Essential Gene Profiles for Human Pluripotent Stem Cells Identify Uncharacterized Genes and Substrate Dependencies
Barbara Mair,
Jelena Tomic,
Sanna N. Masud,
Peter Tonge,
Alexander Weiss,
Matej Usaj,
Amy Hin Yan Tong,
Jamie J. Kwan,
Kevin R. Brown,
Emily Titus,
Michael Atkins,
Katherine S.K. Chan,
Lise Munsie,
Andrea Habsid,
Hong Han,
Marion Kennedy,
Brenda Cohen,
Gordon Keller,
Jason Moffat
Affiliations
Barbara Mair
Donnelly Centre, University of Toronto, Toronto, ON, Canada
Jelena Tomic
Donnelly Centre, University of Toronto, Toronto, ON, Canada
Sanna N. Masud
Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
Peter Tonge
Centre for Commercialization of Regenerative Medicine, Toronto, ON, Canada
Alexander Weiss
Donnelly Centre, University of Toronto, Toronto, ON, Canada
Matej Usaj
Donnelly Centre, University of Toronto, Toronto, ON, Canada
Amy Hin Yan Tong
Donnelly Centre, University of Toronto, Toronto, ON, Canada
Jamie J. Kwan
McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
Kevin R. Brown
Donnelly Centre, University of Toronto, Toronto, ON, Canada
Emily Titus
Centre for Commercialization of Regenerative Medicine, Toronto, ON, Canada
Michael Atkins
McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
Katherine S.K. Chan
Donnelly Centre, University of Toronto, Toronto, ON, Canada
Lise Munsie
Centre for Commercialization of Regenerative Medicine, Toronto, ON, Canada
Andrea Habsid
Donnelly Centre, University of Toronto, Toronto, ON, Canada
Hong Han
Donnelly Centre, University of Toronto, Toronto, ON, Canada
Marion Kennedy
McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
Brenda Cohen
McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
Gordon Keller
McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
Jason Moffat
Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Canadian Institute for Advanced Research, Toronto, ON, Canada; Institute for Biomaterials and BioMedical Engineering, University of Toronto, ON, Canada; Corresponding author
Summary: Human pluripotent stem cells (hPSCs) provide an invaluable tool for modeling diseases and hold promise for regenerative medicine. For understanding pluripotency and lineage differentiation mechanisms, a critical first step involves systematically cataloging essential genes (EGs) that are indispensable for hPSC fitness, defined as cell reproduction in this study. To map essential genetic determinants of hPSC fitness, we performed genome-scale loss-of-function screens in an inducible Cas9 H1 hPSC line cultured on feeder cells and laminin to identify EGs. Among these, we found FOXH1 and VENTX, genes that encode transcription factors previously implicated in stem cell biology, as well as an uncharacterized gene, C22orf43/DRICH1. hPSC EGs are substantially different from other human model cell lines, and EGs in hPSCs are highly context dependent with respect to different growth substrates. Our CRISPR screens establish parameters for genome-wide screens in hPSCs, which will facilitate the characterization of unappreciated genetic regulators of hPSC biology. : Mair et al. establish a robust, inducible CRISPR screening platform for forward genetics in human pluripotent stem cells (hPSCs). Genome-wide proliferation screens identified core essential genes for hPSCs and revealed context-dependent genetic requirements on different substrates. This underlines hPSC plasticity and helps us to understand the genetic wiring of hPSCs. Keywords: human pluripotent stem cells, genome-wide CRISPR screen, functional genomics, essential genes, DRICH1
