Modelling Environment-Dependent Transcriptional Networks using hiPSC-derived Microglia
Nicole G. Coufal1, Dylan Skola2, Claudia Z. Han2, Inge R. Holtman2, Johannes C.M. Schlachetzki2, Monique Pena3, Yin Wu3, Abed Al Fattah Mansour3, Ken Diffenderfer4, Fred H. Gage3, and Christopher K. Glass2
1Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; 2Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA; 3Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037 USA; 4Stem Cell Core, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037 USA
Microglia play essential roles in central nervous system homeostasis, performing diverse functions that include modulation of synaptic networks, production of neuromodulatory factors, and effects on learning and memory. Our recent observation that the brain environment strongly influences human microglia-specific gene expression and regulatory landscapes has implications for understanding the microglial cell fate, signaling between cell types within the brain, and the pathogenic microglial response in disease. However, little is known about the brain-specific signals that regulate environmentally dependent microglial transcriptional network. We examined the environmental contribution to the microglial cell fate in several regards. Firstly, we compared human induced pluripotent stem cell (hiPSC)-derived microglial cells to primary human microglia using unbiased molecular outcomes including transcriptome analysis coupled with histone modifications and assays for chromosome accessibility. By comparing the enhancer repertoires and corresponding epigenetic landscapes of primary and hiPSC-derived microglia we explore the adequacy of hiPSC-derived microglia to model microglial transcriptional networks and pathology. Secondly, we investigated the role of conditioned media and complex cocultures in modulating the microglial transcriptome to replicate the brain-specific environment. Lastly, we manipulated expression of environmentally regulated transcription factors to probe their contribution to the microglial cell fate. These experiments not only inform gene-environment interactions of microglia but also improve hiPSC disease modeling and establish a map of functional enhancers and how they control gene expression.