Scientists from the David Geffen School of Medicine at the University of California, Los Angeles, have developed a high-density yeast cell array to conduct genome-wide functional analyses of cells by performing quantitative and automated readouts of cell fitness.
The array technology, which is described in an open-access article in the May 17 issue of the Proceedings of the National Academy of Sciences, could find use in pharmacogenomics applications such as assessing genotype-dependent drug responses, developing molecularly targeted therapies, and high-throughput functional genomics and drug discovery.
Considering the market success of gene chips and the increasing popularity of protein chips, moving on to "cell chips" seems a natural progression, especially in light of the recent trend towards systems biology and chemical genomics.
Due to the relative sizes of cells as compared with oligos and peptides, a true silicon-based cell chip is more difficult to achieve, at least one with a comparable spotting density. Instead, several companies and academic researchers have successfully arrayed cells on substrates such as microscope slides, microtiter plates, or larger electronic sensing chips.
Although the technology developed by the UCLA researchers also does not use a chip, the researchers claim they have developed a method that allows them to "print" cells on the area of a standard microtiter plate at greater than 10 times the density currently possible.
As detailed in the paper, on which UCLA assistant professor Jing Huang was the principal author, the researchers achieved this by using a contact microarrayer typical of those used to create high-density gene arrays. Specifically, they used a Genemachines microarrayer, manufactured by Genomics Solutions, a Harvard Bioscience company.
They were able to spot 9,600 yeast cell strains in an area of 127 X 85 mm, with a distance of approximately 900 µm between spots.
The significance of this, according to the researchers, is that it allowed them to plate the complete Saccharomyces cerevisiae gene-deletion library — a standard set of about 6,000 yeast deletion strains with full-genome coverage that was created several years ago by the S. cerevisiae Genome Deletion Project.
Huang and colleagues screened the yeast-deletion library for changes in relative fitness in response to the immunosuppressive drug rapamycin, with the goal of identifying all single-gene modifiers of the rapamycin-sensitive Tor pathway.
The researchers imaged the cellular arrays at various concentrations of rapamycin using a custom-made CCD imaging system, and were able to identify 396 yeast strains with altered fitness response to rapamycin. This number included 281 hypersensitive strains and 101 resistant strains. Furthermore, the researchers identified all previously known effectors and downstream targets of Tor, providing proof-of-principle for their method.
"The logic underlying this analysis differs from drug-induced haploinsufficiency screening that aims at identifying direct drug targets, but instead facilitates a global understanding of drug effects at the systems level," the researchers wrote in the paper.
"In the case of rapamycin, its protein targets have been known for more than a decade, but its broad cellular effects, ranging from growth control to possibly lifespan regulation, are only beginning to be understood," the paper continues. "The ability to profile drug effects at the genomic scale in vivo is fundamental to our understanding of molecular and cellular mechanisms and, as we show here, can shed light on the therapeutic limitations and potential unexpected uses of drugs as well."
An example of an unexpected response was the identification of what the researchers call a "rapamycin-enhanced" phenotype in 14 genes whose deletions allowed cells to grow better in the presence of rapamycin than in its absence. The researchers said that 13 of those genes have greater than 30-percent identical homologs at the human level, most of them in mitochondria, thus suggesting that rapamycin may be useful as a treatment in human disease based on mitochondrial malfunction.
Despite the technology's utility in yeast, the researchers also believe that their technology could eventually be useful in large-scale functional genomics studies and drug discovery in bacterial or mammalian cells.
"Although not demonstrated here, the cell array technology is readily adaptable to other types of large-scale screens based on growth, or changes in color/fluorescence or colony morphology," the researchers wrote. "The cell array platform is also applicable to high-throughput investigations of other microbial systems.
"Furthermore, it may be possible to devise analogous systems to array mammalian cells on appropriate substrates," the paper continues. "Such systems will allow high-throughput manipulations of tens of thousands of genetically engineered mammalian cells as an array and complement the use of an elegant mammalian cell array platform developed by the [David] Sabatini laboratory in systematic analyses of gene function and drug mechanisms."
Anne Carpenter, a postdoctoral associate at the Whitehead Institute who has worked with Sabatini to develop the aforementioned mammalian cell arrays, suggested that the transition to other cell types would be a natural one.
"This work is a great example of combining a very powerful classical genetic strategy with modern technology to conduct a systematic screen at unprecedented throughput," Carpenter wrote in an email to CBA News. "These powerful approaches are just now becoming feasible for cells cultured from multicellular organisms using living cell microarray technology, so these next few years should see similar strategies applied to multicellular organisms as well, even human cells.
"We are also eager to see the technologies extended to phenotypes other than just colony growth — like morphology of cells, for example," she added. "This should become more common as software for image analysis continues to improve."
It is unclear whether Huang and colleagues have applied for patents on the cellular array technology, or whether the group is interested in commercialization. Calls to the researchers were not returned in time for this publication.
— Ben Butkus ([email protected])