Hematopoiesis culminates in the production of functionally heterogeneous blood cell types. In zebrafish, the lack of cell surface antibodies has compelled researchers to use fluorescent transgenic reporter lines to label specific blood cell fractions. However, these approaches are limited by the availability of transgenic lines and fluorescent protein combinations that can be distinguished. Here, we have transcriptionally profiled single hematopoietic cells from zebrafish to define erythroid, myeloid, B, and T cell lineages. We also used our approach to identify hematopoietic stem and progenitor cells and a novel NK-lysin 4+ cell type, representing a putative cytotoxic T/NK cell. Our platform also quantified hematopoietic defects in rag2E450fs mutant fish and showed that these fish have reduced T cells with a subsequent expansion of NK-lysin 4+ cells and myeloid cells. These data suggest compensatory regulation of the innate immune system in rag2E450fs mutant zebrafish. Finally, analysis of Myc-induced T cell acute lymphoblastic leukemia showed that cells are arrested at the CD4+/CD8+ cortical thymocyte stage and that a subset of leukemia cells inappropriately reexpress stem cell genes, including bmi1 and cmyb. In total, our experiments provide new tools and biological insights into single-cell heterogeneity found in zebrafish blood and leukemia.

Document Type


Publication Date


Notes/Citation Information

Published in The Journal of Experimental Medicine, v. 213, no. 6, p. 979-992.

© 2016 Moore et al.

This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 3.0 Unported license, as described at http://creativecommons.org/licenses/by-nc-sa/3.0/).

Digital Object Identifier (DOI)


Funding Information

This work was supported by Alex’s Lemonade Stand Foundation (D.M. Langenau), The Live Like Bella Foundation for Childhood Cancer (D.M. Langenau), American Cancer Society (D.M. Langenau), the Massachusetts General Hospital (MGH) Howard Goodman Fellowship (D.M. Langenau), and National Institutes of Health (NIH) grant R24OD016761. F.E. Moore is supported by NIH grant 5F32DK098875-03. Flow cytometry and sorting services were supported by MGH Pathology CNY Flow Cytometry Core shared instrumentation grant 1S10RR023440-01A.

Related Content

Supplemental data can be found at: http://doi.org/10.1084/jem.20152013

JEM_20152013_sm.pdf (1511 kB)
Supplemental Materials

JEM_20152013_Tables.zip (34 kB)
Tables S1-S3