Current opportunities and challenges: genome-wide association studies on pigmentation and skin cancer

Identification of potential therapeutic targets for skin cutaneous melanoma on the basic of transcriptomics

BACKGROUND

Advanced skin cutaneous melanoma (SKCM) is responsible for the majority of skin cancer-related deaths. Apart from the rare BRAF V600F mutation, which can be targeted with specific drugs, there are currently no other novel effective therapeutic targets.

METHODS

We used SMR analysis with cis-expressed quantitative trait locus (cis-eQTL) as the exposure variable and SKCM as the outcome variable to identify potential therapeutic targets for SKCM. Colocalization assays and HEIDI tests are used to test whether SKCM risk and gene expression are driven by common SNPs. Replication analysis further validated the findings, and we also constructed protein-protein interaction networks to explore the relationship between the identified genes and known SKCM targets. Drug prediction and molecular docking further validated the medicinal value of drug targets. Transcriptome differential analysis further validated that there were differences between normal tissues and SKCM for the selected targets.

RESULTS

We identified 13 genes significantly associated with the risk of SKCM, including five protective genes and eight harmful genes. The HEIDI test and co-localization analysis further indicates a causal association between genes (SOX4, MAFF) and SKCM, categorized as Class 1 evidence targets. The remaining 11 genes, except for HELZ2 show a moderately causal association with SKCM, categorized as Class 2 evidence targets. Target druggability predictions from DGIdb suggest that SOX4, MAFF, ACSF3, CDK10, SPG7, and TCF25 are likely to be future drug targets.

CONCLUSION

The study provides genetic evidence for targeting available drug genes for the treatment of SKCM.

Genetics and nonmelanoma skin cancer in kidney transplant recipients

Kidney transplant recipients (KTRs) have a 65- to 250-fold greater risk than the general population of developing nonmelanoma skin cancer. Immunosuppressive drugs combined with traditional risk factors such as UV radiation exposure are the main modifiable risk factors for skin cancer development in transplant recipients. Genetic variation affecting immunosuppressive drug pharmacokinetics and pharmacodynamics has been associated with other transplant complications and may contribute to differences in skin cancer rates between KTRs. Genetic polymorphisms in genes encoding the prednisolone receptor, GST enzyme, MC1R, MTHFR enzyme and COX-2 enzyme have been shown to increase the risk of nonmelanoma skin cancer in KTRs. Genetic association studies may improve our understanding of how genetic variation affects skin cancer risk and potentially guide immunosuppressive treatment and skin cancer screening in at risk individuals.

Mitochondrial DNA copy number in peripheral blood and melanoma risk

Mitochondrial DNA (mtDNA) copy number in peripheral blood has been suggested as risk modifier in various types of cancer. However, its influence on melanoma risk is unclear. We evaluated the association between mtDNA copy number in peripheral blood and melanoma risk in 500 melanoma cases and 500 healthy controls from an ongoing melanoma study. The mtDNA copy number was measured using real-time polymerase chain reaction. Overall, mean mtDNA copy number was significantly higher in cases than in controls (1.15 vs 0.99, P<0.001). Increased mtDNA copy number was associated with a 1.45-fold increased risk of melanoma (95% confidence interval: 1.12-1.97). Significant joint effects between mtDNA copy number and variables related to pigmentation and history of sunlight exposure were observed. This study supports an association between increased mtDNA copy number and melanoma risk that is independent on the known melanoma risk factors (pigmentation and history of sunlight exposure).

Updated field synopsis and systematic meta-analyses of genetic association studies in cutaneous melanoma: the MelGene database

We updated a field synopsis of genetic associations of cutaneous melanoma (CM) by systematically retrieving and combining data from all studies in the field published as of August 31, 2013. Data were available from 197 studies, which included 83,343 CM cases and 187,809 controls and reported on 1,126 polymorphisms in 289 different genes. Random-effects meta-analyses of 81 eligible polymorphisms evaluated in >4 data sets confirmed 20 single-nucleotide polymorphisms across 10 loci (TYR, AFG3L1P, CDK10, MYH7B, SLC45A2, MTAP, ATM, CLPTM1L, FTO, and CASP8) that have previously been published with genome-wide significant evidence for association (P<5 × 10(-8)) with CM risk, with certain variants possibly functioning as proxies of already tagged genes. Four other loci (MITF, CCND1, MX2, and PLA2G6) were also significantly associated with 5 × 10(-8) Collapse

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MESH Headings

• Chromosome Mapping
• Databases, Genetic
• Gene Expression Regulation, Neoplastic
• Genetic Predisposition to Disease
• Genetic Variation
• Genome-Wide Association Study
• Germ-Line Mutation
• Humans
• Linkage Disequilibrium
• Melanoma/genetics
• Odds Ratio
• Polymorphism, Single Nucleotide
• Skin Neoplasms/genetics
• Melanoma, Cutaneous Malignant

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Affiliation(s)

Kyriaki Antonopoulou Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
Irene Stefanaki Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
Christina M Lill Neuropsychiatric Genetics Group, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany; Department of Neurology, Focus Program Translational Neuroscience, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
Foteini Chatzinasiou Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
Katerina P Kypreou Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
Fani Karagianni Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
Emmanouil Athanasiadis Center of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
George M Spyrou Center of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
John P A Ioannidis Department of Medicine, Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, California, USA
Lars Bertram Neuropsychiatric Genetics Group, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany; Department of Medicine, School of Public Health, Imperial College London, London, UK
Evangelos Evangelou Department of Hygiene and Epidemiology, Clinical and Molecular Epidemiology Unit, School of Medicine, University of Ioannina, Ioannina, Greece; Department of Epidemiology and Biostatistics, Imperial College London, St Mary's Campus, London, UK
Alexander J Stratigos Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece.

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Genetic variation in regulatory DNA elements: the case of OCA2 transcriptional regulation

Mutations within the OCA2 gene or the complete absence of the OCA2 protein leads to oculocutaneous albinism type 2. The OCA2 protein plays a central role in melanosome biogenesis, and it is a strong determinant of the eumelanin content in melanocytes. Transcript levels of the OCA2 gene are strongly correlated with pigmentation intensities. Recent studies demonstrated that the transcriptional level of OCA2 is to a large extent determined by the noncoding SNP rs12913832 located 21.5 kb upstream of the OCA2 gene promoter. In this review, we discuss current hypotheses and the available data on the mechanism of OCA2 transcriptional regulation and how this is influenced by genetic variation. Finally, we will explore how future epigenetic studies can be used to advance our insight into the functional biology that connects genetic variation to human pigmentation.

Improved eye- and skin-color prediction based on 8 SNPs

Aim

To improve the 7-plex system to predict eye and skin color by increasing precision and detailed phenotypic descriptions.

Methods

Analysis of an eighth single nucleotide polymorphism (SNP), rs12896399 (SLC24A4), showed a statistically significant association with human eye color (P = 0.007) but a rather poor strength of agreement (κ = 0.063). This SNP was added to the 7-plex system (rs12913832 at HERC2, rs1545397 at OCA2, rs16891982 at SLC45A2, rs1426654 at SLC24A5, rs885479 at MC1R, rs6119471 at ASIP, and rs12203592 at IRF4). Further, the instruction guidelines on the interpretation of genotypes were changed to create a new 8-plex system. This was based on the analysis of an 803-sample training set of various populations. The newly developed 8-plex system can predict the eye colors brown, green, and blue, and skin colors light, not dark, and not light. It is superior to the 7-plex system with its additional ability to predict blue eye and light skin color.

Results

The 8-plex system was tested on an additional 212 samples, the test set. Analysis showed that the number of positive descriptions for eye colors as being brown, green, or blue increased significantly (P = 6.98e-15, z-score: -7.786). The error rate for eye-color prediction was low, at approximately 5%, while the skin color prediction showed no error in the test set (1% in training set).

Conclusions

We can conclude that the new 8-plex system for the prediction of eye and skin color substantially enhances its former version.