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OSU Researchers Advancing Next-Gen Sequencing Test for Detecting Microsatellite Instability

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This article has been updated to include additional information on Caris Life Sciences' next-generation sequencing panel.

NEW YORK (GenomeWeb) – Cancer researchers at Ohio State University are using a $1.4 million grant from the National Cancer Institute to develop a next-generation sequencing-based test that can determine microsatellite instability across a range of tumors and help guide patients to precision medicine trials.

The OSU team, led by Sameek Roychowdhury, developed an MSI-calling software called MANTIS, which they will use as part of the test to identify the hypermutational characteristic in tumors. The researchers plan to add the MSI detection capabilities to a 280-gene NGS panel that OSU's cancer center offers to patients.

"Next-generation sequencing is going to be a great way to expand MSI testing in cancer because today patients are all undergoing NGS for advanced cancers," Roychowdhury said. "It doesn't make sense to have them undergo so many different tests when it can all be bundled into the same assay. Especially with a finite specimen, you can't afford to keep doing multiple tests."

OSU's NGS panel currently detects single-nucleotide variants, indels, and copy number variations, and is intended to help doctors identify potential on- or off-label personalized treatment options for patients, as well as clinical trials that patients might join based on their tumor markers. Roychowdhury's team will add probes for MSI detection so the test can also determine whether a patient's tumor is MSI high or not, and guide them to ongoing trials studying therapies in tumors exhibiting this feature.

Tests that can determine MSI status across a variety of tumors types are needed, especially since the discovery that this hypermutational feature is not restricted to colorectal cancers, where it has been most commonly seen. Recognizing this, the US Food and Drug Administration earlier this year approved Keytruda (pembrolizumab) as a treatment for patients with any advanced solid tumor characterized by high MSI or mismatch repair deficiency after they've progressed on other drugs. 

Mismatch repair deficiency is a condition that makes cancer cells unable to repair the DNA damage that occurs during replication so that they accumulate genetic mutations in repetitive DNA regions called microsatellites. This has been known to cause a hereditary condition called Lynch Syndrome, which increases the risk for colorectal and other cancers.

However, more recent efforts by researchers at Johns Hopkins University showed that these mutationally overloaded tumors not only occurred in 5 percent of colorectal patients, but also with varying frequency in endometrial, gastrointestinal, breast, prostate, bladder, thyroid, and other cancers. This necessitates diagnostics that can detect MSI in different tumors.

In the studies that led to the approval Keytruda's pan-cancer indication, patients' MSI and mismatch repair deficiency status was determined using PCR testing or immunohistochemistry, which currently are the standard diagnostic methods used in this context. But these methods were largely developed for analyzing colon and endometrial tumors, and may be limited in their ability to determine MSI status in other cancers. "If you use a colon cancer test and apply it everywhere else it may or may not work," Roychowdhury said.

OSU's efforts to develop an NGS-based MSI test started with a patient, 60-year-old Rhonda Ball, who had metastatic cancer of unknown origin in her bones, small bowel, and soft tissues. She initially received chemotherapy, but didn't have much response. "A cancer of unknown origin involving three organ sites usually has a terrible prognosis," Roychowdhury said. "Typically, less than six months."

She received NGS panel testing, which identified a number of genetic mutations, including one in KRAS, for which there are still no targeted treatment options. Meanwhile, one of the researchers in Roychowdhury's group dug deeper into her test results and noticed that she had more frameshift mutations than would be expected. The cause, they soon determined, was MSI, and she enrolled in one of the pan-cancer trials for Keytruda open at the university.

"We were very hopeful and very lucky she had a complete radiographic response," Roychowdhury said. "Things have really turned around for her a year and a month later." The experience with this patient spurred Roychowdhury's group to begin developing the MSI-calling software MANTIS.

In JCO Precision Oncology, Roychowdhury's team recently described the ability of MANTIS to analyze whole-exome data from more than 11,000 tumor-normal pairs across nearly 40 cancer types from The Cancer Genome Atlas, the Therapeutically Applicable Research to Generate Effective Treatments, and other external projects. Using MANTIS, researchers were able to identify MSI in 3.8 percent of all cancers assessed in 27 of the tumor types, including adrenocortical carcinoma, cervical cancer, and mesothelioma, cancers where MSI is really uncommon. 

"The purpose of that paper was to identify other cancers where MSI occurs," Roychowdhury said. "Sometimes it occurs very infrequently but sometimes its higher than we expected, too. These are all potentially candidates for therapy now."

Roychowdhury's team determines MSI status in more than 11,000 cases in a matter of weeks. "The neat thing about MANTIS is that we can actually slice the files to look at just the microsatellite loci, so it lets us process the data very quickly," he said. "Other algorithms would take a lot longer to do what we did."

As OSU is developing NGS-based MSI detection capabilities, other labs have begun reporting MSI status as part of NGS panels. Caris Life Sciences reports MSI status as part of its 592-gene NGS panel. In a recently published paper evaluating the response to Keytruda accross different tumor types, researchers used Caris' test to evaluate 32 tumor types accross more than 12,000 cancers and the test identified mismatch repair deficiency in 24 of the tumor types. 

Foundation Medicine is reporting tumor mutational burden within NGS panel test reports. In the JCO Precision Oncology paper, researchers also evaluated characteristics associated with MSI, such as mutational burden, mutational signatures, and somatic variants. They found that adrenocortical carcinoma and cervical cancer that were MSI-high also had higher average mutational burden compared to tumors that were microsatellite-stable.

Roychowdhury's team is hoping to finish validation of the MSI test in the next six-to-nine months. Currently, they are establishing the test's sensitivity/specificity and will move on to limit of detection, reproducibility, and repeatability.

Additionally, Roychowdhury said that his group has partnered with a pharma company to study Keytruda in combination with an IDO-1 inhibitor, which they hypothesize will boost T cell function for patients who have cancer recurrence after first-line immunotherapy treatment. The NGS panel with MSI detection capabilities will be used in this study to evaluate which patients responded to the combination treatment.

Among cancer patients with MSI, the overall response rate to Keytruda is 40 percent. "We get excited about that," he said, noting that not everyone with MSI responds to immunotherapy, however.

Roychowdhury declined to name the pharma partner because the collaboration isn't yet public. He noted, though, that the aim of this combination precision medicine trial is to improve on the 40 percent response rate.