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Comprehensive Genomic Characterization Of Head And Neck Squamous Cell Carcinomas

M. Lawrence, C. Sougnez, L. Lichtenstein, K. Cibulskis, E. Lander, S. Gabriel, G. Getz, A. Ally, M. Balasundaram, I. Birol, R. Bowlby, D. Brooks, Y. Butterfield, Rebecca Carlsen, D. Cheng, A. Chu, Noreen Dhalla, R. Guin, R. Holt, S. Jones, Darlene Lee, H. I. Li, M. Marra, Michael Mayo, R. Moore, A. Mungall, A. G. Robertson, J. Schein, Payal Sipahimalani, Angela Tam, N. Thiessen, T. Wong, A. Protopopov, Netty Santoso, Semin Lee, M. Parfenov, J. Zhang, Harshad S. Mahadeshwar, Jiabin Tang, Xiaojia Ren, Sahil Seth, Psalm S Haseley, D. Zeng, Lixing Yang, A. W. Xu, X. Song, Angeliki Pantazi, C. Bristow, Angela Hadjipanayis, J. Seidman, L. Chin, P. Park, R. Kucherlapati, Rehan Akbani, Tod D. Casasent, W. Liu, Y. Lu, G. B. Mills, Thomas C. Motter, J. Weinstein, L. Diao, J. Wang, Y. Fan, J. Liu, K. Wang, J. T. Auman, S. Balu, T. Bodenheimer, Elizabeth Buda, D. Hayes, K. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, C. Jones, Patrick K. Kimes, Y. Liu, J. S. Marron, S. Meng, P. Mieczkowski, Lisle E. Mose, J. Parker, C. Perou, J. Prins, J. Roach, Y. Shi, Janae V. Simons, Darshan Singh, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, V. Walter, S. Waring, M. Wilkerson, J. Wu, N. Zhao, A. Cherniack, P. Hammerman, A. Tward, C. Pedamallu, G. Saksena, J. Jung, A. I. Ojesina, S. Carter, T. Zack, Steven E. Schumacher, Rameen Beroukhim, S. Freeman, M. Meyerson, J. Cho, Michael S. Noble, D. DiCara, H. Zhang, David I. Heiman, N. Gehlenborg, Doug Voet, P. Lin, S. Frazer, P. Stojanov, Y. Liu, L. Zou, J. Kim, D. M. Muzny, H. doddapaneni, Christie Kovar, Jeffrey S. Reid, Donna Morton, Y. Han, W. Hale, H. Chao, K. Chang, J. Drummond, R. Gibbs, Nipun Kakkar, D. Wheeler, L. Xi, Giovanni Ciriello, M. Ladanyi, W. Lee, Ricardo Ramírez, C. Sander, R. Shen, Rileen Sinha, N. Weinhold, B. Taylor, B. A. Aksoy, Gideon Dresdner, J. Gao, Benjamin E. Gross, Anders Jacobsen, B. Reva, N. Schultz, S. O. Sumer, Y. Sun, T. Chan, L. Morris, Joshua M. Stuart, S. Benz, Sam Ng, C. Benz, C. Yau, S. B. Baylin, L. Cope, L. Danilova, J. Herman, M. Bootwalla, D. Maglinte, P. Laird, T. Triche, D. Weisenberger, D. Berg, N. Agrawal, J. Bishop, P. Boutros, J. Bruce, L. Byers, J. Califano, T. Carey, Z. Chen, H. Cheng, S. Chiosea, E. E. Cohen, B. Diergaarde, A. Egloff, A. El-Naggar, R. Ferris, M. Frederick, J. Grandis, Y. Guo, R. Haddad, T. Harris, Angela B. Y. Hui, J. Lee, S. Lippman, Fei-fei Liu, J. Mchugh, J. Myers, P. Ng, B. Perez-Ordóñez, C. Pickering, M. B. Prystowsky, M. Romkes, A. Saleh, M. Sartor, R. Seethala, T. Seiwert, H. Si, C. V. Waes, Daryl Waggott, Maciej Wiznerowicz, W. Yarbrough, J. Zhang, Zhixiang Zuo, Ken Burnett, D. Crain, J. Gardner, Kevin W Lau, David Mallery, S. Morris, J. Paulauskis, R. Penny, C. Shelton, T. Shelton, M. Sherman, P. Yena, Aaron D. Black, Jay Bowen, J. Frick, J. Gastier‐Foster, H. Harper, Kristen M. Leraas, Tara M. Lichtenberg, N. Ramirez, L. Wise, E. Zmuda, J. Baboud, M. A. Jensen, Ari B. Kahn, Todd Pihl, D. Pot, Deepak Srinivasan, Jessica Walton, Yunhu Wan, Robert A. Burton, T. Davidsen, John A. Demchok, Greg Eley, M. L. Ferguson, K. Shaw, B. Ozenberger, Margi Sheth, H. Sofia, Roy Tarnuzzer, Zhi-Ning Wang, L. Yang, J. Zenklusen, C. Saller, Katherine Tarvin, C. Chen, R. Bollag, P. Weinberger, W. Golusiński, P. Golusiński, M. Ibbs, K. Korski, A. Mackiewicz, W. Suchorska, B. Szybiak, Erin Curley, Christina Beard, C. Mitchell, G. Sandusky, J. Ahn, Z. Khan, J. Irish, J. Waldron, W. William, Sophie C. Egea, C. Gómez-Fernández, Lynn M. Herbert, C. Bradford, D. Chepeha, A. Haddad, Tamara R. Jones, Christine M. Komarck, Mayya Malakh, J. S. Moyer, A. Nguyen, L. Peterson, M. E. Prince, L. Rozek, E. G. Taylor, H. Walline, G. T. Wolf, L. Boice, B. Chera, W. Funkhouser, M. Gulley, T. Hackman, M. Hayward, M. Huang, W. K. Rathmell, Ashley H. Salazar, W. Shockley, C. Shores, L. Thorne, Mark C. Weissler, Sylvia Wrenn, A. Zanation, B. Brown, M. Pham
Published 2015 · Medicine, Biology
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The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations. Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1. Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 mutations and CDKN2A inactivation with frequent copy number alterations including amplification of 3q26/28 and 11q13/22. A subgroup of oral cavity tumours with favourable clinical outcomes displayed infrequent copy number alterations in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and TP53. Other distinct subgroups contained loss-of-function alterations of the chromatin modifier NSD1, WNT pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumours. Therapeutic candidate alterations were identified in most HNSCCs.
This paper references
10.1002/ajmg.a.34156
Adults with Sotos syndrome: review of 21 adults with molecularly confirmed NSD1 alterations, including a detailed case report of the oldest person.
Matthew R Fickie (2011)
GLOBOCAN 2008
Ferlay (2010)
10.1038/nature11404
Comprehensive genomic characterization of squamous cell lung cancers
P. Hammerman (2012)
10.1038/nature04374
Critical role of TRAF3 in the Toll-like receptor-dependent and -independent antiviral response
G. Oganesyan (2006)
10.1002/path.4239
Constitutive activation of distinct NF-κB signals in EBV-associated nasopharyngeal carcinoma.
Grace Tin-Yun Chung (2013)
10.1016/j.devcel.2013.01.020
Regulation of Hippo signaling by EGFR-MAPK signaling through Ajuba family proteins.
B. Reddy (2013)
10.1038/NATURE12222
Comprehensivemolecular characterization of clear cell renal cell carcinoma
C. Creighton (2013)
10.1093/nar/29.1.308
dbSNP: the NCBI database of genetic variation
S. Sherry (2001)
Constitutive activation of distinct NF-kappaB signals in EBV-associated nasopharyngeal carcinoma. The Journal of pathology
Gt Chung
10.3389/fgene.2013.00095
LIM Protein Ajuba Participates in the Repression of the ATR-Mediated DNA Damage Response
Sampada Kalan (2013)
Author manuscript; available in PMC 2015 July 29. Author Manuscript Author Manuscript Author Manuscript Author Manuscript
10.1371/journal.ppat.1003384
Human Papillomavirus (HPV) Upregulates the Cellular Deubiquitinase UCHL1 to Suppress the Keratinocyte's Innate Immune Response
Rezaul Karim (2013)
CD40-induced growth inhibition in epithelial cells is mimicked by Epstein-Barr Virus-encoded LMP1: involvement of TRAF3 as a common mediator.
A. Eliopoulos (1996)
10.1016/j.ccr.2007.07.004
Frequent engagement of the classical and alternative NF-kappaB pathways by diverse genetic abnormalities in multiple myeloma.
C. Annunziata (2007)
reconciling the dual roles of caspase 8 in cell death and survival
A. Oberst (2011)
10.1038/bjc.1990.437
Lack of MHC class I antigens and tumour aggressiveness of the squamous cell carcinoma of the larynx.
Francisco Javier Frutos Esteban (1990)
10.1126/science.1208130
The Mutational Landscape of Head and Neck Squamous Cell Carcinoma
Nicolas Stransky (2011)
LIM protein Ajuba participates in the repression of the ATRmediated DNA damage response. Frontiers in genetics
S Kalan (2013)
10.3233/CLO-2009-0471
Genetic Classification of Oral and Oropharyngeal Carcinomas Identifies Subgroups with a Different Prognosis
Serge J. Smeets (2009)
10.1073/pnas.97.19.10395
Molecular basis for CD40 signaling mediated by TRAF3.
C. Z. Ni (2000)
10.1158/1078-0432.CCR-06-0913
Mutant Epidermal Growth Factor Receptor (EGFRvIII) Contributes to Head and Neck Cancer Growth and Resistance to EGFR Targeting
J. Sok (2006)
10.1083/jcb.201107162
Ajuba is required for Rac activation and maintenance of E-cadherin adhesion
Sébastien Nola (2011)
10.1158/1078-0432.CCR-12-1558
An Epithelial–Mesenchymal Transition Gene Signature Predicts Resistance to EGFR and PI3K Inhibitors and Identifies Axl as a Therapeutic Target for Overcoming EGFR Inhibitor Resistance
L. Byers (2012)
10.1126/science.278.5344.1812
Requirement of NF-kappaB activation to suppress p53-independent apoptosis induced by oncogenic Ras.
M. Mayo (1997)
10.1038/ng.2762
Emerging landscape of oncogenic signatures across human cancers
Giovanni Ciriello (2013)
10.1159/000132342
Integration sites of human papillomavirus 18 DNA sequences on HeLa cell chromosomes.
N. Popescu (1987)
competition for Raf kinase
Park (2001)
10.1038/ncb1608
NUP98–NSD1 links H3K36 methylation to Hox-A gene activation and leukaemogenesis
G. Wang (2007)
10.1038/jid.2012.245
A transposon-based analysis of gene mutations related to skin cancer development.
Rita M Quintana (2013)
T.et al.dbSNP: the NCBIdatabaseofgenetic variation.NucleicAcidsRes
S. Sherry (2001)
10.1038/bjc.1995.346
Frequency of down-regulation of individual HLA-A and -B alleles in cervical carcinomas in relation to TAP-1 expression.
Peter J. Keating (1995)
10.4161/cc.10.18.17350
Network calisthenics
Jeffrey V. Wong (2011)
10.1002/ijc.25516
Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008.
Jacques Ferlay (2010)
10.1371/journal.pone.0056823
Molecular Subtypes in Head and Neck Cancer Exhibit Distinct Patterns of Chromosomal Gain and Loss of Canonical Cancer Genes
Vonn Walter (2013)
Molecular basis for CD40 signaling mediated by TRAF3
Ni (2000)
10.1158/0008-5472.CAN-12-3848
HMGA2 is a driver of tumor metastasis.
A. Morishita (2013)
DeltaNp63 versatilely regulates a Broad NF-kappaB gene program and promotes squamous epithelial proliferation, migration, and inflammation. Cancer research
X Yang (2011)
10.1126/science.1206923
Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1
N. Agrawal (2011)
10.1002/ijc.10398
Effects of pharmacologic antagonists of epidermal growth factor receptor, PI3K and MEK signal kinases on NF-kappaB and AP-1 activation and IL-8 and VEGF expression in human head and neck squamous cell carcinoma lines.
C. Bancroft (2002)
10.1126/science.1220834
Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma
Devendra Singh (2012)
LIM protein Ajuba participates in the repressionof theATR-mediatedDNAdamage
S. Kalan (2013)
10.1016/j.bbrc.2010.05.017
The LIM protein Ajuba is required for ciliogenesis and left-right axis determination in medaka.
Yoko Nagai (2010)
10.1101/gad.1413306
Loss of transforming growth factor-beta type II receptor promotes metastatic head-and-neck squamous cell carcinoma.
Shi-Long Lu (2006)
Author manuscript; available in PMC
10.1128/JVI.01993-10
Acquisition of Host-Derived CD40L by HIV-1 In Vivo and Its Functional Consequences in the B-Cell Compartment † † Supplemental material for this article may be found at http://dx.doi.org/10.1128/JVI.01993-10.
Michaël Imbeault (2010)
10.1126/scisignal.2004324
Ajuba Family Proteins Link JNK to Hippo Signaling
Gongping Sun (2013)
10.1038/sj.onc.1210644
Ajuba negatively regulates the Wnt signaling pathway by promoting GSK-3β-mediated phosphorylation of β-catenin
K. Haraguchi (2008)
10.1002/0471142905.hg1011s57
The Catalogue of Somatic Mutations in Cancer (COSMIC).
S. Forbes (2008)
10.1056/NEJMoa0912217
Human papillomavirus and survival of patients with oropharyngeal cancer.
K. Ang (2010)
10.4161/cc.24573
Polo-like kinase 1 inhibitors, mitotic stress and the tumor suppressor p53
Mourad Sanhaji (2013)
10.1038/nrc2675
Crosstalk of Notch with p53 and p63 in cancer growth control
Gian Paolo Dotto (2009)
10.1006/bbrc.2001.5713
Opposite role of Ras in tumor necrosis factor-alpha-induced cell cycle regulation: competition for Raf kinase.
Seung Jong Park (2001)
control of E2F dynamics in cell cycle entry
J. V. Wong (2011)
10.1158/0008-5472.CAN-10-3445
ΔNp63 versatilely regulates a Broad NF-κB gene program and promotes squamous epithelial proliferation, migration, and inflammation.
X. Yang (2011)
10.1038/ng.2538
Recurrent somatic mutation of FAT1 in multiple human cancers leads to aberrant Wnt activation
L. Morris (2013)
10.1038/nrm3214
It cuts both ways: reconciling the dual roles of caspase 8 in cell death and survival
Andrew Oberst (2011)
10.1038/nature12222
COMPREHENSIVE MOLECULAR CHARACTERIZATION OF CLEAR CELL RENAL CELL CARCINOMA
The Cancer Genome Atlas Research Network (2013)
10.1016/S1359-6349(07)70161-1
Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression.
C. Chung (2004)
10.1158/0008-5472.CAN-05-2749
Somatic mutations lead to an oncogenic deletion of met in lung cancer.
Monica Kong-Beltran (2006)
Ajuba negatively regulates the Wnt signaling pathway by promoting GSK-3beta-mediated phosphorylation of beta-catenin.
K. Haraguchi (2008)



This paper is referenced by
10.1007/s10637-016-0367-2
Phase I trial of dacomitinib, a pan-human epidermal growth factor receptor (HER) inhibitor, with concurrent radiotherapy and cisplatin in patients with locoregionally advanced squamous cell carcinoma of the head and neck (XDC-001)
Amy Prawira (2016)
10.1016/J.TRECAN.2016.04.001
Human papillomaviruses: research priorities for the next decade.
Erika Langsfeld (2016)
10.1101/2020.05.28.122291
SARS-CoV-2 infection induces EMT-like molecular changes, including ZEB1-mediated repression of the viral receptor ACE2, in lung cancer models
C. A. Stewart (2020)
10.1177/0022034515601960
Targeting Head and Neck Cancer Stem Cells
Andrew C. Birkeland (2015)
10.1371/journal.pone.0141695
Similar Squamous Cell Carcinoma Epithelium microRNA Expression in Never Smokers and Ever Smokers
A. Kolokythas (2015)
10.1158/0008-5472.CAN-15-1004
Genomic Profiling of Penile Squamous Cell Carcinoma Reveals New Opportunities for Targeted Therapy.
Andrew S. McDaniel (2015)
10.1371/journal.pone.0181356
ErbB activation signatures as potential biomarkers for anti-ErbB3 treatment in HNSCC
Diego Beltran Alvarado (2017)
10.1002/path.4953
Comprehensive T-cell immunophenotyping and next-generation sequencing of human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinomas.
Kate Poropatich (2017)
10.2217/fon-2016-0073
Induction chemotherapy for head and neck cancer: is there still a role?
Roger Ove (2016)
10.1016/j.ejca.2016.06.006
Human papillomavirus oncoprotein E6 upregulates c-Met through p53 downregulation.
Guoqing Qian (2016)
10.1016/j.oraloncology.2016.04.004
Immune cells and prognosis in HPV-associated oropharyngeal squamous cell carcinomas: Review of the literature.
Camelia Nami Saber (2016)
10.1016/j.cell.2016.12.025
Insertions and Deletions Target Lineage-Defining Genes in Human Cancers
Marcin Imielinski (2017)
10.3390/cancers9040039
Hepatocyte Growth Factor/c-Met Signaling in Head and Neck Cancer and Implications for Treatment
Natalie J. Rothenberger (2017)
10.3390/cancers8100087
Novel Immunotherapeutic Approaches for Head and Neck Squamous Cell Carcinoma
Darrin V Bann (2016)
10.1158/1078-0432.CCR-16-0637
Comprehensive Molecular Characterization of Salivary Duct Carcinoma Reveals Actionable Targets and Similarity to Apocrine Breast Cancer
Martin G Dalin (2016)
10.1159/000452432
Targeted Therapy of Head and Neck Cancer
Damian T. Rieke (2016)
10.3390/ijms161226230
MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma
Steffen Sass (2015)
10.1080/15384101.2016.1148837
Repression of Wnt/β-catenin response elements by p63 (TP63)
Iyoko Katoh (2016)
10.1002/hed.24292
Fibroblast growth factor family aberrations as a putative driver of head and neck squamous cell carcinoma in an epidemiologically low-risk patient as defined by targeted sequencing.
Brittny N. Tillman (2016)
10.1101/313296
Enhanced context reveals the scope of somatic missense mutations driving human cancers
Collin Tokheim (2018)
10.1101/365205
Analysis of head and neck carcinoma progression reveals novel and relevant stage-specific changes associated with immortalisation and malignancy
Ratna Veeramachaneni (2018)
10.1007/978-3-030-03502-0_6
HPV-Associated Oropharyngeal Cancer in the HIV/AIDS Patient.
Jennifer E. Cameron (2019)
10.1038/s41389-019-0144-0
Mechanism for oral tumor cell lysyl oxidase like-2 in cancer development: synergy with PDGF-AB
Faranak Mahjour (2019)
10.1016/j.ctro.2019.05.003
The failure of cetuximab-based de-intensified regimes for HPV-positive OPSCC: A radiobiologists perspective
Thorsten Rieckmann (2019)
10.1097/CCO.0000000000000189
Targeting the immune system in head and neck cancer.
Gilberto de Castro (2015)
10.1101/267245
Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival
Daniele Ramazzotti (2018)
10.3390/cancers7040879
The Tip of the Iceberg: Clinical Implications of Genomic Sequencing Projects in Head and Neck Cancer
Andrew C. Birkeland (2015)
10.3390/jcm7090241
A Review of HPV-Related Head and Neck Cancer
Kazuhiro Kobayashi (2018)
10.3389/fcimb.2020.00143
Human Papilloma Virus Increases ΔNp63α Expression in Head and Neck Squamous Cell Carcinoma
Simona Citro (2020)
10.1101/2020.05.08.085555
Expression of the long noncoding RNA DINO in HPV positive cervical cancer cells reactivates the dormant TP53 tumor suppressor through ATM/CHK2 signaling
Surendra Sharma (2020)
10.1038/s41588-019-0562-0
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition
Bernardo Rodriguez-Martin (2020)
10.1016/j.oraloncology.2019.09.009
Trimodality therapy for HPV-positive oropharyngeal cancer: A population-based study: Trimodality therapy for HPV+ OPC.
Nina N Sanford (2019)
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