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Pellegrini C, Cardelli L, Ghiorzo P, Pastorino L, Potrony M, García-Casado Z, Elefanti L, Stefanaki I, Mastrangelo M, Necozione S, Aguilera P, Rodríguez-Hernández A, Di Nardo L, Rocco T, Del Regno L, Badenas C, Carrera C, Malvehy J, Requena C, Bañuls J, Stratigos AJ, Peris K, Menin C, Calista D, Nagore E, Puig S, Landi MT, Fargnoli MC. High- and intermediate-risk susceptibility variants in melanoma families from the Mediterranean area: A multicentre cohort from the MelaNostrum Consortium. J Eur Acad Dermatol Venereol 2023; 37:2498-2508. [PMID: 37611275 PMCID: PMC10842987 DOI: 10.1111/jdv.19461] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND Most of large epidemiological studies on melanoma susceptibility have been conducted on fair skinned individuals (US, Australia and Northern Europe), while Southern European populations, characterized by high UV exposure and dark-skinned individuals, are underrepresented. OBJECTIVES We report a comprehensive pooled analysis of established high- and intermediate-penetrance genetic variants and clinical characteristics of Mediterranean melanoma families from the MelaNostrum Consortium. METHODS Pooled epidemiological, clinical and genetic (CDKN2A, CDK4, ACD, BAP1, POT1, TERT, and TERF2IP and MC1R genes) retrospective data of melanoma families, collected within the MelaNostrum Consortium in Greece, Italy and Spain, were analysed. Univariate methods and multivariate logistic regression models were used to evaluate the association of variants with characteristics of families and of affected and unaffected family members. Subgroup analysis was performed for each country. RESULTS We included 839 families (1365 affected members and 2123 unaffected individuals). Pathogenic/likely pathogenic CDKN2A variants were identified in 13.8% of families. The strongest predictors of melanoma were ≥2 multiple primary melanoma cases (OR 8.1; 95% CI 3.3-19.7), >3 affected members (OR 2.6; 95% CI 1.3-5.2) and occurrence of pancreatic cancer (OR 4.8; 95% CI 2.4-9.4) in the family (AUC 0.76, 95% CI 0.71-0.82). We observed low frequency variants in POT1 (3.8%), TERF2IP (2.5%), ACD (0.8%) and BAP1 (0.3%). MC1R common variants (≥2 variants and ≥2 RHC variants) were associated with melanoma risk (OR 1.4; 95% CI 1.0-2.0 and OR 4.3; 95% CI 1.2-14.6, respectively). CONCLUSIONS Variants in known high-penetrance genes explain nearly 20% of melanoma familial aggregation in Mediterranean areas. CDKN2A melanoma predictors were identified with potential clinical relevance for cancer risk assessment.
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Affiliation(s)
- C Pellegrini
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - L Cardelli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - P Ghiorzo
- IRCCS Ospedale Policlinico San Martino, Genetica dei Tumori rari, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - L Pastorino
- IRCCS Ospedale Policlinico San Martino, Genetica dei Tumori rari, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - M Potrony
- Department of Biochemistry and Molecular Genetics, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Z García-Casado
- Laboratory of Molecular Biology, Instituto Valenciano de Oncología, València, Spain
| | - L Elefanti
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - I Stefanaki
- 1st Department of Dermatology-Venereology, Andreas Sygros Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - M Mastrangelo
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - S Necozione
- Epidemiology Unit, Department of Life, Health and Environmental Science, University of L'Aquila, L'Aquila, Italy
| | - P Aguilera
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Department of Dermatology, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | | | - L Di Nardo
- UOC Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli - IRCCS, Rome, Italy
- Dermatologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - T Rocco
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
- Dermatology Unit, Ospedale San Salvatore, L'Aquila, Italy
| | - L Del Regno
- UOC Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli - IRCCS, Rome, Italy
- Dermatologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - C Badenas
- Department of Biochemistry and Molecular Genetics, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - C Carrera
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Department of Dermatology, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - J Malvehy
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Department of Dermatology, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - C Requena
- Department of Dermatology, Instituto Valenciano de Oncología, València, Spain
| | - J Bañuls
- Department of Dermatology, Hospital General Universitario de Alicante, Alicante, Spain
| | - A J Stratigos
- 1st Department of Dermatology-Venereology, Andreas Sygros Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - K Peris
- UOC Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli - IRCCS, Rome, Italy
- Dermatologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - C Menin
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - D Calista
- Department of Dermatology, Maurizio Bufalini Hospital, Cesena, Italy
| | - E Nagore
- Department of Dermatology, Instituto Valenciano de Oncología, València, Spain
| | - S Puig
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Department of Dermatology, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - M T Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - M C Fargnoli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
- Dermatology Unit, Ospedale San Salvatore, L'Aquila, Italy
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Newell F, Johansson PA, Wilmott JS, Nones K, Lakis V, Pritchard AL, Lo SN, Rawson RV, Kazakoff SH, Colebatch AJ, Koufariotis LT, Ferguson PM, Wood S, Leonard C, Law MH, Brooks KM, Broit N, Palmer JM, Couts KL, Vergara IA, Long GV, Barbour AP, Nieweg OE, Shivalingam B, Robinson WA, Stretch JR, Spillane AJ, Saw RP, Shannon KF, Thompson JF, Mann GJ, Pearson JV, Scolyer RA, Waddell N, Hayward NK. Comparative Genomics Provides Etiologic and Biological Insight into Melanoma Subtypes. Cancer Discov 2022; 12:2856-2879. [PMID: 36098958 PMCID: PMC9716259 DOI: 10.1158/2159-8290.cd-22-0603] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/01/2022] [Accepted: 09/02/2022] [Indexed: 01/12/2023]
Abstract
Melanoma is a cancer of melanocytes, with multiple subtypes based on body site location. Cutaneous melanoma is associated with skin exposed to ultraviolet radiation; uveal melanoma occurs in the eyes; mucosal melanoma occurs in internal mucous membranes; and acral melanoma occurs on the palms, soles, and nail beds. Here, we present the largest whole-genome sequencing study of melanoma to date, with 570 tumors profiled, as well as methylation and RNA sequencing for subsets of tumors. Uveal melanoma is genomically distinct from other melanoma subtypes, harboring the lowest tumor mutation burden and with significantly mutated genes in the G-protein signaling pathway. Most cutaneous, acral, and mucosal melanomas share alterations in components of the MAPK, PI3K, p53, p16, and telomere pathways. However, the mechanism by which these pathways are activated or inactivated varies between melanoma subtypes. Additionally, we identify potential novel germline predisposition genes for some of the less common melanoma subtypes. SIGNIFICANCE This is the largest whole-genome analysis of melanoma to date, comprehensively comparing the genomics of the four major melanoma subtypes. This study highlights both similarities and differences between the subtypes, providing insights into the etiology and biology of melanoma. This article is highlighted in the In This Issue feature, p. 2711.
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Affiliation(s)
- Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Corresponding Authors: Felicity Newell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3965; E-mail: ; Richard A. Scolyer, Melanoma Institute Australia, 40 Rockland Road, Wollstonecraft, Sydney, NSW 2065, Australia. Phone: 61-2-9515-7011; E-mail: ; and Nicola Waddell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3538;
| | - Peter A. Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - James S. Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Antonia L. Pritchard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Department of Genetics and Immunology, Division of Biomedical Science, University of the Highlands and Islands, Inverness, Scotland, United Kingdom
| | - Serigne N. Lo
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Robert V. Rawson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | | | - Andrew J. Colebatch
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | | | - Peter M. Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Matthew H. Law
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kelly M. Brooks
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Natasa Broit
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,Q-Gen Cell Therapeutics, Brisbane, Queensland, Australia
| | - Jane M. Palmer
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kasey L. Couts
- Center for Rare Melanomas, University of Colorado Cancer Center, Aurora, Colorado
| | - Ismael A. Vergara
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Georgina V. Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Andrew P. Barbour
- Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Omgo E. Nieweg
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Brindha Shivalingam
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Department of Neurosurgery, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia.,Department of Neurosurgery, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - William A. Robinson
- Center for Rare Melanomas, University of Colorado Cancer Center, Aurora, Colorado
| | - Jonathan R. Stretch
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Andrew J. Spillane
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Robyn P.M. Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Kerwin F. Shannon
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - John F. Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Graham J. Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - John V. Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia.,Corresponding Authors: Felicity Newell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3965; E-mail: ; Richard A. Scolyer, Melanoma Institute Australia, 40 Rockland Road, Wollstonecraft, Sydney, NSW 2065, Australia. Phone: 61-2-9515-7011; E-mail: ; and Nicola Waddell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3538;
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Corresponding Authors: Felicity Newell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3965; E-mail: ; Richard A. Scolyer, Melanoma Institute Australia, 40 Rockland Road, Wollstonecraft, Sydney, NSW 2065, Australia. Phone: 61-2-9515-7011; E-mail: ; and Nicola Waddell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3538;
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