The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.
APOBEC-Mediated Cytosine Deamination Links PIK3CA Helical Domain Mutations to Human Papillomavirus-Driven Tumor Development
Open accessAbstract
APOBEC3B cytosine deaminase activity has recently emerged as a significant mutagenic factor in human cancer. APOBEC activity is induced in virally infected cells, and APOBEC signature mutations occur at high frequency in cervical cancers (CESC), over 99% of which are caused by human papillomavirus (HPV). We tested whether APOBEC-mediated mutagenesis is particularly important in HPV-associated tumors by comparing the exomes of HPV+ and HPV- head and neck squamous cell carcinomas (HNSCCs) sequenced by The Cancer Genome Atlas project. As expected, HPV- HNSCC displays a smoking-associated mutational signature, whereas our data suggest that reduced exposure to exogenous carcinogens in HPV+ HNSCC creates a selective pressure that favors emergence of tumors with APOBEC-mediated driver mutations. Finally, we provide evidence that APOBEC activity is responsible for the generation of helical domain hot spot mutations in the PIK3CA gene across multiple cancers. Our findings implicate APOBEC activity as a key driver of PIK3CA mutagenesis and HPV-induced transformation.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Comprehensive molecular portraits of human breast tumours
The Cancer Genome Atlas Network (2012) · Nature · doi:10.1038/nature11412 · Cited by 12,129
Signatures of mutational processes in human cancer
Initiative, A. P. C. G., Alexandrov, L. B., ICGC Breast Cancer Consortium, ICGC MMML-Seq Consortium, PedBrain, I., Nik-Zainal, S., Wedge, D. C., Aparicio, S. A. J. R., Behjati, S., Biankin, A. V., et al. (2013) · Nature · doi:10.1038/nature12477 · Cited by 9,660
Mutational heterogeneity in cancer and the search for new cancer-associated genes
Lawrence, M. S., Stojanov, P., Polak, P., Kryukov, G. V., Cibulskis, K., Sivachenko, A., Carter, S. L., Stewart, C., Mermel, C. H., Roberts, S. A., et al. (2013) · Nature · doi:10.1038/nature12213 · Cited by 5,461
Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes
Parker, J. S., Mullins, M., Cheang, M. C. U., Leung, S., Voduc, D., Vickery, T., Davies, S., Fauron, C., He, X., Hu, Z., et al. (2009) · Journal of Clinical Oncology · doi:10.1200/jco.2008.18.1370 · Cited by 4,721
Human Papillomavirus and Rising Oropharyngeal Cancer Incidence in the United States
Chaturvedi, A. K., Engels, E. A., Pfeiffer, R. M., Hernandez, B. Y., Xiao, W., Kim, E., Jiang, B., Goodman, M. T., Sibug-Saber, M., Cozen, W., et al. (2011) · Journal of Clinical Oncology · doi:10.1200/jco.2011.36.4596 · Cited by 3,638
The Mutational Landscape of Head and Neck Squamous Cell Carcinoma
Stransky, N., Egloff, A. M., Tward, A. D., Kostic, A. D., Cibulskis, K., Sivachenko, A., Kryukov, G. V., Lawrence, M. S., Sougnez, C., McKenna, A., et al. (2011) · Science · doi:10.1126/science.1208130 · Cited by 2,504
Mutational Processes Molding the Genomes of 21 Breast Cancers
Nik-Zainal, S., Alexandrov, L. B., Wedge, D. C., Van Loo, P., Greenman, C. D., Raine, K., Jones, D., Hinton, J., Marshall, J., Stebbings, L. A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.024 · Cited by 1,909
Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1
Agrawal, N., Frederick, M. J., Pickering, C. R., Bettegowda, C., Chang, K., Li, R. J., Fakhry, C., Xie, T.-X., Zhang, J., Wang, J., et al. (2011) · Science · doi:10.1126/science.1206923 · Cited by 1,697
Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts
Mangeat, B., Turelli, P., Caron, G., Friedli, M., Perrin, L., & Trono, D. (2003) · Nature · doi:10.1038/nature01709 · Cited by 1,486
Deciphering Signatures of Mutational Processes Operative in Human Cancer
Alexandrov, L. B., Nik-Zainal, S., Wedge, D. C., Campbell, P. J., & Stratton, M. R. (2013) · Cell Reports · doi:10.1016/j.celrep.2012.12.008 · Cited by 1,277
DNA Deamination Mediates Innate Immunity to Retroviral Infection
Harris, R. S., Bishop, K. N., Sheehy, A. M., Craig, H. M., Petersen-Mahrt, S. K., Watt, I. N., Neuberger, M. S., & Malim, M. H. (2003) · Cell · doi:10.1016/s0092-8674(03)00423-9 · Cited by 1,266
An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers
Roberts, S. A., Lawrence, M. S., Klimczak, L. J., Grimm, S. A., Fargo, D., Stojanov, P., Kiezun, A., Kryukov, G. V., Carter, S. L., Saksena, G., et al. (2013) · Nature Genetics · doi:10.1038/ng.2702 · Cited by 1,167
The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA
Zhang, H., Yang, B., Pomerantz, R. J., Zhang, C., Arunachalam, S. C., & Gao, L. (2003) · Nature · doi:10.1038/nature01707 · Cited by 1,059
Landscape of genomic alterations in cervical carcinomas
Ojesina, A. I., Lichtenstein, L., Freeman, S. S., Pedamallu, C. S., Imaz-Rosshandler, I., Pugh, T. J., Cherniack, A. D., Ambrogio, L., Cibulskis, K., Bertelsen, B., et al. (2014) · Nature · doi:10.1038/nature12881 · Cited by 867
APOBEC3B is an enzymatic source of mutation in breast cancer
Burns, M. B., Lackey, L., Carpenter, M. A., Rathore, A., Land, A. M., Leonard, B., Refsland, E. W., Kotandeniya, D., Tretyakova, N., Nikas, J. B., et al. (2013) · Nature · doi:10.1038/nature11881 · Cited by 838
Mutations induced by ultraviolet light
Pfeifer, G. P., You, Y.-H., & Besaratinia, A. (2005) · Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis · doi:10.1016/j.mrfmmm.2004.06.057 · Cited by 775
Evidence for APOBEC3B mutagenesis in multiple human cancers
Burns, M. B., Temiz, N. A., & Harris, R. S. (2013) · Nature Genetics · doi:10.1038/ng.2701 · Cited by 755
Cytidine Deamination of Retroviral DNA by Diverse APOBEC Proteins
Bishop, K. N., Holmes, R. K., Sheehy, A. M., Davidson, N. O., Cho, S.-J., & Malim, M. H. (2004) · Current Biology · doi:10.1016/j.cub.2004.06.057 · Cited by 619
Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers
Lui, V. W. Y., Hedberg, M. L., Li, H., Vangara, B. S., Pendleton, K., Zeng, Y., Lu, Y., Zhang, Q., Du, Y., Gilbert, B. R., et al. (2013) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0103 · Cited by 589
The AID/APOBEC family of nucleic acid mutators
Conticello, S. G. (2008) · Genome Biology · doi:10.1186/gb-2008-9-6-229 · Cited by 546
Matsumoto, Y., Marusawa, H., Kinoshita, K., Endo, Y., Kou, T., Morisawa, T., Azuma, T., Okazaki, I.-M., Honjo, T., & Chiba, T. (2007) · Nature Medicine · doi:10.1038/nm1566 · Cited by 479
Constitutive Expression of AID Leads to Tumorigenesis
Okazaki, I.-M., Hiai, H., Kakazu, N., Yamada, S., Muramatsu, M., Kinoshita, K., & Honjo, T. (2003) · The Journal of Experimental Medicine · doi:10.1084/jem.20030275 · Cited by 440
Zhao, L., & Vogt, P. K. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712169105 · Cited by 437
Roberts, S. A., Sterling, J., Thompson, C., Harris, S., Mav, D., Shah, R., Klimczak, L. J., Kryukov, G. V., Malc, E., Mieczkowski, P. A., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.03.030 · Cited by 412
Evidence for Editing of Human Papillomavirus DNA by APOBEC3 in Benign and Precancerous Lesions
Vartanian, J.-P., Guétard, D., Henry, M., & Wain-Hobson, S. (2008) · Science · doi:10.1126/science.1153201 · Cited by 331
Oncogenic activities of human papillomaviruses
McLaughlin-Drubin, M. E., & Münger, K. (2009) · Virus Research · doi:10.1016/j.virusres.2009.06.008 · Cited by 321
The landscape of viral expression and host gene fusion and adaptation in human cancer
Tang, K.-W., Alaei-Mahabadi, B., Samuelsson, T., Lindh, M., & Larsson, E. (2013) · Nature Communications · doi:10.1038/ncomms3513 · Cited by 301
Yamanaka, S., Balestra, M. E., Ferrell, L. D., Fan, J., Arnold, K. S., Taylor, S., Taylor, J. M., & Innerarity, T. L. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.18.8483 · Cited by 296
Human papillomavirus in cervical and head-and-neck cancer
Psyrri, A., & DiMaio, D. (2008) · Nature Clinical Practice Oncology · doi:10.1038/ncponc0984 · Cited by 243
Lechner, M., Frampton, G. M., Fenton, T., Feber, A., Palmer, G., Jay, A., Pillay, N., Forster, M., Cronin, M. T., Lipson, D., et al. (2013) · Genome Medicine · doi:10.1186/gm453 · Cited by 217
Self-citationAPOBEC3B Upregulation and Genomic Mutation Patterns in Serous Ovarian Carcinoma
Leonard, B., Hart, S. N., Burns, M. B., Carpenter, M. A., Temiz, N. A., Rathore, A., Vogel, R. I., Nikas, J. B., Law, E. K., Brown, W. L., et al. (2013) · Cancer Research · doi:10.1158/0008-5472.can-13-1753 · Cited by 168
Massive APOBEC3 Editing of Hepatitis B Viral DNA in Cirrhosis
Vartanian, J.-P., Henry, M., Marchio, A., Suspène, R., Aynaud, M.-M., Guétard, D., Cervantes-Gonzalez, M., Battiston, C., Mazzaferro, V., Pineau, P., et al. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000928 · Cited by 166
Chen, Y., Yao, H., Thompson, E. J., Tannir, N. M., Weinstein, J. N., & Su, X. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts665 · Cited by 158
Self-citationCancer-specific mutations in phosphatidylinositol 3-kinase
Vogt, P. K., Kang, S., Elsliger, M., & Gymnopoulos, M. (2007) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2007.05.005 · Cited by 145
Drier, Y., Lawrence, M. S., Carter, S. L., Stewart, C., Gabriel, S., Lander, E. S., Meyerson, M. M., Beroukhim, R., & Getz, G. A. (2012) · Genome Research · doi:10.1101/gr.141382.112 · Cited by 145
Human papillomavirus in a necessary cause of invasive cervical cancer worldwide
(1999) · Pure Amsterdam UMC · doi:10.1002/(sici)1096-9896(199909)189:1 · Cited by 140
Lechner, M., Fenton, T. R., West, J., Wilson, G. A., Feber, A., Henderson, S. R., Thirlwell, C., Dibra, H. K., Jay, A., Butcher, L. M., et al. (2013) · Genome Medicine · doi:10.1186/gm419 · Cited by 128
Self-citationAPOBEC3B mutagenesis in cancer
Kuong, K. J., & Loeb, L. A. (2013) · Nature Genetics · doi:10.1038/ng.2736 · Cited by 101
Base excision repair intermediates are mutagenic in mammalian cells
Simonelli, V. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki749 · Cited by 72
Reward versus Risk: DNA Cytidine Deaminases Triggering Immunity and Disease
Pham, P., Bransteitter, R., & Goodman, M. F. (2005) · Biochemistry · doi:10.1021/bi047481+ · Cited by 71
Roberts, S. A., & Gordenin, D. A. (2014) · BioEssays · doi:10.1002/bies.201300140 · Cited by 57
Cited by
Integrated genomic and molecular characterization of cervical cancer
The Cancer Genome Atlas Research Network (2017) · Nature · doi:10.1038/nature21386 · Cited by 1,479
Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets
Witkiewicz, A. K., McMillan, E. A., Balaji, U., Baek, G., Lin, W.-C., Mansour, J., Mollaee, M., Wagner, K.-U., Koduru, P., Yopp, A., et al. (2015) · Nature Communications · doi:10.1038/ncomms7744 · Cited by 1,115
Biological and therapeutic impact of intratumor heterogeneity in cancer evolution
McGranahan, N., & Swanton, C. (2015) · Cancer Cell · doi:10.1016/j.ccell.2014.12.001 · Cited by 1,077
Co-occurring genomic alterations in non-small-cell lung cancer biology and therapy
Skoulidis, F., & Heymach, J. V. (2019) · Nature Reviews Cancer · doi:10.1038/s41568-019-0179-8 · Cited by 1,019
Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors
Miao, D., Margolis, C. A., Vokes, N. I., Liu, D., Taylor-Weiner, A., Wankowicz, S. M., Adeegbe, D., Keliher, D., Schilling, B., Tracy, A., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0200-2 · Cited by 620
Metadata
- Authors
- Henderson, S., Chakravarthy, A., Su, X., Boshoff, C., & Fenton, T. R.
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2014-06
- Volume
- 7
- Issue
- 6
- Pages
- 1833-1841
- ISSN
- 2211-1247 (ISSN-L)
- OpenAlex
- W2008811015
- Cited by
- 345
- References
- 41
- FWCI
- 10.40
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
