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Startup HealthBioCare Combining cfDNA, Methylation, miRNA Markers for Early Cancer Detection

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NEW YORK – Vienna-based HealthBioCare, a spinout of the University of Vienna is developing a liquid biopsy assay combining cell-free DNA mutations, DNA methylation markers, and microRNAs to improve the detection of multiple cancers via multiple analytes in a single test.

In a recently published pilot study in the journal Cancers, the test classified healthy versus tumor tissue with 95.4 percent accuracy, 97.9 percent sensitivity, and 80 percent specificity.

HealthBioCare now plans to validate the clinical utility of this multi-analyte test in a larger prospective cohort before seeking European regulatory approval for a lab-developed test.

This represents the company's entry into the cancer diagnostics field. HealthBioCare has primarily focused on nutrition-based health interventions but according to Berit Hippe, the company's scientific director, the firm's experience in designing epigenetic tests led to the current study, done in collaboration with the University of Vienna.

For their study, Hippe and her collaborators used real-time qPCR to analyze various combinations of cfDNA mutations, DNA methylation markers, and miRNAs in patient blood samples to identify a subset of each that, when combined, discriminated healthy individuals from those diagnosed with bladder, brain, breast, colorectal, lung, ovarian, pancreas, prostate, and stomach cancers.

Methylation markers on cfDNA provide information on a tumor's tissue of origin and have been used in prior studies to localize cancers of unknown primary origin and to detect metastases. This complements the information gleaned from single nucleotide polymorphisms, which can provide insights into a tumor's biology but often occur in multiple tissues.

While miRNAs are viewed as an attractive cancer screening biomarker for their inherent stability and abundance, research into their use as cancer screening biomarkers remains at an early stage.

"Since a lot of research has been conducted in the area of DNA mutations," Hippe said, "their clinical utility has been established worldwide. MiRNAs are something new. They are exciting, but since there is still not so much information and research on them, they can be risky."

Despite the risk, the idea of improving cancer detection, as well as downstream processes such as minimal residual disease monitoring, using multiple analytes has taken hold.

"If you look at the field for early cancer detection in general, most companies are using at least two analytes, and the most common combination would be methylation and DNA [mutations]," Alexey Aleshin, vice president of Natera, said in an interview.

Last year, for instance, Natera signed an agreement to license Aarhus University's DNA methylation signature for colorectal cancer, which the company plans to combine with its own methylation and circulating tumor DNA technology in a future offering.

The final composition of that test is still a few months away, Aleshin said, adding that the company would likely present some initial data related to it at the end of the year.

Aleshin commented that Natera is looking at emerging data for miRNA and other RNAs in the cancer detection field, although the field is immature at this point, with insufficient evidence and experimental reproducibility.

"We're definitely watching it evolve with great interest, in terms of where miRNAs may fit in," he said.

Given that lack of evidence, it may be telling that initial attempts to combine all three analytes in the HealthBioCare/University of Vienna study resulted in limited gains in specificity, at the cost of sensitivity. The researchers had to perform several rounds of computational analyses to identify a subset of markers contributing to a final classifier.

Given the amount of statistical analysis needed to arrive at this subset, "the power of the study may lie in exposing that too much of a 'good thing' is not necessarily that good," Prem Subramaniam, an associate research scientist at Columbia University specializing in cancer biology, said via email.

Nonetheless, one interesting finding in the study, which HealthBioCare hopes to elaborate on in future studies, was the presence of a prostate cancer-associated androgen receptor mutation called AR p.H875Y in six other cancer types spanning multiple organs.

"To our knowledge," the study's authors wrote, "this is the first time that [the] AR p.H875Y mutation has been reported for bladder, lung, stomach, ovarian, brain, and pancreas cancer."

HealthBioCare is currently planning a larger study, aimed at validating this test's clinical utility. The company aims to analyze the liquid biopsy's performance in all nine cancer types analyzed in the recent study, as well as in liver cancer, for which too few samples were collected to have been included in the earlier analysis. The company intends to recruit approximately 200 people per cancer type, between patients and healthy controls.

As part of that study, HealthBioCare intends to field a new method for stabilizing cell-free DNA and RNA. Although standard methods for isolating and freezing these nucleic acids in plasma were used in the current study, the company said that it developed a stabilization method that allows plasma containing those molecules to be held at room temperature for up to seven days, facilitating sample storage and shipment.

"For the second phase of this project," Elena Tomeva, the study's first author said, "we plan to use this new method for the stabilization of cell-free DNA and RNA in whole blood, [to facilitate] the processing and shipment of samples."

The timeline for that larger study has not been set, as HealthBioCare is currently seeking partners to support it.

"Since we are a small biotech company, we are still looking for investments and financial support," Hippe said via email. "We are open for collaborations with clinical centres and universities."

Research services company System-Biologie helped finance the recent study and plans to continue the collaboration, with the long-term plan of using epigenetic markers to guide development of plant extract-based cancer therapies.

"The ultimate goal is to detect problems early and repair the problem at an early stage," Juerg Daniel Schmid, a member of System-Biologie's board, said via email.

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