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Enzo Biochem Unveils New Molecular Assay Techs, Including TaqMan PCR Challenger

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By Ben Butkus

Enzo Biochem this week disclosed a pair of assay technologies that are expected to drive future growth at the company and that may set new standards for how certain molecular diagnostics are performed, according to Enzo executives.

The first technology, called AmpiProbe, is a nucleic acid amplification chemistry and method that Enzo claims is up to 50 times more sensitive than TaqMan-based real-time PCR, and may allow as many as 20 molecular assays for different targets to be performed on a single clinical sample.

The second innovation is a next-generation version of the company's branched DNA signal amplification assay that the company says has the ability to detect just a single copy of a virus, such as human papillomavirus, that has integrated into a host cell's chromosome, which may allow clinicians to detect HPV-associated cancers earlier than can any existing method.

Further, executives said the company expects to file for approval for the first molecular diagnostic product incorporating the AmpiProbe technology, a laboratory-developed test for an undisclosed target, by the end of January; with an eye toward marketing a product by the end of summer 2012.

Barry Weiner, president of Enzo Biochem, discussed the technologies during a conference call this week recapping the company's financial results for the fiscal first quarter, ended Oct. 31.

Weiner noted that while, for most of its history, Enzo has developed technologies for labeling and detecting DNA and RNA, the two new platforms are the culmination of "a number of years of development work," and really became the central focus of Enzo's molecular diagnostic efforts about five years ago.

AmpiProbe, Weiner said, will enable users to perform "real-time PCR-type amplification and detection in a better, faster, and more economical way." More specifically, Weiner said that an AmpiProbe assay will require a smaller initial sample volume, which in turn will "lower the amount of costly reagents needed to run the tests, thereby reducing costs for the clinical laboratory."

In addition, he said, the increased sensitivity of the AmpiProbe platform reduces the amount of patient sample needed to perform a test. "This can benefit both the physician and patient by reducing the need for a second visit to obtain additional specimens to run follow-up tests," Weiner said. In addition, it may allow labs to run "different multiple tests off the same specimen, thereby potentially reducing what is probably the most expensive component of assays: sample processing," which Weiner said often makes up more than half the cost of a given molecular diagnostic test.

Beyond Multiplexing

Given that this is the first time Enzo has publicly disclosed the AmpiProbe technology, and given its early nature — Weiner said that the company has just recently submitted its first research abstract regarding the technology to a "prestigious clinical organization" — Enzo did not provide a great deal of specifics on how the technology works.

However, in a follow-up interview with PCR Insider, chairman, CEO, and co-founder Elazar Rabbani provided a little more detail, calling the technology the "next generation" of real-time PCR.

"Essentially all real-time PCR or real-time detection [methods] are TaqMan or TaqMan analogs," he said. "And in one form or another, they really have three components: they have a two-primer system and a signaling component. And in most cases, the signal that you generate in each step of amplification sets a new ground level."

"We have reduced the complexity from three parts to only two parts," Rabbani said. "And that system is extremely efficient. We have a two-primer system that amplifies and generates signal at the same time." Enzo has also developed its own signaling dye for use with the assay; and Rabbani said that it has been adapted to be read out in any open commercial system in the marketplace.

The upshot, he said, is that AmpiProbe is "more than 25 times — and that could be increased to 50 times — more sensitive than standard PCR with TaqMan." In many clinical diagnostics applications, he added, this added sensitivity is overkill, noting that "if you have hepatitis virus, for example, there is plenty of it, so to say you are going to detect a single particle … really has no medical relevance."

Instead, the power of AmpiProbe lies in its ability to serve as the basis for molecular diagnostic panels comprising different targets.

"From a single specimen, a single [nucleic acid] purification, we can perform 10 to 20 independent assays without any compromise [in sensitivity]," Rabbani said. "No multiplexing method can go that far. To me multiplexing was always a poor man's excuse for not having enough capability to do independent assays."

This would potentially allow a clinician to take one sample from a patient and test for a variety of important targets without necessitating a return visit. For example, in the case of a gynecological visit, a doctor could use an AmpiProbe assay to test purified nucleic acid from one sample for human papillomavirus, chlamydia, gonorrhea, and other STDs and opportunistic infections, with each assay providing uncompromised sensitivity. In addition, if a test is compromised for some reason, the physician would be able to run the test again using the same sample.

"This is where we really believe the next generation of molecular diagnostics has to go," Rabbani said.

During Enzo's conference call this week, Weiner said that the company's R&D staff is currently running "the last set of correlative studies, which we hope will lead to the filing of our first LDT submission in New York State by quarter's end," which is Jan. 31 for Enzo. "Depending on the time frame for approval, which can be anywhere from three to six or seven months, we hope to have a product … marketed sometime after the end of the summer."

Concurrently, Enzo is developing a series of follow-on products based on AmpiProbe for industry partners to use as research products and potentially develop their own assays, Weiner said. "We are developing this into a format for paneling, meaning we will be offering multiple analytes for our end users to apply," he said. "This will be a continuing process, but it is something we are moving aggressively on."

Branching Out

Enzo's second new technology, while semi-molecular in nature, nonetheless will be an important part of the company's diagnostics strategy moving forward. This technology, a next generation of the company's already-established branched DNA assay method, is a signal-amplification technology that enables direct detection of nucleic acids without the need for target amplification.

The next generation of the bDNA looks to have its killer application in diagnosing diseases hallmarked by specific nucleic acids that have integrated into a host's genetic material, Enzo said.

"Enzo scientists have been able to apply this technology to visualize as little as a single copy of virus that has been actually integrated into a cell … and believe that it may be useful in the development of a better and more sensitive test looking for small amounts of genetic material. Examples of these include a number of assays used to identify specific types of cancer, such as breast and bladder," Weiner said.

"Additionally, this can be used as an even more sensitive predictor of the risk of progression to cervical cancer," he said. "As Enzo continues to increase its HPV testing options … our scientists have also used our next-generation bDNA assay such that it may allow a pathologist to actually visualize the presence of HPV DNA inside of a patient's cell's nucleus, thereby potentially providing more concrete evidence of viral integration while allowing the pathologist to simultaneously study cellular morphology."

Rabbani later added that the company views this technology as complementary to the AmpiProbe assay.

One area where the company sees bDNA being highly applicable is in fluorescent in situ hybridization. "Localized detection of nucleic acid is extremely important in FISH. As you do PCR you diffuse the target, so if you can directly detect chromosomal target by an enhanced signal, that would be very desirable."

Combating Market Softness

Enzo expects both new technologies to breathe life into the company, which saw its Q1 revenues rise less than half a percent to $25.8 million from $25.7 million in the year-ago period.

The company operates two segments: Clinical laboratory services, whose revenues increased to $14.2 million from $12.4 million; and Life Sciences, whose product revenues slid to $9.7 million from $10.2 million year over year. In addition, royalty and licensing fees dropped to $1.9 million from $3.1 million.

The firm's net loss for the quarter increased to $4.5 million, or $.12 per share, from a net loss of $1.1 million, or $.03 per share, a year ago. Enzo ended the quarter with $21.4 million in cash, cash equivalents, and short-term investments.

Weiner said that the weak academic market for life sciences as well as "general tightness in the global economy" contributed to the lackluster Q1 sales. Enzo's Life Sciences division currently offers a number of products such as DNA, RNA, and protein quantification assays; genomics and general molecular biology tools; molecular labels and probes; compound libraries; and enzymatic, protein, and immunological assays.

Weiner said during the conference call that new molecular diagnostic tests Enzo is able to commercialize based on the new technologies will be "immediately salable" upon approval; and that in some cases the company has "already begun the pre-marketing and establishment of the channels to get those products into the market."

He also said that he expects the new technologies to generate revenues through partnerships with pharmaceutical and biotech companies over the coming months.


Have topics you'd like to see covered in PCR Insider? Contact the editor at bbutkus [at] genomeweb [.] com.

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