Single-cell transcriptomics in bone marrow delineates CD56dimGranzymeK+ subset as intermediate stage in NK cell differentiation

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Human natural killer (NK) cells in lymphoid tissues can be categorized into three subsets: CD56 bright CD16 + , CD56 dim CD16 + and CD69 + CXCR6 + lymphoid tissue-resident (lt)NK cells. How the three subsets are functionally and developmentally related is currently unknown. Therefore, we performed single-cell RNA sequencing combined with oligonucleotide-conjugated antibodies against CD56, CXCR6, CD117 and CD34 on fresh bone marrow NK cells. A minor CD56 dim GzmK + subset was identified that shared features with CD56 bright and CD56 dim GzmK - NK cells based on transcriptome, phenotype (NKG2A high CD16 low KLRG1 high TIGIT high ) and functional analysis in bone marrow and blood, supportive for an intermediate subset. Pseudotime analysis positioned CD56 bright , CD56 dim GzmK + and CD56 dim GzmK - cells in one differentiation trajectory, while ltNK cells were developmentally separated. Integrative analysis with bone marrow cells from the Human Cell Atlas did not demonstrate a developmental connection between CD34 + progenitor and NK cells, suggesting absence of early NK cell stages in bone marrow. In conclusion, single-cell transcriptomics provide new insights on development and differentiation of human NK cells.