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

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Hamey, Fiona K 
Lau, Winnie WY 
Kucinski, Iwo 
Wang, Xiaonan 
Diamanti, Evangelia 


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.



basophils, differentiation, mast cells, single-cell RNA sequencing, transcriptomics, Animals, Basophils, Bone Marrow Cells, Cell Differentiation, Mast Cells, Mice, Stem Cells

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Cancer Research UK (21762)
Wellcome Trust (206328/Z/17/Z)
Addenbrooke's Charitable Trust (ACT) (Minute 03/18 B (ii))
Wellcome Trust (105031/D/14/Z)
Bloodwise (18002)
Medical Research Council (MR/S036113/1)
Wellcome Trust (100140/Z/12/Z)
Wellcome Trust (203151/Z/16/Z)
National Institute of Diabetes and Digestive and Kidney Diseases (R24DK106766)
Medical Research Council (MC_PC_12009)
We thank Chiara Cossetti, Gabriela Grondys-Kotarba, and Reiner Schulte at the Cambridge Institute for Medical Research Flow Cytometry Core for their assistance with cell sorting. We also thank the Human Cell Atlas for making the human single-cell transcriptomic data available. J.S.D. is supported by funding from the Swedish Research Council (2015-06322 and 2018-02070), the Swedish Cancer Society, the Åke Wiberg Foundation, the Magnus Bergvall Foundation, the Lars Hierta Memorial Foundation, and Karolinska Institutet. Research in B.G.’s laboratory is supported by Blood Cancer UK (18002), Wellcome (206328/Z/17/Z), CRUK (C1163/A21762), NIH-NIDDK (1 R24 DK106766), MRC (MR/S036113/1) and by core funding from Wellcome and MRC to the Wellcome-MRC Cambridge Stem Cell Institute (203151/Z/16/Z). F.K.H. is funded by a MRC Physical Biology of Stem Cells PhD studentship (MR/K500975/1) and by part of a Wellcome Strategic Award (105031/D/14/Z) awarded to W. Reik, S. Teichmann, J. Nichols, B.D. Simons, T. Voet, S. Srinivas, L. Vallier, B.G. and J.C. Marioni.
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