Mapping malignant T‐cell states and immune circuits in Sézary syndrome by single‐cell analysis

BACKGROUND: Sézary syndrome (SS) and leukaemic mycosis fungoides (MF) are aggressive cutaneous T-cell lymphomas (CTCLs) with poor prognosis and limited treatment options. Single-cell RNA sequencing (scRNA-seq) offers an opportunity to dissect malignant heterogeneity and immune dysregulation yet has been underutilized in leukaemic CTCL. OBJECTIVES: To define transcriptional heterogeneity within malignant T cells, identify immunomodulatory signals shaping the tumour microenvironment and uncover actionable vulnerabilities in SS and leukaemic MF. METHODS: We analysed 144,321 peripheral blood mononuclear cells from 22 patients (SS or leukaemic MF) and 7 healthy controls using scRNA-seq, with CITE-seq and TCR-seq in subsets. Public and prospectively collected datasets were integrated after rigorous per-sample quality control, batch correction and malignancy assignment. Differential gene expression and cell-cell communication analyses were performed using complementary modelling approaches with correction for sparsity and multiple testing. RESULTS: Three transcriptionally distinct malignant T-cell (MTC) subtypes were identified: central memory-like (MTC CM), effector/effector memory-like (MTC E/EM) and regulatory-like (MTC Reg), each with unique expression programmes and putative vulnerabilities. MTC CM, the dominant population, expressed central memory markers, Th2/Th22 skewing and a broader KIR repertoire (KIR3DL2, KIR3DL1, KIR2DL3) than previously reported. MTC E/EM and MTC Reg were enriched for NR4A1 and ITGB1, respectively. Cell-cell communication analysis revealed KIR-MHC-I signalling and suggested that MTC-derived TNF and IL-10 may drive JAK/STAT pathway activity in non-T cells, indicating an underrecognized dimension of tumour-induced immune reprogramming. CONCLUSIONS: This is one of the most comprehensive single-cell studies of leukaemic CTCL to date. We uncover new malignant T-cell states, broaden the known repertoire of KIR expression, and propose mechanisms of immune evasion that may contribute to treatment resistance. These findings lay the groundwork for subtype-specific and microenvironment-informed therapeutic strategies in Sézary syndrome, with potential implications for guiding targeted therapy selection but require validation in larger, independent cohorts.