Single-cell analysis of temporal immune cell dynamics in alopecia areata reveals a causal role for clonally expanded CD8+ T cells in disease

Immune-mediated hair loss in alopecia areata (AA) is driven by CD8+ T cells. Lesional AA skin is characterized by the infiltration of clonally expanded CD8+ T cells, however, the relationship between CD8+ T cell clonality and the pathogenicity is poorly understood. Here, we performed parallel single-cell RNA sequencing and TCR sequencing in the graft-induced C3H/HeJ mouse model of AA to interrogate time-dependent changes in the AA immune landscape. We analyzed T cells derived from both the skin and skin-draining lymph nodes to capture the end organ as well as the site of antigen priming, and found striking hyper-expansion of T cell clones associated with disease onset. Using the highly expanded CD8+ TCR sequences, we generated TCR retrogenic mice and performed depletion experiments to demonstrate that expanded CD8+ T cell clones are both necessary and sufficient for AA onset, establishing the causal relationship between CD8+ T cell clonality and pathogenicity in disease.

Single-cell RNA and T cell receptor sequencing was performed on CD8+ T cells from the skin and skin draining lymph nodes of mice with alopecia areata and ungrafted control mice. The following time points were captured for mice with alopecia areata: baseline (before grafting), and post-grafting weeks 3, 4, 5, 6, 8, 10, 12, 16, 20, and 24. The following time points were captured for ungrafted control mice: weeks 3, 6, 12, 20, and 24.