The head and neck cancer cell oncogenome: a platform for the development of precision molecular therapies

The recent elucidation of the genomic landscape of head and neck squamous cell carcinoma (HNSCC) has provided a unique opportunity to develop selective cancer treatment options. These efforts will require the establishment of relevant HNSCC models for preclinical testing. Here, we performed full exome and transcriptome sequencing of a large panel of HNSCC-derived cells from different anatomical locations and human papillomavirus (HPV) infection status. These cells exhibit typical mutations in TP53, FAT1, CDK2NA, CASP8, and NOTCH1, and copy number variations (CNVs) and mutations in PIK3CA, HRAS, and PTEN that reflect the widespread activation of the PI3K-mTOR pathway. SMAD4 alterations were observed that may explain the decreased tumor suppressive effect of TGF-β in HNSCC. Surprisingly, we identified HPV+ HNSCC cells harboring TP53 mutations, and documented aberrant TP53 expression in a subset of HPV+ HNSCC cases. This analysis also revealed that most HNSCC cells harbor multiple mutations and CNVs in epigenetic modifiers (e.g., EP300, CREBP, MLL1, MLL2, MLL3, KDM6A, and KDM6B) that may contribute to HNSCC initiation and progression. These genetically-defined experimental HNSCC cellular systems, together with the identification of novel actionable molecular targets, may now facilitate the pre-clinical evaluation of emerging therapeutic agents in tumors exhibiting each precise genomic alteration.

[1]  A. Giuliano,et al.  HEAD AND NECK SQUAMOUS CELL CANCER AND THE HUMAN PAPILLOMAVIRUS: SUMMARY OF A NATIONAL CANCER INSTITUTE STATE OF THE SCIENCE MEETING, , 2009 .

[2]  A. Cuddihy,et al.  The human papilloma virus (HPV)-18 E6 oncoprotein physically associates with Tyk2 and impairs Jak-STAT activation by interferon-alpha. , 1999, Oncogene.

[3]  Heather L. Mulder,et al.  The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes , 2014, Nature Communications.

[4]  H. Ohtsuki,et al.  Accumulation of driver and passenger mutations during tumor progression , 2009, Proceedings of the National Academy of Sciences.

[5]  J. Manola,et al.  TP53 mutations and survival in squamous-cell carcinoma of the head and neck. , 2007, The New England journal of medicine.

[6]  G. Peters,et al.  Histone demethylase JMJD3 contributes to epigenetic control of INK4a/ARF by oncogenic RAS. , 2009, Genes & development.

[7]  R. Beart,et al.  Methylation of the 5' CpG island of the p16/CDKN2 tumor suppressor gene in normal and transformed human tissues correlates with gene silencing. , 1995, Cancer research.

[8]  D. Wong,et al.  Dissecting the Akt/Mammalian Target of Rapamycin Signaling Network: Emerging Results from the Head and Neck Cancer Tissue Array Initiative , 2007, Clinical Cancer Research.

[9]  E. Sausville,et al.  Mammalian target of rapamycin, a molecular target in squamous cell carcinomas of the head and neck. , 2005, Cancer research.

[10]  Giacomo Cavalli,et al.  Trithorax group proteins: switching genes on and keeping them active , 2011, Nature Reviews Molecular Cell Biology.

[11]  A. Cuddihy,et al.  The human papilloma virus (HPV)-18 E6 oncoprotein physically associates with Tyk2 and impairs Jak-STAT activation by interferon-α , 1999, Oncogene.

[12]  J. Myers,et al.  Xenograft models of head and neck cancers , 2009, Head & neck oncology.

[13]  Michael J. Ziller,et al.  Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells , 2013, Cell.

[14]  N. Dubrawsky.  Cancer statistics , 1989, CA: a cancer journal for clinicians.

[15]  Pornpimol Charoentong,et al.  ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..

[16]  C. Van Waes,et al.  Role of activated nuclear factor‐κB in the pathogenesis and therapy of squamous cell carcinoma of the head and neck , 2007, Head & neck.

[17]  M. Dawson,et al.  Cancer Epigenetics: From Mechanism to Therapy , 2012, Cell.

[18]  Y. Mitsuishi,et al.  The Keap1–Nrf2 system in cancers: stress response and anabolic metabolism , 2012, Front. Oncol..

[19]  Malini Guha.  Blockbuster dreams for Pfizer's CDK inhibitor , 2013, Nature Biotechnology.

[20]  S A Forbes,et al.  The Catalogue of Somatic Mutations in Cancer (COSMIC) , 2008, Current protocols in human genetics.

[21]  Ruud H. Brakenhoff,et al.  The molecular biology of head and neck cancer , 2011, Nature Reviews Cancer.

[22]  Levi A Garraway,et al.  Genomic Analysis of Head and Neck Squamous Cell Carcinoma Cell Lines and Human Tumors: A Rational Approach to Preclinical Model Selection , 2014, Molecular Cancer Research.

[23]  J. Herman,et al.  Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[24]  A I Saeed,et al.  TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.

[25]  Takafumi Suzuki,et al.  Roles of Keap1–Nrf2 System in Upper Aerodigestive Tract Carcinogenesis , 2012, Cancer Prevention Research.

[26]  Mei Zhao,et al.  Disruptive TP53 Mutation Is Associated with Aggressive Disease Characteristics in an Orthotopic Murine Model of Oral Tongue Cancer , 2011, Clinical Cancer Research.

[27]  P. Pandolfi,et al.  Role of the proto-oncogene Pokemon in cellular transformation and ARF repression , 2005, Nature.

[28]  D. Sidransky,et al.  Head and Neck Cancer in CNonsmokers: A Distinct Clinical and Molecular Entity , 1999, The Laryngoscope.

[29]  P. Meltzer,et al.  The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology. , 2013, Cancer research.

[30]  E. K. Parkinson,et al.  Dysregulated TGF-β1-induced Smad signalling occurs as a result of defects in multiple components of the TGF-β signalling pathway in human head and neck carcinoma cell lines , 2006 .

[31]  L. Liau,et al.  Recurrent somatic mutation of FAT1 in multiple human cancers leads to aberrant Wnt activation , 2013, Nature Genetics.

[32]  P. Harari,et al.  Enhanced radiation sensitivity in HPV-positive head and neck cancer. , 2013, Cancer research.

[33]  Rajiv Sarin,et al.  Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups , 2013, Nature Communications.

[34]  S. Hewitt,et al.  mTOR as a Molecular Target in HPV-Associated Oral and Cervical Squamous Carcinomas , 2012, Clinical Cancer Research.

[35]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[36]  R. Derynck,et al.  Receptor-associated Mad homologues synergize as effectors of the TGF-β response , 1996, Nature.

[37]  G. Clayman,et al.  Resetting the histone code at CDKN2A in HNSCC by inhibition of DNA methylation , 2003, Oncogene.

[38]  M. Soda,et al.  Cancer‐associated missense mutations of caspase‐8 activate nuclear factor‐κB signaling , 2013, Cancer science.

[39]  Adam A. Margolin,et al.  The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity , 2012, Nature.

[40]  Mei Zhao,et al.  Assembly and Initial Characterization of a Panel of 85 Genomically Validated Cell Lines from Diverse Head and Neck Tumor Sites , 2011, Clinical Cancer Research.

[41]  D. Crowe,et al.  Role of microRNA-138 as a potential tumor suppressor in head and neck squamous cell carcinoma. , 2013, International review of cell and molecular biology.

[42]  R. Javier.  Cell polarity proteins: common targets for tumorigenic human viruses , 2008, Oncogene.

[43]  V. Mieulet,et al.  A MAP4 kinase related to Ste20 is a nutrient-sensitive regulator of mTOR signalling. , 2007, The Biochemical journal.

[44]  E. K. Parkinson,et al.  Dysregulated TGF-beta1-induced Smad signalling occurs as a result of defects in multiple components of the TGF-beta signalling pathway in human head and neck carcinoma cell lines. , 2006, International Journal of Oncology.

[45]  K. Nakashiro,et al.  Human FAT1 cadherin controls cell migration and invasion of oral squamous cell carcinoma through the localization of β-catenin. , 2011, Oncology reports.

[46]  T. Wong,et al.  Identification of pyruvate kinase type M2 as potential oncoprotein in squamous cell carcinoma of tongue through microRNA profiling , 2008, International journal of cancer.

[47]  Avi Ma'ayan,et al.  Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool , 2013, BMC Bioinformatics.

[48]  P. Blanchard,et al.  Treatment de‐escalation in HPV‐positive oropharyngeal carcinoma: Ongoing trials, critical issues and perspectives , 2015, International journal of cancer.

[49]  D. Hayes,et al.  The Cancer Genome Atlas: Integrated analysis of genome alterations in squamous cell carcinoma of the head and neck. , 2013 .

[50]  J. Massagué,et al.  Mechanisms of TGF-β Signaling from Cell Membrane to the Nucleus , 2003, Cell.

[51]  D. Sidransky,et al.  Immunohistochemical detection of p53 protein accumulation in head and neck cancer: correlation with p53 gene alterations. , 1999, Human pathology.

[52]  C. Meijer,et al.  Integrated human papillomavirus type 16 and loss of heterozygosity at 11q22 and 18q21 in an oral carcinoma and its derivative cell line. , 1995, Cancer research.

[53]  T. Veldman,et al.  Human papillomavirus E6 and Myc proteins associate in vivo and bind to and cooperatively activate the telomerase reverse transcriptase promoter , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[54]  J. Brugge,et al.  Outgrowth of Single Oncogene-expressing Cells from Suppressive Epithelial Environments , 2012, Nature.

[55]  A. Shahangian,et al.  Critical role of TRAF3 in the Toll-like receptor-dependent and -independent antiviral response , 2006, Nature.

[56]  R. Derynck,et al.  Receptor-associated Mad homologues synergize as effectors of the TGF-beta response. , 1996, Nature.

[57]  S. Warnakulasuriya.  Causes of oral cancer – an appraisal of controversies , 2009, BDJ.

[58]  J. Tschopp,et al.  Induction of TNF Receptor I-Mediated Apoptosis via Two Sequential Signaling Complexes , 2003, Cell.

[59]  D. Pehlivan,et al.  Involvement of EphA2 in head and neck squamous cell carcinoma: mRNA expression, loss of heterozygosity and immunohistochemical studies. , 2008, Oncology reports.

[60]  Zhiyong Wang,et al.  mTOR Co-Targeting in Cetuximab Resistance in Head and Neck Cancers Harboring PIK3CA and RAS Mutations , 2014, Journal of the National Cancer Institute.

[61]  R. Gibbs,et al.  Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers. , 2013, Cancer discovery.

[62]  J. Miller,et al.  Predicting the Functional Effect of Amino Acid Substitutions and Indels , 2012, PloS one.

[63]  Kevin Fung,et al.  Frequent mutations in TP53 and CDKN2A found by next-generation sequencing of head and neck cancer cell lines. , 2012, Archives of otolaryngology--head & neck surgery.

[64]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[65]  Serban Nacu,et al.  Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..

[66]  J. Gutkind,et al.  Exploiting the head and neck cancer oncogenome: widespread PI3K-mTOR pathway alterations and novel molecular targets. , 2013, Cancer discovery.

[67]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[68]  R. Ferris,et al.  Human papillomavirus-16 associated squamous cell carcinoma of the head and neck (SCCHN): a natural disease model provides insights into viral carcinogenesis. , 2005, European journal of cancer.

[69]  A. McKenna,et al.  The Mutational Landscape of Head and Neck Squamous Cell Carcinoma , 2011, Science.

[70]  A. Jemal,et al.  Cancer statistics, 2014 , 2014, CA: a cancer journal for clinicians.

[71]  T. Sasagawa,et al.  A new PCR-based assay amplifies the E6-E7 genes of most mucosal human papillomaviruses (HPV). , 2000, Virus research.

[72]  Christine H Chung,et al.  Human Papillomavirus in Head and Neck Cancer: Its Role in Pathogenesis and Clinical Implications , 2009, Clinical Cancer Research.

[73]  K. Cornetta,et al.  Aberrant expression of the myeloid zinc finger gene, MZF-1, is oncogenic. , 1995, Cancer research.

[74]  R. Lotan,et al.  DPC4, a candidate tumor suppressor gene, is altered infrequently in head and neck squamous cell carcinoma. , 1996, Cancer research.

[75]  D. Sidransky,et al.  Head and neck cancer. , 2001, The New England journal of medicine.

[76]  Simion I. Chiosea,et al.  Frequent mutation of the PI3K pathway in head and neck cancer defines predictive biomarkers. , 2013, Cancer discovery.

[77]  J Silvio Gutkind,et al.  Decreased lymphangiogenesis and lymph node metastasis by mTOR inhibition in head and neck cancer. , 2011, Cancer research.

[78]  J. Massagué,et al.  Mechanisms of TGF-beta signaling from cell membrane to the nucleus. , 2003, Cell.

[79]  Esther Kim,et al.  Human papillomavirus and rising oropharyngeal cancer incidence in the United States. , 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[80]  R. Gibbs,et al.  Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1 , 2011, Science.

[81]  R. Campbell,et al.  Cancer epigenetics drug discovery and development: the challenge of hitting the mark. , 2014, The Journal of clinical investigation.

[82]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[83]  K. Münger,et al.  The human papilloma virus-16 E7 oncoprotein is able to bind to the retinoblastoma gene product. , 1989, Science.