Genome-Scale CRISPR Screens Identify Human Pluripotency-Specific Genes

Abstract

Summary: Human pluripotent stem cells (hPSCs) generate a variety of disease-relevant cells that can be used to improve the translation of preclinical research. Despite the potential of hPSCs, their use for genetic screening has been limited by technical challenges. We developed a scalable and renewable Cas9 and sgRNA-hPSC library in which loss-of-function mutations can be induced at will. Our inducible mutant hPSC library can be used for multiple genome-wide CRISPR screens in a variety of hPSC-induced cell types. As proof of concept, we performed three screens for regulators of properties fundamental to hPSCs: their ability to self-renew and/or survive (fitness), their inability to survive as single-cell clones, and their capacity to differentiate. We identified the majority of known genes and pathways involved in these processes, as well as a plethora of genes with unidentified roles. This resource will increase the understanding of human development and genetics. This approach will be a powerful tool to identify disease-modifying genes and pathways. : Ihry et al. develop a CRISPR/Cas9 genetic screening platform for hPSCs that enables unbiased genome-scale genetic screening. The platform exhibits high performance and accurately detects the dropout of essential genes. Furthermore, proof-of-concept screens exploit hPSC-specific phenotypes to identify regulators of fitness, survival after single-cell dissociation, and pluripotency. Keywords: CRISPR genome-wide screening, human pluripotent stem cells, iPSC, hESC, PAWR, PMAIP1, DDR