Natural variation in gene expression and viral susceptibility revealed by neural progenitor cell villages

Michael F Wells; James Nemesh; Sulagna Ghosh; Jana M Mitchell; Max R Salick; Curtis J Mello; Daniel Meyer; Olli Pietilainen; Federica Piccioni; Ellen J Guss; Kavya Raghunathan; Matthew Tegtmeyer; Derek Hawes; Anna Neumann; Kathleen A Worringer; Daniel Ho; Sravya Kommineni; Karrie Chan; Brant K Peterson; Joseph J Raymond; John T Gold; Marco T Siekmann; Emanuela Zuccaro; Ralda Nehme; Ajamete Kaykas; Kevin Eggan; Steven A McCarroll

doi:10.1016/j.stem.2023.01.010

Natural variation in gene expression and viral susceptibility revealed by neural progenitor cell villages

Cell Stem Cell. 2023 Mar 2;30(3):312-332.e13. doi: 10.1016/j.stem.2023.01.010. Epub 2023 Feb 15.

Authors

Michael F Wells¹, James Nemesh², Sulagna Ghosh², Jana M Mitchell³, Max R Salick⁴, Curtis J Mello², Daniel Meyer², Olli Pietilainen⁵, Federica Piccioni⁶, Ellen J Guss⁷, Kavya Raghunathan⁵, Matthew Tegtmeyer⁸, Derek Hawes⁸, Anna Neumann⁸, Kathleen A Worringer⁹, Daniel Ho⁹, Sravya Kommineni⁹, Karrie Chan⁹, Brant K Peterson⁹, Joseph J Raymond⁹, John T Gold¹⁰, Marco T Siekmann⁷, Emanuela Zuccaro⁷, Ralda Nehme⁵, Ajamete Kaykas⁴, Kevin Eggan¹¹, Steven A McCarroll¹²

Affiliations

¹ Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
² Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
³ Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Insitro, South San Francisco, CA 94080, USA.
⁴ Insitro, South San Francisco, CA 94080, USA.
⁵ Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
⁶ Genetic Perturbation Platform, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA.
⁷ Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
⁸ Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA.
⁹ Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA.
¹⁰ Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Biology, Davidson College, Davidson, NC 28035, USA.
¹¹ Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA. Electronic address: kevin.eggan@bmrn.com.
¹² Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: smccarro@broadinstitute.org.

Abstract

Human genome variation contributes to diversity in neurodevelopmental outcomes and vulnerabilities; recognizing the underlying molecular and cellular mechanisms will require scalable approaches. Here, we describe a "cell village" experimental platform we used to analyze genetic, molecular, and phenotypic heterogeneity across neural progenitor cells from 44 human donors cultured in a shared in vitro environment using algorithms (Dropulation and Census-seq) to assign cells and phenotypes to individual donors. Through rapid induction of human stem cell-derived neural progenitor cells, measurements of natural genetic variation, and CRISPR-Cas9 genetic perturbations, we identified a common variant that regulates antiviral IFITM3 expression and explains most inter-individual variation in susceptibility to the Zika virus. We also detected expression QTLs corresponding to GWAS loci for brain traits and discovered novel disease-relevant regulators of progenitor proliferation and differentiation such as CACHD1. This approach provides scalable ways to elucidate the effects of genes and genetic variation on cellular phenotypes.

Keywords: CACHD1; CRISPR-Cas9 screen; Neurogenin-2; Zika virus; cell villages; neural progenitor cells; neurodevelopmental disorders; proliferation.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Brain / metabolism
Cell Differentiation / genetics
Gene Expression
Humans
Membrane Proteins / metabolism
Neural Stem Cells* / metabolism
RNA-Binding Proteins / metabolism
Zika Virus Infection*
Zika Virus* / metabolism

Substances

IFITM3 protein, human
Membrane Proteins
RNA-Binding Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding