Whole-genome landscapes of major melanoma subtypes

Hayward, Nicholas K.; Wilmott, James S.; Waddell, Nicola; Johansson, Peter A.; Field, Matthew A.; Nones, Katia; Patch, Ann-Marie; Kakavand, Hojabr; Alexandrov, Ludmil B.; Burke, Hazel; Jakrot, Valerie; Kazakoff, Stephen; Holmes, Oliver; Leonard, Conrad; Sabarinathan, Radhakrishnan; Mularoni, Loris; Wood, Scott; Xu, Qinying; Waddell, Nick; Tembe, Varsha; Pupo, Gulietta M.; De Paoli-Iseppi, Ricardo; Vilain, Ricardo E.; Shang, Ping; Lau, Loretta M.  S.; Dagg, Rebecca A.; Schramm, Sarah-Jane; Pritchard, Antonia; Dutton-Regester, Ken; Newell, Felicity; Fitzgerald, Anna; Shang, Catherine A.; Grimmond, Sean M.; Pickett, Hilda A.; Yang, Jean Y.; Stretch, Jonathan R.; Behren, Andreas; Kefford, Richard F.; Hersey, Peter; Long, Georgina V.; Cebon, Jonathan; Shackleton, Mark; Spillane, Andrew J.; Saw, Robyn P.  M.; López-Bigas, Núria; Pearson, John V.; Thompson, John F.; Scolyer, Richard A.; Mann, Graham J.

doi:10.1038/nature22071

Title: Whole-genome landscapes of major melanoma subtypes

Journal Article · Wed May 03 00:00:00 EDT 2017 · Nature (London)

DOI:https://doi.org/10.1038/nature22071· OSTI ID:1357116

Hayward, Nicholas K. ^[1]; Wilmott, James S. ^[2]; Waddell, Nicola ^[3]; Johansson, Peter A. ^[4]; Field, Matthew A. ^[5]; Nones, Katia ^[3]; Patch, Ann-Marie ^[3]; Kakavand, Hojabr ^[6];

^[7]; Burke, Hazel ^[8]; Jakrot, Valerie ^[8]; Kazakoff, Stephen ^[3]; Holmes, Oliver ^[3]; Leonard, Conrad ^[3]; Sabarinathan, Radhakrishnan ^[9]; Mularoni, Loris ^[9]; Wood, Scott ^[3]; Xu, Qinying ^[3]; Waddell, Nick ^[10]; Tembe, Varsha ^[11] more »

Univ. of Sydney, NSW (Australia). Melanoma Inst. Australia; QIMR Berghofer Medical Research Inst., Queensland (Australia)
Univ. of Sydney, NSW (Australia). Melanoma Inst. Australia; Univ. of Sydney, NSW (Australia). Sydney Medical School
QIMR Berghofer Medical Research Inst., Queensland (Australia); Univ. of Queensland, Brisbane (Australia). Inst. for Molecular Bioscience
QIMR Berghofer Medical Research Inst., Queensland (Australia)
James Collk Univ., Queensland (Australia). Australian Inst. of Tropical Health and Medicine
Univ. of Sydney, NSW (Australia). Sydney Medical School
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Univ. of Sydney, NSW (Australia). Melanoma Inst. Australia
Barcelona Inst. of Science and Technology, Barcelona (Spain). Inst. for Research in Biomedicine (IRB Barcelona)
Univ. of Queensland, Brisbane (Australia). Inst. for Molecular Bioscience
Univ. of Sydney, NSW (Australia). Westmead Inst. for Medical Research
Univ. of Sydney, NSW (Australia). Children's Medical Research Inst.
Univ. of Sydney, NSW (Australia). Children's Hospital at Westmead
Bioplatforms Australia, NSW (Australia)
Univ. of Melbourne (Australia). University of Melbourne Centre for Cancer Research
Univ. of Sydney, NSW (Australia). School of Mathematics and Statistics
La Trobe Univ., Melbourne, VIC (Australia). Olivia Newton-John Cancer Research Inst.
Univ. of Sydney, NSW (Australia). Melanoma Inst. Australia; Macquarie Univ., NSW (Australia)
Univ. of Sydney, NSW (Australia). Melanoma Inst. Australia; Univ. of Sydney, NSW (Australia). Centenary Inst.
Univ. of Sydney, NSW (Australia). Melanoma Inst. Australia; Royal North Short Hospital, NSW (Australia). Dept. of Medical Oncology
Peter MacCallum Cancer Centre and Univ. of Melbourne (Australia)
Barcelona Inst. of Science and Technology, Barcelona (Spain). Inst. for Research in Biomedicine (IRB Barcelona); Catalana Inst. of Research and Advanced Studies (ICREA), Barcelona (Spain)
Univ. of Sydney, NSW (Australia). Melanoma Inst. Australia; Univ. of Sydney, NSW (Australia). Sydney Medical School; Royal Prince Alfred Hospital, NSW (Australia). Tissue Pathology and Diagnostic Oncology
Univ. of Sydney, NSW (Australia). Melanoma Inst. Australia; Univ. of Sydney, NSW (Australia). Westmead Inst. for Medical Research

Melanoma of the skin is a common cancer only in Europeans, whereas it arises in internal body surfaces (mucosal sites) and on the hands and feet (acral sites) in people throughout the world. We report analysis of whole-genome sequences from cutaneous, acral and mucosal subtypes of melanoma. The heavily mutated landscape of coding and non-coding mutations in cutaneous melanoma resolved novel signatures of mutagenesis attributable to ultraviolet radiation. But, acral and mucosal melanomas were dominated by structural changes and mutation signatures of unknown aetiology, not previously identified in melanoma. The number of genes affected by recurrent mutations disrupting non-coding sequences was similar to that affected by recurrent mutations to coding sequences. Significantly mutated genes included BRAF, CDKN2A, NRAS and TP53 in cutaneous melanoma, BRAF, NRAS and NF1 in acral melanoma and SF3B1 in mucosal melanoma. Mutations affecting the TERT promoter were the most frequent of all; however, neither they nor ATRX mutations, which correlate with alternative telomere lengthening, were associated with greater telomere length. In most cases, melanomas had potentially actionable mutations, most in components of the mitogen-activated protein kinase and phosphoinositol kinase pathways. The whole-genome mutation landscape of melanoma reveals diverse carcinogenic processes across its subtypes, some unrelated to sun exposure, and extends potential involvement of the non-coding genome in its pathogenesis.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA)

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1357116

Report Number(s):: LA-UR-16-21896

Journal Information:: Nature (London), Vol. 545, Issue 7653; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 819 works

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Pilot study on the correlation between dermoscopic patterns and fluorescence in situ hybridization findings using whole-slide digital imaging for acral volar melanocytic lesions Ogata, Dai; Arai, Eiichi; Goto, Yoshiya The Journal of Dermatology, Vol. 45, Issue 7 https://doi.org/10.1111/1346-8138.14324	journal	April 2018
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Neuroblastoma rat sarcoma mutated melanoma: That’s what we got so far Bertoli, Elisa; Giavarra, Marco; Vitale, Maria Grazia Pigment Cell & Melanoma Research, Vol. 32, Issue 6 https://doi.org/10.1111/pcmr.12819	journal	July 2019
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Functional analysis of RPS27 mutations and expression in melanoma Floristán, Alfredo; Morales, Leah; Hanniford, Douglas Pigment Cell & Melanoma Research, Vol. 33, Issue 3 https://doi.org/10.1111/pcmr.12841	journal	November 2019
Tumor genetic heterogeneity analysis of chronic sun‐damaged melanoma Sanna, Adriana; Harbst, Katja; Johansson, Iva Pigment Cell & Melanoma Research, Vol. 33, Issue 3 https://doi.org/10.1111/pcmr.12851	journal	December 2019
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A genome-wide net to catch and understand cancer Sanjana, Neville E. Science Translational Medicine, Vol. 10, Issue 453 https://doi.org/10.1126/scitranslmed.aat8288	journal	August 2018
Factors Influencing the Efficacy of Anti-PD-1 Therapy in Chinese Patients with Advanced Melanoma Zhao, Lingdi; Yang, Yonghao; Ma, Baozhen Journal of Oncology, Vol. 2019 https://doi.org/10.1155/2019/6454989	journal	September 2019
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The triennial International Pigment Cell Conference (IPCC) Box, Neil F.; Larue, Lionel; Manga, Prashiela Journal of Translational Medicine, Vol. 16, Issue 1 https://doi.org/10.1186/s12967-018-1609-1	journal	October 2018
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Combatting mucosal melanoma: recent advances and future perspectives Tyrrell, Helen; Payne, Miranda Melanoma Management, Vol. 5, Issue 3 https://doi.org/10.2217/mmt-2018-0003	journal	September 2018
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Genome-Wide Analysis of Long Non-Coding RNA Profiles in Canine Oral Melanomas Hitte, Christophe; Le Béguec, Céline; Cadieu, Edouard Genes, Vol. 10, Issue 6 https://doi.org/10.3390/genes10060477	journal	June 2019
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Targeting the ERK Signaling Pathway in Melanoma Savoia, Paola; Fava, Paolo; Casoni, Filippo International Journal of Molecular Sciences, Vol. 20, Issue 6 https://doi.org/10.3390/ijms20061483	journal	March 2019
BRAF Mutations and Dysregulation of the MAP Kinase Pathway Associated to Sinonasal Mucosal Melanomas Colombino, Maria; Paliogiannis, Panagiotis; Cossu, Antonio Journal of Clinical Medicine, Vol. 8, Issue 10 https://doi.org/10.3390/jcm8101577	journal	October 2019
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Multicenter prospective phase II trial of nivolumab in patients with unresectable or metastatic mucosal melanoma Nomura, Motoo; Oze, Isao; Masuishi, Toshiki International Journal of Clinical Oncology, Vol. 25, Issue 5 https://doi.org/10.1007/s10147-020-01618-9	journal	January 2020
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Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma Liu, David; Schilling, Bastian; Liu, Derek Nature Medicine, Vol. 25, Issue 12 https://doi.org/10.1038/s41591-019-0654-5	journal	December 2019
A comprehensive evaluation of pathogenic mutations in primary cutaneous melanomas, including the identification of novel loss-of-function variants Ticha, Ivana; Hojny, Jan; Michalkova, Romana Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-53636-x	journal	November 2019
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The TERT copy number gain is sensitive to telomerase inhibitors in human melanoma Yu, Jinyu; Yu, Jiayi; Wu, Xiaowen Clinical Science, Vol. 134, Issue 2 https://doi.org/10.1042/cs20190890	journal	January 2020
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Role of miRNAs in Melanoma Metastasis Gajos-Michniewicz, Anna; Czyz, Malgorzata Cancers, Vol. 11, Issue 3 https://doi.org/10.3390/cancers11030326	journal	March 2019
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High G2 and S-phase expressed 1 expression promotes acral melanoma progression and correlates with poor clinical prognosis Xu, Tianxiao; Ma, Meng; Chi, Zhihong Cancer Science, Vol. 109, Issue 6 https://doi.org/10.1111/cas.13607	journal	May 2018
Fast‐growing melanoma: a distinct entity or a superficial spreading melanoma with a brief horizontal phase? Peris, K. Journal of the European Academy of Dermatology and Venereology, Vol. 33, Issue 1 https://doi.org/10.1111/jdv.15334	journal	August 2018
Integrated genomic analysis identifies clinically relevant subtypes of renal clear cell carcinoma Wu, Peng; Liu, Jia-Li; Pei, Shi-Mei BMC Cancer, Vol. 18, Issue 1 https://doi.org/10.1186/s12885-018-4176-1	journal	March 2018
Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1 Cifdaloz, Metehan; Osterloh, Lisa; Graña, Osvaldo RWTH Aachen University https://doi.org/10.18154/rwth-conv-222628	text	January 2017
Uveal Versus Cutaneous Melanoma; Same Origin, Very Distinct Tumor Types van der Kooij, Monique K.; Speetjens, Frank M.; van der Burg, Sjoerd H. Cancers, Vol. 11, Issue 6 https://doi.org/10.3390/cancers11060845	journal	June 2019
Micro RNA Transcriptome Profile in Canine Oral Melanoma Rahman, Md. Mahfuzur; Lai, Yu-Chang; Husna, Al Asmaul International Journal of Molecular Sciences, Vol. 20, Issue 19 https://doi.org/10.3390/ijms20194832	journal	September 2019
The identification of patient‐specific mutations reveals dual pathway activation in most patients with melanoma and activated receptor tyrosine kinases in BRAF/NRAS wild‐type melanomas Appenzeller, Silke; Gesierich, Anja; Thiem, Alexander Cancer, Vol. 125, Issue 4 https://doi.org/10.1002/cncr.31843	journal	December 2018
Known and novel roles of the MET oncogene in cancer: a coherent approach to targeted therapy Comoglio, Paolo M.; Trusolino, Livio; Boccaccio, Carla Nature Reviews Cancer, Vol. 18, Issue 6 https://doi.org/10.1038/s41568-018-0002-y	journal	April 2018
Distant metastasis due to heavily pigmented epithelioid melanoma with underlying BRAF V600E, NOTCH1 , ERBB3 , and PTEN mutations Motaparthi, Kiran; George, Eva V.; Guo, Ruifeng Journal of Cutaneous Pathology, Vol. 46, Issue 8 https://doi.org/10.1111/cup.13485	journal	May 2019
Distinct genomic traits of acral and mucosal melanomas revealed by targeted mutational profiling Zou, Zhengyun; Ou, Qiuxiang; Ren, Yu Pigment Cell & Melanoma Research, Vol. 33, Issue 4 https://doi.org/10.1111/pcmr.12865	journal	January 2020
Multisite dependency of an E3 ligase controls monoubiquitylation-dependent cell fate decisions Werner, Achim; Baur, Regina; Teerikorpi, Nia eLife, Vol. 7 https://doi.org/10.7554/elife.35407	journal	July 2018
Matching cell lines with cancer type and subtype of origin via mutational, epigenomic, and transcriptomic patterns Salvadores, Marina; Fuster-Tormo, Francisco; Supek, Fran Science Advances, Vol. 6, Issue 27 https://doi.org/10.1126/sciadv.aba1862	journal	July 2020
Elevated pyrimidine dimer formation at distinct genomic bases underlies promoter mutation hotspots in UV-exposed cancers Elliott, Kerryn; Boström, Martin; Filges, Stefan PLOS Genetics, Vol. 14, Issue 12 https://doi.org/10.1371/journal.pgen.1007849	journal	December 2018
Targeted Therapy and Immunotherapy for Melanoma in Japan Namikawa, Kenjiro; Yamazaki, Naoya Current Treatment Options in Oncology, Vol. 20, Issue 1 https://doi.org/10.1007/s11864-019-0607-8	journal	January 2019
Sentinel Lymph Node Biopsy and Complete Lymph Node Dissection for Melanoma Falk Delgado, Alberto; Zommorodi, Sayid; Falk Delgado, Anna Current Oncology Reports, Vol. 21, Issue 6 https://doi.org/10.1007/s11912-019-0798-y	journal	April 2019
Wavelengths and temporal effects on the response of mammalian cells to UV radiation: Limitations of action spectra illustrated by genotoxicity Douki, Thierry Journal of Photochemistry and Photobiology B: Biology, Vol. 217 https://doi.org/10.1016/j.jphotobiol.2021.112169	journal	April 2021
Antitumour activity of pembrolizumab in advanced mucosal melanoma: a post-hoc analysis of KEYNOTE-001, 002, 006 Hamid, Omid; Robert, Caroline; Ribas, Antoni British Journal of Cancer, Vol. 119, Issue 6 https://doi.org/10.1038/s41416-018-0207-6	journal	September 2018
A deep learning system can accurately classify primary and metastatic cancers based on patterns of passenger mutations Jiao, Wei; Atwal, Gurnit; Polak, Paz https://doi.org/10.1101/214494	posted_content	January 2019
Novel immune signatures associated with dysplastic naevi and primary cutaneous melanoma in human skin Yan, Bernice Y.; Garcet, Sandra; Gulati, Nicholas Experimental Dermatology, Vol. 28, Issue 1 https://doi.org/10.1111/exd.13805	journal	December 2018
Combining molecular and immunohistochemical analyses of key drivers in primary melanomas: interplay between germline and somatic variations Bruno, William; Martinuzzi, Claudia; Dalmasso, Bruna Oncotarget, Vol. 9, Issue 5 https://doi.org/10.18632/oncotarget.23204	journal	December 2017
Sun Exposure and Melanoma, Certainties and Weaknesses of the Present Knowledge Arisi, Mariachiara; Zane, Cristina; Caravello, Simone Frontiers in Medicine, Vol. 5 https://doi.org/10.3389/fmed.2018.00235	journal	August 2018
Biomarkers for Immune Checkpoint Inhibitors in Melanoma Kitano, Shigehisa; Nakayama, Takayuki; Yamashita, Makiko Frontiers in Oncology, Vol. 8 https://doi.org/10.3389/fonc.2018.00270	journal	July 2018
Prognostic Value of Peripheral Inflammatory Markers in Preoperative Mucosal Melanoma: A Multicenter Retrospective Study Wang, Yixi; Zhang, Hao; Yang, Yuhan Frontiers in Oncology, Vol. 9 https://doi.org/10.3389/fonc.2019.00995	journal	October 2019
Melanoma: Genetic Abnormalities, Tumor Progression, Clonal Evolution and Tumor Initiating Cells Testa, Ugo; Castelli, Germana; Pelosi, Elvira Medical Sciences, Vol. 5, Issue 4 https://doi.org/10.3390/medsci5040028	journal	November 2017
Overexpression of microRNA‑21 inhibits the growth and metastasis of melanoma cells by targeting MKK3 Zhou, Meng; Yu, Xiaoqian; Jing, Zhenhai Molecular Medicine Reports https://doi.org/10.3892/mmr.2019.10408	journal	June 2019
The triennial International Pigment Cell Conference (IPCC) Box, Neil F.; Larue, Lionel; Manga, Prashiela arXiv https://doi.org/10.48550/arxiv.1808.05755	preprint	January 2018

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