Single-cell molecular profiling provides a high-resolution map of basophil and mast cell development

Background Basophils and mast cells contribute to the development of allergic reactions. Whereas these mature effector cells are extensively studied, the differentiation trajectories from hematopoietic progenitors to basophils and mast cells are largely uncharted at the single-cell level. Methods We performed multicolor flow cytometry, high-coverage single-cell RNA sequencing analyses, and cell fate assays to chart basophil and mast cell differentiation at single-cell resolution in mouse. Results Analysis of flow cytometry data reconstructed a detailed map of basophil and mast cell differentiation, including a bifurcation of progenitors into two specific trajectories. Molecular profiling and pseudotime ordering of the single cells revealed gene expression changes during differentiation. Cell fate assays showed that multicolor flow cytometry and transcriptional profiling successfully predict the bipotent phenotype of a previously uncharacterized population of peritoneal basophil-mast cell progenitors. Conclusions A combination of molecular and functional profiling of bone marrow and peritoneal cells provided a detailed road map of basophil and mast cell development. An interactive web resource was created to enable the wider research community to explore the expression dynamics for any gene of interest.

Automated summary

The study explored the differentiation pathways of basophils and mast cells at the single-cell level in mice using multicolor flow cytometry, high-coverage single-cell RNA sequencing, and cell fate assays. The results provided a detailed map of differentiation and revealed gene expression changes during the process. Flow cytometry and transcriptional profiling successfully predicted the bipotent phenotype of a previously uncharacterized population of peritoneal basophil-mast cell progenitors.