Is sunlight important to melanoma causation?

From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research

Next-generation sequencing (NGS) applications have flourished in the last decade, permitting the identification of cancer driver genes and profoundly expanding the possibilities of genomic studies of cancer, including melanoma. Here we aimed to present a technical review across many of the methodological approaches brought by the use of NGS applications with a focus on assessing germline and somatic sequence variation. We provide cautionary notes and discuss key technical details involved in library preparation, the most common problems with the samples, and guidance to circumvent them. We also provide an overview of the sequence-based methods for cancer genomics, exposing the pros and cons of targeted sequencing vs. exome or whole-genome sequencing (WGS), the fundamentals of the most common commercial platforms, and a comparison of throughputs and key applications. Details of the steps and the main software involved in the bioinformatics processing of the sequencing results, from preprocessing to variant prioritization and filtering, are also provided in the context of the full spectrum of genetic variation (SNVs, indels, CNVs, structural variation, and gene fusions). Finally, we put the emphasis on selected bioinformatic pipelines behind (a) short-read WGS identification of small germline and somatic variants, (b) detection of gene fusions from transcriptomes, and (c) de novo assembly of genomes from long-read WGS data. Overall, we provide comprehensive guidance across the main methodological procedures involved in obtaining sequencing results for the most common short- and long-read NGS platforms, highlighting key applications in melanoma research.

Mechanisms of UV-induced mutations and skin cancer

Ultraviolet (UV) irradiation causes various types of DNA damage, which leads to specific mutations and the emergence of skin cancer in humans, often decades after initial exposure. Different UV wavelengths cause the formation of prominent UV-induced DNA lesions. Most of these lesions are removed by the nucleotide excision repair pathway, which is defective in rare genetic skin disorders referred to as xeroderma pigmentosum. A major role in inducing sunlight-dependent skin cancer mutations is assigned to the cyclobutane pyrimidine dimers (CPDs). In this review, we discuss the mechanisms of UV damage induction, the genomic distribution of this damage, relevant DNA repair mechanisms, the proposed mechanisms of how UV-induced CPDs bring about DNA replication-dependent mutagenicity in mammalian cells, and the strong signature of UV damage and mutagenesis found in skin cancer genomes.

Anti-genotoxic and anti-mutagenic effects of melatonin supplementation in a mouse model of melanoma

Melanoma, an aggressive skin cancer originating from melanocytes, can metastasize to the lungs, liver, cortex, femur, and spinal cord, ultimately resulting in DNA mutagenic effects. Melatonin is an endogenous hormone and free radical scavenger that possesses the ability to protect the DNA and to exert anti-proliferative effects in melanoma cells. The aim of this study was to evaluate the effects of B16F10 melanoma cells and the effects of melatonin supplementation on genotoxic parameters in murine melanoma models. Thirty-two male C57Bl/6 mice were divided in the following four groups: PBS + vehicle (n = 6), melanoma + vehicle (n = 10), PBS + melatonin (n = 6), and melanoma + melatonin (n = 10). The melanoma groups received a B16F10 cell injection, and melatonin was administered during 60 days. After treatment, tumor sizes were evaluated. DNA damage within the peripheral blood, lungs, liver, cortex, and spinal cord was determined using comet assay, and the mutagenicity within the bone marrow was determined using the micronucleus test. B16F10 cells effectively induced DNA damage in all tissues, and melatonin supplementation decreased DNA damage in the blood, liver, cortex, and spinal cord. This hormone exerts anti-tumor activity via its anti-proliferative, antioxidative, and pro-apoptotic effects. As this result was not observed within the lungs, we hypothesized that melatonin can induce apoptosis in cancer cells, and this was not evaluated by comet assay. This study provides evidence that melatonin can reduce the genotoxicity and mutagenicity caused by B16F10 cells.

Geographic Clusters of Basal Cell Carcinoma in a Northern California Health Plan Population

Importance

Rates of skin cancer, including basal cell carcinoma (BCC), the most common cancer, have been increasing over the past 3 decades. A better understanding of geographic clustering of BCCs can help target screening and prevention efforts.

Objective

Present a methodology to identify spatial clusters of BCC and identify such clusters in a northern California population.

Design, Setting, and Participants

This retrospective study used a BCC registry to determine rates of BCC by census block group, and used spatial scan statistics to identify statistically significant geographic clusters of BCCs, adjusting for age, sex, and socioeconomic status. The study population consisted of white, non-Hispanic members of Kaiser Permanente Northern California during years 2011 and 2012.

Main Outcomes and Measures

Statistically significant geographic clusters of BCC as determined by spatial scan statistics.

Results

Spatial analysis of 28 408 individuals who received a diagnosis of at least 1 BCC in 2011 or 2012 revealed distinct geographic areas with elevated BCC rates. Among the 14 counties studied, BCC incidence ranged from 661 to 1598 per 100 000 person-years. After adjustment for age, sex, and neighborhood socioeconomic status, a pattern of 5 discrete geographic clusters emerged, with a relative risk ranging from 1.12 (95% CI, 1.03-1.21; P = .006) for a cluster in eastern Sonoma and northern Napa Counties to 1.40 (95% CI, 1.15-1.71; P < .001) for a cluster in east Contra Costa and west San Joaquin Counties, compared with persons residing outside that cluster.

Conclusions and Relevance

In this study of a northern California population, we identified several geographic clusters with modestly elevated incidence of BCC. Knowledge of geographic clusters can help inform future research on the underlying etiology of the clustering including factors related to the environment, health care access, or other characteristics of the resident population, and can help target screening efforts to areas of highest yield.

Mitotic regulator Nlp interacts with XPA/ERCC1 complexes and regulates nucleotide excision repair (NER) in response to UV radiation

Cellular response to DNA damage, including ionizing radiation (IR) and UV radiation, is critical for the maintenance of genomic fidelity. Defects of DNA repair often result in genomic instability and malignant cell transformation. Centrosomal protein Nlp (ninein-like protein) has been characterized as an important cell cycle regulator that is required for proper mitotic progression. In this study, we demonstrate that Nlp is able to improve nucleotide excision repair (NER) activity and protects cells against UV radiation. Upon exposure of cells to UVC, Nlp is translocated into the nucleus. The C-terminus (1030-1382) of Nlp is necessary and sufficient for its nuclear import. Upon UVC radiation, Nlp interacts with XPA and ERCC1, and enhances their association. Interestingly, down-regulated expression of Nlp is found to be associated with human skin cancers, indicating that dysregulated Nlp might be related to the development of human skin cancers. Taken together, this study identifies mitotic protein Nlp as a new and important member of NER pathway and thus provides novel insights into understanding of regulatory machinery involved in NER.

Ultraviolet Radiation-Induced Cytogenetic Damage in White, Hispanic and Black Skin Melanocytes: A Risk for Cutaneous Melanoma

Cutaneous Melanoma (CM) is a leading cause of cancer deaths, with reports indicating a rising trend in the incidence rate of melanoma among Hispanics in certain U.S. states. The level of melanin pigmentation in the skin is suggested to render photoprotection from the DNA-damaging effects of Ultraviolet Radiation (UVR). UVR-induced DNA damage leads to cytogenetic defects visualized as the formation of micronuclei, multinuclei and polymorphic nuclei in cells, and a hallmark of cancer risk. The causative relationship between Sun exposure and CM is controversial, especially in Hispanics and needs further evaluation. This study was initiated with melanocytes from White, Hispanic and Black neonatal foreskins which were exposed to UVR to assess their susceptibility to UVR-induced modulation of cellular growth, cytogenetic damage, intracellular and released melanin. Our results show that White and Hispanic skin melanocytes with similar levels of constitutive melanin are susceptible to UVR-induced cytogenetic damage, whereas Black skin melanocytes are not. Our data suggest that the risk of developing UVR-induced CM in a skin type is correlated with the level of cutaneous pigmentation and its ethnic background. This study provides a benchmark for further investigation on the damaging effects of UVR as risk for CM in Hispanics.

Cork extracts reduce UV-mediated DNA fragmentation and cell death

Cork extracts composed of vescalagin/castalagin, gallic acid and ellagic acid reduce UV-mediated cell damage in fibroblasts.

Prospective study of ultraviolet radiation exposure and risk of cancer in the United States

Ecologic studies have reported that solar ultraviolet radiation (UVR) exposure is associated with cancer; however, little evidence is available from prospective studies. We aimed to assess the association between an objective measure of ambient UVR exposure and risk of total and site-specific cancer in a large, regionally diverse cohort [450,934 white, non-Hispanic subjects (50-71 years) in the prospective National Institutes of Health (NIH)-AARP Diet and Health Study] after accounting for individual-level confounding risk factors. Estimated erythemal UVR exposure from satellite Total Ozone Mapping Spectrometer (TOMS) data from NASA was linked to the US Census Bureau 2000 census tract (centroid) of baseline residence for each subject. We used Cox proportional hazards models adjusted for multiple potential confounders to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for quartiles of UVR exposure. Restricted cubic splines examined nonlinear relationships. Over 9 years of follow-up, UVR exposure was inversely associated with total cancer risk (N = 75,917; highest versus lowest quartile; HR = 0.97, 95% CI = 0.95-0.99; p-trend < 0.001). In site-specific cancer analyses, UVR exposure was associated with increased melanoma risk (highest versus lowest quartile; HR = 1.22, 95% CI = 1.13-1.32; p-trend < 0.001) and decreased risk of non-Hodgkin's lymphoma (HR = 0.82, 95% CI = 0.74-0.92) and colon (HR = 0.88, 95% CI = 0.82-0.96), squamous cell lung (HR = 0.86, 95% CI = 0.75-0.98), pleural (HR = 0.57, 95% CI = 0.38-0.84), prostate (HR = 0.91, 95% CI = 0.88-0.95), kidney (HR = 0.83, 95% CI = 0.73-0.94) and bladder (HR = 0.88, 95% CI = 0.81-0.96) cancers (all p-trend < 0.05). We also found nonlinear associations for some cancer sites, including the thyroid and pancreas. Our results add to mounting evidence for the influential role of UVR exposure on cancer.

UV wavelength-dependent DNA damage and human non-melanoma and melanoma skin cancer

Ultraviolet (UV) irradiation from the sun has been epidemiologically and mechanistically linked to skin cancer, a spectrum of diseases of rising incidence in many human populations. Both non-melanoma and melanoma skin cancers are associated with sunlight exposure. In this review, we discuss the UV wavelength-dependent formation of the major UV-induced DNA damage products, their repair and mutagenicity and their potential involvement in sunlight-associated skin cancers. We emphasize the major role played by the cyclobutane pyrimidine dimers (CPDs) in skin cancer mutations relative to that of (6-4) photoproducts and oxidative DNA damage. Collectively, the data implicate the CPD as the DNA lesion most strongly involved in human cancers induced by sunlight.

Rising melanoma incidence rates of the trunk among younger women in the United States

BACKGROUND

Melanoma rates are rising among young women, possibly due to increasing UV radiation to previously protected body sites. Therefore, we examined melanoma incidence trends by age, gender, and body site. Descriptive methods were complemented with the age-period-cohort parameters net drift and longitudinal age trend.

METHODS

Case and population data were obtained from the Surveillance, Epidemiology, and End Results (SEER) 9 Registries Database (1975-2006). Net drift summarized the average annual percentage change in log-linear rates per year of calendar-time (or year of diagnosis). Longitudinal age trend summarized the average annual percentage change by attained age at diagnosis. Early- and late-onset melanomas have low and high longitudinal age trends, respectively.

RESULTS

There were 105,829 melanomas diagnosed in the SEER 9 Registries. The overall age-adjusted incidence rate (IR) for melanoma was 17.7/100,000 person-years. Age-specific IRs were greater among women than men prior to age 40 years. Among women, IRs decreased for all anatomic sites relative to the trunk. The highest net drift occurred in truncal lesions among women (net drift, 3.8%/year of calendar time; 95% confidence interval, 3.5-4.0%). The lowest longitudinal age trends also were observed for truncal lesions among women (longitudinal age trend, 5.4%/year of attained age; 95% confidence interval, 5.1-5.7).

CONCLUSIONS

Although melanoma IRs overall have risen for decades, the combination of high net drift and low longitudinal age trend show that melanomas are rising preferentially on the trunk among young women.

IMPACT

Future surveillance and analytic studies should consider melanoma effect modification by age, gender, and body site.

Divergent cancer pathways for early-onset and late-onset cutaneous malignant melanoma

BACKGROUND

Emerging data suggest that cutaneous malignant melanomas (CMM) may arise through divergent cancer pathways that are linked to intermittent versus accumulated sun exposure. However, numerous questions remain regarding the timing and/or age of exposure.

METHODS

The authors systematically examined the effect of aging on CMM incidence in data from the Surveillance, Epidemiology, and End Results Program of the National Cancer Institute. Standard descriptive epidemiology was supplemented with mathematical models. The impact of advancing age on CMM incidence was assessed by sex, histopathologic classification (superficial spreading melanoma [SSM] or lentigo maligna melanoma [LMM]), and anatomic site (face, head, and neck [FHN] or lower extremity [LE]).

RESULTS

Sex, histopathology, and anatomic site were age-specific effect modifiers for CMM that indicated divergent (bimodal) early-onset and late-onset cancer pathways. Early-onset melanomas were associated predominantly with women, SSM, and LE. Late-onset melanomas were correlated with men, LMM, and FHN. Early- and late-onset melanoma populations were confirmed with age-period-cohort models that were adjusted for period and cohort effects. Two-component mixture models also fit the data better than a single cancer population.

CONCLUSIONS

The current results were consistent with a divergent and age-dependent solar hypothesis for CMM. Early-onset melanomas may represent gene-sun exposure interactions that occur early (and/or intermittently) in life among susceptible individuals. Late-onset melanomas may reflect accumulated, lifelong sun exposure in comparatively less susceptible individuals. Future analytical studies should be powered adequately to account for this age-dependent effect modification both for acknowledged melanoma risk factors (sex, histopathology, and anatomic site) and for suspected melanoma risk factors, such as constituent genetic variants.

UVB and UVA initiate different pathways to p53-dependent apoptosis in melanocytes

The incidence of cutaneous malignant melanoma (CMM) has more than doubled in the past 25 years and continues to increase at over 3% per year across all age groups (Linos et al., this issue), and invasive and disseminated melanoma in young women has increased by almost 10% since 1992 (Purdue et al., 2008). Early detection and excision of CMM can result in successful treatment, but disseminated disease is resistant to current therapies and has a very poor prognosis (Garbe and Eigentler, 2007). Sunlight exposure is a major risk factor for melanoma. In this issue, Waster and llinger investigate the effects of UVB and UVA on melanocytes.

Patterns of photoprotection following CDKN2A/p16 genetic test reporting and counseling

BACKGROUND

The impact of melanoma genetic testing and counseling on photoprotective behaviors is unknown.

OBJECTIVE

To determine if genetic testing and counseling alter compliance with photoprotection recommendations.

METHODS

Reported use of sunscreen, protective clothing, and sun avoidance by 59 members of CDKN2A/p16-mutation positive pedigrees was assessed as a function of mutation status and melanoma history, before, immediately after, and 1 month following test reporting.

RESULTS

Intentions to practice all photoprotective behaviors increased in all participant groups (P < .0001). At 1 month, 33% of participants reported the adoption of a new photoprotective behavior. Subpopulation analyses identified different patterns of change in photoprotection relative to baseline (P < .005), with no net decline in any group.

LIMITATIONS

This initial study of CDKN2A/p16 families is small and awaits replication in a larger sample.

CONCLUSION

Melanoma genetic testing and counseling enhanced intentions to implement photoprotective strategies and did not result in reduced compliance in the CDKN2A/p16-subpopulation.