CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions

Affiliations

¹ Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
² TETRAD Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
³ Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.
⁴ Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA.
⁵ Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
⁶ Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
⁷ Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA.
⁸ Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; FirstGen Internship, Emerson Collective, Palo Alto, CA, USA; University of California, Berkeley, Berkeley, CA, USA.
⁹ Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA. Electronic address: martin.kampmann@ucsf.edu.

PMID: 39814010
PMCID: PMC11886924 (available on 2026-03-05)
DOI: 10.1016/j.neuron.2024.12.016

CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions

Emmy Li et al. Neuron. 2025.

. 2025 Mar 5;113(5):701-718.e8.

doi: 10.1016/j.neuron.2024.12.016. Epub 2025 Jan 14.

Authors

Affiliations

¹ Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
² TETRAD Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
³ Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.
⁴ Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA.
⁵ Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
⁶ Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
⁷ Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA.
⁸ Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; FirstGen Internship, Emerson Collective, Palo Alto, CA, USA; University of California, Berkeley, Berkeley, CA, USA.
⁹ Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA. Electronic address: martin.kampmann@ucsf.edu.

PMID: 39814010
PMCID: PMC11886924 (available on 2026-03-05)
DOI: 10.1016/j.neuron.2024.12.016

Abstract

The complexity of the human brain makes it challenging to understand the molecular mechanisms underlying brain function. Genome-wide association studies have uncovered variants associated with neurological phenotypes. Single-cell transcriptomics have provided descriptions of changes brain cells undergo during disease. However, these approaches do not establish molecular mechanism. To facilitate the scalable interrogation of causal molecular mechanisms in brain cell types, we developed a 3D co-culture system of induced pluripotent stem cell (iPSC)-derived neurons and glia, termed iAssembloids. Using iAssembloids, we ask how glial and neuronal cells interact to control neuronal death and survival. Our CRISPRi-based screens identified that GSK3β inhibits the protective NRF2-mediated oxidative stress response elicited by high neuronal activity. We then investigate the role of APOE-ε4, a risk variant for Alzheimer's disease, on neuronal survival. We find that APOE-ε4-expressing astrocytes may promote neuronal hyperactivity as compared with APOE-ε3-expressing astrocytes. This platform allows for the unbiased identification of mechanisms of neuron-glia cell interactions.

Keywords: APOE; CRISPR interference; CROP-seq; GSK3B; NFE2L2; essential genes; functional genomics; neuron-glia co-culture; neuronal activity; oxidative stress.

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Conflict of interest statement

Declaration of interests M.K. is a co-scientific founder of Montara Therapeutics; serves on the Scientific Advisory Boards of Engine Biosciences, Casma Therapeutics, Alector, and Montara Therapeutics; and is an advisor to Modulo Bio and Recursion Therapeutics. M.K. is an inventor on US Patent 11,254,933 related to CRISPRi and CRISPRa screening and on a US Patent application on in vivo screening methods.

Update of

CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions.
Li E, Benitez C, Boggess SC, Koontz M, Rose IVL, Martinez D, Draeger N, Teter OM, Samelson AJ, Pierce N, Ullian EM, Kampmann M. Li E, et al. bioRxiv [Preprint]. 2024 Nov 24:2023.04.26.538498. doi: 10.1101/2023.04.26.538498. bioRxiv. 2024. Update in: Neuron. 2025 Mar 05;113(5):701-718.e8. doi: 10.1016/j.neuron.2024.12.016. PMID: 37163077 Free PMC article. Updated. Preprint.

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CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions

Affiliations

CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions

Authors

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Abstract

Conflict of interest statement

Update of

References

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