A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 is highly metastatic in vivo

Despite recent advances in melanoma treatment, metastasis and resistance to therapy remain serious clinical challenges. NME1 is a metastasis suppressor, a class of proteins which inhibits metastatic spread of cancer cells without impact on growth of the primary tumor. We have identified a rare subpopulation of cells with markedly reduced expression of NME1 (NME1(LOW)) in human melanoma cell lines. To enable isolation of viable NME1(LOW) cells for phenotypic analysis by fluorescence-activated cell sorting (FACS), a CRISPR-Cas9-mediated approach was used to attach an EGFP coding module to the C-terminus of the endogenous NME1 gene in melanoma cell lines. NME1(LOW) cells displayed enhanced collective invasion in vitro when implanted as 3D aggregates in Matrigel. NME1(LOW) cells were also highly metastatic to lung and liver when xenografted subcutaneously in immune-deficient NSG mice. RNA-seq analysis revealed that NME1(LOW) cells express elevated levels of genes associated with tumor aggressiveness, as well as with morphogenesis of tissues of neural crest-like origin (melanocytes and neurons, bone and heart tissues; GO: 0009653). The highly malignant NME1(LOW) variant of melanoma cells has potential to provide novel therapeutic targets and molecular markers for improved clinical management of patients with advanced melanoma.