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Bai X, Attrill GH, Gide TN, Ferguson PM, Nahar KJ, Shang P, Vergara IA, Palendira U, da Silva IP, Carlino MS, Menzies AM, Long GV, Scolyer RA, Wilmott JS, Quek C. Stroma-infiltrating T cell spatiotypes define immunotherapy outcomes in adolescent and young adult patients with melanoma. Nat Commun 2024; 15:3014. [PMID: 38589406 PMCID: PMC11002019 DOI: 10.1038/s41467-024-47301-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
The biological underpinnings of therapeutic resistance to immune checkpoint inhibitors (ICI) in adolescent and young adult (AYA) melanoma patients are incompletely understood. Here, we characterize the immunogenomic profile and spatial architecture of the tumor microenvironment (TME) in AYA (aged ≤ 30 years) and older adult (aged 31-84 years) patients with melanoma, to determine the AYA-specific features associated with ICI treatment outcomes. We identify two ICI-resistant spatiotypes in AYA patients with melanoma showing stroma-infiltrating lymphocytes (SILs) that are distinct from the adult TME. The SILhigh subtype was enriched in regulatory T cells in the peritumoral space and showed upregulated expression of immune checkpoint molecules, while the SILlow subtype showed a lack of immune activation. We establish a young immunosuppressive melanoma score that can predict ICI responsiveness in AYA patients and propose personalized therapeutic strategies for the ICI-resistant subgroups. These findings highlight the distinct immunogenomic profile of AYA patients, and individualized TME features in ICI-resistant AYA melanoma that require patient-specific treatment strategies.
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Affiliation(s)
- Xinyu Bai
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Grace H Attrill
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Tuba N Gide
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Peter M Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Royal Prince Alfred Hospital, Sydney, NSW, Australia
- NSW Health Pathology, Sydney, NSW, Australia
| | - Kazi J Nahar
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Ping Shang
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Ismael A Vergara
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Umaimainthan Palendira
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | - Ines Pires da Silva
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Westmead and Blacktown Hospitals, Sydney, NSW, Australia
| | - Matteo S Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Westmead and Blacktown Hospitals, Sydney, NSW, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Royal North Shore Hospital, Sydney, NSW, Australia
- Mater Hospital, North Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Royal North Shore Hospital, Sydney, NSW, Australia
- Mater Hospital, North Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Royal Prince Alfred Hospital, Sydney, NSW, Australia
- NSW Health Pathology, Sydney, NSW, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Camelia Quek
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.
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2
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Lee KJ, Soyer HP, Stark MS. The Skin Molecular Ecosystem Holds the Key to Nevogenesis and Melanomagenesis. J Invest Dermatol 2024; 144:456-465. [PMID: 37921715 DOI: 10.1016/j.jid.2023.09.271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/24/2023] [Accepted: 09/18/2023] [Indexed: 11/04/2023]
Abstract
Early detection of melanoma is critical to good patient outcomes, but we still know little about the mechanisms of early melanoma development. Normal epidermis has many of the sequence variants and genetic architecture disruptions found in both benign nevi, melanomas, and other skin cancers, yet continues to behave more or less normally. One hypothesis is that many melanocytes in this context are "tumor competent" but are regulated by the microenvironment provided by the surrounding keratinocytes to inhibit progress to nevi or melanoma. There is evidence of accumulating disorder in several measures of the genomic and epigenomic landscape from normal skin through nevi to melanoma that may be key to promoting nevogenesis and melanomagenesis.
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Affiliation(s)
- Katie J Lee
- Frazer Institute, the University of Queensland, Dermatology Research Centre, Queensland, Australia.
| | - H Peter Soyer
- Frazer Institute, the University of Queensland, Dermatology Research Centre, Queensland, Australia; Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Mitchell S Stark
- Frazer Institute, the University of Queensland, Dermatology Research Centre, Queensland, Australia
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3
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Mojumdar A, Granger C, Lunke M, Cobb JA. Loss of Dna2 fidelity results in decreased Exo1-mediated resection at DNA double-strand breaks. J Biol Chem 2024; 300:105708. [PMID: 38311177 PMCID: PMC10909748 DOI: 10.1016/j.jbc.2024.105708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/13/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024] Open
Abstract
A DNA double-strand break (DSB) is one of the most dangerous types of DNA damage that is repaired largely by homologous recombination or nonhomologous end-joining (NHEJ). The interplay of repair factors at the break directs which pathway is used, and a subset of these factors also function in more mutagenic alternative (alt) repair pathways. Resection is a key event in repair pathway choice and extensive resection, which is a hallmark of homologous recombination, and it is mediated by two nucleases, Exo1 and Dna2. We observed differences in resection and repair outcomes in cells harboring nuclease-dead dna2-1 compared with dna2Δ pif1-m2 that could be attributed to the level of Exo1 recovered at DSBs. Cells harboring dna2-1 showed reduced Exo1 localization, increased NHEJ, and a greater resection defect compared with cells where DNA2 was deleted. Both the resection defect and the increased rate of NHEJ in dna2-1 mutants were reversed upon deletion of KU70 or ectopic expression of Exo1. By contrast, when DNA2 was deleted, Exo1 and Ku70 recovery levels did not change; however, Nej1 increased as did the frequency of alt-end joining/microhomology-mediated end-joining repair. Our findings demonstrate that decreased Exo1 at DSBs contributed to the resection defect in cells expressing inactive Dna2 and highlight the complexity of understanding how functionally redundant factors are regulated in vivo to promote genome stability.
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Affiliation(s)
- Aditya Mojumdar
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Courtney Granger
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Martine Lunke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Jennifer A Cobb
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
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Wang Z, Luo M, Liang Q, Zhao K, Hu Y, Wang W, Feng X, Hu B, Teng J, You T, Li R, Bao Z, Pan W, Yang T, Zhang C, Li T, Dong X, Yi X, Liu B, Zhao L, Li M, Chen K, Song W, Yang J, Li MJ. Landscape of enhancer disruption and functional screen in melanoma cells. Genome Biol 2023; 24:248. [PMID: 37904237 PMCID: PMC10614365 DOI: 10.1186/s13059-023-03087-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/12/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND The high mutation rate throughout the entire melanoma genome presents a major challenge in stratifying true driver events from the background mutations. Numerous recurrent non-coding alterations, such as those in enhancers, can shape tumor evolution, thereby emphasizing the importance in systematically deciphering enhancer disruptions in melanoma. RESULTS Here, we leveraged 297 melanoma whole-genome sequencing samples to prioritize highly recurrent regions. By performing a genome-scale CRISPR interference (CRISPRi) screen on highly recurrent region-associated enhancers in melanoma cells, we identified 66 significant hits which could have tumor-suppressive roles. These functional enhancers show unique mutational patterns independent of classical significantly mutated genes in melanoma. Target gene analysis for the essential enhancers reveal many known and hidden mechanisms underlying melanoma growth. Utilizing extensive functional validation experiments, we demonstrate that a super enhancer element could modulate melanoma cell proliferation by targeting MEF2A, and another distal enhancer is able to sustain PTEN tumor-suppressive potential via long-range interactions. CONCLUSIONS Our study establishes a catalogue of crucial enhancers and their target genes in melanoma growth and progression, and illuminates the identification of novel mechanisms of dysregulation for melanoma driver genes and new therapeutic targeting strategies.
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Affiliation(s)
- Zhao Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China.
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Menghan Luo
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qian Liang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Scientific Research Center, Wenzhou Medical University, Wenzhou, China
| | - Ke Zhao
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuelin Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiangling Feng
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Bolang Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jianjin Teng
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tianyi You
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ran Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zhengkai Bao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Wenhao Pan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Tielong Yang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Chao Zhang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ting Li
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiaobao Dong
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xianfu Yi
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ben Liu
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Li Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Weihong Song
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China.
| | - Jilong Yang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Mulin Jun Li
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
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5
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Liebmann A, Admard J, Armeanu-Ebinger S, Wild H, Abele M, Gschwind A, Seibel-Kelemen O, Seitz C, Bonzheim I, Riess O, Demidov G, Sturm M, Schadeck M, Pogoda M, Bien E, Krawczyk M, Jüttner E, Mentzel T, Cesen M, Pfaff E, Kunc M, Forchhammer S, Forschner A, Leiter-Stöppke U, Eigentler TK, Schneider DT, Schroeder C, Ossowski S, Brecht IB. UV-radiation and MC1R germline mutations are risk factors for the development of conventional and spitzoid melanomas in children and adolescents. EBioMedicine 2023; 96:104797. [PMID: 37716236 PMCID: PMC10511785 DOI: 10.1016/j.ebiom.2023.104797] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/18/2023] Open
Abstract
BACKGROUND Genomic characterisation has led to an improved understanding of adult melanoma. However, the aetiology of melanoma in children is still unclear and identifying the correct diagnosis and therapeutic strategies remains challenging. METHODS Exome sequencing of matched tumour-normal pairs from 26 paediatric patients was performed to study the mutational spectrum of melanomas. The cohort was grouped into different categories: spitzoid melanoma (SM), conventional melanoma (CM), and other melanomas (OT). FINDINGS In all patients with CM (n = 10) germline variants associated with melanoma were found in low to moderate melanoma risk genes: in 8 patients MC1R variants, in 2 patients variants in MITF, PTEN and BRCA2. Somatic BRAF mutations were detected in 60% of CMs, homozygous deletions of CDKN2A in 20%, TERTp mutations in 30%. In the SM group (n = 12), 5 patients carried at least one MC1R variant; somatic BRAF mutations were detected in 8.3%, fusions in 25% of the cases. No SM showed a homozygous CDKN2A deletion nor a TERTp mutation. In 81.8% of the CM/SM cases the UV damage signatures SBS7 and/or DBS1 were detected. The patient with melanoma arising in giant congenital nevus (CNM) demonstrated the characteristic NRAS Q61K mutation. INTERPRETATION UV-radiation and MC1R germline variants are risk factors in the development of conventional and spitzoid paediatric melanomas. Paediatric CMs share genomic similarities with adult CMs while the SMs differ genetically from the CM group. Consistent genetic characterization of all paediatric melanomas will potentially lead to better subtype differentiation, treatment, and prevention in the future. FUNDING Found in Acknowledgement.
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Affiliation(s)
- Alexandra Liebmann
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Sorin Armeanu-Ebinger
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Hannah Wild
- Paediatric Hematology and Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Michael Abele
- Paediatric Hematology and Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Axel Gschwind
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Olga Seibel-Kelemen
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Christian Seitz
- Paediatric Hematology and Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Irina Bonzheim
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Malou Schadeck
- SYNLAB MVZ Human Genetics Freiburg GmbH, Freiburg, Germany
| | - Michaela Pogoda
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany; NGS Competence Center Tübingen, Tübingen, Germany
| | - Ewa Bien
- Department of Paediatrics, Hematology, Oncology, Medical University of Gdansk, Poland
| | - Malgorzata Krawczyk
- Department of Paediatrics, Hematology, Oncology, Medical University of Gdansk, Poland
| | - Eva Jüttner
- Department of Pathology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Thomas Mentzel
- Dermatohistopathology Friedrichshafen, Friedrichshafen, Germany
| | - Maja Cesen
- Department of Paediatric Haematology and Oncology, University Hospital Ljubljana, Ljubljana, Slovenia
| | - Elke Pfaff
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Michal Kunc
- Department of Pathomorphology, Medical University of Gdansk, Poland
| | - Stephan Forchhammer
- Department of Dermatology, Center for Dermatooncology, University Hospital Tübingen, Tübingen, Germany
| | - Andrea Forschner
- Department of Dermatology, Center for Dermatooncology, University Hospital Tübingen, Tübingen, Germany
| | - Ulrike Leiter-Stöppke
- Department of Dermatology, Center for Dermatooncology, University Hospital Tübingen, Tübingen, Germany
| | - Thomas K Eigentler
- Department of Dermatology, Venereology and Allergology, Charite Universitätsmedizin Berlin, Berlin, Germany
| | | | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Ines B Brecht
- Paediatric Hematology and Oncology, University Children's Hospital Tübingen, Tübingen, Germany.
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6
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Argyris PP, Naumann J, Jarvis MC, Wilkinson PE, Ho DP, Islam MN, Bhattacharyya I, Gopalakrishnan R, Li F, Koutlas IG, Giubellino A, Harris RS. Primary mucosal melanomas of the head and neck are characterised by overexpression of the DNA mutating enzyme APOBEC3B. Histopathology 2023; 82:608-621. [PMID: 36416305 PMCID: PMC10107945 DOI: 10.1111/his.14843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 11/24/2022]
Abstract
AIMS Primary head/neck mucosal melanomas (MMs) are rare and exhibit aggressive biologic behaviour and elevated mutational loads. The molecular mechanisms responsible for high genomic instability observed in head/neck MMs remain elusive. The DNA cytosine deaminase APOBEC3B (A3B) constitutes a major endogenous source of mutation in human cancer. A3B-related mutations are identified through C-to-T/-G base substitutions in 5'-TCA/T motifs. Herein, we present immunohistochemical and genomic data supportive of a role for A3B in head/neck MMs. METHODS AND RESULTS A3B protein levels were assessed in oral (n = 13) and sinonasal (n = 13) melanomas, and oral melanocytic nevi (n = 13) by immunohistochemistry using a custom rabbit α-A3B mAb (5210-87-13). Heterogeneous, selective-to-diffuse, nuclear only, A3B immunopositivity was observed in 12 of 13 (92.3%) oral melanomas (H-score range = 9-72, median = 40) and 8 of 13 (62%) sinonasal melanomas (H-score range = 1-110, median = 24). Two cases negative for A3B showed prominent cytoplasmic staining consistent with A3G. A3B protein levels were significantly higher in oral and sinonasal MMs than intraoral melanocytic nevi (P < 0.0001 and P = 0.0022, respectively), which were A3B-negative (H-score range = 1-8, median = 4). A3B levels, however, did not differ significantly between oral and sinonasal tumours (P > 0.99). NGS performed in 10 sinonasal MMs revealed missense NRAS mutations in 50% of the studied cases and one each KIT and HRAS mutations. Publicly available whole-genome sequencing (WGS) data disclosed that the number of C-to-T mutations and APOBEC3 enrichment score were markedly elevated in head/neck MMs (n = 2). CONCLUSION The above data strongly indicate a possible role for the mutagenic enzyme A3B in head/neck melanomagenesis, but not benign melanocytic neoplasms.
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Affiliation(s)
- Prokopios P Argyris
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Jordan Naumann
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Matthew C Jarvis
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Peter E Wilkinson
- Department of Diagnostic and Biological SciencesSchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Dan P Ho
- Department of Diagnostic and Biological SciencesSchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Mohammed N Islam
- Department of Oral and Maxillofacial Diagnostic SciencesUniversity of Florida College of DentistryGainesvilleFLUSA
| | - Indraneel Bhattacharyya
- Department of Oral and Maxillofacial Diagnostic SciencesUniversity of Florida College of DentistryGainesvilleFLUSA
| | - Rajaram Gopalakrishnan
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Faqian Li
- Department of Laboratory Medicine and PathologyMedical School, University of MinnesotaMinneapolisMNUSA
| | - Ioannis G Koutlas
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Alessio Giubellino
- Department of Laboratory Medicine and PathologyMedical School, University of MinnesotaMinneapolisMNUSA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
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7
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El Sharouni MA, Rawson RV, Potter AJ, Paver EC, Wilmott JS, Witkamp AJ, Sigurdsson V, van Diest PJ, Scolyer RA, Thompson JF, Lo SN, van Gils CH. Melanomas in children and adolescents: Clinicopathologic features and survival outcomes. J Am Acad Dermatol 2023; 88:609-616. [PMID: 36509217 DOI: 10.1016/j.jaad.2022.08.067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Melanomas in the first 2 decades of life are uncommon and poorly understood. OBJECTIVE To assess clinicopathologic features and survival of children (≤11 years) and adolescents (12-19 years) diagnosed with melanoma. METHODS A pooled cohort of 514 patients was analyzed (397 Dutch, 117 Australian; 62 children, 452 adolescents). Pathology reports were reevaluated to determine melanoma subtypes. Multivariable Cox models were generated for recurrence-free survival (RFS) and overall survival (OS). RESULTS Melanoma subtypes were conventional melanoma (superficial spreading, nodular, desmoplastic, and acral lentiginous), spitzoid melanoma, and melanoma associated with a congenital nevus in 428, 78, and 8 patients, respectively. Ten-year RFS was 91.5% (95% confidence interval [CI], 82.4%-100%) in children and 86.4% (95% CI, 82.7%-90.3%) in adolescents (P = .32). Ten-year OS was 100% in children and 92.7% (95% CI, 89.8%-95.8%) in adolescents (P = .09). On multivariable analysis possible only for the adolescent cohort due to the small number of children, ulceration status, and anatomic site were associated with RFS and OS, whereas age, sex, mitotic index, sentinel node status and melanoma subtype were not. Breslow thickness >4 mm was associated with worse RFS. LIMITATIONS Retrospective study. CONCLUSIONS Survival rates for children and adolescents with melanomas were high. Ulceration, head or neck location and Breslow thickness >4 mm predicted worse survival in adolescents.
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Affiliation(s)
- Mary-Ann El Sharouni
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Department of Dermatology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Robert V Rawson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Tissue Oncology and Diagnostic Pathology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
| | - Alison J Potter
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Tissue Oncology and Diagnostic Pathology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
| | - Elizabeth C Paver
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Tissue Oncology and Diagnostic Pathology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Arjen J Witkamp
- Department of Surgery, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Vigfús Sigurdsson
- Department of Dermatology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Tissue Oncology and Diagnostic Pathology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.
| | - Serigne N Lo
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Carla H van Gils
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, the Netherlands
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8
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Newell F, Johansson PA, Wilmott JS, Nones K, Lakis V, Pritchard AL, Lo SN, Rawson RV, Kazakoff SH, Colebatch AJ, Koufariotis LT, Ferguson PM, Wood S, Leonard C, Law MH, Brooks KM, Broit N, Palmer JM, Couts KL, Vergara IA, Long GV, Barbour AP, Nieweg OE, Shivalingam B, Robinson WA, Stretch JR, Spillane AJ, Saw RP, Shannon KF, Thompson JF, Mann GJ, Pearson JV, Scolyer RA, Waddell N, Hayward NK. Comparative Genomics Provides Etiologic and Biological Insight into Melanoma Subtypes. Cancer Discov 2022; 12:2856-2879. [PMID: 36098958 PMCID: PMC9716259 DOI: 10.1158/2159-8290.cd-22-0603] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/01/2022] [Accepted: 09/02/2022] [Indexed: 01/12/2023]
Abstract
Melanoma is a cancer of melanocytes, with multiple subtypes based on body site location. Cutaneous melanoma is associated with skin exposed to ultraviolet radiation; uveal melanoma occurs in the eyes; mucosal melanoma occurs in internal mucous membranes; and acral melanoma occurs on the palms, soles, and nail beds. Here, we present the largest whole-genome sequencing study of melanoma to date, with 570 tumors profiled, as well as methylation and RNA sequencing for subsets of tumors. Uveal melanoma is genomically distinct from other melanoma subtypes, harboring the lowest tumor mutation burden and with significantly mutated genes in the G-protein signaling pathway. Most cutaneous, acral, and mucosal melanomas share alterations in components of the MAPK, PI3K, p53, p16, and telomere pathways. However, the mechanism by which these pathways are activated or inactivated varies between melanoma subtypes. Additionally, we identify potential novel germline predisposition genes for some of the less common melanoma subtypes. SIGNIFICANCE This is the largest whole-genome analysis of melanoma to date, comprehensively comparing the genomics of the four major melanoma subtypes. This study highlights both similarities and differences between the subtypes, providing insights into the etiology and biology of melanoma. This article is highlighted in the In This Issue feature, p. 2711.
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Affiliation(s)
- Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Corresponding Authors: Felicity Newell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3965; E-mail: ; Richard A. Scolyer, Melanoma Institute Australia, 40 Rockland Road, Wollstonecraft, Sydney, NSW 2065, Australia. Phone: 61-2-9515-7011; E-mail: ; and Nicola Waddell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3538;
| | - Peter A. Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - James S. Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Antonia L. Pritchard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Department of Genetics and Immunology, Division of Biomedical Science, University of the Highlands and Islands, Inverness, Scotland, United Kingdom
| | - Serigne N. Lo
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Robert V. Rawson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | | | - Andrew J. Colebatch
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | | | - Peter M. Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Matthew H. Law
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kelly M. Brooks
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Natasa Broit
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,Q-Gen Cell Therapeutics, Brisbane, Queensland, Australia
| | - Jane M. Palmer
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kasey L. Couts
- Center for Rare Melanomas, University of Colorado Cancer Center, Aurora, Colorado
| | - Ismael A. Vergara
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Georgina V. Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Andrew P. Barbour
- Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Omgo E. Nieweg
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Brindha Shivalingam
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Department of Neurosurgery, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia.,Department of Neurosurgery, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - William A. Robinson
- Center for Rare Melanomas, University of Colorado Cancer Center, Aurora, Colorado
| | - Jonathan R. Stretch
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Andrew J. Spillane
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Robyn P.M. Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Kerwin F. Shannon
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - John F. Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Graham J. Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - John V. Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia.,Corresponding Authors: Felicity Newell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3965; E-mail: ; Richard A. Scolyer, Melanoma Institute Australia, 40 Rockland Road, Wollstonecraft, Sydney, NSW 2065, Australia. Phone: 61-2-9515-7011; E-mail: ; and Nicola Waddell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3538;
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Corresponding Authors: Felicity Newell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3965; E-mail: ; Richard A. Scolyer, Melanoma Institute Australia, 40 Rockland Road, Wollstonecraft, Sydney, NSW 2065, Australia. Phone: 61-2-9515-7011; E-mail: ; and Nicola Waddell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3538;
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9
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Wang X, Langevin AM, Houghton PJ, Zheng S. Genomic disparities between cancers in adolescent and young adults and in older adults. Nat Commun 2022; 13:7223. [PMID: 36433963 PMCID: PMC9700745 DOI: 10.1038/s41467-022-34959-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022] Open
Abstract
Cancers cause significant mortality and morbidity in adolescents and young adults (AYAs), but their biological underpinnings are incompletely understood. Here, we analyze clinical and genomic disparities between AYAs and older adults (OAs) in more than 100,000 cancer patients. We find significant differences in clinical presentation between AYAs and OAs, including sex, metastasis rates, race and ethnicity, and cancer histology. In most cancer types, AYA tumors show lower mutation burden and less genome instability. Accordingly, most cancer genes show less mutations and copy number changes in AYAs, including the noncoding TERT promoter mutations. However, CTNNB1 and BRAF mutations are consistently overrepresented in AYAs across multiple cancer types. AYA tumors also exhibit more driver gene fusions that are frequently observed in pediatric cancers. We find that histology is an important contributor to genetic disparities between AYAs and OAs. Mutational signature analysis of hypermutators shows stronger endogenous mutational processes such as MMR-deficiency but weaker exogenous processes such as tobacco exposure in AYAs. Finally, we demonstrate a panoramic view of clinically actionable genetic events in AYA tumors.
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Affiliation(s)
- Xiaojing Wang
- grid.267309.90000 0001 0629 5880Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880MD Anderson Mays Cancer Center, UT Health San Antonio, San Antonio, TX USA
| | - Anne-Marie Langevin
- grid.267309.90000 0001 0629 5880MD Anderson Mays Cancer Center, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880Department of Pediatrics, UT Health San Antonio, San Antonio, TX USA
| | - Peter J. Houghton
- grid.267309.90000 0001 0629 5880Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880MD Anderson Mays Cancer Center, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880Department of Molecular Medicine, UT Health San Antonio, San Antonio, TX USA
| | - Siyuan Zheng
- grid.267309.90000 0001 0629 5880Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880MD Anderson Mays Cancer Center, UT Health San Antonio, San Antonio, TX USA
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10
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Muñoz-Barrera A, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Lorenzo-Salazar JM, González-Montelongo R, García-Olivares V, Flores C. From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research. Life (Basel) 2022; 12:1939. [PMID: 36431075 PMCID: PMC9695713 DOI: 10.3390/life12111939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Next-generation sequencing (NGS) applications have flourished in the last decade, permitting the identification of cancer driver genes and profoundly expanding the possibilities of genomic studies of cancer, including melanoma. Here we aimed to present a technical review across many of the methodological approaches brought by the use of NGS applications with a focus on assessing germline and somatic sequence variation. We provide cautionary notes and discuss key technical details involved in library preparation, the most common problems with the samples, and guidance to circumvent them. We also provide an overview of the sequence-based methods for cancer genomics, exposing the pros and cons of targeted sequencing vs. exome or whole-genome sequencing (WGS), the fundamentals of the most common commercial platforms, and a comparison of throughputs and key applications. Details of the steps and the main software involved in the bioinformatics processing of the sequencing results, from preprocessing to variant prioritization and filtering, are also provided in the context of the full spectrum of genetic variation (SNVs, indels, CNVs, structural variation, and gene fusions). Finally, we put the emphasis on selected bioinformatic pipelines behind (a) short-read WGS identification of small germline and somatic variants, (b) detection of gene fusions from transcriptomes, and (c) de novo assembly of genomes from long-read WGS data. Overall, we provide comprehensive guidance across the main methodological procedures involved in obtaining sequencing results for the most common short- and long-read NGS platforms, highlighting key applications in melanoma research.
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Affiliation(s)
- Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
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11
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Larkin KT, Nicolet D, Kelly BJ, Mrózek K, LaHaye S, Miller KE, Wijeratne S, Wheeler G, Kohlschmidt J, Blachly JS, Mims AS, Walker CJ, Oakes CC, Orwick S, Boateng I, Buss J, Heyrosa A, Desai H, Carroll AJ, Blum W, Powell BL, Kolitz JE, Moore JO, Mayer RJ, Larson RA, Stone RM, Paskett ED, Byrd JC, Mardis ER, Eisfeld AK. High early death rates, treatment resistance, and short survival of Black adolescents and young adults with AML. Blood Adv 2022; 6:5570-5581. [PMID: 35788257 PMCID: PMC9577622 DOI: 10.1182/bloodadvances.2022007544] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
Survival of patients with acute myeloid leukemia (AML) is inversely associated with age, but the impact of race on outcomes of adolescent and young adult (AYA; range, 18-39 years) patients is unknown. We compared survival of 89 non-Hispanic Black and 566 non-Hispanic White AYA patients with AML treated on frontline Cancer and Leukemia Group B/Alliance for Clinical Trials in Oncology protocols. Samples of 327 patients (50 Black and 277 White) were analyzed via targeted sequencing. Integrated genomic profiling was performed on select longitudinal samples. Black patients had worse outcomes, especially those aged 18 to 29 years, who had a higher early death rate (16% vs 3%; P=.002), lower complete remission rate (66% vs 83%; P=.01), and decreased overall survival (OS; 5-year rates: 22% vs 51%; P<.001) compared with White patients. Survival disparities persisted across cytogenetic groups: Black patients aged 18 to 29 years with non-core-binding factor (CBF)-AML had worse OS than White patients (5-year rates: 12% vs 44%; P<.001), including patients with cytogenetically normal AML (13% vs 50%; P<.003). Genetic features differed, including lower frequencies of normal karyotypes and NPM1 and biallelic CEBPA mutations, and higher frequencies of CBF rearrangements and ASXL1, BCOR, and KRAS mutations in Black patients. Integrated genomic analysis identified both known and novel somatic variants, and relative clonal stability at relapse. Reduced response rates to induction chemotherapy and leukemic clone persistence suggest a need for different treatment intensities and/or modalities in Black AYA patients with AML. Higher early death rates suggest a delay in diagnosis and treatment, calling for systematic changes to patient care.
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Affiliation(s)
- Karilyn T. Larkin
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Deedra Nicolet
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Benjamin J. Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH
| | - Krzysztof Mrózek
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH
| | - Katherine E. Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH
| | - Saranga Wijeratne
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH
| | - Gregory Wheeler
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH
| | - Jessica Kohlschmidt
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - James S. Blachly
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Alice S. Mims
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Christopher J. Walker
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Christopher C. Oakes
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Shelley Orwick
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Isaiah Boateng
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Jill Buss
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Adrienne Heyrosa
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Helee Desai
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Andrew J. Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - William Blum
- Emory University School of Medicine, Atlanta, GA
| | - Bayard L. Powell
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC
| | - Jonathan E. Kolitz
- Monter Cancer Center, Hofstra Northwell School of Medicine, Lake Success, NY
| | - Joseph O. Moore
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
| | - Robert J. Mayer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Richard M. Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Electra D. Paskett
- Division of Cancer Prevention and Control, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
- The Center for Cancer Health Equity, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - John C. Byrd
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH
| | - Elaine R. Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH
| | - Ann-Kathrin Eisfeld
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
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Eckstein OS, Allen CE, Williams PM, Roy-Chowdhuri S, Patton DR, Coffey B, Reid JM, Piao J, Saguilig L, Alonzo TA, Berg SL, Ramirez NC, Jaju A, Mhlanga J, Fox E, Hawkins DS, Mooney MM, Takebe N, Tricoli JV, Janeway KA, Seibel NL, Parsons DW. Phase II Study of Selumetinib in Children and Young Adults With Tumors Harboring Activating Mitogen-Activated Protein Kinase Pathway Genetic Alterations: Arm E of the NCI-COG Pediatric MATCH Trial. J Clin Oncol 2022; 40:2235-2245. [PMID: 35363510 PMCID: PMC9273373 DOI: 10.1200/jco.21.02840] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
PURPOSE The NCI-COG Pediatric MATCH trial assigns patients age 1-21 years with relapsed or refractory solid tumors, lymphomas, and histiocytic disorders to phase II studies of molecularly targeted therapies on the basis of detection of predefined genetic alterations. Patients with tumors harboring mutations or fusions driving activation of the mitogen-activated protein kinase (MAPK) pathway were treated with the MEK inhibitor selumetinib. METHODS Patients received selumetinib twice daily for 28-day cycles until disease progression or intolerable toxicity. The primary end point was objective response rate; secondary end points included progression-free survival and tolerability of selumetinib. RESULTS Twenty patients (median age: 14 years) were treated. All were evaluable for response and toxicities. The most frequent diagnoses were high-grade glioma (HGG; n = 7) and rhabdomyosarcoma (n = 7). Twenty-one actionable mutations were detected: hotspot mutations in KRAS (n = 8), NRAS (n = 3), and HRAS (n = 1), inactivating mutations in NF1 (n = 7), and BRAF V600E (n = 2). No objective responses were observed. Three patients had a best response of stable disease including two patients with HGG (NF1 mutation, six cycles; KRAS mutation, 12 cycles). Six-month progression-free survival was 15% (95% CI, 4 to 34). Five patients (25%) experienced a grade 3 or higher adverse event that was possibly or probably attributable to study drug. CONCLUSION A national histology-agnostic molecular screening strategy was effective at identifying children and young adults eligible for treatment with selumetinib in the first Pediatric MATCH treatment arm to be completed. MEK inhibitors have demonstrated promising responses in some pediatric tumors (eg, low-grade glioma and plexiform neurofibroma). However, selumetinib in this cohort with treatment-refractory tumors harboring MAPK alterations demonstrated limited efficacy, indicating that pathway mutation status alone is insufficient to predict response to selumetinib monotherapy for pediatric cancers.
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Affiliation(s)
- Olive S. Eckstein
- Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX
| | - Carl E. Allen
- Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX,Carl E. Allen, MD, PhD, Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, 1102 Bates Ave, Suite 1025, Houston, TX 77030; e-mail:
| | | | | | - David R. Patton
- Center for Biomedical Informatics and Information Technology, NCI, NIH, Bethesda, MD
| | - Brent Coffey
- Center for Biomedical Informatics and Information Technology, NCI, NIH, Bethesda, MD
| | | | - Jin Piao
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | - Todd A. Alonzo
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Stacey L. Berg
- Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX
| | - Nilsa C. Ramirez
- Biopathology Center, Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Alok Jaju
- Ann and Robert H. Lurie Children's Hospital, Chicago, IL
| | - Joyce Mhlanga
- Washington University School of Medicine, St Louis, MO
| | | | | | - Margaret M. Mooney
- Division of Cancer Treatment and Diagnosis, Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD
| | - Naoko Takebe
- Division of Cancer Treatment and Diagnosis, Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD
| | - James V. Tricoli
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| | | | - Nita L. Seibel
- Division of Cancer Treatment and Diagnosis, Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD
| | - D. Williams Parsons
- Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX
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Xu H, Gao K, Liu Q, Wang T, Zhang Z, Cai L, Wu Y, Jiang Y. Brain Somatic Variant in Ras-Like Small GTPase RALA Causes Focal Cortical Dysplasia Type II. Front Behav Neurosci 2022; 16:919485. [PMID: 35846790 PMCID: PMC9280360 DOI: 10.3389/fnbeh.2022.919485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/03/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose In our group’s previous study, we performed deep whole-exome sequencing and targeted amplicon sequencing in the postoperative brain tissue of epilepsy patients with focal cortical dysplasia type II (FCD II). We identified the first somatic variant of RALA in the brain tissue of a child with FCD type IIb. RALA encodes a small GTPase of the Ras superfamily. To date, the role of RALA in brain development is not yet known. In this study, we reported that the RALA somatic variant led to FCD type II through activation of the mammalian target of rapamycin (mTOR) pathways. Materials and Methods HEK293T cells were transfected in vitro to analyze the expression of the RalA protein, as well as phosphorylated S6 (P-S6), one of the major markers of mTOR pathway activation, RalA GTPase activity, and the interaction between RalA and its downstream binding effectors. In vivo, wild-type, and mutant RALA plasmids were transfected into the local cortex of mice using in utero electroporation to evaluate the effect of RALA c.G482A on neuronal migration. Results The RALA c.G482A mutation increased RalA protein expression, the abnormal activation of the mTOR pathways, RalA GTPase activity, and binding to downstream effectors. RALA c.G482A local transfection in the embryonic brain in utero induced abnormal cortical neuron migration in mice. Conclusion This study demonstrated for the first time that the somatic gain-of-function variant of RALA activates the mTOR pathway and leads to neuronal migration disorders in the brain, facilitating the development of FCD II. Therefore, RALA brain somatic mutation may be one of the pathogenic mechanisms leading to FCD II, which is always related to drug-resistant epilepsy in children. However, more somatic variations of this gene are required to be confirmed in more FCD II patient brain samples.
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Affiliation(s)
- Han Xu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Kai Gao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Qingzhu Liu
- Children Epilepsy Center, Peking University First Hospital, Beijing, China
| | - Tianshuang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Zhongbin Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Lixin Cai
- Children Epilepsy Center, Peking University First Hospital, Beijing, China
| | - Ye Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
- Children Epilepsy Center, Peking University First Hospital, Beijing, China
- *Correspondence: Ye Wu,
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
- Children Epilepsy Center, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, China
- Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Peking University, Beijing, China
- Institute for Brain Disorders, Beijing, China
- Yuwu Jiang, ,
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14
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Church AJ, Moustafa D, Pinches RS, Hawryluk EB, Schmidt BAR. Genomic comparison of malignant melanoma and atypical Spitz tumor in the pediatric population. Pediatr Dermatol 2022; 39:409-419. [PMID: 35194848 DOI: 10.1111/pde.14935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND/OBJECTIVES The diagnostic distinction between atypical Spitz tumor (AST) and malignant melanoma (MM) in pediatric tumors is challenging. Molecular tests are increasingly used to characterize these neoplasms; however, limited studies are available in pediatric patients. This study aimed to provide a genomic comparison of pediatric MM and AST in the context of comprehensive clinical annotation. METHODS Pediatric patients diagnosed with MM (n=11) and AST (n=12) were compared to a cohort of 693 adult melanoma patients. DNA next-generation sequencing assessed kinase gene fusions, tumor mutational burden, sequence variants, copy number alterations, structural variants, microsatellite instability, and mutational signatures. RESULTS Seven AST cases and eight MM cases were successfully sequenced. Kinase gene fusions were identified in both the MM and AST cohorts (NTRK1, ROS1, and MET). MM cases had TERT, BRAF, and CDKN2A alterations, which were not identified in the AST cohort. Tumor mutational burden (TMB) analysis showed pediatric ASTs had an average of 2.82 mutations/Mb, pediatric MM had an average of 5.7 mutations/Mb, and adult MM cases averaged 18.8 mut/Mb. One pediatric MM case had an elevated TMB of 15 mutations/Mb and a UV mutational signature. CONCLUSIONS These data expand our understanding of pediatric malignant melanoma. The differences between the molecular signatures for AST and MM are not statistically significant, and histopathology remains the gold standard for the diagnosis of pediatric AST and MM at this time. With more data, molecular studies may provide additional support for diagnosis and targeted therapeutics.
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Affiliation(s)
- Alanna J Church
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Danna Moustafa
- Harvard Medical School, Boston, Massachusetts, USA
- Dermatology Section, Department of Immunology, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Robert Seth Pinches
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Elena B Hawryluk
- Harvard Medical School, Boston, Massachusetts, USA
- Dermatology Section, Department of Immunology, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Birgitta A R Schmidt
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
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15
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Colebatch AJ, Paver EC, Vergara IA, Thompson JF, Long GV, Wilmott JS, Scolyer RA. Elevated non-coding promoter mutations are associated with malignant transformation of melanocytic naevi to melanoma. Pathology 2022; 54:533-540. [DOI: 10.1016/j.pathol.2021.12.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/22/2021] [Accepted: 12/02/2021] [Indexed: 10/19/2022]
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16
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Krasnov GS, Ghukasyan LG, Abramov IS, Nasedkina TV. Determination of the Subclonal Tumor Structure in Childhood Acute Myeloid Leukemia and Acral Melanoma by Next-Generation Sequencing. Mol Biol 2021. [DOI: 10.1134/s0026893321040051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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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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Critical evaluation of CNA estimators for DNA data using matching confidence masks and WGS technology. Biomed Signal Process Control 2021. [DOI: 10.1016/j.bspc.2021.103004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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19
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Schiferle EB, Cheon SY, Ham S, Son HG, Messerschmidt JL, Lawrence DP, Cohen JV, Flaherty KT, Moon JJ, Lian CG, Sullivan RJ, Demehri S. Rejection of benign melanocytic nevi by nevus-resident CD4 + T cells. SCIENCE ADVANCES 2021; 7:7/26/eabg4498. [PMID: 34162549 PMCID: PMC8221625 DOI: 10.1126/sciadv.abg4498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/10/2021] [Indexed: 05/05/2023]
Abstract
Melanoma and melanocytic nevi harbor shared lineage-specific antigens and oncogenic mutations. Yet, the relationship between the immune system and melanocytic nevi is unclear. Using a patient-derived xenograft (PDX) model, we found that 81.8% of the transplanted nevi underwent spontaneous regression, while peripheral skin remained intact. Nevus-resident CD4+ T helper 1 cells, which exhibited a massive clonal expansion to melanocyte-specific antigens, were responsible for nevus rejection. Boosting regulatory T cell suppressive function with low-dose exogenous human interleukin-2 injection or treatment with a human leukocyte antigen (HLA) class II-blocking antibody prevented nevus rejection. Notably, mice with rejected nevus PDXs were protected from melanoma tumor growth. We detected a parallel CD4+ T cell-dominant immunity in clinically regressing melanocytic nevi. These findings reveal a mechanistic explanation for spontaneous nevus regression in humans and posit the activation of nevus-resident CD4+ effector T cells as a novel strategy for melanoma immunoprevention and treatment.
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Affiliation(s)
- Erik B Schiferle
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology, Center for Cancer Research, Massachusetts General Hospital Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Se Yun Cheon
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology, Center for Cancer Research, Massachusetts General Hospital Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Seokjin Ham
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong Gu, Daejeon, South Korea
| | - Heehwa G Son
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology, Center for Cancer Research, Massachusetts General Hospital Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jonathan L Messerschmidt
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology, Center for Cancer Research, Massachusetts General Hospital Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Donald P Lawrence
- Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Justine V Cohen
- Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Keith T Flaherty
- Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - James J Moon
- Center for Immunology and Inflammatory Diseases and Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Christine G Lian
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ryan J Sullivan
- Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Shadmehr Demehri
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology, Center for Cancer Research, Massachusetts General Hospital Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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20
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Avery JT, Zhang R, Boohaker RJ. GLI1: A Therapeutic Target for Cancer. Front Oncol 2021; 11:673154. [PMID: 34113570 PMCID: PMC8186314 DOI: 10.3389/fonc.2021.673154] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/30/2021] [Indexed: 12/11/2022] Open
Abstract
GLI1 is a transcriptional effector at the terminal end of the Hedgehog signaling (Hh) pathway and is tightly regulated during embryonic development and tissue patterning/differentiation. GLI1 has low-level expression in differentiated tissues, however, in certain cancers, aberrant activation of GLI1 has been linked to the promotion of numerous hallmarks of cancer, such as proliferation, survival, angiogenesis, metastasis, metabolic rewiring, and chemotherapeutic resistance. All of these are driven, in part, by GLI1’s role in regulating cell cycle, DNA replication and DNA damage repair processes. The consequences of GLI1 oncogenic activity, specifically the activity surrounding DNA damage repair proteins, such as NBS1, and cell cycle proteins, such as CDK1, can be linked to tumorigenesis and chemoresistance. Therefore, understanding the underlying mechanisms driving GLI1 dysregulation can provide prognostic and diagnostic biomarkers to identify a patient population that would derive therapeutic benefit from either direct inhibition of GLI1 or targeted therapy towards proteins downstream of GLI1 regulation.
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Affiliation(s)
- Justin T Avery
- Oncology Department, Drug Discovery Division, Southern Research, Birmingham, AL, United States
| | - Ruowen Zhang
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States
| | - Rebecca J Boohaker
- Oncology Department, Drug Discovery Division, Southern Research, Birmingham, AL, United States
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Acute Increases in Intracellular Zinc Lead to an Increased Lysosomal and Mitochondrial Autophagy and Subsequent Cell Demise in Malignant Melanoma. Int J Mol Sci 2021; 22:ijms22020667. [PMID: 33440911 PMCID: PMC7826594 DOI: 10.3390/ijms22020667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/28/2020] [Accepted: 01/06/2021] [Indexed: 02/07/2023] Open
Abstract
Changes in zinc content and dysregulated zinc homeostatic mechanisms have been recognized in several solid malignancies such as prostate cancer, breast cancer, or pancreatic cancer. Moreover, it has been shown that zinc serum and/or tissue levels are altered in melanoma with varying effects on melanoma development and biology. This study was conducted to explore the effects of acute increases of intracellular zinc in a set of melanoma tissue explants obtained from clinical samples. Measurements of their zinc content showed an extant heterogeneity in total and free intracellular zinc pools associated with varying biological behavior of individual cells, e.g., autophagy levels and propensity to cell death. Use of zinc pyrithione elevated intracellular zinc in a short time frame which resulted in marked changes in mitochondrial activity and lysosomes. These alterations were accompanied by significantly enhanced autophagy flux and subsequent cell demise in the absence of typical apoptotic cell death markers. The present results show for the first time that acutely increased intracellular zinc in melanoma cells specifically enhances their autophagic activity via mitochondria and lysosomes which leads to autophagic cell death. While biologically relevant, this discovery may contribute to our understanding and exploration of zinc in relation to autophagy as a means of controlling melanoma growth and survival.
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Toland AE. The influence of sex, age and sunlight exposure on mutational processes in melanoma. Br J Dermatol 2020; 184:197-198. [PMID: 33372289 DOI: 10.1111/bjd.19336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A E Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
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23
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Vanni I, Casula M, Pastorino L, Manca A, Dalmasso B, Andreotti V, Pisano M, Colombino M, Pfeffer U, Tanda ET, Rozzo C, Paliogiannis P, Cossu A, Ghiorzo P, Palmieri G. Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI). Diagn Pathol 2020; 15:143. [PMID: 33317587 PMCID: PMC7737361 DOI: 10.1186/s13000-020-01052-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/04/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Identification of somatic mutations in key oncogenes in melanoma is important to lead the effective and efficient use of personalized anticancer treatment. Conventional methods focus on few genes per run and, therefore, are unable to screen for multiple genes simultaneously. The use of Next-Generation Sequencing (NGS) technologies enables sequencing of multiple cancer-driving genes in a single assay, with reduced costs and DNA quantity needed and increased mutation detection sensitivity. METHODS We designed a customized IMI somatic gene panel for targeted sequencing of actionable melanoma mutations; this panel was tested on three different NGS platforms using 11 metastatic melanoma tissue samples in blinded manner between two EMQN quality certificated laboratory. RESULTS The detection limit of our assay was set-up to a Variant Allele Frequency (VAF) of 10% with a coverage of at least 200x. All somatic variants detected by all NGS platforms with a VAF ≥ 10%, were also validated by an independent method. The IMI panel achieved a very good concordance among the three NGS platforms. CONCLUSION This study demonstrated that, using the main sequencing platforms currently available in the diagnostic setting, the IMI panel can be adopted among different centers providing comparable results.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Milena Casula
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Antonella Manca
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Bruna Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Marina Pisano
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Maria Colombino
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Ulrich Pfeffer
- Tumor Epigenetics, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Carla Rozzo
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Panagiotis Paliogiannis
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Antonio Cossu
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy.
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy.
| | - Giuseppe Palmieri
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
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Incidence, Survival, and Mortality Trends of Cancers Diagnosed in Adolescents and Young Adults (15-39 Years): A Population-Based Study in The Netherlands 1990-2016. Cancers (Basel) 2020; 12:cancers12113421. [PMID: 33218178 PMCID: PMC7698904 DOI: 10.3390/cancers12113421] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Adolescents and young adults (AYAs, aged 15–39 years) with cancer form a distinct patient population within the oncology care setting that is often overlooked in favour of paediatric and older adult patients. As such, specific knowledge on AYAs and their distinct spectrum of cancers is limited. Worldwide, cancer is increasing and it is among the major causes of death among AYAs. Cancer prognosis among AYAs has also been shown to lag behind that of younger and older patients suffering from similar diseases. To address these problems, better understanding of AYA cancers is needed. This study aims to provide an overview of the specific cancer trends among AYAs and the changes that have occurred in the Netherlands since 1990 in terms of incidence, survival, and mortality. This information will provide a solid foundation from which to guide future studies upon, aimed at acquiring more detailed cancer knowledge within the AYA domain. Abstract Adolescent and young adult (AYA) cancer patients, aged 15–39 years at primary cancer diagnosis, form a distinct, understudied, and underserved group in cancer care. This study aimed to assess long-term trends in incidence, survival, and mortality of AYA cancer patients within the Netherlands. Data on all malignant AYA tumours diagnosed between 1990–2016 (n = 95,228) were obtained from the Netherlands Cancer Registry. European age-standardised incidence and mortality rates with average annual percentage change (AAPC) statistics and five-year relative survival rates were calculated. The overall cancer incidence increased from 54.6 to 70.3 per 100,000 person-years (AAPC: +1.37%) between 1990–2016, and increased for both sexes individually and for most cancer types. Five-year relative survival overall improved from 73.7% in 1990–1999 to 86.4% in 2010–2016 and improved for both sexes and most cancer types. Survival remained poor (<60%) for rhabdomyosarcoma, lung, stomach, liver, bladder, and pancreatic carcinomas, among others. Mortality rates among male AYAs overall declined from 10.8 to 6.6 (AAPC: −1.64%) and from 14.4 to 10.1 per 100,000 person-years (AAPC: −1.81%) for female AYAs since 1990. Mortality rates remained unchanged for male AYAs aged 20–24 and 25–29 years. In conclusion, over the past three decades, there has been a considerable increase in cancer incidence among AYAs in the Netherlands. Meanwhile, the survival improved and the mortality overall declined. Survival at five-years now well exceeds above 80%, but did not do so for all cancer types.
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Abstract
PURPOSE OF REVIEW To inform pediatric providers of the clinical characteristics, underlying genetic drivers, and therapeutic options for skin cancer arising in childhood and adolescence. RECENT FINDINGS The incidence of melanoma in pediatric patients has been declining in the past decades. Pediatric-specific diagnostic criteria should be utilized when assessing lesions concerning for melanoma to better account for the different presentations seen in pediatric disease compared with adults, such as an increased prevalence of amelanotic melanoma or frequent mimic of benign pediatric lesions. Pediatric melanoma often presents with a higher histopathologic stage and a higher Breslow depth as compared with adult melanoma. Pediatric nonmelanoma skin cancer including basal cell carcinoma and squamous cell carcinoma are associated with genetic conditions and immunosuppression, both iatrogenic and inherited. SUMMARY Melanoma in pediatric patients often presents differently from conventional adult melanoma, including Spitz melanoma and melanoma associated with congenital melanocytic nevi. Pediatric patients with nonmelanoma skin cancers should be evaluated for predisposing risk factors. More research on therapeutic options for pediatric skin cancer is vital to understanding the tolerance and response of our pediatric patients to therapies that are more frequently utilized in adult disease.
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Affiliation(s)
- Danna Moustafa
- Harvard Medical School, Boston, Massachusetts, USA.,Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Holly Neale
- University of Massachusetts School of Medicine, Worcester, Massachusetts, USA
| | - Elena B Hawryluk
- Harvard Medical School, Boston, Massachusetts, USA.,Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
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26
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Age Does Matter in Adolescents and Young Adults versus Older Adults with Advanced Melanoma; A National Cohort Study Comparing Tumor Characteristics, Treatment Pattern, Toxicity and Response. Cancers (Basel) 2020; 12:cancers12082072. [PMID: 32726988 PMCID: PMC7464956 DOI: 10.3390/cancers12082072] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Cutaneous melanoma is a common type of cancer in Adolescents and Young Adults (AYAs, 15–39 years of age). However, AYAs are underrepresented in clinical trials investigating new therapies and the outcomes from these therapies for AYAs are therefore unclear. Using prospectively collected nation-wide data from the Dutch Melanoma Treatment Registry (DMTR), we compared baseline characteristics, mutational profiles, treatment strategies, grade 3–4 adverse events (AEs), responses and outcomes in AYAs (n = 210) and older adults (n = 3775) who were diagnosed with advanced melanoma between July 2013 and July 2018. Compared to older adults, AYAs were more frequently female (51% versus 40%, p = 0.001), and had a better Eastern Cooperative Oncology Group performance status (ECOG 0 in 54% versus 45%, p = 0.004). BRAF and NRAS mutations were age dependent, with more BRAF V600 mutations in AYAs (68% versus 46%) and more NRAS mutations in older adults (13% versus 21%), p < 0.001. This finding translated in distinct first-line treatment patterns, where AYAs received more initial targeted therapy. Overall, grade 3–4 AE percentages following first-line systemic treatment were similar for AYAs and older adults; anti-PD-1 (7% versus 14%, p = 0.25), anti-CTLA-4 (16% versus 33%, p = 0.12), anti-PD-1 + anti-CTLA-4 (67% versus 56%, p = 0.34) and BRAF/MEK-inhibition (14% versus 23%, p = 0.06). Following anti-CTLA-4 treatment, no AYAs experienced a grade 3–4 colitis, while 17% of the older adults did (p = 0.046). There was no difference in response to treatment between AYAs and older adults. The longer overall survival observed in AYAs (hazard ratio (HR) 0.7; 95% CI 0.6–0.8) was explained by the increased cumulative incidence of non-melanoma related deaths in older adults (sub-distribution HR 2.8; 95% CI 1.5–4.9), calculated by competing risk analysis. The results of our national cohort study show that baseline characteristics and mutational profiles differ between AYAs and older adults with advanced melanoma, leading to different treatment choices made in daily practice. Once treatment is initiated, AYAs and older adults show similar tumor responses and melanoma-specific survival.
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Vanni I, Tanda ET, Dalmasso B, Pastorino L, Andreotti V, Bruno W, Boutros A, Spagnolo F, Ghiorzo P. Non-BRAF Mutant Melanoma: Molecular Features and Therapeutical Implications. Front Mol Biosci 2020; 7:172. [PMID: 32850962 PMCID: PMC7396525 DOI: 10.3389/fmolb.2020.00172] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023] Open
Abstract
Melanoma is one of the most aggressive tumors of the skin, and its incidence is growing worldwide. Historically considered a drug resistant disease, since 2011 the therapeutic landscape of melanoma has radically changed. Indeed, the improved knowledge of the immune system and its interactions with the tumor, and the ever more thorough molecular characterization of the disease, has allowed the development of immunotherapy on the one hand, and molecular target therapies on the other. The increased availability of more performing technologies like Next-Generation Sequencing (NGS), and the availability of increasingly large genetic panels, allows the identification of several potential therapeutic targets. In light of this, numerous clinical and preclinical trials are ongoing, to identify new molecular targets. Here, we review the landscape of mutated non-BRAF skin melanoma, in light of recent data deriving from Whole-Exome Sequencing (WES) or Whole-Genome Sequencing (WGS) studies on melanoma cohorts for which information on the mutation rate of each gene was available, for a total of 10 NGS studies and 992 samples, focusing on available, or in experimentation, targeted therapies beyond those targeting mutated BRAF. Namely, we describe 33 established and candidate driver genes altered with frequency greater than 1.5%, and the current status of targeted therapy for each gene. Only 1.1% of the samples showed no coding mutations, whereas 30% showed at least one mutation in the RAS genes (mostly NRAS) and 70% showed mutations outside of the RAS genes, suggesting potential new roads for targeted therapy. Ongoing clinical trials are available for 33.3% of the most frequently altered genes.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | | | - Bruna Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | - Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | - Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | - Andrea Boutros
- Medical Oncology, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
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Vanni I, Tanda ET, Spagnolo F, Andreotti V, Bruno W, Ghiorzo P. The Current State of Molecular Testing in the BRAF-Mutated Melanoma Landscape. Front Mol Biosci 2020; 7:113. [PMID: 32695793 PMCID: PMC7338720 DOI: 10.3389/fmolb.2020.00113] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/13/2020] [Indexed: 01/19/2023] Open
Abstract
The incidence of melanoma, among the most lethal cancers, is widespread and increasing. Metastatic melanoma has a poor prognosis, representing about 90% of skin cancer mortality. The increased knowledge of tumor biology and the greater understanding of the immune system role in the anti-tumor response has allowed us to develop a more rational approach to systemic therapies. The discovery of activating BRAF mutations in half of all melanomas has led to the development of molecularly targeted therapy with BRAF and MEK inhibitors, which dramatically improved outcomes of patients with stage IV BRAF-mutant melanoma. More recently, the results of clinical phase III studies conducted in the adjuvant setting led to the combined administration of BRAF and MEK inhibitors also in patients with resected high-risk melanoma (stage III). Therefore, BRAF mutation testing has become a priority to determine the oncologist's choice and course of therapy. In this review, we will report the molecular biology-based strategies used for BRAF mutation detection with the main advantages and disadvantages of the most commonly used diagnostic strategies. The timing of such molecular assessment in patients with cutaneous melanoma will be discussed, and we will also examine considerations and approaches for accurate and effective BRAF testing.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | | | | | - Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
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The prognostic value of tumor mitotic rate in children and adolescents with cutaneous melanoma: A retrospective cohort study. J Am Acad Dermatol 2020; 82:910-919. [DOI: 10.1016/j.jaad.2019.10.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 12/29/2022]
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Abstract
PURPOSE OF REVIEW The current review aims to highlight the frequency of RAS mutations in pediatric leukemias and solid tumors and to propose strategies for targeting oncogenic RAS in pediatric cancers. RECENT FINDINGS The three RAS genes (HRAS, NRAS, and KRAS) comprise the most frequently mutated oncogene family in human cancer. RAS mutations are commonly observed in three of the leading causes of cancer death in the United States, namely lung cancer, pancreatic cancer, and colorectal cancer. The association of RAS mutations with these aggressive malignancies inspired the creation of the National Cancer Institute RAS initiative and spurred intense efforts to develop strategies to inhibit oncogenic RAS, with much recent success. RAS mutations are frequently observed in pediatric cancers; however, recent advances in anti-RAS drug development have yet to translate into pediatric clinical trials. SUMMARY We find that RAS is mutated in common and rare pediatric malignancies and that oncogenic RAS confers a functional dependency in these cancers. Many strategies for targeting RAS are being pursued for malignancies that primarily affect adults and there is a clear need for inclusion of pediatric patients in clinical trials of these agents.
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31
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Close AG, Dreyzin A, Miller KD, Seynnaeve BKN, Rapkin LB. Adolescent and young adult oncology-past, present, and future. CA Cancer J Clin 2019; 69:485-496. [PMID: 31594027 DOI: 10.3322/caac.21585] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 06/26/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022] Open
Abstract
There are nearly 70,000 new cancer diagnoses made annually in adolescents and young adults (AYAs) in the United States. Historically, AYA patients with cancer, aged 15 to 39 years, have not shown the same improved survival as older or younger cohorts. This article reviews the contemporary cancer incidence and survival data through 2015 for the AYA patient population based on the National Cancer Institute's Surveillance, Epidemiology, and End Results registry program and the North American Association of Central Cancer Registries. Mortality data through 2016 from the Centers for Disease Control and Prevention's National Center for Health Statistics are also described. Encouragingly, absolute and relative increases in 5-year survival for AYA cancers have paralleled those of childhood cancers since the year 2000. There has been increasing attention to these vulnerable patients and improved partnerships and collaboration between adult and pediatric oncology; however, obstacles to the care of this population still occur at multiple levels. These vulnerabilities fall into 3 significant categories: research efforts and trial enrollment directed toward AYA malignancies, access to care and insurance coverage, and AYA-specific psychosocial support. It is critical for providers and health care delivery systems to recognize that the AYA population remains vulnerable to provider and societal complacency.
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Affiliation(s)
- Allison G Close
- Division of Hematology/Oncology, University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Alexandra Dreyzin
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | | | - Brittani K N Seynnaeve
- Division of Hematology/Oncology, University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Louis B Rapkin
- Division of Hematology/Oncology, University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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Pellegrini C, Botta F, Massi D, Martorelli C, Facchetti F, Gandini S, Maisonneuve P, Avril MF, Demenais F, Bressac-de Paillerets B, Hoiom V, Cust AE, Anton-Culver H, Gruber SB, Gallagher RP, Marrett L, Zanetti R, Dwyer T, Thomas NE, Begg CB, Berwick M, Puig S, Potrony M, Nagore E, Ghiorzo P, Menin C, Manganoni AM, Rodolfo M, Brugnara S, Passoni E, Sekulovic LK, Baldini F, Guida G, Stratigos A, Ozdemir F, Ayala F, Fernandez-de-Misa R, Quaglino P, Ribas G, Romanini A, Migliano E, Stanganelli I, Kanetsky PA, Pizzichetta MA, García-Borrón JC, Nan H, Landi MT, Little J, Newton-Bishop J, Sera F, Fargnoli MC, Raimondi S. MC1R variants in childhood and adolescent melanoma: a retrospective pooled analysis of a multicentre cohort. THE LANCET. CHILD & ADOLESCENT HEALTH 2019; 3:332-342. [PMID: 30872112 PMCID: PMC6942319 DOI: 10.1016/s2352-4642(19)30005-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/10/2018] [Accepted: 12/21/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Germline variants in the melanocortin 1 receptor gene (MC1R) might increase the risk of childhood and adolescent melanoma, but a clear conclusion is challenging because of the low number of studies and cases. We assessed the association of MC1R variants with childhood and adolescent melanoma in a large study comparing the prevalence of MC1R variants in child or adolescent patients with melanoma to that in adult patients with melanoma and in healthy adult controls. METHODS In this retrospective pooled analysis, we used the M-SKIP Project, the Italian Melanoma Intergroup, and other European groups (with participants from Australia, Canada, France, Greece, Italy, the Netherlands, Serbia, Spain, Sweden, Turkey, and the USA) to assemble an international multicentre cohort. We gathered phenotypic and genetic data from children or adolescents diagnosed with sporadic single-primary cutaneous melanoma at age 20 years or younger, adult patients with sporadic single-primary cutaneous melanoma diagnosed at age 35 years or older, and healthy adult individuals as controls. We calculated odds ratios (ORs) for childhood and adolescent melanoma associated with MC1R variants by multivariable logistic regression. Subgroup analysis was done for children aged 18 or younger and 14 years or younger. FINDINGS We analysed data from 233 young patients, 932 adult patients, and 932 healthy adult controls. Children and adolescents had higher odds of carrying MC1R r variants than did adult patients (OR 1·54, 95% CI 1·02-2·33), including when analysis was restricted to patients aged 18 years or younger (1·80, 1·06-3·07). All investigated variants, except Arg160Trp, tended, to varying degrees, to have higher frequencies in young patients than in adult patients, with significantly higher frequencies found for Val60Leu (OR 1·60, 95% CI 1·05-2·44; p=0·04) and Asp294His (2·15, 1·05-4·40; p=0·04). Compared with those of healthy controls, young patients with melanoma had significantly higher frequencies of any MC1R variants. INTERPRETATION Our pooled analysis of MC1R genetic data of young patients with melanoma showed that MC1R r variants were more prevalent in childhood and adolescent melanoma than in adult melanoma, especially in patients aged 18 years or younger. Our findings support the role of MC1R in childhood and adolescent melanoma susceptibility, with a potential clinical relevance for developing early melanoma detection and preventive strategies. FUNDING SPD-Pilot/Project-Award-2015; AIRC-MFAG-11831.
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Affiliation(s)
- Cristina Pellegrini
- Department of Dermatology and Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Francesca Botta
- Division of Epidemiology and Biostatistics, European Institute of Oncology IRCCS, Milan, Italy; Department of Statistics and Quantitative Methods, University of Milano-Bicocca, Milan, Italy
| | - Daniela Massi
- Division of Pathological Anatomy, Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Claudia Martorelli
- Department of Dermatology and Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Fabio Facchetti
- Pathology Section, Department of Molecular and Translational Medicine, Spedali Civili di Brescia, University of Brescia, Brescia, Italy
| | - Sara Gandini
- Molecular and Pharmaco-Epidemiology Unit, Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Patrick Maisonneuve
- Division of Epidemiology and Biostatistics, European Institute of Oncology IRCCS, Milan, Italy
| | - Marie-Françoise Avril
- APHP, Dermatology Department, Hôpital Cochin and Paris Descartes University, Paris, France
| | - Florence Demenais
- Genetic Variation and Human Diseases Unit (UMR-946), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
| | | | - Veronica Hoiom
- Department of Oncology and Pathology, Cancer Centre, Karolinska Institutet, Stockholm, Sweden
| | - Anne E Cust
- Sydney School of Public Health and Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California, Irvine, CA, USA
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Richard P Gallagher
- British Columbia Cancer and Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada
| | | | - Roberto Zanetti
- Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy
| | - Terence Dwyer
- George Institute for Global Health, Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford, UK
| | - Nancy E Thomas
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marianne Berwick
- Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Susana Puig
- Melanoma Unit, Dermatology Department, Hospital Clinic Barcelona, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi I Sunyer, and CIBER de Enfermedades Raras, Barcelona, Spain
| | - Miriam Potrony
- Melanoma Unit, Dermatology Department, Hospital Clinic Barcelona, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi I Sunyer, and CIBER de Enfermedades Raras, Barcelona, Spain
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy
| | - Chiara Menin
- Diagnostic Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | | | - Monica Rodolfo
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Emanuela Passoni
- Department of Pathophysiology and Transplantation, University of Milan, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Federica Baldini
- Division of Melanoma, Sarcoma and Rare Cancer, European Institute of Oncology IRCCS, Milan, Italy
| | - Gabriella Guida
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Alexandros Stratigos
- 1st Department of Dermatology, Andreas Sygros Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Fezal Ozdemir
- Department of Dermatology, Faculty of Medicine, University of Ege, Izmir, Turkey
| | - Fabrizio Ayala
- Melanoma Unit, Cancer Immunotherapy and Innovative Therapies, IRCCS Istituto Nazionale dei Tumori, Fondazione G Pascale, Napoli, Italia
| | - Ricardo Fernandez-de-Misa
- Dermatology Service, University Hospital Nuestra Senora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Pietro Quaglino
- Dermatologic Clinic, Department of Medical Sciences, University of Torino, Turin, Italy
| | - Gloria Ribas
- Department of Medical Oncology and Haematology, Fundación Investigación Clínico de Valencia, INCLIVA Instituto de Investigación Sanitaria, Valencia, Spain
| | - Antonella Romanini
- US Ambulatori Melanomi, Sarcomi e Tumori Rari, UO Oncologia Medica 1, Azienda Ospedaliero-Universitaria Santa Chiara, Pisa, Italy
| | - Emilia Migliano
- Plastic Surgery, San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - Ignazio Stanganelli
- Skin Cancer Unit, IRCCS Scientific Institute of Romagna for the Study and Treatment of Cancer and University of Parma, Meldola, Italy
| | - Peter A Kanetsky
- Department of Cancer Epidemiology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Jose Carlos García-Borrón
- Department of Biochemistry, Molecular Biology, and Immunology, University of Murcia and IMIB-Arrixaca, Murcia, Spain
| | - Hongmei Nan
- Department of Epidemiology, Richard M Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Julian Little
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, Canada
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Institute of Medical Research at St James', University of Leeds, Leeds, UK
| | - Francesco Sera
- Department of Public Health, Environments and Society, London School of Hygiene & Tropical Medicine, London, UK
| | - Maria Concetta Fargnoli
- Department of Dermatology and Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Sara Raimondi
- Molecular and Pharmaco-Epidemiology Unit, Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy.
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MC1R minor variants and the multiple pathways to melanoma. THE LANCET CHILD & ADOLESCENT HEALTH 2019; 3:287-288. [PMID: 30872113 DOI: 10.1016/s2352-4642(19)30026-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/16/2019] [Indexed: 11/21/2022]
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Quek C, Rawson RV, Ferguson PM, Shang P, Silva I, Saw RPM, Shannon K, Thompson JF, Hayward NK, Long GV, Mann GJ, Scolyer RA, Wilmott JS. Recurrent hotspot SF3B1 mutations at codon 625 in vulvovaginal mucosal melanoma identified in a study of 27 Australian mucosal melanomas. Oncotarget 2019; 10:930-941. [PMID: 30847022 PMCID: PMC6398173 DOI: 10.18632/oncotarget.26584] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/16/2018] [Indexed: 02/03/2023] Open
Abstract
Introduction Clinical outcomes for mucosal melanomas are often poor due to a lack of effective systemic drug therapies. Identifying driver genes in mucosal melanoma may enhance the understanding of disease pathogenesis and provide novel opportunities to develop effective therapies. Results Somatic variant analysis identified SF3B1 (6 of 27: 22%) as the most commonly mutated gene, followed by KIT (3 of 27: 11%). Other less frequently mutated genes (4% otherwise stated) included BRAF (7%), NRAS (7%), ARID2, CTNNB1, DICER1, MAP2K1, NF1, PTEN, SETD2 and TP53. Recurrent SF3B1 p.R625 hotspot mutations were exclusively detected in vulvovaginal (5 of 19: 26%) and anorectal melanomas (3 of 5:60%). The only other SF3B1 mutation was a p.C1123Y mutation that occurred in a conjunctival mucosal melanoma. SF3B1-mutated patients were associated with shorter overall survival (OS; 34.9 months) and progression-free survival (PFS; 16.9 months) compared to non-SF3B1-mutated patients (OS: 79.7 months, log-rank P = 0.1172; PFS: 35.7 months, log-rank P = 0.0963). Conclusion Molecular subgroups of mucosal melanoma with SF3B1 mutations occurred predominantly in the vulvovaginal region. SF3B1 mutations may have a negative prognostic impact. Methods Formalin-fixed biopsies were collected from 27 pathologically-confirmed mucosal melanomas. Genomic DNA was isolated from the tumor tissue and sequenced using a novel dual-strand amplicon sequencing technique to determine the frequency and types of mutations across 45 target genes.
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Affiliation(s)
- Camelia Quek
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Robert V Rawson
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia.,Royal Prince Alfred Hospital, Sydney, Australia
| | - Peter M Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia.,Royal Prince Alfred Hospital, Sydney, Australia
| | - Ping Shang
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Ines Silva
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia.,Royal Prince Alfred Hospital, Sydney, Australia
| | - Kerwin Shannon
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Royal Prince Alfred Hospital, Sydney, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, Sydney, Australia
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia.,Royal Prince Alfred Hospital, Sydney, Australia
| | - Nicholas K Hayward
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia.,Royal North Shore Hospital, Sydney, Australia
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, Sydney, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia.,Royal Prince Alfred Hospital, Sydney, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia
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