Figure 7.

No early NK cell stages detected in bone marrow. (A) To study early NK cell development, our dataset was integrated with the human cell atlas (HCA) bone marrow (BM) single-cell RNA sequencing dataset (8 donors). Progenitor and NK cells were selected and re-clustered (total = 41476 cells). See Figure S8 for the selection procedure. ltNK = lymphoid tissue NK, NK prolif = proliferating NK. (B) For each cluster as visualized in A, the mean mRNA expression (color intensity) and the fraction of cells expressing the mRNA molecule (size) are shown. A selection of progenitor-related genes is depicted. No NK progenitor cluster with combined expression of CD34, CD38, CD7 and MME (CD10) could be identified. (C) Fresh mononuclear cells isolated from bone marrow (n=3), lymph node (n=2), tonsil (n=5) and spleen (n=3) were analyzed for the presence of NK cell development. First, T cells, B cells and monocytes were excluded ( Figure S9 ). Next, the early progenitor cells (CD45^-/dimCD117⁺SSC^high) and NK/ILC/progenitor cells were defined based on a UMAP embedding ( Figure S9 ). Within the NK/ILC/progenitor cells, CD56^bright NK, CD56^dim NK, ltNK cells, and innate lymphoid cells (ILCs, CD127^highCD117⁺) were recognized. In the remaining cells, a population of CD127^lowCD117⁺CD56^+/- cells was identified (yellow), present in lymph node and tonsil, but absent in spleen and bone marrow. (D) subset distribution in the individual tissue samples.