Exome sequencing identifies novel mutation signatures of UV radiation and trichostatin A in primary human keratinocytes

Yao Shen,Wangyong Zeng,Liang Liu,Wootae Ha,Dawn Queen

doi:10.1038/s41598-020-61807-4

Yao Shen, Wangyong Zeng + Show 3 more

Open Access

https://doi.org/10.1038/s41598-020-61807-4

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Abstract

Canonical ultraviolet (UV) mutation type and spectra are traditionally defined by direct sequencing-based approaches to map mutations in a limited number of representative DNA elements. To obtain an unbiased view of genome wide UV mutation features, we performed whole exome-sequencing (WES) to profile single nucleotide substitutions in UVB-irradiated primary human keratinocytes. Cross comparison of UV mutation profiles under different UVB radiation conditions revealed that T > C transition was highly prevalent in addition to C > T transition. We also identified 5′-ACG-3′ as a common sequence motif of C > T transition. Furthermore, our analyses uncovered several recurring UV mutations following acute UVB radiation affecting multiple genes including HRNR, TRIOBP, KCNJ12, and KMT2C, which are frequently mutated in skin cancers, indicating their potential role as founding mutations in UV-induced skin tumorigenesis. Pretreatment with trichostatin A, a pan-histone deacetylase inhibitor that renders chromatin decondensation, significantly decreased the number of mutations in UVB-irradiated keratinocytes. Unexpectedly, we found trichostatin A to be a mutagen that caused DNA damage and mutagenesis at least partly through increased reactive oxidation. In summary, our study reveals new UV mutation features following acute UVB radiation and identifies novel UV mutation hotspots that may potentially represent founding driver mutations in skin cancer development.

Highlights

Today, the most common cancer affecting Caucasians is skin cancer, with a rising incidence globally[1]
While there was an increase in single nucleotide variations (SNVs) number from 4 to 72 h following exposure to identical UVB radiation doses (30 mJ/cm2), we observed no clear trend of dose-dependent changes in SNV numbers (Fig. 1A,B)
In contrast to the large number of mutations reported in human skin tumors[27,28,29], the number of UV-induced SNVs was relatively small, which is attributable to the difference between acute UV radiation and repetitive UV exposure causing accumulation of mutations over time in addition to non-UV mutations during tumor progression

Summary

Introduction

The most common cancer affecting Caucasians is skin cancer, with a rising incidence globally[1] Both genetic risk factors, like skin phototype and family history, as well as environmental factors, including ultraviolet radiation (UVR), chronic arsenic exposure, use of photosensitizing drugs, and immunosuppressed status, all contribute to increasing an individual’s risk for developing skin cancer[2,3,4,5,6,7]. Before generation sequencing technology was developed, studies of UV mutagenesis were largely limited to a few chosen genes or transgenes that allow clonal expansion[19,20,21,22,23,24] While these targeted methods are sensitive and have generated crucial fundamental knowledge of UV mutation characteristics, these mutational profiles may not recapitulate mutagenesis at chromosomal loci across the genome due to their very limited coverage. Subsequent bioinformatics and statistical analyses of the WES data identified novel mutagenic features of UVB radiation, as well as genes that consistently harbor recurring mutations following acute UVB exposure and are present in human skin tumors

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