Seeking to overcome the limitations of high-throughput screening of cells on microplates, researchers at the VTT Technical Research Centre in Finland have developed a miniaturized cell microarray platform that they claim can be used in large-scale gene knockdown analyses.
Using the transfection cell array, the researchers demonstrated that they are able to screen up to 15,000 siRNA molecules in a single array plate. The Finnish scientists discussed the latest version of the array platform, which has been in development for years, in a paper published in BMC Genomics last month.
Paper coauthor Olli Kallioniemi, director of VTT's medical biotechnology division and director of the Institute for Molecular Medicine Finland, told BioArray News this week that the platform was designed to overcome the shortcomings of microplate-based approaches.
"We have had a longstanding interest to develop miniaturized, ultra-high-throughput capabilities for cell-based analyses of gene functions," Kallioniemi said. Such technologies are needed to identify key regulators of cell functions in health and disease, he said.
According to Kallioniemi, cell microarrays enable "genome-scale cell biology." He claimed that cell biology is the "next big challenge for biology" after the structure and function of genomes has been catalogued based on sequencing-based approaches.
"Genes and proteins need to be analyzed and perturbed and visualized where they function, thus in the context of living cells," said Kallioniemi. "Therefore microscopic technologies are key."
Measuring the impact of molecular perturbations on cellular function using microplates has proven a challenge, according to Kallioniemi. "As the number of combinatorial perturbations becomes enormous, current microplate-based technologies for high-throughput analyses of gene function become too expensive and slow for pragmatic reasons," he said.
"Analyzing the combinatorial impact of every gene in the human genome against every other gene will be a huge undertaking requiring millions of experiments," he said. While such an approach would be "completely impossible" using microplate-based approaches, it is "within the realm of future possibilities" with cell arrays.
The VTT researchers have been developing the cell array platform for years. The group's first paper to discuss the cell array concept appeared in 2003 in Genome Research. BioArray News also discussed the platform with Kallioniemi during a site visit to Turku, Finland, in 2008 (BAN 9/16/2008).
The new BMC Genomics paper is the most detailed publication on the approach to date, and showcases what Kallioniemi said represents a "much improved technology that has the potential to develop into a robust and quick method that a very broad group of scientists could find useful."
More specifically, Kallioniemi and fellow researchers claim in the paper that their approach is cheaper and consumes less siRNAs and reagents than microplate-based approaches, in addition to being flexible and high throughput.
To validate the method, Kallioniemi and fellow researchers, including VTT scientist and lead author Juha Rantala, tested a panel of 92 adherent cell types, including primary human cells, ultimately demonstrating the systematic screening of 492 GPCR-coding genes for impact on growth and survival of cultured human prostate cancer cells.
According to the paper, the VTT researchers can create transfection cell arrays with sample densities allowing screening of up to 15,000 siRNA molecules in a single array plate. With future development of higher capacity time-lapse microscopic imagers, the platform could be used for high-throughput time-lapse microscopic analyses, the authors claim.
According to Kallioniemi, the applications for the approach are "amazingly broad." He said that "whatever cell biologists and molecular biologists can do with adherent cells today, they could do in a genomic-scale tomorrow with the help of the cell microarrays."
While genome-scale analysis of gene function is the "primary application," other applications include exploration of key signaling pathways, cellular processes, visualization of localization of proteins and protein complexes in cells, combinatorial strategies to knock down multiple genes, and exploration of gene-drug interactions.
Kallioniemi also noted that VTT's approach relies on a Matrigel-based substrate that the cells grow on, which he and fellow researchers believe can generate a "somewhat more physiological growth environment for the cells," as compared to classical plastic-based 2D cell cultures.
Currently, Kallioniemi and the other VTT scientists are working with "both corporate and academic partners to try to propagate the widespread application of the technology," he said. Still, he cautioned that it will "take some years to optimize and modify a research technology into a robust and standardized product, but we believe this will be possible."
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