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Han CZ, Li RZ, Hansen E, Trescott S, Fixsen BR, Nguyen CT, Mora CM, Spann NJ, Bennett HR, Poirion O, Buchanan J, Warden AS, Xia B, Schlachetzki JCM, Pasillas MP, Preissl S, Wang A, O'Connor C, Shriram S, Kim R, Schafer D, Ramirez G, Challacombe J, Anavim SA, Johnson A, Gupta M, Glass IA, Levy ML, Haim SB, Gonda DD, Laurent L, Hughes JF, Page DC, Blurton-Jones M, Glass CK, Coufal NG. Human microglia maturation is underpinned by specific gene regulatory networks. Immunity 2023; 56:2152-2171.e13. [PMID: 37582369 PMCID: PMC10529991 DOI: 10.1016/j.immuni.2023.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/11/2023] [Accepted: 07/21/2023] [Indexed: 08/17/2023]
Abstract
Microglia phenotypes are highly regulated by the brain environment, but the transcriptional networks that specify the maturation of human microglia are poorly understood. Here, we characterized stage-specific transcriptomes and epigenetic landscapes of fetal and postnatal human microglia and acquired corresponding data in induced pluripotent stem cell (iPSC)-derived microglia, in cerebral organoids, and following engraftment into humanized mice. Parallel development of computational approaches that considered transcription factor (TF) co-occurrence and enhancer activity allowed prediction of shared and state-specific gene regulatory networks associated with fetal and postnatal microglia. Additionally, many features of the human fetal-to-postnatal transition were recapitulated in a time-dependent manner following the engraftment of iPSC cells into humanized mice. These data and accompanying computational approaches will facilitate further efforts to elucidate mechanisms by which human microglia acquire stage- and disease-specific phenotypes.
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Affiliation(s)
- Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rick Z Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily Hansen
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Samantha Trescott
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Bethany R Fixsen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Celina T Nguyen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Cristina M Mora
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hunter R Bennett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olivier Poirion
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Justin Buchanan
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anna S Warden
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Bing Xia
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Martina P Pasillas
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sebastian Preissl
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Allen Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Shreya Shriram
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Roy Kim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Danielle Schafer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Gabriela Ramirez
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Jean Challacombe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samuel A Anavim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Avalon Johnson
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Mihir Gupta
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ian A Glass
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA
| | - Michael L Levy
- Department of Neurosurgery, University of California, San Diego-Rady Children's Hospital, San Diego, CA 92123, USA
| | - Sharona Ben Haim
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - David D Gonda
- Department of Neurosurgery, University of California, San Diego-Rady Children's Hospital, San Diego, CA 92123, USA
| | - Louise Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92696, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Nicole G Coufal
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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