Mapping phenotypic heterogeneity in melanoma onto the epithelial-hybrid-mesenchymal axis

Abstract

Epithelial to mesenchymal transition (EMT) is a well-studied hallmark of epithelial-like cancers that is characterized by loss of epithelial markers and gain of mesenchymal markers. Interestingly, melanoma, which is derived from melanocytes of the skin, also undergo phenotypic plasticity toward mesenchymal-like phenotypes under the influence of various micro-environmental cues. Our study connects EMT to the phenomenon of de-differentiation (i.e., transition from proliferative to more invasive phenotypes) observed in melanoma cells during drug treatment. By analyzing 78 publicly available transcriptomic melanoma datasets, we found that de-differentiation in melanoma is accompanied by upregulation of mesenchymal genes, but not necessarily a concomitant loss of an epithelial program, suggesting a more 'one-dimensional' EMT that leads to a hybrid epithelial/ mesenchymal phenotype. Samples lying in the hybrid epithelial/mesenchymal phenotype also correspond to the intermediate phenotypes in melanoma along the proliferative-invasive axis - neural crest and transitory ones. Interestingly, as melanoma cells progress along the invasive axis, the mesenchymal signature does not increase monotonically. Instead, we observe a peak in mesenchymal scores followed by a decline, as cells further de-differentiate. This biphasic response recapitulates the dynamics of melanocyte development, suggesting close interactions among genes controlling differentiation and mesenchymal programs in melanocytes. Similar trends were noted for metabolic changes often associated with EMT in carcinomas in which progression along mesenchymal axis correlates with the downregulation of oxidative phosphorylation, while largely maintaining glycolytic capacity. Overall, these results provide an explanation for how EMT and de-differentiation axes overlap with respect to their transcriptional and metabolic programs in melanoma.

Quantitative landscapes reveal trajectories of cell-state transitions associated with drug resistance in melanoma

“… 6 , 7 Although the classification started as a binary system for metastatic and non-metastatic samples, intermediate phenotypes displaying features of both the extreme phenotypes have also been identified. 5 , 8 , 9 , 10 , 11 A recent study classified melanoma samples into four phenotypes: melanocytic, transitory, neural crest stem cell like (NCSC) and undifferentiated (in a decreasing order of proliferative behavior, or in an increasing order of invasive traits). 12 Treatment of melanocytic samples with BRAF inhibitors (BRAFi) or MEK inhibitors (MEKi) can cause cells to follow a distinct de-differentiation trajectory, where they first transition to being intermediate phenotypes on the proliferative-invasive axis (transitory and NCSC) and finally get undifferentiated.…”