The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins
Open accessAbstract
Genotypic differences greatly influence susceptibility and resistance to disease. Understanding genotype-phenotype relationships requires that phenotypes be viewed as manifestations of network properties, rather than simply as the result of individual genomic variations. Genome sequencing efforts have identified numerous germline mutations, and large numbers of somatic genomic alterations, associated with a predisposition to cancer. However, it remains difficult to distinguish background, or 'passenger', cancer mutations from causal, or 'driver', mutations in these data sets. Human viruses intrinsically depend on their host cell during the course of infection and can elicit pathological phenotypes similar to those arising from mutations. Here we test the hypothesis that genomic variations and tumour viruses may cause cancer through related mechanisms, by systematically examining host interactome and transcriptome network perturbations caused by DNA tumour virus proteins. The resulting integrated viral perturbation data reflects rewiring of the host cell networks, and highlights pathways, such as Notch signalling and apoptosis, that go awry in cancer. We show that systematic analyses of host targets of viral proteins can identify cancer genes with a success rate on a par with their identification through functional genomics and large-scale cataloguing of tumour mutations. Together, these complementary approaches increase the specificity of cancer gene identification. Combining systems-level studies of pathogen-encoded gene products with genomic approaches will facilitate the prioritization of cancer-causing driver genes to advance the understanding of the genetic basis of human cancer.
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.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Nearly 3800 virus–host protein interactions were identified by Rozenblatt-Rosen et al. in a single study of DNA tumor virus proteins from four viruses, HPV, EBV, adenovirus Ad5, and human polyomavirus [91].”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [91]
In the citing paper
“the cellular transcriptional regulators cAMP-response element binding protein and EP300 were only found to associate with the E6 oncoprotein of HPV from cutaneous subtypes and not mucosal subtypes.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [91]
In the citing paper
“The identified associations stemmed from 54 viral and 1079 host proteins that pointed to viral subtype-specificity in interactions.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [91]
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
Hallmarks of Cancer: The Next Generation
Hanahan, D., & Weinberg, R. A. (2011) · Cell · doi:10.1016/j.cell.2011.02.013 · Cited by 66,590
A method and server for predicting damaging missense mutations.
Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S., & Sunyaev, S. R. (2010) · Nature Methods · doi:10.1038/nmeth0410-248 · Cited by 13,194
The landscape of somatic copy-number alteration across human cancers
Beroukhim, R., Mermel, C. H., Porter, D., Wei, G., Raychaudhuri, S., Donovan, J., Barretina, J., Boehm, J. S., Dobson, J., Urashima, M., et al. (2010) · Nature · doi:10.1038/nature08822 · Cited by 4,017
Self-citationCOSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
Forbes, S. A., Bindal, N., Bamford, S., Cole, C., Kok, C. Y., Beare, D., Jia, M., Shepherd, R., Leung, K., Menzies, A., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq929 · Cited by 2,278
Interactome Networks and Human Disease
Vidal, M., Cusick, M. E., & Barabási, A.-L. (2011) · Cell · doi:10.1016/j.cell.2011.02.016 · Cited by 1,771
Self-citationGenomewide Association Studies and Assessment of the Risk of Disease
Manolio, T. A. (2010) · New England Journal of Medicine · doi:10.1056/nejmra0905980 · Cited by 1,512
Notch signalling in solid tumours: a little bit of everything but not all the time
Ranganathan, P., Weaver, K. L., & Capobianco, A. J. (2011) · Nature reviews. Cancer · doi:10.1038/nrc3035 · Cited by 841
Exploring the Genomes of Cancer Cells: Progress and Promise
Stratton, M. R. (2011) · Science · doi:10.1126/science.1204040 · Cited by 711
A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection
Shapira, S. D., Gat‐Viks, I., Shum, B. O. V., Dricot, A., DeGrace, M. M., Wu, L., Gupta, P. B., Hao, T., Silver, S. J., Root, D. E., et al. (2009) · Cell · doi:10.1016/j.cell.2009.12.018 · Cited by 630
Self-citationMolecular Linkage Between the Kinase ATM and NF-κB Signaling in Response to Genotoxic Stimuli
Wu, Z., Shi, Y., Tibbetts, R. S., & Miyamoto, S. (2006) · Science · doi:10.1126/science.1121513 · Cited by 515
Cited by
Sorted by citations
A Proteome-Scale Map of the Human Interactome Network
Rolland, T., Taşan, M., Charloteaux, B., Pevzner, S. J., Zhong, Q., Sahni, N., Yi, S. S., Lemmens, I. H., Fontanillo, C., Mosca, R., et al. (2014) · Cell · doi:10.1016/j.cell.2014.10.050 · Cited by 1,381
Self-citationPhenomapping for Novel Classification of Heart Failure With Preserved Ejection Fraction
Shah, S. J., Katz, D. H., Selvaraj, S., Burke, M. A., Yancy, C. W., Gheorghiade, M., Bonow, R. O., Huang, C.-C., & Deo, R. C. (2015) · Circulation · doi:10.1161/circulationaha.114.010637 · Cited by 1,157
Self-citationThe BioGRID interaction database: 2013 update
Chatr‐aryamontri, A., Breitkreutz, B., Heinicke, S., Boucher, L., Winter, A. G., Stark, C., Nixon, J., Ramage, L., Kolas, N. K., O’Donnell, L., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1158 · Cited by 1,021
Structure and dynamics of molecular networks: A novel paradigm of drug discovery
Csermely, P., Korcsmáros, T., Kiss, H., London, G., & Nussinov, R. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.01.016 · Cited by 911
The BioGRID interaction database: 2015 update
Chatr‐aryamontri, A., Breitkreutz, B., Oughtred, R., Boucher, L., Heinicke, S., Chen, D., Stark, C., Breitkreutz, A., Kolas, N. K., O’Donnell, L., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1204 · Cited by 911
Metadata
- Authors
- Rozenblatt-Rosen, O., Deo, R. C., Padi, M., Adelmant, G., Calderwood, M. A., Rolland, T., Grace, M., Dricot, A., Askenazi, M., Tavares, M., Pevzner, S. J., Abderazzaq, F., Byrdsong, D., Carvunis, A.-R., Chen, A. A., Cheng, J., Correll, M., Duarte, M., Fan, C., Feltkamp, M. C., Ficarro, S. B., Franchi, R., Garg, B. K., Gulbahce, N., Hao, T., Holthaus, A. M., James, R., Korkhin, A., Litovchick, L., Mar, J. C., Pak, T. R., Rabello, S., Rubio, R., Shen, Y., Singh, S., Spangle, J. M., Tasan, M., Wanamaker, S., Webber, J. T., Roecklein-Canfield, J., Johannsen, E., Barabási, A.-L., Beroukhim, R., Kieff, E., Cusick, M. E., Hill, D. E., Münger, K., Marto, J. A., Quackenbush, J., Roth, F. P., DeCaprio, J. A., & Vidal, M.
- Affiliations
- Harvard University (US)
- Brigham and Women's Hospital (US)
- Boston University (US)
- Dana-Farber Cancer Institute (US)
- Leiden University Medical Center (NL)
- Simmons University (US)
- Northeastern University (US)
- Mount Sinai Hospital (CA)
- Broad Institute (US)
- Corresponding author
- Marto, Jarrod A.
- Quackenbush, John
- Roth, Frederick P.
- DeCaprio, James A.
- Vidal, Marc
- ORCID
- Deo, Rahul C.
- Padi, Megha
- Adelmant, Guillaume
- Calderwood, Michael A.
- Rolland, Thomas
- Askenazi, Manor
- Carvunis, Anne-Ruxandra
- Chen, Alyce A.
- Cheng, Jingwei
- Feltkamp, Mariet C.
- Ficarro, Scott B.
- Gulbahce, Natali
- Hao, Tong
- Litovchick, Larisa
- Mar, Jessica C.
- Pak, Theodore R.
- Spangle, Jennifer M.
- Wanamaker, Shelly
- Webber, James T.
- Johannsen, Eric
- Beroukhim, Rameen
- Hill, David E.
- Münger, Karl
- Marto, Jarrod A.
- Quackenbush, John
- Roth, Frederick P.
- DeCaprio, James A.
- Vidal, Marc
- Venue
- Nature
- Published
- 2012-07
- Volume
- 487
- Issue
- 7408
- Pages
- 491-495
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3408847
- OpenAlex
- W2085540051
- Cited by
- 378
- References
- 32
- Citations by year
- 2026: 8 · 2025: 9 · 2024: 18 · 2023: 14 · 2022: 18 · 2021: 24 · 2020: 32 · 2019: 24 · 2018: 31 · 2017: 31 · 2016: 31 · 2015: 36 · 2014: 43 · 2013: 42 · 2012: 16
- FWCI
- 17.60
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Heart, Lung, and Blood Institute (K08HL098361, T32HL007208)
- National Human Genome Research Institute (R01HG001715, K25HG006031, P50HG004233)
- National Cancer Institute (R01CA081135, R01CA093804, P01CA050661, R01CA047006, R01CA085180, K08CA122833, R01CA131354, R01CA066980, R01CA063113, U01CA141583)
- National Institute of General Medical Sciences (F32GM095284)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Health Sciences › Medicine › Oncology › Viral-associated cancers and disorders
- Health Sciences › Medicine › Epidemiology › Cervical Cancer and HPV Research
- Keywords
- cancer driver genes, DNA tumor viruses, human papillomavirus, Epstein-Barr virus, adenovirus, polyomavirus, Notch signaling, apoptosis, passenger mutations, genotype-phenotype correlation, host-virus interaction
- MeSH terms
- Adenoviridae, Herpesvirus 4, Human, Humans, Neoplasms, Oncogenic Viruses, Polyomavirus, Viral Proteins, Signal Transduction, Genome, Human, Gene Expression Regulation, Neoplastic, Open Reading Frames, Two-Hybrid System Techniques, Gene Expression Profiling, Papillomaviridae, Receptors, Notch, Genes, Neoplasm, Host-Pathogen Interactions
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
