A forward genetics approach to define driver mutations in bile duct cancer

Cholangiocarcinoma is an aggressive malignancy of the bile ducts in the liver and has a poor prognosis, with 75% of patients dying in the first year after diagnosis and 5-10 per cent of patients surviving more than five years. Understanding the genetics of cholangiocarcinoma has been hampered by relatively small sample sizes, where whole exome sequencing (WES) has yielded a broad mutational profile that does not provide a standout mutational signature that can be targeted therapeutically.

We aim to use computational tools to conduct a combined analysis of 413 cholangiocarcinoma WES datasets. We will then define driver mutations using algorithms that predict the likelihood of a mutation being oncogenic. These computationally derived mutations will be used to conduct a forward genetic screen in bile duct organoids using Cas9/CRISPR. The expectation is that neutral mutations will be filtered out and we will be able to derive a list of functional oncogenic mutations. This combination of in silico and in vitro methodology will determine bona fide oncogenes from a highly-triaged list of candidate mutations.

This methodology will be important in identifying oncogenes in cholangiocarcinoma and other rare cancers or cancers which have diverse mutational spectra.