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Paradise Genomics Seeks Partners to Translate Gene Expression Profiles Into Clinical Dx Assays

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NEW YORK – Paradise Genomics has exited stealth mode with a process for determining highly accurate disease-specific gene expression profiles from cells found in whole blood samples, and is now seeking commercialization partners to turn these "bioprofiles" into clinical gene expression-based diagnostic assays.

So far, the Northbrook, Illinois-based company has developed profiles for celiac disease, major depressive disorder (MDD), and bipolar disorder, and is working on bioprofiles for several kinds of cancer, intestinal metaplasia, attention deficit hyperactivity disorder, post-traumatic stress disorder, and fibromyalgia.

The company, founded in 2011, chose to focus on whole blood cells because, as CSO and Cofounder Scott Magnuson describes it, "from a practical standpoint, blood is circulating all over your body and it 'sees' every different disease in every physiological state immediately."

Essentially, the idea is that disease-related cellular signals, such as tumor cell-related angiogenic factors, trigger a response from other circulating cells, which is reflected in gene expression changes. Paradise's technology detects these changes and maps them to a corresponding physiological condition.

The approach is uncommon in the diagnostics field although the underlying biological process is fairly well known.

Past studies, for instance, have found whole-blood gene expression profiles associated with vasospasms in subarachnoid hemorrhage, the responses of dendritic cells to pathogens, and in the body's response to sepsis, among other things.

Ash Alizadeh, a professor of medicine and expert in oncology gene expression profiling at Stanford University, suggested that a noisy background may prove a stumbling block in commercial development of this approach.

"From what I have seen thus far," he said, "I think the [signal-to-noise ratio] profile of these gene expression profile signals has yet to demonstrate sufficient robustness to be considered ready for prime time for use as diagnostics." Alizadeh is also scientific cofounder at Foresight Diagnostics, which is developing liquid biopsy tests for early cancer detection.

Michael Falduto, Paradise's cofounder and chief technology officer, explained that this is precisely the area in which the firm has made some of its biggest strides. In internal studies, Paradise has used its expression profiling method, which makes use of Agilent's Whole Genome Microarrays, to distinguish disease states from healthy cells with accuracies ranging from 95 percent to 100 percent. This enhanced accuracy is due largely to a proprietary sample preparation procedure, which Falduto and Magnuson refined at their earlier venture, GenUs BioSystems, which remains in business as a microarray services provider.

"Hybridization is where we are able to decrease background a lot," he said, explaining that a strong emphasis on sample preparation facilitates a high degree of reproducibility in the firm's discovery process.

"And then in data analysis," Falduto added, "because it's so reproducible, we're really able to find those genes that are differentially expressed [at a] pretty low level."

Although Paradise's process is a trade secret, Falduto and Magnuson explained that much of it came down to refining well-known processes.

The low signal-to-noise ratio also enables Paradise to detect signals across a broader dynamic range than standard RNA sequencing techniques, contributing to the accuracy of its profiling tech, Magnuson said. 

Paradise claims that its 92-mRNA celiac disease bioprofile, for instance, proved 100 percent accurate at diagnosing the disorder in a study of 22 biopsy-positive celiac patients and 16 unaffected controls.

The company is currently exploring partnerships with "a couple" companies, in the hopes of developing the celiac bioprofile as a lab-developed test.

"We would rather not be the CLIA lab running this as an LDT," Magnuson said, "because that would take up all of our time."

Paradise has also developed gene expression profiles of bipolar and major depressive disorders, and claims that the expression of only four mRNAs is sufficient to differentiate the two. Below a certain level of expression of these mRNAs, Falduto said, the firm could identify clinically confirmed bipolar patients with 100 percent accuracy, although a few MDD patients might still fall below the threshold and be evaluated for bipolar disorder.

Nonetheless, any improvement in rapidly discriminating between the two disorders, whose symptoms often overlap, could save months of testing and analysis, as well as lower the risk of misdiagnosis and being prescribed suboptimal medication.

"They're very different disorders with very different therapies and very different drugs that work in those two disorders," Falduto said. "So the potential of having a biological test to accurately diagnose bipolar disorder will make a huge difference to medical practice."

The profiles for bipolar, MDD, and celiac disease are currently at the most mature stage, and Paradise is looking for partners to help further develop and commercialize both of them. The company has several other profiles in the pipeline, including for several cancer indications.

"Colon cancer, lung cancer, and gastric cancer also are showing really good promise in our accuracy levels and in what we could potentially do with the early diagnostics for those cancers," Falduto said.

Despite the large number of players in the cancer liquid biopsy field, Falduto and Magnuson feel that their approach makes them unique in terms of the technology being offered.

"Nobody is really doing discovery in the way that we're doing it for cancer diagnostics," Falduto said.

For instance, the firm has discovered three genes whose expression Falduto and Magnuson say can be used to diagnose non-small cell lung cancer and that were previously unknown to associate with that disease.

Paradise currently employs seven people, focusing on bioprofile discovery and validation.

"Right now," Magnuson said, "we need to keep it that way for funding reasons, but we'll grow as we can."

The firm is privately funded and has so far raised approximately $2.5 million. Paradise expects more funding rounds to be forthcoming but as yet has no specific timeline.

Paradise hopes to have a viable test on the market within the next two years.

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