RNA-seq data reveal distinct transcriptional profiles of different FACS CD4⁺ T-cell populations and identify recurrent novel aberrancies. (A) Principal component (PC) analysis of the gene expression profiles displays clustering of normal FACS CD4⁺ T-cell populations regardless of donor (SS/HC, encircled in green) as opposed to Sézary subsets (encircled in red). (B) Heatmap (including log₂CPM−2 to 10) shows that phenotypically functionally distinct CD4⁺ T-cell subsets (Th2 and Th17) derived from HCs harbor characteristic lineage-specifying gene expression profiles. This was most prominently observed in GATA3 and RORA/RORC genes that are known to prime naïve CD4⁺ T cells toward Th2 and Th17 functional subsets, respectively. To a less prominent extent, phenotypically distinct functional subsets isolated from the same patient with SS showed variation in the expression of lineage-specifying signature genes. (C) Volcano plot depicting the significantly DEGs in tumor populations from 3 patients with SS in comparison with phenotypically normal CD4⁺ T-cell populations from the same patients. Shown are log₂ fold changes (FC) (x-axis) with selected genes highlighted. Dashed lines at −5 and 5 indicate the chosen log₂FC cutoff values. (D) List of biological processes and corresponding significance [(−log10) adjusted P value] that are involved in SS based on gene ontology enrichment analysis conducted on the top up- and downregulated DEGs (log₂FC ≥5, FDR <0.05) between tumor and normal subsets from patients with SS.