Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi

Variation in CDKN2A at 9p21.3 influences childhood acute lymphoblastic leukemia risk

Using data from a genome-wide association study of 907 individuals with childhood acute lymphoblastic leukemia (cases) and 2,398 controls and with validation in samples totaling 2,386 cases and 2,419 controls, we have shown that common variation at 9p21.3 (rs3731217, intron 1 of CDKN2A) influences acute lymphoblastic leukemia risk (odds ratio = 0.71, P = 3.01 x 10(-11)), irrespective of cell lineage.

Genome-wide association study identifies five new breast cancer susceptibility loci

Breast cancer is the most common cancer in women in developed countries. To identify common breast cancer susceptibility alleles, we conducted a genome-wide association study in which 582,886 SNPs were genotyped in 3,659 cases with a family history of the disease and 4,897 controls. Promising associations were evaluated in a second stage, comprising 12,576 cases and 12,223 controls. We identified five new susceptibility loci, on chromosomes 9, 10 and 11 (P = 4.6 x 10(-7) to P = 3.2 x 10(-15)). We also identified SNPs in the 6q25.1 (rs3757318, P = 2.9 x 10(-6)), 8q24 (rs1562430, P = 5.8 x 10(-7)) and LSP1 (rs909116, P = 7.3 x 10(-7)) regions that showed more significant association with risk than those reported previously. Previously identified breast cancer susceptibility loci were also found to show larger effect sizes in this study of familial breast cancer cases than in previous population-based studies, consistent with polygenic susceptibility to the disease.

IGFBP7 is not required for B-RAF-induced melanocyte senescence

Induction of senescence permanently restricts cellular proliferation after oncogenic stimulation thereby acting as a potent barrier to tumor development. The relevant effector proteins may therefore be fundamental to cancer development. A recent study identified IGFBP7 as a secreted factor mediating melanocyte senescence induced by oncogenic B-RAF, which is found commonly in cutaneous nevi. In contrast to the previous report, we demonstrate that B-RAF signaling does not induce IGFBP7 expression, nor the expression of the IGFBP7 targets, BNIP3L, SMARCB1, or PEA15, in human melanocytes or fibroblasts. We also found no correlation between B-RAF mutational status and IGFBP7 protein expression levels in 22 melanoma cell lines, 90 melanomas, and 46 benign nevi. Furthermore, using a lentiviral silencing strategy we show that B-RAF induces senescence in melanocytes and fibroblasts, irrespective of the presence of IGFBP7. Therefore, we conclude that the secreted protein IGFBP7 is dispensable for B-RAF(V600E)-induced senescence in human melanocytes.

Architecture of inherited susceptibility to common cancer

This Timeline article looks back at 40 years of research into the inherited genetic basis of cancer and the insights these studies have yielded. Early epidemiological research provided evidence for the 'two-hit' model of cancer predisposition. During the 1980s and 1990s linkage and positional cloning analyses led to the identification of high-penetrance cancer susceptibility genes. The past decade has seen a shift from models of predisposition based on single-gene causative mutations to multigenic models. These models suggest that a high proportion of cancers may arise in a genetically susceptible minority as a consequence of the combined effects of common low-penetrance alleles and rare disease-causing variants that confer moderate cancer risks.

Management of melanoma families

In this review we have aimed to focus on the clinical management of familial melanoma patients and their relatives. Along this line three major topics will be discussed: (1) management/screening of familial melanoma families: what is advised and what is the evidence thereof; (2) variability of families worldwide with regard to clinical phenotype, including cancer spectrum and likelihood of finding germline mutations and (3) background information for clinicians on the molecular biology of familial melanoma and recent developments in this field.

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

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

Familial melanoma: a meta-analysis and estimates of attributable fraction

Melanoma commonly clusters in families, and the recent identification of numerous genotypes predicting higher risks of melanoma has led to the widespread perception that this cancer is predominantly a genetic disease. We conducted a systematic review of the literature and meta-analysis to quantify the contribution of familial factors to melanoma, estimated by the population attributable fraction (PAF). Eligible studies were those that permitted quantitative assessment of the association between histologically confirmed melanoma and family history of the disease; we identified 22 such studies using citation databases, followed by manual review of retrieved references. We calculated summary RRs using weighted averages of the log RR, taking into account random effects, and used these to estimate the PAF. Overall, family history was associated with a significant 2-fold increased risk of melanoma (odds ratio, 2.06; 95% confidence interval, 1.72-2.45); however, there was significant heterogeneity (P = 0.01). The pooled estimate for population-based studies (n = 11) was 2.03 (1.70-2.43), and 2.51 (1.55-4.07) for clinic/hospital-based studies (n = 11), both with significant heterogeneity (P = 0.049 and P = 0.013, respectively). Two studies used record linkage to verify family history in relatives; the pooled risk estimate from these two studies was 2.52 (2.11-3.00) with no evidence of heterogeneity (P = 0.258). Estimates of PAF associated with a positive family history ranged from 0.007 for Northern Europe to 0.064 for Australia (0.040 for all regions combined). Our findings suggest that only a small percentage of melanoma cases (always <7%) are attributable to familial risk; the majority of melanomas are presumably attributable to other factors.

Increased risk of second primary cancers after a diagnosis of melanoma

OBJECTIVE

To quantify the risk of subsequent primary cancers among patients with primary cutaneous malignant melanoma.

DESIGN

Population-based registry study.

SETTING

We evaluated data from 9 cancer registries of the Surveillance, Epidemiology, and End Results program from 1973-2006.

PARTICIPANTS

We included 89 515 patients who survived at least 2 months after their initial melanoma diagnosis.

RESULTS

Of the patients with melanoma, 10 857 (12.1%) developed 1 or more subsequent primary cancers. The overall risk of a subsequent primary cancer increased by 28% (observed to expected [O:E] ratio = 1.28). One quarter of the cancers were subsequent primary melanomas (O:E = 8.61). Women with head and neck melanoma and patients younger than 30 had markedly increased risks (O:E = 13.22 and 13.40, respectively) of developing a subsequent melanoma. Second melanomas were more likely to be thin than were the first of multiple primary melanomas (thickness at diagnosis <1.00 mm, 77.9% vs 70.3%, respectively; P < .001). Melanoma survivors had increased risk of developing several cancers; the most common cancers with elevated risks were breast, prostate, and non-Hodgkin lymphoma (O:E = 1.10, 1.15, and 1.25, respectively).

CONCLUSIONS

Melanoma survivors have an approximately 9-fold increased risk of developing subsequent melanoma compared with the general population. The risk remains elevated more than 20 years after the initial melanoma diagnosis. This increased risk may be owing to behavioral factors, genetic susceptibility, or medical surveillance. Although the percentage of subsequent primary melanomas thicker than 1 mm is lower than for the first of multiple primary melanomas, it is still substantial. Melanoma survivors should remain under surveillance not only for recurrence but also for future primary melanomas and other cancers.

[What's new in oncodermatology?]

Several epidemiologic studies using the Surveillance, Epidemiology and End results program, have shown that the incidence of melanoma and of cutaneous lymphomas has clearly increased in the United States. Two independent groups have reported genome-wide association studies identifying variants associated to an increased risk of melanoma. Tumor stem cells were found to have an increased frequency when compared to previously reported studies, and also a greater plasticity. The Merkel cell polyoma virus seems rather ubiquitous, since it has been evidenced, without clonal integration, in several other types of cutaneous tumors, and even in healthy skin, with an increased frequency in photo-exposed skin and in immunodepressed patients. A recent study demonstrates for the first time a link between the exposure to pesticides and the occurrence of lymphomas. Another study has evidenced the association between topical treatments with steroids and the occurrence of lymphomas, especially cutaneous lymphomas. The risk is increased with the length of treatment and the potency of steroids. Adjuvant treatment of high-risk melanomas with alpha interferon does not achieve better results with the adjunction of a 4 weeks high-dose induction period, and development of autoantibodies is not significantly associated to an increased relapse free survival after correction of the time related biais. In contrast, the effect of interferon on relapse free survival, distant metastasis free survival and overall survival seems better in the subgroup of melanoma with primary ulceration. The development of new specific inhibitors of c-kit or BRAF is a great hope for the targeted treatment of peculiar groups of advanced melanomas. The main objectives of the new 2009-2013 Cancer Plan is to optimize the structuration of health organization in the field of oncology.

Gene expression profiling of paraffin-embedded primary melanoma using the DASL assay identifies increased osteopontin expression as predictive of reduced relapse-free survival

PURPOSE

Gene expression studies in melanoma have been few because tumors are small and cryopreservation is rarely possible. The purpose of this study was to evaluate the Illumina DASL Array Human Cancer Panel for gene expression studies in formalin-fixed melanoma primary tumors and to identify prognostic biomarkers.

EXPERIMENTAL DESIGN

Primary tumors from two studies were sampled using a tissue microarray needle. Study 1: 254 tumors from a melanoma cohort recruited from 2000 to 2006. Study 2: 218 tumors from a case-control study of patients undergoing sentinel node biopsy.

RESULTS

RNA was obtained from 76% of blocks; 1.4% of samples failed analysis (transcripts from <250 of the 502 genes on the DASL chip detected). Increasing age of the block and increased melanin in the tumor were associated with reduced number of genes detected. The gene whose expression was most differentially expressed in association with relapse-free survival in study 1 was osteopontin (SPP1; P = 2.11 x 10(-6)) and supportive evidence for this was obtained in study 2 used as a validation set (P = 0.006; unadjusted data). Osteopontin level in study 1 remained a significant predictor of relapse-free survival when data were adjusted for age, sex, tumor site, and histologic predictors of relapse. Genes whose expression correlated most strongly with osteopontin were PBX1, BIRC5 (survivin), and HLF.

CONCLUSION

Expression data were obtained from 74% of primary melanomas and provided confirmatory evidence that osteopontin expression is a prognostic biomarker. These results suggest that predictive biomarker studies may be possible using stored blocks from mature clinical trials.

Moderate- to low-risk variant alleles of cutaneous malignancies and nevi: lessons from genome-wide association studies

Cutaneous malignancies, especially malignant melanoma, exhibit great genetic heterogeneity. As a result, some individuals and families have particularly increased risk due to genetic predisposition to the disease. The susceptibility alleles range from rarely occurring, heritable, high-risk variants to ubiquitously occurring low-risk variants. Although until now the focus has been mostly towards the familial high-risk genes, the development of genome-wide association studies has uncovered a number of moderate- to low-risk predisposition alleles. The ability to specifically identify genetic variation associated with visible pigmentation traits and disease risk has provided a much richer view of the genetics of cutaneous malignancies. In this review, we provide an update on the recently identified risk loci. Existing clinical data, combined with vast genome information, will provide a better understanding of the biology of disease, and increased accuracy in risk prediction.

Genome-wide association study identifies three loci associated with melanoma risk

We report a genome-wide association study of melanoma conducted by the GenoMEL consortium based on 317K tagging SNPs for 1,650 selected cases and 4,336 controls, with replication in an additional two cohorts (1,149 selected cases and 964 controls from GenoMEL, and a population-based case-control study in Leeds of 1,163 cases and 903 controls). The genome-wide screen identified five loci with genotyped or imputed SNPs reaching P < 5 x 10(-7). Three of these loci were replicated: 16q24 encompassing MC1R (combined P = 2.54 x 10(-27) for rs258322), 11q14-q21 encompassing TYR (P = 2.41 x 10(-14) for rs1393350) and 9p21 adjacent to MTAP and flanking CDKN2A (P = 4.03 x 10(-7) for rs7023329). MC1R and TYR are associated with pigmentation, freckling and cutaneous sun sensitivity, well-recognized melanoma risk factors. Common variants within the 9p21 locus have not previously been associated with melanoma. Despite wide variation in allele frequency, these genetic variants show notable homogeneity of effect across populations of European ancestry living at different latitudes and show independent association to disease risk.