Diversity of peripheral blood human NK cells identified by single-cell RNA sequencing

• Published in: Blood advances Vol. 4; no. 7; pp. 1388 - 1406
• Main Authors: Smith, Samantha L., Kennedy, Philippa R., Stacey, Kevin B., Worboys, Jonathan D., Yarwood, Annie, Seo, Seungmae, Solloa, Everardo Hegewisch, Mistretta, Brandon, Chatterjee, Sujash S., Gunaratne, Preethi, Allette, Kimaada, Wang, Ying-Chih, Smith, Melissa Laird, Sebra, Robert, Mace, Emily M., Horowitz, Amir, Thomson, Wendy, Martin, Paul, Eyre, Steve, Davis, Daniel M.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 14-04-2020; American Society of Hematology
• Subjects: Cytomegalovirus; Cytomegalovirus Infections; Humans; Immunobiology and Immunotherapy; Killer Cells, Natural; Receptors, KIR; Sequence Analysis, RNA
• ISSN: 2473-9529; 2473-9537
• DOI: 10.1182/bloodadvances.2019000699

Human natural killer (NK) cells in peripheral blood perform many functions, and classification of specific subsets has been a longstanding goal. We report single-cell RNA sequencing of NK cells, comparing gene expression in unstimulated and interleukin (IL)-2–activated cells from healthy cytomegalovirus (CMV)-negative donors. Three NK cell subsets resembled well-described populations; CD56brightCD16−, CD56dimCD16+CD57−, and CD56dimCD16+CD57+. CD56dimCD16+CD57− cells subdivided to include a population with higher chemokine mRNA and increased frequency of killer-cell immunoglobulin-like receptor expression. Three novel human blood NK cell populations were identified: a population of type I interferon–responding NK cells that were CD56neg; a population exhibiting a cytokine-induced memory-like phenotype, including increased granzyme B mRNA in response to IL-2; and finally, a small population, with low ribosomal expression, downregulation of oxidative phosphorylation, and high levels of immediate early response genes indicative of cellular activation. Analysis of CMV+ donors established that CMV altered the proportion of NK cells in each subset, especially an increase in adaptive NK cells, as well as gene regulation within each subset. Together, these data establish an unexpected diversity in blood NK cells and provide a new framework for analyzing NK cell responses in health and disease.
•Single-cell RNA sequencing reveals an unexpected diversity of healthy human blood NK cells, each population with a distinct transcriptome.•For the first time, we describe a population of NK cells with low ribosomal expression, which may be linked to cellular activation.
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