A CRISPRi/a platform in human iPSC-derived microglia uncovers regulators of disease states

Microglia are emerging as key drivers of neurological diseases. However, we lack a systematic understanding of the underlying mechanisms. Here, we present a screening platform to systematically elucidate functional consequences of genetic perturbations in human induced pluripotent stem cell-derived...

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Published in:Nature neuroscience Vol. 25; no. 9; pp. 1149 - 1162
Main Authors: Dräger, Nina M, Sattler, Sydney M, Huang, Cindy Tzu-Ling, Teter, Olivia M, Leng, Kun, Hashemi, Sayed Hadi, Hong, Jason, Aviles, Giovanni, Clelland, Claire D, Zhan, Lihong, Udeochu, Joe C, Kodama, Lay, Singleton, Andrew B, Nalls, Mike A, Ichida, Justin, Ward, Michael E, Faghri, Faraz, Gan, Li, Kampmann, Martin
Format: Journal Article
Language:English
Published: United States Nature Publishing Group 01.09.2022
Subjects:
Brain - metabolism
Clustered Regularly Interspaced Short Palindromic Repeats - genetics
Colony-stimulating factor
CRISPR
Disease
Gene sequencing
Genes
Genomes
Humans
Induced Pluripotent Stem Cells - metabolism
Macrophage colony-stimulating factor
Microglia
Microglia - metabolism
Neurodegeneration
Neurological diseases
Osteopontin
Perturbation
Phagocytosis
Phagocytosis - genetics
Pluripotency
Stem cells
Therapeutic targets
Transcription activation
Transcription factors
ISSN:1097-6256, 1546-1726, 1546-1726
Online Access:Get full text
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Summary:Microglia are emerging as key drivers of neurological diseases. However, we lack a systematic understanding of the underlying mechanisms. Here, we present a screening platform to systematically elucidate functional consequences of genetic perturbations in human induced pluripotent stem cell-derived microglia. We developed an efficient 8-day protocol for the generation of microglia-like cells based on the inducible expression of six transcription factors. We established inducible CRISPR interference and activation in this system and conducted three screens targeting the 'druggable genome'. These screens uncovered genes controlling microglia survival, activation and phagocytosis, including neurodegeneration-associated genes. A screen with single-cell RNA sequencing as the readout revealed that these microglia adopt a spectrum of states mirroring those observed in human brains and identified regulators of these states. A disease-associated state characterized by osteopontin (SPP1) expression was selectively depleted by colony-stimulating factor-1 (CSF1R) inhibition. Thus, our platform can systematically uncover regulators of microglial states, enabling their functional characterization and therapeutic targeting.
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ISSN:1097-6256
1546-1726
1546-1726
DOI:10.1038/s41593-022-01131-4