The Surprising Diversity of UV-Induced Mutations

Abstract

Ultraviolet (UV) light is the most pervasive environmental mutagen and the primary cause of skin cancer. Genome sequencing of melanomas and other skin cancers has revealed that the vast majority of somatic mutations in these tumors are cytosine-to-thymine (C>T) substitutions in dipyrimidine sequences, which, together with tandem CC>TT substitutions, comprise the canonical UV mutation "signature". These mutation classes are caused by DNA damage directly induced by UV absorption, namely cyclobutane pyrimidine dimers (CPDs) or 6-4 pyrimidine-pyrimidone photoproducts (6-4PP), which form between neighboring pyrimidine bases. However, many of the key driver mutations in melanoma do not fit this mutation signature, but instead are caused by T>A, T>C, C>A, or AC>TT substitutions, frequently occurring in non-dipyrimidine sequence contexts. This article describes recent studies indicating that UV light causes a more diverse spectrum of mutations than previously appreciated, including many of the mutation classes observed in melanoma driver mutations. Potential mechanisms for these diverse mutation signatures are discussed, including UV-induced pyrimidine-purine photoproducts and indirect DNA damage induced by UVA light. Finally, the article reviews recent findings indicating that human DNA polymerase eta normally suppresses these non-canonical UV mutation classes, which can potentially explain why canonical C>T substitutions predominate in human skin cancers.

Keywords: DNA repair; UVA; atypical photoproducts; reactive oxygen species; skin cancer; ultraviolet light.

Figure 1

Passaging assay for UV mutagenesis in yeast. Yeast cells are spotted onto plates containing rich media, UV irradiated, and allowed to grow in standard culture condition. The resulting cell spots are then diluted, re‐spotted onto fresh plates, and subjected to the same process for a total of fifteen passages. Cells from each spot are struck for isolation and whole genome sequencing is performed on genomic DNA extracted from a clonal isolate obtained from each spot.

Figure 2

Differing mutation spectra of UV‐exposed yeast and human skin cancers. A) Mutation spectrum derived from whole genome sequencing data from UVB‐exposed wild‐type yeast cells. The fraction of total mutations associated with each mutation class and trinucleotide context is depicted. Data are from.^{[ 33 ]} B) Mutation spectra derived from whole genome sequencing of sporadic human skin cancers, including squamous cell carcinomas (SCC), basal cell carcinomas (BCC), and melanomas (MEL). The fraction of total mutations associated with each mutation class and tri‐nucleotide context is depicted. Figure is reproduced and adapted under terms of the Creative Commons Attribution 4.0 International License.^{[ 34 ]} 2023, The Authors, published by Nature Communications.

Figure 3

Non‐canonical UV‐induced mutations are enriched in UVB passaged yeast. Mutation spectrum from UVB‐irradiated yeast (same as Figure 2A) is depicted.^{[ 33 ]} The putative lesion responsible for each mutation class is indicated. Mutations occurring in dipyrimidine contexts (i.e., CT, TT, and TC) likely originate from CPDs or 6‐4 PPs, which are the two most prevalent UV lesions, which can potentially explain UV‐induced C>A, T>C, and a subset of T>A mutations. In contrast, mutations occurring in NTA contexts likely originate from atypical thymine‐adenine photoproducts and yield T>A/A>T mutations.

Figure 4

Mutation spectra of human XPV^−/− tumors and yeast rad30∆ mutants show greater similarity. A) Mutation spectra of whole genome sequencing of sporadic skin cancers (top panel; see Figure 2 legend for more details) versus XPV^−/− tumors (bottom panel) reveals increased proportion of C>A, T>A, and T>C substitutions in XPV mutant tumors. This effect is primarily reflected in 3′ TT dinucleotide sequences for many of the T>A and T>C substitutions, suggesting an important role for XPV/POLH in error‐free bypass of UV‐induced TT photoproducts. C>A substitutions were primarily noted in NCA sequence contexts and were highly enriched in XPV^−/− tumors. Transcriptional asymmetry analysis (not depicted) indicates that these mutations were actually TG>TT substitutions, potentially originating from a thymine‐guanine (TG) photoproduct. Figure is reproduced and adapted under terms of the Creative Commons Attribution 4.0 International License.^{[ 34 ]} 2023, The Authors, published by Nature Communications. B) Mutation spectra derived from whole genome sequencing of UVC‐exposed WT yeast (top panel) and rad30∆ deletion (bottom panel) passaging isolates. Similar to XPV^−/− tumors, yeast data reflects an increase in C>A mutations in NCA sequence contexts in the rad30∆ mutant. Transcriptional asymmetry analysis (not depicted) CA>AA substitutions are likely TG>TT substitutions. Conversely, rad30∆ in yeast also caused a decreased frequency of T>C substitutions in TT dipyrimidines, suggesting an error‐prone bypass of TT photoproducts by Rad30 in yeast. Further, loss of Rad30 in yeast had no effect on T>A substitutions, suggesting yeast Rad30 may not be able to bypass TA photoproducts in an error‐free manner. Both POLH and Rad30 seem to serve a protective effect against C>T substitutions, particularly in the 3′ position of dipyrimidines. Data from WT and rad30∆ mutant yeast exposed to 15 doses of UVC light are depicted.^[32]

Figure 5

Model of how species‐specific differences in DNA polymerase eta impact UV mutation spectra in yeast and human cells. A) Human XPV/POLH suppresses UV‐induced C>A, T>A, and T>C mutations due to error‐free bypass of the causative lesions. Note, while UV‐induced C>T mutations comprise the vast majority of the mutation spectra in skin cancers, C>A, T>A, and T>C mutations do occur at low frequency, even though they are not depicted in model. Structure of human POLH from PDB ID: 4J9S and visualized using Pymol. B) Yeast Rad30 does not suppress UV‐induced T>A mutations and stimulates UV‐induced T>C mutations, likely due to error‐prone bypass of 6‐4PP or CPD lesions. Yeast Rad30 does suppress UV‐induced C>A and, to a lesser extent, C>T mutations. Structure of yeast Rad30 from PDB ID: 3MFH and visualized using Pymol.