We describe a novel microarray based-method for the screening of oncogenic human papillomavirus 18 (HPV-18) molecular variants. Due to the fact that sequencing methodology may underestimate samples containing more than one variant we designed a specific and sensitive stacking DNA hybridization assay. This technology can be used to discriminate between three possible phylogenetic branches of HPV-18. Probes were attached covalently on glass slides and hybridized with single-stranded DNA targets. Prior to hybridization with the probes, the target strands were pre-annealed with the three auxiliary contiguous oligonucleotides flanking the target sequences. Screening HPV-18 positive cell lines and cervical samples were used to evaluate the performance of this HPV DNA microarray. Our results demonstrate that the HPV-18’s variants hybridized specifically to probes, with no detection of unspecific signals. Specific probes successfully reveal detectable point mutations in these variants. The present DNA oligoarray system can be used as a reliable, sensitive and specific method for HPV-18 variant screening. Furthermore, this simple assay allows the use of inexpensive equipment, making it accessible in resource-poor settings.
References
[1]
Walboomers, J.M.; Jacobs, M.V.; Manos, M.M.; Bosch, F.X.; Kummer, J.A.; Shah, K.V.; Snijders, P.J.F.; Peto, J.; Meijer, C.J.L.M.; Mu？oz, N. Human papillomavirus is a necessary cause of invasive cervical cancer worldwide. J. Pathol. 1999, 189, 12–19.
[2]
Chaturvedi, A.K.; Katki, H.A.; Hildesheim, A.; Rodríguez, A.C.; Quint, W.; Schiffman, M.; van Doorn, L.-J.; Porras, C.; Wacholder, S.; Gonzalez, P.; et al. Human papillomavirus infection with multiple types: Pattern of coinfection and risk of cervical disease. J. Infect. Dis. 2011, 203, 910–920.
[3]
Munoz, N.; Bosch, F.X.; de Sanjosé, S.; Shah, K.V. The role of HPV in the etiology of cervical cancer. Mutant. Res. 1994, 305, 293–301.
[4]
Jemal, A.; Bray, F.; Center, M.M.; Ferlay, J.; Ward, E.; Forman, D. Global cancer statistics. CA Cancer J. Clin. 2011, 61, 69–90.
[5]
Boshart, M.; Boshart, M.; Gissmann, L.; Ikenberg, H.; Kleinheinz, A.; Scheurlen, W.; zur Hausen, H. A new type of papillomavirus DNA, its presence in genital cancer biopsies and in cell lines derived from cervical cancer. EMBO J. 1984, 3, 1151–1157.
[6]
Beaudenon, S.; Beaudenon, S.; Kremsdorf, D.; Croissant, O.; Jablonska, S.; Wain-Hobson, S.; Orth, G. A novel type of human papillomavirus associated with genital neoplasias. Nature 1986, 321, 246–249.
[7]
Walker, J.; Bloss, J.D.; Liao, S.Y.; Berman, M.; Bergen, S.; Wilczynski, S.P. Human papillomavirus genotype as a prognostic indicator in carcinoma of the uterine cervix. Obstet. Gynecol. 1989, 74, 781–785.
[8]
Kurman, R.J.; Schiffman, M.H.; Lancaster, W.D.; Reid, R.; Jenson, A.B.; Temple, G.F.; Lorincz, A.T. Analysis of individual human papillomavirus types in cervical neoplasia: A possible role for type 18 in rapid progression. Am. J. Obstet. Gynecol. 1988, 159, 293–296.
[9]
Burger, R.A.; Monk, B.J.; Kurosaki, T.; Anton-Culver, H.; Vasilev, S.A.; Berman, M.L.; Wilczynski, S.P. Human papillomavirus type 18: Association with poor prognosis in early stage cervical cancer. J. Natl. Cancer Inst. 1996, 88, 1361–1368.
[10]
Schwartz, S.M.; Daling, J.R.; Shera, K.A.; Madeleine, M.M.; McKnight, B.; Galloway, D.A.; Porter, P.L.; McDougall, J.K. Human papillomavirus and prognosis of invasive cervical cancer: A population-based study. J. Clin. Oncol. 2001, 19, 1906–1915.
[11]
Ong, C.K.; Chan, S.Y.; Campo, M.S.; Fujinaga, K.; Mavromara-Nazos, P.; Labropoulou, V.; Pfister, H.; Tay, S.K.; ter Meulen, J.; Villa, L.L. Evolution of human papillomavirus type 18: An ancient phylogenetic root in Africa and intratype diversity reflect coevolution with human ethnic groups. J. Virol. 1993, 67, 6424–6431.
[12]
Chan, S.Y.; Ho, L.; Ong, C.K.; Chow, V.; Drescher, B.; Dürst, M.; ter Meulen, J.; Villa, L.; Luande, J.; Mgaya, HN. Molecular variants of human papillomavirus type 16 from four continents suggest ancient pandemic spread of the virus and its coevolution with humankind. J. Virol. 1992, 66, 2057–2066.
[13]
Yamada, T.; Manos, M.M.; Peto, J.; Greer, C.E.; Munoz, N.; Bosch, F.X.; Wheeler, C.M. Human papillomavirus type 16 sequence variation in cervical cancers: A worldwide perspective. J. Virol. 1997, 71, 2463–2472.
[14]
Pande, S.; Jain, N.; Prusty, B.K.; Bhambhani, S.; Gupta, S.; Sharma, R.; Batra, S.; Das, B.C. Human papillomavirus type 16 variant analysis of E6, E7, and L1 genes and long control region in biopsy samples from cervical cancer patients in north India. J. Clin. Microbiol. 2008, 46, 1060–1066.
[15]
Bernard, H.U.; Chan, S.Y.; Delius, H. Evolution of papillomaviruses. Curr. Top Microbiol. Immunol. 1994, 186, 33–54.
[16]
Lopez-Saavedra, A.; González-Maya, L.; Ponce-de-León, S.; García-Carrancá, A.; Mohar, A.; Lizano, M. Functional implication of sequence variation in the long control region and E2 gene among human papillomavirus type 18 variants. Arch. Virol. 2009, 154, 747–754.
[17]
Villa, L.L.; Sichero, L.; Rahal, P.; Caballero, O.; Ferenczy, A.; Rohan, T.; Franco, E.L. Molecular variants of human papillomavirus types 16 and 18 preferentially associated with cervical neoplasia. J. Gen. Virol. 2000, 81, 2959–2968.
[18]
Hildesheim, A.; Wang, S.S. Host and viral genetics and risk of cervical cancer: A review. Virus Res. 2002, 89, 229–240.
[19]
Cento, V.; Rahmatalla, N.; Ciccozzi, M.; Perno, C.F.; Ciotti, M. Intratype variations of HPV 31 and 58 in Italian women with abnormal cervical cytology. J. Med. Virol. 2011, 83, 1752–1761.
[20]
Sichero, L.; Franco, E.L.; Villa, L.L. Different P105 promoter activities among natural variants of human papillomavirus type 18. J. Infect. Dis. 2005, 191, 739–742.
[21]
Pista, A.; Oliveira, A.; Barateiro, A.; Costa, H.; Verdasca, N.; Paix？o, M.T. Molecular variants of human papillomavirus type 16 and 18 and risk for cervical neoplasia in Portugal. J. Med. Virol. 2007, 79, 1889–1897.
[22]
Lizano, M.; García-Carrancá, A. Molecular variants of human papillomaviruses types 16, 18, and 45 in tumors of the uterine cervix in Mexico. Gac. Med. Mex. 1997, 133, 43–48.
[23]
The European Bioinformatics Center. ClustalW2. Available online: http://www.ebi.ac.uk/Tools/msa/clustalw2/ (accessed on 21 December 2012).
Beattie, W.G.; Lin, M.; Saralinda, L.; Turner, R.; Varma, S.; Dat, D.; Kenneth, Dao.; Beattie, L. Hybridization of DNA targets to glass-tethered oligonucleotide probes. Mol. Biotechnol. 1995, 4, 213–225.
[26]
Maldonado-Rodriguez, R.; Beattie, K.L. Analysis of nucleic acids by tandem hybridization on oligonucleotide microarrays. Methods Mol. Biol. 2001, 170, 157–171.
[27]
Reyes-Lopez, M.A.; Méndez-Tenorio, A.; Maldonado-Rodríguez, R.; Doktycz, M.J.; Fleming, J.T.; Beattie, K.L. Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridization. Nucleic Acids Res. 2003, 31, 779–789.
[28]
Rangel-Lopez, A.; Maldonado-Rodríguez1, R.; Salcedo-Vargas, M.; Espinosa-Lara, J.M.; Méndez-Tenorio, A.; Beattie, K.L. Low density DNA microarray for detection of most frequent TP53 missense point mutations. BMC Biotechnol. 2005, 5, 8, doi:10.1186/1472-6750-5-8.
[29]
Ho, L.; Chan, S.Y.; Chow, V.; Chong, T.; Tay, S.K.; Villa, L.L.; Bernard, H.U. Sequence variants of human papillomavirus type 16 in clinical samples permit verification and extension of epidemiological studies and construction of a phylogenetic tree. J. Clin. Microbiol. 1991, 29, 1765–1772.
[30]
Icenogle, J.P.; Laga, M.; Miller, D.; Manoka, A.T.; Tucker, R.A.; Reeves, W.C. Genotypes and sequence variants of human papillomavirus DNAs from human immunodeficiency virus type 1-infected women with cervical intraepithelial neoplasia. J. Infect. Dis. 1992, 166, 1210–1216.
[31]
Xi, L.F.; Nancy, B.; Kiviat, A.H.; Denise, A.; Galloway, C.M.; Wheeler, J.H.; Laura, A.K. Human papillomavirus type 16 and 18 variants: Race-related distribution and persistence. J. Natl. Cancer Inst. 2006, 98, 1045–1052.
[32]
Felsenstein, J. Confidence limits on phylogenyes: An approach using the bootstrap. Evolution 1985, 39, 783–791.
[33]
Tamura, K.; Nei, M.; Kumar, S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. USA 2004, 101, 11030–11035.
[34]
Saitou, N.; Nei, M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4, 406–425.
[35]
Tamura, K.; Peterson, D.; Peterson, N.; Stecher, G.; Nei, M.; Kumar, S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28, 2731–2739.
[36]
Penny, M.; Bartolini, R.; Mosqueira, N.R.; LaMontagne, D.S.; Mendoza, M.A.; Ramos, I.; Winkler, J.L.; Villafana, J.; Janmohamed, A.; Jumaan, A.O. Strategies to vaccinate against cancer of the cervix: Feasibility of a school-based HPV vaccination program in Peru. Vaccine 2011, 29, 5022–5030.
[37]
Park, T.C.; Kim, C.J.; Koh, Y.M.; Lee, K.H.; Yoon, J.H.; Kim, J.H.; Namkoong, S.E.; Park, J.S. Human papillomavirus genotyping by the DNA chip in the cervical neoplasia. DNA Cell Biol. 2004, 23, 119–125.
[38]
Pierik, A.; Zwanenburg, C.; Moerland, E.; Broer, D.; Stapert, H.; van den Brule, A.J.C. Rapid genotyping of human papillomavirus by post-PCR array-based hybridization techniques. J. Clin. Microbiol. 2011, 49, 1395–1402.
[39]
Klaassen, C.H.; Prinsen, C.F.; de Valk, H.A.; Horrevorts, A.M.; Jeunink, M.A.; Thunnissen, F.B. DNA microarray format for detection and subtyping of human papillomavirus. J. Clin. Microbiol. 2004, 42, 2152–2160.
[40]
Maki, H.; Kiyomi, F.-A.; Osamu, Y.O. Evidence for a promoter-like activity in the short non-coding region of human papillomaviruses. J. Gen. Virol. 1996, 77, 453–458.
[41]
Hecht, J.L.; Kadish, A.S.; Jiang, G.; Burk, R.D. Genetic characterization of the human papillomavirus (HPV) 18 E2 gene in clinical specimens suggests the presence of a subtype with decreased oncogenic potential. Int. J. Cancer 1995, 60, 369–376.
[42]
Lizano, M.; Berumen, J.; Guido, M.C.; Casas, L.; García-Carrancá, A. Association between human papillomavirus type 18 variants and histopathology of cervical cancer. J. Natl. Cancer Inst. 1997, 89, 1227–1231.
[43]
Burk, R.D.; Terai, M.; Gravitt, P.E.; Brinton, L.A.; Kurman, R.J.; Barnes, W.A.; Greenberg, M.D.; Hadjimichael, O.C.; Fu, L.; McGowan, L.; Mortel, R.; Schwartz, P.E.; Hildesheim, A. Distribution of human papillomavirus types 16 and 18 variants in squamous cell carcinomas and adenocarcinomas of the cervix. Cancer Res. 2003, 63, 7215–7220.
[44]
Melchers, W.J.; Herbrink, P.; Walboomers, J.M.; Meijer, C.J.; vd Drift, H.; Lindeman, J.; Quint, W.G. Optimization of human papillomavirus genotype detection in cervical scrapes by a modified filter in situ hybridization test. J. Clin. Microbiol. 1989, 27, 106–110.
Samiotaki, M.; Kwiatkowski, M.; Ylitalo, N.; Landegren, U. Seven-color time-resolved fluorescence hybridization analysis of human papilloma virus types. Anal. Biochem. 1997, 253, 156–161.
[47]
Kleter, B.; van Doorn, L.J.; Schrauwen, L.; Molijn, A.; Sastrowijoto, S.; ter Schegget, J.; Lindeman, J.; ter Harmsel, B.; Burger, M.; Quint, W. Development and clinical evaluation of a highly sensitive PCR-reverse hybridization line probe assay for detection and identification of anogenital human papillomavirus. J. Clin. Microbiol. 1999, 37, 2508–2517.
