E.L. Lowry

TCR sequencing facilitates diagnosis and identifies mature T cells as the cell of origin in CTCL

High-throughput TCR sequencing can accurately diagnose and discriminate CTCL cells in skin. Discriminating taste for CTCL Cutaneous T cell lymphoma (CTCL) is a potentially debilitating disease, but early stages resemble rashes of less dangerous inflammatory skin diseases. Now, Kirsch et al. report that high-throughput TCR sequencing (HTS) can be used to distinguish CTCL from benign inflammatory disease by identifying T cell clones. This diagnostic was more sensitive and specific than the current standard of care and was also able to determine therapeutic response and identify early recurrence. The authors then used HTS to gain insight into CTCL pathogenesis, reporting that the malignancy derived from mature T cells that may have a specialized niche in the skin. Early diagnosis of cutaneous T cell lymphoma (CTCL) is difficult and takes on average 6 years after presentation, in part because the clinical appearance and histopathology of CTCL can resemble that of benign inflammatory skin diseases. Detection of a malignant T cell clone is critical in making the diagnosis of CTCL, but the T cell receptor γ (TCRγ) polymerase chain reaction (PCR) analysis in current clinical use detects clones in only a subset of patients. High-throughput TCR sequencing (HTS) detected T cell clones in 46 of 46 CTCL patients, was more sensitive and specific than TCRγ PCR, and successfully discriminated CTCL from benign inflammatory diseases. HTS also accurately assessed responses to therapy and facilitated diagnosis of disease recurrence. In patients with new skin lesions and no involvement of blood by flow cytometry, HTS demonstrated hematogenous spread of small numbers of malignant T cells. Analysis of CTCL TCRγ genes demonstrated that CTCL is a malignancy derived from mature T cells. There was a maximal T cell density in skin in benign inflammatory diseases that was exceeded in CTCL, suggesting that a niche of finite size may exist for benign T cells in skin. Last, immunostaining demonstrated that the malignant T cell clones in mycosis fungoides and leukemic CTCL localized to different anatomic compartments in the skin. In summary, HTS accurately diagnosed CTCL in all stages, discriminated CTCL from benign inflammatory skin diseases, and provided insights into the cell of origin and location of malignant CTCL cells in skin.

Clinically resolved psoriatic lesions contain psoriasis-specific IL-17–producing αβ T cell clones

In psoriasis, an IL-17–mediated inflammatory skin disease, skin lesions resolve with therapy, but often recur in the same locations when therapy is discontinued. We propose that residual T cell populations in resolved psoriatic lesions represent the pathogenic T cells of origin in this disease. Utilizing high-throughput screening (HTS) of the T cell receptor (TCR) and immunostaining, we found that clinically resolved psoriatic lesions contained oligoclonal populations of T cells that produced IL-17A in both resolved and active psoriatic lesions. Putative pathogenic clones preferentially utilized particular V&bgr; and V&agr; subfamilies. We identified 15 TCR&bgr; and 4 TCR&agr; antigen receptor sequences shared between psoriasis patients and not observed in healthy controls or other inflammatory skin conditions. To address the relative roles of &agr;&bgr; versus &ggr;&dgr; T cells in psoriasis, we carried out TCR/&dgr; HTS. These studies demonstrated that the majority of T cells in psoriasis and healthy skin are &agr;&bgr; T cells. &ggr;&dgr; T cells made up 1% of T cells in active psoriasis, less than 1% in resolved psoriatic lesions, and less than 2% in healthy skin. All of the 70 most frequent putative pathogenic T cell clones were &agr;&bgr; T cells. In summary, IL-17–producing &agr;&bgr; T cell clones with psoriasis-specific antigen receptors exist in clinically resolved psoriatic skin lesions. These cells likely represent the disease-initiating pathogenic T cells in psoriasis, suggesting that lasting control of this disease will require suppression of these resident T cell populations.

High-throughput sequencing of the T cell receptor β gene identifies aggressive early-stage mycosis fungoides

The malignant T cell clone frequency in cutaneous T cell lymphoma lesions is an independent prognostic indicator for early disease progression and death. Predicting progression in a T cell lymphoma Mycosis fungoides (MF) is an often indolent cutaneous T cell lymphoma identifiable by the T cell receptor gene TCRB in skin biopsies. de Masson et al. performed high-throughput sequencing of MF skin lesions to determine whether the frequency of the most abundant TCRB sequence could predict the fraction of cases that progress to more aggressive disease. This tumor clone frequency (TCF) outperformed commonly used prognostic indicators of disease progression and overall survival in MF, and was particularly useful in early-stage disease. The TCF may thus help identify which MF patients in the same clinical disease stage are in fact more likely to progress to life-threatening disease. Mycosis fungoides (MF), the most common cutaneous T cell lymphoma (CTCL) is a malignancy of skin-tropic memory T cells. Most MF cases present as early stage (stage I A/B, limited to the skin), and these patients typically have a chronic, indolent clinical course. However, a small subset of early-stage cases develop progressive and fatal disease. Because outcomes can be so different, early identification of this high-risk population is an urgent unmet clinical need. We evaluated the use of next-generation high-throughput DNA sequencing of the T cell receptor β gene (TCRB) in lesional skin biopsies to predict progression and survival in a discovery cohort of 208 patients with CTCL (177 with MF) from a 15-year longitudinal observational clinical study. We compared these data to the results in an independent validation cohort of 101 CTCL patients (87 with MF). The tumor clone frequency (TCF) in lesional skin, measured by high-throughput sequencing of the TCRB gene, was an independent prognostic factor of both progression-free and overall survival in patients with CTCL and MF in particular. In early-stage patients, a TCF of >25% in the skin was a stronger predictor of progression than any other established prognostic factor (stage IB versus IA, presence of plaques, high blood lactate dehydrogenase concentration, large-cell transformation, or age). The TCF therefore may accurately predict disease progression in early-stage MF. Early identification of patients at high risk for progression could help identify candidates who may benefit from allogeneic hematopoietic stem cell transplantation before their disease becomes treatment-refractory.