Defining and comparing the immune composition of Cutaneous T-cell Lymphoma to Atopic Dermatitis and Psoriasis, using single-cell transcriptome profiling

Abstract

Cutaneous T-cell Lymphoma (CTCL) is an extra nodal form of non-Hodgkin lymphoma, characterised by a clonal malignant proliferation of T-cells primarily in the skin. Mycosis fungoides (MF) is the commonest type of CTCL. Whilst early-stage MF can be indolent in nature, approximately a quarter of patients will progress to advanced stage disease with a poor prognosis. A diagnostic challenge, CTCL can frequently be misdiagnosed as a benign inflammatory dermatosis, including atopic dermatitis (AD) and psoriasis. Contributing to the difficulty in identifying diagnostic and prognostic markers for CTCL are benign reactive T-cells, which along with antigen presenting cells (APCs) contribute to the heterogeneous cutaneous tumour microenvironment. However, the development of single-cell RNA sequencing (scRNA-seq) provides the ability to simultaneously sequence both the TCR and transcriptome of individual T-cells to identify clonally expanded cells, as well as profile complex heterogeneous cellular tissues. In this study, scRNA-seq of healthy, AD and psoriasis skin was first performed to characterise the populations of T-cells and APCs in steady state and their aberrations in disease, revealing clonally expanded disease-specific cytokine producing T-cells and increased Mac2 macrophages in lesional AD and psoriasis. Subsequently, scRNA-seq was performed on 8 lesional skin biopsies from patients with MF, successfully identifying and characterising the malignant T-cells memory and exhaustion phenotype, as well as their expression of unique markers and inflammatory profile. Transcriptome profiling of non neoplastic cells within MF suggests that benign reactive T-cells lack inflammatory cytokine expression and are recruited into the tumour microenvironment, which is enrichened in MoDC3 cells. Gene expression indicates that macrophages are polarised and potentially contribute to the migration and retention of T-cells into lesional CTCL skin. In this study scRNA-seq has provided new insights into the heterogeneity of lesional CTCL, as well as providing an invaluable resource for future studies into CTCL and benign inflammatory dermatoses.