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Pastorino L, Dalmasso B, Allavena E, Vanni I, Ugolini F, Baroni G, Croce M, Guadagno A, Cabiddu F, Andreotti V, Bruno W, Zoppoli G, Ferrando L, Tanda ET, Spagnolo F, Menin C, Gangemi R, Massi D, Ghiorzo P. Ataxia-Telangiectasia Mutated Loss of Heterozygosity in Melanoma. Int J Mol Sci 2022; 23:ijms232416027. [PMID: 36555667 PMCID: PMC9786167 DOI: 10.3390/ijms232416027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
ATM germline pathogenic variants were recently found enriched in high-risk melanoma patients. However, ATM loss of heterozygosity (LOH) has never been investigated in melanoma and, therefore, a causal association with melanoma development has not been established yet. The purpose of this study was to functionally characterize 13 germline ATM variants found in high-risk melanoma patients-and classified by in silico tools as pathogenic, uncertain significance, or benign-using multiple assays evaluating ATM/pATM expression and/or LOH in melanoma tissues and cell lines. We assessed ATM status by Immunohistochemistry (IHC), Western Blot, Whole-Exome Sequencing/Copy Number Variation analysis, and RNA sequencing, supported by Sanger sequencing and microsatellite analyses. For most variants, IHC results matched those obtained with in silico classification and LOH analysis. Two pathogenic variants (p.Ser1135_Lys1192del and p.Ser1993ArgfsTer23) showed LOH and complete loss of ATM activation in melanoma. Two variants of unknown significance (p.Asn358Ile and p.Asn796His) showed reduced expression and LOH, suggestive of a deleterious effect. This study, showing a classic two-hit scenario in a well-known tumor suppressor gene, supports the inclusion of melanoma in the ATM-related cancer spectrum.
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Affiliation(s)
- Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
- Genetica dei Tumori Rari, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Bruna Dalmasso
- Genetica dei Tumori Rari, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Eleonora Allavena
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
| | - Irene Vanni
- Genetica dei Tumori Rari, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Filippo Ugolini
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, 50134 Florence, Italy
| | - Gianna Baroni
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, 50134 Florence, Italy
| | - Michela Croce
- Bioterapie, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Antonio Guadagno
- Anatomia Patologica, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Francesco Cabiddu
- Anatomia Patologica, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Virginia Andreotti
- Genetica dei Tumori Rari, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - William Bruno
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
- Genetica dei Tumori Rari, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
- Clinica di Medicina Interna a Indirizzo Oncologico, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Lorenzo Ferrando
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
- Clinica di Medicina Interna a Indirizzo Oncologico, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Enrica Teresa Tanda
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
- Oncologia Medica 2, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Francesco Spagnolo
- Oncologia Medica 2, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Chiara Menin
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padua, Italy
| | - Rosaria Gangemi
- Bioterapie, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Daniela Massi
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, 50134 Florence, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
- Genetica dei Tumori Rari, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Correspondence:
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Astiazaran-Symonds E, Graham C, Kim J, Tucker MA, Ingvar C, Helgadottir H, Pastorino L, van Doorn R, Sampson JN, Zhu B, Bruno W, Queirolo P, Fornarini G, Sciallero S, Carter B, Hicks B, Hutchinson A, Jones K, Stewart DR, Chanock SJ, Freedman ND, Landi MT, Höiom V, Puig S, Gruis N, Yang XR, Ghiorzo P, Goldstein AM. Gene-Level Associations in Patients With and Without Pathogenic Germline Variants in CDKN2A and Pancreatic Cancer. JCO Precis Oncol 2022; 6:e2200145. [PMID: 36409970 PMCID: PMC10166474 DOI: 10.1200/po.22.00145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/28/2022] [Accepted: 10/03/2022] [Indexed: 11/22/2022] Open
Abstract
PURPOSE Pancreatic ductal adenocarcinoma (PDAC) is a component of familial melanoma due to germline pathogenic variants (GPVs) in CDKN2A. However, it is unclear what role this gene or other genes play in its etiology. MATERIALS AND METHODS We analyzed 189 cancer predisposition genes using parametric rare-variant association (RVA) tests and nonparametric permutation tests to identify gene-level associations in PDAC for patients with (CDKN2A+) and without (CDKN2A-) GPV. Exome sequencing was performed on 84 patients with PDAC, 47 CDKN2A+ and 37 CDKN2A-. After variant filtering, various RVA tests and permutation tests were run separately by CDKN2A status. Genes with the strongest nominal associations were evaluated in patients with PDAC from The Cancer Genome Atlas and the UK Biobank (UKB). A secondary analysis including only GPV from UKB was also performed. RESULTS In RVA tests, ERCC4 and RET showed the most compelling evidence as plausible PDAC candidate genes for CDKN2A+ patients. In contrast, the findings in CDKN2A- patients provided evidence for HMBS, EPCAM, and MRE11 as potential new candidate genes and confirmed ATM, BRCA2, and PALB2 as PDAC genes, consistent with findings in The Cancer Genome Atlas and the UKB. As expected, CDKN2A- patients were more likely to harbor GPVs from the 189 genes investigated. When including only GPVs from UKB, significant associations with PDAC were seen for ATM, BRCA2, and CDKN2A. CONCLUSION These results suggest that variants in other genes likely play a role in PDAC in all patients and that PDAC in CDKN2A+ patients has a distinct etiology from PDAC in CDKN2A- patients.
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Affiliation(s)
- Esteban Astiazaran-Symonds
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- National Human Genome Research Institute, NIH, Bethesda, MD
- Department of Medicine, College of Medicine-Tucson, University of Arizona, Tucson, AZ
| | - Cole Graham
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | | | | | - Hildur Helgadottir
- Department of Oncology Pathology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Joshua N. Sampson
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Paola Queirolo
- Melanoma Sarcoma and Rare Tumors, IEO European Institute of Oncology, Milano, Italy
| | - Giuseppe Fornarini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Stefania Sciallero
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | | | - Neal D. Freedman
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | | | - Veronica Höiom
- Department of Oncology Pathology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Susana Puig
- Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona and CIBERER, Barcelona, Spain
| | - Nelleke Gruis
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
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Bruno W, Dalmasso B, Barile M, Andreotti V, Elefanti L, Colombino M, Vanni I, Allavena E, Barbero F, Passoni E, Merelli B, Pellegrini S, Morgese F, Danesi R, Calò V, Bazan V, D'Elia AV, Molica C, Gensini F, Sala E, Uliana V, Soma PF, Genuardi M, Ballestrero A, Spagnolo F, Tanda E, Queirolo P, Mandalà M, Stanganelli I, Palmieri G, Menin C, Pastorino L, Ghiorzo P. Predictors of germline status for hereditary melanoma: 5 years of multi-gene panel testing within the Italian Melanoma Intergroup. ESMO Open 2022; 7:100525. [PMID: 35777164 PMCID: PMC9434136 DOI: 10.1016/j.esmoop.2022.100525] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/26/2022] [Accepted: 05/29/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The incidence of cutaneous melanoma is increasing in Italy, in parallel with the implementation of gene panels. Therefore, a revision of national genetic assessment criteria for hereditary melanoma may be needed. The aim of this study was to identify predictors of susceptibility variants in the largest prospective cohort of Italian high-risk melanoma cases studied to date. MATERIALS AND METHODS From 25 Italian centers, we recruited 1044 family members and germline sequenced 940 cutaneous melanoma index cases through a shared gene panel, which included the following genes: CDKN2A, CDK4, BAP1, POT1, ACD, TERF2IP, MITF and ATM. We assessed detection rate according to familial status, region of origin, number of melanomas and presence and type of non-melanoma tumors. RESULTS The overall detection rate was 9.47% (5.53% analyzing CDKN2A alone), ranging from 5.14% in sporadic multiple melanoma cases (spoMPM) with two cutaneous melanomas to 13.9% in familial cases with at least three affected members. Three or more cutaneous melanomas in spoMPM cases, pancreatic cancer and region of origin predicted germline status [odds ratio (OR) = 3.23, 3.15, 2.43, P < 0.05]. Conversely, age > 60 years was a negative independent predictor (OR = 0.13, P = 0.008), and was the age category with the lowest detection rate, especially for CDKN2A. Detection rate was 19% when cutaneous melanoma and pancreatic cancer clustered together. CONCLUSIONS Gene panel doubled the detection rate given by CDKN2A alone. National genetic testing criteria may need a revision, especially regarding age cut-off (60) in the absence of strong family history, pancreatic cancer and/or a high number of cutaneous melanomas.
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Affiliation(s)
- W Bruno
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy; University of Genoa, Department of Internal Medicine and Medical Specialties (DiMI), Genoa, Italy.
| | - B Dalmasso
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy
| | - M Barile
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy
| | - V Andreotti
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy
| | - L Elefanti
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - M Colombino
- Unit of Cancer Genetics, Institute of Genetics and Biomedical Research of the National Research Council (IRGB-CNR), Sassari, Italy
| | - I Vanni
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy; University of Genoa, Department of Internal Medicine and Medical Specialties (DiMI), Genoa, Italy
| | - E Allavena
- University of Genoa, Department of Internal Medicine and Medical Specialties (DiMI), Genoa, Italy
| | - F Barbero
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy
| | - E Passoni
- Dermatology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - B Merelli
- Oncology Unit, ASST Papa Giovanni XXIIII, Bergamo, Italy
| | - S Pellegrini
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy; Department of Surgery, Oncology and Gastroenterology (DISCOG), University of Padua, Padua, Italy
| | - F Morgese
- Oncology Unit, AOU Ospedali Riuniti di Ancona, Ancona, Italy
| | - R Danesi
- Romagna Cancer Registry, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - V Calò
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - V Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, Palermo, Italy
| | - A V D'Elia
- Institute of Medical Genetics, ASUFC University Hospital of Udine, Udine, Italy
| | - C Molica
- Medical Oncology Unit, S. Maria della Misericordia Hospital, Perugia, Italy
| | - F Gensini
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', University of Florence, Florence, Italy
| | - E Sala
- Cytogenetics and Medical Genetics Unit, H San Gerardo ASST Monza, Monza, Italy
| | - V Uliana
- Medical Genetics Unit, AOU di Parma, Parma, Italy
| | - P F Soma
- Casa di Cura Gibiino, Catania, Italy
| | - M Genuardi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Medical Genetics Unit, Rome, Italy; Università Cattolica del Sacro Cuore, Department of Life Sciences and Public Health, Rome, Italy
| | - A Ballestrero
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy; University of Genoa, Department of Internal Medicine and Medical Specialties (DiMI), Genoa, Italy
| | - F Spagnolo
- IRCCS Ospedale Policlinico San Martino, Medical Oncology 2, Genoa, Italy
| | - E Tanda
- IRCCS Ospedale Policlinico San Martino, Medical Oncology 2, Genoa, Italy
| | - P Queirolo
- Division of Medical Oncology for Melanoma, Sarcoma, and Rare Tumors, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - M Mandalà
- Medical Oncology Unit, S. Maria della Misericordia Hospital, Perugia, Italy; Department of Surgery and Medicine, University of Perugia, Perugia, Italy
| | - I Stanganelli
- Skin Cancer Unit, IRCCS IRST Istituto Scientifico Romagnolo per lo Studio dei Tumori 'Dino Amadori' (IRST) IRCCS, Meldola, Italy; Dermatologic Unit, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - G Palmieri
- Unit of Cancer Genetics, Institute of Genetics and Biomedical Research of the National Research Council (IRGB-CNR), Sassari, Italy
| | - C Menin
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - L Pastorino
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy; University of Genoa, Department of Internal Medicine and Medical Specialties (DiMI), Genoa, Italy
| | - P Ghiorzo
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy; University of Genoa, Department of Internal Medicine and Medical Specialties (DiMI), Genoa, Italy
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4
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Pellegrini C, Raimondi S, Di Nardo L, Ghiorzo P, Menin C, Manganoni MA, Palmieri G, Guida G, Quaglino P, Stanganelli I, Massi D, Pastorino L, Elefanti L, Tosti G, Queirolo P, Leva A, Maurichi A, Rodolfo M, Fargnoli MC. Melanoma in children and adolescents: analysis of susceptibility genes in 123 Italian patients. J Eur Acad Dermatol Venereol 2021; 36:213-221. [PMID: 34664323 DOI: 10.1111/jdv.17735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/02/2021] [Indexed: 01/12/2023]
Abstract
BACKGROUND A polygenic inheritance involving high, medium and low penetrance genes has been suggested for melanoma susceptibility in adults, but genetic information is scarce for paediatric patients. OBJECTIVE We aim to analyse the major high and intermediate melanoma risk genes, CDKN2A, CDK4, POT1, MITF and MC1R, in a large multicentre cohort of Italian children and adolescents in order to explore the genetic context of paediatric melanoma and to reveal potential differences in heritability between children and adolescents. METHODS One-hundred-twenty-three patients (<21 years) from nine Italian centres were analysed for the CDKN2A, CDK4, POT1, MITF, and MC1R melanoma predisposing genes. The rate of gene variants was compared between sporadic, familial and multiple melanoma patients and between children and adolescents, and their association with clinico-pathological characteristics was evaluated. RESULTS Most patients carried MC1R variants (67%), while CDKN2A pathogenic variants were found in 9% of the cases, the MITF E318K in 2% of patients and none carried CDK4 or the POT1 S270N pathogenic variant. Sporadic melanoma patients significantly differed from familial and multiple cases for the young age at diagnosis, infrequent red hair colour, low number of nevi, low frequency of CDKN2A pathogenic variants and of the MC1R R160W variant. Melanoma in children (≤12 years) had more frequently spitzoid histotype, were located on the head/neck and upper limbs and had higher Breslow thickness. The MC1R V92M variant was more common in children than in adolescents. CDKN2A common polymorphisms and MC1R variants were associated with a high number of nevi. CONCLUSION Our results confirm the scarce involvement of the major high-risk susceptibility genes in paediatric melanoma and suggest the implication of MC1R gene variants especially in the children population.
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Affiliation(s)
- C Pellegrini
- Dermatology, Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - S Raimondi
- Molecular and Pharmaco-Epidemiology Unit, Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - L Di Nardo
- Dermatology, Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.,Dermatology, Department of Translational Medicine and Surgery, Catholic University of Rome, Italy
| | - P Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, and Department of Internal Medicine and Medical Specialties, University of Genoa, Italy
| | - C Menin
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - M A Manganoni
- Department of Dermatology, Spedali Civili di Brescia, University of Brescia, Brescia, Italy
| | - G Palmieri
- Unit of Cancer Genetics, Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Sassari, Italy
| | - G Guida
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari 'A. Moro', Bari, Italy
| | - P Quaglino
- Dermatologic Clinic, Department of Medical Sciences, University of Torino, Turin, Italy
| | - I Stanganelli
- Skin Cancer Unit, IRCCS-IRST Scientific Institute of Romagna for the Study and Treatment of Cancer, Meldola and University of Parma, Parma, Italy
| | - D Massi
- Department of Health Sciences, University of Florence, Florence, Italy
| | - L Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, and Department of Internal Medicine and Medical Specialties, University of Genoa, Italy
| | - L Elefanti
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - G Tosti
- Division of Melanoma, Sarcoma and Rare Cancer, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - P Queirolo
- Division of Melanoma, Sarcoma and Rare Cancer, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - A Leva
- Melanoma and Sarcoma Unit, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - A Maurichi
- Melanoma and Sarcoma Unit, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M Rodolfo
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M C Fargnoli
- Dermatology, Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
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5
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Yang R, Wang Z, Li J, Pi X, Gao R, Ma J, Qing Y, Zhou S. The Identification of the Metabolism Subtypes of Skin Cutaneous Melanoma Associated With the Tumor Microenvironment and the Immunotherapy. Front Cell Dev Biol 2021; 9:707677. [PMID: 34458265 PMCID: PMC8397464 DOI: 10.3389/fcell.2021.707677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/06/2021] [Indexed: 01/22/2023] Open
Abstract
Skin cutaneous melanoma (SKCM) is a highly aggressive and resistant cancer with immense metabolic heterogeneity. Here, we performed a comprehensive examination of the diverse metabolic signatures of SKCM based on non-negative matrix factorization (NMF) categorization, clustering SKCM into three distinct metabolic subtypes (C1, C2, and C3). Next, we evaluated the metadata sets of the metabolic signatures, prognostic values, transcriptomic features, tumor microenvironment signatures, immune infiltration, clinical features, drug sensitivity, and immunotherapy response of the subtypes and compared them with those of prior publications for classification. Subtype C1 was associated with high metabolic activity, low immune scores, and poor prognosis. Subtype C2 displayed low metabolic activity, high immune infiltration, high stromal score, and high expression of immune checkpoints, demonstrating the drug sensitivity to PD-1 inhibitors. The C3 subtype manifested moderate metabolic activity, high enrichment in carcinogenesis-relevant pathways, high levels of CpG island methylator phenotype (CIMP), and poor prognosis. Eventually, a 90-gene classifier was produced to implement the SKCM taxonomy and execute a consistency test in different cohorts to validate its reliability. Preliminary validation was performed to ascertain the role of SLC7A4 in SKCM. These results indicated that the 90-gene signature can be replicated to stably identify the metabolic classification of SKCM. In this study, a novel SKCM classification approach based on metabolic gene expression profiles was established to further understand the metabolic diversity of SKCM and provide guidance on precisely targeted therapy to patients with the disease.
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Affiliation(s)
- Ronghua Yang
- Department of Burn Surgery and Skin Regeneration, The First People's Hospital of Foshan, Foshan, China
| | - Zhengguang Wang
- Department of Orthopedics, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jiehua Li
- Department of Dermatology, The First People's Hospital of Foshan, Foshan, China
| | - Xiaobing Pi
- Department of Dermatology, The First People's Hospital of Foshan, Foshan, China
| | - Runxing Gao
- Department of Anesthesiology, The First People's Hospital of Foshan, Foshan, China
| | - Jun Ma
- Department of Burns, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yi Qing
- Department of Oncology, Affiliated Hospital of Chengdu University, Chengdu, China
| | - Sitong Zhou
- Department of Dermatology, The First People's Hospital of Foshan, Foshan, China
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Chan SH, Chiang J, Ngeow J. CDKN2A germline alterations and the relevance of genotype-phenotype associations in cancer predisposition. Hered Cancer Clin Pract 2021; 19:21. [PMID: 33766116 PMCID: PMC7992806 DOI: 10.1186/s13053-021-00178-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023] Open
Abstract
Although CDKN2A is well-known as a susceptibility gene for melanoma and pancreatic cancer, germline variants have also been anecdotally associated with a broader range of neoplasms including neural system tumors, head and neck squamous cell carcinomas, breast carcinomas, as well as sarcomas. The CDKN2A gene encodes for two distinct tumor suppressor proteins, p16INK4A and p14ARF, however, the independent association of germline alterations affecting these two proteins with cancer is under-appreciated. Here, we reviewed CDKN2A germline alterations reported among individuals and families with cancer in the literature, specifically addressing the cancer phenotypes in relation to the molecular consequence on p16INK4A and p14ARF. While melanoma is observed to associate with variants affecting both p16INK4A and p14ARF transcripts, it is noted that variants affecting p14ARF are more frequently observed with a heterogenous range of cancers. Finally, we reflected on the implications of this inferred genotype-phenotype association in clinical practice and proposed that clinical management of CDKN2A germline variant carriers should involve dedicated cancer genetics services, with multidisciplinary input from various healthcare professionals.
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Affiliation(s)
- Sock Hoai Chan
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Jianbang Chiang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore.
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, 308232, Singapore.
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Avitabile M, Succoio M, Testori A, Cardinale A, Vaksman Z, Lasorsa VA, Cantalupo S, Esposito M, Cimmino F, Montella A, Formicola D, Koster J, Andreotti V, Ghiorzo P, Romano MF, Staibano S, Scalvenzi M, Ayala F, Hakonarson H, Corrias MV, Devoto M, Law MH, Iles MM, Brown K, Diskin S, Zambrano N, Iolascon A, Capasso M. Neural crest-derived tumor neuroblastoma and melanoma share 1p13.2 as susceptibility locus that shows a long-range interaction with the SLC16A1 gene. Carcinogenesis 2020; 41:284-295. [PMID: 31605138 PMCID: PMC7346310 DOI: 10.1093/carcin/bgz153] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 08/28/2019] [Accepted: 09/04/2019] [Indexed: 12/27/2022] Open
Abstract
Neuroblastoma (NB) and malignant cutaneous melanoma (CMM) are neural crest cells (NCC)-derived tumors and may have a shared genetic basis, but this has not been investigated systematically by genome-wide association studies (GWAS). We took a three-staged approach to conduct cross-disease meta-analysis of GWAS for NB and CMM (2101 NB cases and 4202 controls; 12 874 CMM cases and 23 203 controls) to identify shared loci. Findings were replicated in 1403 NB cases and 1403 controls of European ancestry and in 636 NB, 508 CMM cases and 2066 controls of Italian origin. We found a cross-association at locus 1p13.2 (rs2153977, odds ratio = 0.91, P = 5.36 × 10-8). We also detected a suggestive (P < 10-7) NB-CMM cross-association at 2q37.1 with opposite effect on cancer risk. Pathway analysis of 110 NB-CMM risk loci with P < 10-4 demonstrated enrichment of biological processes such as cell migration, cell cycle, metabolism and immune response, which are essential of human NCC development, underlying both tumors. In vitro and in silico analyses indicated that the rs2153977-T protective allele, located in an NB and CMM enhancer, decreased expression of SLC16A1 via long-range loop formation and altered a T-box protein binding site. Upon depletion of SLC16A1, we observed a decrease of cellular proliferation and invasion in both NB and CMM cell lines, suggesting its role as oncogene. This is the largest study to date examining pleiotropy across two NC cell-derived tumors identifying 1p13.2 as common susceptibility locus for NB and CMM risk. We demonstrate that combining genome-wide association studies results across cancers with same origins can identify new loci common to neuroblastoma and melanoma arising from tissues which originate from neural crest cells. Our results also show 1p13.2 confer risk to neuroblastoma and melanoma by regulating SLC16A1.
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Affiliation(s)
- Marianna Avitabile
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | | | - Alessandro Testori
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Antonella Cardinale
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Zalman Vaksman
- Division of Oncology and Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vito Alessandro Lasorsa
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | | | - Matteo Esposito
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | | | | | | | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, Meibergdreef, Amsterdam, The Netherlands
| | - Virginia Andreotti
- Dipartimento di Medicina Oncologica Integrata, Università degli Studi di Genova,Genova, Italy
| | - Paola Ghiorzo
- Dipartimento di Medicina Oncologica Integrata, Università degli Studi di Genova,Genova, Italy
| | - Maria Fiammetta Romano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Stefania Staibano
- Dipartimento di Scienze Biomediche Avanzate, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Massimiliano Scalvenzi
- Dipartimento di Medicina clinica e Chirurgia, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Fabrizio Ayala
- National Cancer Institute, ‘Fondazione G. Pascale’-IRCCS, Naples, Italy
| | - Hakon Hakonarson
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Marcella Devoto
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Translational and Precision Medicine, University of Rome Sapienza, Rome, Italy
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute Brisbane, Queensland, Australia
| | - Mark M Iles
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Kevin Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharon Diskin
- Division of Oncology and Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicola Zambrano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
- IRCCS SDN, Naples, Italy
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Insights into Genetic Susceptibility to Melanoma by Gene Panel Testing: Potential Pathogenic Variants in ACD, ATM, BAP1, and POT1. Cancers (Basel) 2020; 12:cancers12041007. [PMID: 32325837 PMCID: PMC7226507 DOI: 10.3390/cancers12041007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/20/2022] Open
Abstract
The contribution of recently established or candidate susceptibility genes to melanoma missing heritability has yet to be determined. Multigene panel testing could increase diagnostic yield and better define the role of candidate genes. We characterized 273 CDKN2A/ARF and CDK4-negative probands through a custom-designed targeted gene panel that included CDKN2A/ARF, CDK4, ACD, BAP1, MITF, POT1, TERF2IP, ATM, and PALB2. Co-segregation, loss of heterozygosity (LOH)/protein expression analysis, and splicing characterization were performed to improve variant classification. We identified 16 (5.9%) pathogenic and likely pathogenic variants in established high/medium penetrance cutaneous melanoma susceptibility genes (BAP1, POT1, ACD, MITF, and TERF2IP), including two novel variants in BAP1 and 4 in POT1. We also found four deleterious and five likely deleterious variants in ATM (3.3%). Thus, including potentially deleterious variants in ATM increased the diagnostic yield to about 9%. Inclusion of rare variants of uncertain significance would increase the overall detection yield to 14%. At least 10% of melanoma missing heritability may be explained through panel testing in our population. To our knowledge, this is the highest frequency of putative ATM deleterious variants reported in melanoma families, suggesting a possible role in melanoma susceptibility, which needs further investigation.
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Ciccarese G, Dalmasso B, Bruno W, Queirolo P, Pastorino L, Andreotti V, Spagnolo F, Tanda E, Ponti G, Massone C, Drago F, Parodi A, Ghigliotti G, Pizzichetta MA, Ghiorzo P. Clinical, pathological and dermoscopic phenotype of MITF p.E318K carrier cutaneous melanoma patients. J Transl Med 2020; 18:78. [PMID: 32054529 PMCID: PMC7017513 DOI: 10.1186/s12967-020-02253-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 01/31/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The p.E318K variant of the Melanocyte Inducing Transcription Factor (MITF) has been implicated in genetic predisposition to melanoma as an intermediate penetrance allele. However, the impact of this variant on clinico-phenotypic, as well as on dermoscopic patterns features of affected patients is not entirely defined. The purpose of our study was to assess the association between the p.E318K germline variant and clinic-phenotypical features of MITF+ compared to non-carriers (MITF-), including dermoscopic findings of melanomas and dysplastic nevi. METHODS we retrospectively analyzed a consecutive series of 1386 patients recruited between 2000 and 2017 who underwent genetic testing for CDKN2A, CDK4, MC1R and MITF germline variants in our laboratory for diagnostic/research purposes. The patients were probands of melanoma-prone families and apparently sporadic single or multiple primary melanoma patients. For all, we collected clinical, pathological information and dermoscopic images of the histopathologically diagnosed melanomas and dysplastic nevi, when available. RESULTS After excluding patients positive for CDKN2A/CDK4 pathogenic variants and those affected by non-cutaneous melanomas, our study cohort comprised 984 cutaneous melanoma patients, 22 MITF+ and 962 MITF-. MITF+ were more likely to develop dysplastic nevi and multiple primary melanomas. Nodular melanoma was more common in MITF+ patients (32% compared to 19% in MITF-). MITF+ patients showed more frequently dysplastic nevi and melanomas with uncommon dermoscopic patterns (unspecific), as opposed to MITF- patients, whose most prevalent pattern was the multicomponent. CONCLUSIONS MITF+ patients tend to develop melanomas and dysplastic nevi with histopathological features, frequency and dermoscopic patterns often different from those prevalent in MITF- patients. Our results emphasize the importance of melanoma prevention programs for MITF+ patients, including dermatologic surveillance with digital follow-up.
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Affiliation(s)
- Giulia Ciccarese
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy.,Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
| | - Bruna Dalmasso
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy.,Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
| | - William Bruno
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy. .,Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy.
| | - Paola Queirolo
- IRCCS Ospedale Policlinico San Martino, Medical Oncology 2, Genoa, Italy
| | - Lorenza Pastorino
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy.,Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
| | - Virginia Andreotti
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy.,Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
| | - Francesco Spagnolo
- IRCCS Ospedale Policlinico San Martino, Medical Oncology 2, Genoa, Italy
| | - Enrica Tanda
- IRCCS Ospedale Policlinico San Martino, Medical Oncology 2, Genoa, Italy
| | - Giovanni Ponti
- Department of Diagnostic and Clinical Medicine and Public Health, Division of Clinical Pathology, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Francesco Drago
- Department of Health Sciences (Di.S.Sal.), University of Genoa, Genoa, Italy.,IRCCS Ospedale Policlinico San Martino, Section of Dermatology, Genoa, Italy
| | - Aurora Parodi
- Department of Health Sciences (Di.S.Sal.), University of Genoa, Genoa, Italy.,IRCCS Ospedale Policlinico San Martino, Section of Dermatology, Genoa, Italy
| | - Giovanni Ghigliotti
- IRCCS Ospedale Policlinico San Martino, Section of Dermatology, Genoa, Italy
| | - Maria Antonietta Pizzichetta
- Dermatology Clinic - National Cancer Institute, Medical Oncology and Preventive Oncology Aviano, University of Trieste, Aviano, Italy
| | - Paola Ghiorzo
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy.,Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
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10
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Dalmasso B, Pastorino L, Ciccarese G, Andreotti V, Grillo F, Mastracci L, Spagnolo F, Ballestrero A, Queirolo P, Bruno W, Ghiorzo P. CDKN2A germline mutations are not associated with poor survival in an Italian cohort of melanoma patients. J Am Acad Dermatol 2018; 80:1263-1271. [PMID: 30274933 DOI: 10.1016/j.jaad.2018.07.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 07/16/2018] [Accepted: 07/19/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Cyclin dependent kinase inhibitor 2A gene (CDKN2A) germline mutations have recently been associated with poor survival in patients with melanoma. Despite the high mutation rate in our cohort (up to 10% in patients with apparently sporadic melanoma), information on the impact of CDKN2A on survival in this cohort is lacking. OBJECTIVE To investigate whether poor survival associated with CDKN2A germline mutations was confirmed in a high mutation-prevalence cohort of Italian patients with melanoma undergoing a mutation-based follow-up. METHODS A total of 1239 patients with cutaneous melanoma were tested for CDKN2A mutational status and then assigned to a follow-up scheme according not only to family history but also to CDKN2A mutational status, as follow-up intervals were more frequent for CDKN2A germline mutation-positive (MUT+) patients. From this cohort, we selected 106 MUT+ patients (with familial melanoma or apparently sporadic melanoma) and 199 CDKN2A germline mutation-negative (MUT-) patients with sporadic melanoma who were matched by age and sex and had a similar tumor stage distribution. RESULTS We found no difference in overall survival (hazard ratio, 0.85; 95% confidence interval, 0.48-1.52; P = .592,) or melanoma-specific survival (hazard ratio, 0.86; 95% confidence interval, 0.38-1.95; P = .718,) between MUT+ and MUT- patients. MUT+ patients were more likely to develop multiple melanomas and to undergo surgical excision of dysplastic nevi than were MUT- patients. LIMITATIONS Retrospective study. CONCLUSION CDKN2A mutations were not associated with survival in our cohort.
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Affiliation(s)
- Bruna Dalmasso
- Department of Internal Medicine and Medical Specialties, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Giulia Ciccarese
- Department of Internal Medicine and Medical Specialties, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Virginia Andreotti
- Department of Internal Medicine and Medical Specialties, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Federica Grillo
- Department of Surgical and Diagnostic Sciences, Pathology Unit, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Luca Mastracci
- Department of Surgical and Diagnostic Sciences, Pathology Unit, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Francesco Spagnolo
- Department of Medical Oncology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specialties, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Paola Queirolo
- Department of Medical Oncology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - William Bruno
- Department of Internal Medicine and Medical Specialties, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy.
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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11
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Bruno W, Martinuzzi C, Dalmasso B, Andreotti V, Pastorino L, Cabiddu F, Gualco M, Spagnolo F, Ballestrero A, Queirolo P, Grillo F, Mastracci L, Ghiorzo P. Combining molecular and immunohistochemical analyses of key drivers in primary melanomas: interplay between germline and somatic variations. Oncotarget 2018; 9:5691-5702. [PMID: 29464027 PMCID: PMC5814167 DOI: 10.18632/oncotarget.23204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/15/2017] [Indexed: 01/15/2023] Open
Abstract
Due to the high mutational somatic burden of Cutaneous Malignant Melanoma (CMM) a thorough profiling of the driver mutations and their interplay is necessary to explain the timing of tumorigenesis or for the identification of actionable genetic events. The aim of this study was to establish the mutation rate of some of the key drivers in melanoma tumorigenesis combining molecular analyses and/or immunohistochemistry in 93 primary CMMs from an Italian cohort also characterized for germline status, and to investigate an interplay between germline and somatic variants. BRAF mutations were present in 68% of cases, while CDKN2A germline mutations were found in 16 % and p16 loss in tissue was found in 63%. TERT promoter somatic mutations were detected in 38% of cases while the TERT -245T>C polymorphism was found in 51% of cases. NRAS mutations were found in 39% of BRAF negative or undetermined cases. NF1 was expressed in all cases analysed. MC1R variations were both considered as a dichotomous variable or scored. While a positive, although not significant association between CDKN2A germline mutations, but not MC1R variants, and BRAF somatic mutation was found, we did not observe other associations between germline and somatic events. A yet undescribed inverse correlation between TERT -245T>C polymorphism and the presence of BRAF mutation was found. It is possible to hypothesize that -245T>C polymorphism could be included in those genotypes which may influence the occurrence of BRAF mutations. Further studies are needed to investigate the role of -245T>C polymorphism as a germline predictor of BRAF somatic mutation status.
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Affiliation(s)
- William Bruno
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Claudia Martinuzzi
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Bruna Dalmasso
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Virginia Andreotti
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Marina Gualco
- Pathology Unit, Ospedale Policlinico San Martino, Genoa, Italy
| | - Francesco Spagnolo
- Department of Medical Oncology, Ospedale Policlinico San Martino, Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Paola Queirolo
- Department of Medical Oncology, Ospedale Policlinico San Martino, Genoa, Italy
| | - Federica Grillo
- Department of Surgical and Diagnostic Sciences, Pathology Unit, University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Luca Mastracci
- Department of Surgical and Diagnostic Sciences, Pathology Unit, University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
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12
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Bruno W, Andreotti V, Bisio A, Pastorino L, Fornarini G, Sciallero S, Bianchi-Scarrà G, Inga A, Ghiorzo P. Functional analysis of a CDKN2A 5'UTR germline variant associated with pancreatic cancer development. PLoS One 2017; 12:e0189123. [PMID: 29216274 PMCID: PMC5720692 DOI: 10.1371/journal.pone.0189123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/20/2017] [Indexed: 11/18/2022] Open
Abstract
CDKN2A coding region germline variants are associated with pancreatic adenocarcinoma (PC) susceptibility. Recently, we described functional germline 5’UTR CDKN2A variants from melanoma patients affecting the post-transcriptional regulation of p16INK4a mRNA that is dependent, at least in part, on an Internal Ribosome Entry Site (IRES) in the 5’UTR region. Here we describe a 5’UTR c.-201_-198delinsCTTT CDKN2A variant (frequency 0.0028 based on 350 PC patients), which seems to be private to PC, since it has never been found in public databases nor in thousands of melanoma patients tested. Functional analyses confirmed IRES activity of the 5’UTR in BX-PC3 PC cells and revealed a functional impact of the identified variant. Using gene reporter assays we observed reduced translation potential in cells treated with the mTOR inhibitor Torin1, a condition that favors the assessment of IRES activity. At the endogenous gene level we quantified allelic imbalance among polysome-associated mRNAs using a patient-derived cell line heterozygous for the c.-201_-198delinsCTTT. Overall, we conclude that this very rare private variant can be considered a potential mutation, specifically associated with PC. Our data indicate that sequencing of the entire 5'UTR of CDKN2A should be included in routine screening of PC cases with suspected inherited susceptibility.
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Affiliation(s)
- William Bruno
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Virginia Andreotti
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Alessandra Bisio
- Centre for Integrative Biology (CIBIO) and University of Trento, Trento, Italy
| | - Lorenza Pastorino
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | | | | | - Giovanna Bianchi-Scarrà
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Alberto Inga
- Centre for Integrative Biology (CIBIO) and University of Trento, Trento, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
- * E-mail:
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13
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Bruno W, Martinuzzi C, Andreotti V, Pastorino L, Spagnolo F, Dalmasso B, Cabiddu F, Gualco M, Ballestrero A, Bianchi-Scarrà G, Queirolo P, Grillo F, Mastracci L, Ghiorzo P. Heterogeneity and frequency of BRAF mutations in primary melanoma: Comparison between molecular methods and immunohistochemistry. Oncotarget 2017; 8:8069-8082. [PMID: 28039443 PMCID: PMC5352383 DOI: 10.18632/oncotarget.14094] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/24/2016] [Indexed: 11/25/2022] Open
Abstract
Finding the best technique to identify BRAF mutations with a high sensitivity and specificity is mandatory for accurate patient selection for target therapy. BRAF mutation frequency ranges from 40 to 60% depending on melanoma clinical characteristics and detection technique used.Intertumoral heterogeneity could lead to misinterpretation of BRAF mutational status; this is especially important if testing is performed on primary specimens, when metastatic lesions are unavailable.Aim of this study was to identify the best combination of methods for detecting BRAF mutations (among peptide nucleic acid - PNA-clamping real-time PCR, immunohistochemistry and capillary sequencing) and investigate BRAF mutation heterogeneity in a series of 100 primary melanomas and a subset of 25 matched metastatic samples.Overall, we obtained a BRAF mutation frequency of 62%, based on the combination of at least two techniques. Concordance between mutation status in primary and metastatic tumor was good but not complete (67%), when agreement of at least two techniques were considered. Next generation sequencing was used to quantify the threshold of detected mutant alleles in discordant samples. Combining different methods excludes that the observed heterogeneity is technique-based. We propose an algorithm for BRAF mutation testing based on agreement between immunohistochemistry and PNA; a third molecular method could be added in case of discordance of the results. Testing the primary tumor when the metastatic sample is unavailable is a good option if at least two methods of detection are used, however the presence of intertumoral heterogeneity or the occurrence of additional primaries should be carefully considered.
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Affiliation(s)
- William Bruno
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Claudia Martinuzzi
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Virginia Andreotti
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | | | - Bruna Dalmasso
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | | | - Marina Gualco
- Department of Pathology, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Giovanna Bianchi-Scarrà
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Paola Queirolo
- Department of Medical Oncology, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Federica Grillo
- Department of Surgical and Diagnostic Sciences, Pathology Unit, University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Luca Mastracci
- Department of Surgical and Diagnostic Sciences, Pathology Unit, University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
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14
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Bisio A, Latorre E, Andreotti V, Bressac-de Paillerets B, Harland M, Scarra GB, Ghiorzo P, Spitale RC, Provenzani A, Inga A. The 5'-untranslated region of p16INK4a melanoma tumor suppressor acts as a cellular IRES, controlling mRNA translation under hypoxia through YBX1 binding. Oncotarget 2016; 6:39980-94. [PMID: 26498684 PMCID: PMC4741874 DOI: 10.18632/oncotarget.5387] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/05/2015] [Indexed: 12/20/2022] Open
Abstract
CDKN2A/p16INK4a is an essential tumor suppressor gene that controls cell cycle progression and replicative senescence. It is also the main melanoma susceptibility gene. Here we report that p16INK4a 5'UTR mRNA acts as a cellular Internal Ribosome Entry Site (IRES). The potential for p16INK4a 5'UTR to drive cap-independent translation was evaluated by dual-luciferase assays using bicistronic and monocistronic vectors. Results of reporters' relative activities coupled to control analyses for actual bicistronic mRNA transcription, indicated that the wild type p16INK4a 5'UTR could stimulate cap-independent translation. Notably, hypoxic stress and the treatment with mTOR inhibitors enhanced the translation-stimulating property of p16INK4a 5'UTR. RNA immunoprecipitation performed in melanoma-derived SK-Mel-28 and in a patient-derived lymphoblastoid cell line indicated that YBX1 can bind the wild type p16INK4a mRNA increasing its translation efficiency, particularly during hypoxic stress. Modulation of YBX1 expression further supported its involvement in cap-independent translation of the wild type p16INK4a but not a c.-42T>A variant. RNA SHAPE assays revealed local flexibility changes for the c.-42T>A variant at the predicted YBX1 binding site region. Our results indicate that p16INK4a 5'UTR contains a cellular IRES that can enhance mRNA translation efficiency, in part through YBX1.
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Affiliation(s)
- Alessandra Bisio
- Laboratory of Transcriptional Networks, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Elisa Latorre
- Laboratory of Genomic Screening, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Virginia Andreotti
- Laboratory of Genetics of Rare Hereditary Cancers, DiMI, University of Genoa, Italy and IRCCS AOU San Martino-IST, Genoa, Italy
| | | | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Giovanna Bianchi Scarra
- Laboratory of Genetics of Rare Hereditary Cancers, DiMI, University of Genoa, Italy and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Paola Ghiorzo
- Laboratory of Genetics of Rare Hereditary Cancers, DiMI, University of Genoa, Italy and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Alessandro Provenzani
- Laboratory of Genomic Screening, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
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Martinuzzi C, Pastorino L, Andreotti V, Garuti A, Minuto M, Fiocca R, Bianchi-Scarrà G, Ghiorzo P, Grillo F, Mastracci L. A combination of immunohistochemistry and molecular approaches improves highly sensitive detection of BRAF mutations in papillary thyroid cancer. Endocrine 2016; 53:672-80. [PMID: 26296380 DOI: 10.1007/s12020-015-0720-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/08/2015] [Indexed: 12/19/2022]
Abstract
The optimal method for BRAF mutation detection remains to be determined despite advances in molecular detection techniques. The aim of this study was to compare, against classical Sanger sequencing, the diagnostic performance of two of the most recently developed, highly sensitive methods: BRAF V600E immunohistochemistry (IHC) and peptide nucleic-acid (PNA)-clamp qPCR. BRAF exon 15 mutations were searched in formalin-fixed paraffin-embedded tissues from 86 papillary thyroid carcinoma using the three methods. The limits of detection of Sanger sequencing in borderline or discordant cases were quantified by next generation sequencing. BRAF mutations were found in 74.4 % of cases by PNA, in 71 % of cases by IHC, and in 64 % of cases by Sanger sequencing. Complete concordance for the three methods was observed in 80 % of samples. Better concordance was observed with the combination of two methods, particularly PNA and IHC (59/64) (92 %), while the combination of PNA and Sanger was concordant in 55 cases (86 %). Sensitivity of the three methods was 99 % for PNA, 94.2 % for IHC, and 89.5 % for Sanger. Our data show that IHC could be used as a cost-effective, first-line method for BRAF V600E detection in daily practice, followed by PNA analysis in negative or uninterpretable cases, as the most efficient method. PNA-clamp quantitative PCR is highly sensitive and complementary to IHC as it also recognizes other mutations besides V600E and it is suitable for diagnostic purposes.
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Affiliation(s)
- Claudia Martinuzzi
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
- Department of Surgical Sciences (DISC), University of Genoa, Genoa, Italy
| | - Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
| | - Virginia Andreotti
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
| | - Anna Garuti
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
| | - Michele Minuto
- Department of Surgical Sciences (DISC), University of Genoa, Genoa, Italy
- Surgery 1 Unit, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Roberto Fiocca
- Department of Surgical Sciences (DISC), University of Genoa, Genoa, Italy
- Pathology Unit, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Giovanna Bianchi-Scarrà
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
- Genetics of Rare Tumors, IRCCS AOU San Martino-IST, University of Genoa, Genoa, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy.
- Genetics of Rare Tumors, IRCCS AOU San Martino-IST, University of Genoa, Genoa, Italy.
| | - Federica Grillo
- Department of Surgical Sciences (DISC), University of Genoa, Genoa, Italy
- Pathology Unit, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Luca Mastracci
- Department of Surgical Sciences (DISC), University of Genoa, Genoa, Italy
- Pathology Unit, IRCCS AOU San Martino-IST, Genoa, Italy
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16
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Bruno W, Pastorino L, Ghiorzo P, Andreotti V, Martinuzzi C, Menin C, Elefanti L, Stagni C, Vecchiato A, Rodolfo M, Maurichi A, Manoukian S, De Giorgi V, Savarese I, Gensini F, Borgognoni L, Testori A, Spadola G, Mandalà M, Imberti G, Savoia P, Astrua C, Ronco AM, Farnetti A, Tibiletti MG, Lombardo M, Palmieri G, Ayala F, Ascierto P, Ghigliotti G, Muggianu M, Spagnolo F, Picasso V, Tanda ET, Queirolo P, Bianchi-Scarrà G. Multiple primary melanomas (MPMs) and criteria for genetic assessment: MultiMEL, a multicenter study of the Italian Melanoma Intergroup. J Am Acad Dermatol 2016; 74:325-32. [PMID: 26775776 DOI: 10.1016/j.jaad.2015.09.053] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/24/2015] [Accepted: 09/29/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND Multiple primary melanoma (MPM), in concert with a positive family history, is a predictor of cyclin-dependent kinase (CDK) inhibitor 2A (CDKN2A) germline mutations. A rule regarding the presence of either 2 or 3 or more cancer events (melanoma and pancreatic cancer) in low or high melanoma incidence populations, respectively, has been established to select patients for genetic referral. OBJECTIVE We sought to determine the CDKN2A/CDK4/microphthalmia-associated transcription factor mutation rate among Italian patients with MPM to appropriately direct genetic counseling regardless of family history. METHODS In all, 587 patients with MPM and an equal number with single primary melanomas and control subjects were consecutively enrolled at the participating centers and tested for CDKN2A, CDK4, and microphthalmia-associated transcription factor. RESULTS CDKN2A germline mutations were found in 19% of patients with MPM versus 4.4% of patients with single primary melanoma. In familial MPM cases the mutation rate varied from 36.6% to 58.8%, whereas in sporadic MPM cases it varied from 8.2% to 17.6% in patients with 2 and 3 or more melanomas, respectively. The microphthalmia-associated transcription factor E318K mutation accounted for 3% of MPM cases altogether. LIMITATIONS The study was hospital based, not population based. Rare novel susceptibility genes were not tested. CONCLUSION Italian patients who developed 2 melanomas, even in situ, should be referred for genetic counseling even in the absence of family history.
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Affiliation(s)
- William Bruno
- Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy; Genetics of Rare Cancers, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Lorenza Pastorino
- Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy; Genetics of Rare Cancers, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy.
| | - Paola Ghiorzo
- Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy; Genetics of Rare Cancers, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Virginia Andreotti
- Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy
| | - Claudia Martinuzzi
- Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy; Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, Istituto Oncologico Veneto (IOV)-IRCCS, Padua, Italy
| | - Lisa Elefanti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, Istituto Oncologico Veneto (IOV)-IRCCS, Padua, Italy
| | - Camilla Stagni
- Section of Oncology and Immunology, Department of Surgery, Oncology, and Gastroenterology, University of Padua, Padua, Italy
| | - Antonella Vecchiato
- Melanoma and Soft Tissue Sarcoma Unit, Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Monica Rodolfo
- Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Andrea Maurichi
- Melanoma and Sarcoma Surgery Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Siranoush Manoukian
- Medical Genetics Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | | | - Imma Savarese
- Department of Dermatology, University of Florence, Florence, Italy
| | - Francesca Gensini
- Unit of Medical Genetics, Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Lorenzo Borgognoni
- Plastic Surgery Unit, Regional Melanoma Referral Center, Santa Maria Annunziata Hospital, Florence, Italy
| | - Alessandro Testori
- Division of Dermatoncological Surgery, European Institute of Oncology, Milan, Italy
| | - Giuseppe Spadola
- Division of Dermatoncological Surgery, European Institute of Oncology, Milan, Italy
| | - Mario Mandalà
- Medical Oncology Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | | | - Paola Savoia
- Department of Medical Sciences, Dermatology Section, University of Turin, Turin, Italy
| | - Chiara Astrua
- Department of Medical Sciences, Dermatology Section, University of Turin, Turin, Italy
| | - Anna Maria Ronco
- Dermatoncological Surgery Unit, Presidio Sanitario Gradenigo, Turin, Italy
| | | | | | | | - Giuseppe Palmieri
- Cancer Genetics Unit, Institute of Biomolecular Chemistry, National Research Council, Sassari, Italy
| | - Fabrizio Ayala
- Department of Melanoma, National Cancer Institute Pascale Foundation, Naples, Italy
| | - Paolo Ascierto
- Department of Melanoma, National Cancer Institute Pascale Foundation, Naples, Italy
| | - Giovanni Ghigliotti
- Dermatology Unit, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Marisa Muggianu
- Department of Plastic and Reconstructive Surgery, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Francesco Spagnolo
- Department of Plastic and Reconstructive Surgery, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Virginia Picasso
- Department of Medical Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria (AOU) San Martino-Istituto Nazionale dei Tumori (IST) Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Enrica Teresa Tanda
- Department of Medical Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria (AOU) San Martino-Istituto Nazionale dei Tumori (IST) Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Paola Queirolo
- Department of Medical Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria (AOU) San Martino-Istituto Nazionale dei Tumori (IST) Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Giovanna Bianchi-Scarrà
- Department of Internal Medicine, Medical Specialties and Surgical Science and Integrated Diagnostics, University of Genoa, Genoa, Italy; Genetics of Rare Cancers, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
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17
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Andreotti V, Bisio A, Bressac-de Paillerets B, Harland M, Cabaret O, Newton-Bishop J, Pastorino L, Bruno W, Bertorelli R, De Sanctis V, Provenzani A, Menin C, Fronza G, Queirolo P, Spitale RC, Bianchi-Scarrà G, Inga A, Ghiorzo P. The CDKN2A/p16(INK) (4a) 5'UTR sequence and translational regulation: impact of novel variants predisposing to melanoma. Pigment Cell Melanoma Res 2016; 29:210-21. [PMID: 26581427 DOI: 10.1111/pcmr.12444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/13/2015] [Indexed: 12/20/2022]
Abstract
Many variants of uncertain functional significance in cancer susceptibility genes lie in regulatory regions, and clarifying their association with disease risk poses significant challenges. We studied 17 germline variants (nine of which were novel) in the CDKN2A 5'UTR with independent approaches, which included mono and bicistronic reporter assays, Western blot of endogenous protein, and allelic representation after polysomal profiling to investigate their impact on CDKN2A mRNA translation regulation. Two of the novel variants (c.-27del23, c.-93-91delAGG) were classified as causal mutations (score ≥3), along with the c.-21C>T, c.-34G>T, and c.-56G>T, which had already been studied by a subset of assays. The novel c.-42T>A as well as the previously described c.-67G>C were classified as potential mutations (score 1 or 2). The remaining variants (c.-14C>T, c.-20A>G, c.-25C>T+c.-180G>A, c.-30G>A, c.-40C>T, c.-45G>A, c.-59C>G, c.-87T>A, c.-252A>T) were classified as neutral (score 0). In conclusion, we found evidence that nearly half of the variants found in this region had a negative impact on CDKN2A mRNA translation, supporting the hypothesis that 5'UTR can act as a cellular Internal Ribosome Entry Site (IRES) to modulate p16(INK) (4a) translation.
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Affiliation(s)
- Virginia Andreotti
- Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy
- Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Alessandra Bisio
- Laboratory of Transcriptional Networks, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | | | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Odile Cabaret
- Department of Biopathology and INSERM U1186, Gustave Roussy, Villejuif, France
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy
- Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy
| | - William Bruno
- Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy
- Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Roberto Bertorelli
- NGS Core Facility, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Veronica De Sanctis
- NGS Core Facility, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Alessandro Provenzani
- Laboratory of Genomic Screening, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | - Paola Queirolo
- Medical Oncology Unit, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Giovanna Bianchi-Scarrà
- Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy
- Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy
- Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy
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18
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Baker MJ, Goldstein AM, Gordon PL, Harbaugh KS, Mackley HB, Glantz MJ, Drabick JJ. An interstitial deletion within 9p21.3 and extending beyond CDKN2A predisposes to melanoma, neural system tumours and possible haematological malignancies. J Med Genet 2016; 53:721-727. [PMID: 26794401 DOI: 10.1136/jmedgenet-2015-103446] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/25/2015] [Accepted: 12/22/2015] [Indexed: 11/04/2022]
Abstract
Familial atypical multiple mole melanoma syndrome (FAMMM) is characterised by dysplastic naevi, malignant melanoma and pancreatic cancer. Given that large deletions involving CDKN2A (cyclin-dependent kinase inhibitor 2A) account for only 2% of cases, we describe a family that highlights the co-occurrence of both melanoma and neural system tumours to aid clinical recognition and propose a management strategy. A patient with multiple neurofibromas was referred with a provisional diagnosis of neurofibromatosis type 1 (NF1). Prior molecular testing, though, had failed to identify an NF1 mutation by sequencing and multiplex ligation-dependent probe amplification. His family history was significant for multiple in situ/malignant melanomas at young ages and several different cancers reminiscent of an underlying syndrome. A search of the Familial Cancer Database, FaCD Online, highlighted several families with cutaneous melanoma and nervous system tumours who were subsequently identified to have large deletions spanning CDKN2A Although sequencing of CDKN2A and TP53 failed to identify a mutation, a heterozygous CDKN2A deletion was identified by targeted array comparative genomic hybridisation (CGH). Whole-genome oligonucleotide array CGH and SNP analysis identified an interstitial deletion of at least 1.5 Mb within 9p21.3 and spanning approximately 25 genes. Identification of the underlying molecular abnormality permits predictive testing for at-risk relatives. Given the young cancer diagnoses, a surveillance regimen was developed and a clinical team organised for ongoing management so that genetic testing could be offered to both adults and minor children. Surveillance recommendations addressed cancer risks associated with FAMMM, and other cancers exhibited by this family with a large contiguous gene deletion.
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Affiliation(s)
- Maria J Baker
- Department of Medicine, Penn State Milton S. Hershey Medical Center, Penn State Hershey Cancer Institute, Hershey, Pennsylvania, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, Genetic Epidemiology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Patricia L Gordon
- Department of Pediatrics, Penn State Milton S. Hershey Medical Center, Penn State Hershey Cancer Institute, Hershey, Pennsylvania, USA
| | - Kimberly S Harbaugh
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Penn State Hershey Cancer Institute, Hershey, Pennsylvania, USA
| | - Heath B Mackley
- Department of Radiation Oncology, Penn State Milton S. Hershey Medical Center, Penn State Hershey Cancer Institute, Hershey, Pennsylvania, USA
| | - Michael J Glantz
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Penn State Hershey Cancer Institute, Hershey, Pennsylvania, USA
| | - Joseph J Drabick
- Department of Medicine, Penn State Milton S. Hershey Medical Center, Penn State Hershey Cancer Institute, Hershey, Pennsylvania, USA
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19
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Frigerio S, Disciglio V, Manoukian S, Peissel B, Della Torre G, Maurichi A, Collini P, Pasini B, Gotti G, Ferrari A, Rivoltini L, Massimino M, Rodolfo M. A large de novo 9p21.3 deletion in a girl affected by astrocytoma and multiple melanoma. BMC MEDICAL GENETICS 2014; 15:59. [PMID: 24884915 PMCID: PMC4036080 DOI: 10.1186/1471-2350-15-59] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 05/05/2014] [Indexed: 11/10/2022]
Abstract
Background Association of melanoma, neural system tumors and germ line mutations at the 9p21 region in the CDKN2A, CDKN2B and CDKN2BAS genes has been reported in a small number of families worldwide and described as a discrete syndrome in melanoma families registered as a rare disease, the melanoma–astrocytoma syndrome. Case presentation We here studied two young patients developing melanoma after radiotherapy for astrocytoma, both reporting lack of family history for melanoma or neural system tumors at genetic counselling. Patient A is a girl treated for anaplastic astrocytoma at 10 years and for multiple melanomas on the scalp associated to dysplastic nevi two years later. Her monozygotic twin sister carried dysplastic nevi and a slow growing, untreated cerebral lesion. Direct sequencing analysis showed no alterations in melanoma susceptibility genes including CDKN2A, CDK4, MC1R and MITF or in TP53. By microsatellite analysis, multiplex ligation-dependent probe amplification, and array comparative genomic hybridization a deletion including the CDKN2A, CDKN2B and CDKN2BAS gene cluster was detected in both twin sisters, encompassing a large region at 9p21.3 and occurring de novo after the loss of one paternal allele. Patient B is a boy of 7 years when treated for astrocytoma then developing melanoma associated to congenital nevi on the head 10 years later: sequencing and multiplex ligation-dependent probe amplification revealed a normal profile of the CDKN2A/CDKN2B/CDKN2BAS region. Array comparative genomic hybridization confirmed the absence of deletions at 9p21.3 and failed to reveal known pathogenic copy number variations. Conclusions By comparison with the other germ line deletions at the CDKN2A, CDKN2B and CDKN2BAS gene cluster reported in melanoma susceptible families, the deletion detected in the two sisters is peculiar for its de novo origin and for its extension, as it represents the largest constitutive deletion at 9p21.3 region identified so far. In addition, the two studied cases add to other evidence indicating association of melanoma with exposure to ionizing radiation and with second neoplasm after childhood cancer. Melanoma should be considered in the monitoring of pigmented lesions in young cancer patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Monica Rodolfo
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, Milan 20133, Italy.
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20
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KAWAGUCHI TAKUYA, YOSHIKAWA KAZUHIRO, KAWAMOTO KEIJI, YOSHIMURA KUNIKAZU, OSHIGE HIDEYUKI, ASAI AKIO. Molecular targeting of neuroblastoma with a novel p16INK4a transporter system. Int J Oncol 2014; 44:1879-85. [DOI: 10.3892/ijo.2014.2372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 02/18/2014] [Indexed: 11/05/2022] Open
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21
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Ghiorzo P, Bonelli L, Pastorino L, Bruno W, Barile M, Andreotti V, Nasti S, Battistuzzi L, Grosso M, Bianchi-Scarrà G, Queirolo P. MC1R variation and melanoma risk in relation to host/clinical and environmental factors in CDKN2A positive and negative melanoma patients. Exp Dermatol 2013; 21:718-20. [PMID: 22804906 DOI: 10.1111/j.1600-0625.2012.01549.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Host, environmental and genetic factors differently modulate cutaneous melanoma (CM) risk across populations. Currently, the main genetic risk determinants are germline mutations in the major known high-risk susceptibility genes, CDKN2A and CDK4, and variants of the low-risk gene MC1R, which is key in the pigmentation process. This case-control study aimed at investigating the influence of the main host and environmental risk factors and of MC1R variation on CM risk in 390 CDKN2A-negative and 49 CDKN2A-positive Italian individuals. Multivariate analysis showed that MC1R variation, number of nevi and childhood sunburns doubled CM risk in CDKN2A-negative individuals. In CDKN2A-positive individuals, family history of CM and presence of atypical nevi, rather than MC1R status, modified risk (20.75- and 2.83-fold, respectively). Occupational sun exposure increased CM risk (three to sixfold) in both CDKN2A-negative and CDKN2A-positive individuals, reflecting the occupational habits of the Ligurian population and the geographical position of Liguria.
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Affiliation(s)
- Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy.
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22
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Domingo-Fernandez R, Watters K, Piskareva O, Stallings RL, Bray I. The role of genetic and epigenetic alterations in neuroblastoma disease pathogenesis. Pediatr Surg Int 2013; 29:101-19. [PMID: 23274701 PMCID: PMC3557462 DOI: 10.1007/s00383-012-3239-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/12/2012] [Indexed: 12/11/2022]
Abstract
Neuroblastoma is a highly heterogeneous tumor accounting for 15 % of all pediatric cancer deaths. Clinical behavior ranges from the spontaneous regression of localized, asymptomatic tumors, as well as metastasized tumors in infants, to rapid progression and resistance to therapy. Genomic amplification of the MYCN oncogene has been used to predict outcome in neuroblastoma for over 30 years, however, recent methodological advances including miRNA and mRNA profiling, comparative genomic hybridization (array-CGH), and whole-genome sequencing have enabled the detailed analysis of the neuroblastoma genome, leading to the identification of new prognostic markers and better patient stratification. In this review, we will describe the main genetic factors responsible for these diverse clinical phenotypes in neuroblastoma, the chronology of their discovery, and the impact on patient prognosis.
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Affiliation(s)
- Raquel Domingo-Fernandez
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Karen Watters
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Olga Piskareva
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Raymond L. Stallings
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Isabella Bray
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
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Ghiorzo P, Pastorino L, Queirolo P, Bruno W, Tibiletti MG, Nasti S, Andreotti V, Paillerets BBD, Bianchi Scarrà G. Prevalence of the E318K MITF germline mutation in Italian melanoma patients: associations with histological subtypes and family cancer history. Pigment Cell Melanoma Res 2012; 26:259-62. [PMID: 23167872 DOI: 10.1111/pcmr.12047] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 11/13/2012] [Indexed: 12/20/2022]
Abstract
A French and an Australian study have recently identified a rare germline functional variant in the microphthalmia-associated transcription factor (MITF) (E318K) that predisposes to familial and sporadic melanoma and to renal cell carcinoma (RCC), showing a new link between two tumour types with different risk factors and between deregulated sumoylation and cancer. The aim of this study was to test the prevalence of the MITF E318K mutation in 667 Italian melanoma patients. We observed significant associations between histological subtypes and family cancer history. Carriers exhibited a nearly threefold higher risk of developing melanoma compared with controls. Carriers were also more likely to have developed multiple primary melanomas (6.40-fold), compared with wt patients. Carriers with a personal and/or family history of pancreatic cancer and kidney cancer had a nearly 31- and eightfold higher risk of developing melanoma compared with wt patients. Our findings further support MITF as a medium-penetrance melanoma susceptibility gene, highlight a potential association with histological subtypes and suggest that MITF may predispose to pancreatic cancer.
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Affiliation(s)
- P Ghiorzo
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy.
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24
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Bourdeaut F, Isidor B, Ferrand S, Thomas C, Moreau A, Leclair MD, David A, Pierron G, Le Caignec C, Delattre O. Homozygous PTEN deletion in neuroblastoma arising in a child with Cowden syndrome. Am J Med Genet A 2011; 155A:1763-6. [PMID: 21671387 DOI: 10.1002/ajmg.a.34066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 03/13/2011] [Indexed: 11/06/2022]
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Patra CR, Bhattacharya R, Mukhopadhyay D, Mukherjee P. Fabrication of gold nanoparticles for targeted therapy in pancreatic cancer. Adv Drug Deliv Rev 2010; 62:346-61. [PMID: 19914317 PMCID: PMC2827658 DOI: 10.1016/j.addr.2009.11.007] [Citation(s) in RCA: 238] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2009] [Accepted: 10/17/2009] [Indexed: 12/18/2022]
Abstract
The targeted delivery of a drug should result in enhanced therapeutic efficacy with low to minimal side effects. This is a widely accepted concept, but limited in application due to lack of available technologies and process of validation. Biomedical nanotechnology can play an important role in this respect. Biomedical nanotechnology is a burgeoning field with myriads of opportunities and possibilities for advancing medical science and disease treatment. Cancer nanotechnology (1-100 nm size range) is expected to change the very foundations of cancer treatment, diagnosis and detection. Nanomaterials, especially gold nanoparticles (AuNPs) have unique physico-chemical properties, such as ultra small size, large surface area to mass ratio, and high surface reactivity, presence of surface plasmon resonance (SPR) bands, biocompatibility and ease of surface functionalization. In this review, we will discuss how the unique physico-chemical properties of gold nanoparticles may be utilized for targeted drug delivery in pancreatic cancer leading to increased efficacy of traditional chemotherapeutics.
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Affiliation(s)
- Chitta Ranjan Patra
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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26
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Bisio A, Nasti S, Jordan JJ, Gargiulo S, Pastorino L, Provenzani A, Quattrone A, Queirolo P, Bianchi-Scarrà G, Ghiorzo P, Inga A. Functional analysis of CDKN2A/p16INK4a 5'-UTR variants predisposing to melanoma. Hum Mol Genet 2010; 19:1479-91. [PMID: 20093296 DOI: 10.1093/hmg/ddq022] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Germline CDKN2A mutations are observed in 20-50% of melanoma-prone families. We identified melanoma patients that were heterozygous for non-coding germline variants in the 5'-UTR of CDKN2A (c.-21C > T; c.-25C > T&c.-180G > A; c.-56G > T; c.-67G > C) and examined their impact on the p16(INK4a) 5'-UTR activity using two luciferase-based reporter vectors that differ in basal transcription level and that were transfected into the melanoma-derived WM266-4 and in the breast cancer-derived MCF7 cells. The wild-type 5'-UTR sequence, containing a reported SNP (c.-33G > C) and a known melanoma-predisposing mutation (c.-34G > T), was included as controls. Results revealed that the variants at -21 and -34 severely reduced the reporter activity. The variants at -56 and at -25&-180 exhibited a milder impact, while results with c.-67G > C were dependent on the plasmid type. Quantification of the luciferase mRNA indicated that the effects of the variants were mainly post-transcriptional. Using a bicistronic dual-luciferase reporter plasmid, we confirmed that c.-21C > T and c.-34G > T had a severe negative impact in both cell lines. We also applied a polysomal profiling technique to samples heterozygous for the 5'-UTR variants, including patient-derived lymphoblasts. Analysis of allelic imbalance indicated that in addition to the c.-21C > T variant, the c.-56T > G and c.-67G > C variants also reduced mRNA translation efficiency. Overall, our results suggest that the c.-21C > T sequence variant is a melanoma-predisposing mutation. The c.-25C > T&c.-180G > A and particularly the c.-56G > T variants showed a range of intermediate functional defects in the different assays, and were not observed in the control population. We propose that these variants should be considered as potential mutations.
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Affiliation(s)
- Alessandra Bisio
- Unit of Molecular Mutagenesis and DNA Repair, National Institute for Cancer Research IST, 16132 Genoa, Italy
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Genomic rearrangements of the CDKN2A locus are infrequent in Italian malignant melanoma families without evidence of CDKN2A/CDK4 point mutations. Melanoma Res 2009; 18:431-7. [PMID: 19011513 DOI: 10.1097/cmr.0b013e328319412f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Predisposition to familial cutaneous malignant melanoma has been associated with mutations in the CDKN2A and CDK4 genes. However, only a small subgroup of melanoma pedigrees harbour CDKN2A or CDK4 germline mutations. It is possible that other types of CDKN2A rearrangements, not detectable by routine PCR-based approaches, are involved in a fraction of melanoma cases negative for point sequence changes. In order to gain insights on the possible role of CDKN2A large deletions or duplications in melanoma susceptibility in the Italian population, we screened a series of 124 cutaneous malignant melanoma families referred to five national medical/cancer genetics centres. All probands were negative for point mutations in CDKN2A and CDK4. All samples were tested by MLPA (multiplex ligation-dependent probe amplification), and the results were confirmed by real-time quantitative PCR in a subset of 53 cases. No genomic rearrangements were detected in this series, one of the largest so far investigated. These data suggest that large deletions/duplications in the CDKN2A locus are infrequently involved in the development of familial melanoma in the Italian population. Based on these results, routine search for these rearrangements in CDKN2A- and CDK4-mutation negative melanoma families is not warranted, although it would be reasonable to pursue it in selected cases with very strong family history and/or showing linkage to 9p21.
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Abstract
Amelanotic melanoma (AM) is a rare subtype of melanoma with little or no clinically visible pigment; it is more difficult to diagnose than pigmented melanoma (PM), and has a worse prognosis. In the attempt to find a genetic explanation for the distinction between AM and PM, we conducted a case-case study, matching AM and PM patients, and testing them for germline mutations in high- (p16INK4A, p14ARF, CDK4) and low-penetrance (MC1R) melanoma susceptibility genes. Similar CDKN2A mutations were found in both sets of melanomas. A p14ARF splice germline mutation was detected for the first time in an Italian family with AM. This rare mutation, which has been described only once previously, may be involved in predisposition to the amelanotic phenotype in combination with germline MC1R variants and coordinate somatic expression of pigmentation genes and their regulators.
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Bruno W, Ghiorzo P, Battistuzzi L, Ascierto PA, Barile M, Gargiulo S, Gensini F, Gliori S, Guida M, Lombardo M, Manoukian S, Menin C, Nasti S, Origone P, Pasini B, Pastorino L, Peissel B, Pizzichetta MA, Queirolo P, Rodolfo M, Romanini A, Scaini MC, Testori A, Tibiletti MG, Turchetti D, Leachman SA, Bianchi Scarrà G. Clinical genetic testing for familial melanoma in Italy: a cooperative study. J Am Acad Dermatol 2009; 61:775-82. [PMID: 19500876 DOI: 10.1016/j.jaad.2009.03.039] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 03/02/2009] [Accepted: 03/20/2009] [Indexed: 11/27/2022]
Abstract
BACKGROUND The Italian Society of Human Genetics' (SIGU) recommendations on genetic counseling and testing for hereditary melanoma state that clinical genetic testing can be offered to Italian melanoma families with at least two affected members. OBJECTIVE In the framework of a cooperative study, we sought to establish the frequency of cyclin-dependent kinase inhibitor 2A mutations in melanoma families that underwent clinical genetic counseling and testing in accordance with the SIGU recommendations at 9 centers in different Italian regions. METHODS Cyclin-dependent kinase inhibitor 2A testing was conducted by direct sequencing and multiplex ligation-dependent probe amplification analysis in melanoma families with at least two affected members. RESULTS A total of 33% (68/204) of the families harbored cyclin-dependent kinase inhibitor 2A mutations. In the 145 families with two affected members the mutation frequency was 25%. Three novel mutations, L94P, A86T, and c.407dupG, were identified among the cases and not in 200 controls. LIMITATIONS We were unable to perform separate analyses for individual centers, as in some cases the number of families was too small. CONCLUSIONS The availability of clinical genetic testing for melanoma to families with just two affected members in the same branch is justified in Italy in terms of the likelihood of identifying a mutation.
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Affiliation(s)
- William Bruno
- Department of Oncology, Biology, and Genetics, University of Genoa, Genoa, Italy.
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Pastorino L, Bonelli L, Ghiorzo P, Queirolo P, Battistuzzi L, Balleari E, Nasti S, Gargiulo S, Gliori S, Savoia P, Abate Osella S, Bernengo MG, Bianchi Scarrà G. CDKN2A mutations and MC1R variants in Italian patients with single or multiple primary melanoma. Pigment Cell Melanoma Res 2008; 21:700-9. [DOI: 10.1111/j.1755-148x.2008.00512.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Helsing P, Nymoen DA, Ariansen S, Steine SJ, Maehle L, Aamdal S, Langmark F, Loeb M, Akslen LA, Molven A, Andresen PA. Population-based prevalence of CDKN2A and CDK4 mutations in patients with multiple primary melanomas. Genes Chromosomes Cancer 2008; 47:175-84. [PMID: 18023021 DOI: 10.1002/gcc.20518] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The presence of multiple primary cutaneous melanomas (MPM) has been advocated as guidance to identifying melanoma families. Frequencies of CDKN2A mutations in materials of sporadic MPM cases from pigmented lesion clinics vary between 8 and 15%. Patients with MPM have therefore been regarded as good candidates for CDKN2A mutational screening. We describe a population-based study where all persons in Norway diagnosed with MPM between 1953 and 2004 (n = 738 alive per April 2004) were invited to participate. Three-hundred-and-ninety patients (52.8%) responded confidentially. Mutations in CDKN2A were found in 6.9% of the respondents. Eighty-one MPM patients (20.8%) reported that they belonged to melanoma families, and 17 (21.0%) of these harboured a CDKN2A mutation, compared to 3.2% of the nonfamilial cases. The probability of finding a CDKN2A mutation increased when the patients had three or more melanomas, or a young age of onset of first melanoma. We identified five novel CDKN2A variants (Ala57Gly, Pro81Arg, Ala118Val, Leu130Val, and Arg131Pro) and four that previously have been reported in melanoma families (Glu27X, Met53Ile, Arg87Trp, and Ala127Pro). A large deletion (g.13623_23772del10150) encompassing exon 1alpha and the 5' part of exon 2 was detected in six patients with a family history of melanoma. Three patients, belonging to the same family, had the CDK4 Arg24His mutation. The frequency of CDKN2A mutations was lower than previously reported in other studies, an observation which probably is due to the population-based design of our study.
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Affiliation(s)
- Per Helsing
- Department of Dermatology, Rikshospitalet-Radiumhospitalet Medical Center, N-0027 Oslo, Norway
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Peters G. Tumor Suppression for ARFicionados: The Relative Contributions of p16INK4a and p14ARF in Melanoma. J Natl Cancer Inst 2008; 100:757-9. [DOI: 10.1093/jnci/djn156] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Ghiorzo P, Gargiulo S, Nasti S, Pastorino L, Battistuzzi L, Bruno W, Bonelli L, Taveggia P, Pugliese V, Borgonovo G, Mastracci L, Fornarini G, Romagnoli P, Iiritano E, Savarino V, Bianchi-Scarrà G. Predicting the risk of pancreatic cancer: on CDKN2A mutations in the melanoma-pancreatic cancer syndrome in Italy. J Clin Oncol 2007; 25:5336-7; author reply 5337-8. [PMID: 18024887 DOI: 10.1200/jco.2007.13.5624] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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The p.G23S CDKN2A founder mutation in high-risk melanoma families from Central Italy. Melanoma Res 2007; 17:387-92. [DOI: 10.1097/cmr.0b013e3282f1d328] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kannengiesser C, Dalle S, Leccia MT, Avril MF, Bonadona V, Chompret A, Lasset C, Leroux D, Thomas L, Lesueur F, Lenoir G, Sarasin A, Bressac-de Paillerets B. New founder germline mutations of CDKN2A in melanoma-prone families and multiple primary melanoma development in a patient receiving levodopa treatment. Genes Chromosomes Cancer 2007; 46:751-60. [PMID: 17492760 DOI: 10.1002/gcc.20461] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Germline mutations in the CDKN2A gene have been shown to predispose individuals to cutaneous malignant melanoma. Here, we describe three melanoma-prone families and one isolated patient affected by multiple melanoma who carried a tandem germline mutation of CDKN2A at the nucleotide level, [c.339G>C;c.340C>T], [p.Leu113Leu;p.Pro114Ser]. We also describe three other melanoma-prone families that carried a missense germline CDKN2A mutation, c.167G>T, p.Ser56Ile. All these families and patients resided in southeast France. We analyzed six 9p21 markers where the CDKN2A gene is located and found that carrier haplotypes for both mutations were consistent with two respective common founder ancestors. In one family, we identified two fourth-degree relatives homozygous for the Ser56Ile mutation, indicating a possible consanguinity. Furthermore, we observed that a carrier of the founder CDKN2A [p.Leu113Leu;p.Pro114Ser] mutation as well as two MC1R moderate-risk variants, [p.Arg151Cys(+)p.Arg163Gln] developed 22 primary melanomas in the three years that followed initiation of levodopa therapy for Parkinson's disease. This observation suggests that there is a need for reconsideration of the hypothesis that levodopa may play a role in melanoma development, at least when in the context of a high-risk genetic background.
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