A Web-based database of genetic association studies in cutaneous melanoma enhanced with network-driven data exploration tools

Polygenic Risk Score Analysis of 37 SNPs Associated with Melanoma Risk in Colombian Population

Melanoma incidence is increasing, with distinct genetic and clinical patterns observed in the Latin American population. This study aimed to evaluate melanoma risk in a Colombian cohort through polygenic risk analysis using 37 variants across nine genes previously associated with melanoma. We performed polygenic risk score (PRS) analysis on 85 melanoma patients and 165 controls. Genotyping was performed for 37 melanoma-associated SNPs, and on the basis of previous GWAS reports, individual PRSs were calculated for each participant. The participants were then stratified into quartiles to examine risk gradients. In addition, phenotypic features such as eye and hair color were evaluated, and genetic models and haplotype analyses were performed, adjusting for sex and family history of cancer. PRS quartile stratification revealed a clear risk gradient. Notably, 31.8% of the melanoma cases were clustered in the highest-risk quartile (Q4), with a maximum PRS of 1.04. Variants in TYR, TYRP1, CDKN2A, and HERC2 significantly contributed to risk, and light brown eye and hair colors were strongly associated with increased melanoma risk. Moreover, a protective haplotype in the OCA2-HERC2 region was identified among males. The integration of the PRS with clinical and phenotypic factors has potential for improving melanoma risk stratification in the Colombian population, warranting further investigation in larger, diverse cohorts.

Common genetic variants and pathways in diabetes and associated complications and vulnerability of populations with different ethnic origins

Diabetes mellitus is a complex and heterogeneous metabolic disorder which is often pre- or post-existent with complications such as cardiovascular disease, hypertension, inflammation, chronic kidney disease, diabetic retino- and nephropathies. However, the frequencies of these co-morbidities vary among individuals and across populations. It is, therefore, not unlikely that certain genetic variants might commonly contribute to these conditions. Here, we identified four single nucleotide polymorphisms (rs5186, rs1800795, rs1799983 and rs1800629 in AGTR1, IL6, NOS3 and TNFA genes, respectively) to be commonly associated with each of these conditions. We explored their possible interplay in diabetes and associated complications. The variant allele and haplotype frequencies at these polymorphic loci vary among different super-populations (African, European, admixed Americans, South and East Asians). The variant alleles are particularly highly prevalent in different European and admixed American populations. Differential distribution of these variants in different ethnic groups suggests that certain drugs might be more effective in selective populations rather than all. Therefore, population specific genetic architectures should be considered before considering a drug for these conditions.

Dissecting the Mutational Landscape of Cutaneous Melanoma: An Omic Analysis Based on Patients from Greece

Melanoma is a lethal type of skin cancer, unless it is diagnosed early. Formalin-fixed, paraffin-embedded (FFPE) tissue is a valuable source for molecular assays after diagnostic examination, but isolated nucleic acids often suffer from degradation. Here, for the first time, we examine primary melanomas from Greek patients, using whole exome sequencing, so as to derive their mutational profile. Application of a bioinformatic framework revealed a total of 10,030 somatic mutations. Regarding the genes containing putative protein-altering mutations, 73 were common in at least three patients. Sixty-five of these 73 top common genes have been previously identified in melanoma cases. Biological processes related to melanoma were affected by varied genes in each patient, suggesting differences in the components of a pathway possibly contributing to pathogenesis. We performed a multi-level analysis highlighting a short list of candidate genes with a probable causative role in melanoma.

UNR/CSDE1 Drives a Post-transcriptional Program to Promote Melanoma Invasion and Metastasis

RNA binding proteins (RBPs) modulate cancer progression through poorly understood mechanisms. Here we show that the RBP UNR/CSDE1 is overexpressed in melanoma tumors and promotes invasion and metastasis. iCLIP sequencing, RNA sequencing, and ribosome profiling combined with in silico studies unveiled sets of pro-metastatic factors coordinately regulated by UNR as part of RNA regulons. In addition to RNA steady-state levels, UNR was found to control many of its targets at the level of translation elongation/termination. Key pro-oncogenic targets of UNR included VIM and RAC1, as validated by loss- and gain-of-function studies. Our results identify UNR as an oncogenic modulator of melanoma progression, unravel the underlying molecular mechanisms, and identify potential targets for this therapeutically challenging malignancy.

Prediction of Melanoma Risk in a Southern European Population Based on a Weighted Genetic Risk Score

Many single nucleotide polymorphisms (SNPs) have been described as putative risk factors for melanoma. The aim of our study was to validate the most prominent genetic risk loci in an independent Greek melanoma case-control dataset and to assess their cumulative effect solely or combined with established phenotypic risk factors on individualized risk prediction. We genotyped 59 SNPs in 800 patients and 800 controls and tested their association with melanoma using logistic regression analyses. We constructed a weighted genetic risk score (GRSGWS) based on SNPs that showed genome-wide significant (GWS) association with melanoma in previous studies and assessed their impact on risk prediction. Fifteen independent SNPs from 12 loci were significantly associated with melanoma (P < 0.05). Risk score analysis yielded an odds ratio of 1.36 per standard deviation increase of the GRSGWS (P = 1.1 × 10(-7)). Individuals in the highest 20% of the GRSGWS had a 1.88-fold increase in melanoma risk compared with those in the middle quintile. By adding the GRSGWS to a phenotypic risk model, the C-statistic increased from 0.764 to 0.775 (P = 0.007). In summary, the GRSGWS is associated with melanoma risk and achieves a modest improvement in risk prediction when added to a phenotypic risk model.

Genetic epidemiology of malignant melanoma susceptibility

Germline CDKN2A mutations were the first to be associated with familial melanoma. MC1R polymorphisms are associated, in conformity with epidemiological observations, with fair skin phenotype and a moderately increased risk for melanoma. The wider implementation of genome-wide association studies along with improved whole exome sequencing techniques made possible the identification of novel high-penetrant mutations (TERT, MITF, POT1, BAP1) beyond the established pathways of pigmentation and nevus count suggesting an additional role for pathways involved in cell cycle control and DNA repair. A multitude of common polymorphisms in the general population have been associated through candidate gene studies with a low risk for melanoma, supporting the hypothesis of a complex disease.

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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