In situ profiling of plasma cell clonality with image-based single-cell transcriptomics

Image-based single-cell transcriptomics can identify diverse cell types in intact tissues. However, in adaptive immunity, V(D)J recombination generates unique immune receptors in cells of the same type, leading to important functional variation that is not yet defined by these methods. Here we introduce B cell receptor multiplexed error-robust fluorescence in situ hybridization (BCR-MERFISH), which measures plasma cell clonality based on V gene usage in combination with transcriptome profiling. We demonstrate that BCR-MERFISH accurately identifies V gene usage in cell culture and in mice with restricted or native plasma cell diversity. We then use BCR-MERFISH to elucidate the microbiota-dependent changes in plasma cell abundance, clonal diversity, and public clonotype usage in the mouse gut and the non-uniform distribution of plasma cell clones along the mouse ileum. Given that tissue context is an essential modulator of plasma cell dynamics, we anticipate that BCR-MERFISH may offer new insights into a wide range of immunological questions.