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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 6

Unmutated IgM/D B cells lack a naive B cell signature.

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Unmutated IgM/D B cells lack a naive B cell signature.
(A) Cells with un...
(A) Cells with unmutated IgM BCR sequences visualized as black dots over a UMAP projection of B cell single-cell transcriptomes. (B) Differential gene expression of 3 marker genes associated with naive B cells after normalization (cell gene expression was Z-scored for each grouping and pseudobulk averages were calculated). (C) enrichR pathway analysis (Reactome 2016) of the top 40 genes upregulated in unmutated IgM memory B cells compared with all other memory B cells. Red bars correspond to significantly associated gene ontology assignments (P < 0.05 by Wilcoxon’s test). Horizontal bars show the mean frequency of each comparison and frequencies belonging to the same subject are connected with lines. Data for the same n = 6 subjects from cohort 1 are shown for A, while B only shows the n = 5 subjects with unmutated IgM memory B cells in EM lesions. Statistical differences are shown only when significant for a paired t test (**P < 0.01). EM, erythema migrans; BCR, B cell receptor.

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