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

doi:10.1016/j.celrep.2019.02.041

Essential Gene Profiles for Human Pluripotent Stem Cells Identify Uncharacterized Genes and Substrate Dependencies

Cell Rep. 2019 Apr 9;27(2):599-615.e12. doi: 10.1016/j.celrep.2019.02.041.

Authors

Barbara Mair¹, Jelena Tomic¹, Sanna N Masud², Peter Tonge³, Alexander Weiss¹, Matej Usaj¹, Amy Hin Yan Tong¹, Jamie J Kwan⁴, Kevin R Brown¹, Emily Titus³, Michael Atkins⁵, Katherine S K Chan¹, Lise Munsie³, Andrea Habsid¹, Hong Han¹, Marion Kennedy⁴, Brenda Cohen⁴, Gordon Keller⁵, Jason Moffat⁶

Affiliations

¹ Donnelly Centre, University of Toronto, Toronto, ON, Canada.
² Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
³ Centre for Commercialization of Regenerative Medicine, Toronto, ON, Canada.
⁴ 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.
⁵ 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.
⁶ 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. Electronic address: j.moffat@utoronto.ca.

PMID: 30970261
DOI: 10.1016/j.celrep.2019.02.041

Abstract

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.

Keywords: DRICH1; essential genes; functional genomics; genome-wide CRISPR screen; human pluripotent stem cells.

Publication types

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

MeSH terms

Cell Differentiation
Clustered Regularly Interspaced Short Palindromic Repeats / genetics*
Gene Expression Regulation / genetics*
Genes, Essential / genetics*
Humans
Pluripotent Stem Cells / metabolism*

Grants and funding

MOP-142375/CIHR/Canada