Integrative genetic analysis suggests that skin color modifies the genetic architecture of melanoma

Pervasive Induction of Regulatory Mutation Microclones in Sun-exposed Skin

Carcinogen-induced mutations are thought near-random, with rare cancer-driver mutations underlying clonal expansion. Using high-fidelity Duplex Sequencing to reach a mutation frequency sensitivity of 4×10 -9 per nt, we report that sun exposure creates pervasive mutations at sites with ∼100-fold UV-sensitivity in RNA-processing gene promoters - cyclobutane pyrimidine dimer (CPD) hyperhotspots - and these mutations have a mini-driver clonal expansion phenotype. Numerically, human skin harbored 10-fold more genuine mutations than previously reported, with neonatal skin containing 90,000 per cell; UV signature mutations increased 8,000-fold in sun-exposed skin, averaging 3×10 -5 per nt. Clonal expansion by neutral drift or passenger formation was nil. Tumor suppressor gene hotspots reached variant allele frequency 0.1-10% via 30-3,000 fold clonal expansion, in occasional biopsies. CPD hyperhotspots reached those frequencies in every biopsy, with modest clonal expansion. In vitro, tumor hotspot mutations arose occasionally over weeks of chronic low-dose exposure, whereas CPD hyperhotspot mutations arose in days at 1000-fold higher frequencies, growing exponentially. UV targeted mini-drivers in every skin cell.

Cyclobutane Pyrimidine Dimer Hyperhotspots as Sensitive Indicators of Keratinocyte UV Exposure†

The dominant DNA damage generated by UV exposure is the cyclobutane pyrimidine dimer (CPD), which alters skin cell physiology and induces cell death and mutation. Genome-wide nucleotide-resolution analysis of CPDs in melanocytes and fibroblasts has identified "CPD hyperhotspots", pyrimidine-pyrimidine sites hundreds of fold more susceptible to the generation of CPDs than the genomic average. Identifying hyperhotspots in keratinocytes could enable measuring individual past UV exposure in small skin samples and predicting future skin cancer risk. We therefore exposed neonatal human epidermal keratinocytes to narrowband UVB and quantified CPDs using the adductSeq high-throughput DNA sequencing method. Keratinocytes contained thousands of CPD hyperhotspots, with a UVB-sensitivity up to 550 fold greater than the genomic average. As with melanocytes, the most sensitive sites were located in promoter regions at ETS-family transcription factor binding sequence motifs, near RNA processing genes. Moreover, they lay at sequence motifs bound to ETS1 in CpG islands. These genes were specifically upregulated in skin and the CPD hyperhotspots were mutated in a fraction of keratinocyte cancers. Crucially for their biological importance and practical application, CPD hyperhotspot locations and UV-sensitivity ranking demonstrated high reproducibility across experiments and across skin donors. CPD hyperhotspots are therefore sensitive indicators of UV exposure.

Skin Cancer in People of Color: A Systematic Review

BACKGROUND

People of African, Asian, Hispanic or Latino, Pacific Islander, and Native Indian descent are considered people of color by the Skin of Color Society (SOCS).

OBJECTIVES

In this study, we assess incidence, risk factors, clinical characteristics, histopathology, treatment, and survival for skin malignancies in people of color as defined by the SOCS, by systematically reviewing the literature.

METHODS

An electronic literature search of the PubMed, EMBASE, and MEDLINE databases was performed. Articles published from 1 January 1990 through 12 December 2020 were included in the search.

RESULTS

We identified 2666 publications potentially meeting the study criteria. Titles and abstracts of these studies were reviewed and 2353 were excluded. The full text of 313 articles were evaluated and 251 were included in this review.

CONCLUSION

Differences in incidence, patterns, treatment, and survival exist among people of color for cutaneous malignancies. Further research and initiatives are needed to account for and mitigate these differences.

Slip versus Slop: A Head-to-Head Comparison of UV-Protective Clothing to Sunscreen

Simple Summary

Photoprotection reduces invasive melanoma incidence and mortality, but not all sun protection modalities are created equal. Dermatologists have long debated the pros and cons of photoprotective clothing and sunscreen, but few studies compare the effectiveness of these two modalities head-to-head. This study uses both in vitro and in vivo techniques to compare the ultraviolet radiation (UVR) protective capacity of four modern textiles and two commercially available, broad-spectrum sunscreens.

Abstract

Ultraviolet radiation (UVR) exposure is the most important modifiable risk factor for skin cancer development. Although sunscreen and sun-protective clothing are essential tools to minimize UVR exposure, few studies have compared the two modalities head-to-head. This study evaluates the UV-protective capacity of four modern, sun-protective textiles and two broad-spectrum, organic sunscreens (SPF 30 and 50). Sun Protection Factor (SPF), Ultraviolet Protection Factor (UPF), Critical Wavelength (CW), and % UVA- and % UVB-blocking were measured for each fabric. UPF, CW, % UVA- and % UVB-blocking were measured for each sunscreen at 2 mg/cm² (recommended areal density) and 1 mg/cm² (simulating real-world consumer application). The four textiles provided superior UVR protection when compared to the two sunscreens tested. All fabrics blocked erythemogenic UVR better than the sunscreens, as measured by SPF, UPF, and % UVB-blocking. Each fabric was superior to the sunscreens in blocking full-spectrum UVR, as measured by CW and % UVA-blocking. Our data demonstrate the limitations of sunscreen and UV-protective clothing labeling and suggest the combination of SPF or UPF with % UVA-blocking may provide more suitable measures for broad-spectrum protection. While sunscreen remains an important photoprotective modality (especially for sites where clothing is impractical), these data suggest that clothing should be considered the cornerstone of UV protection.

Estimating prevalence of human traits among populations from polygenic risk scores

The genetic basis of phenotypic variation across populations has not been well explained for most traits. Several factors may cause disparities, from variation in environments to divergent population genetic structure. We hypothesized that a population-level polygenic risk score (PRS) can explain phenotypic variation among geographic populations based solely on risk allele frequencies. We applied a population-specific PRS (psPRS) to 26 populations from the 1000 Genomes to four phenotypes: lactase persistence (LP), melanoma, multiple sclerosis (MS) and height. Our models assumed additive genetic architecture among the polymorphisms in the psPRSs, as is convention. Linear psPRSs explained a significant proportion of trait variance ranging from 0.32 for height in men to 0.88 for melanoma. The best models for LP and height were linear, while those for melanoma and MS were nonlinear. As not all variants in a PRS may confer similar, or even any, risk among diverse populations, we also filtered out SNPs to assess whether variance explained was improved using psPRSs with fewer SNPs. Variance explained usually improved with fewer SNPs in the psPRS and was as high as 0.99 for height in men using only 548 of the initial 4208 SNPs. That reducing SNPs improves psPRSs performance may indicate that missing heritability is partially due to complex architecture that does not mandate additivity, undiscovered variants or spurious associations in the databases. We demonstrated that PRS-based analyses can be used across diverse populations and phenotypes for population prediction and that these comparisons can identify the universal risk variants.

Developing indices to identify hotspots of skin cancer vulnerability among the Non-Hispanic White population in the United States

PURPOSE

Skin cancer is the most common, yet oftentimes preventable, cancer type in the United States. Exposure to ultraviolet radiation from sunlight is the most prominent environmental risk factor for skin cancer. Besides environmental exposure, demographic characteristics such as race, age, and socioeconomic status may make some groups more vulnerable. An exploratory spatial clustering method is described for identifying clusters of vulnerability to skin cancer incidence and mortality based on composite indices, which combine data from environmental and demographic risk factors.

METHODS

Based on county-level ultraviolet data and demographic risk factors, two vulnerability indices for skin cancer were generated using an additive percentile rank approach. With these indices, univariate local Moran's I spatial autocorrelation identified significant clusters, or hotspots, of neighboring counties with high overall vulnerability indices. Clusters were identified separately for skin cancer incidence and mortality.

RESULTS

Counties with high vulnerabilities were spatially distributed across the United States in a pattern that generally increased to the South and West. Clusters of counties with high skin cancer incidence vulnerability were mostly observed in Utah and Colorado, even with highly conservative levels of significance. Meanwhile, clusters for skin cancer mortality vulnerability were observed in southern Alabama and west Florida as well as across north Alabama, north Georgia and up through the Tennessee-North Carolina area.

CONCLUSIONS

Future skin cancer research and screening initiatives may use these innovative composite vulnerability indices and identified clusters to better target resources based on anticipated risk from underlying demographic and environmental factors.

Clinical Presentations of Melanoma in African Americans, Hispanics, and Asians

BACKGROUND

Skin cancer has traditionally been studied in Caucasian skin. Although it does occur with increased relative frequency in Caucasians, patients with skin of color suffer from elevated morbidity and mortality when diagnosed with skin cancer.

OBJECTIVE

To detail the unique demographic, clinical, and genetic features of melanoma in patients with skin of color, including Hispanic, African American, and Asian patients.

MATERIALS AND METHODS

A PubMed search was conducted spanning dates 1947 to June 2017. A total of 246 articles were screened, from which 69 were included in this review.

RESULTS

Relative to Caucasians, melanoma has unique demographic, clinical, and genetic features in African Americans, Hispanics, and Asians that include gender and subtype predominance.

CONCLUSION

Familiarization with these unique presentations of skin cancer in skin of color is imperative to accurate identification and treatment of cutaneous malignancies in these populations and ultimately to improved disease-related outcomes.

Accelerating cancer without mutations

Mice get melanoma faster when they have common, inherited variants in a few genes that control cell-wide changes but also respond to the environment.

Different genetic mechanisms mediate spontaneous versus UVR-induced malignant melanoma

Genetic variation conferring resistance and susceptibility to carcinogen-induced tumorigenesis is frequently studied in mice. We have now turned this idea to melanoma using the collaborative cross (CC), a resource of mouse strains designed to discover genes for complex diseases. We studied melanoma-prone transgenic progeny across seventy CC genetic backgrounds. We mapped a strong quantitative trait locus for rapid onset spontaneous melanoma onset to Prkdc, a gene involved in detection and repair of DNA damage. In contrast, rapid onset UVR-induced melanoma was linked to the ribosomal subunit gene Rrp15. Ribosome biogenesis was upregulated in skin shortly after UVR exposure. Mechanistically, variation in the 'usual suspects' by which UVR may exacerbate melanoma, defective DNA repair, melanocyte proliferation, or inflammatory cell infiltration, did not explain melanoma susceptibility or resistance across the CC. Instead, events occurring soon after exposure, such as dysregulation of ribosome function, which alters many aspects of cellular metabolism, may be important.