Study of the molecular evolution of melanoma sheds new light on how cancer metastasizes

For the first time, research has uncovered distinct molecular patterns that elucidate the molecular evolution of melanoma distant metastases. Results of a study conducted by dermato-oncologist and researcher Mohammed Kashani-Sabet, M.D., and colleagues at Sutter’s California Pacific Medical Center (CPMC) Research Institute were published in the Journal of Investigative Dermatology. Their study includes previously unreported findings of molecular pathways potentially selected for in the metastatic cascade.

“Our research shows copy number alterations (CNAs) in distinct genes or pathways may be enriched in distinct nodes in the melanoma progression cascade,” says Dr. Kashani, medical director of CPMC's Center for Melanoma Research and Treatment. “The presence of three particular patterns of CNA suggests unique selection pressures may exist in the melanoma metastasis cascade. Overall, these findings contribute to our understanding of the clonal evolution of melanoma distant metastasis in matched tissues from individual patients—and these findings may have implications for the metastatic cascade of other types of cancer.”

Melanoma can metastasize to virtually any organ either early or late in the course of the disease, and melanoma-related deaths are mostly due to the progression of distant metastases. Data from experimental models suggest lymph node metastases can promote the development of distant metastases, resulting in a prevailing model of cancer metastasis in which distant metastases develop from pre-existing lymph node metastases. But Dr. Kashani says the evolution of primary melanoma to lymph node and distant metastasis is incompletely understood.

“Until now, it’s been unclear whether distinct molecular factors are gained or lost in the melanoma metastasis paradigm, and therefore are potentially selected for in the development of melanoma distant metastasis. Molecular analyses have demonstrated clear evidence of intra-tumor heterogeneity in the primary tumor, resulting in subclones that likely have differential capacities for metastasis. Our research was aimed at better characterizing whether and how the mutational frequency of a given driver gene changes in the melanoma metastasis cascade, and whether distant melanoma metastasis can develop from a minority clonal population in the primary tumor.”

In the study, Dr. Kashani and colleagues assessed CNAs and frequency of driver mutations in melanoma using a matched cohort of 17 patients with primary melanoma, lymph node and distant metastasis in whom tissue was available for analysis. Copy number gain was defined as the cancer cell fraction (i.e., percent of tumor cells) harboring three or more copies of a given gene, whereas copy number loss was defined as the cancer cell fraction (i.e., percent of tumor cells) with a ratio of the gene’s copy number relative to its centromeric probe less than 0.8.

Fluorescence in situ hybridization (FISH) analysis of several genes with known CNA in melanoma was performed, including MITF, PTEN, PHIP, NCOA3, BPTF and ERBB2. Next-generation sequencing (NGS) was performed to analyze the presence or absence of various oncogenic mutations in the same 17-patient cohort using a 56-gene pan-cancer panel. 

FISH analysis revealed cancer cell fractions with monotonic CNAs, including PHIP gain and PTEN loss, in the metastatic cascade. By contrast, the cancer cell fraction with CNAs for BPTF and MITF was reduced in lymph node metastases but increased in distant metastases. Separately, the cancer cell fraction with NCOA3 CNA was comparable in primary tumors and lymph nodes yet increased in distant metastases.

By contrast, NGS analysis did not identify a consistent pattern of changes in variant allele frequency (VAF) and, surprisingly, showed decreased VAF in distant metastases and distinct drivers in lymph node versus distant metastases. 

“These results suggest enrichment of the PI3K and MITF pathways in the transition through the metastatic cascade, and provide evidence that distant melanoma metastasis does not always emanate from lymph node metastasis. Our findings advance understanding of clonal patterns of melanoma metastasis, with possible implications for targeted therapy.”

Melanoma is the fifth-most common malignancy in the United States. Distant metastasis from the primary tumor occurs via either the lymphatic or vascular route (or both). In most melanoma patients, regional lymph node metastasis predates distant metastasis and is a powerful predictor of melanoma-specific survival.

Dr. Kashani says the next steps of the research will be to replicate the study in a larger sample size, enabling conclusions regarding possible differences in molecular profiles based on sites of distant metastasis.

The study was supported by the California Pacific Medical Center Foundation through the Cancer Avatar Program and by the Kimberlee Swig Fund.