CRISPRi-based screen of autism spectrum disorder risk genes in microglia uncovers roles of ADNP in microglia endocytosis and synaptic pruning
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Autism Spectrum Disorders (ASD) are a set of neurodevelopmental disorders with complex biology. The identification of ASD risk genes from exome-wide association studies and de novo variation analyses has enabled mechanistic investigations into how ASD-risk genes alter development. Most functional genomics studies have focused on the role of these genes in neurons and neural progenitor cells. However, roles for ASD risk genes in other cell types are largely uncharacterized. There is evidence from postmortem tissue that microglia, the resident immune cells of the brain, appear activated in ASD. Here, we used CRISPRi-based functional genomics to systematically assess the impact of ASD risk gene knockdown on microglia activation and phagocytosis. We developed an iPSC-derived microglia-neuron coculture system and high-throughput flow cytometry readout for synaptic pruning to enable parallel CRISPRi-based screening of phagocytosis of beads, synaptosomes, and synaptic pruning. Our screen identified ADNP, a high-confidence ASD risk genes, as a modifier of microglial synaptic pruning. We found that microglia with ADNP loss have altered endocytic trafficking, remodeled proteomes, and increased motility in coculture.
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SHIP1 negatively regulates myeloid cell proliferation.
“previous reports showing that SHIP1 negatively regulates myeloid cell proliferation52,53.”
From INPP5D/SHIP1 regulates endo-lysosomal function and cargo-selective phagocytosis in human microglia (2025) · cites this paper as [53]
The Results passages in our copy discuss ADNP knockdown and microglial activation, but do not address whether SHIP1 regulates myeloid-cell proliferation. Searches for “SHIP1 negatively regulates myeloid cell proliferation” and “SHIP1 INPP5D proliferation” found no passage supporting that point. No page numbers were provided for the indexed passages. (LLM, conf=0.72)
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- Authors
- Teter, O. M., McQuade, A., Hagan, V., Liang, W., Dräger, N. M., Sattler, S. M., Holmes, B. B., Castillo, V. C., Papakis, V., Leng, K., Boggess, S., Nowakowski, T. J., Wells, J., & Kampmann, M.
- Affiliations
- University of California, San Francisco (US)
- Corresponding author
- Kampmann, Martin
- ORCID
- Venue
- Molecular Psychiatry
- Published
- 2025-04-06
- Volume
- 30
- Issue
- 9
- Pages
- 4176-4193
- ISSN
- 1359-4184 (ISSN-L)
- 1476-5578
- PMC
- PMC12339388
- OpenAlex
- W4409190508
- Cited by
- 38
- References
- 62
- Citations by year
- 2026: 30 · 2025: 7 · 2024: 1
- FWCI
- 13.35
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Molecular Psychiatry (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by)
- Funders
- U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (U01 MH115747, R01 MH125516)
- National Science Foundation (2034836)
- Alzheimer's Association (AARF-22-973222)
- Larry L. Hillblom Foundation (2022-A-016-FEL)
- Topics
- Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- autism spectrum disorder, ASD risk genes, microglia, ADNP, synaptic pruning, microglial phagocytosis, microglial motility, microglial activation
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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