samples