ETS transcription factors induce a unique UV damage signature that drives recurrent mutagenesis in melanoma

Abstract

Recurrent mutations are frequently associated with transcription factor (TF) binding sites (TFBS) in melanoma, but the mechanism driving mutagenesis at TFBS is unclear. Here, we use a method called CPD-seq to map the distribution of UV-induced cyclobutane pyrimidine dimers (CPDs) across the human genome at single nucleotide resolution. Our results indicate that CPD lesions are elevated at active TFBS, an effect that is primarily due to E26 transformation-specific (ETS) TFs. We show that ETS TFs induce a unique signature of CPD hotspots that are highly correlated with recurrent mutations in melanomas, despite high repair activity at these sites. ETS1 protein renders its DNA binding targets extremely susceptible to UV damage in vitro, due to binding-induced perturbations in the DNA structure that favor CPD formation. These findings define a mechanism responsible for recurrent mutations in melanoma and reveal that DNA binding by ETS TFs is inherently mutagenic in UV-exposed cells.

Intragenomic variability and extended sequence patterns in the mutational signature of ultraviolet light

“…Assessment of signals of selection in cancer involves determination of expected mutation rates/probabilities, which may be improved by considering mutational signatures 4 . When applied to recurrent promoter mutations, common in melanoma 31,32 , we found that a regular trinucleotide model failed to give higher mutation probability estimates for non-TERT recurrent sites, generally believed to be passengers [12][13][14][15] , compared to TERT promoter mutations (C228T and C250T) 33,34 , which are established drivers (Fig. 5e).…”

“…Notably, it has been shown that 5mC facilitates CPD formation by UVB (280-315 nm), the main inducer of CPDs in sunlight, but not by UVC (100-280 nm) 25,26 , which does not penetrate the atmosphere. Despite this, genome-wide studies of CPD formation in human cells to date have all been performed using UVC 14,15,27,28 . To address this, we mapped CPDs genome-wide in human A375 melanoma cells immediately following exposure to UVB (310 nm), using a protocol based on T4 endonuclease V digestion and Illumina sequencing as described previously for UVC 15 (Fig.…”

“…These signals may in part be detectable by simply considering a larger number of patterns, or using a position weight matrix still centered at the position of interest 9 , but this will obscure longer patterns occurring at highly asymmetric or variable positions relative to the mutation [12][13][14][15] . To address this, we devised an extended mutational signature model that considers the central trinucleotide as well presence/absence of longer pentamer patterns at flexible locations within a +/-10 bp context around a given position, here focusing on the predominant C>T mutations (Fig.…”

“…While trinucleotide patterns are informative of whether a UV photoproduct can form, thus providing key information regarding mutation probability, it is also clear that longer motifs may be important [9][10][11][12][13][14][15] .…”

“…However, studies of UV-induced DNA damage in melanoma exome data 9 as well as smaller target templates 10,11 support that presence of thymines in positions beyond the immediate neighboring bases may confer elevated mutation rates. Additionally, it is known that ETS transcription factor binding site sequences (TTCCG) are associated with strongly elevated CPD formation and mutation rates in melanoma, but only in promoter regions and notably at positions that are variable relative to the motif [12][13][14][15] . These intricacies of the underlying mutational process may contribute to recurrent mutations in skin cancers, but cannot be captured using trinucleotide-based UV mutational signatures.…”