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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. 6 — Macrophage and dendritic cell remodeling after therapy. A Boxplot showing cellular fractions of each macrophage and DC cluster 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. 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. B Heatmap of module scores of M0, M1, and M2 signatures among macrophage clusters. C Boxplots of average M0, M1, and M2 signature scores for macrophages in TN (n = 3), MPR (n = 4), and NMPR (n = 8) patients. One-sided t-test was used. D Heatmap of normalized expression of DC marker genes among clusters. E The developmental trajectory of DCs inferred by Monocle2. mregDCs (DC_LAMP3) could derive from cDC1s (DC_XCR1) or cDC2s (DC_CD1C). F Boxplots of average antigen presentation signature scores for DCs in TN (n = 2, one sample with less than 10 DC cells was removed), MPR (n = 4), and NMPR (n = 8) patients. One-sided t-test was used. G Summary of selected ligand-receptor interactions from CellPhoneDB among cancer cells and cDC2s (DC_CD1C) cells