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

ABSTRACT: Human Natural Killer (NK) cells in peripheral blood perform many functions and classification of specific subsets has been a long-standing goal. Here, we report single cell RNA-sequencing of NK cells, comparing gene expression in unstimulated and IL-2 activated cells, from healthy CMV-negative donors. Three NK cell subsets resembled well-described populations, CD56brightCD16-, CD56dimCD16+CD57- and CD56dimCD16+CD57+. CD56dimCD16+CD57- cells sub-divided to include a population with higher chemokine mRNA and increased frequency of KIR expression. Three novel human blood NK cell populations were identified as: a population of type I interferon responding NK cells which 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, down-regulation of oxidative phosphorylation and high levels of immediate early response genes indicative of cellular activation. Analysis of CMV-positive 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 analysing NK cell responses in health and disease.

ORGANISM(S): Homo sapiens

PROVIDER: GSE144191 | GEO | 2020/01/25

REPOSITORIES: GEO

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

Project description:Human Natural Killer (NK) cells in peripheral blood perform many functions but classification of specific subsets has been a long-standing problem. Here, we report single-cell RNA sequencing of NK cells from healthy CMV-negative donors, comparing gene expression in unstimulated and IL-2 activated cells. Unsupervised clustering identified seven NK cell subsets. Three resembled well-described populations, CD56brightCD16-, CD56dimCD16+CD57- and CD56dimCD16+CD57+. CD56dimCD16+CD57- cells sub-divided to include a population with higher chemokine mRNA and increased frequency of KIR expression. Three novel human blood NK cell populations were identified as: a population of type I interferon responding NK cells which were CD56neg; a population exhibiting an in-vivo cytokine-induced memory-like phenotype, including increased granzyme B mRNA in response to IL-2, and finally, a small population, with low ribosomal expression, down-regulation of oxidative phosphorylation and high levels of immediate early response genes indicative of cellular activation. Human cytomegalovirus positive donors also included a higher frequency of adaptive NK cells. Together, these data establish an unexpected diversity in blood NK cells and provide a new framework for analysing NK cell responses in health and disease.

2020-01-29 | GSE144430 | GEO

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2013-07-01 | E-GEOD-47855 | biostudies-arrayexpress

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Project description:CD56brightCD16-, CD56dimNKG2A+ and CD56dimNKG2A- NK cells subsets were FACS sorted and their transcriptional profile were compared after whole genome microarray analysis.

2010-08-10 | E-MEXP-2798 | biostudies-arrayexpress

a26bf570-482e-435d-a268-fddc7e54b31d - samples

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