Forward genetic screening in engineered colorectal cancer organoids identifies novel regulators of metastasis

Cancer is the second leading cause of death globally, and this is due primarily to metastatic dissemination to distal sites. Metastatic outgrowth requires that cancer cells delaminate from the primary tumor, intravasate, survive in circulation, extravasate, then migrate to and proliferate at a distal site. Recurrent genetic drivers of metastasis have remained elusive, suggesting that, unlike the initial steps of oncogenic transformation and primary tumor development, drivers of metastasis may be variable. Here, we develop a framework for interrogating pathways governing metastasis by applying CRISPR/Cas9-based forward genetic screening in a genetically defined tumor-organoid model of colorectal adenocarcinoma. We conduct in vitro screens for invasion and migration alongside orthotopic, in vivo screens for gain of metastatic potential in a syngeneic mouse model, identifying suppressors of metastasis both unique to the in vivo setting as well as common to both models. Specifically, we identify Ctnna1 and Bcl2l13 as bona fide metastasis suppressors acting through distinct mechanisms, with CTNNA1 loss promoting carcinoma cell invasion and migration through an atypical EMT-like mechanism, and BCL2L13 loss promoting cell survival after extracellular matrix detachment and non-cell-autonomous changes to macrophage polarization. Ultimately, this study provides a proof-of-principle that high-content forward genetic screening can be performed in tumor-organoid models in vivo and identifies novel regulators of colon cancer metastasis. Overall design: Engineered colorectal adenocarcinoma organoids expressing a control or Bcl2l13-targeted sgRNA were implanted into the ceca syngeneic mice. 2 replicate primary tumors from both genotypes were isolated and subjected to scRNA-seq. 2 liver metatases were isolated from sgBcl2l13-implanted mice. Control sgRNA cells were used as reference