LyP vs advanced-stage CTCLs: single-cell profiling reveals markers of self-limited vs aggressive disease behavior

Cutaneous T-cell lymphomas (CTCL) encompass a broad spectrum from highly indolent to aggressive systemic disease, but underlying mechanisms remain only poorly understood. Using single-cell RNA sequencing, we profiled samples from patients with self-limited, spontaneously regressing lymphomatoid papulosis (LyP) lesions of CD4+, CD8+, or T-cell receptor γδ (TCR-γδ)+ clonal phenotypes and compared the results with samples from patients with advanced-stage CTCL (aCTCL) variants, namely CD4+ mycosis fungoides (MF), CD8+ primary cutaneous aggressive epidermotropic CD8+ cytotoxic T-cell lymphoma, and TCR-γδ+ MF, that all led to a documented lethal disease outcome. Within T cells, transcriptomic differences between LyP and the aCTCL group were primarily found among malignant clones, with only relatively minor differences within the polyclonal T-cell infiltrates. When compared with all aCTCL diagnoses, LyP top clones consistently exhibited a hyperactivated cytotoxic phenotype, characterized by the enrichment of tumor necrosis factor α (TNF-α), interleukin-2 (IL-2)/STAT5, interferon gamma, hypoxia, and complement activation pathways, irrespective of their CD4, CD8, or TCR-γδ lineage. In line, LyP lesions contained SPP1+ macrophages expressing M1-associated markers (IL1B, TNF, and IRF1), consistent with a cytotoxic, type 1-skewed immune microenvironment, that were largely absent across aCTCL diagnoses. LyP samples further expressed markers of vascular dysfunction and stress (C2CD4B, IL6, and CEBPD), corroborated by the morphological signs of lymphocytic vasculitis and necrosis in a subset of patients. Along with a signal of an insufficient coping response to hypoxia, these stromal reactions might be critical contributors to spontaneous lesion regression in LyP. Collectively, this study reveals mediators associated with the self-limited behavior of LyP lesions, which might be relevant for future immunomodulatory treatment strategies in CTCL.