Single-cell RNA sequencing reveals markers of disease progression in primary cutaneous T-cell lymphoma

Abstract

Background In early-stage mycosis fungoides (MF), the most common primary cutaneous T-cell lymphoma, limited skin involvement with patches and plaques is associated with a favorable prognosis. Nevertheless, approximately 20–30% of cases progress to tumors or erythroderma, resulting in poor outcome. At present, factors contributing to this switch from indolent to aggressive disease are only insufficiently understood. Methods In patients with advanced-stage MF, we compared patches with longstanding history to newly developed plaques and tumors by using single-cell RNA sequencing, and compared results with early-stage MF as well as nonlesional MF and healthy control skin. Results Despite considerable inter-individual variability, lesion progression was uniformly associated with downregulation of the tissue residency markers CXCR4 and CD69, the heat shock protein HSPA1A, the tumor suppressors and immunoregulatory mediators ZFP36 and TXNIP, and the interleukin 7 receptor (IL7R) within the malignant clone, but not in benign T cells. This phenomenon was not only found in conventional TCR-αβ MF, but also in a case of TCR-γδ MF, suggesting a common mechanism across MF subtypes. Conversely, malignant cells in clinically unaffected skin from MF patients showed upregulation of these markers. Conclusions Our data reveal a specific panel of biomarkers that might be used for monitoring MF disease progression. Altered expression of these genes may underlie the switch in clinical phenotype observed in advanced-stage MF.

Spatially Guided and Single Cell Tools to Map the Microenvironment in Cutaneous T-Cell Lymphoma

“…These findings supported that the reactive lymphocytic infiltrate of the skin microenvironment demonstrates an immune-suppressive profile, particularly in advanced stages [ 50 ]. However, it is still to be determined if malignant T cells originate from Tregs or gain Treg-like properties during disease progression according to recent single-cell transcriptomic studies [ 51 ].…”

Single‐cell transcriptomics in human skin research: available technologies, technical considerations and disease applications

“…29 Lesion progression correlated with downregulation of tissueresident memory T-cell markers CXCR4 and CD69, heat shock protein HSPA1A, immunoregulatory molecules ZFP36 and TXNIP, and interleukin receptor IL7R. 75 Furthermore, because malignant cells can spread from the skin in later stages, the authors profiled with scRNA-seq and simultaneous V-D-J sequencing the tumor microenvironment of skin, blood and lymph node in a patient with advanced MF. 76 They found skin tissue-resident memory T cells that could switch to a more central memory-like phenotype in circulation and could explain their migratory behaviour.…”

“…ScRNA-seq was employed to profile the matrisome gene expression of the tumor microenvironment cells, revealing the absence of collagen I myofibroblasts and elevated expression of collagen VI by fibroblasts instead 74. Rindler et al discerned disease progression in primary cutaneousT-cell lymphoma by performing scRNA-seq αβ and T-cell receptor sequencing on skin samples from patients with different stages of mycosis fungoides (MF), the most frequent type of this malignancy 75.…”

Single-cell RNA sequencing analyses of primary cutaneous B-cell disorders reveal distinct molecular patterns consistent with clinical behavior

“…Data from healthy control samples in a previously published dataset from our laboratory are available under GEO accession number GSE173205. 11…”

“…Skin punch biopsies were taken after obtaining written informed consent, under a protocol approved by the Ethics Committee of the Medical University of Vienna (EK 1360/2018). After processing using the Skin Dissociation Kit by Miltenyi Biotech (Bergisch Gladbach, Germany), [11][12][13] single-cell suspensions were subjected to scRNA-seq using the Chromium Single Cell Controller and Single Cell 5' Library & Gel Bead Kit v1.1 (10X Genomics, Pleasanton, CA) according to the manufacturer's protocol. TCR and BCR sequences were enriched from cDNA using the VDJ Kit workflow by 10X Genomics.…”