Abstract
High-throughput measurement of gene-expression and immune receptor repertoires have recently become powerful tools in the study of adaptive immune response. However, despite their now-widespread use, both tend to discard cell identity by treating cell populations in bulk, and therefore lose the correlation between genetic variability and gene-expression at the single cell level. In order to recover this information, we developed a method to simultaneously measure gene expression profiles and genome mutations in single cells. We applied this method by quantifying the relationships between gene expression and antibody mutation in ensembles of individual B-cells from immunized mice. The results reveal correlations reflecting the manner in which information propagates between a B-cell’s antigen receptors, its gene expression, and its mutagenic machinery, and demonstrate the power of this approach to illuminate both heterogeneity and physiology in cell populations.
Highlights
The mammalian adaptive immune system is comprised of Tcells and B-cells that produce receptors specific to antigens
AbT cells are necessary for the generation of germinal center B cell response, cd T cells can recognize the same antigens as B-cells and may affect B cell development [7]
Single PE+ and PE- B-cells were sorted and pre-amplified with primers specific both to sequences flanking the variable regions of the Ig heavy- and light-chains (Figure 1, Table S4 in File S1) and a panel of genes noted for their expression in differentiating B cells (Table S5 in File S1)
Summary
The mammalian adaptive immune system is comprised of Tcells and B-cells that produce receptors specific to antigens. Antigen-engagement of antibody receptors on B-cell surfaces results in B-cell activation, up-regulation of the enzyme AID [1], and the consequent hypermutation of the antibodyencoding gene; the variants created by these mutations are yet another source of diversity. AID induces antibody class-switching, whereby the non-mutated constant region of the antibody heavy chain gene, initially expressed as IgM and IgD classes, may change to IgG, IgA, or IgE. Because such diversification of antibody receptors, which fine-tunes adaptive immune response, both affects and is affected by the geneexpression of B-cells that produce them, co-variation between receptor sequence and immune gene-expression may be expected to reflect direct and indirect mechanisms of feedback between them. While high-throughput measurements have examined both independently in bulk samples [2], [3], [4], [5], no combined cellto-cell analysis of these two critical components of immune response has yet been performed
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