Single cell immunophenotyping of the Lyme erythema migrans lesion (TCR)

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 single cell transcriptomics with B cell and T cell receptor sequencing to characterize the cutaneous immune response in the EM lesion, focusing on B cells. Here, in an expanded sample size, we profiled T cell responses in the EM lesions in comparison to autologous uninvolved skin. In addition to CD4+IFNG+ T cell subsets known to be abundant in the EM, we identified clonal expansion of CD8+GZMK+IFNG+ T cells that comprised the only T cell population with significant differential expression of interferon regulated genes. This subset included IFNG+ cells with low cytotoxic gene expression, which may promote inflammation. While FOXP3+ regulatory T cells also were increased in EM, we found that the CD4+FOXP3- effector T cell subset contained cells with the highest differential expression of IL-10. Fibroblasts, endothelial cells, and pericytes expressed a broader array of chemokines than macrophages. These studies represent the first comprehensive interrogation of the cutaneous T cell response to Bb infection using single cell transcriptomics and provide insight into the orchestration of the skin immune response to this vector-borne pathogen. Overall design: we performed single-cell RNA and B cell receptor sequencing using 10x Genomics on PBMCs and whole skin cell digests of biopsies of paired EM lesions and autologous uninvolved skin from 13 subjects with Lyme disease.