(23e) Multi-Omics Approaches to Decipher Human Melanoma Initiation

Melanoma is the most aggressive skin cancer that arises in skin pigment cells called melanocytes. Developmentally, melanocytes are derived from a short-lived embryonic stem cell population called neural crest stem cells. Recent evidence suggests that when melanocytes turn cancerous, they activate a developmental program similar to embryonic neural crest cells¹. In addition, melanoma cells also utilize molecular machinery of neural crest cells to spread to different parts of the body (metastasis) and in acquiring resistance against currently used drugs². Taken together, these observations suggest that melanocytes possibly de-differentiate into neural crest cell-like state during melanoma initiation and this neural crest-like state further drives melanoma progression. However, it is not clear, what is the epigenetic landscape of this dedifferentiated stage that melanocytes acquire in order to initiate melanoma. Moreover, it is not known whether these epigenetic signatures actually endow dedifferentiated melanocytes with melanomagenic potential and drive melanoma growth under permissible oncogenic environment. BRAF mutation where a valine is substituted by a glutamate at position 600 (BRAF (V600E)) is the most common mutation found in melanomas (in 80% primary and 68% metastatic melanomas)³.

In this work, we identified global gene expression changes upon BRAF (V600E) overexpression in early melanocyte developmental context as well as in primary human melanocytes. Importantly, quantitative examination of cis-regulatory histone marks (H3K27Ac and H3K27me3) discovered over 700 enhancers that were differentially enriched between wild type and BRAF (V600E) mutant cells indicating their potential role in mediating transcriptional changes in early melanoma-genesis. Particularly, in mutant cells, the putative enhancers involved in cell proliferation (e.g., CDKN2A) displayed higher H3K27Ac marks in agreement with their more proliferative status while this active enhancer mark was depleted at melanocyte differentiation genes such as EDNRB suggesting BRAF(V600E) commits cells towards more melanoma-like cell state by simultaneously affecting both cell-cycle and cell differentiation programs. Our study identified earliest gene expression changes and associated epigenetic events that are involved in reprogramming of normal melanocytes into melanoma like-cells upon BRAF (V600E) overexpression. This study has generated a plethora of novel candidate enhancers that will fuel more studies towards identifying novel molecular mechanisms involved in the melanoma initiation and will potentially pave the way for development of novel diagnostics and therapeutics.

References:

1 Kaufman, C. K. et al. A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation. Science 351, aad2197, doi:10.1126/science.aad2197 (2016).

2 Johannessen, C. M. et al. A melanocyte lineage program confers resistance to MAP kinase pathway inhibition. Nature 504, 138-142, doi:10.1038/nature12688 (2013).

3 Pollock, P. M. et al. High frequency of BRAF mutations in nevi. Nature genetics 33, 19-20, doi:10.1038/ng1054 (2003).