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bioRxiv · 10.64898/2026.07.21.739939

iPSC-Derived Microglia-like Cells Exhibit Protocol-Dependent Transcriptomic Features and Robust Phagocytosis of Glioma Cells

Walker, M. N.·Tang, H.·Silvers, C.·Roth, S.·Tiek, D.·Hu, B.·Cheng, S.-Y.·Song, X.
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Abstract

Microglia are the brain-resident macrophages and key regulators of the brain tumor microenvironment. Although induced pluripotent stem cell-derived microglia (iMG) provide a valuable model for studying human microglial, systematic comparisons of differentiation protocols are limited, and their utility for modeling microglia-tumor cell interactions remains underexplored. Here, we analyzed 54 public RNA-seq datasets representing 22 iMG differentiation protocols, including embryoid body (EB)-based, two-dimensional (2D), transcription factor-induced, and coculture-based approaches. Most iMG closely resembled primary human microglia, although substantial protocol-dependent differences were observed. iMG generated using EB-based protocols showed higher TMEM119 expression, whereas those generated using 2D-based protocols showed higher P2RY12 expression. A widely adopted EB-based protocol showed the highest phagocytosis gene signature. Using this protocol, we generated iMG that efficiently phagocytosed patient-derived glioma stem-like cells and upregulated inflammatory and immunoregulatory genes following phagocytosis. These findings provide a transcriptomic benchmark for current iMG models and support their use in investigating microglia-glioma interactions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/739939v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@893ebforg.highwire.dtl.DTLVardef@769c08org.highwire.dtl.DTLVardef@fe06ccorg.highwire.dtl.DTLVardef@1705d70_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Walker, M. N., Tang, H., Silvers, C., Roth, S., Tiek, D., Hu, B., Cheng, S.-Y., Song, X.. 2026-07-22. iPSC-Derived Microglia-like Cells Exhibit Protocol-Dependent Transcriptomic Features and Robust Phagocytosis of Glioma Cells. https://doi.org/10.64898/2026.07.21.739939

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