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Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells
Ruoyi Jiang, Hailong Meng, Khadir Raddassi, Ira Fleming, Kenneth B. Hoehn, Kenneth R. Dardick, Alexia A. Belperron, Ruth R. Montgomery, Alex K. Shalek, David A. Hafler, Steven H. Kleinstein, Linda K. Bockenstedt
Ruoyi Jiang, Hailong Meng, Khadir Raddassi, Ira Fleming, Kenneth B. Hoehn, Kenneth R. Dardick, Alexia A. Belperron, Ruth R. Montgomery, Alex K. Shalek, David A. Hafler, Steven H. Kleinstein, Linda K. Bockenstedt
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Research Article Immunology Infectious disease

Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells

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Abstract

The skin lesion erythema migrans (EM) is an initial sign of the Ixodes tick–transmitted Borreliella spirochetal infection known as Lyme disease. T cells and innate immune cells have previously been shown to predominate the EM lesion and promote the reaction. Despite the established importance of B cells and antibodies in preventing infection, the role of B cells in the skin immune response to Borreliella is unknown. Here, we used single-cell RNA-Seq in conjunction with B cell receptor (BCR) sequencing to immunophenotype EM lesions and their associated B cells and BCR repertoires. We found that B cells were more abundant in EM in comparison with autologous uninvolved skin; many were clonally expanded and had circulating relatives. EM-associated B cells upregulated the expression of MHC class II genes and exhibited preferential IgM isotype usage. A subset also exhibited low levels of somatic hypermutation despite a gene expression profile consistent with memory B cells. Our study demonstrates that single-cell gene expression with paired BCR sequencing can be used to interrogate the sparse B cell populations in human skin and reveals that B cells in the skin infection site in early Lyme disease expressed a phenotype consistent with local antigen presentation and antibody production.

Authors

Ruoyi Jiang, Hailong Meng, Khadir Raddassi, Ira Fleming, Kenneth B. Hoehn, Kenneth R. Dardick, Alexia A. Belperron, Ruth R. Montgomery, Alex K. Shalek, David A. Hafler, Steven H. Kleinstein, Linda K. Bockenstedt

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Figure 1

Schematic demonstration of study workflow.

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Schematic demonstration of study workflow.
EM and uninvolved skin sample...
EM and uninvolved skin samples were first isolated from patients by punch biopsy and submitted for scRNA-Seq. In cohort 1 (n = 6), paired PBMCs were prepared as unpaired bulk TCRB and IGH repertoires from bulk RNA and also submitted for repertoire sequencing using the 10× Genomics Chromium platform. The characteristics of B cells and T cells found in both compartments were analyzed based on gene expression and features of their respective V(D)J sequences. Cohort 2 (n = 4) subject samples were sequenced using a nanowell-based single-cell transcriptome approach (Seq-Well) to support findings from cohort 1. EM, erythema migrans; sc, single-cell.

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ISSN 2379-3708

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