Single-cell transcriptomics in bone marrow delineates CD56dimGranzymeK+ subset as intermediate stage in NK cell differentiation
Janine Melsen, Monique M. van Ostaijen-ten Dam, Dorenda J. A. Schoorl, Pieter J. Schol, Daphne A. L. van den Homberg, Arjan C. Lankester, Gertjan Lugthart, Marco W. Schilham
Abstract
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.