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. 2023 Mar 3;15:14. doi: 10.1186/s13073-023-01164-9

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© The Author(s) 2023

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 3 — T/NK cell remodeling after therapy. A UMAP plot of T/NK cells colored by clusters. B Heatmap of normalized expression of canonical T/NK cell marker genes among clusters. TRM, tissue-resident memory. C Boxplots of the average cytotoxic and exhausted signature scores for CD8+ T cells in TN (n = 3), MPR (n = 4), and NMPR (n = 8) patients. Center line indicates the median, lower, and upper hinges represent the 25th and 75th percentiles, respectively, and whiskers denote 1.5× interquartile range. One-sided t-test was used. D Boxplots of the average cytotoxic and exhausted signature scores for NK cells in TN (n = 3), MPR (n = 4), and NMPR (n = 8) patients. One-sided t-test was used. E Boxplot showing cellular fractions of each T/NK cluster in TN (n = 3), MPR (n = 4), and NMPR (n = 8) patients. All differences with adjusted P < 0.10 are indicated. One-sided unpaired Wilcoxon test was used and the P values were adjusted by the FDR method. F Summary of selected ligand-receptor interactions from CellPhoneDB between cancer cells and CD16+ NK cells in MPR patients. G Boxplots of the average exhausted signature scores for Tregs in TN (n = 3), MPR (n = 4), and NMPR (n = 8) patients. One-sided t-test was used. H The developmental trajectory of CD8+ T cells inferred by Monocle2. The memory CD8+ T cells (CD8_IL7R) and effector memory (CD8_GZMK) T cells were the roots of differentiation, and the exhausted CD8+ T cells (CD8_HAVCR2) were in the end-point state. I Heatmap of the top differential genes in memory (CD8_IL7R) cells along the pseudo-time (lower panel). The distribution of CD8_IL7R cells during the transition (divided into 2 phases: resting and activated) in TN, MPR, and NMPR patients, along with the pseudo-time (upper panel)