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SkylineDx Partners With Mayo Clinic on Melanoma Risk Test Study Ahead of Planned US Trial

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NEW YORK – Dutch molecular diagnostics firm SkylineDx and the Mayo Clinic have launched a study to evaluate and introduce a new molecular test for primary cutaneous melanoma.

The test relies on an eight-gene expression signature as well as other information to predict the risk of regional metastasis at the time of diagnosis. Those with a negative result are less likely to experience regional metastasis. SkylineDx believes its test could be used to select certain patients for sentinel lymph node biopsies, while ruling out the need for surgical intervention in others.

The pilot study with the Mayo Clinic is the final step before Rotterdam-based SkylineDx commences a US trial for the test next year.

That trial "is expected to confirm the predictive utility of our test compared to the real sentinel lymph node outcome," said SkylineDx CEO Dharminder Chahal. "If the accrual across the US goes as scheduled, the first results will be available in 2021."

Chahal noted that the new collaboration with Mayo follows a joint development agreement the company inked last year with Rochester, Minnesota-based Mayo to commercialize molecular risk factors associated with sentinel lymph node positivity in primary melanoma. The work was initially published by Alexander Meves, a Mayo Clinic dermatologist, in a 2015 Journal of Clinical Oncology paper.

SkylineDX was founded in 2013 after it acquired all the assets of Skyline Diagnostics, a defunct molecular diagnostics firm that had been developing microarray-based, gene-expression tests for multiple myeloma and acute myeloid leukemia. Chahal said that the company continues to support these tests, called MMprofiler and AMLprofiler, both of which run on Thermo Fisher Scientific Affymetrix microarrays and are offered as CE-IVD kits in Europe and as laboratory-developed tests in the US.

Melanoma is the most recent area of interest for SkylineDx. Chahal said that the Rotterdam-based firm is always hunting for potential new diagnostics, though, and the work with Mayo Clinic resulted from its internal biomarker scouting and screening process. The resulting effort, dubbed the Falcon Research & Development Program, includes a variety of studies and projects, the first of which is called the Merlin Study Initiative and covers the new test.

Chahal said that SkylineDx used Affymetrix arrays to develop the new test, but has decided to transfer it to a Thermo Fisher QuantStudio 5 quantitative PCR platform, given the smaller number of genes tested. For instance, the signature in its MMprofiler test relies on 92 genes, but the melanoma test covers eight genes.

More specifically, the test combines the expression of eight genes from the primary tumor with other tumor characteristics, such as histopathology, and patient data to predict the risk of nodal metastasis. If the risk is 5 percent or higher, patients are encouraged to undergo a biopsy. Currently, the decision of who should undergo a biopsy is based on histopathology alone. Those found to have a risk lower than 5 percent can safely forgo a surgical intervention, according to Chahal. "This reduces the amount of unnecessary sentinel lymph node [biopsies] dramatically," he said.

There are other studies and tests in process under the Falcon R&D Program. Another, called the Peregrine Study Initiative is in the "advanced stages of research," Chahal said. Here the aim is to develop a test that predicts a melanoma patient's prognosis, enabling clinicians prescribe early adjuvant therapy to those who are likelier to progress faster. Other projects are too early stage to discuss at this time, Chahal noted.

"This is a complex disease with many questions and we believe a lot of these questions can be answered with genomics," he said.

In the US, the melanoma risk test should be available as an LDT next year. The company is also planning submissions to the US Food and Drug Administration and European regulatory authorities under the new In Vitro Diagnostic Regulation. In Europe, SkylineDx aims to provide the test through its  diagnostics service next year and market a CE-IVD kit in 2021.

All analysis of samples in the US will be processed at its new facility in San Diego, which SkylineDx established in March 2018 and currently houses 10 of the company's 45 employees worldwide. The lab was CLIA compliant in 2018 and certified by the College of American Pathologists (CAP) in April of this year.

Skyline previously had a sales presence in the Boston area, but the San Diego site has become the center of its US operations. "It's the third major biotech hub in the US, has good infrastructure in terms of the laboratory world and the airport is close," Chahal said of the decision. "For a central lab, it's located in a good place."

Earlier this month, SkylineDx announced that it received €20 million ($21.9 million) to further develop its melanoma test. Chahal noted that the firm will have to face off against competitors like Castle Biosciences, which sells a gene expression-based melanoma recurrence test called DecisionDx-Melanoma, and completed a $73 million IPO in July.

"That's why fundraising is so important to us, so we can make a lot of progress," said Chahal. Last year, the Netherlands Enterprise Agency also granted SkylineDx €2.7 million to develop the melanoma test.

While the lion's share of the new funds will go into clinical validation and utility trials for the melanoma risk test, it will also support the development of the prognostic assay and others. Some of the funding will also support GESTURE, a machine-learning tool that can be used to develop gene expression signatures.

GESTURE is an acronym for Gene Expression-based Simulated Treatment Using Similarity between Patients. The tool derives predictive classifiers from gene expression datasets with different treatment arms and survival data. SkylineDx discussed the use of the tool for selecting therapies for multiple myeloma patients in a July 2018 paper in Nature Communications.

While that study focused on multiple myeloma patients, the tool could potentially be used in other instances, such as in guiding melanoma treatments, according to Chahal. SkylineDX called an earlier version of the tool TOPSPIN, which stood for Treatment Outcome Prediction Using Similarity Between Patients.

"It's early days," Chahal said of GESTURE. "It's not a test yet, but it's a groundbreaking algorithm."

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