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Mitochondrial Genomics Firm Eyes MDx for Cancer

By Tony Fong

NEW YORK (GenomeWeb News) – Leveraging expertise in mitochondrial genomics, a Canadian firm is readying to transition from an R&D shop to a commercial entity.

This week, Mitomics beefed up its management team and board with new additions, and in the coming weeks the firm will launch its first cancer diagnostic test, called Prostate Core Mitomic Test for prostate cancer, as a lab-developed test.

The Thunder Bay, Ontario-based firm also changed its name from Genesis Genomics this week to align its public identity with its lead technology called Mitomic Technology, the basis of its prostate cancer test.

While the life science space abounds with companies focusing on nuclear genomics, Mitomics is one of the only ones specializing in mitochondrial genomics. Another firm, Medomics, headquartered in Azusa, Calif., develops gene-sequencing-based tests for mitochondrial diseases and launched its MitoDx test a year ago.

Founded in 2001 by Ryan Parr, Mark Birch-Machin, and Robert Thayer, Mitomics has hedged its future on the promise of mitochondrial genomics from the start.

"All of the research and development we've done historically has been based on large-scale deletions of mitochondrial DNA that resides within the genome," Robert Poulter, president and CEO of Mitomics, told GenomeWeb Daily News. "And [we're] able to determine specific deletions and alterations associated with that genome and relate it back to specific types of diseases."

The advantage of focusing on the mitochondrial genome, he added, is that because mitochondria are present in every cell in a human, "for any given cell, we literally have hundreds of samples of DNA that we can analyze to detect whether these large-scale deletions are present within that genome.

"Mitochondria are highly sensitive to changes that are going on in the cell," he added, "and as a result, it's almost nature's ideally designed biosensor for what's happening in your body."

In the case of cancer, mitochondrial deletions can indicate the presence of cancerous cells "long before any current nuclear [genomics] or other technologies." Because mitochondria are "at the forefront" of cellular stress, "they are able to indicate at a very early stage that the cell or the organ is moving toward cancer," said Poulter.

A study published earlier this year in Nature, also points to the potential of mtDNA for use as disease biomarkers, especially for cancer. While the assumption has been that the mitochondrial genome of any individual is homoplasmic, meaning that mtDNA is the same within an individual, the researchers discovered "widespread heterogeneity (heteroplasmy) in the mtDNA of normal human cells," they said in their study.

In cancer cells, they found mtDNA variation to be even greater. In an analysis of blood samples from two patients with colorectal cancer before and after surgery, the researchers found different levels of cancer-associated mtDNA mutations, and added that mtDNA was more concentrated and more detectable in blood than nuclear DNA sequences associated with the tumor.

In an e-mail, Parr, now the chief scientific officer for Mitomics, said that the Nature study "affirms that the mitochondrial genome is a very biologically active and dynamic molecule … [and] draws attention to what many already know — this molecule has an important clinical and therapeutic role to play in cancer detection, diagnosis, and management."

The study, he added, "serves to highlight the utility of these active properties within the mitochondrial genome and confirm the use of the mitochondrial genome as a biosensor for the detection of cancer. Importantly, irrespective of the subtle variations noted in this study, a multitude of studies have easily demonstrated that there is a significant difference in the level, frequency, and number of somatic alterations between normal and malignant tissue."

The Mitomic Technology, which was developed in house at Mitomics, is a method for detecting whether a deletion in mtDNA may be indicative of disease. The company has a patent application filed with the US Patent and Trademark Office for the technology as it applies to sun damage, prostate cancer, and other cancers. In it, the company says that, in general, the method works by first determining the load in the mtDNA of a biological sample and the identity of the mtDNA. Then the mtDNA of the sample is compared to a database of "interpopulation and intrapopulation variation" and deletions associated with cancer.

Deletions in the mtDNA of the sample are identified by any number of techniques including sequencing, PCR, denaturing HPLC, and hybridization to micorarrays, gene chips, or biochips.

Mitomics' Prostate Core Mitomic Test is PCR-based. While Poulter would not specify a launch date, he said that it will be introduced in the "coming weeks." The test, which uses negative biopsy tissue, was previewed in May at the annual meeting of the American Urological Association, and Mitomics is working with CLIA laboratories to validate and implement the test. Poulter declined to identify the labs.

The company also is eyeing FDA approval for the test, though Poulter would say only that "the FDA factors very much into our future strategy."

The test would be ordered after a patient's biopsy came back negative. Typically, a biopsy involves 12 needle cores removed from the prostate, and if all the cores are negative for cancer, Mitomics' diagnostic test would then be used to analyze the 12 cores to determine whether, in spite of the negative biopsy results, changes are underway in the DNA that are, in fact, indicative of cancer.

If the specific biomarker exists, there is a likelihood that the cancer has been missed and another biopsy may be necessary.

In a study published online in January in Prostate Cancer and Prostatic Diseases, Mitomics' researchers said that at "an empirically established cycle threshold cutoff of 31, the test has a sensitivity of 84 percent, a specificity of 54 percent, and a negative predictive value of 91 percent," meaning that the test is able to predict true-negatives with 91 percent accuracy.

The test was able to predict the presence of a missed tumor in 17 of 20 men a year before diagnosis, the researchers wrote.

As it prepares the test for launch, Mitomics also is developing a similar prostate cancer test using the Mitomic Technology on body fluids. Fluid-based tests for other indications are also being developed.

"We're looking for non-invasive ways of early detection of these diseases," Poulter said.

The fluid-based prostate cancer test is slated to be Mitomics' second test to be commercially available, in about one year. In about two years, the company hopes to bring a prostate cancer prognosis test to market. Mitomics has not determined whether that test will be fluid or tissue based.

Mitomics is also developing tests for lung, colorectal, ovarian, and breast cancers as well as other cancers and has programs in non-cancer disease areas, though Poulter declined to elaborate.

As Mitomics continues on its commercialization path, the company this week hired Jason Dulude as chief financial officer and Chris Merritt as vice president of sales and marketing, a newly created position. At the same time, it added three members to its board — Vijay Aggarwa, CEO of Vaxigenex and managing partner of Channel Group; Kenneth Fallon, chairman of Osteotech; and Jim LaFrance, President and CEO of LaFrance Consulting Group.

Poulter arrived at Mitomics in 2007 in order to guide Mitomics through its commercialization mode, and in 2008 the company partnered with Dermaglow, a Canadian skin care firm, on DermaDNA, a system to measure an individual's DNA damage from sun exposure. The system consisted of a DNA test and products to prevent and repair DNA damage.

The prostate cancer test, however, is "really product number one" for Mitomics, Poulter said. "And this will be the key source of our early-stage revenues."

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