Cutaneous Melanoma Susceptibility Research Articles

861P Association of genetic variants in JAK/STAT signaling pathway with cutaneous melanoma susceptibility

Janus kinase signal transducer and activator of transcription (JAK/STAT) signaling pathway is involved in cell proliferation, angiogenesis, apoptosis inhibition, metastasis, and immune suppression. Due to these multiple functions, this pathway regulates cutaneous melanoma (CM) development and progression. The JAK1, JAK2 and STAT3 proteins are encoded by polymorphic genes. This study aimed to verify whether single-nucleotide variants (SNVs) in JAK1 (c.1648+1272G>A, c.991-27C>T), JAK2 (c.-1132G>T, c.-139G>A) and STAT3 (c.*1671T>C, c.-1937C>G) altered risk, clinicopathological aspects, survival of CM patients, as well as protein activity. CM patients (N = 248) and controls (N = 274) were included in this study. Genotyping was performed by real-time polymerase chain reaction (PCR) and JAK1, JAK2 and STAT3 expression was assessed by quantitative PCR (qPCR). STAT3 c.-1937C>G SNV was investigated by luciferase, qPCR, western blot, apoptosis, and cell cycle assays in SKMEL-28 cells with CC or GG genotype. In addition, fourteen melanoma cell lines with different genotypes were used to analyze STAT3 expression with non-intervention. Individuals with STAT3 c.*1671TT and c.-1937CC genotypes, and TC haplotype of both SNVs were under 2.0-fold increased risk of CM. Specific JAK1, JAK2 and STAT3 combined genotypes were associated with up to 4.0-fold increased risk of CM. Higher luciferase activity (4,013.34 vs. 2,463.32 arbitrary unit (AU); p = 0.009), STAT3 expression by qPCR (649.20 vs. 0.04 AU; p = 0.003) and western blot (1.69 vs. 1.16 AU; p = 0.01), and percentage of cells in S phase of cell cycle (57.54 vs. 30.73 %; p = 0.04) were more frequent in SKMEL-28 with STAT3 c.-1937CC than with GG genotype. CM cell lines with CC genotype presented higher STAT3 protein levels than those with GG genotype (1.93 versus 1.27 AU, p = 0.0027). Our data present for the first-time preliminary evidence that JAK1, JAK2 and STAT3 SNVs alter risk and clinical aspects of CM patients. If validated in a further epidemiological study, our data can be used to select individuals at high-risk of CM, who should receive special attention in tumor prevention and early detection.

Integrated Analysis of Coexpression and Exome Sequencing to Prioritize Susceptibility Genes for Familial Cutaneous Melanoma

The application of whole-exome sequencing has led to the identification of high- and moderate-risk variants that contribute to cutaneous melanoma susceptibility. However, confirming disease-causing variants remains challenging. We applied a gene coexpression network analysis to prioritize the candidate genes identified from whole-exome sequencing of 34 melanoma-prone families, with at least three affected members sequenced per family (N= 119 cases). A coexpression network was constructed from genotype-tissue expression project, skin melanoma from the cancer genome atlas, and primary melanocyte cultures. We performed module-specific enrichment and focused on modules associated with pigmentation processes because they are the best-studied and most well-known risk factors for melanoma susceptibility. We found that pigmentation-associated modules across the four expression datasets examined were enriched for well-known melanoma susceptibility genes plus genes associated with pigmentation. We also used network properties to prioritize genes within pigmentation modules as candidate susceptibility genes. Integrating information from coexpression network analysis and variant prioritization, we identified 36 genes (such as DCT, TPCN2, TRPM1, ATP10A, and EPHA5) as potential melanoma risk genes in the families. Our approach also allowed us to link families with private gene mutations on the basis of gene coexpression patterns and thereby may provide an innovative perspective in gene identification in high-risk families.

Family-based whole-exome sequencing identifies rare variants potentially related to cutaneous melanoma predisposition in Brazilian melanoma-prone families.

Genetic predisposition accounts for nearly 10% of all melanoma cases and has been associated with a dozen moderate- to high-penetrance genes, including CDKN2A, CDK4, POT1 and BAP1. However, in most melanoma-prone families, the genetic etiology of cancer predisposition remains undetermined. The goal of this study was to identify rare genomic variants associated with cutaneous melanoma susceptibility in melanoma-prone families. Whole-exome sequencing was performed in 2 affected individuals of 5 melanoma-prone families negative for mutations in CDKN2A and CDK4, the major cutaneous melanoma risk genes. A total of 288 rare coding variants shared by the affected relatives of each family were identified, including 7 loss-of-function variants. By performing in silico analyses of gene function, biological pathways, and variant pathogenicity prediction, we underscored the putative role of several genes for melanoma risk, including previously described genes such as MYO7A and WRN, as well as new putative candidates, such as SERPINB4, HRNR, and NOP10. In conclusion, our data revealed rare germline variants in melanoma-prone families contributing with a novel set of potential candidate genes to be further investigated in future studies.

Gender-specific associations between polymorphisms of the circadian gene RORA and cutaneous melanoma susceptibility

BackgroundMelanoma is the deadliest of skin cancers and has an increasing annual incidence worldwide. It is a multi-factorial disease most likely arising from both genetic predisposition and environmental exposure to ultraviolet light. Genetic variability of the components of the biological circadian clock is recognized to be a risk factor for different type of cancers. Moreover, two variants of a clock gene, RORA, have been associated with melanoma patient’s prognosis. Our aim is to test the hypothesis that specific single nucleotide polymorphisms (SNPs) of the circadian clock genes may significantly influence the predisposition to develop cutaneous melanoma or the outcome of melanoma patients.MethodsWe genotyped 1239 subjects, 629 cases of melanoma and 610 healthy controls in 14 known SNPs of seven selected clock genes: AANAT, CLOCK, NPAS2, PER1, PER2, RORA, and TIMELESS. Genotyping was conducted by q-PCR. Multivariate logistic regression was employed for susceptibility of melanoma assessment, modeled additively. Subgroup analysis was performed by gender. For the female subgroup, a further discrimination was performed by age. For prognosis of melanoma assessment, multivariate Cox proportional hazard regression was employed. The Benjamini–Hochberg method was utilized as adjustment for multiple comparisons.ResultsWe identified two RORA SNPs statistically significant with respect to the association with melanoma susceptibility. Considering the putative role of RORA as a nuclear steroid hormone receptor, we conducted a subgroup analysis by gender. Interestingly, the RORA rs339972 C allele was associated with a decreased predisposition to develop melanoma only in the female subgroup (OR 0.67; 95% CI 0.51–0.88; P = 0.003) while RORA rs10519097 T allele was associated with a decreased predisposition to develop melanoma only in the male subgroup (OR 0.62; 95% CI 0.44–0.87; P = 0.005). Moreover, the RORA rs339972 C allele had a decreased susceptibility to develop melanoma only in females aged over 50 years old (OR 0.67; 95% CI 0.54–0.83; P = 0.0002). None of the studied SNPs were significantly associated with the prognosis.ConclusionsOverall, we cannot ascertain that circadian pathway genetic variation is involved in melanoma susceptibility or prognosis. Nevertheless, we identified an interesting relationship between melanoma susceptibility and RORA polymorphisms acting in sex-specific manner and which is worth further future investigation.

A Single Center Retrospective Review of Patients from Central Italy Tested for Melanoma Predisposition Genes.

Cutaneous malignant melanoma (CMM) is one of the most common skin cancers worldwide. CMM pathogenesis involves genetic and environmental factors. Recent studies have led to the identification of new genes involved in CMM susceptibility: beyond CDKN2A and CDK4, BAP1, POT1, and MITF were recently identified as potential high-risk melanoma susceptibility genes. This study is aimed to evaluate the genetic predisposition to CMM in patients from central Italy. From 1998 to 2017, genetic testing was performed in 888 cases with multiple primary melanoma and/or familial melanoma. Genetic analyses included the sequencing CDKN2A, CDK4, BAP1, POT1, and MITF in 202 cases, and of only CDKN2A and CDK4 codon 24 in 686 patients. By the evaluation of the personal and familial history, patients were divided in two clinical categories: “low significance” and “high significance” cases. 128 patients (72% belonging to the “high significance” category, 28% belonging to the “low significance” category) were found to carry a DNA change defined as pathogenic, likely pathogenic, variant of unknown significance (VUS)-favoring pathogenic or VUS. It is important to verify the genetic predisposition in CMM patients for an early diagnosis of further melanomas and/or other tumors associated with the characterized genotype.

Using whole-exome sequencing and protein interaction networks to prioritize candidate genes for germline cutaneous melanoma susceptibility

Although next-generation sequencing has demonstrated great potential for novel gene discovery, confirming disease-causing genes after initial discovery remains challenging. Here, we applied a network analysis approach to prioritize candidate genes identified from whole-exome sequencing analysis of 98 cutaneous melanoma patients from 27 families. Using a network propagation method, we ranked candidate genes by their similarity to known disease genes in protein–protein interaction networks and identified gene clusters with functional connectivity. Using this approach, we identified several new candidate susceptibility genes that warrant future investigations such as NGLY1, IL1RN, FABP2, PRKDC, and PROSER2. The propagated network analysis also allowed us to link families that did not have common underlying genes but that carried variants in genes that interact on protein–protein interaction networks. In conclusion, our study provided an analysis perspective for gene prioritization in the context of genetic heterogeneity across families and prioritized top potential candidate susceptibility genes in our dataset.

Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility

Most genetic susceptibility to cutaneous melanoma remains to be discovered. Meta-analysis genome-wide association study (GWAS) of 36,760 melanoma cases (67% newly-genotyped) and 375,188 controls identified 54 significant loci with 68 independent SNPs. Analysis of risk estimates across geographical regions and host factors suggests the acral melanoma subtype is uniquely unrelated to pigmentation. Combining this meta-analysis with nevus count and hair color GWAS, and transcriptome association approaches, uncovered 31 potential secondary loci, for a total of 85 cutaneous melanoma susceptibility loci. These findings provide substantial insights into cutaneous melanoma genetic architecture, reinforcing the importance of nevogenesis, pigmentation, and telomere maintenance together with identifying potential new pathways for cutaneous melanoma pathogenesis.

Insights into Genetic Susceptibility to Melanoma by Gene Panel Testing: Potential Pathogenic Variants in ACD, ATM, BAP1, and POT1.

The contribution of recently established or candidate susceptibility genes to melanoma missing heritability has yet to be determined. Multigene panel testing could increase diagnostic yield and better define the role of candidate genes. We characterized 273 CDKN2A/ARF and CDK4-negative probands through a custom-designed targeted gene panel that included CDKN2A/ARF, CDK4, ACD, BAP1, MITF, POT1, TERF2IP, ATM, and PALB2. Co-segregation, loss of heterozygosity (LOH)/protein expression analysis, and splicing characterization were performed to improve variant classification. We identified 16 (5.9%) pathogenic and likely pathogenic variants in established high/medium penetrance cutaneous melanoma susceptibility genes (BAP1, POT1, ACD, MITF, and TERF2IP), including two novel variants in BAP1 and 4 in POT1. We also found four deleterious and five likely deleterious variants in ATM (3.3%). Thus, including potentially deleterious variants in ATM increased the diagnostic yield to about 9%. Inclusion of rare variants of uncertain significance would increase the overall detection yield to 14%. At least 10% of melanoma missing heritability may be explained through panel testing in our population. To our knowledge, this is the highest frequency of putative ATM deleterious variants reported in melanoma families, suggesting a possible role in melanoma susceptibility, which needs further investigation.

Abstract 1638: Whole-exome sequencing and protein interaction networks to prioritize candidate genes for cutaneous melanoma susceptibility

Abstract Background: Known cutaneous malignant melanoma (CMM) genes account for melanoma risk in less than 40% of melanoma-prone families, suggesting the existence of additional risk genes or other modifiers. Whole exome sequencing (WES) of high-risk families usually results in the identification of a large number of potential disease-causing genes. However, prioritizing these genes and finding the true disease-causing ones have been challenging. We hypothesize that physically interacting proteins might have a similar effect on cell function and therefore, might produce a shared phenotype or increase the risk when mutated. To test this hypothesis, we applied a network approach integrating WES and protein-protein interaction (PPI) data to detect and prioritize rare variants in melanoma-prone families. Methods: We conducted WES analysis on germline DNA of 212 patients from 45 CMM families (2-5 affected people in a family) without known mutations. Variants that were rare (<1% in public and our in-house control datasets), loss-of-function or missense predicted to be deleterious, and showed complete disease co-segregation (present in all affected members within a family) were included in the network analysis. For this analysis, we only focused on genes that interact with known CMM genes (gene list in Goldstein AM, et al. Hum Mol Genet, 2017) which we used as seed proteins. We then applied a degree-aware algorithm (DADA) to rank the set of candidate genes from WES with respect to the set of known CMM genes using human PPI networks. The goal of DADA is to prioritize a candidate set of genes based on their association level with genes known to be related to the disease. Network proximity calculations of the candidates with respect to the seed set were based on Random Walk with Restarts method. We used high quality and scored human proteins interactions collected from InWeb_IM. In the primary analysis, the network contains 625,641 interactions, aggregated from 8 source databases and spanning 87% of reviewed human proteins. We also conducted additional analyses with CMM PPI subnetworks generated using high confidence interaction data from different sources to compare results. Results: The WES analysis described above identified 546 genes that harbored rare variants, likely affect protein function and co-segregated in affected members in CMM families. After applying DADA across all networks, the rankings of these genes were fairly consistent. Top genes included both known CMM genes (such as MC1R, CDKN2B, KITLG, and TINF2) and genes that have not yet been associated with CMM susceptibility (such as FOXK1, AR, LEF1, RGL4, PABPC1, CHEK2, CTBP2, and BLM). These results highlight the importance of known CMM genes and their networks in CMM susceptibility, and demonstrate the potential value of network approaches in gene prioritization. Further evaluation of novel genes is in progress. Citation Format: Sally Yepes, Margaret Tucker, Hela Koka, Kristine Jones, Aurelie Vogt, Laurie Burdette, Wen Luo, Bin Zhu, Meredith Yeager, Belynda Hicks, Neal D. Freedman, Stephen J. Chanock, Alisa M. Goldstein, Xiaohong R. Yang. Whole-exome sequencing and protein interaction networks to prioritize candidate genes for cutaneous melanoma susceptibility [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1638.

Quantitative assessment of the association between XRCC1 Arg399Gln and Arg194Trp polymorphisms and risk of cutaneous melanoma.

Accumulating evidence has suggested that the XRCC1 Arg399Gln and Arg194Trp polymorphisms might be related to cutaneous melanoma susceptibility. However, epidemiologic findings have been inconsistent. We have assessed reported studies by meta-analysis to perform a more precise estimation of the association between the XRCC1 two polymorphisms (Arg399Gln, Arg194Trp) and risk of cutaneous melanoma. A total of seven eligible articles were selected for this meta-analysis, including 3454 cases and 3811 controls for the XRCC1 Arg399Gln polymorphism and 1256 cases and 1575 controls for the XRCC1 Arg194Trp polymorphism. Overall, no significant associations were found in all genetic models when the studies were pooled into the meta-analysis for the Arg399Gln and Arg194Trp polymorphisms. When stratified by source of control, significant associations were found for the Arg399Gln polymorphism in the population-based subgroup under AA versus GG [odds ratio (OR)=1.43, 95% confidence interval (CI)=1.08-1.88]; the dominant model AA/GA versus GG (OR=1.25, 95% CI=1.04-1.51); and the recessive model AA versus GA/GG (OR=1.31, 95% CI=1.01-1.68). No significant associations were found for the Arg194Trp polymorphism in the subgroup analysis. This meta-analysis suggested that the XRCC1 Arg399Gln polymorphism was a risk factor for cutaneous melanoma in population-based subgroup.

Quantitative assessment of the influence of X-ray repair cross-complementing group 3 rs861539 polymorphism and cutaneous melanoma susceptibility.

Previous studies evaluating the association between X-ray repair cross-complementing group 3 (XRCC3) rs861539 polymorphism and cutaneous melanoma susceptibility reported conflicting findings. To draw a more precise association between XRCC3 rs861539 polymorphism and cutaneous melanoma susceptibility, we searched PubMed, EMBASE and Web of Science for case-control studies. A total of eight case-control studies including 3463 cases of melanoma and 4216 controls were included in the meta-analysis. Overall, no significant associations were found between XRCC3 rs861539 polymorphism and cutaneous melanoma susceptibility under all four genetic models (TT vs CC: OR 0.99, 95% CI 0.86-1.14; TC vs CC: OR 0.92, 95% CI 0.83-1.01; dominant model: OR 0.94, 95% CI 0.85-1.03; recessive model: OR 1.05, 95% CI 0.92-1.19). In the subgroup by source of control, no significant associations were found in hospital-based and population-based subgroup. This meta-analysis suggested that the XRCC3 rs861539 polymorphism was not a risk factor for cutaneous melanoma susceptibility.

Prevalence of GermlineBAP1, CDKN2A, andCDK4Mutations in an Australian Population-Based Sample of Cutaneous Melanoma Cases

Mutations in Cyclin-Dependent Kinase Inhibitor 2A (CDKN2A) and Cyclin-Dependent Kinase 4 (CDK4) contribute to susceptibility in approximately 40% of high-density cutaneous melanoma (CMM) families and about 2% of unselected CMM cases. BRCA-1 associated protein-1 (BAP1) has been more recently shown to predispose to CMM and uveal melanoma (UMM) in some families; however, its contribution to CMM development in the general population is unreported. We sought to determine the contribution of these genes to CMM susceptibility in a population-based sample of cases from Australia. We genotyped 1,109 probands from Queensland families and found that approximately 1.31% harbored mutations in CDKN2A, including some with novel missense mutations (p.R22W, p.G35R and p.I49F). BAP1 missense variants occurred in 0.63% of cases but no CDK4 variants were observed in the sample. This is the first estimate of the contribution of BAP1 and CDK4 to a population-based sample of CMM and supports the previously reported estimate of CDKN2A germline mutation prevalence.

Long telomere length and a TERT-CLPTM1 locus polymorphism association with melanoma risk

Telomere length has been associated with the development of cancer. Studies have shown that shorter telomere length may be related to a decreased risk of cutaneous melanoma. Furthermore, deregulation of the telomere-maintaining gene complexes, has been related to this oncogenic process. Some variants in these genes seem to be correlated with a change in telomerase expression. We examined the effect of 10 single nucleotide polymorphisms (SNPs) in the TERT gene (encoding telomerase), one SNP in the related TERT-CLPTM1L locus and one SNP in the TRF1 gene with telomere length, and its influence on melanoma risk in 970 Spanish cases and 733 Spanish controls.Genotypes were determined using KASP technology, and telomere length was measured by quantitative polymerase chain reaction (PCR) on DNA extracted from peripheral blood leucocytes.Our results demonstrate that shorter telomere length is associated with a decreased risk of melanoma in our population (global p-value, 2.69×10−11), which may be caused by a diminution of proliferative potential of nevi (melanoma precursor cells). We also obtained significant results when we tested the association between rs401681 variant (TERT-CLPTM1L locus) with melanoma risk (Odds ratio, OR; 95% confidence interval, CI=1.24 (1.08–1.43); p-value, 3×10−3).This is the largest telomere-related study undertaken in a Spanish population to date. Furthermore, this study represents a comprehensive analysis of some of the most relevant telomere pathway genes in relation to cutaneous melanoma susceptibility.

Blood DNA methylation, nevi number, and the risk of melanoma.

Germline mutations determining increased cutaneous malignant melanoma (CMM) risk have been identified in familial and sporadic CMM cases, but they account only for a small proportion of CMM cases. Recent evidence suggests that germline epimutations (e.g. DNA methylation alterations), which can be inherited similarly to genomic mutations and can be detected in normal body cells (including blood), might increase susceptibility to cancer. The aim of the study was to identify germline epimutations of genes that were found to be mutated in familial CMM (p16, p14, CDK4, MC1R, hTERT), immune and inflammatory genes (ICAM-1, TNFα), DNA mismatch repair gene (MLH1), and repetitive elements (ALU, LINE-1, HERV-w). We measured DNA methylation using bisulfite pyrosequencing in peripheral blood mononuclear cells from 167 CMM cases and 164 sex-matched and age-matched controls. We used multivariable logistic regression models to evaluate the association between methylation levels and CMM status or presence of dysplastic nevi. We found an association between the risk of CMM and peripheral blood mononuclear cell methylation levels of TNFα [odds ratio (OR)=1.11, 95% confidence interval (CI)=1.03-1.18], CDK4 (OR=0.76, 95% CI=0.64-0.91), and MLH1 (OR=1.12, 95% CI=1.02-1.22). In control participants, the risk of developing dysplastic nevi was associated with methylation levels of TNFα (OR=0.81, 95% CI=0.69-0.95), hTERT (OR=0.90, 95% CI=0.82-0.99), and ALU (OR=1.56, 95% CI=1.02-2.39). Epimutations in CMM susceptibility genes and in genes involved in response to oxidative damage are associated with the risk of developing CMM or dysplastic nevi. Further studies measuring methylation levels of these genes in prospectively collected samples are warranted to further elucidate their role in the development and progression of CMM.

The contribution of large genomic deletions at the CDKN2A locus to the burden of familial melanoma

Mutations in two genes encoding cell cycle regulatory proteins have been shown to cause familial cutaneous malignant melanoma (CMM). About 20% of melanoma-prone families bear a point mutation in the CDKN2A locus at 9p21, which encodes two unrelated proteins, p16INK4a and p14ARF. Rare mutations in CDK4 have also been linked to the disease. Although the CDKN2A gene has been shown to be the major melanoma predisposing gene, there remains a significant proportion of melanoma kindreds linked to 9p21 in which germline mutations of CDKN2A have not been identified through direct exon sequencing. The purpose of this study was to assess the contribution of large rearrangements in CDKN2A to the disease in melanoma-prone families using multiplex ligation-dependent probe amplification. We examined 214 patients from independent pedigrees with at least two CMM cases. All had been tested for CDKN2A and CDK4 point mutation, and 47 were found positive. Among the remaining 167 negative patients, one carried a novel genomic deletion of CDKN2A exon 2. Overall, genomic deletions represented 2.1% of total mutations in this series (1 of 48), confirming that they explain a very small proportion of CMM susceptibility. In addition, we excluded a new gene on 9p21, KLHL9, as being a major CMM gene.

High- and low-penetrance cutaneous melanoma susceptibility genes

The aim of this review is to report the current understanding of the molecular genetics of melanoma predisposition. To date, two high-penetrance melanoma susceptibility genes, cyclin-dependent kinas inhibitor (CDKN)2A on chromosome 9p21 and cyclin-dependent kinase (CDK4) on 12q13, have been identified. Germline inactivating mutations of the CDKN2A gene are the most common cause of inherited susceptibility to melanoma. Worldwide, a few families have been found to harbor CDK4 mutations. However, predisposing alterations to familial melanoma are still unknown in a large proportion of kindreds. Other melanoma susceptibility loci have been mapped through genome-wide linkage analysis, although the putative causal genes at these loci have yet to be identified. Much ongoing research is being focused on the identification of low-penetrance melanoma susceptibility genes that confer a lower melanoma risk with more frequent variations. Specific variants of the MC1R gene have been demonstrated to confer an increase in melanoma risk. In addition, conflicting data are available on other potential low-penetrance genes encoding proteins involved in pigmentation, cell growth and differentiation, DNA repair or detoxifying of metabolites.

HLA class I and class II frequencies in patients with cutaneous malignant melanoma from southeastern Spain: the role of HLA-C in disease prognosis

Available data have led to a controversy on the relationship between human leukocyte antigen (HLA) and cutaneous malignant melanoma susceptibility or prognosis. Moreover, the influence of HLA-C on melanoma has not yet been well established. Therefore, the aim of the current study was to analyze the possible influence of the HLA system on melanoma susceptibility and prognosis in the Spanish population. For this purpose, HLA-A and HLA-B serotyping and HLA-C, HLA-DRB1, and HLA-DQB1 genotyping by polymerase chain reactions using sequence-specific oligonucleotide (PCR-SSO) and sequence-specific primer (PCR-SSP) were performed in 174 melanoma patients and 227 ethnically matched controls. The number of controls was increased up to 356 for HLA-C typing. Patients were stratified according to the histological subtypes of melanoma, sentinel lymph node status, tumor thickness, and ulceration of primary lesion. No HLA-A, HLA-B, HLA-DRB1, or HLA-DQB1 relationship with melanoma was observed for susceptibility or disease prognosis. However, the analysis of HLA-C locus showed that individuals homozygous for HLA-C(Lys80) were significantly more frequent within the patient than the control group. Remarkably, individuals homozygous for group 2 HLA-C alleles (HLA-C(Lys80)) seem to be associated with metastatic progression of melanoma. In contrast, we found a negative association between group 1 HLA-C alleles (HLA-C(Asn80)) and disease susceptibility or metastasis development. In conclusion, although an association with HLA-A, HLA-B, HLA-DRB1, or HLA-DQB1 was not demonstrated, the study of the HLA-C locus revealed that the analysis of the dimorphism at position 80 in the alpha1 helix may help to evaluate the risk and prognosis of melanoma in our population.

ICAM‐1 polymorphisms and development of cutaneous malignant melanoma

Tumour growth in cutaneous malignant melanoma (CMM) is mediated by cell adhesion molecules, including intercellular adhesion molecule-1 (ICAM-1). ICAM-1 expression is associated with increasing Breslow thickness of vertical growth-phase tumours and, in patients with stage 1 disease, may be associated with disease free and patient survival. In this study we have investigated whether two single nucleotide polymorphisms (SNPs) in the ICAM-1 gene encoding amino acid substitutions in codons 241 and 469 of the expressed ICAM-1 molecule are associated with susceptibility to and markers of prognosis (including tumour Breslow thickness) in CMM. A total of 164 CMM patients and 264 cancer-free controls were genotyped for these SNPs by the 5' nuclease assay for allelic discrimination (TaqMan). No genotypes showed any significant associations with CMM susceptibility, although there was a non-significant increase in frequency of the ICAM-1 469 AA genotype among CMM patients vs. controls (38.4% vs. 29.9%; P = 0.11). However, the ICAM-1 241 GG genotype was significantly decreased in frequency among patients with primary invasive tumours of greater Breslow thickness (72.5% vs. 91.2%; P = 0.013; OR = 0.25 (0.072-0.85)). These results provide no evidence for a role for the ICAM-1 codon 241 and 469 SNPs in determining susceptibility to CMM, but provide preliminary evidence that the role of ICAM-1 polymorphism in modulating tumour growth in CMM requires further investigation in a larger study group.

Cytokine gene single nucleotide polymorphisms and susceptibility to and prognosis in cutaneous malignant melanoma.

Cutaneous malignant melanoma (CMM) is a potentially fatal malignancy in which exposure to UV light is the most important risk factor. Several lines of evidence suggest that CMM patients develop an immune response to their tumours, although, in most cases, anti-tumour immune responses are insufficient to abrogate tumour development. Polymorphism in genes regulating the immune response and cell growth may result in increased susceptibility to and/or poorer prognosis in certain individuals. In this study, we addressed whether single nucleotide polymorphisms (SNPs) associated with differential expression of selected pro- and anti-inflammatory cytokines and growth factors [interleukin (IL)-1beta-35 and -511, IL-2 -330, IL-4 -590, IL-6 -174, IL-8 -251, interferon (IFN)-gamma+874 and transforming growth factor (TGF)beta1 +915] or as markers of candidate cytokine genes (IL-12 +1188) are associated with susceptibility to or known prognostic indicators (e.g. initial tumour growth phase, Breslow thickness, mitotic count in vertical growth phase tumours, tumour regression) in CMM. One hundred and sixty-nine British caucasian CMM patients and 261 controls were included in the study and all SNPs were genotyped by ARMS-PCR. No SNP genotypes or alleles showed significant associations with CMM susceptibility and only the IL-1beta-511 TT genotype was associated with thinner invasive tumours at presentation, as assessed by Breslow thickness at the clinically significant cut-off point of 1.5 mm [occurring in 2/51 (3.9%) thicker vs. 14/78 (17.9%) thinner tumours (P = 0.03; relative risk = 0.29 (95% confidence interval 0.05-0.95)]. These findings suggest that - with the possible exception of IL-1beta- genetic variation associated with differential expression of the selected pro- and anti-inflammatory cytokines is unlikely to play a major role in susceptibility to and prognosis in CMM.

CDKN2A as a uveal and cutaneous melanoma susceptibility gene

A few families have been described whose members are affected by either cutaneous melanoma (CM) or uveal melanoma (UM), suggesting that a common susceptibility could exist. Although CDKN2A is the main CM predisposing gene, thus far no germline CDKN2A mutations have been described in families with both CM and UM. We report a Gly67Ser missense CDKN2A germline mutation in a melanoma-prone family, where one carrier was affected by UM and the other by a CM. Immunohistochemistry performed on the UM tissue block revealed loss of CDKN2A protein staining in tumor cells. These observations demonstrate that CDKN2A is also a UM susceptibility gene.