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

Abstract

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.