CRISPR screens in physiologic medium reveal conditionally essential genes in human cells

Nicholas J Rossiter; Kimberly S Huggler; Charles H Adelmann; Heather R Keys; Ross W Soens; David M Sabatini; Jason R Cantor

doi:10.1016/j.cmet.2021.02.005

CRISPR screens in physiologic medium reveal conditionally essential genes in human cells

Cell Metab. 2021 Jun 1;33(6):1248-1263.e9. doi: 10.1016/j.cmet.2021.02.005. Epub 2021 Mar 1.

Authors

Nicholas J Rossiter¹, Kimberly S Huggler², Charles H Adelmann³, Heather R Keys⁴, Ross W Soens², David M Sabatini⁵, Jason R Cantor⁶

Affiliations

¹ Morgridge Institute for Research, Madison, WI 53715, USA.
² Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
³ Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁴ Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
⁵ Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: sabatini@wi.mit.edu.
⁶ Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; University of Wisconsin Carbone Cancer Center, Madison, WI 53705, USA. Electronic address: jcantor@morgridge.org.

Abstract

Forward genetic screens across hundreds of cancer cell lines have started to define the genetic dependencies of proliferating human cells and how these vary by genotype and lineage. Most screens, however, have been carried out in culture media that poorly reflect metabolite availability in human blood. Here, we performed CRISPR-based screens in traditional versus human plasma-like medium (HPLM). Sets of conditionally essential genes in human cancer cell lines span several cellular processes and vary with both natural cell-intrinsic diversity and the combination of basal and serum components that comprise typical media. Notably, we traced the causes for each of three conditional CRISPR phenotypes to the availability of metabolites uniquely defined in HPLM versus conventional media. Our findings reveal the profound impact of medium composition on gene essentiality in human cells, and also suggest general strategies for using genetic screens in HPLM to uncover new cancer vulnerabilities and gene-nutrient interactions.

Keywords: CRISPR; HPLM; conditional gene essentiality; gene-nutrient interaction; genetic screen; physiologic medium.

Publication types

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

MeSH terms

CRISPR-Cas Systems*
Cell Line, Tumor
Culture Media*
Humans

Substances

Culture Media

Abstract

Publication types

MeSH terms

Substances

Grants and funding