Human induced pluripotent stem cell-derived macrophages share ontogeny with MYB-independent tissue-resident macrophages

Tissue-resident macrophages such as microglia, Kupffer and Langerhans cells derive from Myb-independent yolk sac (YS) progenitors generated before the emergence of hematopoietic stem cells (HSCs). Myb-independent YS-derived resident macrophages self-renew locally, independently of circulating monocytes and HSCs. In contrast, adult blood monocytes as well as infiltrating, gut and dermal macrophages derive from Myb-dependent HSCs. These findings are derived from the mouse, using gene knock-outs and lineage tracing, but their applicability to human development has not been formally demonstrated. Here we use human induced pluripotent stem cells (iPSCs) as a tool to model human hematopoietic development. By using a CRISPR-Cas9 knock-out strategy we show that human iPSC-derived monocytes/macrophages develop in a MYB-independent, RUNX1 and SPI1 (PU.1)-dependent fashion. This result makes human iPSC-derived macrophages developmentally related to and a good model for MYB-independent tissue-resident macrophages such as alveolar and kidney macrophages, microglia, Kupffer and Langerhans cells. The human hiPSC-AH016-3 has been used for all CRISPR-Cas9 mediated gene targeting in this study. iPSC-AH016-3 has been targeted using a double nicking CRISPR-Cas9 strategy for the knock-out of MYB, SPI1 and RUNX1. Seven lines were generated: a WT control line which underwent CRISPR-Cas9 transfection and single cell cloning but is unmodified, 3 MYB double allele knock-outs, a MYB single allele knock-out, a SPI1 double allele knock-out and a RUNX1 double allele knock-out. SNP datasets were generated from knock-out and control lines. Note that the parental line AH016 clone 3 used as the target line in this current study, has been published previously therefore datasets are not given here [GSM2055806. Sandor C RP, Lang C, Heger A, Booth H, Vowles J, Witty L, Bowden R, Hu M, Cowley SA, Wade-Martins R, Webber C (2017) Transcriptomic profiling of purified patient-derived dopamine neurons identifies convergent perturbations and therapeutics for Parkinson’s disease. Human Molecular Genetics.]