Blood-based detection of BRAF and NRAS DNA as biomarkers in patients with stage I

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Abstract Melanoma remains a highly morbid disease in the United States. With a relatively young age of onset, the toll of melanoma in terms of "life-years lost" is second only to breast cancer among the major solid tumor malignancies. Despite advances in early detection, the number of deaths from melanoma has continued to rise. Five-year survival rates are dismal, with only 3%-14%% of patients with distant metastatic disease (stage IV) achieving that milestone. In addition, the only commonly used serologic marker of disease activity in the US, serum lactate dehydrogenase, has a poor sensitivity to detect disease progression leading clinicians to rely on expensive imaging studies to monitor disease. Overall, the annual estimated costof treating melanoma in the United States is over $3.1 billion. Beginning in 2002 activating mutations in the serine-threonine kinase BRAF were identified at high rates in primary and metastatic melanoma, and subsequent in-vitro and animal model experiments demonstrated BRAF to be an oncogene in melanoma. The V600E substitution is a mutation hotspot, accounting for greater than 90% of the BRAF mutations identified in melanoma. Earlier this month the results of a Phase III randomized trial of Vemurafenib, a second generation small molecule inhibitor of the BRAFV600E protein, demonstrated improved disease-free and overall survival at 6 months. The trial was limited to patients with metastatic melanoma tumors that had the BRAFV600E as determined by genotyping of a biopsy specimen. Thus, knowledge of the BRAF genotype of a patient's metastatic melanomas will be an essential step for proper therapeutic decision-making. Based on our clinical trial experience, tumor genotyping often takes 1-2 weeks or longer if there are difficulties obtaining a metastatic tumor specimen for analysis. In addition, we and others have found that multiple metastases from individual patients may be discordant for the BRAF mutation (i.e. one tumor is mutant, a second tumor from the same patient is wild-type). Genotyping of a single tumor biopsy from individual patients, therefore, may inadvertently render some patients ineligible for a BRAF inhibitor who might otherwise derive benefit. We have patented and licensed a highly sensitive approach to detect mutant BRAF DNA in patient blood samples. Our Preliminary Data demonstrate that this approach is feasible in melanoma patients, as the results of blood-based testing are highly associated with the BRAF genotype of the tumor. In the current proposal we will work with our industry collaborator, Molecular MD to further optimize our blood-based methodology, and rigorously demonstrate its utility as both a molecular diagnostic biomarker of metastatic melanoma genotype and response-predictive biomarker that can differentiate between patients that will have a longer versus shorter duration of progression-free survival while under treatment with the new agents that inhibit mutant BRAF.