NEW YORK (GenomeWeb) – Molecular diagnostics test developer RiboMed has begun expanding its epigenetics-based diagnostics offering beyond CLIA-lab oncology testing services. The firm recently won funding to apply its core technology to develop a non-invasive endometriosis diagnostic, with the intent of ultimately offering the test as an IVD.
RiboMed currently provides testing services for oncology, particularly brain cancers, from a CLIA lab in Phoenix, Arizona, using a few proprietary technologies.
The firm has developed a system for quantitatively measuring gene-specific DNA methylation at high sensitivity and with an extremely low failure rate, said founder and CEO Michelle Hanna. This is possible even with degraded samples and low concentrations of targets, she added.
The "secret sauce" in all RiboMed assays, Hanna said, is a proprietary technology called coupled abscription PCR signaling, or CAPS.
The method can detect small DNA targets of fewer than 50 base pairs using a technique called abortive transcription, whereby a proprietary RNA polymerase performs reiterative synthesis of short RNA abortive transcripts, or abscripts, from an artificial start site that is added to gene targets using PCR.
The method yields "hundreds to thousands of abscripts per minute per amplicon," Hanna said, and abscripts in turn cause fluorescence of molecular beacon molecules. It also works independently of the target type or sequence, and thus can be used to detect DNA, RNA, or protein, as well as DNA methylation.
A second RiboMed technology, called MethylMeter, was described in Epigenomics in 2016. It is basically an application of CAPS for DNA methylation detection, Hanna said.
The process first involves using a methylated CpG binding protein the firm has developed, called MethylMagnet, to separate methylated and unmethylated DNA, followed by measurement of DNA copy number in each fraction to get a readout of methylation of each target gene.
RiboMed currently offers some of its reagents, such as the MethylMagnet binding protein, as RUO products, and the MethylMeter test itself is currently available as a service in its clinical lab. The firm is also in the process of scaling up manufacturing of the core reagents so that it can make them available in kit form and provide them to other CLIA labs, a process that should be completed sometime in 2020, Hanna said.
RiboMed was initially founded in Phoenix, Arizona in 1999. The company moved to San Diego for a few years, but recently returned. "Now that we have a functioning CLIA lab, the environment for expansion is better in Phoenix," said Hanna, particularly considering the requirements for scaling up reagent manufacturing.
In addition, RiboMed develops gene-specific DNA methylation assays for clients, particularly offering methylation assays to pharma companies developing new treatments for brain cancer, Hanna said.
In general, "because of its high sensitivity and low failure rate, the technology is the perfect platform for clinical diagnostic tests, including those involving liquid biopsies," Hanna said.
In 2016, RiboMed began collaborating with Tocagen, a company developing cancer-selective gene therapies for patients with recurrent high-grade gliomas. RiboMed has developed an assay, called GliomaStrat, that stratifies brain tumors into high grade or low grades, and can be used to predict response to a chemotherapy drug called temozolomide, or TMZ. Tocagen is using this test to guide treatment as part of its development of a product to stimulate a patient's anti-cancer immune response.
RiboMed is also targeting researchers who have identified potentially clinically relevant DNA methylation biomarkers that may wish to translate their panels to successful clinical tests, Hanna said.
"Every time I present our data, I hear stories about low sensitivity and high failure rates with bisulfite-based tests, even when working with a single gene," she said, adding that attempts to develop multi-gene DNA methylation biomarker panels often fail. These issues are the primary barrier to the translation of potentially beneficial panels to commercially available diagnostic assays, and the RiboMed technology can offer a solution to the problem of high failure rates, Hanna said.
RiboMed will continue to work on oncology assays and offer its tumor stratification tests in its CLIA lab. But the firm has also now expanded to endometriosis test development.
It was awarded new funding this month — totaling $164,306 for one year — from the National Institute of Child Health and Development under a call for proposals to develop non-invasive diagnostics to improve gynecologic health.
"We saw the opportunity to apply our platform technology outside of oncology, in an area of unmet need," Hanna said regarding the expansion.
Although approximately ten percent of women of childbearing age suffer from endometriosis, there is currently no easy method for detection, and the average time from onset of painful symptoms to diagnosis is about seven years, Hanna said. "Because of this debilitating disease, millions of women suffer for decades from pain, productivity loss, and infertility."
The goal of the project is to develop a noninvasive test that will allow for early detection, potentially leading to treatment before significant damage is done to a woman's reproductive system.
The project also fits well with an existing collaboration with the University of Arizona Cancer Center to identify epigenetic biomarkers for diagnosis and treatment of ovarian cancer, Hanna said.
Previous research has suggested an epigenetic component to endometriosis, including variations in methylation of genes known to be involved in the aberrant hormonal, immunologic, and inflammatory aspects of the illness.
"We have selected a subset of these genes for which disease-associated dysregulation of DNA methylation is implicated for further analysis and clinical validation using our MethylMeter technology," Hanna said.
For Phase I, the company will refine this biomarker panel and optimize its assays in tissue culture using samples from an endometrial tissue and DNA bank. RiboMed will then work to clinically validate the assay.
"The goal is to produce an affordable diagnostic test that will be available for women presenting with the symptoms of endometriosis," Hanna said. The test will initially be offered in RiboMed's lab, but the firm will also perform the additional clinical validation required to get US Food and Drug Administration clearance for an IVD. "As we did with our brain tumor stratification panel, GliomaStrat, we will also offer the tests as RUO kits to the research community," Hanna said.
Currently, the new funding is the only grant funding the firm has, although it also has ongoing contracts with companies to test brain tumors as part of their clinical trials.
The firm had previously been funded by the Defense Advanced Research Projects Agency, or DARPA, to develop a handheld bioterrorism monitor with Northrop Grumman, but this project did not ultimately result in a product. RiboMed developed tests for detection of protein toxins and RNA viruses, Hanna said, and had achieved the sensitivity and specificity goals by the end of Phase III. "But the project required the prime contractor to develop a handheld detector that contained a mass spectrometer on a chip, and that never happened," she said.