iPSC-derived macrophages: the differentiation protocol affects cell immune and metabolic characteristics and differentiation trajectories

The generation of human macrophages from induced pluripotent stem cells (iMacs) is a rapidly developing approach used to create disease models, screen drugs, study macrophage-pathogen interactions and develop macrophage-based cell therapy. To generate iMacs, different types of protocols have been suggested, all thought to result in the generation of similar iMac populations. However, direct comparison of iMacs generated using different protocols has not been performed. We have compared the productivity, the differentiation trajectories and the characteristics of iMacs generated using two widely used protocols and found significant differences in: (i) protocol productivity; (ii) dynamic changes in the expression of genes related to inflammation and lipid homeostasis following iMac differentiation; and (iii) the transcriptomic profiles of terminally differentiated iMacs, including the expression of genes involved in inflammatory response (e.g., CCL2, CCL8, NLRP2), antigen presentation (e.g., HLA class II, CD74, CFSF) and lipid homeostasis (e.g., LDRL, MSR1, OLR1, RETN). The results document for the first time the dependence of fine iMac characteristics on the type of differentiation protocol, which is important for further development of the field and various iMac applications.