PHATE analysis reveals circulating putative precancerous intermediate CD4⁺T-cell populations in CTCL. (A) Representative UMAP plot of CD4⁺ T cells from a patient with CTCL resulted in 2 major separate annotated clusters: CTCL cells (red) and non-CTCL CD4⁺ T cells (blue+purple). (C) The non-CTCL CD4⁺ T cells were further divided into 2 clusters: population 1 (blue), and population 2 (purple). (B,D) The dominant TCR clonotype is highlighted in yellow over the same UMAP. A group of cells containing the dominant clonotype fell within the non-CTCL CD4⁺ T-cell population upon unsupervised clustering. A comparison of the mean frequency of the dominant (malignant) TCR clonotype vs all other TCR clonotypes in the non-CTCL CD4⁺ T-cell population 2 (E) and in the total non-CTCL CD4⁺ T-cell population (F) revealed that the dominant clonotype frequency was overrepresented in both populations (n = 10, paired t test). (G) PHATE mapping revealed the non-CTCL CD4⁺ T-cell population 2 to be an intermediate group of cells (purple) falling between normal CD4⁺ T cells (blue) and CTCL cells (red). (H) This intermediate group contained cells with the dominant clonotype, highlighted in yellow throughout the PHATE map. UMAP, Uniform Manifold Approximation and Projection.