Rapid characterization of candidate loss of function genes in primary organoid culture.

77 Background: Genome scale sequencing efforts have identified chromosomal deletions and non-synonymous mutations as putative drivers of gastro-intestinal cancer. There is a need to rapidly validate these drivers in robust models. The culture of primary, non-transformed tissues in vitro as three-dimensional organoids that accurately recapitulate organ structure and physiology serves as an ideal model for such validation, and many other applications in biology. Methods: Mouse wild type and p53 flox/flox upper digestive tract tissue containing epithelial and mesenchymal components were cultured in an air-liquid interface and subjected to adenovirus expressing either a functional control or Cre recombinase. Resultant organoids were passaged at confluency until dysplasia was evident in histology. A lentiviral shRNA (loss-of-function) screen was then conducted, where proliferative activity was measured with barcode reads from the pooled library. Results: p53-null organoids showed histology consistent with human gastrointestinal cancer. These organoids were also able to form small tumors when injected subcutaneously into immune-deficient mice. The pooled lentiviral shRNA screen functionally validated candidate drivers. Conclusions: Gastrointestinal organoids are a suitable model for the introduction of oncogenic mutations in a tractable and replicable format. In future work we will validate loss-of function and gain-of-function screens with CRISPRi/a libraries, and replicate these screens in human gastrointestinal organoids.