Single-cell RNA sequencing unveils the clonal and transcriptional landscape of cutaneous T-cell lymphomas

Abstract Purpose: Clonal malignant T lymphocytes constitute only a fraction of T cells in mycosis fungoides (MF) skin tumors and in the leukemic blood of Sézary syndrome (SS), the classic types of cutaneous T-cell lymphomas. However, lack of markers specific for malignant lymphocytes prevents distinguishing them from benign T cells, thus delaying diagnosis and the development of targeted treatments. Here we applied single-cell methods to assess the transcriptional profiles of both malignant T-cell clones and reactive T lymphocytes directly in MF/SS patient samples. Methods: Single-cell RNA sequencing was employed to profile the T-cell immune repertoire simultaneously with gene expression in CD3+ lymphocytes from MF and healthy skin biopsies as well as from SS and control blood samples. Transcriptional data were validated in additional advanced-stage MF/SS skin and blood samples byimmunofluorescence microscopy. Results: Several non-overlapping clonotypes are expanded in the skin and blood of individual advanced-stage MF/SS patient samples, including a dominant malignant clone as well as additional minor malignant and reactive clones. While we detected up-regulation of patient-specific as well as MF- and SS-specific oncogenic pathways within individual malignant clones, we also detected upregulation of several common pathways that included genes associated with cancer cell metabolism, cell cycle regulation, de novo nucleotide biosynthesis, and invasion. Conclusions: Our analysis unveils new insights into MF/SS pathogenesis by providing an unprecedented report of the transcriptional profile of malignant T-cell clones in the skin and blood of individual patients and offers novel prospective targets for personalized therapy.