The phenotypic landscape of essential human genes

Luke Funk; Kuan-Chung Su; Jimmy Ly; David Feldman; Avtar Singh; Brittania Moodie; Paul C Blainey; Iain M Cheeseman

doi:10.1016/j.cell.2022.10.017

The phenotypic landscape of essential human genes

Cell. 2022 Nov 23;185(24):4634-4653.e22. doi: 10.1016/j.cell.2022.10.017. Epub 2022 Nov 7.

Authors

Luke Funk¹, Kuan-Chung Su², Jimmy Ly², David Feldman³, Avtar Singh³, Brittania Moodie², Paul C Blainey⁴, Iain M Cheeseman⁵

Affiliations

¹ Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA; Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
² Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
³ Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA.
⁴ Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA. Electronic address: pblainey@broadinstitute.org.
⁵ Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address: icheese@wi.mit.edu.

Abstract

Understanding the basis for cellular growth, proliferation, and function requires determining the roles of essential genes in diverse cellular processes, including visualizing their contributions to cellular organization and morphology. Here, we combined pooled CRISPR-Cas9-based functional screening of 5,072 fitness-conferring genes in human HeLa cells with microscopy-based imaging of DNA, the DNA damage response, actin, and microtubules. Analysis of >31 million individual cells identified measurable phenotypes for >90% of gene knockouts, implicating gene targets in specific cellular processes. Clustering of phenotypic similarities based on hundreds of quantitative parameters further revealed co-functional genes across diverse cellular activities, providing predictions for gene functions and associations. By conducting pooled live-cell screening of ∼450,000 cell division events for 239 genes, we additionally identified diverse genes with functional contributions to chromosome segregation. Our work establishes a resource detailing the consequences of disrupting core cellular processes that represents the functional landscape of essential human genes.

Keywords: CRISPR-Cas9; cell division; essential genes; functional genomics; high-content screening; in situ sequencing; microscopy; mitosis; morphology; optical pooled screening.

Publication types

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

MeSH terms

CRISPR-Cas Systems*
Gene Knockout Techniques
Genes, Essential*
HeLa Cells
Humans
Phenotype

Abstract

Publication types

MeSH terms

Grants and funding