Multimodal single-cell analysis of cutaneous T-cell lymphoma reveals distinct subclonal tissue-dependent signatures

Abstract

Cutaneous T cell lymphoma (CTCL) is a heterogeneous group of mature T cell neoplasms characterized by the accumulation of clonal malignant CD4+ T cells in the skin. The most common variant of CTCL, Mycosis Fungoides, is confined to the skin in early stages but can be accompanied by extracutaneous dissemination of malignant T cells to the blood and lymph nodes in advanced stages of disease. Sézary Syndrome, a leukemic form of disease is characterized by significant blood involvement. Little is known about the transcriptional and genomic relationship between skin and blood residing malignant T cells in CTCL. To identify and interrogate malignant clones in matched skin and blood from leukemic MF and SS patients, we combine T cell receptor clonotyping, with quantification of gene expression and cell surface markers at the single cell level. Our data reveals clonal evolution at a transcriptional and genetic level within the malignant populations of individual patients. We highlight highly consistent transcriptional signatures delineating skin-derived and blood-derived malignant T cells. Analysis of these two populations suggests that environmental cues, along with genetic aberrations, contribute to transcriptional profiles of malignant T cells. Our findings indicate that the skin microenvironment in CTCL promotes a transcriptional response supporting rapid malignant expansion, as opposed to the quiescent state observed in the blood, potentially influencing efficacy of therapies. These results provide insight into tissue-specific characteristics of cancerous cells and underscore the need to address the patients' individual malignant profiles at the time of therapy to eliminate all sub-clones.

Transcriptional Heterogeneity and the Microbiome of Cutaneous T-Cell Lymphoma

“…In skin samples, several upregulated pathways were unmasked: T-cell activation, TCR ligation, mitogen-induced transcripts, and cell cycle. Vice versa, T-cell quiescence and markers for resting T-cells were upregulated in blood counterparts [53]. Strikingly, some of those genes were also outlined by Rindler et al in blood of an advanced stage MF patient [54].…”

“…Hence, bulk sequencing will determine average values of fluctuating percentages of malignant and benign cells and cannot assess unique transcriptome expression of tumour cells and its microenvironment [42,46]. Five studies utilized scRNA-seq for CTCL: Three investigated SS [51,52] with one study including a single MF subject [53] and two examined exclusively MF [12,54]. Gaydosik et al [12] sequenced single cells of five advanced stage (IIB-IVA) MF patients.…”

“…Herrera et al [53] interrogated surface marker expression, TCR-repertoire and transcriptome of matched skin and blood from SS and one leukemic MF patient on the single cell level. Malignant T-cells were defined based on clonal TCR sequences and transcriptional and surface marker patterns distinct to non-malignant T-cells.…”

The Microenvironment’s Role in Mycosis Fungoides and Sézary Syndrome: From Progression to Therapeutic Implications

“…Due to MF's indolent course and the frequency of relapses in MF and SS, treatments focused on the host immune system's role are warranted. A recent finding showed that genetic aberrations and microenvironment cells may promote a transcriptional response fostering rapid malignant expansion, potentially influencing the response to scheduled treatments [193]. Knowledge of the role of the microenvironment and its interaction with neoplastic cells is an unmet need in the light of developing new treatment approaches.…”

Natural Barcodes for Longitudinal Single Cell Tracking of Leukemic and Immune Cell Dynamics

“…Single-cell sequencing of TCR now enables phenotyping of individual T cell clones (31,32) and permits tracking of antigen-specific T cells across tissue compartments and following therapeutic interventions such as immune checkpoint blockade or vaccination (33)(34)(35). Further, TCR is used to phenotype malignant T cells, for example in angioimmunoblastic (36) or cutaneous T cell lymphoma (37,38).…”