Using Single Cell Analysis to identify therapeutic vulnerabilities in leptomeningeal melanoma metastases

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Project summary The long-term goal of this research program is to develop therapeutic strategies that improve the outcome of patients with disseminated melanoma. Melanoma is a highly metastatic tumor, with a propensity to disseminate to the skin, lungs and brain. In ~5% of cases, patients also develop leptomeningeal melanoma metastases (LMM: e.g. melanoma cell infiltration into the pia mater, the arachnoid membranes and cerebrospinal fluid) which have an even worse prognosis and a median survival of 8-10 weeks. It is likely that the leptomeninges represent “sanctuary sites” for melanoma cells that evade both targeted and immune therapies. At this time, no therapeutic strategies have been identified that are effective against LMM. Melanomas are genetically heterogeneous, suggesting that distinct genetic clones/patterns of mutation determine which cells home to the brain and leptomeninges. Progress in this area has been limited due to the technical difficulties of obtaining specimens from the leptomeninges, cerebrospinal fluid (CSF) and sub-arachnoid space. Recently our group has begun the routine collection of CSF from patients with LMM, which we have shown to contain circulating melanoma cells (circulating tumor cells: CTCs). We have also established protocols to obtain serial CSF samples from patients undergoing off-label treatment BRAF-MEK inhibitor treatment for LMM. Methods for the isolation and amplification of RNA and DNA from single cells have become available and are ideally suited for analyzing rare populations of cells, such as those found in the CSF. The overarching goal of this R21 is to define the genetic and transcriptional profiles of the CTCs from patients with LMM and to identify novel therapeutic targets for these tumors. We will use the Fluidigm C1 platform to perform sophisticated single cell RNA and DNA analysis to define the clonal relationship between LMM CTCs and matched melanoma specimens from other sites. We will then collect serial CSF specimens from LMM patients undergoing treatment with targeted therapy and will determine how treatment drives clonal selection. Validation experiments will be performed in which BRAF-mutant LMM cells are orthotopically implanted into the leptomeninges of mice and treated with personalized drug combinations based upon dabrafenib-trametinib and drugs targeted against the actionable mutations/pathways that we identify. These studies are expected to provide critical new insights into the biology of brain and leptomeningeal melanoma metastases and form the groundwork for the development of clinically relevant drug combinations.