CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer’s disease

Genetic variants associated with complex traits often lie in distal enhancers. While candidate enhancers have been mapped genome wide, their functional state and gene targets in specific cell types remain unclear. Here we present AstroREG, a resource of enhancer-gene interactions in human primary astrocytes, generated by combining CRISPR inhibition (CRISPRi), single-cell RNA-seq and machine learning. By functionally testing nearly 1,000 PsychENCODE enhancers, we identified more than 150 regulatory interactions, revealing enhancers that control key astrocyte functions and genes implicated in Alzheimer's disease. The CRISPRi screen also provided valuable ground-truth data from a primary cell type for training and benchmarking prediction models of enhancer activity. We thus developed EGrf, a random forest (RF) model trained on these data, and applied it genome wide to predict regulatory interactions with high specificity. Together, our data provide a comprehensive functional map of enhancer-mediated regulation in a key glial cell type, shedding light on brain function and disease.

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Publication Details

Journal
Nature Neuroscience
Published
2025-12-18
DOI
https://doi.org/10.1038/s41593-025-02154-3
Citations
2
Primary Topic
Single-cell and spatial transcriptomics
Type
article
Field-Weighted Citation Impact
1.61
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CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer’s disease

Kieran Walsh, Sébastien Bagot, Akira Gokoolparsadh, Guang Yang et al.
2 citations
Nature Neuroscience
Single-cell and spatial transcriptomics
1.61
article

CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer’s disease

Kieran Walsh, Sébastien Bagot, Akira Gokoolparsadh, Guang Yang, Gavin J Sutton, Vladimir Sytnyk, Joseph Rosenbluh, Irina Voineagu, J. Wang, Ryan Lister, Nicole F. Oldham Green, Javier Pérez‐Burillo, Hamid Alinejad-Rokny, Johann A. Gagnon-Bartsch, Charles A. Herring, Grant Pfundstein, Yuheng Liang, Steve Miles, Hannah G Danon
article en
2 citations

Abstract

Genetic variants associated with complex traits often lie in distal enhancers. While candidate enhancers have been mapped genome wide, their functional state and gene targets in specific cell types remain unclear. Here we present AstroREG, a resource of enhancer-gene interactions in human primary astrocytes, generated by combining CRISPR inhibition (CRISPRi), single-cell RNA-seq and machine learning. By functionally testing nearly 1,000 PsychENCODE enhancers, we identified more than 150 regulatory interactions, revealing enhancers that control key astrocyte functions and genes implicated in Alzheimer's disease. The CRISPRi screen also provided valuable ground-truth data from a primary cell type for training and benchmarking prediction models of enhancer activity. We thus developed EGrf, a random forest (RF) model trained on these data, and applied it genome wide to predict regulatory interactions with high specificity. Together, our data provide a comprehensive functional map of enhancer-mediated regulation in a key glial cell type, shedding light on brain function and disease.

Nature NeuroscienceVol. 29(3)
The University of Western Australia (AU), University of Michigan (US), Discovery Institute (US), Harry Perkins Institute of Medical Research (AU), UNSW Sydney (AU), Queen Elizabeth II Medical Centre (AU), ARC Centre of Excellence in Plant Energy Biology (AU), New South Wales Institute of Psychiatry (AU), Sydney Institute of Marine Science (AU), Macquarie University (AU)
Openalex Percentile: Top 14%
Single-cell and spatial transcriptomics
1.61
DOIOpen Access PDFOpenAlex
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