Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a five-year survival below 15% in Australia. The poor prognosis is due to a combination of late detection and lack of effective treatments. Most patients are diagnosed with advanced diseases, where cytotoxic chemotherapy is the only modality to prolong survival. FOLFIRINOX is currently the most efficacious and commonly used regimen in PDAC, but most patients rapidly develop resistance and relapse within a short period of time. Chemoresistance is a major bottleneck towards improving the survival outcome of PDAC patients, but the underpinning mechanisms are poorly understood. This highlights the usefulness of unbiased, systemic exploration of the resistance mechanisms to be able to improve the efficacy of our current chemotherapeutic regimen.
To perform this analysis at scale whilst accurately recapitulating the disease, we used patient derived organoids (PDOs) established from chemo-naive surgical or biopsy samples. This three-dimensional system is considered physiologically relevant and allows us to maintain key signatures of the original tumour.
Aiming to identify genes crucial for the survival of PDAC cells under FOLFIRINOX, we performed a whole genome CRISPR-Cas9 loss of function screen under chemotherapeutic pressure using PDOs. In the primary screen, 19114 genes were invalidated individually in PDOs derived from a primary PDAC tumour. Genes whose invalidation sensitised PDAC cells to FOLFIRINOX were identified using MaGECK, and the top 1000 candidates were selected for a secondary screen. We performed the secondary screen in 4 PDOs, including 2 from primary PDAC tumours, 1 from omental metastasis, and 1 from liver metastasis, to cover different stages of the disease. Over 30 robust gene hits were identified across multiple organoids, including candidates that are novel in the context of chemoresistance, as well as a few genes that have been previously described in the literature. Currently, we are exploring the mechanism of action of the top candidates and their draggability or the possibility of drug repurposing. The ultimate outcomes of this project will not only contribute to the knowledge of chemoresistance but also foster translation towards novel combination treatments for PDAC patients.