Single-Cell RNA Sequencing Reveals Tissue Compartment-Specific Plasticity of Mycosis Fungoides Tumor Cells

Abstract

Mycosis fungoides (MF) is the most common primary cutaneous T-cell lymphoma. While initially restricted to the skin, malignant cells can appear in blood, bone marrow and secondary lymphoid organs in later disease stages. However, only little is known about phenotypic and functional properties of malignant T cells in relationship to tissue environments over the course of disease progression. We thus profiled the tumor micromilieu in skin, blood and lymph node in a patient with advanced MF using single-cell RNA sequencing combined with V-D-J T-cell receptor sequencing. In skin, we identified clonally expanded T-cells with characteristic features of tissue-resident memory T-cells (TRM, CD69+CD27-NR4A1+RGS1+AHR+). In blood and lymph node, the malignant clones displayed a transcriptional program reminiscent of a more central memory-like phenotype (KLF2+TCF7+S1PR1+SELL+CCR7+), while retaining tissue-homing receptors (CLA, CCR10). The skin tumor microenvironment contained potentially tumor-permissive myeloid cells producing regulatory (IDO1) and Th2-associated mediators (CCL13, CCL17, CCL22). Given their expression of PVR, TNFRSF14 and CD80/CD86, they might be under direct control by TIGIT+CTLA4+CSF2+TNFSF14+ tumor cells. In sum, this study highlights the adaptive phenotypic and functional plasticity of MF tumor cell clones. Thus, the TRM-like phenotype enables long-term skin residence of MF cells. Their switch to a TCM-like phenotype with persistent skin homing molecule expression in the circulation might explain the multi-focal nature of MF.

CCR7 in Blood Cancers – Review of Its Pathophysiological Roles and the Potential as a Therapeutic Target

“…Indeed, single-cell RNA sequencing of skin biopsies from one patient with aggressive disease showed that malignant clones in PB and LN displayed a transcriptional program reminiscent of a more central CCR7 + memory-like phenotype, while retaining tissue-homing receptors (i.e. CLA, CCR10) (172). Nonetheless, evidence of CCR7 protein expression in MF samples is scarce.…”

Malignant and Benign T Cells Constituting Cutaneous T-Cell Lymphoma

“…As the malignant cells in CTCL are rather heterogeneous, with multiple mutant subclones in the same lesions [ 97 , 98 ], and exist along with their benign counterparts, it was difficult to identify the common and specific characteristics of the malignant cells. Recently, clarifying malignant T cells and their properties by high-throughput sequencing analyses, including single-cell RNA sequencing, has enabled the discovery of the common gene expression signatures of malignant T cells.…”

“…While the expression of T RM markers, especially CD103, in tumor-infiltrating T cells is associated with a stronger antitumor effect in various solid malignant tumors, as described above [ 69 , 70 , 71 , 72 , 73 , 74 ], benign T cells in CTCL lesions possess less T RM (CD69 + CD103 + ) phenotype [ 97 , 118 ]. From the perspective of suppressive functions in antitumor immunity, these benign Th1 cells more frequently express immune checkpoint molecules, such as the programmed cell death 1, lymphocyte activation gene 3 (LAG-3), and cytotoxic T-lymphocyte-associated protein 4 [ 97 ]. The benign Tc1 cells also highly express LAG-3, consistent with their less inflammatory phenotype, with the decreased production of cytotoxic molecules [ 97 ].…”

“…From the perspective of suppressive functions in antitumor immunity, these benign Th1 cells more frequently express immune checkpoint molecules, such as the programmed cell death 1, lymphocyte activation gene 3 (LAG-3), and cytotoxic T-lymphocyte-associated protein 4 [ 97 ]. The benign Tc1 cells also highly express LAG-3, consistent with their less inflammatory phenotype, with the decreased production of cytotoxic molecules [ 97 ]. Furthermore, as the disease progresses, CTCL lesions are shifted to the Th2 environment [ 119 ].…”

“…Among the various cells constituting TME, for example, tumor-associated macrophages (TAM) are increased in MF and SS lesions with the increased expression of CCL18 and CCL22, which promote a Th2-biased microenvironment, as mentioned above [ 123 , 127 ]. Indeed, malignant T cells of CTCL highly express CCR4, which is a receptor of CCL18 and CCL22 and also serves as a T RM marker [ 7 , 97 ]. Additionally, in a murine CTCL model, depletion of TAM results in a decrease in tumor size and an increase in tumor-infiltrating CD8 T cells and in the level of antitumor cytokines [ 128 ].…”