Single-cell immunophenotyping identifies CD8+GZMK+IFNG+ T cells as a key immune population in cutaneous Lyme disease

The skin lesion erythema migrans (EM) is the first clinical sign of Lyme disease, an infection due to the tick-transmitted bacterium Borrelia burgdorferi (Bb). Previously, we used scRNA-Seq to characterize the cutaneous immune response in the EM lesion, focusing on B cells. Here, with an expanded sample size, we profiled T cell responses in EM lesions compared to autologous uninvolved skin. In addition to CD4+ T cell subsets known to be abundant in the EM lesion, we identified clonally expanded CD8+GZMK+IFNG+ T cells that comprised cells with high or intermediate IFNG expression. These cells exhibited significant differential expression of IFN-regulated genes and included subsets with low cytotoxic gene expression, suggesting an inflammatory potential that may contribute to early defense against Bb within the EM lesion. In addition, we found that endothelial cells, fibroblasts, and pericytes were the main producers of key T cell-recruiting chemokines. These studies using single-cell transcriptomics with adaptive immune receptor sequencing provide a comprehensive interrogation of the cutaneous T cell response to Bb infection and insight into the orchestration of the skin barrier defense to this vector-borne pathogen.