Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing

J Exp Med. 2017 Oct 2;214(10):2875-2887. doi: 10.1084/jem.20170976. Epub 2017 Sep 6.


Recent advances in single-cell, transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. In this study, we used massively parallel, single-cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow, constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner, our approach was useful in characterizing immune-cell deficiencies within DNA-protein kinase catalytic subunit (prkdc), interleukin-2 receptor γ a (il2rga), and double-homozygous-mutant fish, identifying blood cell losses in T, B, and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types, including two classes of natural killer immune cells, classically defined and erythroid-primed hematopoietic stem and progenitor cells, mucin-secreting kidney cells, and kidney stem/progenitor cells. In total, our work provides the first, comprehensive, single-cell, transcriptomic analysis of kidney and marrow cells in the adult zebrafish.

MeSH terms

  • Animals
  • Animals, Genetically Modified
  • Cell Lineage / genetics
  • Cell Lineage / physiology
  • Gene Expression Profiling
  • Hematopoiesis, Extramedullary / genetics*
  • Hematopoiesis, Extramedullary / physiology
  • Hematopoietic Stem Cells
  • Kidney / cytology*
  • Kidney / metabolism
  • RNA / genetics*
  • Sequence Analysis, RNA
  • Zebrafish / anatomy & histology*
  • Zebrafish / genetics
  • Zebrafish / metabolism


  • RNA