Melanoma Susceptibility Gene Research Articles

A cryptic BAP1 splice mutation in a family with uveal and cutaneous melanoma, and paraganglioma

Inactivating germ line BRCA1-associated protein-1 (BAP1) mutations have recently been reported in families with uveal or cutaneous malignant melanoma (UMM, CMM), mesothelioma, and meningioma. Although apparently predisposing to a wide range of tumors, the exact tumor spectrum associated with germ line BAP1 mutations has yet to be established. Here, we report a novel germ line BAP1 splice mutation, c.1708C>G (p.Leu570fs*40), in a multiple-case Danish UMM family with a spectrum of other tumors. Whole-exome sequencing identified an apparent missense mutation of BAP1 in UMM, CMM, as well as paraganglioma, breast cancer, and suspected mesothelioma cases in the family. Bioinformatic analysis and splicing assays demonstrated that this mutation creates a strong cryptic splice donor, resulting in aberrant splicing and a truncating frameshift of the BAP1 transcript. Somatic loss of the wild-type allele was also confirmed in the UMM and paraganglioma tumors. Our findings further support BAP1 as a melanoma susceptibility gene and extend the potential predisposition spectrum to paraganglioma.

MC1R variants predisposing to concomitant primary cutaneous melanoma in a monozygotic twin pair

BackgroundConcomitant primary cutaneous melanoma in monozygotic twins has been reported in only two pairs but in neither of them genetic analysis was performed. Two high-penetrance susceptibility genes, CDKN2A and CDK4 and one low-penetrance gene, MC1R, are well-defined genetic risk factors for melanoma. MITF has been recently identified as a novel intermediate risk melanoma-predisposing gene.Case presentationWe describe the extraordinary occurrence of a primary cutaneous invasive melanoma in two 44-year-old identical, female twins, on the same body site within 30 days of each other and report for the first time the genetic analysis of melanoma susceptibility genes in both twins. Data on characteristics of the twins were collected through a standardized questionnaire and skin examination. Exons 1α, 1β, 2 and 3 of CDKN2A, exon 2 of CDK4, the entire open reading frame of MC1R and the recently described MITF c.952 G > A (p.Glu318Lys) variant were investigated by direct sequencing. Sequencing analysis of the high-penetrance susceptibility genes showed no changes in CDKN2A and in exon 2 of the CDK4 gene. Both patients were heterozygous for the same CDKN2A UTR c.*29C > G variant. Interestingly, the same two heterozygous variants of the MC1R were identified in both twins: the c.451C > T (p.Arg151Cys) and the c.456C > A (p.Tyr152*) variants. Neither patient showed the c.952 G > A (p.Glu318Lys) substitution in the MITF gene.ConclusionsIdentification of two high-risk MC1R variants in our identical twins in the absence of CDKN2A and CDK4 mutations highlights the contribution of low penetrance genes, such as MC1R, in melanoma susceptibility.

Perceptions of genetic research and testing among members of families with an increased risk of malignant melanoma

BackgroundSeveral melanoma susceptibility genes have been identified. As part of the international genetic research programme of the GenoMEL consortiums research on genetic mutations in melanoma families, the aim of this study was to examine family members’ views about their risk of melanoma, gene testing and genetic research. MethodsSelf-report data were gathered using online and paper-based surveys available in four languages among 312 individuals (62% from Europe, 18% from Australia, 13% from the United States of America (USA) and 7% from Israel). ResultsFifty three percent had been diagnosed with a melanoma, and 12% had a positive susceptibility gene test result. Respondents with many moles and freckles were more likely to perceive themselves at risk for developing melanoma (odds ratio [OR]Freckles=2.24 with 95% confidence interval [CI]=1.18–4.26; ORMany moles=6.92, 95%CI=2.37–20.23). Respondents who had received a non-informative (negative) genetic test result were much less likely to perceive themselves at increased risk (OR=0.17, 95% CI=0.04–0.73). Safe-guards were perceived as important to protect genetic information, but there was also support for the storage and exchange of such information. Overall, respondents were in favour of genetic testing, even if current knowledge about melanoma risk genes is still limited. Contrary to previous studies, participants reported that a non-informative (negative) genetic test result, although not necessarily indicative of lower risk of melanoma, would be likely to reduce their practise of preventive behaviours. ConclusionsParticipants were influenced by their phenotype and test results in risk estimations. They expressed positive views on genetic research and towards genetic testing, but reported that a non-informative (negative) test result might be associated with an (erroneous) perception of reduced risk and fewer preventive behaviours. These results highlight the urgency of improving the quality of genetic counselling and increasing the effectiveness of communication regarding genetic test results.

Germline melanoma susceptibility and prognostic genes: A review of the literature

In recent years, there have been increasing efforts to identify germline genetic variants that may alter melanoma susceptibility and prognosis. The findings of these studies have indicated the presence of rare, high-penetrance alleles with large effects, such as CDKN2A and CDK4, more common, moderately penetrant genes like MC1R, and very common, low-penetrance polymorphisms with small effects that are related to pigmentation, nevus count, immune responses, DNA repair, metabolism, and the vitamin D receptor. The study of these low-penetrance single nucleotide polymorphisms is relatively new; thus many of them are termed 'candidate melanoma susceptibility or prognostic genes.' This review summarizes the research on germline polymorphisms that have been implicated in melanoma susceptibility and prognosis in order to provide a framework for additional studies to meet the ultimate goal of predicting a patient's risk of, and prognosis in, cutaneous malignant melanoma.

From GWAS to genome sequencing: complementary approaches to identify melanoma predisposition genes

Family and twin studies indicate that melanoma susceptibility has a strong genetic component. Very rarely, melanoma runs in families in which there is an inherited mutation in a single ‘high penetrance’ gene, but in the general population melanoma susceptibility is thought to be governed by variation in a series of ‘low penetrance’ genes. We sought to identify new melanoma risk genes of both classes by conducting an Australian genome-wide association study (GWAS) of ~2200 melanoma cases and ~4300 matched controls (from the AMFS and Q-MEGA studies), in parallel with whole-genome sequencing of cases from densely affected melanoma families with follow up genotyping of interesting variants in the GWAS sample and other highly case-loaded melanoma families. Genotyping of the GWAS sample was carried out using Illumina Hap610K or OMNI 1M arrays. All 25 SNPs that reached genome-wide statistical significance (i.e. p<5 x 10-8) map to chromosomal regions/genes previously associated with melanoma (e.g. MC1R, ASIP, OCA2, MTAP/CDKN2A and SLC45A2). However, two other genomic regions had multiple adjacent SNPs with low p values. These were the focus of a replication study using melanoma GWAS data generated by groups from the MD Anderson Cancer Center and the International Melanoma Genetics Consortium (GenoMEL). Both independent GWAS data sets support the original Australian findings and thus indicate that the PARP1 gene and another broad region on 1q (which includes SETDB1, a recently identified melanoma oncogene) are novel low penetrance melanoma risk loci. The three known high penetrance melanoma susceptibility genes (CDKN2A, CDK4 and ARF) account for less than half of all ‘familial’ melanoma. We sought to identify other genes responsible for susceptibility in multi-case melanoma families using a next-generation sequencing approach. Families were chosen on the basis that they did not have a mutation in CDKN2A, CDK4 or ARF; and had at least 5 melanoma cases. Whole-genome or exome sequencing was carried out on X cases from Y families. No convincing evidence has yet been obtained to support the identification of a new familial melanoma gene, however, follow up genotyping of several novel SNPs in the GWAS sample showed that a non-synonymous variant in the MITF gene is associated with melanoma in the general population. This type of integrated approach should help accelerate the discovery of new loci that play a role in the aetiology of melanoma.

Multiple melanoma susceptibility factors function in an ultraviolet radiation response pathway in skin

Exposure to ultraviolet radiation (UVR) and the familial melanoma susceptibility gene p16 (CDKN2A) are among the major risk factors which have been identified to contribute to the development of melanoma, and also significantly contribute to squamous cell carcinoma. We have previously shown that UVR induces p16(CDKN2A) expression in melanoma and keratinocyte cell lines and human skin, but the regulatory mechanisms controlling this expression are unknown. To determine the mechanism by which UVR induces p16(CDKN2A) expression in melanocytes and keratinocytes in the epidermis. We have used an in vitro cell lines model of the UVR response in skin to assess the changes in p16(CDKN2A) expression and the signalling pathways regulating these changes, and validated these findings in whole human skin cultures. We show that UVR-induced ERK signalling, mediated by BRAF, regulates p16(CDKN2A) expression at the transcriptional, and possibly translational level. This study demonstrates the biological connection between the known melanoma genes p16 (CDKN2A) and BRAF in a normal physiological response to UVR in the skin, and highlights the importance of defects in this biological pathway to melanoma and squamous cell carcinoma development.

Pathway-Based Analysis of a Melanoma Genome-Wide Association Study: Analysis of Genes Related to Tumour-Immunosuppression

Systemic immunosuppression is a risk factor for melanoma, and sunburn-induced immunosuppression is thought to be causal. Genes in immunosuppression pathways are therefore candidate melanoma-susceptibility genes. If variants within these genes individually have a small effect on disease risk, the association may be undetected in genome-wide association (GWA) studies due to low power to reach a high significance level. Pathway-based approaches have been suggested as a method of incorporating a priori knowledge into the analysis of GWA studies. In this study, the association of 1113 single nucleotide polymorphisms (SNPs) in 43 genes (39 genomic regions) related to immunosuppression have been analysed using a gene-set approach in 1539 melanoma cases and 3917 controls from the GenoMEL consortium GWA study. The association between melanoma susceptibility and the whole set of tumour-immunosuppression genes, and also predefined functional subgroups of genes, was considered. The analysis was based on a measure formed by summing the evidence from the most significant SNP in each gene, and significance was evaluated empirically by case-control label permutation. An association was found between melanoma and the complete set of genes (pemp = 0.002), as well as the subgroups related to the generation of tolerogenic dendritic cells (pemp = 0.006) and secretion of suppressive factors (pemp = 0.0004), thus providing preliminary evidence of involvement of tumour-immunosuppression gene polymorphisms in melanoma susceptibility. The analysis was repeated on a second phase of the GenoMEL study, which showed no evidence of an association. As one of the first attempts to replicate a pathway-level association, our results suggest that low power and heterogeneity may present challenges.

Abstract A84: Reduced LINE-1 methylation in peripheral blood mononuclear cells is associated with risk of melanoma in families segregating CDKN2A germline mutations

Abstract Background: CDKN2A is a major susceptibility gene for familial melanoma, but its incomplete penetrance suggests that other factors may modify the effect of this gene in melanoma-prone families. Epigenetic changes involving reduced levels of global DNA methylation in blood have been associated with genomic instability and cancer risk. In addition, genetic background has the potential to influence epigenetic processes through cis- or trans-regulatory variation. Therefore, we hypothesize that the CDKN2A carrier mutation state may be an important factor influencing global DNA methylation in predisposed individuals and that aberrant methylation may be an indicator of modified risk in individuals from melanoma-prone families segregating CDKN2A germline mutations. Methods: We measured the overall level of genomic DNA methylation using bisulfite pyrosequencing at four CpG sites (CpG1, CpG2, CpG3 and CpG4) of the Long Interspersed Nucleotide Element-1 (LINE-1) sequences in peripheral blood mononuclear cells (PBMCs) from 42 CDKN2A mutation positive cases (20 males and 22 females) and 73 controls (29 CDKN2A carrier controls [9 males and 20 females] and 44 non-carrier controls [19 males and 25 females]) in 26 families with CDKN2A mutations. LINE-1 methylation was reported as the average (of all 4 CpGs) and as site-specific percentage methylation. Odds' ratios (OR) and P-values were obtained by comparing melanoma cases to controls using unconditional logistic regression with adjustment for family correlation (using the generalized estimating equations [GEE] approach), age, sex, number of moles and with melanoma status as the outcome variable. Percentage LINE-1 methylation was categorized using tertiles with the highest tertile as the reference. Results: Male gender was significantly associated with higher average LINE-1 methylation (P=&amp;lt;0.001) and methylation at all CpG sites (P=&amp;lt;0.03). In contrast, age, solar injury, dysplastic nevi (DN) and number of moles were not associated with average LINE-1 methylation. Although mean levels of LINE-1 methylation were similar in melanoma cases, carrier controls, and non-carrier controls, after adjusting for family correlation, age, sex and number of moles, low average LINE-1 methylation (tertile 1) was significantly associated with increased risk of melanoma (OR=3.87, 95% confidence interval [CI]: 1.11–13.5, P=0.033, compared to all controls; OR=1.83, 95% CI: 1.09–11.7, P=0.035, compared to carrier controls; and OR=3.43, 95% CI: 1.17–10.0, P= 0.024, compared to non-carrier controls). This association was observed for most CpG sites with the most significant association seen for site 3 and risk of melanoma compared to all controls (OR=5.18, 95% CI: 1.54–17.4, P=0.008). We observed no significant association between average or CpG site-specific LINE-1 methylation and CDKN2A mutation status among controls although the comparison was limited by small sample size. Conclusions: Melanoma cases from families segregating CDKN2A germline mutations have significantly lower LINE-1 global methylation in their PBMCs compared to controls. Changes in LINE-1 methylation in PBMCs from CDKN2A mutation positive cases may reflect a potential genetic background influence on global DNA methylation in these individuals. Further studies are needed to clarify these preliminary observations. Citation Information: Cancer Prev Res 2011;4(10 Suppl):A84.

Genome‐wide linkage analysis of Swedish families to identify putative susceptibility loci for cutaneous malignant melanoma

Cutaneous malignant melanoma is a clinically and genetically heterogeneous disorder which is caused by an interaction between hereditary and environmental factors. In Sweden, a small portion of the inherited susceptibility is explained by the presence of germline mutations in the tumor suppressor gene CDKN2A. But still, the genetic background of melanoma susceptibility is largely unknown. Here, we conducted a genome-wide linkage scan on melanoma-prone families using high-density single-nucleotide polymorphisms (SNPs) arrays to identify novel melanoma susceptibility genes. We investigated 35 families of Swedish origin without CDKN2A mutations. Nonparametric and parametric multipoint linkage analyses were performed. After removal of SNPs in strong linkage disequilibrium, the strongest evidence of linkage was detected on chromosome 17p11-12 (logarithm (base 10) of odds (LOD) scores of 2.76) using parametric linkage analysis assuming a dominant trait with full penetrance. Analyses were also performed on a subset of families with low age at diagnosis (mean age ≤ 47 years), to obtain a more homogenous subset. This subgroup analysis based on 22 families yielded suggestive evidence of linkage to the chromosomal regions 11p12-p11 and 18q22 (multipoint LOD scores of 2.10 and 2.02, respectively). Also, the 17p region that was detected in the complete family set showed suggestive linkage in this cohort (multipoint LOD scores of 2.01). Our data suggest that these chromosomal regions, 17p12-p11 in particular as it was present in both analyses, may harbor genes involved in the susceptibility of malignant melanoma in the Swedish population.

Genetic and functional evaluation of MITF as a candidate gene for cutaneous melanoma predisposition in pigs

Cutaneous melanoma arises from transformed melanocytes and is caused mainly by environmental effects such as ultraviolet radiation and to a lesser extent by predisposing genetic variants. Only a few susceptibility genes for cutaneous melanoma have been identified so far in human; therefore, animal models represent a valuable alternative for genetic studies of this disease. In a previous quantitative trait locus (QTL) study, several susceptibility regions were identified in a swine biomedical model, the MeLiM (Melanoblastoma-bearing Libechov minipig) pigs. This article details the fine-mapping of a QTL located on SSC13 (Sus scrofa chromosome 13) through an increase in marker density. New microsatellites were used to confirm the results of the first analysis, and MITF (microphthalmia-associated transcription factor) was selected as a candidate gene for melanoma development. A single-marker association analysis was performed with single-nucleotide polymorphisms (SNPs) spread over the locus, but it did not reveal a significant association with diverse melanoma-related traits. In parallel, MITF alternative transcripts were characterized and their expression was investigated in different porcine tissues. The obtained results showed a complex transcriptional regulation concordant with the one present in other mammals. Notably, the ratio between MITF+ and MITF- isoforms in melanoma samples followed the same pattern as in human tumors, which highlights the adequacy of the MeLiM pig as a model for human melanoma. In conclusion, although MITF does not seem to be the causal gene of the QTL initially observed, we do not exclude a prominent role of its transcription and function in the outbreak and evolution of the tumors observed in pigs.

Impact of population genetic substructure on association studies and risk assessment for melanoma.

8521 Background: Genetic substructure due to varying allele frequencies between populations can confound association studies. Ancestry informative genetic marker (AIMs) data combined with statistical adjustment can reveal spurious associations and identify population specific risk markers. In melanoma, AIMs may also be risk markers, e.g. pigment genes contribute to melanoma susceptibility and segregate with ancestry. We have thus developed a strategy to adjust for population genetic substructure (PGS) using AIMs, while identifying potentially novel genes associated with melanoma. Methods: 326 melanoma patients and 400 controls of European ancestry from the New York area were studied. Tag SNPs spanning 14 candidate genes and 75 AIMs were genotyped and odds ratios (OR), unadjusted and adjusted for PGS, computed. Results: A PGS model based on all AIMs separated cases and controls, suggesting that some AIMs were associated with melanoma. An algorithm was developed to select AIMs least capable of separating cases and controls to infer PGS and validated using simulations. The resulting model, which was reproduced using 49 additional AIMs, separated Northern (NE) and Southern Europeans (SE) and was used to adjust ORs. Three classes of SNPs were identified 1. Associated before and after PGS correction in both groups (10 SNPs localized to MATP, TYR and ERCC5). 2. Not associated in unadjusted analysis, but significantly associated with melanoma in NEs (6 SNPs localized to XPC, ERCC4, OCA2, ASIP and TYR). 3. Associated with melanoma before but not after adjustment. To determine if AIMs that separate cases and controls can identify novel melanoma genes, we genotyped 16 SNPs localized to 4 genes that house candidate AIMs. Four SNPs at 2 different loci were associated with melanoma (e.g. AIM1: OR=0.35, p=0.01; AIM2: OR=1.77, p=0.03). Conclusions: Our approach demonstrated that ancestry is a significant confounding factor in identifying melanoma susceptibility genes. Melanoma risk markers vary significantly between groups and a DNA based risk assessment model will require adjustment for ancestry. We have also identified potentially novel susceptibility melanoma genes for futher study.

Abstract 869: Characterization of malignant melanoma families with CDK4 germ-line mutation

Abstract Background: CDKN2A (p16) and CDK4 are high-risk susceptibility genes for cutaneous melanoma. CDKN2A is the major identified high-risk gene and CDKN2A-mutated families have been extensively characterized. Melanoma families with CDK4 mutation are very rare. Only 10 such families have been published and a systematic investigation of their phenotype is lacking. Aim of study: We evaluated all known CDK4-mutated families with regard to phenotypic features of their melanocytic disease. We also examined if common variants of the melanocortin-1 receptor (MC1R) gene had an effect on age of melanoma onset. Methods: CDK4-melanoma families, previously ascertained by different research groups, were selected for this study either by contacting the authors of published papers or by requests via the GenoMEL Melanoma Genetics Consortium. Phenotypic data related to melanoma and pigmentation were collected via a standardized form. For all family members with available DNA, exon 2 of CDK4 and the complete coding region of the MC1R gene were sequenced. Results: Thirteen CDK4 families (including three unpublished) were enrolled in the study. Altogether, 83 subjects with malignant melanoma, having a total of 125 melanomas, were verified in the pedigrees. The mean and median age of melanoma diagnosis was 38.5 years and 36.5 years, respectively. Of the 83 melanoma-positive subjects, 29 (34.9%) had multiple primary melanoma. Superficially spreading melanoma was the most common histological diagnosis (52.2%). DNA was available from 198 members of the pedigrees, and 81 tested positive for either the CDK4 R24H or R24C mutation; 117 subjects including 39 spouses tested negative. Subjects with the CDK4 mutation or with verified melanoma had a much higher prevalence of atypical nevi (79.5% and 77.2%, respectively) than CDK4-negative family members (26.0%; p&amp;lt;0.001 for both groups). The pedigrees included only one verified case of pancreatic cancer, occurring in a non-tested subject with melanoma. There did not appear to be evidence for a predisposition to other non-melanoma cancers. The analysis of MC1R gene variants is ongoing. Conclusion: CDK4-positive melanoma families are phenotypically similar to families with a CDKN2A mutation with regard to age of melanoma diagnosis, histological tumor type and the presence of atypical nevi/multiple melanomas. In a clinical setting, the CDK4 gene should therefore be examined if a melanoma family is negative for a CDKN2A mutation. Although based on only 13 CDK4 families, mutation carriers do not appear to have an increased predisposition to pancreatic cancer as noted in some pedigrees with CDKN2A mutations. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 869. doi:10.1158/1538-7445.AM2011-869

Contribution of CDKN2A/P16 INK4A, P14 ARF, CDK4 and BRCA1/2 germline mutations in individuals with suspected genetic predisposition to uveal melanoma

Uveal melanoma arises from melanocytes of the uveal tract (iris, ciliary body and choroid) and represents the most common intraocular malignancy in adults. Some rare clinical situations (young age at diagnosis, bilateral or multifocal forms, association with cutaneous malignant melanoma and/or familial aggregations of melanomas) are suggestive of genetic susceptibility. The aim of this study was to evaluate the contribution of CDKN2A/P16INK4A, P14ARF and CDK4 gene germline mutations in a series of patients with uveal melanoma recruited in a single institution with a clinical presentation indicative of genetic predisposition. Molecular analyses were proposed to 36 patients and were performed in 25 cases. The contribution of BRCA1/2 gene germline mutations in patients with uveal melanoma and a personal and/or family history of breast/ovarian cancers was also evaluated. Molecular analysis of BRCA1/2 genes was proposed to 35 patients and was performed in 25 patients. No deleterious germline mutation was identified in either group of patients. These results indicate that the CDKN2A/P16INK4A, P14ARF, CDK4 genes are not responsible for the vast majority of genetic susceptibility to uveal melanoma. They also suggest that one case of uveal melanoma in a family with a history of breast cancer is not sufficient to justify BRCA1/2 genetic testing when the classical criteria for molecular analysis are not present. International studies are ongoing in melanoma-prone families in an attempt to identify uveal melanoma susceptibility loci and genes.

Revised UK guidelines for the management of cutaneous melanoma 2010

These guidelines for the management of cutaneous melanoma present an evidence-based guidance for treatment, with identification of the strength of evidence available at the time of preparation of the guidelines, and a brief overview of epidemiology, diagnosis, investigation, and follow-up.

Genetic analysis of three important genes in pigmentation and melanoma susceptibility: CDKN2A, MC1R and HERC2/OCA2

The CDKN2A gene is regarded as the major familial malignant melanoma (MM) susceptibility gene. Human pigmentation is one of the main modulators of individual risk of developing MM. Therefore, the genes involved in the determination of skin colour and tanning response are potentially implicated in MM predisposition and may be useful predictors of MM risk in the general population. The human melanocortin-1 receptor gene (MC1R) plays a crucial role in pigmentation and also appears to be important in MM. The OCA2 gene has emerged as a new and significant determinant of human iris colour variation. We present a case-control study in Spanish population including 390 consecutive patients with melanoma and 254 control subjects. Sequence analysis of the entire coding region and genotyping of 5 tag-SNPs in the genomic region of MC1R was performed. We identified 27 variants, two reaching statistical significance [R160W (OR: 4.18, 95% CI: 1.24-14.04, P = 0.02) and D294H (OR: 3.10, 95% CI: 1.37-7.01, P = 0.01)] and we detected two novel non-synonymous changes: V92L and T308M. Odds ratio for carrying two functional variants was 4.25 (95% CI: 2.30-7.84, P = 3.63 x 10(-6)). Haplotypes of the entire MC1R region have been established, and we observed an enrichment of a rare European haplotype similar to African values carrying variants V92M and I155T. In addition, three potentially functional SNPs were selected in p16/CDKN2A and in the promoter region of OCA2/HERC2. Our data for CDKN2A gene did not reach statistically significant results for any of the two studied alleles. We found that the variant allele A > G of OCA2/HERC2 (rs12913832) was associated with pigmentation features: eye, hair and skin colour; P-values = 1.8 x 10(-29), 9.2 x 10(-16), 1.1 x 10(-3), respectively, validating previous results.

Melanocortin 1 receptorgenotype: an important determinant of the damage response of melanocytes to ultraviolet radiation

The melanocortin 1 receptor gene is a main determinant of human pigmentation, and a melanoma susceptibility gene, because its variants that are strongly associated with red hair color increase melanoma risk. To test experimentally the association between melanocortin 1 receptor genotype and melanoma susceptibility, we compared the responses of primary human melanocyte cultures naturally expressing different melanocortin 1 receptor variants to α-melanocortin and ultraviolet radiation. We found that expression of 2 red hair variants abolished the response to α-melanocortin and its photoprotective effects, evidenced by lack of functional coupling of the receptor, and absence of reduction in ultraviolet radiation-induced hydrogen peroxide generation or enhancement of repair of DNA photoproducts, respectively. These variants had different heterozygous effects on receptor function. Microarray data confirmed the observed differences in responses of melanocytes with functional vs. nonfunctional receptor to α-melanocortin and ultraviolet radiation, and identified DNA repair and antioxidant genes that are modulated by α-melanocortin. Our findings highlight the molecular mechanisms by which the melanocortin 1 receptor genotype controls genomic stability of and the mutagenic effect of ultraviolet radiation on human melanocytes.

Abstract ED3-2: Understanding melanoma using GWAS and systems biology

Abstract In this review I will discuss progress made in understanding the genetic determinants of susceptibility to melanoma and outcome from melanoma using genome wide association studies (GWAS) and approaches based more upon systems biology. In very recent years the first GWAS identifying hereditary susceptibility genes have been published as have the first larger scale gene expression studies. In the next few years, bioinformatics developments will allow integration of data from these and other system-wide approaches, in a multi-disciplinary fashion to better understand complex interactions between biological pathways and both the cellular environment and that of the organism. Family studies are usually the first approach to identifying high penetrance susceptibility genes for cancer in general and for melanoma these lead to the identification of germline mutations in CDKN2A and CDK4 as the most common genes underlying susceptibility in families with 4 or more cases of melanoma. The melanoma genetics consortium GenoMEL at www.genomel.org is directed towards understanding the clinical relevance of these mutations. More recently, GWAS studies confirmed the role of MC1R variants as the most common low risk susceptibility genes (1), although this was previously recognised as a result of a small candidate gene study in 1996 (2) perhaps showing the value of taking multiple approaches. Other pigment genes have been identified as low risk susceptibility genes using a combination of agnostic and candidate gene approaches (3) and the evolution of new techniques was demonstrated by Brown et al who developed DNA pooling in GWAS which identified a locus near to the agouti signalling protein gene as a melanoma susceptibility gene (4). These GWAS have therefore identified susceptibility loci in genes predicted from epidemiological studies, which identified sun-sensitive phenotypes as associated with melanoma risk. Epidemiological studies also identified large numbers of melanocytic nevi as associated with increased risk and GWAS studies designed to identify nevus genes were therefore carried out to identify both nevus and melanoma susceptibility genes (5). Thus the melanoma field has benefitted from GWAS technology in conjunction with epidemiology to identify pathways involved in susceptibility. It is perhaps disappointing that so far the agnostic approach has failed to identify new biological pathways of note but there are some interesting clues and the GWAS data existing already are being interrogated using newer informatics approaches. It is likely that new relevant biological pathways will be identified in the very near future. It is crucial to increase our understanding of the genetic determinants of outcome for melanoma patients not least to improve the response to therapies for stage IV melanoma. In recent years genomics has lead to major progress in understanding the biological pathways important to tumour progression, which has lead to the clinical trials with the most hopeful chemotherapeutic agent for melanoma, a specific inhibitor of mutant Braf. Biological complexity is evident however and it seems likely that we require a quantum leap in understanding to provide therapeutic options for all patients. Systems biological approaches will be of fundamental importance here aided by new technologies/platforms which allow us to work with small paraffin embedded melanoma tumours such as the Illumina DASL platform (6). Citation Information: Clin Cancer Res 2010;16(7 Suppl):ED3-2

Malignant Melanoma–a Genetic Overview

Malignant melanoma, a potentially lethal skin neoplasm, is characterized by a complex and heterogeneous etiology. Both incidences and deaths associated with melanoma are increasing in Caucasian populations. While exposure to ultraviolet radiation through sun-exposure is the major risk factor; the host factors including skin type and number of moles are critical in predisposition. The CDKN2A is a high penetrance melanoma susceptibility gene as carriers of the mutations are predisposed to the disease within familial settings. The gene is also somatically altered to varying degrees in sporadic melanoma. The CDK4 gene due to occurrence of activation mutations in a few families worldwide represents another melanoma susceptibility locus. The variants within the melanocortin receptor 1 (MC1R) gene, which encodes a melanocyte specific surface receptor with a key role in pigmentation, are associated with high risk phenotypes and increased risk of melanoma. Melanoma tumors are characterized by activation of the RAS-RAF-MEK-ERK pathway through either autocrine growth factor stimulation or oncogenic mutations in the B-RAF or N-RAS genes. Somatic mutations in the B-RAF gene are complemented by those in the N-RAS gene and represent the major genetic alterations. The mutations in the B-RAF gene in melanoma due to occurrence in melanocytic nevi represent early events that additionally require loss of cell cycle inhibitors like CDKN2A for melanoma progression and development. The sequence of events points to the cooperative collaboration between different genetic pathways in tumor development that can be and are being used as targets for developing specific therapeutic agents.

Role of key-regulator genes in melanoma susceptibility and pathogenesis among patients from South Italy

BackgroundSeveral genetic alterations have been demonstrated to contribute to the development and progression of melanoma. In this study, we further investigated the impact of key-regulator genes in susceptibility and pathogenesis of such a disease.MethodsA large series (N = 846) of sporadic and familial cases originating from South Italy was screened for germline mutations in p16CDKN2A, BRCA2, and MC1R genes by DHPLC analysis and automated DNA sequencing. Paired primary melanomas and lymph node metastases from same patients (N = 35) as well as melanoma cell lines (N = 18) were analyzed for somatic mutations in NRAS, BRAF, and p16CDKN2A genes.ResultsFor melanoma susceptibility, investigations at germline level indicated that p16CDKN2A was exclusively mutated in 16/545 (2.9%) non-Sardinian patients, whereas BRCA2 germline mutations were observed in 4/91 (4.4%) patients from North Sardinia only. Two MC1R germline variants, Arg151Cys and Asp294His, were significantly associated with melanoma in Sardinia. Regarding genetic events involved in melanoma pathogenesis at somatic level, mutually-exclusive mutations of NRAS and BRAF genes were observed at quite same rate (about two thirds) in cultured and in vivo melanomas (either primary or metastatic lesions). Conversely, p16CDKN2A gene alterations were observed at increased rates moving from primary to metastatic melanomas and melanoma cell lines. Activation of the ERK gene product was demonstrated to be consistently induced by a combination of molecular alterations (NRAS/BRAF mutations and p16CDKN2A silencing).ConclusionOur findings further clarified that: a) mutation prevalence in melanoma susceptibility genes may vary within each specific geographical area; b) multiple molecular events are accumulating during melanomagenesis.

DNA repair gene polymorphisms and risk of cutaneous melanoma: a systematic review and meta-analysis

Polymorphisms of DNA repair-related genes might modulate cancer predisposition. We performed a systematic review and meta-analysis of the available evidence regarding the relationship between these polymorphisms and the risk of developing cutaneous melanoma. Relevant studies were searched using PubMed, Medline, Embase, Cancerlit, Cochrane and ISI Web of Knowledge databases. Data were gathered according to the Meta-analysis Of Observational Studies in Epidemiology (MOOSE) guidelines. The model-free approach was adopted to perform the meta-analysis of the retrieved data. We identified 20 original reports that describe the relationship between melanoma risk and the single-nucleotide polymorphisms (SNPs) of 16 genes (cases = 4195). For seven SNPs considered in at least two studies, the findings were heterogeneous. Data were suitable for meta-analysis only in the case of the XPD/ERCC2 SNP rs13181 (cases = 2308, controls = 3698) and demonstrated that the variant C allele is associated with increased melanoma risk (odds ratio = 1.12, 95% confidence interval = 1.03-1.21, P = 0.01; population attributable risk = 9.6%). This is the first meta-analysis suggesting that XPD/ERCC2 might represent a low-penetrance melanoma susceptibility gene. Much work is still to be done before definitive conclusions can be drawn on the role of DNA repair alterations in melanomagenesis since for the other genes involved in this highly complex process, the available information is scarce or null.