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Epigenetics Firm Epigentek Focusing on 'Sixth DNA Base'

By Tony Fong

NEW YORK (GenomeWeb News) – A Brooklyn, NY-based epigenetics firm has developed a method for identifying a potentially critical DNA nucleotide that only recently was discovered to be in humans and may play a vital role in switching genes on and off and in the development of diseases such as cancer.

The company, called Epigentek, began making available in late June the first version of its MethylFlash Hydroxymethylated DNA Quantification kit for 5-hydroxymethylcytosine identification and differentiation. In the next month, the firm anticipates launching three other MethylFlash kits, William Lee, the company's sales and marketing manager, told GenomeWeb Daily News.

Epigenetics is still a young science and while a number of life-science firms dabble in the field, Epigentek is one of a very small number of pure-play companies in the space — according to Lee, Epigentek is the only tool company operating exclusively in epigenetics. But as the body of epigenetics research continues to expand and the direction of genomics-related research delves beyond the DNA level to the epigenetic level, Epigentek sees the field as the next big opportunity in the genomics space, Lee said.

Epigentek offers more than 700 proprietary products, but at the moment, the company describes its MethylFlash technology as potentially a breakthrough in epigenetics research.

The technology is for identifying and quantifying a DNA nitrogen base that was first observed nearly 60 years ago but only last year was detected in mammals. Before that, a paper had hinted at the presence of 5-hydroxymethylcytosine, or 5-hmC, in mammals but the finding could never be confirmed, and 5-hmC was assumed to exist only in simple life forms, such as bacterial viruses.

Much of 5-hmC's function — and how and if it may be different from its forerunner, 5-methylcytosine, or 5-mC — remains unknown, but it is believed that 5-hmC may play a role in turning genes on and off, and 5-hmC has been called the "sixth DNA base." Last year when the study about its presence in mammals was announced, Nathaniel Heintz, in whose lab the work was done, said the finding "will electrify the field of epigenetics."

To date, identification of 5-hmC has been possible primarily by mass spectrometry and liquid chromatography, instruments that can be expensive and require technical expertise to use. Epigentek's technology changes that by now making it possible for any researcher in any lab to identify 5-hmC, Lee said.

He declined to describe the technology in great detail, saying it was proprietary, but said it is in a 96-well plate format coated with a substrate that binds to a 5-hmC antibody. The format is similar to an ELISA and all that's needed is a microplate reader, "so that way it gives access to individuals to efficiently detect 5-hmC in every lab," Lee said.

According to Epigentek, the kits can be used in any species, including humans, fungi, plants, bacteria, and viruses, and in different forms such as cultured cells, frozen tissues, paraffin-embedded tissues, plasma/serum samples, and body fluid samples.

Importantly, the MethylFlash technology can differentiate 5-hmC from 5-mC, something that other DNA methylation-based approaches, such as enzymatic digestion or bisulfite treatment cannot do. Mass spec-based methods can be used to differentiate the two bases, but not easily.

"Right now, this is the only method of efficiently differentiating and determining between 5-mhC and 5-mC," Lee said. This ability, he added, could have significant implications for not only future epigenetics research but past ones as well.

"People who've been looking at 5-mC using [mass spectrometery and HPLC] might have also been inclusive of 5-hmC but just didn't know it," Lee said. Variations in methylation data from earlier experiments can now be attributed to the presence of 5-hmC, "which means researchers can go back and reevaluate their data" easily using the MethylFlash approach, he said.

The ability of the technology to differentiate 5-hmC from 5-mC was demonstrated in unpublished research done by Epigentek researchers in which they found that 5-hmC is abundant in normal human brains and colon tissues but "significantly" decreased in colon cancer tissue and cells, according to the company. The scientists also found that human brains had 30 percent higher levels of 5-hmC than 5-mC, and colon tissues had 15 percent higher levels of 5-hmC than 5-mC.

The MethylFlash kits — which sell for $300 in a 48-well plate format and $600 in a 96-well plate format — would have use for any researcher who does DNA methylation, a major area of research in epigenetics, Lee said. By his estimates, DNA methylation experiments make up at least one-quarter of all epigenetics research.

Lee acknowledged that epigenetics is still an emerging science and may not yet have the same commercial potential as other life science research fields, such as next-generation sequencing, but "we have a vision that epigenetics is going to be the next big thing in life sciences," he said. "Just as genetics has taken off … and has become so huge now, we feel that epigenetics is that next stepping stone."

Lee declined to disclose any financial information about the company, which has 15 employees.

According to market research firm Global Industry Analysts, the worldwide epigenetics space is projected to reach more than $18 billion by 2015, driven by research into cellular malfunction and disease development. Therapeutics firms such as Celgene, CellCentric, and Constellation Pharmaceuticals, which recently announced the completion of a Series B financing round that raised $22 million, have embraced epigenetics and are using the science in their new drug and therapeutic target development programs.

In the life-science tools space, several large vendors have products for epigenetics researchers, though they are mostly limited to chromatin immunoprecipitation and DNA methylation kits. These competitors include Affymetrix, Illumina, and Life Technologies' Invitrogen business. Also, Thermo Fisher Scientific in March introduced an agarose ChIP kit.

In 2008, Millipore and Agilent Technologies announced a collaboration to develop ChIP-on-chip kits to facilitate genetic research by protein scientists. And last year Roche Nimblegen and Sigma-Aldrich announced a deal coupling Roche's ChIP-chip microarrays with Sigma-Aldrich's GenomePlex platform to allow the study of epigenetic interactions between DNA and DNA-binding proteins.

Unlike those firms, however, Epigentek is focused solely on epigenetics and plans on staying that way. In addition to providing tools to the research community, the company is working to develop epigenetics-based diagnostics. Lee declined to elaborate on the work and would say only that the firm has two products in clinical trials.

Meanwhile, the company is preparing for additional launches of its MethylFlash technology. In the next month, three other MethylFlash products will become available, Lee said. One will be for the identification of 5-mC. That and the kit launched last month are both colorimetric, and Epigentek also plans to introduce fluorometric versions of them.

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