Single‐cell RNA sequencing profiling in a patient with discordant primary cutaneous B‐cell and T‐cell lymphoma reveals micromilieu‐driven immune skewing

Abstract

Summary Background Primary cutaneous lymphomas comprise a heterogeneous group of B‐cell and T‐cell malignancies which often show an indolent course, but can progress to aggressive disease in a subset of patients. Diagnosis is often delayed owing to clinical and histopathological similarities with benign inflammatory conditions. Especially during early disease, cancer cells are present at relatively low percentages compared with the inflammatory infiltrate, an interplay that is currently only insufficiently understood. Objectives To improve diagnostics and perform molecular characterization of a complex type of primary cutaneous lymphoma. Methods Single‐cell RNA sequencing (scRNA‐seq) was performed and combined with T‐cell and B‐cell receptor sequencing. Results We were able to diagnose a patient with concurrent mycosis fungoides (MF) and primary cutaneous follicle centre lymphoma (PCFCL), appearing in mutually exclusive skin lesions. Profiling of tumour cells and the tissue microenvironment revealed a type‐2 immune skewing in MF, most likely guided by the expanded clone that also harboured upregulation of numerous pro‐oncogenic genes. By contrast, PCFCL lesions exhibited a more type‐1 immune phenotype, consistent with its indolent behaviour. Conclusions These data not only illustrate the diagnostic potential of scRNA‐seq, but also allow the characterization of specific clonal populations that shape the unique tissue microenvironment in clinically distinct types of lymphoma skin lesions.

Phenotypic plasticity of malignant T cells in blood and skin of a Sézary syndrome patient revealed by single cell transcriptomics

“…In summary, we demonstrate that the single cell transcriptome of SS cells, which are present in circulating blood and skin, reveals a new level of tumor heterogeneity in SS, thereby confirming the potential of scRNAseq to improve our understanding of CTCL (40)(41)(42). The existence of two distinct phenotypes of the same malignant monoclonal T-cell population driven by the tumor microenvironment represents a new finding, extending previous reports of phenotype plasticity.…”

Single‐cell transcriptomics in human skin research: available technologies, technical considerations and disease applications

“…A single patient's samples with concurrent MF and primary cutaneous follicle centre lymphoma (PCFCL)—the most common cutaneous B‐cell lymphoma—appearing in separate lesions were analysed with scRNA‐seq and combined T‐cell and B‐cell receptor sequencing 77 77 . Finally, Gayodosik and colleagues employed scRNA‐seq on lymphocytes purified from skin biopsies of advanced stage cutaneous T‐cell lymphoma patients and confirmed a large inter‐ and intratumor T‐cell gene expression heterogeneity 78 …”

“…76 A single patient's samples with concurrent MF and primary cutaneous follicle centre lymphoma (PCFCL)-the most common cutaneous B-cell lymphoma-appearing in separate lesions were analysed with scRNA-seq and combined Tcell and B-cell receptor sequencing. 77 Two co-occurring clonal malignancies were unveiled, with the T-cell clone expressing Th2-related markers while the PCFCL lesions exhibited a more Th1 skewed gene expression profile and this was reflected in the tumors micromilieu. 77 Finally, Gayodosik and colleagues employed scRNA-seq on lymphocytes purified from skin biopsies of advanced stage cutaneous T-cell lymphoma patients and confirmed a large inter-and intratumor Tcell gene expression heterogeneity.…”

“…77 Two co-occurring clonal malignancies were unveiled, with the T-cell clone expressing Th2-related markers while the PCFCL lesions exhibited a more Th1 skewed gene expression profile and this was reflected in the tumors micromilieu. 77 Finally, Gayodosik and colleagues employed scRNA-seq on lymphocytes purified from skin biopsies of advanced stage cutaneous T-cell lymphoma patients and confirmed a large inter-and intratumor Tcell gene expression heterogeneity. 78 Patient-specific enriched cell subpopulations and markers were outlined, demonstrating the efficiency of scRNA-seq as a diagnostic and informational tool for personalized medicine.…”

“…They found skin tissue‐resident memory T cells that could switch to a more central memory‐like phenotype in circulation and could explain their migratory behaviour 76 . A single patient's samples with concurrent MF and primary cutaneous follicle centre lymphoma (PCFCL)—the most common cutaneous B‐cell lymphoma—appearing in separate lesions were analysed with scRNA‐seq and combined T‐cell and B‐cell receptor sequencing 77 77 .…”