Supporting data for "Identifying genetic vulnerabilities in patient-derived gastric cancer organoids by CRISPR-Cas9 screening"

Identifying vulnerabilities for the many tumor subtypes to devise precision treatment strategies remains a challenging task. CRISPR screens facilitate the discovery of cancer vulnerabilities that can be exploited therapeutically, but screening has been limited to two-dimensional (2D) monolayer cell line culture that does not recapitulate in vivo environment. Here we establish the CRISPR dropout screening pipeline in patient-derived gastric cancer organoids. Our organoid-based CRISPR subpool library screens uncover common and differential vulnerabilities in a panel of organoids derived from patients with distinct gastric cancer subtypes. We then extend the CRISPR dropout screening to a genome-wide scale and exemplify organoid-dependent vulnerabilities with metabolic regulators as prioritized targets that are not revealed when using 2D and even three-dimensional (3D) spheroid cultures of cell lines. We further demonstrate the in vivo relevance of metabolic vulnerability identified using tumor organoids. Together, our work underscores the power of utilizing organoid-based CRISPR dropout screening for revealing more clinically relevant vulnerabilities, paving way to the development of precision therapeutic treatments.