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

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

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Article number4943
JournalScientific reports
Volume10
Issue number1
DOIs
StatePublished - Mar 18 2020

Bibliographical note

Funding Information:
We thank Dr. Angela Christiano for her generous support. We also thank Dr. Wioletta Czaja for her insightful comments, Rong Du for her excellent technical assistance with cell culture work, and support from the Molecular Pathology Shared Resources at the Herbert Irving Cancer Research Center at Columbia University Medical Center. This work was supported in part by NIH/NIAMS grant K01AR064315, the Prevent Cancer Foundation award, the Columbia University Herbert Irving Comprehensive Cancer Center (P30CA013696), and the Columbia University Skin Disease Research Center (P30AR44535).

Publisher Copyright:
© 2020, The Author(s).

Keywords

  • Computational Biology/methods
  • DNA Damage
  • Genomic Instability
  • Humans
  • Hydroxamic Acids/pharmacology
  • Keratinocytes/drug effects
  • Mutation
  • Polymorphism, Single Nucleotide
  • Protein Synthesis Inhibitors/pharmacology
  • Ultraviolet Rays
  • Whole Exome Sequencing

PubMed: MeSH publication types

  • Research Support, Non-U.S. Gov't
  • Journal Article
  • Research Support, N.I.H., Extramural

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