Researchers led by The University of Texas MD Anderson Cancer Center (TX, USA) have developed an innovative approach to rapidly screen for genes that are crucial in the development of pancreatic cancer.
Published recently in Cell Reports, the team led by Alessandro Carugo (MD Anderson Cancer Center) carried out functional genetic screens on mice carrying patient-derived xenografts (PDX). The resulting data highlighted the importance of the WDR5 gene, which protects pancreatic tumors from DNA damage, working alongside the MYC promoter gene to allow tumor proliferation and survival.
The novel approach to genetic screening of these human tumors in PDX mice allows for more realistic gene function evaluations that would otherwise be established via screening tumor cells lines, which do not represent the true genetic complexity of an actual tumor.
This new method, named Patient-Based in Vivo Lethality to Optimize Treatment (PILOT), is currently being applied as part of MD Anderson’s Moon Shots Program. The program aims to reduce cancer deaths through the rapid development of new treatments, prevention programs and early detection methods based on the latest research. The technology is currently analyzing PDXs for a range of cancers including pancreatic, lung, colorectal and head and neck.
“With PILOT, instead of expanding the sample to challenge it with different drugs one at a time in many mice, we apply many more tests to a few mice to identify genomic drivers,” Carugo commented. “What’s really different here is that we are applying functional screening on patient-derived xenografts.”
Where researchers would normally expand PDX tissue, transplant it into approximately 30 mice and then test one drug against the tumor in each mouse, PILOT allows for the analysis of hundreds of genes in a lesser number of mice.
To test a primary tumor’s capacity to engraft into the mouse, a tracking library of molecular ’barcodes’ is delivered into the sample to assess the levels of tumor-initiating cells. This in turn provides a faster readout of engraftment efficacy in what would otherwise be an extensive process.
Once engrafting efficacy has been assured, a library of short hairpin RNAs (shRNA) are applied to the sample to silence specific genes. By analyzing the depletion of shRNAs in the tumor, researchers are able to identify individual genes involved in promoting proliferation.
In this study, Carugo and colleagues chose shRNA specific to genes involved in chromatin regulation, as chromatin regulation directly affects gene transcription and mutations in chromatin regulators are a hallmark of pancreatic cancer. Once the top 15–30% of depleted shRNAs were identified after multiple screens, WDR5 was implicated as the key gene.
The WDR5 protein product is a vital component of the COMPASS complex involved in regulating chromatin function and has been previously demonstrated to be upregulated in prostate and bladder cancers.
This study confirmed high WDR5 expression in pancreatic cancer, with subsequent experiments where the gene was knocked down demonstrating reduced tumor proliferation and increased survival in the mice.
Further studies highlighted synergy between WDR5 and MYC in protecting pancreatic cancer from DNA damage. Although there is no current method for targeting WDR5 or MYC individually, there may be a possibility of interrupting their interaction.
“This new technology allows us to more rapidly identify genetic drivers that maintain a tumor and thus potentially find new ways to treat it,” commented Giulio Draetta (MD Anderson Cancer Center).
PILOT is also being used with other shRNA libraries aimed at different genes in various other cancer subtypes.