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

Melsen, J.E.; Ostaijen-ten Dam, M.M. van; Schoorl, D.J.A.; Schol, P.J.; Homberg, D.A.L. van den; Lankester, A.C.; ... ; Schilham, M.W. (2022)

Article / Letter to editor

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.

• spectral cytometry
• single-cell RNA sequencing
• natural killer cells (NK cells)
• bone marrow
• pseudotime analysis

• All authors: Melsen, J.E.; Ostaijen-ten Dam, M.M. van; Schoorl, D.J.A.; Schol, P.J.; Homberg, D.A.L. van den; Lankester, A.C.; Lugthart, G.; Schilham, M.W.
• Date: 2022-11-24
• Journal: Frontiers in Immunology
• Volume: 13
• DOI: doi:10.3389/fimmu.2022.1044398