VANCOUVER, BC — Eppendorf Array Technologies has established itself in the array market by selling condition-specific gene expression assays, but this August it will add a stem cell transcription factor chip to its portfolio, according to a company official.
Margit Stadler, the product manager for Eppendorf’s TF array line, told BioArray News at the World Microarray Congress here last week that the company sees an opportunity in the nascent stem-cell research market for content that is currently not widely available in an array-based format.
Eppendorf, based in Namur, Belgium, launched its first chip-based transcription factor assay for the mitogen-activated protein kinase pathway, called the TF Chip MAPK Kit, in April 2006, and the TF Chip Stem Cell Kit confirms Eppendorf’s interest in marketing TF assays, mainly to the academic market. However, the privately held firm is also optimistic about the product’s potential in the industrial market, particularly for biotechs, and a 96-well plate format is being considered to meet that need.
Stadler said that Eppendorf began developing these predefined, low-density assays two years ago on its DualChip platform, which enables users to run two assays at the same time to increase the power of their results. To date, the company has released gene-expression chips for at least 14 different research areas, from human cancer to rat inflammation, based on the firm’s DualChip platform. Eppendorf has also commercialized a DualChip-based kit for testing for the presence of genetically modified organisms, which is mandated for foods sold in the European Union.
Stadler said that Eppendorf’s interest in TF assays blossomed recently when the company hired R&D personnel with experience in that area. After some internal deliberation, the firm decided to roll out TF chips for MAPK first and then stem cells.
“We thought that the MAPK pathway and the transcription factors involved in that pathway would be of crucial interest to many researchers because the MAPK pathway is involved in so many other reactions like inflammation and other disequilibrium of processes in a cell,” Stadler said.
The company decided to focus on stem cell TFs next “because there isn’t any tool for measuring the differentiation of stem cells in that way,” she said. “At the moment the tools [researchers] are using force them to do a lot of work, especially data mining … to find out different gene expression patterns for different developmental stages of stem cells,” Stadler added.
Indeed, Eppendorf isn’t the only array firm trying to reach stem cell researchers. Both Invitrogen and Illumina have recently engaged researchers at the Burnham Institute in stem-cell related projects (see BAN 4/17/2007). However neither firm has launched a specific “stem cell array,” let alone one that tests for transcription factors.
Affymetrix has also worked with stem cell researchers who have used its 100K SNP mapping product and mitochondrial resequencing array. Additionally, SuperArray and Miltenyi Biotec both sell stem cell arrays, but those are not tailored to transcription factor studies.
According to Stadler, Eppendorf’s array includes probes for 12 different transcription factors associated with stem cells in various model organisms, including human, mouse, and rat. To compile the master list of genes for the array, Eppendorf engaged researchers and culled the literature for content. “We had extensive communication with stem cell researchers to find out what factors would be most important to them,” Stadler said.
“Our R&D people did an extensive literature search to get an idea of what would be interesting for researchers. They also sent questionnaires to researchers,” she added.
At the moment, users can monitor 12 different transcription factors that are “not restricted to human embryonic stem cells,” which is expected to be of interest to customers doing basic research based on mouse and rat models, Stadler said.
Eppendorf is hoping that the new chip will capture the attention of a growing sector in academia while array giants like Affy, Illumina, and Agilent duke it out in more established application areas like SNP genotyping, miRNAs, and array comparative genomic hybridization.
“At the moment the tools [researchers] are using force them to do a lot of work, especially data mining … to find out different gene expression patterns for different developmental stages of stem cells.”
Stadler said that the chip will be the only array of its kind on the market. “You can purchase some single-factor arrays from suppliers but you can monitor one TF in one assay, not multiplex,” she said.
Stadler said that, for the moment, the TF Chip Stem Cell Kit will be targeted at the academic market “because the stem cell field is mostly academic.” She said, however, that Eppendorf’s line of expression arrays could complement the newer TF arrays, and that industrial clients, like biotechs, might want to use the two together to measure both expression and transcription factors, “which are telling you a different story about the same cell,” she said.
Eppendorf’s assays are designed for use with its Silverquant Microarray Detection and Scanning System, which is based on its Silverquant label technique that employs silver particles to label an experiment, rather than fluorescence. According to Stadler, the gray-versus-black labeling strategy has allowed Eppendorf to reduce the cost for its instrumentation because its scanner is about a third of the price of a fluorescent scanner.
Building on Silverquant, Stadler said that Eppendorf is considering optimizing its products for 96-well plates to achieve higher penetration among industrial users who prefer that format over the 1X3 inch slides that Eppendorf’s platform currently uses.
Stadler said that the availability of a higher-throughput option could also boost adoption of TF assays outside of academia, particularly those using the chips for quality control.
“This would be interesting for a lot of biotech companies doing a lot of cell research,” she said. “They could use it as a QC tool for the cells to be sure that the cells are doing what they want them to do,” she said.
However, the MAPK product is likely to enter the industrial market before the stem cell kit, she said. “I think the market for stem cells is different from the market for MAPK. And the whole stem cell research area is still in its infancy. That is a much younger market than the market for kinase assays or something like that,” Stadler added.