Finding the right drug to target a specific molecule is like finding a small needle in a giant haystack. With thousands of drug compounds to screen through in a short period, scientists start the search with a process known as high-throughput cell-based screening, thereby sieving out a small handful of candidate compounds for further detailed testing.
The challenge is intensified in the case of hepatocellular carcinoma or liver cancer, for which the most aggressive form express high levels of a fetal oncogene known as SALL4. Existing screening methods use either patient-derived cells or cells genetically engineered to express high levels of SALL4; each approach has its drawbacks.
“Cells from genetically distinct patients could have oncogenes other than SALL4 at varying levels, so we cannot conclude if the compounds identified are truly targeting SALL4,” explained Justin Tan, a Junior Principal Investigator at A*STAR’s Genome Institute of Singapore (GIS). “On the other hand, while engineering allows us to compare cells that are genetically identical other than their SALL4 levels, the compounds found could be interfering with the upregulation mechanism and not have anything to do with the underlying cancer biology.”
“To overcome the disadvantages of both systems, we simply combined both into our screening platform,” Tan said. By comparing the responses of both types of SALL4-overexpressing cells, the team was able to tease out the impact of genetic variability induced by genetic manipulation while providing biologically relevant findings.
“It also increases the efficiency and effectiveness of drug discovery. This saves time and money since fewer compounds need to be validated after the screen,” said Tan.
From an initial panel comprising more than 22,000 small molecules and natural product extracts, the team identified five compounds that killed SALL4-overexpressing liver cancer cells. Of the five, four were found to inhibit an oxygen-dependent energy-generating process called oxidative phosphorylation, suggesting that SALL4-expressing cells are metabolically distinct from other liver cancers.
“Our results showed that more aggressive liver cancers and even non-small cell lung cancer are ‘addicted’ to this pathway for their metabolic needs, potentially making them more sensitive towards inhibitors of the SALL4 metabolic pathway,” added Wai Leong Tam, one of the senior investigators of the study.
Further testing showed that one of the compounds, oligomycin, when used in combination with sorafenib, the current standard-of-care drug for liver cancer, was more potent at suppressing SALL4-expressing tumors in mice when compared to sorafenib alone.
While seeking industry partnerships to develop candidate compounds for clinical testing, the team is also utilizing this screening strategy in combination with whole-metabolome CRISPR knockout screens and genomic analyses to target genes involved in other cancers.