Single-cell transcriptomics links malignant T cells to the tumor immune landscape in cutaneous T cell lymphoma

Cutaneous T cell lymphoma (CTCL) represents a heterogeneous group of non-Hodgkin lymphoma distinguished by the presence of clonal malignant T cells. The heterogeneity of malignant T cells and the complex tumor microenvironment remain poorly characterized. With single-cell RNA analysis and bulk whole-exome sequencing on 19 skin lesions from 15 CTCL patients, we decipher the intra-tumor and inter-lesion diversity of CTCL patients and propose a multi-step tumor evolution model. We further establish a subtyping scheme based on the molecular features of malignant T cells and their pro-tumorigenic microenvironments: the T(CyEM) group, demonstrating a cytotoxic effector memory T cell phenotype, shows more M2 macrophages infiltration, while the T(CM) group, featured by a central memory T cell phenotype and adverse patient outcome, is infiltrated by highly exhausted CD8(+) reactive T cells, B cells and Tregs with suppressive activities. Our results establish a solid basis for understanding the nature of CTCL and pave the way for future precision medicine for CTCL patients.