Single-cell analysis of Sézary syndrome reveals novel markers and shifting gene profiles associated with treatment

Abstract

Cutaneous T cell lymphomas (CTCLs) are a spectrum of diseases with varied clinical courses caused by malignant clonal proliferation of skin-tropic T cells. Most patients have an indolent disease course managed with skin-directed therapies. In contrast, others, especially in advanced stages of disease or with specific forms, have aggressive progression and poor median survival. Sézary syndrome (SS), a leukemic variant of CTCL, lacks highly consistent phenotypic and genetic markers that may be leveraged to prevent the delay in diagnosis experienced by most patients with CTCL and could be useful for optimal treatment selection. Using single-cell mRNA and T-cell receptor sequencing of peripheral blood immune cells in SS, we extensively mapped the transcriptomic variations of nearly 50 000 T cells of both malignant and nonmalignant origins. We identified potential diverging SS cell populations, including quiescent and proliferative populations shared across multiple patients. In particular, the expression of AIRE was the most highly upregulated gene in our analysis, and AIRE protein expression could be observed over a variety of CTCLs. Furthermore, within a single patient, we were able to characterize differences in cell populations comparing malignant T cells over the course of treatment with histone deacetylase inhibition and photopheresis. New cellular clusters after progression on the therapy notably exhibited increased expression of the transcriptional factor FOXP3, a master regulator of regulatory T cell function, raising the potential implication of an evolving mechanism of immune evasion.

Novel Biomarkers in Cutaneous T Cell Lymphomas

“…In sorted CD4+ T cells they found DNM3 overexpression in 75% of SS. In a recent high throughput single-cell RNASeq analysis of SS 15 , Borcherding et al have found DNM3 among top ten overlap with the study of Booken et al 30 .…”

Molecular techniques drive cutting edge advancements in management of cutaneous T cell lymphoma

“…In a separate study of patients with SS, tumor cells commonly exhibited activating mutations in CCR4 and CARD1 , and ZEB1 was deleted in over half of the patients ( 2 ). AIRE , which encodes for a protein that functions in central immune tolerance, was upregulated in 58% of malignant cells in SS versus 8.7% of non-malignant cells in one study ( 56 ).…”

Advances in single-cell RNA sequencing and its applications in cancer research

“…ACH-derived GCB cells potentially undergo independent clonal evolution and support tumorigenesis in AITL via the CD40-CD40LG axis [ 134 ] Adult T cell leukemia-lymphoma 2021 Human 10 × Genomics NBDC: JGAS000301 Identified possible molecular mechanisms of multistep tumorigenesis and revealed the transcriptomic changes in identical infected clones over time during multistep tumorigenesis [ 267 ] 2022 Human 10 × Genomics GEO: GSE195674 Identified a novel subset of CAFs, suggesting a potential target for targeted therapy to enhance treatment [ 268 ] Cutaneous T cell lymphoma 2019 Human 10 × Genomics Correspondence with authors FOXP3 was identified as the most important factor to predict early disease in patients with CTCL. Transcriptome differences within a clonal tumor can be used to predict disease stage and thereby offer guidance for therapy [ 73 ] 2021 Human 10 × Genomics GSE173205 Identified a specific panel of biomarkers that might be used for monitoring MF disease progression [ 217 ] 2022 Human 10 × Genomics GSE124899 and GSE14658 New cellular clusters after progression of the therapy notably exhibited increased expression of the transcriptional factor FOXP3 , raising the potential implication of an evolving mechanism of immune evasion [ 209 ] 2022 Human 10 × Genomics GSE182861 Provided unprecedented new insights into MF/SS pathogenesis by reporting the transcriptional profile of malignant T-cell clones in the skin and blood ...…”