NEW YORK (GenomeWeb News) – A new study has narrowed in on shared, overlapping sets of genes contributing to yeast reactions to a range of small molecules — chemogenomic signatures that are expected to aid future efforts to understand and predict drug responses in yeast and mammalian cells.
As they reported online today in Science, researchers from the University of Toronto and other centers in Canada, the US, Belgium, and France did a series of chemogenomic assays known as haploinsufficiency profiling (HIP) and homozygous profiling (HOP) in yeast cells to gauge small molecule effects.
By systematically applying 3,250 small molecule compounds to thousands of yeast strains missing one or both copies of individual genes, the team tracked down more than 300 small molecule compounds that interfere with the function of 121 yeast genes.
The broader screen also revealed a few dozen key chemogenomic signatures that can pop up when yeast cells are exposed to various compounds. Those shared sets of genes with functional ties to drug response appear promising not only for understanding the biological consequences of small molecule exposure, but also for predicting the effects of previously uncharacterized compounds.
"The gist of the paper is really about understanding the number of ways a cell can respond to a drug," senior author Guri Giaever told GenomeWeb Daily News.
Giaever was affiliated with the University of Toronto when the study started. She is currently based at the University of British Columbia's Faculty of Pharmaceutical Sciences.
She and her colleagues took a loss-of-function genomic approach for their small molecule profiling study. Starting from around 50,000 small molecule compounds with potential drug effects, they focused in on 3,250 compounds that appeared to hamper the growth of wild-type yeast cells.
"Only about 10 percent of compounds inhibited growth," noted co-author Corey Nislow, a researcher with the University of Toronto when the study began, who is currently based at UBC. "We further winnowed [those 5,000 compounds] using what we know about their chemical structures."
After identifying compounds that elicited a measurable effect on cell growth, the team turned to its chemogenomic tools to take a closer look at how and why that growth inhibition occurs, Nislow told GWDN.
For the HIP assays, the researchers systematically applied each of the compounds to roughly 1,100 yeast strains, each missing one copy of a given gene to look for instances in which a small molecule hindered the function of the remaining copy of a yeast gene.
In the case of the HOP experiments, meanwhile, the team tracked functional defects in a set of roughly 4,800 yeast strains, each missing both copies of a different non-essential gene. That arm of the study helped in defining pathways acting in parallel to mediate small molecule response.
Together, the study's authors explained, results from the HIP and HOP analyses offered a glimpse at the suite of genes and pathways at the heart of yeast cell responses to the compounds assessed.
For instance, the work highlighted 317 small molecules that interfered with the functions of 121 essential yeast genes. Among them were compounds already noted for their drug effects as well as small molecules with still undetermined drug roles.
The researchers also picked up on the presence of 45 major chemogenomic signatures associated with cellular response to the small molecules, as well as a few more minor signatures. Those signatures represent sets of genes that are important for growth in the presence of a given compound, Giaever noted, explaining that "every gene that has a signal in the [fitness] signature is important for growth."
"In retrospect, it's not that surprising that the cell has a way of integrating all these signals, if you consider drug stress a signal," Nislow added. "The cell has evolved ways of integrating these signals such that it has a best way to respond."
The chemogenomic response signatures proved useful for predicting the effects of some uncharacterized compounds, too. For example, at least 20 of the small molecules tested appeared to prompt cellular responses resembling those found in cells treated with DNA damaging drugs, suggesting that the new compounds likely produce similar effects.
The team argued that the patterns identified in yeast cells may also help in determining the functional consequences of applying such compounds to mammalian cells — a notion supported by follow-up experiments on human leukemia cells treated with an apparent mitochondrial-inhibiting drug.
Similarly, the researchers saw a pair of genes that seem to have a strong influence on cellular response to compounds known as cationic amphiphilic drugs, which sometimes build up as fatty deposits in humans treated with the drugs.
Though more research is needed to verify a functional role for similar genes in mammalian cells, such results hint that yeast screens or functionally relevant gene genotyping may help in predicting which patients may be prone to adverse reactions to cationic amphiphilic drugs.
Along with future studies aimed at applying findings from the current study to mammalian cells, the study's authors are gearing up to look at how yeast cell responses to small molecules change depending on their environmental conditions and corresponding metabolic changes.
"Our systems-level view of the cellular response to small molecules provides a resource for the exploration of multifaceted relationships among genes, biological processes, chemical structures, and response signatures," Giaever and her co-authors wrote.
"We expect that these signatures … represent fundamental small molecule response systems that are present across eukaryotic cells," they concluded. "Accordingly, we expect that many of our 317 chemical-genetic probes will be directly applicable to mammalian cell biology and may support novel targets as opportunities to pursue for therapeutic intervention."