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Epitome Biosystems Developing Phosphoarray; Tool Will Compete With Invitrogen s New Chips

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A year and a half after it was founded, Epitome Biosystems has received a $500,000 Phase II Small Business Innovation Research grant from the National Science Foundation to develop an array of protein kinases with known phosphorylation sites, the company said this week.

The new array, scheduled to be launched in about nine months, will probably contain 30 or 40 proteins that together have up to 100 different phosphorylation sites, said Neal Gordon, president of the Waltham, Mass.-based company. The array will compete with phosphoarrays produced by BioSource International, which was recently acquired by Invitrogen (see briefs).


"A number of people are looking at using mass spectrometry quantitatively in a clinical setting, but I think it's more likely that an antibody array would take hold in a clinical setting. It's more high throughput, simple to use, and you can interrogate a lot of samples quickly."

The array uses a technology called Proteome Epitope Tag, or PET. With PET technology, scientists first look at the corresponding DNA sequence for a protein of interest and figure out what pieces of sequence exist that make the protein unique.

They then make a synthetic version of this unique fragment, called an EpiTag. The EpiTag, which is usually about seven or eight amino acids long, is then injected into rabbits that raise antibodies to the peptides.

To quantitate the amount of phosphorylation of a specific protein, Epitome uses a sandwich assay. An array of EpiTag antibodies is presented on a chip. Digested sample proteins are applied to the chip, and the chip is washed so that only sample peptides that recognize the antibodies remain on the chip. An antibody to the phophorylation site of interest is then applied to the chip, and the chip is washed again. Now the amount of phosphorylation can be quantified by measuring the amount of phosphosite antibody that remains.

"The specificity at the protein level is being introduced by the antibody," Gordon explained. "There's a lot of consensus around phosphorylation sites, so some phosphosite antibodies are just not as specific [as EpiTags]. We make it so that the specificity is not at the phosphosite, but at the peptide [that is near the phosphosite]."

Kevin Reagan, the executive vice president of technical operations at BioSource International, said that Epitome's technology sounds similar to the technology used by BioSource to produce phosphoarrays. BioSource released the first commercially available planar phosphoarray in January (see ProteoMonitor 1/21/2005).

Reagan said he could not comment at this point on whether there are any intellectual property violation issues involved with Epitome and BioSource.

"I think [Epitome's new array] validates the approach," said Reagan. "It confirms that there is a market need when other companies begin to copy it. In a sense it really comes down to which marker it is that people will find most useful. We recognize that people will expand on the technology, and it is expected that we will be the leader in the menu."

Following the launch of its Mercatur Phosphoarray, which contains 10 analytes, BioSource launched a phosphosite antibody set for studying the Akt pathway and for studying neurodegeneration, first on its ELISA platform, then on its Luminex platform. It is now working on launching them in its planar phosphoarray format.

Within Invitrogen, BioSource is collaborating with Proteometrix, which was itself acquired by Invitrogen last year, to develop more protein arrays.

Gordon said that aside from launching the cell-signaling array, Epitome is also working on producing quantitative biomarker arrays, which scientists could use to measure how much of a specific biomarker is present in a sample.


"The $64,000 question is 'Which is the right panel?'. We're working with a lot of knowledgeable people to try to determine which are the right proteins to multiplex together."

Rather than being used for discovery proteomics, quantitative biomarker arrays should be used in "measurement proteomics," Gordon said, where thousands and thousands of samples need to be processed to see how much of a biomarker is present.

"A number of people are looking at using mass spectrometry quantitatively in a clinical setting, but I think it's more likely that an antibody array would take hold in a clinical setting," Gordon said. "It's more high throughput, simple to use, and you can interrogate a lot of samples quickly."

Gordon said he expects his company to launch a quantitative cancer-biomarker array within about nine months. Other arrays will probably be put together based upon a disease, or on an organ-specific level.

"The $64,000 question is 'Which is the right panel?'" said Gordon. "We're working with a lot of knowledgeable people to try to determine which are the right proteins to multiplex together."

Aside from commercializing ready-made quantitative antibody arrays, Epitome is also looking at creating custom arrays for customers, Gordon said.

"We can go from not having anything to having a working product within four to six months," said Gordon. "What we're going after is creating measurement tools for proteins and panels that don't exist today."

Potential customers for Epitome's custom arrays include pharma companies and partners of Epitome, such as EMD Biosciences (see ProteoMonitor 9/23/2005).

"As we generate more and more content, the number of panels that you can get out of that becomes pretty large, and we're not sure ultimately what's going to be the preferred product," said Gordon. "We are working collaboratively with a lot of end users to figure out what measurement panel makes sense."

— Tien Shun Lee ([email protected])

 

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