LOGIN TO YOUR ACCOUNT

Username
Password
Remember Me
Or use your Academic/Social account:

CREATE AN ACCOUNT

Or use your Academic/Social account:

Congratulations!

You have just completed your registration at OpenAire.

Before you can login to the site, you will need to activate your account. An e-mail will be sent to you with the proper instructions.

Important!

Please note that this site is currently undergoing Beta testing.
Any new content you create is not guaranteed to be present to the final version of the site upon release.

Thank you for your patience,
OpenAire Dev Team.

Close This Message

CREATE AN ACCOUNT

Name:
Username:
Password:
Verify Password:
E-mail:
Verify E-mail:
*All Fields Are Required.
Please Verify You Are Human:
fbtwitterlinkedinvimeoflicker grey 14rssslideshare1
Languages: English
Types: Doctoral thesis
Subjects: RC0254

Classified by OpenAIRE into

mesheuropmc: virus diseases, female genital diseases and pregnancy complications
DNA methylation helps regulate transcriptional activity and is widely studied in cancer biology. This investigation aimed to establish the significance of Human Papillomavirus (HPV) DNA methylation in HPV-associated disease both in terms of basic biology and as a potential biomarker.\ud Assays to assess DNA methylation and gene expression were developed and evaluated. Pyrosequencing was used to assess DNA methylation of four regions of the HPV16 genome (E2, L1/L2, enhancer, promoter). Gene expression was assessed using quantitative PCR with assays for E2, E6 and E7. HPV integration was assessed using Detection of Integrated Papillomavirus Sequences (DIPS).\ud The relationship between HPV methylation, gene expression and integration was explored in vitro and in vivo using cell cultures and clinical cohorts. A variety of sample materials were used including short term and immortal cell lines, cervical cancer biopsies, cytology samples and Vulval Intraepithelial Neoplasia (VIN) biopsies.\ud In general, hypermethylation of the HPV genome was associated with low HPV gene expression and the presence of integrated HPV genomes.\ud To better understand the potential clinical utility of HPV DNA methylation, the relationship between HPV DNA methylation and various stages of cervical disease was determined. The HPV genome was progressively hypermethylated with increasing severity of cervical disease and certain regions of the HPV genome were more affected than others. A longitudinal study was also performed in order to determine a relationship between HPV methylation and clinical outcome. Differences in HPV methylation among patients who had persistent HPV infection and low grade disease, persistent infection and high grade disease and patients that cleared HPV infections were observed. Throughout the study the potential application of a HPV biomarker was considered and the correct biomarker design procedures were referred to. Several of the early biomarker development steps were successfully achieved.
  • The results below are discovered through our pilot algorithms. Let us know how we are doing!

    • The NSC Study - DNA Methylation and Disease Grade .......................................96 5.1.2. Hypothesis 2: There is a Difference in DNA Methylation among the Different Disease Grades....................................................................................................................97 6.1.1. Hypothesis 1: DNA Methylation Varies among Regions of the HPV Genome and among the CpGs within Each Region................................................................................118 6.1.2.
    • Hypothesis 2: DNA Methylation of the HPV16 Genome Varied over Time.......119 6.1.3. Hypothesis 3: There are DNA Methylation Differences among the Outcome Groups ...........................................................................................................................127 6.1.4. Hypothesis 4: The Level of DNA Methylation of the CRISP Samples Should be Comparable to the Disease Grade Study..........................................................................134 6.1.5. Hypothesis 5a: There is an Association between DNA Methylation and Outcome Cytology ...........................................................................................................................135 6.1.6. Hypothesis 5b: There is a Relationship between Outcome Cytology and Outcome Histology ...........................................................................................................137 6.2.
    • 1.1.3. HPV Genome and Gene Products 1.1.3.1. The Long Control Region
    • The LCR of HPV varies between types, however most HPV LCRs contain binding sites for the same subset of factors, the most significant of which appear to be YY1, CDP, Ap1, Sp1 and TBP (Spink and Laimins, 2005, O'Connor et al., 2000, Ai et al., 2000). For the promoter region, YY1 and CDP binding is associated with repression of P97. The expression of YY1 and CDP decreases upon differentiation alleviating these repressive effects (O'Connor et al., 1996, O'Connor et al., STUNKEL, W. & BERNARD, H. U. 1999. The chromatin structure of the long control region of human papillomavirus type 16 represses viral oncoprotein expression. J Virol, 73, 1918-30.
    • STUNKEL, W., HUANG, Z., TAN, S. H., O'CONNOR, M. J. & BERNARD, H. U. 2000. Nuclear matrix attachment regions of human papillomavirus type 16 repress or activate the E6 promoter, depending on the physical state of the viral DNA. J Virol, 74, 2489-501.
    • SUN, C., REIMERS, L. L. & BURK, R. D. 2011. Methylation of HPV16 genome CpG sites is associated with cervix precancer and cancer. Gynecologic Oncology, 121, 59-63.
    • SUN, L. L., CAO, D. Y., YANG, J. X., LI, H., ZHOU, X. R., SONG, Z. Q., CHENG, X. M., CHEN, J. & SHEN, K. 2012. Population-based case-control study on DAPK1, RAR-beta2 and MGMT methylation in liquid-based cytology. Arch Gynecol Obstet, 285, 1433-9.
    • SURANI, M. A. H., BARTON, S. C. & NORRIS, M. L. 1984. Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature, 308, 548-550.
    • SUTTER, D., WESTPHAL, M. & DOERFLER, W. 1978. Patterns of integration of viral DNA sequences in the genomes of adenovirus type 12-transformed hamster cells. Cell, 14, 569-85.
    • SZYF, M., ELIASSON, L., MANN, V., KLEIN, G. & RAZIN, A. 1985. Cellular and viral DNA hypomethylation associated with induction of Epstein-Barr virus lytic cycle. Proc Natl Acad Sci U S A, 82, 8090-4.
    • SZYF, M., PAKNESHAN, P. & RABBANI, S. A. 2004. DNA demethylation and cancer: therapeutic implications. Cancer Lett, 211, 133-43.
    • TAKAI, D. & JONES, P. A. 2002. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A, 99, 3740-5.
    • TAKIZAWA, T., NAKASHIMA, K., NAMIHIRA, M., OCHIAI, W., UEMURA, A., YANAGISAWA, M., FUJITA, N., NAKAO, M. & TAGA, T. 2001. DNA Methylation Is a Critical Cell-Intrinsic Determinant of Astrocyte Differentiation in the Fetal Brain. Developmental Cell, 1, 749- 758.
    • TAN, S. H., BAKER, C. C., STUNKEL, W. & BERNARD, H. U. 2003. A transcriptional initiator overlaps with a conserved YY1 binding site in the long control region of human papillomavirus type 16. Virology, 305, 486-501.
    • TAN, S. H., LEONG, L. E., WALKER, P. A. & BERNARD, H. U. 1994. The human papillomavirus type 16 E2 transcription factor binds with low cooperativity to two flanking sites and represses the E6 promoter through displacement of Sp1 and TFIID. J Virol, 68, 6411-20.
    • TAO, Q. & ROBERTSON, K. D. 2003. Stealth technology: how Epstein-Barr virus utilizes DNA methylation to cloak itself from immune detection. Clin Immunol, 109, 53-63.
    • TASKER, G. L. & WOJNAROWSKA, F. 2003. Lichen sclerosus. Clinical and Experimental Dermatology, 28, 128-133.
    • TAZI, J. & BIRD, A. 1990. Alternative chromatin structure at CpG islands. Cell, 60, 909-920.
    • THAIN, A., JENKINS, O., CLARKE, A. R. & GASTON, K. 1996. CpG methylation directly inhibits binding of the human papillomavirus type 16 E2 protein to specific DNA sequences. J Virol, 70, 7233-5.
    • THIERRY, F. 2009. Transcriptional regulation of the papillomavirus oncogenes by cellular and viral transcription factors in cervical carcinoma. Virology, 384, 375-9.
    • THIERRY, F., SPYROU, G., YANIV, M. & HOWLEY, P. 1992. Two AP1 sites binding JunB are essential for human papillomavirus type 18 transcription in keratinocytes. J Virol, 66, 3740-8.
    • THOMAS, M. C. & CHIANG, C. M. 2005. E6 oncoprotein represses p53-dependent gene activation via inhibition of protein acetylation independently of inducing p53 degradation. Mol Cell, 17, 251-64.
    • THORLAND, E. C., MYERS, S. L., GOSTOUT, B. S. & SMITH, D. I. 2003. Common fragile sites are preferential targets for HPV16 integrations in cervical tumors. Oncogene, 22, 1225-37.
    • THORLAND, E. C., MYERS, S. L., PERSING, D. H., SARKAR, G., MCGOVERN, R. M., GOSTOUT, B. S. & SMITH, D. I. 2000. Human papillomavirus type 16 integrations in cervical tumors frequently occur in common fragile sites. Cancer Res, 60, 5916-21.
    • TODD, R. W., ETHERINGTON, I. J. & LUESLEY, D. M. 2002. The effects of 5% imiquimod cream on high-grade vulval intraepithelial neoplasia. Gynecol Oncol, 85, 67-70.
    • TRISTRAM, A. & FIANDER, A. 2005. Clinical responses to Cidofovir applied topically to women with high grade vulval intraepithelial neoplasia. Gynecol Oncol, 99, 652-5.
    • TURAN, T., KALANTARI, M., CALLEJA-MACIAS, I. E., CUBIE, H. A., CUSCHIERI, K., VILLA, L. L., SKOMEDAL, H., BARRERA-SALDAƑA, H. A. & BERNARD, H.-U. 2006. Methylation of the human papillomavirus-18 L1 gene: A biomarker of neoplastic progression? Virology, 349, 175-183.
    • TURAN, T., KALANTARI, M., CUSCHIERI, K., CUBIE, H. A., SKOMEDAL, H. & BERNARD, H. U. 2007. High-throughput detection of human papillomavirus-18 L1 gene methylation, a candidate biomarker for the progression of cervical neoplasia. Virology, 361, 185-93.
    • TURKER, M. S. 2002. Gene silencing in mammalian cells and the spread of DNA methylation. Oncogene, 21, 5388-93.
    • UNGER, E. R., STEINAU, M., RAJEEVAN, M. S., SWAN, D., LEE, D. R. & VERNON, S. D. 2004. Molecular markers for early detection of cervical neoplasia. Dis Markers, 20, 103-16.
    • VAN DE NIEUWENHOF, H. P., BULTEN, J., HOLLEMA, H., DOMMERHOLT, R. G., MASSUGER, L. F. A. G., VAN DER ZEE, A. G. J., DE HULLU, J. A. & VAN KEMPEN, L. C. L. T. 2011. Differentiated vulvar intraepithelial neoplasia is often found in lesions, previously diagnosed as lichen sclerosus, which have progressed to vulvar squamous cell carcinoma. Mod Pathol, 24, 297-305.
    • VAN DE NIEUWENHOF, H. P., VAN DER AVOORT, I. A. M. & DE HULLU, J. A. 2008. Review of squamous premalignant vulvar lesions. Critical Reviews in Oncology/Hematology, 68, 131-156.
    • VAN DE NIEUWENHOF, H. P., VAN KEMPEN, L. C. L. T., DE HULLU, J. A., BEKKERS, R. L. M., BULTEN, J., MELCHERS, W. J. G. & MASSUGER, L. F. A. G. 2009. The Etiologic Role of HPV in Vulvar Squamous Cell Carcinoma Fine Tuned. Cancer Epidemiology Biomarkers & Prevention, 18, 2061-2067.
    • VAN TINE, B. A., DAO, L. D., WU, S.-Y., SONBUCHNER, T. M., LIN, B. Y., ZOU, N., CHIANG, C.-M., BROKER, T. R. & CHOW, L. T. 2004a. Human papillomavirus (HPV) origin-binding protein associates with mitotic spindles to enable viral DNA partitioning. Proc Natl Acad Sci U S A, 101, 4030-4035.
    • VAN TINE, B. A., KAPPES, J. C., BANERJEE, N. S., KNOPS, J., LAI, L., STEENBERGEN, R. D. M., MEIJER, C. L. J. M., SNIJDERS, P. J. F., CHATIS, P., BROKER, T. R., MOEN, P. T., JR. & CHOW, L. T. 2004b. Clonal Selection for Transcriptionally Active Viral Oncogenes during Progression to Cancer. J Virol, 78, 11172-11186.
    • VAN TINE, B. A., KNOPS, J., BROKER, T. R., CHOW, L. T. & MOEN, P. T., JR. 2001. In situ analysis of the transcriptional activity of integrated viral DNA using tyramide-FISH. Dev Biol (Basel), 106, 381-5.
    • VANDESOMPELE, J., DE PRETER, K., PATTYN, F., POPPE, B., VAN ROY, N., DE PAEPE, A. & SPELEMAN, F. 2002. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol, 3, RESEARCH0034.
    • VELDMAN, T., LIU, X., YUAN, H. & SCHLEGEL, R. 2003. Human papillomavirus E6 and Myc proteins associate in vivo and bind to and cooperatively activate the telomerase reverse transcriptase promoter. Proc Natl Acad Sci U S A, 100, 8211-6.
    • VENUTI, A., PAOLINI, F., NASIR, L., CORTEGGIO, A., ROPERTO, S., CAMPO, M. S. & BORZACCHIELLO, G. 2011. Papillomavirus E5: the smallest oncoprotein with many functions. Mol Cancer, 10, 140.
    • VINOKUROVA, S. & VON KNEBEL DOEBERITZ, M. 2011. Differential Methylation of the HPV 16 Upstream Regulatory Region during Epithelial Differentiation and Neoplastic Transformation. PloS one, 6, e24451.
    • VINOKUROVA, S., WENTZENSEN, N., KRAUS, I., KLAES, R., DRIESCH, C., MELSHEIMER, P., KISSELJOV, F., DURST, M., SCHNEIDER, A. & VON KNEBEL DOEBERITZ, M. 2008. Typedependent integration frequency of human papillomavirus genomes in cervical lesions. Cancer Res, 68, 307-13.
    • W.H.O. 2010. Immunization, Vaccines and Biologicals: Human papillomavirus (HPV) [Online]. World Health Organisation. Available: http://www.who.int/immunization/topics/hpv/en/ [Accessed 5/09/2011 2011].
    • WALDMAN, T., KINZLER, K. W. & VOGELSTEIN, B. 1995. p21 Is Necessary for the p53-mediated G1 Arrest in Human Cancer Cells. Cancer Res, 55, 5187-5190.
    • WANG-JOHANNING, F., LU, D. W., WANG, Y., JOHNSON, M. R. & JOHANNING, G. L. 2002. Quantitation of human papillomavirus 16 E6 and E7 DNA and RNA in residual material from ThinPrep Papanicolaou tests using real-time polymerase chain reaction analysis. Cancer, 94, 2199-2210.
    • WANG, J. C. 1979. Helical repeat of DNA in solution. Proceedings of the National Academy of Sciences, 76, 200-203.
    • WATT, P. M., KUMAR, R. & KEES, U. R. 2000. Promoter demethylation accompanies reactivation of the HOX11 proto-oncogene in leukemia. Genes Chromosomes Cancer, 29, 371-7.
    • WEBER, M., DAVIES, J. J., WITTIG, D., OAKELEY, E. J., HAASE, M., LAM, W. L. & SCHUBELER, D. 2005. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet, 37, 853-62.
    • WELLS, S. I., FRANCIS, D. A., KARPOVA, A. Y., DOWHANICK, J. J., BENSON, J. D. & HOWLEY, P. M. 2000. Papillomavirus E2 induces senescence in HPV-positive cells via pRB- and p21(CIP)-dependent pathways. Embo J, 19, 5762-71.
    • WENTZENSEN, N., BERGERON, C., CAS, F., ESCHENBACH, D., VINOKUROVA, S. & VON KNEBEL DOEBERITZ, M. 2005. Evaluation of a nuclear score for p16INK4a-stained cervical squamous cells in liquid-based cytology samples. Cancer, 105, 461-7.
    • WENTZENSEN, N., SHERMAN, M. E., SCHIFFMAN, M. & WANG, S. S. 2009. Utility of methylation markers in cervical cancer early detection: Appraisal of the state-of-the-science. Gynecologic Oncology, 112, 293-299.
    • WENTZENSEN, N. & VON KNEBEL DOEBERITZ, M. 2007. Biomarkers in cervical cancer screening. Dis Markers, 23, 315-30.
    • WILEY, D. J., HUH, J., RAO, J. Y., CHANG, C., GOETZ, M., POULTER, M., MASONGSONG, E., CHANG, C. I. & BERNARD, H. U. 2005. Methylation of human papillomavirus genomes in cells of anal epithelia of HIV-infected men. J Acquir Immune Defic Syndr, 39, 143-51.
    • WILSON, A. S., POWER, B. E. & MOLLOY, P. L. 2007. DNA hypomethylation and human diseases. Biochimica et biophysica acta, 1775, 138-62.
    • WILSON, V. G., WEST, M., WOYTEK, K. & RANGASAMY, D. 2002. Papillomavirus E1 Proteins: Form, Function, and Features. Virus Genes, 24, 275-290.
    • WOJDACZ, T. K. & DOBROVIC, A. 2007. Methylation-sensitive high resolution melting (MSHRM): a new approach for sensitive and high-throughput assessment of methylation. Nucl. Acids Res., gkm013.
    • WOO, Y. L., DAMAY, I., STANLEY, M., CRAWFORD, R. & STERLING, J. 2007. The use of HPV Linear Array Assay for multiple HPV typing on archival frozen tissue and DNA specimens. J Virol Methods, 142, 226-30.
    • WOODMAN, C. B., COLLINS, S., WINTER, H., BAILEY, A., ELLIS, J., PRIOR, P., YATES, M., ROLLASON, T. P. & YOUNG, L. S. 2001. Natural history of cervical human papillomavirus infection in young women: a longitudinal cohort study. Lancet, 357, 1831-6.
    • WOODMAN, C. B. J., COLLINS, S. I. & YOUNG, L. S. 2007. The natural history of cervical HPV infection: unresolved issues. Nat Rev Cancer, 7, 11-22.
    • WU, J., ISSA, J. P., HERMAN, J., BASSETT, D. E., JR., NELKIN, B. D. & BAYLIN, S. B. 1993. Expression of an exogenous eukaryotic DNA methyltransferase gene induces transformation of NIH 3T3 cells. Proc Natl Acad Sci U S A, 90, 8891-5.
    • WU, S. C. & ZHANG, Y. 2010. Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol, 11, 607-20.
    • XU, M., LUO, W., ELZI, D. J., GRANDORI, C. & GALLOWAY, D. A. 2008. NFX1 interacts with mSin3A/histone deacetylase to repress hTERT transcription in keratinocytes. Mol Cell Biol, 28, 4819-28.
    • YEE, C., KRISHNAN-HEWLETT, I., BAKER, C. C., SCHLEGEL, R. & HOWLEY, P. M. 1985. Presence and expression of human papillomavirus sequences in human cervical carcinoma cell lines. Am J Pathol, 119, 361-6.
    • YODER, J. A., WALSH, C. P. & BESTOR, T. H. 1997. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet, 13, 335-40.
    • YOU, J., CROYLE, J. L., NISHIMURA, A., OZATO, K. & HOWLEY, P. M. 2004. Interaction of the Bovine Papillomavirus E2 Protein with Brd4 Tethers the Viral DNA to Host Mitotic Chromosomes. Cell, 117, 349-360.
    • YUGAWA, T. & KIYONO, T. 2009. Molecular mechanisms of cervical carcinogenesis by high-risk human papillomaviruses: novel functions of E6 and E7 oncoproteins. Rev Med Virol, 19, 97-113.
    • ZHENG, Z. M. & BAKER, C. C. 2006. Papillomavirus genome structure, expression, and posttranscriptional regulation. Front Biosci, 11, 2286-302.
    • ZHENG, Z. M., TAO, M., YAMANEGI, K., BODAGHI, S. & XIAO, W. 2004. Splicing of a capproximal human Papillomavirus 16 E6E7 intron promotes E7 expression, but can be restrained by distance of the intron from its RNA 5' cap. J Mol Biol, 337, 1091-108.
    • ZHOU, J., GISSMANN, L., ZENTGRAF, H., MULLER, H., PICKEN, M. & MULLER, M. 1995. Early phase in the infection of cultured cells with papillomavirus virions. Virology, 214, 167- 176.
    • ZHOU, J., LIU, W. J., PENG, S. W., SUN, X. Y. & FRAZER, I. 1999. Papillomavirus Capsid Protein Expression Level Depends on the Match between Codon Usage and tRNA Availability. J Virol, 73, 4972-4982.
    • ZILBERMAN, D., GEHRING, M., TRAN, R. K., BALLINGER, T. & HENIKOFF, S. 2007. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet, 39, 61-69.
    • ZILBERMAN, D. & HENIKOFF, S. 2007. Genome-wide analysis of DNA methylation patterns. Development, 134, 3959-3965.
    • ZUR HAUSEN, H. 1976. Condylomata acuminata and human genital cancer. Cancer Res, 36, 794.
    • ZUR HAUSEN, H. 1977. Human papillomaviruses and their possible role in squamous cell carcinomas. Curr Top Microbiol Immunol, 78, 1-30.
    • ZUR HAUSEN, H. 1991. Viruses in human cancers. Science, 254, 1167-1173.
    • ZUR HAUSEN, H., MEINHOF, W., SCHEIBER, W. & BORNKAMM, G. 1974. Attempts to detect virus-secific DNA in human tumors. I. Nucleic acid hybridizations with complementary RNA of human wart virus. Int J Cancer, 13, 650-656.
  • Inferred research data

    The results below are discovered through our pilot algorithms. Let us know how we are doing!

    Title Trust
    67
    67%
  • No similar publications.

Share - Bookmark

Cite this article