Importantly, iMGLs, Fetal MG, and Adult MG express canonical microglial genes such as P2RY12, GPR34, C1Q, CABLES1, BHLHE41, TREM2, ITAM PROS1, APOE, SLCO2B1, SLC7A8, PPARD, and CRYBB1 (Figure 2C and Table S1). When compared to monocytes, iMGLs express the myeloid genes, RUNX1, PU.1, and CSF1R (Figure S3C), but do not express monocyte-specific transcription factors, IRF1, KLF4, NR4A1 (Abdollahi et al., 1991; Hanna et al., 2011; Lavin et al., 2014) (Figure S3D). Differential analysis between iMGLs, CD14 M, and CD16 M (Figure S3F) further emphasized that iMGLs predominantly express microglial genes (greater than two-fold change and p<0.001) including CX3CR1, TGFBR1, RGS10, and GAS6, but not monocyte and macrophage genes KLF2, TREM1, MPO, ITGAL, and ADGRE5. At the protein level, iMGLs, like primary microglia, are CD45lo compared to CD45hi MD-Mφ, and express the microglia surface proteins Cx3cr1, Tgfbr1, P2ry12 and Pros1 (Figures S2A and S4A). Collectively, unbiased whole-transcriptome analysis and protein expression of key microglial markers strongly establishes iMGLs as a cell model that highly resembles primary human microglia that can be used to study microglia physiology and function in human health and disease.
