Heterogeneity of human bone marrow and blood natural killer cells defined by single-cell transcriptome

Nat Commun. 2019 Sep 2;10(1):3931. doi: 10.1038/s41467-019-11947-7.


Natural killer (NK) cells are critical to both innate and adaptive immunity. However, the development and heterogeneity of human NK cells are yet to be fully defined. Using single-cell RNA-sequencing technology, here we identify distinct NK populations in human bone marrow and blood, including one population expressing higher levels of immediate early genes indicative of a homeostatic activation. Functionally matured NK cells with high expression of CX3CR1, HAVCR2 (TIM-3), and ZEB2 represents terminally differentiated status with the unique transcriptional profile. Transcriptomic and pseudotime analyses identify a transitional population between CD56bright and CD56dim NK cells. Finally, a donor with GATA2T354M mutation exhibits reduced percentage of CD56bright NK cells with altered transcriptome and elevated cell death. These data expand our understanding of the heterogeneity and development of human NK cells.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bone Marrow / metabolism*
  • Bone Marrow Cells / metabolism
  • CD56 Antigen / genetics
  • CD56 Antigen / metabolism
  • CX3C Chemokine Receptor 1 / genetics
  • CX3C Chemokine Receptor 1 / metabolism
  • Genetic Heterogeneity
  • Hepatitis A Virus Cellular Receptor 2 / genetics
  • Hepatitis A Virus Cellular Receptor 2 / metabolism
  • Humans
  • Killer Cells, Natural / immunology
  • Killer Cells, Natural / metabolism*
  • Single-Cell Analysis / methods*
  • Transcriptome / genetics*
  • Zinc Finger E-box Binding Homeobox 2 / genetics
  • Zinc Finger E-box Binding Homeobox 2 / metabolism


  • CD56 Antigen
  • CX3C Chemokine Receptor 1
  • CX3CR1 protein, human
  • HAVCR2 protein, human
  • Hepatitis A Virus Cellular Receptor 2
  • ZEB2 protein, human
  • Zinc Finger E-box Binding Homeobox 2