The scientists at Hayward, Calif.-based Biolog have turned the concept of microarraying inside out: Instead of measuring thousands of different genes from a cell, Biolog’s Phenotype Microarrays, which company scientists outline in a June 25 paper published in Genome Research, measure the effect of one gene on thousands of different cell conditions.
“Gene expression arrays provide a snapshot of gene expression in cells under one particular growth condition,” said Biolog founder Barry Bochner, the lead author on the paper. “The next thing you need to know is how the cell changes with gene expression.”
In the paper, “Phenotype Microarrays for High-Throughput Phenotypic Testing and Assay of Gene Function,” Bochner and his colleagues described the use of E. coli Phenotype Microarrays to simultaneously test 700 phenotypes of E. coli cells in order to measure the effect of different genes or gene knockouts on numerous cellular activities.
Phenotype Microarrays (PMs) consist of microwells of live bacterial cells arrayed in 96-well microtiter plates. Each well contains a different cell culture medium that brings out a different function or phenotype of the cells. Tetrazolium dye, which is added to each well, detects cell respiration by turning purple when respiration byproducts cause it to be chemically reduced. Purple wells indicate normally functioning cells, while loss of purple color reflects the degree to which cell function is compromised by a particular gene change or external condition.
To read the PMs, Biolog has designed the Omnilog, an instrument that cycles microplates in front of a CCD camera and records the images. The company said the instrument could simultaneously read up to 50 microplates in five minutes.
The article describes several different experiments with PMs. First, the researchers compared a normal E. coli strain in which a mutation was inserted to inactivate a xylos catabolism gene. Using the PMs, the researchers found that this “knockout” also caused the cell to lose function for maltose and maltotriose metabolism.
They also tested E. coli strains with loss of function in a gene whose function was previously unknown, as well as several genes with well-validated functions. The results from these tests, the researchers said, showed that the PM technology accurately displayed phenotypic changes predicted from previous information about gene function, as well as leading to new discoveries about additional gene function.
This ability to elucidate gene function could make the PM a valuable tool in characterizing cell lines, the researchers said. “Although not surveying every gene, it can still provide an important tool in basic biological research as well as in maintenance of cell lines used to produce everything from beer to pharmaceuticals.”
Currently, Biolog offers 700-assay PMs for twelve different bacteria species at $200 a pair, but plans to introduce a human cell line. The company also is planning to commercialize 2000-assay PMs it has developed.
Biolog has licensed the technology to a number of non-profit research centers, but is now focusing its efforts for the microbial arrays on pharmaceutical and biotech companies developing antibiotics and antifungals. “We are already in discussions with about ten companies in that arena,” said Bochner.
When the human arrays are added to its portfolio, Biolog believes this PM technology could find an important niche in the pharmaceutical research arena. “There’s a huge need to understand the function of the genes so they can pick which are the best drug targets,” Bochner said.
The PM technology can also be used to test the effect of drug compounds on cell metabolism. “In our technology, we can see how drugs respond under thousands of different states of the cell,” Bochner said.
The arrays do have some drawbacks, however. Before the cells are tested, genetics work is required to do the gene knockouts on the cells. To alleviate this step for researchers, the company plans to do some of this work itself, and then offer the gene function results in a single database — similar in principle to Lexicon Genetics’ Omnibank knockout mouse database.
But in order to quickly execute its commercialization plans, Biolog is going to have to raise some funds. The 16-year-old company, which has been self-funded through Small Business Innovation Research (SBIR) grants, as well as sales of other microbiology products, is now in the process of conducting a $10 million private offering. “We’ve been profitable for ten out of the past 11 years now, so we can move ahead even without the funding,” said Bochner. “But we do want to get it so we can accelerate the development of the PM technology.