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. 2022 Sep 14;8:92. doi: 10.1038/s41421-022-00434-x

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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. 5 — a UMAP plot exhibiting the identified clusters of T cells in the 10× dataset. b Histogram showing cell type percentages of different T cells from collected samples in the 10× dataset. c Dot plots presenting the normalized expression levels of corresponding markers of T cell clusters in the 10× dataset. d Scatterplot showing DEGs of T cells from tumor tissues compared with normal tissues in both CD4⁺ and CD8⁺ T cells. e Violin plots showing expression of the exhaustion and cytotoxicity gene sets in CD8⁺ T cells from tumor and normal tissues. The P value was calculated by t-test. f Representative IHC staining of TIM3 in adjacent normal and primary tumor tissues (original magnification 100×). The rows of the paired normal and tumor samples are from the same patients, and three individual patients are listed. Scale bar, 100 μm. g Dot plot showing the expression of interaction pairs in epithelial cell and T cell pairs with different signatures.