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

Nature Methods · 10 Nov 2026 · Journal Article · Open access

Yang, Aceves-Salvador + more

The abstract is read at the publisher; the summary is JClub's.

BCR-MERFISH accurately identifies plasma cell V gene usage and clonality in mice, including settings with restricted or native plasma cell diversity, enabling in situ receptor profiling.

Why it matters: Image-based single-cell transcriptomics can classify cell types but does not define functional variation from V(D)J-generated immune receptors within the same cell type.
What they did: The authors developed BCR-MERFISH, combining V gene usage via multiplexed error-robust fluorescence in situ hybridization with transcriptome profiling, and validated it in cell culture and mouse models.
The result: In the mouse gut, BCR-MERFISH reveals microbiota-dependent changes in plasma cell abundance, clonal diversity, and public clonotype usage, and shows non-uniform clone distribution along the ileum.

AI summary of the abstract · may contain errors · not medical advice · read the paper.

Open access
4 cites

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

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