Single-cell RNA sequencing identifies malignant lymphocytes in cutaneous T-cell lymphoma


Skin-homing memory T cells are affected by the uncommon clonal disease called cutaneous T-cell lymphoma (CTCL). The two most common types are the leukemic Sezary syndrome, which is distinguished by circulating malignant T cells, and the skin-limited mycosis fungoides, in which malignant T cells are primarily located in the dermo-epidermal junction of the skin. Only a small portion of the T cells in the two most prevalent types of cutaneous T-cell lymphomas, mycosis fungoides skin tumors and leukemic blood of Sezary syndrome are clonally malignant. However, the inability to distinguish malignant lymphocytes from benign T cells makes it difficult to obtain a diagnosis and successful specialized treatments.

Despite the fact that mycosis fungoides skin tumors and the blood of Sezary syndrome patients include large numbers of T lymphocytes, it is challenging to distinguish between benign and malignant lymphocytes because there are no unique markers for recognizing and separating the malignant cells. This hinders the development of tailored medicines and delays diagnosis, which has an adverse effect on clinical results. Most clinical tests used to identify T-cell clonality are only partially selective and specific. Mycosis fungoides skin tumors and the leukemic blood of Sezary syndrome only contain a small percentage of T cells that are clonally malignant. Moreover, the lack of malignant lymphocyte-specific markers makes it difficult to tell them apart from benign T cells, delaying diagnosis and the creation of tailored therapies.

To directly assess the transcriptional profiles of expanded malignant clones and reactive T lymphocytes in mycosis fungoides/Sezary syndrome samples, scientists at the University of Pittsburgh School of Medicine: Alyxzandria Gaydosik and Dr. Patrizia Fuschiotti together with Dr. Connor Stonesifer, Alexandra Khaleel, and Professor Larisa Geskin from Columbia University Medical Center employed single-cell RNA sequencing for high-resolution profiling of the T-cell immune repertoire concurrent with gene expression. The research team used the most recent developments in to simultaneously establish the T-cell immunological repertoire and the transcriptome of enlarged T-cell clones in leukemic blood from Sezary syndrome patients as well as in mycosis fungoides skin tumors. Within each advanced stage mycosis fungoides/Sezary syndrome sample, they identified a diverse clonotype expansion in terms of the number of expanded clones, the utilization of the TCR V, D, and J genes, the CDR3 sequences, and the gene expression.  These findings offer robust rationales for developing novel therapeutic approaches.

The research team demonstrated that a number of nonoverlapping clonotypes, including a dominant malignant clonotype and additional minor reactive and malignant clones, are expanded in the skin and blood of distinct advanced-stage mycosis fungoides/Sezary syndrome patient samples. In contrast to secondary somatic mutations of assembled CDR3 domains, the authors showed that multiple clonotype expansion in mycosis fungoides/Sezary syndrome is caused by antigen-driven mechanisms. The notion is supported by the fact that the rearranged clonal TCRs were made up of nonoverlapping combinations of different germline genes and also found no evidence of RAG1/2 gene expression in the enlarged clonotypes.

Another exciting finding by the authors was the observation that cells from the minor benign clones inside most tumors appear to be developmentally related to the dominant clones, which raises the possibility that benign reactive lymphocytes could change. The epithelial adherens remodelling pathway is also upregulated, which is important since it suggests that substantial linked activities occur in malignant cells. Using elegant experimental molecular studies the researchers showed that several pathways related to invasion, de novo nucleotide biosynthesis, cell cycle regulation, and cancer cell metabolism, were also upregulated.

In conclusion, the new study now published in the journal Clinical Cancer Research offers novel potential targets for customized therapy and sheds new light on the pathogenesis of mycosis fungoides/Sezary syndrome by providing an unprecedented report of the transcriptional profile of malignant T-cell clones in the skin and blood of individual patients. Future studies will focus on identifying novel prospective targets for treatment of mycosis fungoides/Sezary syndrome.


Gaydosik AM, Stonesifer CJ, Khaleel AE, Geskin LJ, Fuschiotti P. Single-cell RNA sequencing unveils the clonal and transcriptional landscape of cutaneous T-cell lymphomas. Clinical Cancer Research. 2022 Apr 14:OF1-3.

Go To Clinical Cancer Research.