SALT LAKE CITY DNA-methylation analysis appears to be gathering momentum as an approach parallel to or even competing with genotyping and gene-expression analysis in pharmacogenomics applications.
After recently hinting at a move toward, Sequenom has taken the plunge and announced a service offering in that market. When asked whether Sequenom intended to look into fetal gene expression in maternal blood, Harry Stylli told Pharmacogenomics Reporter that "if you look at methylation markers, they're involved in gene regulation."
But Sequenom is not focused on fetal DNA-methylation diagnostics not yet, at least. The recently launched detection service and a software add-on for performing methylation detection with its MassArray platform, due in the first quarter of next year, are research-only offerings that make good on a September pledge to enter the methylation market, as well as the market for quantitative gene expression.
"Unlike the expression field and the genotyping area, where people have accumulated a lot of data already, in terms of methylation, it's a much more wide-open area because the biological knowledge base doesn't exist yet."
Sequenom officials will not say one way or the other whether the company intends to pursue clinical diagnostics in this arena, but the recent declaration by Harry Stylli, the company's CEO, that Sequenom is committed to molecular diagnostics, along with methylation's obvious ties to disease and fetal DNA detection, certainly hint at diagnostics applications for the technology. Although DNA-methylation is one of the less-common biomarker analysis methods, there are indications that the technology will make its way into guiding drug-prescription choices, and it is already making inroads in predictive screening.
"We can see the field is moving toward methylation for expression analysis," Christian Jurinke, Sequenom's director of product development, told Pharmacogenomics Reporter at the American Society for Human Genetics conference held here last week. Diagnostics applications for which methylation analysis is suited could include cancer prognosis and cancer drug-therapy monitoring, he said.
Another possible application of the methylation technology couples it with Sequenom's intellectual property in fetal DNA analysis, as foreshadowed by Stylli. The company is looking at using methylation detection as a "quality control tool" to distinguish fetal from maternal DNA in serum, Jurinke said. "We believe methylation is very useful there," he added.
Sequenom has not yet decided whether it would pursue US Food and Drug Administration clearance for molecular diagnostics coming out of the MassArray methylation analysis system, said Jurinke.
"Mass spec is a very sensitive technology that can be adapted to run many, many genes at the same time," said Jorge Leon, president of the consulting firm Leomics and acting chief scientific officer and vice president of business development of Orion Genomics. "So I think that Sequenom could be very critical in two aspects," he said. "One is that this could be perhaps the best technology available right now to detect multiple methylation markers at the same time I'm talking 10, 20, 30, 40," with methylation-based cancer diagnostic assays possibly requiring the use of that many genes, he said. "If you do real-time PCR on that, it's going to be a nightmare."
"The other advantage is that it might be very sensitive," said Leon. "In combination with the enzymatic approach, the platform could be more sensitive than real-time PCR for detecting DNA in serum," he said. "So if they prove that, then [theirs] will be the platform of choice, but that remains to be seen."
Outside of the fetal DNA applications, the field seems to be picking up steam. Other players in the methylation-detection market include Ann Arbor, Mich.-based Rubicon Genomics, Berlin-based Epigenomics, St. Louis, Mo.-based Orion Genomics, Amsterdam, The Netherlands-based Oncomethylome; and Uppsala, Sweden-based Biotage.
The Methylation Landscape
Of these, Rubicon made the most recent news, announcing this week that it had signed an agreement with Abbott Molecular to develop and commercialize its methylation detection technology, MethylPlex, for prostate- and bladder-cancer diagnosis and prognosis from urine and serum samples. "We anticipate having products on the market before five years," along with FDA clearance, said John Langmore, the firm's vice president of commercial development, in an interview this week.
Rubicon is not now developing any products that are directly tied to guiding drug treatment, but "anything that you do in diagnostics could become a tool in pharmacogenomics as well," Langmore said.
Pharmacogenomics tools based on methylation would range as broadly in application and disease area as tools based on gene expression, said Langmore. But "unlike the expression field and the genotyping area, where people have accumulated a lot of data already, in terms of methylation, it's a much more wide-open area because the biological knowledge base doesn't exist yet," he said.
Other indications in which methylation may prove useful in diagnosis and treatment include cardiovascular disease and autoimmune diseases, but Rubicon is looking for more collaboration partners to help them develop further cancer tests, Langmore said.
Epigenomics works with pharma companies in clinical studies, and uses intellectual property from the collaborations to help develop diagnostic products to run on one of several platforms, such as Roche's TaqMan, said Oliver Schacht, the firm's CFO in an interview.
This week, Epigenomics said in a statement that it was unable to validate candidate methylation markers "for technical reasons," in a study of its Tamoxifen treatment-response diagnostic that the company is carrying out with partner Roche Diagnostics. Ideally, the Epigenomics-Roche test would inform physicians which patients to treat with chemotherapy, in addition to Tamoxifen or aromatase inhibitors, Schacht said. Tamoxifen is an AstraZeneca product.
In addition to the Tamoxifen-related diagnostic, the company is working with Roche on four other diagnostics one early-detection test each for colon, prostate, and breast cancer; and a prognostic test for prostate cancer. The company is also working with Qiagen, which plans to produce a bisulfite kit for treating DNA samples prior to analysis using one of Epigenomics' kits. Epigenomics hopes to launch its first products next year.
Like Langmore, Schacht likens the size of the market for methylation diagnostics to that of RNA expression diagnostics.
Orion Genomics said in August that it will be collaborating with Washington University researchers to discover DNA methylation-based biomarkers of a tumor's response to certain drugs, with the goal of eventually producing a cancer test. "We're in discovery for three specific diagnostic tests right now, and two more will enter discovery in the near future. We should be in development in the first or second quarter next year of our first test," Nate Lakey, the company's CEO, told Pharmacogenomics Reporter.
Like most of the firms approaching diagnostics using methylation detection, Orion is working on cancer screening diagnostics, "as well as one therapy-selection paradigm," Lakey said. "We're looking at lung, breast … cervical cancer, ovarian cancer, colon cancer those are our initial focus," he said. Lakey declined to disclose which drug the therapy-selection assay addresses.
The market for methylation-based diagnostics is "absolutely huge," said Lakey, although he was unable to provide a more precise estimate. "There is evidence that epigenetics is involved in obesity, diabetes, psychiatric disorders, some infectious disease paradigms, immunity, autoimmunity these are huge research markets, but no one has made a clean connection" between methylation and these areas, he said. As many as 1,500 papers in the last three years discuss methylation's role in cancer, however, "so the cancer research market is absolutely hot right now," he added.
OncoMethylome is working on screening assays as well, and in many of the same areas as its competitors: prostate; lung; colorectal; breast; cervical; and bladder cancer; and glioma. The company could not be contacted for comment before deadline.
Biotage is the only direct competitor for Sequenom's DNA-methylation service interviewed for this article. "We've had a DNA-methylation detection service for about a year," said Rene Myers, the company's vice president of technology support for its biosystems group. In May, the company launched two methylation-detection tests based on its pyrosequencing technology an assay to check the status of the gene MLH1, which is implicated in colon, gastric, and endometrial cancers, and a test for the gene p16, which is implicated in several tumors.
One likely avenue for methylation in pharmacogenomics involves cancer drugs that alter DNA methylation. "What you need is a way to monitor, in the short term, the decrease in methylation the reversion to normal phenotype," said Langmore. This application would probably find its first uses in stratifying patients in clinical trials before it became available for clinicians, he said.
The taxane class of cancer drugs, such as Bristol-Myers Squibb's taxol, may prove to be another arena in which methylation status will help doctors make prescription decisions, said Orion's Jorge Leon. "We know that methylation is heavily involved in the pathway of taxol response, so there's a possibility that methylation plays a role," although it's not yet known exactly what that role is, he said.
Taxanes are typically prescribed for metastatic ovarian and colon and prostate cancer. Several studies have examined the use of the methylation status of the CHFR gene as a marker of taxane sensitivity.
Chris Womack ([email protected])