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Investigating DNA Methylation As a Potential Mediator Between Pigmentation Genes, Pigmentary Traits and Skin Cancer

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Investigating DNA Methylation As a Potential Mediator Between Pigmentation Genes, Pigmentary Traits and Skin Cancer Genetics of DNA Methylation Consortium (2020). Investigating DNA methylation as a potential mediator between pigmentation genes, pigmentary traits and skin cancer. Pigment Cell & Melanoma Research. https://doi.org/10.1111/pcmr.12948 Publisher's PDF, also known as Version of record License (if available): CC BY Link to published version (if available): 10.1111/pcmr.12948 Link to publication record in Explore Bristol Research PDF-document This is the final published version of the article (version of record). It first appeared online via Wliey at https://doi.org/10.1111/pcmr.12948 . Please refer to any applicable terms of use of the publisher. University of Bristol - Explore Bristol Research General rights This document is made available in accordance with publisher policies. Please cite only the published version using the reference above. Full terms of use are available: http://www.bristol.ac.uk/red/research-policy/pure/user-guides/ebr-terms/ Received: 28 May 2020 | Revised: 16 October 2020 | Accepted: 17 November 2020 DOI: 10.1111/pcmr.12948 ORIGINAL ARTICLE Investigating DNA methylation as a potential mediator between pigmentation genes, pigmentary traits and skin cancer Carolina Bonilla1,2 | Bernardo Bertoni3 | Josine L. Min2,4 | Gibran Hemani2,4 | Genetics of DNA Methylation Consortium | Hannah R. Elliott2,4 1Departamento de Medicina Preventiva, Faculdade de Medicina, Universidade de São Abstract Paulo, São Paulo, Brazil Pigmentation characteristics are well-known risk factors for skin cancer. 2 Population Health Sciences, Bristol Medical Polymorphisms in pigmentation genes have been associated with these traits and School, University of Bristol, Bristol, UK 3Departamento de Genética, Facultad de with the risk of malignancy. However, the functional relationship between genetic Medicina, Universidad de la República, variation and disease is still unclear. This study aims to assess whether pigmenta- Montevideo, Uruguay tion SNPs are associated with pigmentary traits and skin cancer via DNA methyla- 4MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK tion (DNAm). Using a meta-GWAS of whole-blood DNAm from 36 European cohorts (N = 27,750; the Genetics of DNA Methylation Consortium, GoDMC), we found that Correspondence Carolina Bonilla, Departamento de Medicina 19 out of 27 SNPs in 10 pigmentation genes were associated with 391 DNAm sites Preventiva, Faculdade de Medicina, across 30 genomic regions. We examined the effect of 25 selected DNAm sites on Universidade de São Paulo, Av. Dr. Arnaldo 455, CEP 01246-903 São Paulo, Brazil. pigmentation traits, sun exposure phenotypes and skin cancer and on gene expres- Email: [email protected] sion in whole blood. We uncovered an association of DNAm site cg07402062 with Funding information red hair in the Avon Longitudinal Study of Parents and Children (ALSPAC). We also 23andme; Wellcome Trust, Grant/Award found that the expression of ASIP and CDK10 was associated with hair colour, mela- Number: 088806, 208806/Z/17/Z and 217065/Z/19/Z; Universidade de São Paulo, noma and basal cell carcinoma. Our results indicate that DNAm and expression of Grant/Award Number: 88887.160006/2017- pigmentation genes may play a role as potential mediators of the relationship be- 00; Biotechnology and Biological Sciences Research Council, Grant/Award Number: tween genetic variants, pigmentation phenotypes and skin cancer and thus deserve BB/1025263/1 and BBI025751/1; further scrutiny. Royal Society, Grant/Award Number: 208806/Z/17/Z; Medical Research Council, Grant/Award Number: MC-UU_12013/2, KEYWORDS MC_UU_00011/5, MC_UU_12013/1 and ALSPAC, ASIP, DNA methylation, GoDMC, MC1R, pigmentation, skin cancer MC_UU_12013/8; University of Bristol; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Grant/Award Number: 88887.160006/2017-00 1 | INTRODUCTION skin cancers although it has a low incidence, while non-melanoma skin cancer (NMSC) shows high incidence yet considerably lower The incidence of skin cancer, comprising malignant melanoma, mortality rates compared to melanoma (Apalla et al., 2017). To date, basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), recognized risk factors for melanoma and NMSC include fair skin, has increased rapidly in the past decades (Cahoon et al., 2015; Hu light-coloured eyes, red hair, freckles and melanocytic naevi as well et al., 2009; Rees et al., 2014). Melanoma is the most aggressive of as genetic variants, some of which underlie these skin pigmentation This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd Pigment Cell Melanoma Res. 2020;00:1–13. wileyonlinelibrary.com/journal/pcmr | 1 2 | BONILLA ET al. and sun sensitivity phenotypes (Gordon, 2013). Even though there are missense and nonsense polymorphisms in pigmentation genes Significance strongly associated with skin cancer, particularly in the gene MC1R Several genetic variants in pigmentation-related genes (Nasti & Timares, 2015), it is not fully understood how non-coding have been associated with skin cancer, particularly in pop- variation in these genes relates to malignancy. ulations of European ancestry. DNA methylation was in- DNA methylation (DNAm) is an epigenetic modification with vestigated as a potential link between pigmentation SNPs, a prospective role in cancer aetiology. The association of global pigmentation phenotypes and skin cancer. DNA methyla- whole-blood DNA hypomethylation with cancer is well known and tion sites near MC1R and ASIP were strongly associated has also been described for melanoma (Cappetta et al., 2015; Shen with pigmentation SNPs, gene expression, hair colour, mel- et al., 2017). In addition, recent studies have shown the presence anoma and basal cell carcinoma in an analysis that included of hypomethylation in skin biopsy samples that were exposed to data from the Genetics of DNA Methylation consortium, sunlight or artificial ultraviolet radiation (Grönniger et al., 2010; the Avon Longitudinal Study of Parents and Children and Holzscheck et al., 2020; Vandiver et al., 2015). Inter-individual the UK Biobank. Further evaluation of the role played by DNAm variation at specific sites, measured in peripheral blood, has DNA methylation in these relationships is warranted. been uncovered as a predictor of a number of complex trait risk fac- tors as well as all-cause mortality (McCartney et al., 2018). DNAm has the potential to be used as a molecular biomarker to diagnose disease or to assess prognosis in those affected by disease and is a robustly associated with pigmentation traits and skin cancer, in 36 promising candidate leading towards the realization of personalized cohorts of European descent. We then analysed the association of medicine (Nikolouzakis et al., 2020). pigmentation SNP-associated DNAm sites with sun exposure and This study investigated whether DNAm plays a role in the rela- pigmentation phenotypes in participants of the Avon Longitudinal tionship between genetic variants, pigmentation-related skin cancer Study of Parents and Children (ALSPAC). Finally, using summary risk factors and skin cancer. First, we examined the effect of genetic data-based Mendelian randomization (SMR), we explored whether variation on DNAm levels in peripheral blood across 10 regions SNP-related DNAm was likely to causally underlie the expression • blood DNAm vs 27 pigmentation SNPs • regression - GoDMC • pigmentation/sun exposure traits vs blood DNAm • regression – ALSPAC • CIT - ALSPAC • blood gene expression vs blood DNAm • SMR – eQTL browser/CAGE/GTEx & McRae et al. (2018) FIGURE 1 Stages of analysis implemented and datasets used in this study. From the 391 unique DNA methylation (DNAm) sites associated • pigmentation/sun exposure/skin cancer vs skin gene expression with pigmentation SNPs, 25 were • SMR – UKB & GTEx selected for further analysis as depicted. GoDMC, Genetics of DNA methylation consortium; ALSPAC, Avon Longitudinal Study of Parents and Children; CIT, causal inference test; SMR, summary data-based Mendelian randomization; eQTL browser, • pigmentation/sun exposure/skin cancer vs blood DNAm blood eQTL browser; CAGE, Cap Analysis • SMR – UKB & McRae et al. (2018) of Gene Expression; GTEx, Genotype- Tissue Expression consortium; UKB, UK Biobank BONILLA ET al. | 3 of genes associated with pigmentation phenotypes and skin cancer. 2.2 | DNA methylation and pigmentation/sun The purpose of this work was to carry out an integrative analysis to exposure phenotypes in the Avon Longitudinal evaluate the joint contribution of genetic and epigenetic risk factors Study of Parents and Children (ALSPAC) to skin cancer susceptibility. As this is the first instance of such an analysis involving genes associated with pigmentation traits and skin Cohort description and information regarding the collection of cancer, the clinical relevance of our findings will depend on subse- DNAm data in ALSPAC can be found in the Methods S1. quent replication and further investigation of the genes and path- ways that we described here. 2.2.1 | Regression analysis 2 | MATERIALS AND METHODS The pigmentation/sun exposure phenotypes evaluated included the following: skin reflectance, freckles, moles, sunburning, tanning abil- The different stages of this study are depicted in Figure 1. ity, hair colour and eye colour. We examined DNAm at the nearest time point with
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