Despite an increase in the number of molecular epidemiological studies conducted in recent years to evaluate the association between human papillomavirus (HPV) and the risk of breast carcinoma, these studies remain inconclusive. Here we aim to detect HPV DNA in various tissues from patients with breast carcinoma using the method of HPV capture combined with massive paralleled sequencing (MPS). To validate the confidence of our methods, 15 cervical cancer samples were tested by PCR and the new method. Results showed that there was 100% consistence between the two methods.DNA from peripheral blood, tumor tissue, adjacent lymph nodes and adjacent normal tissue were collected from seven malignant breast cancer patients, and HPV type 16(HPV16) was detected in 1/7, 1/7, 1/7and 1/7 of patients respectively. Peripheral blood, tumor tissue and adjacent normal tissue were also collected from two patients with benign breast tumor, and 1/2, 2/2 and 2/2 was detected to have HPV16 DNA respectively. MPS metrics including mapping ratio, coverage, depth and SNVs were provided to characterize HPV in samples. The average coverage was 69% and 61.2% for malignant and benign samples respectively. 126 SNVs were identified in all 9 samples. The maximum number of SNVs was located in the gene of E2 and E4 among all samples. Our study not only provided an efficient method to capture HPV DNA, but detected the SNVS, coverage, SNV type and depth. The finding has provided further clue of association between HPV16 and breast cancer.
References
[1]
Parkin DM, Bray F, Ferlay J, Pisani P (2005) Global cancer statistics, 2002. CA Cancer J Clin 55: 74–108. doi: 10.3322/canjclin.55.2.74
[2]
Campeau PM, Foulkes WD, Tischkowitz MD (2008) Hereditary breast cancer: new genetic developments, new therapeutic avenues. Hum Genet 124: 31–42. doi: 10.1007/s00439-008-0529-1
[3]
Armstrong B, Doll R (1975) Environmental factors and cancer incidence and mortality in different countries, with special reference to dietary practices. Int J Cancer 15: 617–631. doi: 10.1002/ijc.2910150411
[4]
Parkin DM (2006) The global health burden of infection-associated cancers in the year 2002. Int J Cancer 118: 3030–3044. doi: 10.1002/ijc.21731
[5]
Antonsson A, Bialasiewicz S, Rockett RJ, Jacob K, Bennett IC, et al. (2012) Exploring the prevalence of ten polyomaviruses and two herpes viruses in breast cancer. PLoS One 7: e39842. doi: 10.1371/journal.pone.0039842
[6]
Silva RG Jr, da Silva BB (2011) No evidence for an association of human papillomavirus and breast carcinoma. Breast Cancer Res Treat 125: 261–264. doi: 10.1007/s10549-010-1129-z
[7]
zur Hausen H (2009) Papillomaviruses in the causation of human cancers - a brief historical account. Virology 384: 260–265. doi: 10.1016/j.virol.2008.11.046
[8]
Acevedo-Nuno E, Gonzalez-Ojeda A, Vazquez-Camacho G, Balderas-Pena Luz Ma A, Moreno-Villa H, et al. (2004) Human papillomavirus DNA and protein in tissue samples of oesophageal cancer, Barrett's oesophagus and oesophagitis. Anticancer Res 24: 1319–1323.
[9]
Schiffman M, Rodriguez AC, Chen Z, Wacholder S, Herrero R, et al. (2010) A population-based prospective study of carcinogenic human papillomavirus variant lineages, viral persistence, and cervical neoplasia. Cancer Res 70: 3159–3169. doi: 10.1158/0008-5472.can-09-4179
[10]
Gheit T, Cornet I, Clifford GM, Iftner T, Munk C, et al. (2011) Risks for persistence and progression by human papillomavirus type 16 variant lineages among a population-based sample of Danish women. Cancer Epidemiol Biomarkers Prev 20: 1315–1321. doi: 10.1158/1055-9965.epi-10-1187
[11]
Di Lonardo A, Venuti A, Marcante ML (1992) Human papillomavirus in breast cancer. Breast Cancer Res Treat 21: 95–100. doi: 10.1007/bf01836955
[12]
de Villiers EM, Sandstrom RE, zur Hausen H, Buck CE (2005) Presence of papillomavirus sequences in condylomatous lesions of the mamillae and in invasive carcinoma of the breast. Breast Cancer Res 7: R1–11.
[13]
Damin AP, Karam R, Zettler CG, Caleffi M, Alexandre CO (2004) Evidence for an association of human papillomavirus and breast carcinomas. Breast Cancer Res Treat 84: 131–137. doi: 10.1023/b:brea.0000018411.89667.0d
[14]
Kroupis C, Markou A, Vourlidis N, Dionyssiou-Asteriou A, Lianidou ES (2006) Presence of high-risk human papillomavirus sequences in breast cancer tissues and association with histopathological characteristics. Clin Biochem 39: 727–731. doi: 10.1016/j.clinbiochem.2006.03.005
[15]
Gumus M, Yumuk PF, Salepci T, Aliustaoglu M, Dane F, et al. (2006) HPV DNA frequency and subset analysis in human breast cancer patients' normal and tumoral tissue samples. J Exp Clin Cancer Res 25: 515–521.
[16]
Lindel K, Forster A, Altermatt HJ, Greiner R, Gruber G (2007) Breast cancer and human papillomavirus (HPV) infection: no evidence of a viral etiology in a group of Swiss women. Breast 16: 172–177. doi: 10.1016/j.breast.2006.09.001
[17]
de Cremoux P, Thioux M, Lebigot I, Sigal-Zafrani B, Salmon R, et al. (2008) No evidence of human papillomavirus DNA sequences in invasive breast carcinoma. Breast Cancer Res Treat 109: 55–58. doi: 10.1007/s10549-007-9626-4
[18]
Wrede D, Luqmani YA, Coombes RC, Vousden KH (1992) Absence of HPV 16 and 18 DNA in breast cancer. Br J Cancer 65: 891–894.
[19]
Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966–1967. doi: 10.1093/bioinformatics/btp336
[20]
Li R, Li Y, Fang X, Yang H, Wang J, et al. (2009) SNP detection for massively parallel whole-genome resequencing. Genome Res 19: 1124–1132. doi: 10.1101/gr.088013.108
[21]
Li W, Zeng X, Lee NP, Liu X, Chen S, et al. (2013) HIVID: An efficient method to detect HBV integration using low coverage sequencing. Genomics 102: 338–344. doi: 10.1016/j.ygeno.2013.07.002
[22]
Gillison ML, Koch WM, Capone RB, Spafford M, Westra WH, et al. (2000) Evidence for a causal association between human papillomavirus and a subset of head and neck cancers. J Natl Cancer Inst 92: 709–720. doi: 10.1093/jnci/92.9.709
[23]
Chen AC, Keleher A, Kedda MA, Spurdle AB, McMillan NA, et al. (2009) Human papillomavirus DNA detected in peripheral blood samples from healthy Australian male blood donors. J Med Virol 81: 1792–1796. doi: 10.1002/jmv.21592
[24]
Widschwendter A, Brunhuber T, Wiedemair A, Mueller-Holzner E, Marth C (2004) Detection of human papillomavirus DNA in breast cancer of patients with cervical cancer history. J Clin Virol 31: 292–297. doi: 10.1016/j.jcv.2004.06.009
[25]
Masterson PJ, Stanley MA, Lewis AP, Romanos MA (1998) A C-terminal helicase domain of the human papillomavirus E1 protein binds E2 and the DNA polymerase alpha-primase p68 subunit. J Virol 72: 7407–7419
[26]
Blakaj DM, Fernandez-Fuentes N, Chen Z, Hegde R, Fiser A, et al. (2009) Evolutionary and biophysical relationships among the papillomavirus E2 proteins. Front Biosci 14: 900–917. doi: 10.2741/3285
[27]
Shang Q, Wang Y, Fang Y, Wei L, Chen S, et al. (2011) Human Papillomavirus Type 16 Variant Analysis of E6, E7, and L1 Genes and Long Control Region in Identification of Cervical Carcinomas in Patients in Northeast China,. JOURNAL OFCLINICALMICROBIOLOGY 49: 2656–2663 doi: 10.1128/jcm.02203-10
[28]
Smith B, Chen Z, Reimers L, van Doorslaer K, Schiffman M, et al. (2011) Sequence Imputation of HPV16 Genomes for Genetic Association Studies,. Plos one 6: e21375. doi: 10.1371/journal.pone.0021375
[29]
Liu X, Liu GB, Pang ZJ, Xing FQ (2005) Sequence polymorphism of human papillomavirus type 16 E7 in cervical cancer]. Di Yi Jun Yi Da Xue Xue Bao 25: 1272–1275.
[30]
Kimura M (1977) Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267: 275–276. doi: 10.1038/267275a0
[31]
Miyata T, Miyazawa S, Yasunaga T (1979) Two types of amino acid substitutions in protein evolution. J Mol Evol 12: 219–236. doi: 10.1007/bf01732340
[32]
Buck CB, Cheng N, Thompson CD, Lowy DR, Steven AC, et al. (2008) Arrangement of L2 within the Papillomavirus Capsid. J Virol 82: 5190–5197. doi: 10.1128/jvi.02726-07
[33]
Sun M, Gao L, Liu Y, Zhao Y, Wang X, et al. (2012) Whole Genome Sequencing and Evolutionary Analysis of Human Papillomavirus Type 16 in Central China. PLoS ONE 7(5): e36577. doi: 10.1371/journal.pone.0036577
[34]
Wang T, Chang P, Wang L, Yao Q, Guo W, et al. (2012) The role of human papillomavirus infection in breast cancer. Med Oncol 29: 48–55. doi: 10.1007/s12032-010-9812-9
