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Germany's PepPerPrint Designing Next-Gen Peptide Array Printer; Plans Year-End Debut


PepPerPrint, an eight-year-old spinout of the German Cancer Research Center, is working with partners to develop a new laser printer that will be designed to quadruple the density of the firm's peptide array platform.

CEO Volker Stadler said that the company is working with the Fraunhofer Institute for Manufacturing Engineering and Automation IPA in Stuttgart and KMS Automation in Schramberg to bring the instrument online by the end of 2009.

Once the company scales up its offering, it hopes to attract interest from researchers studying peptides, many of whom are still spotting their own arrays.

"Each assay is more beneficial to a user the more data points they get per assay," Stadler said. "Our goal is to be able to put as many peptides onto the same area as possible."

Stadler spoke to BioArray News during Select Biosciences' Advances in Microarray Technology conference, held in Stockholm, Sweden, last week.

PepPerPrint, based in Heidelberg, has been working with Fraunhofer for several years to develop the new printer. Its method, developed at DKFZ, uses dry immunohistochemistry to generate arrays of thousands of peptides. Dry amino acids are first encapsulated in toner powder in a state where they cannot react or decay. They are then arrayed onto a glass slide to create peptide arrays (see BAN 6/10/2008).

Based on this, Fraunhofer last year developed for PepPerPrint a special laser printer capable of printing 20 different types of amino acid toners. The toners are arrayed on a surface and then heated in a generic laboratory oven at approximately 180 degrees Fahrenheit until the dry toner powder melts away.

Slides are then washed, and a second layer of amino acids is printed atop the first layer. The process repeats itself to generate peptides that are 15 to 20 amino acids in length.

Using its current printer, PepPerPrint can generate arrays of nearly 5,500 peptides on a standard 1x3-inch glass slide and up to 156,000 peptides on a 20x20 cm glass plate. Once the new, automated scanner comes on line later this year, though, PepPerPrint will be able to print more than 20,000 peptides per slide, or roughly 500,000 on a glass plate.

"We do not believe that this is the end of the laser printing technology's capabilities," said Stadler. "Within two or three years, we will be able to enhance the array density to maybe more than a million peptides on large-scale areas, which would correlate to 50,000 peptides on a [1x3-inch] slide," he said.

Beyond density, the new instrument being designed at Fraunhofer and KMS will be intended to overcome several constraints of PepPerPrint's current laser printer. For example, PepPerPrint to date has had to manually align its printers with the printing surface, an adjustment that requires micron-level resolution and typically takes the firm two weeks to accomplish.

"Once the existing laser printer is adjusted, it works well for months, but to adjust it takes weeks," said Stadler. "Once we load a toner cartridge, we have to readjust it. This is laborious."

The new printer, in contrast, will employ diodes that adjust the toner cartridge using register marks on the slide, eliminating the need for manual adjustment.

Separate from the work with Fraunhofer and KMS, PepPerPrint is also working with the University of Heidelberg to develop a microfluidics-based platform for peptide research. Pairing a microchip platform with combinatorial synthesis, PepPerPrint is able to already produce 10,000 peptides per square centimeter, Stadler said. He declined to elaborate on when the new platform could become available.

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'Stimulating the Market'

Though PepPerPrint is eager to upgrade its offering, it is serving a market of undetermined size. That is because unlike the genomic arrays manufactured by large companies like Affymetrix, Agilent Technologies, Illumina, or Roche NimbleGen, there have been few companies that have managed to successfully produce catalog peptide arrays at a price that is attractive for researchers.

"Right now, it costs roughly €5 [$7] per peptide to make an array," said Stadler. "But who is willing to give €5,000 for an array of 1,000 peptides? No one," he said. "If such an array costs €250, though, things become interesting." Stadler said PepPerPrint can spot a peptide for around €.05.

PepPerPrint believes its future market lies in converting researchers making their own chips to using its custom design service. "A huge number of people are spotting their own arrays," said Stadler. "But if it becomes so easy that you sit on your web browser, you design your array, send the data to the supplier, and then get the chip back in a few weeks, it becomes much more attractive for customers.

"If a peptide doesn't cost several euros per molecule, but only several cents, then there is the chance to play a comparable role in protein research that DNA chips in DNA research do," he added. "Just by providing a new technology and new products that are better in terms of array complexity and price, we hope we can stimulate the market."

Though the market is nascent, PepPerPrint has competitors. Earlier this month, TheraCode, a subsidiary of Marburg, Germany-based BioNTech, snatched up Berlin-based JPT Peptide Technologies for €5 million. JPT provides peptide-based services as well as high-content peptide arrays, peptide tools, and peptide libraries for the development of vaccines (see BAN 5/19/2009).

Houston-based LC Sciences is another firm that offers peptide array synthesis and services, as do Köln, Germany-based Intavis; Rockville, Md-based 20/20 GeneSystems; and Nantes, France-based ProtNeteomix. Most of these firm's offerings target users that are interested in biomarker discovery, particularly in oncology research.

The majority of PepPerPrint's collaborations so far have been with research institutes, though the company is also working with biotech and pharmaceutical companies, said Stadler. However, he predicts the firm's arrays will be affordable enough for academics and government-sponsored researchers "who are sitting in labs and have to rely on grant money to run their experiments."

PepPerPrint meantime is trying to score its own kind of grant. The company is looking for venture capital to support a "scale up of its technology, more automation, and better quality control," Stadler said.

"This is a question of money," he said. "The technology itself is working and we are earning money selling a product that is already available. I think our capital needs are very low for a biotech company, and we believe that the market is there for our peptide chips."

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