HPVbase - A knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Kumar Gupta, Amit ^a   Kumar, Manoj ^a  

^a INSTITUTE OF MICROBIAL TECHNOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RNA; TUMOR MARKER;

BIOSYNTHESIS; CARCINOMA; DNA METHYLATION; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; HUMAN; METABOLISM; PAPILLOMAVIRIDAE; PAPILLOMAVIRUS INFECTION; VIROLOGY; VIRUS DNA CELL DNA INTERACTION;

BIOMARKERS, TUMOR; CARCINOMA; DATABASES, GENETIC; DNA METHYLATION; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MICRORNAS; PAPILLOMAVIRIDAE; PAPILLOMAVIRUS INFECTIONS; RNA, NEOPLASM; VIRUS INTEGRATION;

EID: 84937963805     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep12522     Document Type: Article

References (50)

1. de Villiers, E. M., Fauquet, C., Broker, T. R., Bernard, H. U. & zur Hausen, H. Classification of papillomaviruses. Virology 324, 17-27, doi: 10.1016/j.virol.2004.03.033 (2004).
2. Doorbar, J. Molecular biology of human papillomavirus infection and cervical cancer. Clin Sci (Lond) 110, 525-541, doi: 10.1042/CS20050369 (2006).
3. Munoz, N. et al. Epidemiologic classification of human papillomavirus types associated with cervical cancer. N Engl J Med 348, 518-527, doi: 10.1056/NEJMoa021641 (2003).
4. Mantovani, F. & Banks, L. The human papillomavirus E6 protein and its contribution to malignant progression. Oncogene 20, 7874-7887, doi: 10.1038/sj.onc.1204869 (2001).
5. Munger, K. et al. Biological activities and molecular targets of the human papillomavirus E7 oncoprotein. Oncogene 20, 7888-7898, doi: 10.1038/sj.onc.1204860 (2001).
6. Moody, C. A. & Laimins, L. A. Human papillomavirus oncoproteins: pathways to transformation. Nat Rev Cancer 10, 550-560, doi: 10.1038/nrc2886 (2010).
7. Doorbar, J. et al. The biology and life-cycle of human papillomaviruses. Vaccine 30 Suppl 5, F55-70, doi: 10.1016/j.vaccine. 2012.06.083 (2012).
8. Schiffman, M. & Wentzensen, N. Human papillomavirus infection and the multistage carcinogenesis of cervical cancer. Cancer Epidemiol Biomarkers Prev 22, 553-560, doi: 10.1158/1055-9965.EPI-12-1406 (2013).
9. Boulet, G. A., Horvath, C. A., Berghmans, S. & Bogers, J. Human papillomavirus in cervical cancer screening: important role as biomarker. Cancer Epidemiol Biomarkers Prev 17, 810-817, doi: 10.1158/1055-9965.EPI-07-2865 (2008).
10. Woodman, C. B., Collins, S. I. & Young, L. S. The natural history of cervical HPV infection: unresolved issues. Nat Rev Cancer 7, 11-22, doi: 10.1038/nrc2050 (2007).
11. Sahasrabuddhe, V. V., Luhn, P. & Wentzensen, N. Human papillomavirus and cervical cancer: biomarkers for improved prevention efforts. Future Microbiol 6, 1083-1098, doi: 10.2217/fmb.11.87 (2011).
12. Schwarz, E. et al. Structure and transcription of human papillomavirus sequences in cervical carcinoma cells. Nature 314, 111-114 (1985).
13. zur Hausen, H. Papillomaviruses and cancer: from basic studies to clinical application. Nat Rev Cancer 2, 342-350, doi: 10.1038/nrc798 (2002).
14. Schmitz, M., Driesch, C., Jansen, L., Runnebaum, I. B. & Durst, M. Non-random integration of the HPV genome in cervical cancer. PLoS One 7, e39632, doi: 10.1371/journal.pone.0039632 (2012).
15. Akagi, K. et al. Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability. Genome Res 24, 185-199, doi: 10.1101/gr.164806.113 (2014).
16. Parfenov, M. et al. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A 111, 15544-15549, doi: 10.1073/pnas.1416074111 (2014).
17. Ojesina, A. I. et al. Landscape of genomic alterations in cervical carcinomas. Nature 506, 371-375, doi: 10.1038/nature12881 (2014).
18. Xu, B. et al. Multiplex Identification of Human Papillomavirus 16 DNA Integration Sites in Cervical Carcinomas. PLoS One 8, e66693, doi: 10.1371/journal.pone.0066693 (2013).
19. Jeon, S. & Lambert, P. F. Integration of human papillomavirus type 16 DNA into the human genome leads to increased stability of E6 and E7 mRNAs: implications for cervical carcinogenesis. Proc Natl Acad Sci U S A 92, 1654-1658 (1995).
20. Wentzensen, N., Vinokurova, S. & von Knebel Doeberitz, M. Systematic review of genomic integration sites of human papillomavirus genomes in epithelial dysplasia and invasive cancer of the female lower genital tract. Cancer Res 64, 3878-3884, doi: 10.1158/0008-5472.CAN-04-0009 (2004).
21. Thorland, E. C., Myers, S. L., Gostout, B. S. & Smith, D. I. Common fragile sites are preferential targets for HPV16 integrations in cervical tumors. Oncogene 22, 1225-1237, doi: 10.1038/sj.onc.1206170 (2003).
22. Matovina, M., Sabol, I., Grubisic, G., Gasperov, N. M. & Grce, M. Identification of human papillomavirus type 16 integration sites in high-grade precancerous cervical lesions. Gynecol Oncol 113, 120-127, doi: 10.1016/j.ygyno.2008.12.004 (2009).
23. Klaes, R. et al. Detection of high-risk cervical intraepithelial neoplasia and cervical cancer by amplification of transcripts derived from integrated papillomavirus oncogenes. Cancer Res 59, 6132-6136 (1999).
24. Bird, A. The essentials of DNA methylation. Cell 70, 5-8 (1992).
25. Robertson, K. D. DNA methylation and human disease. Nat Rev Genet 6, 597-610, doi: 10.1038/nrg1655 (2005).
26. Clarke, M. A. et al. Human papillomavirus DNA methylation as a potential biomarker for cervical cancer. Cancer Epidemiol Biomarkers Prev 21, 2125-2137, doi: 10.1158/1055-9965.EPI-12-0905 (2012).
27. Turan, T. et al. High-throughput detection of human papillomavirus-18 L1 gene methylation, a candidate biomarker for the progression of cervical neoplasia. Virology 361, 185-193, doi: 10.1016/j.virol.2006.11.010 (2007).
28. Brandsma, J. L. et al. Distinct human papillomavirus type 16 methylomes in cervical cells at different stages of premalignancy. Virology 389, 100-107, doi: 10.1016/j.virol.2009.03.029 (2009).
29. Crosbie, E. J., Einstein, M. H., Franceschi, S. & Kitchener, H. C. Human papillomavirus and cervical cancer. Lancet 382, 889-899, doi: 10.1016/S0140-6736(13)60022-7 (2013).
30. Reshmi, G. & Pillai, M. R. Beyond HPV: oncomirs as new players in cervical cancer. FEBS Lett 582, 4113-4116, doi: 10.1016/j. febslet.2008.11.011 (2008).
31. Gomez-Gomez, Y., Organista-Nava, J. & Gariglio, P. Deregulation of the miRNAs expression in cervical cancer: human papillomavirus implications. Biomed Res Int 2013, 407052, doi: 10.1155/2013/407052 (2013).
32. Zheng, Z. M. & Wang, X. Regulation of cellular miRNA expression by human papillomaviruses. Biochim Biophys Acta 1809, 668-677, doi: 10.1016/j.bbagrm.2011.05.005 (2011).
33. Kim, V. N. Small RNAs: classification, biogenesis, and function. Mol Cells 19, 1-15 (2005).
34. Engels, B. M. & Hutvagner, G. Principles and effects of microRNA-mediated post-transcriptional gene regulation. Oncogene 25, 6163-6169, doi: 10.1038/sj.onc.1209909 (2006).
35. Lee, J. W. et al. Altered MicroRNA expression in cervical carcinomas. Clin Cancer Res 14, 2535-2542, doi: 10.1158/1078-0432. CCR-07-1231 (2008).
36. Winter, J. & Diederichs, S. MicroRNA biogenesis and cancer. Methods Mol Biol 676, 3-22, doi: 10.1007/978-1-60761-863-8-1 (2011).
37. Zhang, L. et al. microRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci U S A 103, 9136-9141, doi: 10.1073/pnas.0508889103 (2006).
38. Wang, X. et al. microRNAs are biomarkers of oncogenic human papillomavirus infections. Proc Natl Acad Sci U S A 111, 4262-4267, doi: 10.1073/pnas.1401430111 (2014).
39. Wentzensen, N. et al. Methylation of HPV18, HPV31, and HPV45 genomes and cervical intraepithelial neoplasia grade 3. J Natl Cancer Inst 104, 1738-1749, doi: 10.1093/jnci/djs425 (2012).
40. Patel, D. A. et al. Patterns of cellular and HPV 16 methylation as biomarkers for cervical neoplasia. J Virol Methods 184, 84-92, doi: 10.1016/j.jviromet.2012.05.022 (2012).
41. Mirabello, L. et al. Elevated methylation of HPV16 DNA is associated with the development of high grade cervical intraepithelial neoplasia. Int J Cancer 132, 1412-1422, doi: 10.1002/ijc.27750 (2013).
42. Brandsma, J. L. et al. Methylation of Twelve CpGs in Human Papillomavirus Type 16 (HPV16) as an Informative Biomarker for the Triage of Women Positive for HPV16 Infection. Cancer Prev Res (Phila), doi: 10.1158/1940-6207.CAPR-13-0354 (2014).
43. Ling, H., Fabbri, M. & Calin, G. A. MicroRNAs and other non-coding RNAs as targets for anticancer drug development. Nature reviews. Drug discovery 12, 847-865, doi: 10.1038/nrd4140 (2013).
44. Qureshi, A., Thakur, N., Monga, I., Thakur, A. & Kumar, M. VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets. Database (Oxford) 2014, doi: 10.1093/database/bau103 (2014).
45. Zhao, X. et al. Dr.VIS: a database of human disease-related viral integration sites. Nucleic Acids Res 40, D1041-1046, doi: 10.1093/nar/gkr1142 (2012).
46. Yang, X. et al. Dr.VIS v2.0: an updated database of human disease-related viral integration sites in the era of high-throughput deep sequencing. Nucleic Acids Res 43, D887-892, doi: 10.1093/nar/gku1074 (2015).
47. Van Doorslaer, K. et al. The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis. Nucleic Acids Res 41, D571-578, doi: 10.1093/nar/gks984 (2013).
48. Zhang, G. L. et al. HPVdb: a data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology. Database (Oxford) 2014, bau031, doi: 10.1093/database/bau031 (2014).
49. Hsu, S. D. et al. miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res 42, D78-85, doi: 10.1093/nar/gkt1266 (2014).
50. Skinner, M. E., Uzilov, A. V., Stein, L. D., Mungall, C. J. & Holmes, I. H. JBrowse: a next-generation genome browser. Genome Res 19, 1630-1638, doi: 10.1101/gr.094607.109 (2009).