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Bio-Me Eyes PCR-Based Microbiome Profiling Technology for Future CDx

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NEW YORK ─ Microbiome profiling technology startup Bio-Me is kicking off a project to accelerate development of a companion diagnostic test that it believes can improve response rates to immune checkpoint inhibitor (ICI) cancer treatments.

The Oslo, Norway-based startup anticipates its qPCR-based Precision Microbiome Profiling technology will serve as a tool that helps clinicians address clinical challenges associated with how the gut microbiome influences the efficacy of ICI treatments.

The firm is launching the new project on the back of a €2 million ($2.2 million) grant it recently received from the Research Council of Norway, which Bio-Me expects to use to apply for regulatory approvals of its CDx around 2025.

Founded in 2016 by its CEO Morten Isaksen, the company anticipates that it will take until around then to launch a test for clinical use that provides results within hours to clinicians looking to treat their cancer patients with immune checkpoint inhibitors. However, Bio-Me is already seeing the potential of the technology to improve patient response rates for such treatments, Isaksen said in an interview.

Though the company has a few years of test development and validation ahead of it, its tool may prove to be what clinicians need to better match patients with ICI treatments, said Odd Terje Burstugun, principal clinician at Oslo-based Vestre Viken Hospital Trust, which is a collaborator in the project with Bio-Me, NTNU/HUNT4 Biobank, and Thermo Fisher Scientific.

Immune checkpoint inhibitors work well for patients with immune systems that respond to the treatments. However, response rates are generally well below what clinicians and their patients would like to see, and the treatments sometimes produce toxic side effects, said Burstugun, who is an oncologist at Drammen Hospital, part of Vestre Viken Health Trust.

Given the link between the gut microbiome and efficacy of ICI treatments, "response rates should increase substantially if we can use this tool to be more intelligent about how we determine which therapy combination suits a specific patient," Burstugun added.

To develop its approach, Bio-Me is leveraging published information derived from the sequencing of microbiome bacterial amplicons as well as deep shotgun sequencing, whole-genome sequencing, and other data. Sequencing approaches are frequently employed by researchers for exploration and discovery of microbiome molecular markers, and Bio-Me leverages the results of these studies for biomarker identification, but the firm's microbiome profiling technology is being designed to use qPCR for testing and response prediction.

To develop its assays, Bio-Me uses Thermo Fisher Scientific's OpenArray platform, a PCR–based technology for gene expression analysis, genotyping, microRNA analysis, and digital PCR applications. Bio-Me's microbiome profiling panels enable drilling down to the species level and detecting strains within a species for each qPCR reaction, Isaksen said.

One version of its precision microbiome profiling panel uses 56 through-holes with each one enabling a PCR reaction, he noted. Such a panel would detect 53 target bacteria, while the remaining holes are used as control elements for the assay. The setup enables running profiles involving those 53 bacteria for each of 192 samples within two hours, Isaksen said.

The firm is further developing algorithms that use the presence of identified bacteria biomarkers in fecal samples to predict patients' potential to respond to a given ICI therapy.

Though the company is developing panels for academic research, its focus is on clinical applications, where issues of test turnaround time, accuracy, and reproducibility are needed, Isaksen said. Its microbiome profiling panels provide direct quantification, detecting the number of bacterial DNA molecules in each sample, which is the level of data needed for microbiome analysis, he added. 

The company's focus areas include illnesses associated with inflammation of the digestive tract, as well as cancers. For example, Bio-Me is seeking to apply its technology to distinguish between Crohn's disease and ulcerative colitis in children and adults.

However, its immediate focus is on kicking off the project funded by the Research Council of Norway, in which the company anticipates developing and using qPCR panels to test up to 1,000 patient fecal samples.

For the first two years of the project, the investigators expect to devote most of their time and resources to identifying and fine tuning the selection of biomarkers to use in their panel, Isaksen said. They will also devote part of that time to training and fine-tuning the companion diagnostic test's prediction algorithm.

In 2022, a year before the expected end of the project, the group anticipates conducting an interventional study in which clinicians will seek to validate the tool in a clinical setting involving patients undergoing lung cancer treatments.

Though use of Bio-Me's microbiome profiling as a companion diagnostic test may be years off, microbiome profiling, in general, for diagnostic testing is being explored by research organizations and companies. Researchers led by the University of California, San Diego, for example, have discovered unique microbial DNA signatures in the tissue and blood of cancer patients, leading to the development of a microbiome-based oncology diagnostic tool.

A UK research group has reported using metagenomic nanopore sequencing to rapidly diagnose preterm infants with suspected necrotizing enterocolitis, a life-threatening gut condition.

Further, OraSure Technologies plans to combine metagenomics sequencing with the microbiome services and sample collection technologies of its CoreBiome and DNA GenoTek subsidiaries to provide an end-to-end solution for microbiome analysis.

Bio-Me has deliberately opted for PCR over sequencing for its precision microbiome profiling tool because it believes its PCR technology can be more affordable and could provide turnaround times that are better aligned with what are required by clinicians looking to prescribe better ICI treatments.

The microbiome profiling technology has the potential to lift patient response rates well above the current 30 percent rate when it is used in combination with microbiome-modifying agents that are under development to increase the efficacy of ICIs, Isaksen said. Bio-Me is evaluating potential partners for its project that have suitable microbiome modifying agents.

Though the firm has yet to publish a study describing the technology and it applications, it anticipates published peer-reviewed studies will be available before the end of this year, Isaksen said.

The company continues to seek additional financing so that it can take on "more ambitious" plans for its microbiome profiling technology, he added.

Burstugun said that if the microbiome profiling tool can be launched it will cater to some important concerns of patients and clinicians. "By providing a sample at a doctor's office or by mail, the test will be convenient and easy to take," he said. "Also, the prospect of having a result in a short time is a very important point for this indication. We can't wait for weeks to have a result if we are to use such a tool to decide which treatment to use."

The timeline for availability of the test, however, is heavily dependent on "how the current project pans out," Burstugun added.

Isaksen anticipates that Bio-Me will eventually seek regulatory approval for its tool from the US Food and Drug Administration, as well as CE marking.

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