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. 2021 Sep 28;20:124. doi: 10.1186/s12943-021-01419-2

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© The Author(s) 2021

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. 8 — Comparison of lesional with nonlesional MF and healthy control skin. A UMAP of 32,958 subclustered cells from lymphocyte clusters TC-1, TC-2, TC-3/NK and TC-4 of Fig. S8, integrated from 7 MF patients with lesional and nonlesional biopsies, and 4 healthy control samples, according to similarity of their transcriptome, resulting in 8 different color-coded clusters, split according to tissue of origin. B Feature plots showing expression of selected T cell and NK cell marker genes. Normalized expression level for each cell is color-coded (red) and overlaid onto UMAP plots. C Frequencies of cell clusters within groups. D-E UMAP plots of individual patients colored according to most common monoclonal (red) and polyclonal (green) αβ TCR; cells without TCR are displayed in grey; photographs of biopsy sites for nonlesional (green arrow) and lesional (red arrow) skin. Percentages denote frequencies of malignant cells among all TCR+ cells for each plot. F UMAP of four healthy control biopsies; the single most frequent clone for each sample is depicted in blue (P112), orange (P115), purple (P116) or yellow (P121); all other TCR+ cells are shown in green, and cells without detectable TCR in grey. G Distribution of the malignant clone (red), polyclonal TCR+ cells (green), and cells without detectable TCR, as percentages for each cluster in lesional and nonlesional biopsies. H Violin plots showing distribution of normalized gene expression levels in nonlesional (green), lesional (red) and healthy control skin (blue) for the top expanded αβ TCR clone, as well as helper T cells, regulatory T cells, and cytotoxic T cells. I Volcano plot showing differentially expressed genes (DEGs) of the malignant clone, as well as polyclonal helper, cytotoxic and regulatory T cells between lesional and nonlesional MF biopsies. Differential gene expression was defined as log fold change >∣0.25∣ as calculated by logistic regression and Bonferroni correction. Regulatory T cells: FOXP3+ cells with polyclonal TCRs. Cytotoxic T cells: CD8A+ FOXP3- cells with polyclonal TCRs. Helper T cells: CD4+ FOXP3- cells with polyclonal TCRs. UMAP: Uniform Manifold Approximation and Projection