Profile of HBV Integration in the Plasma DNA of Hepatocellular Carcinoma Patients

Author(s): Weiyang Li*, Xiaofang Cui*, Qing Huo, Yanwei Qi, Yuhui Sun, Meihua Tan, Qingsheng Kong*.

Journal Name: Current Genomics

Volume 20 , Issue 1 , 2019

Submit Manuscript
Submit Proposal

Graphical Abstract:


Abstract:

Background: Hepatitis B Viral (HBV) infection is one of the major causes of Hepatocellular Carcinoma (HCC). Mounting evidence had provided that the HBV integration might be a critical contributor of HCC carcinogenesis.

Objective and Methods: To explore the profile of HBV integration in the plasma DNA, the method of next-generation sequencing, HBV capture and bioinformatics had been employed to screen for HBV integration sites in the plasma samples.

Results: In the initial experiment, a total of 87 breakpoints were detected in the 20 plasma samples. The distribution of breakpoints showed that there was significant enrichment of breakpoints in the region of intron. Furthermore, the HBV breakpoints were prone to occur in the region of X protein (1,700-2,000bp) in the plasma samples. The pathway analysis had revealed that the HBV integrations sites were specifically enriched in the cancer pathway.

Conclusion: Altogether, our results had provided direct evidence for the HBV integration in plasma DNA, and they might be potentially useful for future HCC prognosis and diagnosis.

Keywords: Hepatocellular carcinoma, Plasma, HBV integration, Cell free DNA, HBV genome, Breakpoints.

[1]
Lin, C.L.; Liao, L.Y.; Wang, C.S.; Chen, P.J.; Lai, M.Y.; Chen, D.S.; Kao, J.H. Basal core-promoter mutant of hepatitis B virus and progression of liver disease in hepatitis B e antigen-negative chronic hepatitis B. Liver Int., 2005, 25(3), 564-570.
[2]
Petruzziello, A. Epidemiology of Hepatitis B virus (HBV) and Hepatitis C virus (HCV) related hepatocellular carcinoma. Open Virol. J., 2018, 12(1), 26-32.
[3]
Sagnelli, E.; Felaco, F.M.; Rapicetta, M.; Stroffolini, T.; Petruzziello, A.; Annella, T.; Chionne, P.; Pasquale, G.; Filippini, P.; Peinetti, P. Interaction between HDV and HBV infection in HBsAg-chronic carriers. Infection, 1991, 19(3), 155-158.
[4]
Perz, J.F.; Armstrong, G.L.; Farrington, L.A.; Hutin, Y.J.; Bell, B.P. The contributions of hepatitis B virus and hepatitis C virus infections to cirrhosis and primary liver cancer worldwide. J. Hepatol., 2006, 45(4), 529-538.
[5]
Sherman, M. Hepatocellular carcinoma: Epidemiology, risk factors, and screening. Semin. Liver Dis., 2005, 25(2), 143-154.
[6]
Aghemo, A.; Colombo, M. Hepatocellular carcinoma in chronic hepatitis C: From bench to bedside. Semin. Immunopathol., 2013, 35(1), 111-120.
[7]
Romeo, R.; Petruzziello, A.; Pecheur, E.I.; Facchetti, F.; Perbellini, R.; Galmozzi, E.; Khan, N.U.; Di Capua, L.; Sabatino, R.; Botti, G.; Loquercio, G. Hepatitis delta virus and hepatocellular carcinoma: An update. Epidemiol. Infect., 2018, 146(13), 1612-1618.
[8]
Stroffolini, T.; Sagnelli, E.; Rapicetta, M.; Felaco, F.M.; Filippini, P.; Annella, T.; Petruzziello, A.; Chionne, P.; Sarrecchia, B.; Piccinino, F. Hepatitis B virus DNA in chronic HBsAg carriers: Correlation with HBeAg/anti-HBe status, anti-HD and liver histology. Hepatogastroenterology, 1992, 39(1), 62-65.
[9]
Araujo, N.M.; Waizbort, R.; Kay, A. Hepatitis B virus infection from an evolutionary point of view: How viral, host, and environmental factors shape genotypes and subgenotypes. Infect. Genet. Evol., 2011, 11(6), 1199-1207.
[10]
Tanaka, M.; Katayama, F.; Kato, H.; Tanaka, H.; Wang, J.; Qiao, Y.L.; Inoue, M. Hepatitis B and C virus infection and hepatocellular carcinoma in China: A review of epidemiology and control measures. J. Epidemiol., 2011, 21(6), 401-416.
[11]
Jiang, Z.; Jhunjhunwala, S.; Liu, J.; Haverty, P.M.; Kennemer, M. Guan, Y.; Lee, W.; Carnevali, P.; Stinson, J.; Johnson, S.; Diao, J.; Yeung, S.; Jubb, A.; Ye, W.; Wu, T.D.; Kapadia, S.B.; de Sauvage, F.J.; Gentleman, R.C.; Stern, H.M.; Seshagiri, S.; Pant, K.P.; Modrusan, Z.; Ballinger, D.G.; Zhang, Z. The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Res., 2012, 22(4), 593-601.
[12]
Sung, W.K.; Zheng, H.; Li, S.; Chen, R.; Liu, X.; Li, Y.; Lee, N.P.; Lee, W.H.; Ariyaratne, P.N.; Tennakoon, C.; Mulawadi, F.H.; Wong, K.F.; Liu, A.M.; Poon, R.T.; Fan, S.T.; Chan, K.L.; Gong, Z.; Hu, Y.; Lin, Z.; Wang, G.; Zhang, Q.; Barber, T.D.; Chou, W.C.; Aggarwal, A.; Hao, K.; Zhou, W.; Zhang, C.; Hardwick, J.; Buser, C.; Xu, J.; Kan, Z.; Dai, H.; Mao, M.; Reinhard, C.; Wang, J.; Luk, J.M. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat. Genet., 2012, 44(7), 765-769.
[13]
Lau, C.C.; Sun, T.; Ching, A.K.; He, M.; Li, J.W.; Wong, A.M.; Co, N.N.; Chan, A.W.; Li, P.S.; Lung, R.W.; Tong, J.H.; Lai, P.B.; Chan, H.L.; To, K.F.; Chan, T.F.; Wong, N. Viral-human chimeric transcript predisposes risk to liver cancer development and progression. Cancer Cell, 2014, 25(3), 335-349.
[14]
Hanahan, D.; Weinberg, R.A. Hallmarks of cancer: The next generation. Cell, 2011, 144(5), 646-674.
[15]
Edman, J.C.; Gray, P.; Valenzuela, P.; Rall, L.B.; Rutter, W.J. Integration of hepatitis B virus sequences and their expression in a human hepatoma cell. Nature, 1980, 286(5772), 535-538.
[16]
Brechot, C.; Pourcel, C.; Louise, A.; Rain, B.; Tiollais, P. Presence of integrated hepatitis B virus DNA sequences in cellular DNA of human hepatocellular carcinoma. Nature, 1980, 286(5772), 533-535.
[17]
Tu, T.; Budzinska, M.A.; Shackel, N.A.; Jilbert, A.R. Conceptual models for the initiation of hepatitis B virus-associated hepatocellular carcinoma. Liver Int., 2015, 35(7), 1786-1800.
[18]
Li, W.; Zeng, X.; Lee, N.P.; Liu, X.; Chen, S.; Guo, B.; Yi, S.; Zhuang, X.; Chen, F.; Wang, G.; Poon, R.T.; Fan, S.T.; Mao, M.; Li, Y.; Li, S.; Wang, J. Jianwang; Xu, X.; Jiang, H.; Zhang, X. HIVID: An efficient method to detect HBV integration using low coverage sequencing. Genomics, 2013, 102(4), 338-344.
[19]
Li, H.; Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 2009, 25(14), 1754-1760.
[20]
Wang, K.; Li, M.; Hakonarson, H. ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucl Acid Res., 2010, 38(16), e164.
[21]
Huang da W.; Sherman, B.T.; Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 2009, 4(1), 44-57.
[22]
Huang da W.; Sherman, B.T.; Lempicki, R.A. Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucl Acid Res., 2009, 37(1), 1-13.
[23]
Jahr, S.; Hentze, H.; Englisch, S.; Hardt, D.; Fackelmayer, F.O.; Hesch, R.D.; Knippers, R. DNA fragments in the blood plasma of cancer patients: Quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res., 2001, 61(4), 1659-1665.
[24]
Anker, P.; Mulcahy, H.; Chen, X.Q.; Stroun, M. Detection of circulating tumour DNA in the blood (plasma/serum) of cancer patients. Cancer Metast Rev., 1999, 18(1), 65-73.
[25]
Elshimali, Y.I.; Khaddour, H.; Sarkissyan, M.; Wu, Y.; Vadgama, J.V. The clinical utilization of circulating cell free DNA (CCFDNA) in blood of cancer patients. Int. J. Mol. Sci., 2013, 14(9), 18925-18958.
[26]
Fleischhacker, M.; Schmidt, B. Circulating nucleic acids (CNAs) and cancer--a survey. Biochim. Biophys. Acta, 2007, 1775(1), 181-232.
[27]
Holdenrieder, S.; Von Pawel, J.; Nagel, D.; Stieber, P. Long-term stability of circulating nucleosomes in serum. Anticancer Res., 2010, 30(5), 1613-1615.
[28]
Thakur, B.K.; Zhang, H.; Becker, A.; Matei, I.; Huang, Y.; Costa-Silva, B.; Zheng, Y.; Hoshino, A.; Brazier, H.; Xiang, J.; Williams, C.; Rodriguez-Barrueco, R.; Silva, J.M.; Zhang, W.; Hearn, S.; Elemento, O.; Paknejad, N.; Manova-Todorova, K.; Welte, K.; Bromberg, J.; Peinado, H.; Lyden, D. Double-stranded DNA in exosomes: a novel biomarker in cancer detection. Cell Res., 2014, 24(6), 766-769.
[29]
Tamkovich, S.N.; Cherepanova, A.V.; Kolesnikova, E.V.; Rykova, E.Y.; Pyshnyi, D.V.; Vlassov, V.V.; Laktionov, P.P. Circulating DNA and DNase activity in human blood. Ann. N. Y. Acad. Sci., 2006, 1075(1), 191-196.
[30]
Tamkovich, S.N.; Vlasov, V.V.; Laktionov, P.P. Circulating deoxyribonucleic acids in blood and their using in medical diagnostics. Mol. Biol., 2008, 42(1), 12-23.
[31]
Tamkovich, S.N.; Litviakov, N.V.; Bryzgunova, O.E.; Dobrodeev, A.Y.; Rykova, E.Y.; Tuzikov, S.A.; Zav’ialov, A.A.; Vlassov, V.V.; Cherdyntseva, N.V.; Laktionov, P.P. Cell-surface-bound circulating DNA as a prognostic factor in lung cancer. Ann. N. Y. Acad. Sci., 2008, 1137(1), 214-217.
[32]
Choi, J.J.; Reich, C.F., 3rd; Pisetsky, D.S. The role of macrophages in the in vitro generation of extracellular DNA from apoptotic and necrotic cells. Immunology, 2005, 115(1), 55-62.
[33]
Adey, A.; Burton, J.N.; Kitzman, J.O.; Hiatt, J.B.; Lewis, A.P.; Martin, B.K.; Qiu, R.; Lee, C.; Shendure, J. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line. Nature, 2013, 500(7461), 207-211.


Rights & PermissionsPrintExport Cite as


Article Details

VOLUME: 20
ISSUE: 1
Year: 2019
Page: [61 - 68]
Pages: 8
DOI: 10.2174/1389202919666181002144336
Price: $58

Article Metrics

PDF: 25
HTML: 4
EPUB: 1
PRC: 1