Unravelling enhancer landscapes in melanoma

Enhancers are regulatory genomic regions that play an important role in gene regulatory networks. Through the binding of sequence-specific transcription factors, enhancers cooperatively regulate the expression of their target genes and, ultimately, a cell's phenotype. Melanoma is one of the most dangerous and difficult to treat human cancers. Both cellular heterogeneity and plasticity of melanoma cell states are thought to contribute to its aggressiveness and its ease to acquire drug resistance. The aim of this PhD research was to unravel enhancer landscapes in melanoma to improve our understanding of the regulatory logic underlying different melanoma cell states. Since enhancers are generally located in accessible chromatin, they can be profiled using chromatin accessibility profiling methods such as ATAC-seq. Firstly, we used both bulk and single-cell ATAC-seq on melanoma cell lines following knock-down of the transcription factor SOX10. Loss of SOX10 mimics the switch from a melanocytic melanoma state towards a more invasive mesenchymal-like state. The generated data thus allowed us to study the epigenomic dynamics and heterogeneity during melanoma phenotype switching. Next, by generating chromatin accessibility data in melanoma cell lines across six species, we were able to show the conservation of the two main melanoma states and their master regulators across several species. We performed an in-depth investigation of the melanoma enhancer code by combining comparative epigenomics and deep learning. This led to our hypothesis that SOX10 functions as a 'pioneer' factor in melanocytic melanoma by priming enhancers and making them accessible for the binding of other transcription factors, namely TFAP2A, MITF and RUNX. Building on this work, via a massively parallel reporter assay, we identified MITF and ETS as the putative main contributors to enhancer activity in melanocytic melanoma. Lastly, through the use of a microfluidics-based single-cell migration device, we were able to demonstrate that melanoma cells in an intermediate transcriptomic state also display an intermediate and heterogeneous migratory capacity. Altogether, this research has led to a better understanding of the melanoma enhancer code and the specific roles of transcription factors and regulatory regions important in melanoma cell states.

Publication year:2020

Accessibility:Open