Single-cell analysis of before and after HDACi therapy shows diverging cell populations. (A) UMAP projection of malignant T cells at initial sample collection (T1, n = 2603) and after HDACi progression (T2, n = 2778) with percent of cells in clusters by time point. (B) Violin plots of cluster-specific gene markers compared with the entire cohort of malignant T cells across both time points. (C) Density plots of the principal component analysis of ssGSEA results by malignant T-cell clusters. (D) Trajectory manifold of malignant T cells using the monocle R package with both the Seurat clusters and time point displayed. (E) Median mRNA expression of the top 20 significantly (adjusted P value < .05) upregulated markers by transition state. (F) Venn diagram of the overlap in significant genes between the transcriptional states in the cell trajectory and comparing HDACi-resistant vs -sensitive patients with SS in GSE132053¹⁰ with a selection of the 33 overlapping genes displayed as violin plots. Significant genes were defined as log-fold change ≥ 0.5 and adjusted P value < .05. (G) Gene expression patterns of significantly expressed genes by transition state that are previously reported upregulated in an HDACi-resistant SS¹⁰ along the cell trajectory manifold.