Skin cells: genomic DNA changes from UV light is especially common


For the first time, scientists have measured the different types of genomic DNA changes that occur in skin cells, finding that mutations from ultraviolet (UV) light is especially common, but Black individuals have lower levels of UV damage compared to white people.

Dmitry Gordenin and colleagues at the National Institute of Environmental Health Sciences, report these findings January 14 in PLOS Genetics.

The DNA in our skin cells suffer damage from sources inside and outside the body, leading to genomic changes such as mutations that may lead to cancer.

UV light is the major source of these mutations, but byproducts of cellular metabolism, like free radicals, and DNA copying errors that occur during cell division also cause genomic changes. These mutation-causing mechanisms are well known, but previously, no one had been able to accurately measure the relative contributions from each source.

In their new paper, Gordenin and his colleagues quantified the amounts of each type of genomic changes by sequencing the genomes of skin cells donated from 21 Black and white individuals, ranging in age from 25 to 79.

The researchers discovered that the total amount of genomic changes from metabolic byproducts accumulates as a person gets older, while the amount of genomic changes caused by UV damage is unrelated to a person’s age.

Additionally, they showed that genomic changes from UV light is common, even in skin cells typically shielded from the sun, but it was less prevalent in Black donors compared to white donors.

The researchers suspect that Black individuals may be better protected from UV light due to having higher levels of the skin pigment melanin. Supporting this idea, is the fact that Black people have much lower rates of skin cancer compared to white people.

Overall, the new study provides an accurate estimate of the genomic changes that occur in skin cells due to different types of DNA damage, and establishes the normal range of somatic genomic changes across a wide range of ages and of different races, providing a baseline for future research.

The authors add, “The new study provides an accurate estimate of the genomic changes that occur in skin cells due to different types of DNA damage, and establishes the normal range of somatic genomic changes across a wide range of ages and of different races, providing a baseline for future research.”

Cells within the human body encounter a vast variety of DNA damaging agents throughout an individual’s lifetime. By some estimates, cells may receive 70,000 DNA lesions per day [1,2].

Erroneous repair or lack of repair of these lesions would lead to a variety of genome changes including somatic single base substitutions, insertions and deletions, rearrangements and copy number changes. Large-scale sequencing studies of single cells, clonally expanded single cells and bulk cells from healthy humans have demonstrated that healthy human tissues are genetically mosaic with thousands of somatic mutations [3–11].

Analysis of such accumulated somatic genome changes have enabled elucidation of the sources of the mutation-initiating lesions as well as the various DNA repair pathways that may be involved in error-prone repair of DNA damage in human cancers [12–15].

Since at least half of the somatic genome changes seen in cancers originate in healthy pre-cancerous cells [16], it is imperative to establish the sources of DNA damage and their impacts on genome stability in healthy cancer-free tissues.

Skin is the largest tissue in the human body and forms the first line of defense against environmental toxins and DNA damaging agents, with ultraviolet (UV) radiation being the most potent environmental mutagen in skin cells. In fact, melanoma genomes have the highest burdens of mutations with UV-induced mutation signatures predominating amongst the mutation signatures identified in this cancer type [12,13].

The pathogenic impact of UV-radiation in generating genome instability is multifaceted. UV-induced DNA lesions are a source of replicative polymerase stalling [17,18] and require translesion synthesis (TLS) over cyclobutane pyrimidine dimers (CPD) and pyrimidine 6–4 pyrimidone (6-4PP) [19–27].

Error-prone TLS over UV-induced lesions leads to C➔T changes in the yCn motif (y is any pyrimidine, n is any nucleotide, mutated base is capitalized). Cytosines within a CPD may also be deaminated to uracils and upon copying by the canonical DNA polymerases or by the TLS polymerase, Pol η, would be fixed as yCn➔yTn changes or to CC➔TT changes in the next round of replication [19,21].

Error-prone TLS across thymine CPDs can also lead to T➔C changes [19,21,28,29] preferring nTt➔nCt motif [8]. Altogether, these base-substitution motifs derived from experimental data constitute a significant part of mutation signature SBS7b extracted by non-negative matrix factorization analysis from mutation catalogs of thousands of whole-genome sequenced human cancers [13].

In the absence of TLS across UV-induced lesion it would not result in base substitutions but can lead to impediment of replication fork progression. Restart of a stalled replication fork can result in the formation of single-stranded gaps in the sister DNA molecules and later convert to double strand breaks (DSBs) [30,31].

Inaccurate repair of such a DSB via homologous recombination (HR) or non-homologous end joining (NHEJ) can lead to a structural changes, copy number variation or generate a small insertion or a deletion.

In agreement with UV radiation being the major source of DNA damage in skin cells, various studies have demonstrated that C➔T changes in the yCn context is the most prevalent base substitution in skin fibroblasts, melanocytes, and keratinocytes. In addition, human skin cells also carry CC➔TT changes and T➔C in the nTt motifs [7,8,32,33].

Moreover, we previously demonstrated that fibroblasts obtained from sun-exposed body sites carry a higher mutation burden along with a higher contribution of a UV-mutation signature than fibroblasts obtained from sun-shielded sites [8]. Our findings were also supported in the study by Tang wherein they demonstrated higher mutation burden in melanocytes from sun-exposed body sites than sun-shielded body sites via either whole exome sequencing or targeted sequencing of 509 cancer-associated genes in single melanocytes [33].

In summary, numerous studies have established and verified the prominent mutagenic effects of the bypass of UV-induced lesions by translesion polymerases generating a characteristic base substitution signature in skin cells. However, the broad spectrum of somatic genome instability, including consequences of UV-induced DSBs in cells of healthy human skin have neither been established nor characterized by mutation signature analysis.

In addition to environmental DNA damage, cells may also accumulate somatic genome changes due to endogenous DNA damage or errors during DNA replication in the form of base substitutions, small insertions or deletions (indels), and gross chromosomal rearrangements.

Somatic mutations in skin cells have been measured either by deep sequencing of bulk tissue [32] or whole-genome sequencing of single cell-derived induced pluripotent stem cells [5] or single cell-derived clonal lineages [7,8]. However, due to either small sample sizes or difficulties in accurately identifying somatic indels and chromosomal rearrangements using induced pluripotent stem cells or bulk cells, none of these studies have been able to adequately characterize the different sources of DNA damage and their mutagenic outcomes in skin cells from healthy donors [34].

Here, we present an integrated analysis of the various types of somatic genome changes that are found in skin fibroblasts and melanocytes from a total of 21 donors ranging in ages from 25 to 79 years. Unlike previous studies, our cohort contains both White and African American donors, allowing a better estimation of the impacts of skin color on mutagenesis in skin cells.

Our work provides the normal range of the burden and types of somatic genome instability in human skin cells. We show here that in skin cells, endogenous DNA damage in the form of spontaneously deaminated cytosines at CpG motifs, oxidative DNA damage, as well as DNA replication errors, are a substantial source of somatic mutagenesis.

Additionally, UV-induced DNA damage is prevalent even in sun-shielded skin cells and manifests as single base substitutions arising from DNA synthesis over lesions by TLS and by deletions of five or more nucleotides arising from end-joining repair of UV-induced DSBs.

Our analysis also highlights the differences in the outcomes of UV-induced DSBs and DSBs induced by endogenous DNA damage in cancer-free skin cells. Overall, we provide a comprehensive analysis of the various UV-induced and endogenous genome de-stabilizing processes that operate in healthy skin cells.

Fig 1
UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin
Fig 1
Schematics and total base substitutions identified per clonal lineage in this study.
(A) Schematics of the study design. From each donor, we obtained blood for whole-genome sequencing. In addition, we obtained skin biopsies from the hips of the donors from which fibroblasts and melanocyte clonal lineages were obtained. Fibroblasts were grown up to a million cells and their DNA was directly used for whole-genome sequencing, while melanocytes grew up to 10,000 cells and the DNA was whole-genome amplified and thereafter sequenced. (B) The total base substitutions in each clonal lineage versus the age of the donors. The pink filled circles denote melanocyte clones. The x-axis denotes the ages of the donors, while the y-axis denotes the number of base substitutions. The solid black line is the linear regression line for the samples, while the dotted black curves are the 95% confidence intervals. The source data for this figure is in S1 and S2 Tables.

More information: Saini N, Giacobone CK, Klimczak LJ, Papas BN, Burkholder AB, Li J-L, et al. (2021) UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin. PLoS Genet 17(1): e1009302. … journal.pgen.1009302


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