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Discovering the causes of cancer and the means of prevention
 

MelaNostrum Consortium Research

Case-Control Study

MelaNostrum Consortium

The MelaNostrum case-control study consists of melanoma patients recruited from hospitals, universities, and clinical centers affiliated with Consortium members from Italy, Spain, Greece, Croatia, southern France, and Cyprus, along with controls recruited at each site. Clinical and phenotypic information, such as number of melanocytic nevi (moles) and freckles, skin type, hair and eye color, and sunburns, as well as environmental exposures, are collected by clinical examination, interviews, and/or self-report. Data and biospecimens collected from participants of this study are used to investigate melanoma risk and progression associated with genetic, phenotypic, and environmental factors.

Case-control Study Projects

ΜelanoQ: A questionnaire of standardized epidemiologic and clinical variables for melanoma risk assessment

Contact: Alex Stratigos

MelanoQ is a questionnaire designed by members of the MelaNostrum Consortium to standardize the collection of epidemiologic and clinical data used for melanoma risk assessment. The questionnaire consists of four sections: A. demographic data; B. phenotypic and sun exposure risk factors and lifestyle habits; C. clinical examination, and medical and family history; and D. diagnostic data on melanoma. The aim of the questionnaire is to standardize the collection of data for use in pooled and meta-analyses and to provide guidance for the design of clinical, epidemiologic, and translational studies of melanoma.

Genome-wide association study (GWAS)

Contact: Maria Teresa Landi

Genome-wide association studies (GWAS) have identified several genetic variants – mainly in the proximity of genes that are related to pigmentation, nevus (mole) density, DNA repair, or telomere maintenance – that are associated with melanoma risk. GWAS studies of melanoma risk, however, have included few individuals of Mediterranean descent. This case-control study compares genetic variants among melanoma patients from Mediterranean countries to healthy people from the general populations of those countries. Investigators then combine these results with results from Northern-European, American, and Australian populations in order to investigate the similarities and the differences in the pathways leading to melanoma development.

Characterization of non-acral sporadic cutaneous melanoma unrelated to common, known risk factors

Contact: Eduardo Nagore

Most cutaneous melanomas develop through patterns of either:
•    sun sensitivity (i.e. fair pigmentation of skin and hair) and chronic sun damage, or
•    melanocytic nevi (moles) and intermittent sun exposure

However, a small percentage of non-acral melanomas are unrelated to common, known risk factors. This study seeks to identify and characterize these melanomas and better understand their clinical features. This work can be of great clinical importance because melanomas that develop in the absence of common risk factors tend to be asymptomatic and occur at young ages.

Analyses of phenotypic characteristics, sun exposure, and genetic variants in southern Europe, northern Europe, and Australia

Contact: Mengying Li

Individuals with many melanocytic nevi (moles) and fair pigmentation are known to be at increased risk of cutaneous melanoma. Both melanocytic nevus count and pigmentation characteristics have a genetic component. Pigmentation is associated with sun sensitivity and may also influence an individual’s sun exposure behavior. In this study, casual inference analyses and additional approaches are conducted in melanoma cases and controls from three populations that differ in pigmentation characteristics and intensity of sun exposure – southern European (darker pigmentation, intense sun), northern European (fairer pigmentation, moderate sun), and Australian (fairer pigmentation, intense sun) – to better understand the complex patterns of association between phenotypic characteristics, genetic variants, and melanoma risk. 

Combining common genetic variants and non-genetic risk factors to predict risk of cutaneous melanoma

Contact: Maria Teresa Landi

Because melanoma is highly curable when detected early, it is critically important to identify individuals at high risk for melanoma in order to improve survival and morbidity associated with this disease. Melanoma risk is thought to have a strong genetic component; in fact, melanoma heritability is among the highest of any cancer. However, melanoma risk prediction models have only included single nucleotide polymorphisms (SNPs) that reached statistical significance in genome-wide association studies (GWAS) or few candidate SNPs. This study uses different approaches to build polygenic risk scores (PRS) to capture the underlying genetic risk for melanoma. The largest meta-analysis of melanoma GWAS is used to build the PRS models; the performance is validated in additional genotyped cases and controls from the MelaNostrum Consortium. The PRS with the greatest predictive performance is combined with traditional risk factors (e.g. pigmentation, nevi, sun exposure) to stratify individuals based on melanoma risk. Model calibration in prospective cohort studies is planned.

A Mendelian Randomization Study of melanoma risk factors

Contact: Evangelos Evangelou

Several modifiable factors have been associated with risk of melanoma. Mendelian randomization is a tool to investigate which of these associations, if any, are causal factors in the development of melanoma. Genetic variants that only alter disease risk through the effect of the variant on specific modifiable factors (e.g. a variant that affects vitamin D levels) can be used as unbiased proxies for investigating risks of melanoma due to these modifiable factors. Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) associated with diet-related factors, including alcohol, beta-carotene, coffee, retinol, and vitamin D. A previous study analyzing data from melanoma patients in the UK Biobank found no significant associations between these SNPs and dietary factors. In this follow-up study, data from the UK Biobank is combined with data from MelaNostrum to investigate whether any significant associations are observed when including a large population of people of Mediterranean descent. In addition to exploring SNPs associated with diet-related factors, this study will also include BMI, sex, and hormonal factors in the analyses.

Family Study

Individuals with two or more first-degree relatives with a history of melanoma are at greater risk of developing melanoma than the general population. Only a portion of these familial melanomas are attributable to the heritable genetic risks that have been identified to date or to the risk factors shared among close relatives (e.g. pigmentation and sun exposure patterns). The MelaNostrum Family Study seeks to further understand familial melanoma risk by sequencing data from Mediterranean/Southern European populations. The sequencing data are then analyzed together with that from Northern European and Australian families – offering an opportunity to study familial melanoma risk across different populations.

Family study projects

Whole exome sequencing to identify rare and common variants and melanoma risk in familial settings

Contact: Maria Teresa Landi

A portion of familial melanoma risk is hereditary in nature. A few susceptibility genes have already been identified, including CDKN2A and CDK4 – both of which have a role in cell cycle progression. Collaborative research involving members of the MelaNostrum Consortium has identified a rare variant in the Protection of Telomeres 1 (POT1) as a high susceptibility gene. The variant arose as a founder mutation in the area of Romagna, Italy. Whole-exome sequencing – sequencing of the protein coding regions of DNA – in melanoma-prone families, excluding those with known mutations in high penetrant susceptibility genes, is being performed to continue investigating rare genetic variants associated with melanoma risk in a familial setting. Using polygenic risk scores (PRS), this study also investigates the contribution of common susceptibility variants in the presence or absence of rare variants in known high penetrance susceptibility genes.

A subset of the families will undergo whole genome sequencing analysis to potentially identify noncoding variants affecting melanoma risk. Families were selected based on certain factors, including having a large number of affected individuals per family, multiple melanomas, young age at melanoma onset, and low PRS.

ATM mutations in melanoma susceptibility

Contact: Paola Ghiorzo

ATM is a gene that plays an important role in DNA repair. Consequently, ATM is associated with predisposition to certain cancers. Genome-wide association studies (GWAS) have established ATM as a low-penetrance melanoma susceptibility gene, and population studies have linked specific ATM genetic variants with increased melanoma risk. To better understand the role of ATM in melanoma susceptibility, this study evaluates ATM gene variants observed in melanoma-prone families. ATM data are collected from melanoma-prone families, unrelated melanoma patients, and disease-free individuals. The number of loss of function (inactivation) and missense (amino acid substitution) ATM variants in melanoma-prone family members and melanoma patients will be identified and compared to disease-free controls.

Evaluation of specific candidate melanoma susceptibility genes in families

Contact: Susana Puig

Beyond the known high-penetrance susceptibility genes, others candidate genes have shown higher expression in several cancers, including melanoma, than in normal healthy tissue. Although the specific function of the genes has not been well established, genome analyses of melanoma-prone families have identified variants of these genes as one of the likely discriminators between family members that develop melanoma from those who do not. These observations provide a rationale for assessing the possible role of loss of function (inactivation) and missense (amino acid substitution) variants in these genes among melanoma-prone families.

Evaluation of pigmentation genes as modifying factors for the development of melanoma in CDKN2A mutation carriers from Mediterranean countries

Contact: Susana Puig

Fair skin and hair, and sun sensitivity are known risk factors for melanoma development. Variants in genes associated with pigmentation have been linked to increased risk of melanoma. These genes may also modify the risk of melanoma in individuals with mutations in the CDKN2A gene – a gene involved in regulating the progression of the cell cycle and one of the key known factors for inherited susceptibility to melanoma. This study seeks to evaluate the role of variants in pigmentation genes common in Mediterranean populations as modifying factors for the development of melanoma in CDKN2A mutation carriers from Mediterranean countries.

Tissue Study

The MelaNostrum Consortium conducts a molecular classification project using formalin-fixed paraffin-embedded (FFPE) tissue samples collected from primary melanoma tumors, re-excision from areas around the tumor, and metastatic site tissue. Whole genome methylation profiling and sequencing will be performed on the DNA extracted from these tissues to explore the determinants of melanoma progression in relation to immunological markers.

Tissue study projects

Pilot study – Examination of methylation levels in primary tumors and metastatic lesions from melanoma patients

Contact: Mario Mandala

DNA extraction, mutational calling, and DNA methylation (chemical "tags" that modulate gene expression) profiling from formalin-fixed, paraffin-embedded (FFPE) melanoma tumor and surrounding tissue can present challenges, including DNA degradation (fragmentation) from FFPE preservation and oxidation of DNA by melanin. Therefore, a pilot study is being conducted to test the feasibility of measuring whole genome methylation levels and whole exome sequencing in DNA from FFPE samples. The current pilot study tests the quantity and quality of DNA extracted using different kits and approaches, and conducts methylation profiling using the Infinium MethylationEPIC array. The results will inform the protocol and technologies to be used in a larger study of primary and metastatic melanoma tissues. With the extensive pathology data, particularly on lymphocyte infiltration and the presence of other inflammatory cells, the investigators can examine the link between molecular changes and tissue microenvironment.

Study of the progression from nevi to melanoma

Contact: Maria Teresa Landi

Converging lines of evidence suggest that melanoma comprises biologically distinct subtypes arising through multiple causal pathways. The distribution of melanoma subtypes differ by age, anatomical location of the cancer, and sun exposure. Somatic mutation patterns vary across melanoma subtypes, though the large majority of studies suggesting this phenomenon were based on metastatic melanomas alone.

To further understand the heterogeneity of melanoma, and to determine a predictive pattern of progression for dysplastic nevi (a melanoma precursor and risk factor), the investigators plan to conduct tissue-based analyses of precursors, melanoma tumors and metastases within existing study populations. They aim to investigate the tumor evolutionary patters, tumor microenvironment, and cells of origin of different melanoma subtypes. These cases are well annotated with detailed clinical and epidemiological data, and have sufficient biological samples. To this end, researchers are conducting pilot investigations testing different approaches for single-nucleus RNA sequencing and oligo cell DNA sequencing from frozen specimens. Results from the pilot investigations will inform the design and approach of the overall study.

Molecular landscape and etiology of acral lentiginous melanoma

Contact: Maria Teresa Landi

Acral lentiginous melanoma (ALM) is a rare subtype of melanoma associated with poor survival. Unlike other cutaneous melanoma subtypes, ALM has not been linked to sun exposure, and much of its risk factors and exposures remain unknown. Further, a recent genome-wide association study from the Consortium has shown that ALM is not linked with pigmentation genes. The Mediterranean population, with its relatively darker pigmentation, has a higher proportion of the ALM subtype than other fairer-skinned populations. To better understand the etiology and possibly inform the prevention and treatment of ALM, this study will characterize the genomic landscape of the ALM melanoma subtype through whole exome sequencing and RNA sequencing. The researchers aim to investigate the endogenous and exogenous processes involved in the development of this tumor and their correlation with host factors. Additionally, to increase the sample size for this investigation, the researchers plan to work with the Sanger Institute as well as collaborators from Mexico and other countries.