Case-Control Study
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 and countries in Latin America and Northern Africa, 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. For the study of acral lentiginous melanoma, questions on mechanical stress, trauma, and weight-bearing locations, as well as an anatomical classification system that maps tumor subsite to defined pressure and friction zones are included.
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 to increase the statistical power to identify novel genetic loci related to melanoma risk.
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 younger ages.
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. The largest meta-analysis of melanoma GWAS is used to build polygenic risk scores (PRS) and absolute risk is estimated, with model calibration in prospective cohorts. The PRS is combined with traditional risk factors (e.g. pigmentation, nevi, sun exposure) to improve risk prediction and identify individuals who could benefit from screening and improved surveillance for melanoma early detection.
MELCAYA (Melanoma in Children, Adolescents, and Young Adults)
Contact: Susana Puig
In childhood, adolescence and young adults (CAYA), melanoma is under-studied and non-existing tailored clinical guidelines and standardized approaches lead to a very low diagnostic accuracy. The MELCAYA project aims to understand risk factors and determinants of melanoma to improve the prevention, diagnosis and prognosis of melanomas in CAYAs through a strong international consortium with experts from 10 countries in different disciplines (e.g. oncology, paediatrics, ethics, policy making), and sectors (e.g. academic centers, SMEs, hospitals, patient associations). MELCAYA will work on different approaches. 1) By integrating existing reference European cohorts and registries, studies of genetic and environmental risk factors and progression of melanoma in CAYA will be performed through different omic methods, and a novel taxonomy of CAYA melanoma will be generated. 2) MELCAYA will also develop image-based robust and trustworthy machine learning tools and a pan-European second-opinion platform for better diagnosis specifically designed for CAYA. 3) Moreover, the validation of minimally and non-invasive disruptive tools based on artificial intelligence and volatilomics detection from exhaled breath and skin will lead to earlier detection and more accurate prognosis of melanoma in CAYA. 4) Finally, through the evidence gathered, MELCAYA will design and implement public health strategies and will actively involve patients and the general population. The results of MELCAYA will maximize its impact by making its data and results accessible and re-usable through integration into UNCAN.eu.
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 high-risk individuals from the Consortium. 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 genetic variants in melanoma high-risk individuals
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, as well as telomere genes. 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 familial aggregation.
Whole genome sequencing to identify rare, structural and non-coding genetic variants in melanoma high-risk individuals
Contact: Maria Teresa Landi, Paola Ghiorzo, and Kevin Brown
A subset of the families is undergoing 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. In the analysis of the first set of WGS data, we found a recurrent intergenic founder deletion at chr.9p21 associated with a markedly increased CM risk (OR=27.5; P=1.27×10⁻⁶) through disruption of regulatory elements governing CDKN2A. This work establishes this deletion as a high-penetrance genetic locus and highlights the role of non-coding variation in cancer predisposition.
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 are being 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 is being performed on the DNA extracted from these tissues to explore the determinants of melanoma progression in relation to immunological markers.
Tissue study projects
Molecular profiling and imaging of paired primary and metastatic melanomas - NOPRIMME
Contact: Cristina Pellegrini
Characterizing the genomic features of primary and metastatic cancers is essential for improving our understanding of the biological processes that drive cancer progression. The primary objective of this study is to investigate intra-patient molecular and immunologic heterogeneity in paired primary and metastatic tumor tissues. Secondary objectives will include analyses of specific sample subgroups, subject to sample availability, such as skin and lymph node metastases; differences between metastases arising through lymphatic versus hematogenous spread; imaging features of primary melanoma that may predict patterns of dissemination; and circulating serum biomarkers. This study will integrate multimodal data, including whole-exome sequencing, RNA sequencing, lipidomics, spatial profiling, circulating biomarkers, and imaging data.
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 differs by age, melanoma anatomical location, and sun exposure. Somatic mutation patterns vary across melanoma subtypes, although most studies 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 patterns, 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. Currently, researchers are conducting pilot investigations testing different approaches for single-nucleus RNA sequencing and oligo cell DNA sequencing from frozen specimens of normal skin, nevi, dysplastic nevi, and melanoma from the same patients. Results from the pilot investigations will inform the design and approach of the full-scale study.
Molecular landscape and etiology of acral lentiginous melanoma
Contact: Maria Teresa Landi, Carlos Castaneda, Alehandro Ruiz, Ketty Peris
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 genome-wide association study from the Consortium has shown that ALM is not linked with pigmentation genes. The MelaNostrum Consortium includes populations with relatively darker pigmentation and a higher proportion of the ALM subtype than other fairer-skinned populations. Understanding ALM cell of origin and evolution, tumor-immune interactions relevant to prognosis, and therapeutic vulnerabilities will improve early detection and clinical outcomes. The ALM plantar location suggests a role for trauma or mechanical stress in its etiology, but this hypothesis remains untested in large studies. Subpopulations of melanocytes with anatomical site-specific enrichment have been identified, and the transcriptional signature of the volar-enriched subpopulation is retained in ALM, suggesting that it could be the ALM cell of origin. We will study ALM genomic and immune architecture across body sites, ancestry groups, and clinical features, we will also use snRNA-seq and methylation to verify whether volar melanocytes are ALM cells of origin. We will develop deep learning approaches to capture histologic features, molecular states, and spatial tumor-TME interfaces. The long-term goal is to develop biomarkers for early detection and prognostication and engage the communities to raise awareness of this tumor, especially where ALM burden is highest and CM screening is least accessible.