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Unraveling Genetic Susceptibility to Melanoma

March 2012 - Linkage Newsletter

by Victoria A. Fisher, M.P.H., and Wendy Schneider-Levinson

Tenure-track investigator Kevin Brown, Ph.D., Laboratory of Translational Genomics, has added a new chapter to DCEG’s history of discovering the genetic factors that contribute to the risk of melanoma. As reported in a recent Nature article, Dr. Brown and colleagues used whole-genome sequencing to identify a novel, recurrent mutation, the E318K variant, in MITF. MITF is a gene that predisposes people to familial and sporadic melanoma (see Figure 1).

The MITF gene, or microphthalmia-associated transcription factor, helps control the development and function of pigment-producing cells called melanocytes. MITF has been considered an important gene in melanoma tumors for many years, being somatically amplified or mutated in some subsets of melanoma while strongly overexpressed in others.

Dr. Brown’s paper describes the latest in a series of major DCEG findings on the genetics of melanoma. The ultimate goal of this research is the prevention and early detection of melanoma in high-risk individuals. The application of novel research approaches has been enabled by the large body of clinical and epidemiological data, as well as biospecimens, that have been collected over years of family and case-control studies.

A History of Genetic Detective Work

DCEG first began investigating possible genetic linkages to melanoma during the late 1970s under the leadership of Mark H. Greene, M.D., now Chief of the Clinical Genetics Branch. Margaret A. Tucker, M.D., Director of DCEG’s Human Genetics Program, was a postdoctoral fellow working with Dr. Greene at the time of the initial investigation, and she later led and expanded the effort in melanoma research. Over time, the Genetic Epidemiology Branch (GEB) evaluated and prospectively followed approximately 80 multigenerational families with more than 1,800 members, some for up to 30 years. The investigators gathered detailed family histories, performed clinical examinations, and phenotyped the families. The goal was to identify high-risk susceptibility genes for melanoma, understand the risk factors for sporadic and familial cases, and provide better guidance for screening and clinical practice. 

One of the first major clinical findings in these families was the identification and characterization of dysplastic nevi, the unusual moles seen in melanoma families. In a large case-control study, Dr. Tucker later showed that dysplastic nevi are precursors to both familial and sporadic melanoma, a finding that has had a significant impact on clinical screening protocols.

Gathering the Pieces of the Melanoma Puzzle

The first linkage analysis of familial melanoma, based on 23 genetic markers, was conducted in 1983 by Lynn R. Goldin, Ph.D., now Deputy Chief of GEB, who found suggestive evidence of linkage on the short arm of chromosome 1. In 1994, Alisa M. Goldstein, Ph.D. (GEB), and Dr. Tucker identified the first melanoma susceptibility gene—CDKN2A, a tumor suppressor gene found in roughly 40 percent of melanoma-prone families. CDKN2A codes for p16 and p14 proteins and also has been found to be associated with pancreatic cancer, although the precise mechanism underlying that association has yet to be understood. The two researchers identified a second melanoma susceptibility gene in 1996—CDK4, which encodes cyclin-dependent kinase 4, an oncogene, and accounts for approximately 2 percent of melanoma-prone families. Dr. Goldstein also demonstrated that another gene, MC1R, is a modifier of melanoma risk in American families with CDKN2A mutations. Individuals with MC1R variants are more likely to have multiple melanomas that start at an earlier age.

Further studies were performed through GenoMEL (the Melanoma Genetics Consortium), which was established in 1997 with initial funding through NCI and is composed of researchers from approximately 20 countries. The creation of GenoMEL provided a larger number of familial melanoma patients in whom mutations in the high-risk melanoma genes could be studied and better characterized. Dr. Goldstein has led multiple analyses within GenoMEL, including a study that identified differences in the risk of melanoma and other tumors associated with mutations in CDKN2A across geographic locales. That study also detected a strong association between pancreatic cancer and CDKN2A mutations.

In 2006, Maria Teresa Landi, M.D., Ph.D. (GEB), reported on data from case-control studies in Italy and San Francisco showing that Caucasians with a germline variant of MC1R, the gene encoding the melanocortin-1 receptor, were more likely to develop melanoma with BRAF mutations. Following up on her finding by examining the association in a much larger number of subjects in GenoMEL, Dr. Landi and colleagues found three areas of significant association with melanoma: on 16q24 marking MC1R, on 11q12-q14 near TYR, and on 9p21 near MTAP. In subsequent larger studies, four more loci have been identified, in ATM, MX2, and CASP8, as well as on 1q21.3.

Along with Ruth A. Kleinerman, M.P.H., of the Radiation Epidemiology Branch, Dr. Tucker and colleagues found that patients with inherited retinoblastoma, a rare cancer of the eye that tends to develop in early childhood, had a significantly higher risk of developing melanoma and that a family history of retinoblastoma further increased their risk. This work suggests that the tumor suppressor gene RB may play a role in melanoma as well as retinoblastoma.

Harnessing New Technology

In more recent years, investigators have harnessed next-generation DNA sequencing technology to make critical discoveries. For example, exome sequencing has become a common means of interrogating the protein-coding regions of a genome at a relatively low cost. Other new techniques include high-resolution array-based comparative genomic hybridization (array-CGH), which detects genomic copy number variations, or alterations of the DNA of a genome that result in an abnormal number of copies of a section of DNA; chromatin immunoprecipitation (ChIP) sequencing, which is used to analyze protein interactions with DNA; and molecular profiling, which provides a powerful means of classifying tumors based on their underlying biology.

Xiaohong Rose Yang, Ph.D., M.P.H. (GEB), is employing these new techniques in her search for genetic variation and regulation of genes linked to melanoma susceptibility within the American families. In collaboration with Dr. Meg Gerstenblith of the Case Western Reserve University School of Medicine in Cleveland, Ohio, Dr. Yang is launching a study that will identify clinically and etiologically relevant subtypes of melanoma using integrated molecular profiling approaches. She and other scientists are assessing the feasibility of conducting molecular profiling analyses on DNA and RNA extracted from melanoma tissue blocks. “With improved awareness and earlier diagnoses, most melanoma tumors diagnosed in the U.S. are small,” said Dr. Tucker. “With this pilot study, we will assess whether enough tumor material is available in routinely collected pathology tissue blocks for the molecular analyses.”

Translating Research Into Clinical Practice

The DCEG melanoma research program has always had a strong translational clinical component. Following melanoma-prone families over the long term has enabled investigators to develop recommendations for managing risk factors and has changed clinical practice for screening. Mary Fraser, a former clinical research nurse in GEB, spent considerable time educating members of melanoma-prone families on ways to reduce their risk of the disease and how to recognize dysplastic nevi and other warning signs of early-stage melanoma. GEB also developed a tool to measure exposure to the sun based on lifetime history of residence, and developed a risk prediction model that can be used by primary care providers to plan for screening of individuals not in melanoma-prone families. In addition, to inform study participants, clinicians, and the public, DCEG has published a melanoma atlas, videos, newsletters, and brochures, including a recent award-winning brochure targeting populations of color and their physicians titled Anyone Can Get Skin Cancer (see the July 2011 issue of Linkage).

Thanks to the long-term investment in these resources, DCEG investigators are poised to apply novel technologies and approaches that will help unlock the complexities of melanoma genetics, including gene-environment interactions, and to translate the findings to facilitate the prevention, early detection, and treatment of this disease.

View related information: NCI Melanoma Home Page

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