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Fig. 5 | Molecular Cancer

Fig. 5

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

Fig. 5

Gene expression in patch and plaque lesions of a γδ TCR+ MF patient. A Pictures of patch and plaque lesions; black circles indicate biopsy location. B Relative distribution of cells within individual clusters in patch vs. plaque lesions. C UMAP of 22,051 cells integrated from two skin biopsies according to similarity of their transcriptome, resulting in 26 different color-coded clusters (C0-C25), split according to tissue of origin. D UMAP plots of patch and plaque samples colored according to most common monoclonal γδ TCR (red), polyclonal αβ (green) or polyclonal γδ TCRs (blue), and cells without detectable TCR (grey). Percentages denote frequencies of malignant cells among all TCR+ cells per plot. E Feature plots showing expression of selected T cell marker genes. Normalized expression level for each cell is color-coded (red) and overlaid onto UMAP plots. F Total numbers of differentially expressed genes (DEGs) within each cluster comparing plaque with patch lesions, projected onto an UMAP plot. Differential gene expression was defined as log fold change >0.25 and adjusted p < 0.05 as calculated by logistic regression and Bonferroni correction. G Volcano plot of DEGs of the malignant clone between patch and plaque lesions. H Violin plots of T cell clusters showing distribution of normalized gene expression levels of the six uniformly differentially expressed genes in patch (turquoise) and plaque (red) lesions. Malignant clone: top expanded γδ clone. Helper T cells: CD4+ FOXP3- cells with polyclonal TCRs. Regulatory T cells: FOXP3+ cells with polyclonal TCRs. Cytotoxic T cells: CD8A+ FOXP3- cells with polyclonal TCRs. UMAP: Uniform Manifold Approximation and Projection

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