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Summit Biolabs Commercializing Tests for Head and Neck Cancer Recurrence, COVID-19

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NEW YORK – Startup Summit Biolabs is leveraging a newly forged agreement with the Colorado Center for Personalized Medicine (CCPM) to commercialize a saliva-based assay for head and neck squamous cell cancer (HNSCC) recurrence, as well as a suite of assays for COVID-19 detection and diagnosis.

The firm's HNSCC recurrence testing platform, dubbed HNKlear, uses quantitative methylation-specific PCR (qMS-PCR) to detect methylated microRNA biomarkers linked to HNSCC in a patient's saliva following frontline treatment.

Originally spun out in 2018 as Summit Dx by associate otolaryngology, dermatology, and pathology professor Shi-Long Lu at the Colorado University Anschutz Medical Campus, the Aurora, Colorado-based firm rebranded as Summit Biolabs earlier this year. The firm exclusively licenses IP related to the detection of viral contagions in saliva, which was jointly developed by Lu's team, researchers at Washington University in St. Louis, and Summit Biolabs.

Summit Biolabs CEO Bob Blomquist explained that Lu, who serves as the company's CSO and president, initially wanted to find out if he could reliably detect oral oncogenic human papillomavirus (HPV) in patient saliva samples.

HPV infects a patient's skin and mucous-lined areas, often leaving warts in these areas and potentially causing HNSCC. In rare cases where HPV fails to be removed or treated, the virus can eventually cause cellular damage that leads to tumor growth in a patient's throat, tongue, and tonsils.

Lu's team then expanded its approach earlier this year to develop an assay to detect SARS-CoV-2, the RNA-based virus that causes COVID-19.

"When the pandemic hit, we were starting to raise money for HNSCC detection," Blomquist said. "But now we believe we can detect RNA viruses in a patient's liquid sample with our platform."

Summit Biolabs' HNKlear workflow begins by collecting up to 5 ml of a patient's saliva sample using different collection techniques, including DNA Genotek devices and centrifuge tubes using Summit Bio's "secret sauce to stabilize the virus," Blomquist noted. Bisulfite conversion on extracted cell-free DNA is then performed before using qMS-PCR to identify potential miRNA biomarkers linked to HNSCC. 

"Compared to using blood-based tests, the [HNSCC] is located to a patient's salivary glands, so you can use the markers earlier in the saliva than in blood," Blomquist said. "The cancer also has to be more advanced before it breaks the membrane and enters the blood, [suggesting that] we can detect HNSCC earlier in saliva before blood-based liquid biopsies."

 Lu's team initially published data on the qMS-PCR based method for detecting HNSCC in a 2018 Clinical Epigenetics study, developing a panel of "methylation of genomic loci encoding microRNA" (mgmiR) biomarkers from a cohort of 315 HNSCC and control patients. The group found that a qMS-PCR panel containing seven biomarkers had a clinical sensitivity of 77 percent and specificity of 86 percent when using patient saliva samples, and sensitivity and specificity of 93 percent and 92 percent, respectively, in tissue samples.

In a retrospective study presented at the American Association for Cancer Research's "Advances in Liquid Biopsies" conference in January, Lu and his colleagues used the qMS-PCR approach to screen for HNSCC biomarkers in a patient cohort that included 281 tissue samples (189 cancer and 92 controls) and 194 saliva samples (86 cancer and 108 controls). Using the previously developed seven-biomarker panel, the team found that the assay had a clinical sensitivity of 85 percent and a specificity of 95 percent in saliva samples, compared to a clinical sensitivity of 92 percent and specificity of 98 percent in tissue samples.

"The preliminary data that we have [suggests that] we can detect HNSCC in saliva up to a year earlier than a physician can detect in standard clinical practice for observing recurrence," Blomquist said. "If you can detect [recurrence] early, you could hopefully guide treatment for and deescalate treatment after recurrence."

Lu and his colleagues are now performing a longitudinal prospective study for HNSCC recurrence, monitoring a cohort of 43 patients following curative treatment.

Summit Biolabs is also developing COVID-19 detection tests using the same analysis platform, collection methods, and stabilizing solution as the HNSCC assay.

Blomquist elaborated that Summit Biolabs is developing three different assays that will look at viral RNA: COVIDCount, a quantitative test for SARS-CoV-2, including viral load determination for diagnostic use in symptomatic individuals;  COVIDClear, a PCR-based nucleic acid test for diagnostic use in symptomatic individuals; and COVIDFast, an extraction-free, PCR-based nucleic acid test for screening asymptomatic individuals. The firm is aiming to provide a 24-hour turnaround time for these tests.

The company has received IRB approval to begin a clinical study comparing viral RNA detection between matched patient saliva and nasopharyngeal or anterior nares specimens in asymptomatic individuals. Starting in November, the team will collect samples from up to 2,000 subjects at two undisclosed study sites in Colorado.  

"There are a few things we have to work out before developing other tests like tests for viral antigens in saliva," Blomquist said. "As a small company, we want to initially see if we can detect the virus, and then later address the next phase of the pandemic by observing quantitative information."

CCPM collaboration

Summit Biolabs will partner with Kristy Crooks, assistant professor of pathology at CU School of Medicine, and her team at the CCPM to commercialize the HSNCC and COVID-19 assays as laboratory-developed tests at the group's CLIA-approved lab. Crooks noted that her team will look at genetic data of patients in the CCPM's clinical database to see how the group can best utilize it for different patient populations.

"We were already a high-throughput clinical laboratory with liquid handlers, so we could easily adapt our existing system to do 1,000 tests a day, [while] most other clinical labs on campuses our size don't have that sophistication," Crooks said. "It just happened that we had the appropriate instrument for the COVID-19 test that we had planned to leverage for a test we were developing, but it was mostly idle."

Brian Harry, assistant professor of pathology at CU School of Medicine, added that CCPM's annotated biobank acts as a resource for designing new methods for cancer detection such as HNKlear.

"The hope is that the CCPM-Summit collaboration will begin with saliva and COVID-19, and to make the testing available to groups that haven't had testing options previously, such as disadvantaged and underserved communities," Harry explained. "Beyond COVID-19, CCPM's clinical and research expertise and biobank laboratory of over 50,000 samples provide fertile ground to work with Summit to develop assays for early cancer detection."

Blomquist said that Summit Biolabs may eventually use the HNKlear technology and CCPM's resources to develop a screening assay for early detection of HNSCC in high-risk individuals following the launch of its recurrence panel in 2023

Summit Biolabs also hopes to have at least one COVID-19 binary running by the end of this year, Blomquist noted.

Since launching in 2018, Summit Biolabs has raised about $300,000 between academic funding, including a SPARK Colorado grant, as well as private financing. The firm hopes to raise more than $3.5 million in a current funding round to further advance the HNKlear platform.

In addition to receiving a patent from the US Patent and Trademark Office earlier this year related to HNSCC detection, Summit Biolabs has also filed other IP related to viral detection in saliva, including viral contagions, and methods for collecting saliva specimens.

"We filed the application earlier this year [for saliva collection], and found that other academic groups …such as Yale and Rutgers, were doing the same for COVID-19 detection," Blomquist said. "The key is detecting it early and reliably, but also to have a stabilizing solution so that you can send a sample from, say a rural area, to a lab."

Blomquist envisions the COVID-19 assays to cost the end user around $100, but he hopes to drive the cost lower depending on the results of validation studies and the firm's ability to increase testing throughput.

Blomquist believes that users might purchase Summit's COVID-19 tests over those from bigger, more established companies for multiple reasons, including the ease of saliva sample collection over nasopharyngeal swabs.

"Doctors and others that are trying to deploy testing are interested in how much virus is present [to] answer clinical questions," Blomquist said. "The reliability of our saliva test results because of our expertise in saliva-based diagnostics, quantitative SARS-CoV-2 viral load indication… and the confidence we will create from medically driven clinical validation … will generate [end-user interest]."