Fig. 6: Effect on macrophage differentiation of ICAM1, LSP1, PRKCB and ZEB2 KO.

a (left) Schematic illustration of the in vitro differentiation protocols from iPSC to macrophages (MAC, top) or dendritic cells (DC, bottom) used to evaluate the effects of ICAM1, LSP1, PRKCB or ZEB2 knock-outs (KO). Samples were collected at day0 and day31 of the protocols and profiled with scRNAseq. (right) Computational workflow diagram for cell type annotation. Briefly, cell type annotations were transferred from scRNAseq data of the macrophages (Discovery data set) and DC protocols described in the previous sections. b UMAP projections of scRNAseq data from both KO protocols labelled by time point. c UMAP projections of scRNAseq data generated from the iPSC-to-macrophages KO protocol (one UMAP per KO and wild type) coloured by cell type. d UMAP projections of scRNAseq data generated from the iPSC-to-DC KO protocol (one UMAP per KO plus wild type) coloured by cell type. e Dot plot showing the average expression of intermediate monocyte–associated genes in the monocytes produced by each KO and the wild type in the iPSC-to-DC protocol. f Dot plot showing the average expression of genes associated to myeloid-derived suppressor cells in the monocytes produced by each KO and the wild type in the iPSC-to-DC protocol. g (left) Dot plot showing the average expression of M2-associated genes in the macrophages produced by each KO and the wild type in the iPSC-to-macrophages protocol. (right) Transcription factor activities computed with DoRothEA for macrophages produced by each KO and the wild type.