Prospective isolation according to melanin pigment content of melanoma cells with heterogeneous potentials for disease propagation

Functional variation between cancer cells (intra-tumoral heterogeneity) poses a major challenge to treating and managing cancer patients. Melanomas are typically composed of cancer cells with heterogeneous content of melanin pigment. Pigment production is a hallmark of normal melanocytic differentiation, however the functional consequences of melanin production in melanoma cells remains poorly understood owing to a lack of experimental approaches for detection of pigment in unfixed cells. Here, we describe a novel flow cytometric method for high purity separation of viable melanoma cells based on their content of melanin pigment, exploiting the infrared light scattering properties of melanin. By fluorescence-activated cell sorting, we show that melanoma cells with low-pigment content (LPCs) in culture and in patient tumors are far more abundant than high-pigment cells (HPCs), and have substantially increased potentials for colony formation in vitro and for tumor formation in vivo. RNAseq analysis revealed activation of P53 in HPCs associated with perturbed cell cycling, whereas LPCs displayed upregulation of MYC-associated transcription and activated ribosome biogenesis. The latter was reduced by topoisomerase 2 beta targeting with CX-5461, which also induced senescent HPC phenotypes and irreversible loss of clonogenic activity. These data illuminate an inverted pyramid hierarchical model of melanoma cell propagation wherein abundant LPCs frequently renew their own malignant potential to propagate disease, but also rarely generate HPCs that lose this ability in a manner that may be promoted as an anti-melanoma strategy.