In situ profiling of plasma cell clonality with image-based single-cell transcriptomics
Evan Yang1,2, Jose Aceves-Salvador1,2, Carlos Castrillon1
1Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
Insights
New BCR-MERFISH technology identifies plasma cell clones by V-gene usage. This method reveals microbiota-driven changes in mouse gut plasma cells, enhancing our understanding of adaptive immunity.
Area of Science:
- Immunology
- Molecular Biology
- Genomics
Background:
- Single-cell transcriptomics identifies cell types but misses functional variation in adaptive immunity due to unique immune receptors.
- V(D)J recombination creates diverse B-cell receptors within the same cell type, a key aspect not captured by current methods.
Purpose of the Study:
- To introduce a novel method, B-cell-receptor multiplexed error robust fluorescence in situ hybridization (BCR-MERFISH), for distinguishing plasma cell clones.
- To analyze plasma cell diversity and distribution in response to microbiota in the mouse gut.
Main Methods:
- Developed BCR-MERFISH to combine V-gene usage with transcriptome profiling for plasma cell identification.
- Validated BCR-MERFISH in cell culture and in mice with varying plasma cell diversity.
- Applied BCR-MERFISH to study mouse gut plasma cells and their response to microbiota.
Main Results:
- BCR-MERFISH accurately identifies V-gene usage in various settings.
- Revealed microbiota-dependent alterations in plasma cell abundance and clonal diversity in the mouse gut.
- Demonstrated non-uniform spatial distribution of plasma cell clones along the mouse ileum.
Conclusions:
- BCR-MERFISH provides a powerful tool to dissect plasma cell heterogeneity and function.
- The study highlights the impact of microbiota on adaptive immunity and plasma cell dynamics.
- BCR-MERFISH is anticipated to offer new insights into diverse immunological questions by integrating tissue context.
Abstract:
Image-based single-cell transcriptomics can identify diverse cell types within intact tissues. However, in adaptive immunity, V(D)J recombination generates unique immune receptors within 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 distinguishes plasma cell clones 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 reveal 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. As 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.
