Show simple item record

dc.contributor.authorFreeman, Samuel Spenser Sharpe
dc.contributor.authorJung, Joonil
dc.contributor.authorOjesina, Akinyemi
dc.contributor.authorMeyerson, Matthew L.
dc.date.accessioned2018-05-17T19:40:26Z
dc.date.available2018-05-17T19:40:26Z
dc.date.issued2014-10
dc.identifier.issn0027-8424
dc.identifier.issn1091-6490
dc.identifier.urihttp://hdl.handle.net/1721.1/115484
dc.description.abstractPrevious studies have established that a subset of head and neck tumors contains human papillomavirus (HPV) sequences and that HPV-driven head and neck cancers display distinct biological and clinical features. HPV is known to drive cancer by the actions of the E6 and E7 oncoproteins, but the molecular architecture of HPV infection and its interaction with the host genome in head and neck cancers have not been comprehensively described. We profiled a cohort of 279 head and neck cancers with next generation RNA and DNA sequencing and show that 35 (12.5%) tumors displayed evidence of high-risk HPV types 16, 33, or 35. Twenty-five cases had integration of the viral genome into one or more locations in the human genome with statistical enrichment for genic regions. Integrations had a marked impact on the human genome and were associated with alterations in DNA copy number, mRNA transcript abundance and splicing, and both inter- and intrachromosomal rearrangements. Many of these events involved genes with documented roles in cancer. Cancers with integrated vs. nonintegrated HPV displayed different patterns of DNA methylation and both human and viral gene expressions. Together, these data provide insight into the mechanisms by which HPV interacts with the human genome beyond expression of viral oncoproteins and suggest that specific integration events are an integral component of viral oncogenesis.en_US
dc.publisherNational Academy of Sciences (U.S.)en_US
dc.relation.isversionofhttp://dx.doi.org/10.1073/PNAS.1416074111en_US
dc.rightsArticle is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.en_US
dc.sourcePNASen_US
dc.titleCharacterization of HPV and host genome interactions in primary head and neck cancersen_US
dc.typeArticleen_US
dc.identifier.citationParfenov, M. et al. “Characterization of HPV and Host Genome Interactions in Primary Head and Neck Cancers.” Proceedings of the National Academy of Sciences 111, 43 (October 2014): 15544–15549en_US
dc.contributor.departmentBroad Institute of MIT and Harvarden_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Biologyen_US
dc.contributor.mitauthorFreeman, Samuel Spenser Sharpe
dc.contributor.mitauthorJung, Joonil
dc.contributor.mitauthorOjesina, Akinyemi
dc.contributor.mitauthorMeyerson, Matthew L
dc.relation.journalProceedings of the National Academy of Sciencesen_US
dc.type.urihttp://purl.org/eprint/type/JournalArticleen_US
eprint.statushttp://purl.org/eprint/status/PeerRevieweden_US
dc.date.updated2018-05-07T15:10:08Z
dspace.orderedauthorsParfenov, M.; Pedamallu, C. S.; Gehlenborg, N.; Freeman, S. S.; Danilova, L.; Bristow, C. A.; Lee, S.; Hadjipanayis, A. G.; Ivanova, E. V.; Wilkerson, M. D.; Protopopov, A.; Yang, L.; Seth, S.; Song, X.; Tang, J.; Ren, X.; Zhang, J.; Pantazi, A.; Santoso, N.; Xu, A. W.; Mahadeshwar, H.; Wheeler, D. A.; Haddad, R. I.; Jung, J.; Ojesina, A. I.; Issaeva, N.; Yarbrough, W. G.; Hayes, D. N.; Grandis, J. R.; El-Naggar, A. K.; Meyerson, M.; Park, P. J.; Chin, L.; Seidman, J. G.; Hammerman, P. S.; Kucherlapati, R.; Ally, A.; Balasundaram, M.; Birol, I.; Bowlby, R.; Butterfield, Y. S. N.; Carlsen, R.; Cheng, D.; Chu, A.; Dhalla, N.; Guin, R.; Holt, R. A.; Jones, S. J. M.; Lee, D.; Li, H. I.; Marra, M. A.; Mayo, M.; Moore, R. A.; Mungall, A. J.; Robertson, A. G.; Schein, J. E.; Sipahimalani, P.; Tam, A.; Thiessen, N.; Wong, T.; Protopopov, A.; Santoso, N.; Lee, S.; Parfenov, M.; Zhang, J.; Mahadeshwar, H. S.; Tang, J.; Ren, X.; Seth, S.; Haseley, P.; Zeng, D.; Yang, L.; Xu, A. W.; Song, X.; Pantazi, A.; Bristow, C.; Hadjipanayis, A.; Seidman, J.; Chin, L.; Park, P. J.; Kucherlapati, R.; Akbani, R.; Casasent, T.; Liu, W.; Lu, Y.; Mills, G.; Motter, T.; Weinstein, J.; Diao, L.; Wang, J.; Fan, Y. H.; Liu, J.; Wang, K.; Auman, J. T.; Balu, S.; Bodenheimer, T.; Buda, E.; Hayes, D. N.; Hoadley, K. A.; Hoyle, A. P.; Jefferys, S. R.; Jones, C. D.; Kimes, P. K.; Marron, J. S.; Meng, S.; Mieczkowski, P. A.; Mose, L. E.; Parker, J. S.; Perou, C. M.; Prins, J. F.; Roach, J.; Shi, Y.; Simons, J. V.; Singh, D.; Soloway, M. G.; Tan, D.; Veluvolu, U.; Walter, V.; Waring, S.; Wilkerson, M. D.; Wu, J.; Zhao, N.; Cherniack, A. D.; Hammerman, P. S.; Tward, A. D.; Pedamallu, C. S.; Saksena, G.; Jung, J.; Ojesina, A. I.; Carter, S. L.; Zack, T. I.; Schumacher, S. E.; Beroukhim, R.; Freeman, S. S.; Meyerson, M.; Cho, J.; Chin, L.; Getz, G.; Noble, M. S.; DiCara, D.; Zhang, H.; Heiman, D. I.; Gehlenborg, N.; Voet, D.; Lin, P.; Frazer, S.; Stojanov, P.; Liu, Y.; Zou, L.; Kim, J.; Lawrence, M. S.; Sougnez, C.; Lichtenstein, L.; Cibulskis, K.; Lander, E.; Gabriel, S. B.; Muzny, D.; Doddapaneni, H.; Kovar, C.; Reid, J.; Morton, D.; Han, Y.; Hale, W.; Chao, H.; Chang, K.; Drummond, J. A.; Gibbs, R. A.; Kakkar, N.; Wheeler, D.; Xi, L.; Ciriello, G.; Ladanyi, M.; Lee, W.; Ramirez, R.; Sander, C.; Shen, R.; Sinha, R.; Weinhold, N.; Taylor, B. S.; Aksoy, B. A.; Dresdner, G.; Gao, J.; Gross, B.; Jacobsen, A.; Reva, B.; Schultz, N.; Sumer, S. O.; Sun, Y.; Chan, T.; Morris, L.; Stuart, J.; Benz, S.; Ng, S.; Benz, C.; Yau, C.; Baylin, S. B.; Cope, L.; Danilova, L.; Herman, J. G.; Bootwalla, M.; Maglinte, D. T.; Laird, P. W.; Triche, T.; Weisenberger, D. J.; Van Den Berg, D. J.; Agrawal, N.; Bishop, J.; Boutros, P. C.; Bruce, J. P.; Byers, L. A.; Califano, J.; Carey, T. E.; Chen, Z.; Cheng, H.; Chiosea, S. I.; Cohen, E.; Diergaarde, B.; Egloff, A. M.; El-Naggar, A. K.; Ferris, R. L.; Frederick, M. J.; Grandis, J. R.; Guo, Y.; Haddad, R. I.; Hammerman, P. S.; Harris, T.; Hayes, D. N.; Hui, A. B.; Lee, J. J.; Lippman, S. M.; Liu, F.-F.; McHugh, J. B.; Myers, J.; Ng, P. K. S.; Perez-Ordonez, B.; Pickering, C. R.; Prystowsky, M.; Romkes, M.; Saleh, A. D.; Sartor, M. A.; Seethala, R.; Seiwert, T. Y.; Si, H.; Tward, A. D.; Van Waes, C.; Waggott, D. M.; Wiznerowicz, M.; Yarbrough, W.; Zhang, J.; Zuo, Z.; Burnett, K.; Crain, D.; Gardner, J.; Lau, K.; Mallery, D.; Morris, S.; Paulauskis, J.; Penny, R.; Shelton, C.; Shelton, T.; Sherman, M.; Yena, P.; Black, A. D.; Bowen, J.; Frick, J.; Gastier-Foster, J. M.; Harper, H. A.; Lichtenberg, T. M.; Ramirez, N. C.; Wise, L.; Zmuda, E.; Baboud, J.; Jensen, M. A.; Kahn, A. B.; Pihl, T. D.; Pot, D. A.; Srinivasan, D.; Walton, J. S.; Wan, Y.; Burton, R.; Davidsen, T.; Demchok, J. A.; Eley, G.; Ferguson, M. L.; Shaw, K. R. M.; Ozenberger, B. A.; Sheth, M.; Sofia, H. J.; Tarnuzzer, R.; Wang, Z.; Yang, L.; Zenklusen, J. C.; Saller, C.; Tarvin, K.; Chen, C.; Bollag, R.; Weinberger, P.; Golusinski, W.; Golusinski, P.; Ibbs, M.; Korski, K.; Mackiewicz, A.; Suchorska, W.; Szybiak, B.; Wiznerowicz, M.; Burnett, K.; Curley, E.; Gardner, J.; Mallery, D.; Penny, R.; Shelton, T.; Yena, P.; Beard, C.; Mitchell, C.; Sandusky, G.; Agrawal, N.; Ahn, J.; Bishop, J.; Califano, J.; Khan, Z.; Bruce, J. P.; Hui, A. B.; Irish, J.; Liu, F.-F.; Perez-Ordonez, B.; Waldron, J.; Boutros, P. C.; Waggott, D. M.; Myers, J.; Lippman, S. M.; Egea, S.; Gomez-Fernandez, C.; Herbert, L.; Bradford, C. R.; Carey, T. E.; Chepeha, D. B.; Haddad, A. S.; Jones, T. R.; Komarck, C. M.; Malakh, M.; McHugh, J. B.; Moyer, J. S.; Nguyen, A.; Peterson, L. A.; Prince, M. E.; Rozek, L. S.; Sartor, M. A.; Taylor, E. G.; Walline, H. M.; Wolf, G. T.; Boice, L.; Chera, B. S.; Funkhouser, W. K.; Gulley, M. L.; Hackman, T. G.; Hayes, D. N.; Hayward, M. C.; Huang, M.; Rathmell, W. K.; Salazar, A. H.; Shockley, W. W.; Shores, C. G.; Thorne, L.; Weissler, M. C.; Wrenn, S.; Zanation, A. M.; Chiosea, S. I.; Diergaarde, B.; Egloff, A. M.; Ferris, R. L.; Romkes, M.; Seethala, R.; Brown, B. T.; Guo, Y.; Pham, M.; Yarbrough, W. G.en_US
dspace.embargo.termsNen_US
mit.licensePUBLISHER_POLICYen_US


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record