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. 2024 Mar 28;56(4):652–662. doi: 10.1038/s41588-024-01688-9

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© The Author(s) 2024

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 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/.

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Extended Data Fig. 9 — (a) Bar plots showing the ratio of CD4+ (left) and CD4+/PD1+ double-positive (right) cells to PanCK+ cells in whole Ultivue tissue slides from average risk (AR; n = 10), high-risk BRCA1(HR-BR1; n = 11, p=) and high-risk BRCA2 (HR-BR2; n = 8) donors. The p-values are calculated with one-way non-parametric Wilcox test with * (**) indicating p < 0.05 (p < 0.005) respectively. The AR vs HR-BR1 (CD4+PD1 : PanCK) comparison has p = 0.028. Error bars show the standard error of the mean. (b) Bar plots showing the ratio of CD8+ (left) and CD8+/PD1+ double-positive (right) cells to PanCK+ cells in whole Ultivue tissue slides from average risk (AR; n = 10), high-risk BRCA1(HR-BR1; n = 11) and high-risk BRCA2 (HR-BR2; n = 8) donors. The p-values are calculated with one-way non-parametric Wilcox test with * (**) indicating p < 0.05 (p < 0.005) respectively. The AR vs HR-BR1 (CD8 : PanCK) comparison has p = 0.0041, AR vs HR-BR2 (CD8 : PanCK) comparison has p = 0.049 and AR vs HR-BR1 (CD8+PD1 : PanCK) comparison has p = 0.028. Error bars show the standard error of the mean. (c) Bar plots showing the percentage of TIGIT+ (left), HAVCR2+ (middle) and GZMH+ (right) cells from the immunofluorescence images (n = 2 for AR and HR-BR2, n = 3 for HR-BR1) shown in Fig. 5 and Supplementary Figs. 19–22. (d) Bar plot showing the percentage of CD3+ cells located in non-epithelial epithelial areas (ie. not intercalated with the epithelium) in HR-BR1 (n = 11) and HR-BR2 (n = 8) donors compared to AR (n = 10) donors in whole Ultivue slides (see Methods). No significant differences were found with one-way non-parametric Wilcox test. Error bars show the standard error of the mean. (e) Example segmentation and calling of positive cells of an immunofluorescence (GZMH) image (AR n = 2, HR-BR1 n = 3, HR-BR2 n = 2).