KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease
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Understanding transcriptional regulatory networks (TRNs) in microglia is key to uncovering mechanisms driving central nervous system (CNS) disorders. Human iPSC-derived models offer a tractable system for studying microglia, yet variability between lines has limited reproducibility. Here, we use the standardized KOLF2.1J iTF line to rapidly generate microglia-like cells (iTF-Microglia) and profile TRNs under homeostatic and inflammatory conditions. iTF-Microglia closely resemble primary brain microglia at both transcriptomic and epigenomic levels. Integrative analyses reveal microglia-enriched candidate cis -regulatory elements (cCREs) and dynamic enhancer remodeling upon differentiation and LPS+IFNG stimulation, involving key transcription factors (TFs) including NF-κB, IRF, and STAT families. TRNs active in iTF-Microglia are enriched for genetic variants linked to Alzheimer’s disease and other CNS disorders. These findings establish KOLF2.1J iTF-Microglia as a reproducible and genetically tractable platform for studying human microglial gene regulation and provide mechanistic insight into how TRN remodeling may contribute to CNS disease risk.
