VANCOUVER, BC — Eppendorf will release a new version of its TF Chip MAPK, a transcription-factor assay for the mitogen-activated protein kinase pathway, before the end of September, according to a company official.
Peter Herzer, a senior scientist for the Hamburg, Germany-based company, told BioArray News this week that the second version of the TF Chip MAPK will feature 12 transcription factors. The first chip, released in April 2006, contained eight.
Speaking during the Fourth Annual World Microarray Congress, held here this week, Herzer said that the new MAPK assay will include the transcription factors AP1 (c-Jun), ATF2, c-Myc, Elk-1, MEF2, NFATc1, p53, and STAT1, as well as new additions HSF1, NFkB (p50), PPARg, and Sp1.
The MAPK pathway is known to regulate cellular functions such as cell growth, differentiation, immune-mediated inflammatory responses, and apoptosis.
“With this new content, we now fully cover the whole MAPK cascade, [and] also the NFkB and heat stress cascades, which are more than frequently co-activated together with MAPK, in particular upon physical stress, inflammation, or viral infections,” Herzer said.
“Several of those new TFs are [based on] feedback from our customers and scientists in the field [about] what they want to see in addition to what is already on there,” he added. “NF-kappa B, for example, is a natural part of the MAPK cascade and is, to date, the most studied TF.”
Eppendorf chose the MAPK pathway for its first TF-themed array because it believes it to be one of the “most well-studied signaling cascades” that is related to both pathological and physiological stress, said Herzer.
While Eppendorf has historically been known for its line of theme gene expression arrays, the company has focused in recent years on developing a portfolio of transcription factor arrays, including the TF Chip MAPK, as well as the TF Chip Stem Cell, which launched last year (see BAN 7/3/2007).
It has also been a season for upgrades at Eppendorf. Last month, the company released an upgraded version of its DualChip GMO Microarray Kit that enables users to test food, feed, and seed products for 12 different European Union-authorized and unauthorized genetically modified organisms in parallel (see BAN 5/27/2008).
“Pharmas haven’t gotten into stem cell research yet. They are still watching it.”
The TF Chip MAPK, like all of Eppendorf’s arrays, is designed for use with its Silverquant Microarray Detection and Scanning System, which is based on its Silverquant label technique that employs silver particle precipitation on nanogold particles, rather than fluorescence, to label an experiment. The arrays are sold in Eppendorf’s DualChip format, which enables customers to run two assays simultaneously.
Herzer said that in some ways, the nature of Eppendorf’s Silverquant platform made TF-themed arrays a natural fit for the company. “We have a lot of experience in TF assays, and in combination with the Silverquant detection system, it was a natural decision because we can here look at proteins,” he said.
“Developing TF arrays nicely complements the different gene-expression arrays from our portfolio, and combining proteomics and genomics levels of investigation provides information [that] is more than additive,” Herzer added.
TF Chip Stem Cell
Eppendorf last year began selling the TF Chip Stem Cell, which includes probes for 12 different transcription factors associated with stem cell differentiation, pluripotency, or cell death in various model organisms, including human, mouse, and rat. According to Herzer, the chip marks a “real opportunity” for Eppendorf to win over new customers.
“Stem-cell research is increasing, especially concerning adult stem cells, for which new niches are constantly discovered,” he said. “Scientists want to know, ‘What is their differentiation potential? How pluripotent are they? How adapted are their culture conditions? Are they growing? Are they dying?’ Most of the time, you don’t know what cells are doing until they have differentiated. With this research tool, we can look at what cells are doing while they are doing it,” said Herzer.
When the company was launching the array last year, Eppendorf product manager Margit Stadler told BioArray News that the it would most likely find a user base in academia, with perhaps some early-stage interest from biotech companies (see BAN 7/3/2007).
A year on, Herzer confirmed that Stadler’s market predictions have turned out to be accurate. “Most of the interest is coming from academics and small biotechs who have the freedom to do this kind of research, especially in states like California, because of the huge government funds available,” he said. “Pharmas haven’t gotten into stem cell research yet. They are still watching it.”
Herzer said that while the company has no immediate plans to update the chip, upgrades are likely as new transcription factors become increasingly popular in studies.
“Some key TFs, like Nanog and Sox2, are of particular interest to the stem-cell community, and those assays are under development,” he said. “Stem cell research on hematopoietic, neuronal, and pancreatic differentiation is also increasing. Any kit that comes out will be a Stem Cell II with markers for those applications.”
Gauging the competition for arrays like the TF Chip MAPK or the TF Chip Stem Cell is tough. Herzer said that transcription factors are typically studied in well-based assays, and stem-cell research mainly uses cell-surface markers, which are less specific than TFs, and not adapted to multiplex detection.
Other array firms have dabbled in these areas, however. In 2005, for instance, Sigma Aldrich launched its Panorama Ab Microarray — MAPK & PKC Pathways Kit, which it recommends for "studying protein expression in cell or tissue extracts" and said is "compatible with various species including human, mouse, and rat" (see BAN 8/3/2005).
As for Eppendorf, Herzer said that the firm is likely to introduce new arrays in the future as the market demands them. “We are constantly getting input from scientists about what TFs they want on an array,” he said. “If we get enough encouragement for certain TFs, then we could think about creating a product for that.”