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Fig. 8 | Molecular Cancer

Fig. 8

From: Single-cell RNA sequencing reveals markers of disease progression in primary cutaneous T-cell lymphoma

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

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