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Viome Life Sciences Prepares Clinical Study of Microbial Transcriptome Test in Oral, Throat Cancer


NEW YORK – Viome Life Sciences is further expanding into the cancer diagnostics space with preparations for a pivotal clinical study of its CancerDetect saliva test.

Last year, the firm, previously better known for its microbiome-based wellness products, published a description of its diagnostic classifier for oral cancer — which relies on microbial transcriptome, or metatranscriptome, profiling — in NPJ Genomic Medicine and is now planning a clinical study of the classifier's clinical utility.

In addition to the cancer study, Viome is collaborating on several other clinical studies across various disease indications, including diabetes and irritable bowel syndrome (IBS).

Revenue from Viome's consumer wellness products helps fund the firm's clinical studies, according to Guruduth Banavar, the firm's chief technology officer. "This was always our vision — to collect data from consumers, do the analysis, and then get into therapeutics and diagnostics," he said.

Last year, the company determined it had achieved a "critical mass" of data collected from consumers, stored and analyzed on its newly branded ViOS platform, enabling it to begin its foray into diagnostics and therapeutics research.

By having achieved this critical mass, Banavar said, "we decided that we would formally create a new business unit for the health sciences [business]."

The ViOS platform combines biological samples — largely blood, stool, and saliva, although Viome has begun collecting other types, such as cerebrospinal fluid — with machine learning-driven metatranscriptomic analysis to discover biomarkers and identify potential therapeutic targets for further research, as well as to construct predictive models for a variety of disorders.

The platform's database currently boasts some 325,000 samples and continues to grow by an estimated 10,000 samples per month, Banavar said, all coming from Viome customers.

Other self-reported clinical data often accompanies these samples, such as an individual's medical history, medications, symptoms, lifestyle habits, and diet.

Banavar estimated that roughly 200,000 people have bought Viome's microbiome-based wellness tests and an additional 11,000 to 12,000 people maintain monthly subscriptions to the company's products, such as supplements, probiotics, and prebiotics.

Viome did not say how much revenue its wellness business generated last year, but it also raised $54 million in pre-Series C funding last November, bringing its total amount raised to $125 million.

Viome was further buoyed by receiving breakthrough device designation for its CancerDetect oral and throat cancer early detection test from the US Food and Drug Administration last year.

"The FDA breakthrough designation gave us the confidence that we have some support from the regulatory and scientific communities, and that this is worth going after," Banavar said.

In Viome's recently published study, the classifier demonstrated up to 83 percent sensitivity and 97.9 percent specificity, but the firm needs stronger results from a more controlled study to pursue FDA approval for CancerDetect, which is currently offered as a lab-developed test.

"The microbiome is undoubtedly important for oral carcinogenesis," said Jiyoung Ahn, a professor of population health at the NYU Grossman School of Medicine, "but to be used as a tool for cancer diagnosis and risk assessment, these should be evaluated in a rigorous study setting," specifically a large prospective study with multiple independent replications.

Viome is preparing to launch a pivotal study within the next couple of months to validate CancerDetect's effectiveness compared to histopathology and imaging analysis. The trial will take place at several US locations and Viome aims to recruit "thousands" of participants, although the final number is still being discussed with the FDA. "We've signed off on the protocol, and it should start recruiting very shortly," Banavar said.

While Ahn largely applauded the firm's work in evaluating the links between the salivary metatranscriptome and cancer, she cautioned that in the therapeutics space, "we have a very limited understanding of whether the oral microbiome influences the response to cancer therapy in oral cancer patients."

One factor that could complicate evaluating therapeutics based on microbiome transcriptional responses, Ahn explained, is that it is unknown how stable the microbiome remains over the course of therapy, with active research efforts across multiple cancer indications ongoing.

Although still in very early stages, Viome also plans to use its metatranscriptomic tools and expertise to pursue cancer therapeutics through collaborations with other drug developers.

"We're taking the next step now, of getting into drug development," Banavar said, adding that Viome plans to create lead molecules based on analyses made using ViOS.

Once the company has a preclinical candidate, it plans to look for clinical trial partners.

Beyond cancer, Viome is investigating several potential therapeutic targets for IBD, coming from both human and microbiome gene signatures, although Banavar said it was too early to comment on results.

"Our ViOS platform has enabled a rapid way — just a couple of months — to identify novel targets for IBD on the human host side, on the microbiome side, as well as the interactions between the host and microbes," he said.

The company is also collaborating on clinical studies in other, undisclosed metabolic disorders with Advent Health, and in obesity and insomnia with the Mayo Clinic.

"Our interventional metabolic study with Advent Health is an adaptive study that includes hundreds of participants," Banavar said. "These protocols are already approved by IRB and we will soon be starting to recruit these patients."

Other studies with Advent Health are being planned, he added, and the Mayo Clinic study is still being designed.

Despite the pivot toward diagnostics and therapeutics, Viome does remain committed to growing its personalized nutrition program.

The company recently published a preprint on BioRxiv, using ViOS stool and blood sample data to make personalized dietary recommendations for people with IBS, type 2 diabetes, depression, and anxiety.

Viome currently employs approximately 150 people and expects to double in size over the next year or two. The company is located in Seattle and New York City, with its biopharma operations largely located in Seattle and computational biology operations mainly in NYC. Banavar said he expects the majority of near-term hiring to focus on the Seattle location.