Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state

Abstract

Transcriptional reprogramming of proliferative melanoma cells into a phenotypically distinct invasive cell subpopulation is a critical event at the origin of metastatic spreading. Here we generate transcriptome, open chromatin and histone modification maps of melanoma cultures; and integrate this data with existing transcriptome and DNA methylation profiles from tumour biopsies to gain insight into the mechanisms underlying this key reprogramming event. This shows thousands of genomic regulatory regions underlying the proliferative and invasive states, identifying SOX10/MITF and AP-1/TEAD as regulators, respectively. Knockdown of TEADs shows a previously unrecognized role in the invasive gene network and establishes a causative link between these transcription factors, cell invasion and sensitivity to MAPK inhibitors. Using regulatory landscapes and in silico analysis, we show that transcriptional reprogramming underlies the distinct cellular states present in melanoma. Furthermore, it reveals an essential role for the TEADs, linking it to clinically relevant mechanisms such as invasion and resistance.

A Preclinical Model of Malignant Peripheral Nerve Sheath Tumor-like Melanoma Is Characterized by Infiltrating Mast Cells

“…We obtained a ranked gene list (t-test values as ranking parameter) and performed GSEA using the C2-curated gene set collection of the BROAD molecular signature database (MSigDB) that was extended by gene sets representing the so-called "proliferative" and "invasive" melanoma cell states (Supplementary Tables S1 and S2). "Invasive" human melanoma cell lines are characterized by an epithelial-mesenchymal transition (EMT)-like phenotype in contrast with the melanocytic "proliferative" cell state, as described by Hoek and colleagues and Verfaillie and colleagues (12,19). We found that MPNST-like mouse melanomas showed significant enrichments of the "invasive" (Hoek/Verfaillie), EMT, collagen, and (neural crest) stem cell gene signatures, suggesting reactivated neural crest pathways ( Fig.…”

“…jsp) with 10K permutations (permutation type ¼ gene set as the only available option in GSEAPreranked). The VERFAILLIE_IN-VASIVE and VERFAILLIE_PROLIFERATIVE gene sets were retrieved from the original publication (12). The HOEK_INVA-SIVE and HOEK_PROLIFERATIVE gene sets were retrieved from http://www.jurmo.ch/work_97.php.…”

Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic

“…ChIP-seq, RNA-seq, and public data ChIP-seq against H3K27ac was performed and analyzed as described before (Verfaillie et al 2015). RNA-seq for MCF7 TP53 knockdown was extracted and performed as described previously (Janky et al 2014).…”

Take ACTION to characterize the functional identity of single cells

“…http://dx.doi.org/10.1101/081273 doi: bioRxiv preprint first posted online Oct. 15, 2016; are also highly significant (Fisher's test p-value of subclass B = 7.9 × 10 −11 , and that for subclass C = 9.3 × 10 −14 ) for known markers of the proliferative state [16]. Further analysis of these factors, however, reveals that while both of these subclasses are highly MITF-associated, the degree of association is higher for subclass C. Examining downstream targets of MITF that are activated in each subclass (see Supplementary Text 8), we identified that GPNMB, MLANA, PMEL, and TYR are shared between two subclasses, whereas ACP5, CDK2, CTSK, DCT, KIT, OCA2 and TRPM1/P1 are unique to subclass C. Besides MITF and SOX10, there are 38 other factors identified for subclass B and 17 other factors for subclass C. In particular, wellknown oncogenes TP53 and MYC are differentially activated in subclass B and subclass C, respectively.…”

“…In addition, both have SOX10 as active too. These two factors are canonical markers for melanoma cells in the "proliferative" state [16]. Both of these subclasses 8 .…”