UV-induced Mutations Research Articles

Ultrasensitive profiling of UV-induced mutations identifies thousands of subclinical facial tumors in tuberous sclerosis complex.

BackgroundTuberous sclerosis complex (TSC) is a neurogenetic syndrome due to loss-of-function mutations in TSC2 or TSC1, characterized by tumors at multiple body sites, including facial angiofibroma (FAF). Here, an ultrasensitive assessment of the extent and range of UV-induced mutations in TSC facial skin was performed.MethodsA multiplex high-sensitivity PCR assay (MHPA) was developed, enabling mutation detection at extremely low (<0.1%) variant allele frequencies (VAFs).ResultsMHPA assays were developed for both TSC2 and TP53, and applied to 81 samples, including 66 skin biopsies. UV-induced second-hit mutation causing inactivation of TSC2 was pervasive in TSC facial skin with an average of 4.8 mutations per 2-mm biopsy at median VAF 0.08%, generating more than 150,000 incipient facial tumors (subclinical “micro-FAFs”) in the average TSC subject. The MHPA analysis also led to the identification of a refined UV-related indel signature and a recurrent complex mutation pattern, consisting of both a single-nucleotide or dinucleotide variant and a 1- to 9-nucleotide deletion, in cis.ConclusionTSC facial skin can be viewed as harboring a patchwork of clonal fibroblast proliferations (micro-FAFs) with indolent growth, a small proportion of which develop into clinically observable FAF. Our observations also expand the spectrum of UV-related mutation signatures.FundingThis work was supported by the TSC Alliance; the Engles Family Fund for Research in TSC and LAM; and the NIH, National Heart, Lung, and Blood Institute (U01HL131022-04 and Intramural Research Program).

RumAB genes from SXT/R391 ICEs confer UV-induced mutability to Proteus mirabilis hosts and improve conjugation after UV irradiation

Proteus mirabilis is one of the Enterobacteriales species that has been deemed as non-mutable by DNA damaging agents. A genomic analysis of P. mirabilis genomes shows that this species often does not carry pol V-encoding genes in its chromosome, which are responsible for SOS mutagenesis in other bacteria. On the other hand, the highly active umuDC homologs rumAB are carried in the mobile integrative conjugative elements (ICEs) from the SXT/R391 family that are frequently found in this species. Here we show that isolates devoid of SXT/R391 are indeed weakly or non-mutable by UV-light exposure, in contrast to isolates carrying SXT/R391 elements, some of which are mutable under these conditions. SXT/R391-bearing isolates display a variable behavior regarding UV-induced mutagenesis, despite the functionality of rumAB homologs carried by them. We also show that the globally dispersed ICEPmiJpn1 confers UV mutability to otherwise non-mutable isolates and demonstrate that this phenomenon is dependent on rumAB genes. Finally, we investigated whether rumAB genes could play a role in the conjugation of ICEPmiJpn1 and found that these genes improve the conjugation of SXT/R391 by a small margin. Taken together, these results show that the presence of rumAB in SXT/R391 ICEs endows the hosts with damage-inducible mutagenesis ability and promotes a small but significant enhancement in element transfer after exposure to UV light.

246 Epidermal ablation reduces keratinocyte cancer occurrence by reducing skin mutation burden caused by chronic ultraviolet radiation

Ultra-Violet (UV) radiation from sunlight is the main carcinogen driving keratinocyte cancers of the skin. The accumulation of UV-induced mutations on sun-exposed areas leads to field cancerisation. Knowing the regenerative property of the skin, we investigated if epidermal ablation removes mutations on the epidermis and allows less mutated cells from the deeper part of the skin to repopulate the ablated surface. Patients with history of multiple epidermal cancers were subjected to epidermal ablation on their forearms with three different depths of laser (600nm, 400nm and fractional laser).

Plants growing in Colombia as sources of active ingredients for sunscreens

Introduction Plants can be sources of photoprotective/antigenotoxic compounds that prevent cellular mutations involved in skin cancer and aging by regulating UV-induced mutability. Purpose The study was aimed at investigating the sunscreen properties of plants growing in Colombia. Materials and Methods Ultraviolet (UV) radiation-absorption capability of different plant extracts was examined. In vitro photoprotection efficacies were evaluated using in vitro indices such as sun protection factor (SPFin vitro) and critical wavelength (λc). Pearson correlation analysis was used to examine the relationship between SPFin vitro and complementary UVB- antigenotoxicity estimates (%GI) based on SOS Chromotest database. The cytotoxicity in human fibroblasts was studied using the trypan blue exclusion assay. Major compounds of promising plant extracts were determined by gas chromatography coupled to mass spectrometry (GC/MS). Results We showed that plant extracts have sunscreen properties against UVB, whereas broad-spectrum radiation protection efficacy was poor. SPFin vitro and %GI were correlated (R = 0.71, p < 0.0001) for the plant extracts under study. Three extracts obtained from Achyrocline satureioides, Chromolaena pellia, and Lippia origanoides species resulted to possess high protection efficacy and relatively low cytotoxicity in human fibroblasts. These plant extracts contained major compounds such as α-pinene, trans-β-caryophyllene, γ-muurolene, γ-cadinene and caryophyllene oxide in A. Satureioides extract, trans-β-caryophyllene, caryophyllene oxide, squalene and α-amyrin in C. pellia extract, and p-cymene, carvacrol, trans-β-caryophyllene and pinocembrin in L. origanoides extract. Conclusions Plants growing in Colombia contain compounds which ca be useful for potential sunscreens. SPFin vitro and %GI estimates were correlated, but %GI estimates were more sensitive detecting activity at lower plant extract concentrations. Our results supported the need to use DNA damage detection assays as a complement to photoprotection efficacy measurement.

Chronic UV radiation–induced RORγt+ IL-22–producing lymphoid cells are associated with mutant KC clonal expansion

Chronic ultraviolet (UV) radiation exposure is the greatest risk factor for cutaneous squamous cell carcinoma (cSCC) development, and compromised immunity accelerates this risk. Having previously identified that epidermal Langerhans cells (LC) facilitate the expansion of UV-induced mutant keratinocytes (KC), we sought to more fully elucidate the immune pathways critical to cutaneous carcinogenesis and to identify potential targets of intervention. Herein, we reveal that chronic UV induces and LC enhance a local immune shift toward RORγt+ interleukin (IL)-22/IL-17A-producing cells that occurs in the presence or absence of T cells while identifying a distinct RORγt+ Sca-1+ CD103+ ICOS+ CD2+/- CCR6+ intracellular CD3+ cutaneous innate lymphoid cell type-3 (ILC3) population (uvILC3) that is associated with UV-induced mutant KC growth. We further show that mutant KC clone size is markedly reduced in the absence of RORγt+ lymphocytes or IL-22, both observed in association with expanding KC clones, and find that topical application of a RORγ/γt inhibitor during chronic UV exposure reduces local expression of IL-22 and IL-17A while markedly limiting mutant p53 KC clonal expansion. We implicate upstream Toll-like receptor signaling in driving this immune response to chronic UV exposure, as MyD88/Trif double-deficient mice also show substantially reduced p53 island number and size. These data elucidate key immune components of chronic UV-induced cutaneous carcinogenesis that might represent targets for skin cancer prevention.

Merkel Cell Polyomavirus‒Negative Merkel Cell Carcinoma Originating from In Situ Squamous Cell Carcinoma: A Keratinocytic Tumor with Neuroendocrine Differentiation

Although virus-negative Merkel cell carcinoma (MCC) is characterized by a high frequency of UV-induced mutations, the expression of two viral oncoproteins is regarded as a key mechanism driving Merkel cell polyomavirus‒positive MCC. The cells in which these molecular events initiate MCC oncogenesis have yet not been identified for both MCC subsets. A considerable proportion of virus-negative MCC is found in association with squamous cell carcinoma (SCC), suggesting (i) coincidental collision, (ii) one providing a niche for the other, or (iii) one evolving from the other. Whole-exome sequencing of four combined tumors consisting of SCC in situ and Merkel cell polyomavirus‒negative MCC showed many mutations shared between SCC and MCC in all cases, indicating a common ancestry and thereby a keratinocytic origin of these MCCs. Moreover, analyses of the combined cases as well as of pure SCC and MCC suggest that RB1 inactivation in SCC facilitates MCC development and that epigenetic changes may contribute to the SCC/MCC transition.

Periodic Graphics: The chemistry of how our skin responds to the sun

Chemical educator and Compound Interest blogger Andy Brunning illuminates the biochemistry behind sunlight’s effects on our skin To download a pdf of this article, visit http://cenm.ag/sunskin. References used to create this graphic: Clancy, Suzanne. “ DNA Damage & Repair: Mechanisms for Maintaining DNA Integrity .” Nat. Educ. (2008). De Gruijl, Frank R., Henk J. van Kranen, and Leon H. F. Mullenders. “UV-Induced DNA Damage, Repair, Mutations and Oncogenic Pathways in Skin Cancer.” J. Photochem. Photobiol. , B (Oct. 2001). DOI: 10.1016/S1011-1344 (01)00199-3. Hopkins, Ryan. “ How Ultraviolet Light Reacts in Cells .” SciBytes (blog). Feb. 14, 2015. Soyer, H. Peter, and Katie Lee. “ Explainer: What Happens to Your Skin When You Get Sunburnt? ” Conversation, March 9, 2016. A collaboration between C&EN and Andy Brunning, author of the popular graphics blog Compound Interest To see more of Brunning’s work, go to compoundchem.com . To see all of C&EN’s Periodic

Biochemical and photochemical mechanisms that produce different UV-induced mutation spectra.

Although UV-induced mutagenesis has been studied extensively, the precise mechanisms that convert UV-induced DNA damage into mutations remain elusive. One well-studied mechanism involves DNA polymerase (Pol) η and ζ, which produces C > T transitions during translesion synthesis (TLS) across pyrimidine dimers. We previously proposed another biochemical mechanism that involves multiple UV-irradiations with incubation in the dark in between. The incubation facilitates spontaneous deamination of cytosine in a pyrimidine dimer, and the subsequent UV irradiation induces photolyase-independent (direct) photoreversal that converts cytosine into monomeric uracil residue. In this paper, we first demonstrate that natural sunlight can induce both mutational processes in vitro. The direct photoreversal was also reproduced by monochromatic UVB at 300 nm. We also demonstrate that post-irradiation incubation in the dark is required for both mutational processes, suggesting that cytosine deamination is required for both the Pol η/ζ-dependent and the photoreversal-dependent mechanisms. Another Y-family polymerase Pol ι also mediated a mutagenic TLS on UV-damaged templates when combined with Pol ζ. The Pol ι-dependent mutations were largely independent of post-irradiation incubation, indicating that cytosine deamination was not essential for this mutational process. Sunlight-exposure also induced C > A transversions which were likely caused by oxidation of guanine residues. Finally, we constructed in vitro mutation spectra in a comparable format to cancer mutation signatures. While both Pol η-dependent and photoreversal-dependent spectra showed high similarities to a cancer signature (SBS7a), Pol ι-dependent mutation spectrum has distinct T > A/C substitutions, which are found in another cancer signature (SBS7d). The Pol ι-dependent T > A/C substitutions were resistant to T4 pyrimidine dimer glycosylase-treatment, suggesting that this mutational process is independent of cis-syn pyrimidine dimers. An updated model about multiple mechanisms of UV-induced mutagenesis is discussed.

072 Targeting field cancerisation in epidermal cancers

Ultra-Violet (UV) radiation from sunlight is the main carcinogen driving epidermal cancers of the skin. The accumulation of UV-induced mutations on sun-exposed areas leads to field cancerisation. Knowing the regenerative property of the skin, we investigated if epidermal ablation removes mutations on the epidermis and allows less mutated cells from the deeper part of the skin to repopulate the ablated surface. Patients with history of multiple epidermal cancers were subjected to epidermal ablation on their forearms with three different depths of laser (600nm, 400nm and fractional laser). Deep targeted DNA sequencing of 151 cancer related genes had revealed the mutation burdens on ablated and non-ablated epidermis. There were 12.9 mutations per Megabase (Muts/Mb) found in non-ablated control epidermis compared to 2.55 Muts/Mb in 600nm, 4.45 Muts/Mb in 400nm and 3.58 Muts/Mb in fractional laser ablated and regenerated epidermis (n=7). To evaluate the efficacy of epidermal ablation on epidermal cancers formation, we utilised a UVB inducible Basal Cell Carcinomas (BCC) murine model (K14Cre/ER::Ptch1lox/+ ). These mice were subjected to a total of 20 weeks of UVB radiation. Half of the dorsal epidermis was dermabrased after the first 10 weeks of radiation. Wholemount staining of a BCC biomarker, Keratin-17 (K17), revealed a significant reduction in the number of K17 patches in dermabrased area (0.35 patches/mm2 ± 0.04 compared to 0.07 patches/mm2 ± 0.03) suggesting dermabrsasion can be used to reduce BCC occurrence. Overall, our findings propose a potential technique to reverse the photo-damage process by removing the mutations accumulated on the epidermis. This study may also pave the way to a larger clinical trial of epidermal ablation as an adjuvant therapy for high-risk epidermal cancer patients.

491 Functional genomics screen identifies alternative targetable pathways for Merkel cell carcinoma

Merkel cell carcinoma (MCC) is a rare, aggressive neuroendocrine skin cancer. Most MCC tumors have Merkel cell polyomavirus integrated into the host genome (virus-positive MCC; VP-MCC), whereas virus-negative MCC (VN-MCC) tumors bear UV-induced mutations. Immune checkpoint inhibitors (ICI) are the first-line treatment for metastatic MCC, but the majority of patients are either not candidates for ICI or have disease progression while on treatment. In order to identify alternative therapeutic targets for these patients, we performed a druggable genome RNAi screen in MKL-2 (VP-MCC) and MCC26 (VN-MCC) cell lines. We screened >25,000 siRNA for their ability to reduce MCC viability at 72 hours. The main gene functions identified as essential to MCC viability included cell proliferation (VP- and VN-MCC) and apoptosis (VP-MCC). These results were corroborated by a follow-up RNAi screen including the two original cell lines, WaGa (VP-MCC), MCC13 (VN-MCC), and UISO (VN-MCC). Interestingly, many essential gene products identified in our screen were targets of compounds that selectively reduced MCC viability in an independent high-throughput MCC viability screen of ∼4000 small molecules. High-priority lead compounds supported by both screens showed efficacy in preclinical xenograft mouse models of MCC. Overall, our discovery and validation of novel targetable pathways have identified alternative treatment approaches for metastatic MCC.

Detection and analysis of UV-induced mutations in the chromosomal DNA of Arabidopsis

Under natural conditions, plants are exposed to solar ultraviolet (UV) radiation, which damages chromosomal DNA. Although plant responses to UV-induced DNA damage have recently been elucidated in detail, revealing a set of DNA repair mechanisms and translesion synthesis (TLS), limited information is currently available on UV-induced mutations in plants. We previously reported the development of a supF-based system for the detection of a broad spectrum of mutations in the chromosomal DNA of Arabidopsis. In the present study, we used this system to investigate UV-induced mutations in plants. The irradiation of supF-transgenic plants with UV-C (500 and 1000 J/m2) significantly increased mutation frequencies (26- and 45-fold, respectively). G:C to A:T transitions (43–67% of base substitutions) dominated in the mutation spectrum and were distributed throughout single, tandem, and multiple base substitutions. Most of these mutations became undetectable with the subsequent illumination of UV-irradiated plants with white light for photoreactivation (PR). These results indicated that not only G:C to A:T single base substitutions, but also tandem and multiple base substitutions were caused by two major UV-induced photoproducts, cyclobutane-type pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (6-4 PPs). In contrast, a high proportion of A:T to T:A transversions (56% of base substitutions) was a characteristic feature of the mutation spectrum obtained from photoreactivated plants. These results define the presence of the characteristic feature of UV-induced mutations, and provide insights into DNA repair mechanisms in plants.

An Easily Accessible Microfluidic Chip for High-Throughput Microalgae Screening for Biofuel Production

Microalgae are important green energy resources. With high efficiency in fixing carbon dioxide, microalgae are broadly applied for biofuel production. Integrating various cultivation parameters, we applied ultraviolet (UV) mutagenesis, one of the most common approaches, to induce genomic mutation in microalgae and thus enhance the production of lipid content, but the screening process is convoluted and labor-intensive. In this study, we aimed to develop an accessible microfluidic platform to optimize the biofuel production of microalgae. Instead of traditional lithography, we designed hanging-drop microfluidic chips that were fabricated using a cheap computer numerical control (CNC) micro-milling technique. On each chip, we cultured in parallel Botryococcus braunii, one of the most common freshwater microalgae for biofuel production, in sets of ten separated hanging drops (~30 µL each); we monitored their growth in each individual drop for more than 14 days. To optimize the culturing conditions, using drops of varied diameter, we first identified the influence of cell density on algae growth and lipid production. After introducing UV-induced random mutations, we quantified the lipid content of the microalgae in situ; the optimized UV-C dosage was determined accordingly. In comparison with wild-type B. braunii, the results showed increased biomass growth (137%) and lipid content (149%) of the microalgae mutated with the desired UV process. Moreover, we showed a capacity to modulate the illumination on an addressed chip area. In summary, without using an external pump system, we developed a hanging-drop microfluidic system for long-term microalgae culturing, which can be easily operated using laboratory pipettes. This microfluidic system is expected to facilitate microalgae mutation breeding, and to be applied for algae cultivation optimization.

Pph3 Phosphatase Participates in the Regulation of the Error-Free Branch of Postreplication DNA Repair in Yeast Saccharomyces cerevisiae

The phosphatase complex PPH3 consists of three subunits: catalytic Pph3 and auxiliary Pph2 and Psy4. Pph3 also forms a double complex with subunit Psy2, which binds to kinase Rad53 and dephosphorylates it without recruiting the third subunit. The triple complex dephosphorylates γH2A. We have previously shown that gene HSM6 corresponds to gene PSY4 on the genetic map of Saccharomyces cerevisiae. Mutation hsm6-1 increases the rate of spontaneous and UV-induced mutagenesis. In this work, we have shown that mutations in gene PPH3 increase the rate of spontaneous reparative mutagenesis sevenfold, while mutations pph3Δ and hsm6-1 show an epistatic effect. At high doses, the frequency of UV-induced mutations in mutants pph3Δ, psy4Δ, and hsm6-1 is the same and exceeds the level of mutagenesis in the wild-type strain by approximately twofold. All mutants show a higher (approximately 10-fold) frequency of γ-induced mutations compared to the wild-type strain. The combination of mutations in genes encoding PPH3 subunits and mutations in MMS2 and XRS2, which control an error-free postreplication repair pathway, leads to blocking of PPH3-specific UV-induced mutagenesis. Thus, we have identified the PPH3 complex as a novel factor involved in the regulation of the error-free branch of postreplication repair. The double mutant for genes PTC2 and PTC3, encoding the other two phosphatases that dephosphorylate Rad53, does not differ from the wild-type strain with respect to UV-induced mutagenesis and survival. This means that hyperphosphorylation of only the Pph3-specific sites of protein Rad53 and histone H2A increases the level of UV mutagenesis.

UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin.

Human skin is continuously exposed to environmental DNA damage leading to the accumulation of somatic mutations over the lifetime of an individual. Mutagenesis in human skin cells can be also caused by endogenous DNA damage and by DNA replication errors. The contributions of these processes to the somatic mutation load in the skin of healthy humans has so far not been accurately assessed because the low numbers of mutations from current sequencing methodologies preclude the distinction between sequencing errors and true somatic genome changes. In this work, we sequenced genomes of single cell-derived clonal lineages obtained from primary skin cells of a large cohort of healthy individuals across a wide range of ages. We report here the range of mutation load and a comprehensive view of the various somatic genome changes that accumulate in skin cells. We demonstrate that UV-induced base substitutions, insertions and deletions are prominent even in sun-shielded skin. In addition, we detect accumulation of mutations due to spontaneous deamination of methylated cytosines as well as insertions and deletions characteristic of DNA replication errors in these cells. The endogenously induced somatic mutations and indels also demonstrate a linear increase with age, while UV-induced mutation load is age-independent. Finally, we show that DNA replication stalling at common fragile sites are potent sources of gross chromosomal rearrangements in human cells. Thus, somatic mutations in skin of healthy individuals reflect the interplay of environmental and endogenous factors in facilitating genome instability and carcinogenesis.

Effects of β-HPV on DNA damage response pathways to drive carcinogenesis: a review.

The DDR is a complex signaling network responsible for the preservation of genomic integrity. Beta human papillomaviruses (β-HPVs) are able to destabilize the host genome by attenuating the DDR machinery at the molecular scale following expression of the oncogenes E6 and E7. In the event of β-HPV infection, the E6- and E7-mediated inhibition of the DDR enhances the oncogenicity of UV-induced mutations to enable carcinogenesis in an otherwise immunocompetent host, marking an important mechanistic divergence from the alpha genus of HPVs. In this review, we summarize recent updates to build upon the 'hit-and-run' hypothesis of β-HPV pathomechanism and highlight strain-dependent variations. Simultaneously, we illuminate points within the β-HPV-DDR interface that may unravel new insights for HPV viral genetics, genus-specific mechanistic models, and developments in targeted molecular therapy of β-HPV-related cancers.

Genome shuffling improves pigment and other bioactive compound production in Monascus purpureus.

Monascus purpureus, a pigment-producing ascomycetous fungus, has been traditionally used for red rice preparation using solid-state fermentation. The objective of this study was to develop an improved pigment-producing strain of M. purpureus MTCC 1090 through genome shuffling followed by detailed analytical estimations of pigments and other bioactive compounds produced by the fusant. Protoplast formation was optimum with 12h-old mycelia incubated at 30 °C with cellulase, lyticase, and chitinase (40:1:1) for 5 h. Four UV-induced mutants that produced 13.1-39.5% higher amount of yellow, orange, and red pigments in fermented low-grade (cheap) broken rice were used as parents for genome shuffling. After the first round of fusion, four fusants with 35.9-60.52% higher pigment production capabilities were fused again, and finally the fusant F2-19 with distinct culture characteristic was selected under multi-selection pressure. It consistently produced 67%, 70%, and 76% higher content of yellow, orange, and red pigments respectively ascompared to the wild-type. High-performance liquid chromatography (HPLC) analysis also reveals clear variation in pigment productions between wild-type and the fusant. Furthermore, HPLC analysis of F2-19 fermented rice extract confirms the production of 186 ± 8.71 and 3810 ± 29.81 mg/kg mevinolin and gamma-aminobutyric acid respectively. Citrinin was not detected. F2-19 fermented rice also has high antioxidant activity (7.92 ± 0.32 mg/g trolox equivalent), with good amount of phenolics (18.0 ± 0.95 mg/g gallic acid equivalent) and flavonoids (2.7 ± 0.26 mg/g quercetin equivalent). Thus, genome shuffling was successfully implemented on M. purpureus for the first time to develop a citrinin-free, better-performing fusant that holds future biotechnological potential. KEY POINTS: • Genome shuffling was performed by recursive protoplast fusion in Monascus purpureus. • The selected fusant, F2-19, was used in solid-state fermentation using low-grade rice. • It produced 67-76% higher content of yellow, orange, and red pigments than the wild-type. • HPLC detected 186 mg/kg mevinolin and 3810 mg/kg γ-aminobutyric acid, but no citrinin. • F2-19 shows high antioxidant activity with good amount of phenolics and flavonoids. Graphical abstract.

Atypical UV Photoproducts Induce Non-canonical Mutation Classes Associated with Driver Mutations in Melanoma

SUMMARYSomatic mutations in skin cancers and other ultraviolet (UV)-exposed cells are typified by C>T and CC>TT substitutions at dipyrimidine sequences; however, many oncogenic “driver” mutations in melanoma do not fit this UV signature. Here, we use genome sequencing to characterize mutations in yeast repeatedly irradiated with UV light. Analysis of ~50,000 UV-induced mutations reveals abundant non-canonical mutations, including T>C, T>A, and AC>TT substitutions. These mutations display transcriptional asymmetry that is modulated by nucleotide excision repair (NER), indicating that they are caused by UV photoproducts. Using a sequencing method called UV DNA endonuclease sequencing (UVDE-seq), we confirm the existence of an atypical thymine-adenine photoproduct likely responsible for UV-induced T>A substitutions. Similar non-canonical mutations are present in skin cancers, which also display transcriptional asymmetry and dependence on NER. These include multiple driver mutations, most prominently the recurrent BRAF V600E and V600K substitutions, suggesting that mutations arising from rare, atypical UV photoproducts may play a role in melanomagenesis.

Actinic Keratoses: Reconciling the Biology of Field Cancerization with Treatment Paradigms

This Perspective briefly reviews the relationship between UV-induced mutations in habitually sun-exposed human skin and subsequent development of actinic keratoses (AKs) and skin cancers. It argues that field therapy rather than AK-selective therapy is the more logical approach to cancer prevention and hypothesizes that treatment early in the process of field cancerization, even prior to the appearance of AKs, may be more effective in preventing cancer as well as more beneficial for and better tolerated by at-risk individuals. Finally, the Perspective encourages use of rapidly advancing DNA analysis techniques to quantify mutational burden in sun-damaged skin and its reduction by various therapies.

Multi-site clonality analysis uncovers pervasive heterogeneity across melanoma metastases

Metastatic melanoma carries a poor prognosis despite modern systemic therapies. Understanding the evolution of the disease could help inform patient management. Through whole-genome sequencing of 13 melanoma metastases sampled at autopsy from a treatment naïve patient and by leveraging the analytical power of multi-sample analyses, we reveal evidence of diversification among metastatic lineages. UV-induced mutations dominate the trunk, whereas APOBEC-associated mutations are found in the branches of the evolutionary tree. Multi-sample analyses from a further seven patients confirmed that lineage diversification was pervasive, representing an important mode of melanoma dissemination. Our analyses demonstrate that joint analysis of cancer cell fraction estimates across multiple metastases can uncover previously unrecognised levels of tumour heterogeneity and highlight the limitations of inferring heterogeneity from a single biopsy.

Human genes differ by their UV sensitivity estimated through analysis of UV-induced silent mutations in melanoma.

We hypothesized that human genes differ by their sensitivity to ultraviolet (UV) exposure. We used somatic mutations detected by genome-wide screens in melanoma and reported in the Catalog Of Somatic Mutations In Cancer. As a measure of UV sensitivity, we used the number of silent mutations generated by C>T transitions in pyrimidine dimers of a given transcript divided by the number of potential sites for this type of mutations in the transcript. We found that human genes varied by UV sensitivity by two orders of magnitude. We noted that the melanoma-associated tumor suppressor gene CDKN2A was among the top five most UV-sensitive genes in the human genome. Melanoma driver genes have a higher UV-sensitivity compared with other genes in the human genome. The difference was more prominent for tumor suppressors compared with oncogene. The results of this study suggest that differential sensitivity of human transcripts to UV light may explain melanoma specificity of some driver genes. Practical significance of the study relates to the fact that differences in UV sensitivity among human genes need to be taken into consideration whereas predicting melanoma-associated genes by the number of somatic mutations detected in a given gene.