Fig. 2: CDK9 is overexpressed in CTCL and defines a unique malignant T cell population.

a Immunohistochemistry (IHC) staining of CDK9 of tissues collected from healthy donors (Normal) and CTCL patients. b Immunofluorescent staining of tissue sections from Normal and CTCL patients using antibodies against CD4 and CDK9. DAPI (4’,6-diamidino-2-phenylindole) was used for nucleus staining. c Western blot analysis of samples from healthy donors (Normal) and CTCL cell lines using indicated antibodies. n = 3, independent experiments, a representative example is shown. Band intensities were analyzed and compared using Image J. Relative densitometric values are provided below the blot images. d Differential expression of CDK9 in patients with CTCL from the indicated datasets. NLCT non large-cell transformation. P values were calculated by one-tailed t test. e UMAP projection of CTCL dataset GSE165623 including cells from skin, blood and lymph node across a patient with advanced MF. f Dot plot of CTCL dataset GSE165623 showing the average expression levels and cell expression proportions of selected cell lineage markers. g Violin plots of T cell clusters in CTCL datasets GSE165623 and GSE171811 exhibiting the specific expression of CDK9 and proliferating markers. CDK9^high cluster number was labeled in red. h UMAP projections of three cell cycle phases in CTCL datasets GSE165623, GSE171811, and GSE128531 respectively, T cell clusters were labeled using the bold black text and CDK9^high cluster was indicated by the dotted oval (top panel). Percentage of cells in each phase of cell cycle was shown, with CDK9^high cluster number labeled in red (bottom panel). i UMAP plots of T cells from GSE165623 and GSE171811 datasets, cells with the top expanded TCR α or β chain CDRs amino acid sequence per patient are colored in red (malignant), the polyclonal α or β TCRs are labeled in blue (polyclonal), and cells without detectable TCR are displayed in gray (remaining). Cell distribution was presented with contour graphs and summarized in the accompanying bar chart. The CDK9^high cluster was labeled in red (right panel). j UMAP representation split by tissues of T cells from GSE165623. Malignant T cells from skin, blood, and lymph node are colored by dark cyan, red, and purple. CDK9^high cluster number was labeled using the bold black text and cells were indicated by the dotted oval.