iPSC-Derived Microglia-like Cells Exhibit Protocol-Dependent Transcriptomic Features and Robust Phagocytosis of
Maya N Walker1, Hui Tang2, Caylee Silvers1
1The Ken & Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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.
Insights
Induced pluripotent stem cell-derived microglia (iMG) models show promise for studying brain tumors. This study benchmarks iMG protocols, finding an embryoid body method best models microglia-glioma interactions.
Area of Science:
- Neuroscience
- Immunology
- Stem Cell Biology
Background:
- Microglia are crucial regulators of the brain tumor microenvironment.
- Induced pluripotent stem cell-derived microglia (iMG) offer a model for human microglia research.
- Limited systematic comparisons exist for iMG differentiation protocols and their use in microglia-tumor studies.
Purpose of the Study:
- To systematically compare transcriptomic profiles of iMG generated by various differentiation protocols.
- To evaluate the utility of different iMG models for studying microglia-glioma interactions.
- To establish a benchmark for iMG models in cancer research.
Main Methods:
- Analysis of 54 public RNA-seq datasets from 22 iMG differentiation protocols (EB-based, 2D, transcription factor-induced, coculture).
- Transcriptomic profiling and comparison of iMG populations.
- Functional assessment of iMG phagocytosis and inflammatory response using patient-derived glioma stem-like cells.
Main Results:
- Most iMG models closely resembled primary human microglia, with protocol-dependent variations observed.
- Embryoid body (EB)-based protocols yielded iMG with higher TMEM119 expression, while 2D protocols showed higher P2RY12 expression.
- A specific EB-based protocol demonstrated superior phagocytosis gene signatures and enabled iMG to phagocytose glioma cells, upregulating immune response genes.
Conclusions:
- Transcriptomic analysis provides a benchmark for evaluating iMG differentiation protocols.
- The optimized EB-based protocol effectively models microglia-glioma interactions.
- iMG models are valuable tools for investigating the role of microglia in glioma pathogenesis and response.
