Integrated transcriptome and trajectory analysis of cutaneous T-cell lymphoma identifies putative precancer populations.

Cutaneous T-cell lymphoma (CTCL) incidence increases with age, and blood involvement portends a worse prognosis. To advance our understanding of CTCL development and identify potential therapeutic targets, we performed integrative analyses of paired single-cell RNA and TCR sequencing of peripheral blood CD4+ T-cells from CTCL patients to reveal disease unifying features. The malignant CD4+ T-cells of CTCL show highly diverse transcriptomic profiles across patients, with most displaying a mature Th2 differentiation and T-cell exhaustion phenotype. TCR-CDR3 peptide prediction analysis suggested limited diversity between CTCL samples, consistent with a role for a common antigenic stimulus. PHATE affinity-based transition analysis identified putative precancerous circulating populations characterized by an intermediate stage of gene expression and mutation level between the normal CD4+ T-cells and malignant CTCL cells. We further revealed the therapeutic potential of targeting CD82 and JAK that endow the malignant CTCL cells with survival and proliferation advantages.