A Dual-Reporter System for Real-Time Monitoring and High-throughput CRISPR/Cas9 Library Screening of the Hepatitis C Virus

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Ren, Qingpeng ^a   Li, Chan ^a   Yuan, Pengfei ^a   Cai, Changzu ^a   Zhang, Linqi ^b   Luo, Guangxiang George ^a,c   Wei, Wensheng ^a  

^a PEKING UNIVERSITY   (China)

^b Tsinghua University   (China)

^c University of Alabama at Birmingham   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS PROTEIN;

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; GENE LIBRARY; GENETICS; HELA CELL LINE; HEPACIVIRUS; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; REPORTER GENE; SPECTROFLUOROMETRY; VIRUS ENTRY;

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; GENE LIBRARY; GENES, REPORTER; HELA CELLS; HEPACIVIRUS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SPECTROMETRY, FLUORESCENCE; VIRAL PROTEINS; VIRUS INTERNALIZATION;

EID: 84924371138     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep08865     Document Type: Article

References (51)

1. Choo, Q. L. et al. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 244, 359-362 (1989).
2. Andreoni, M. et al. HIV-HCV co-infection: epidemiology, pathogenesis and therapeutic implications. Eur Rev Med Pharmacol Sci 16, 1473-1483 (2012).
3. Moradpour, D., Penin, F. & Rice, C. M. Replication of hepatitis C virus. Nat Rev Microbiol 5, 453-463 (2007).
4. Pileri, P. et al. Binding of hepatitis C virus to CD81. Science 282, 938-941 (1998).
5. Scarselli, E. et al. The human scavenger receptor class B type I is a novel candidate receptor for the hepatitis C virus. EMBO J 21, 5017-5025 (2002).
6. Evans, M. J. et al. Claudin-1 is a hepatitis C virus co-receptor required for a late step in entry. Nature 446, 801-805 (2007).
7. Ploss, A. et al. Human occludin is a hepatitis C virus entry factor required for infection of mouse cells. Nature 457, 882-886 (2009).
8. Lupberger, J. et al. EGFR and EphA2 are host factors for hepatitis Cvirus entry and possible targets for antiviral therapy. Nature Medicine 17, 589-595 (2011).
9. Sainz, B., Jr. et al. Identification of the Niemann-Pick C1-like 1 cholesterol absorption receptor as a new hepatitis C virus entry factor. Nat Med 18, 281-285 (2012).
10. Witteveldt, J. et al. CD81 is dispensable for hepatitis C virus cell-to-cell transmission in hepatoma cells. J Gen Virol 90, 48-58 (2009).
11. Brimacombe, C. L. et al. Neutralizing antibody-resistant hepatitis C virus cell-to-cell transmission. J Virol 85, 596-605 (2011).
12. Fofana, I. et al. A novel monoclonal anti-CD81 antibody produced by genetic immunization efficiently inhibits Hepatitis C virus cell-cell transmission. PLoS One 8, e64221 (2013).
13. Catanese, M. T. et al. Different requirements for scavenger receptor class B type I in hepatitis C virus cell-free versus cell-to-cell transmission. J Virol 87, 8282-8293 (2013).
14. Lindenbach, B. D. & Rice, C. M. The ins and outs of hepatitis C virus entry and assembly. Nat Rev Microbiol 11, 688-700 (2013).
15. Lee, J. C., Yu, M. C., Lien, T. W., Chang, C. F. & Hsu, J. T. High-throughput cell-based screening for hepatitis C virus NS3/4A protease inhibitors. Assay Drug Dev Technol 3, 385-392 (2005).
16. Tai, A. W. et al. A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Cell Host Microbe 5, 298-307 (2009).
17. Tanaka, Y. et al. Establishment of an indicator cell system for hepatitis C virus. Microbiol Immunol 54, 206-220 (2010).
18. Jones, C. T. et al. Real-time imaging of hepatitis C virus infection using a fluorescent cell-based reporter system. Nat Biotechnol 28, 167-171 (2010).
19. Hsu, E. C. et al. Modified apoptotic molecule (BID) reduces hepatitis C virus infection in mice with chimeric human livers. Nature Biotechnol 21, 519-525 (2003).
20. Lei, Y. et al. MAVS-mediated apoptosis and its inhibition by viral proteins. PLoS ONE 4, e5466 (2009).
21. Chockalingam, K., Simeon, R. L., Rice, C. M. & Chen, Z. A cell protection screen reveals potent inhibitors of multiple stages of the hepatitis C virus life cycle. Proc Natl Acad Sci U S A 107, 3764-3769 (2010).
22. Su, A. I. et al. Genomic analysis of the host response to hepatitis C virus infection. Proc Natl Acad Sci U S A 99, 15669-15674 (2002).
23. Markusic, D.,Oude-Elferink, R.,Das, A. T., Berkhout, B. &Seppen, J. Comparison of single regulated lentiviral vectors with rtTA expression driven by an autoregulatory loop or a constitutive promoter. Nucleic Acids Res 33, e63 (2005).
24. Das, A. T. et al.Viral evolution as a tool to improve the tetracycline-regulated gene expression system. J Biol Chem 279, 18776-18782 (2004).
25. Meylan, E. et al. Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus. Nature 437, 1167-1172 (2005).
26. Shin, K. J. et al. A single lentiviral vector platform for microRNA-based conditional RNA interference and coordinated transgene expression. Proc Natl Acad Sci U S A 103, 13759-13764 (2006).
27. Salomon, B. et al. A truncated herpes simplex virus thymidine kinase phosphorylates thymidine and nucleoside analogs and does not cause sterility in transgenic mice. Mol Cell Biol 15, 5322-5328 (1995).
28. Han, Q. et al. Compensatory mutations in NS3 and NS5A proteins enhance the virus production capability of hepatitis C reporter virus. Virus Res 145, 63-73 (2009).
29. Wakita, T. et al. Production of infectious hepatitis C virus in tissue culture from a cloned viral genome. Nat Med 11, 791-796 (2005).
30. Matthews, S. J. & Lancaster, J. W. Telaprevir: a hepatitis C NS3/4A protease inhibitor. Clin Ther 34, 1857-1882 (2012).
31. Zhou, Y. et al.High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509, 487-491 (2014).
32. Li, W. et al. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biology 15, 554, doi:10.1186/s13059-014-0554-4 (2014).
33. Yang, J. et al. ULtiMATE system for rapid assembly of customized TAL effectors. PLoS One 8, e75649 (2013).
34. Zeisel, M. B., Fofana, I., Fafi-Kremer, S. & Baumert, T. F. Hepatitis C virus entry into hepatocytes: Molecular mechanisms and targets for antiviral therapies. J Hepatol 54, 566-576 (2011).
35. Carloni, G., Crema, A., Valli, M. B., Ponzetto, A. & Clementi, M. HCV infection by cell-to-cell transmission: choice or necessity? Curr Mol Med 12, 83-95 (2012).
36. Kim, C. S., Jung, J. H., Wakita, T., Yoon, S. K. & Jang, S. K. Monitoring the antiviral effect of alpha interferon on individual cells. J Virol 81, 8814-8820 (2007).
37. Schaller, T. et al. Analysis of hepatitis C virus superinfection exclusion by using novel fluorochrome gene-tagged viral genomes. J Virol 81, 4591-4603 (2007).
38. Koutsoudakis, G. et al. Characterization of the early steps of hepatitis C virus infection by using luciferase reporter viruses. J Virol 80, 5308-5320 (2006).
39. Pacini, L., Bartholomew, L., Vitelli, A. & Migliaccio, G. Reporter substrates for assessing the activity of the hepatitis C virus NS3-4A serine protease in living cells. Anal Biochem 331, 46-59 (2004).
40. Breiman, A. et al. A hepatitis C virus (HCV) NS3/4A protease-dependent strategy for the identification and purification of HCV-infected cells. J Gen Virol 87, 3587-3598 (2006).
41. Lei, Y. F. et al. Development of a cell-based assay for monitoring hepatitis C virus ns3/4a protease activity. Acta Virol 52, 133-141 (2008).
42. Pan, K. L., Lee, J. C., Sung, H. W., Chang, T. Y. & Hsu, J. T. Development of NS3/4A protease-based reporter assay suitable for efficiently assessing hepatitis C virus infection. Antimicrob Agents Chemother 53, 4825-4834 (2009).
43. Lee, J. C. et al. A cell-based reporter assay for inhibitor screening of hepatitis C virus RNA-dependent RNA polymerase. Anal Biochem 403, 52-62 (2010).
44. Li, X. D., Sun, L., Seth, R. B., Pineda, G. & Chen, Z. J. Hepatitis C virus protease NS3/4A cleaves mitochondrial antiviral signaling protein off the mitochondria to evade innate immunity. Proc Natl Acad Sci U S A 102, 17717-17722 (2005).
45. Miller, J. C. et al. A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29, 143-148, doi:10.1038/nbt.1755 (2011).
46. Cong, L. et al. Multiplex Genome Engineering Using CRISPR/Cas Systems. Science, doi:10.1126/science.1231143 (2013).
47. Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823-826, doi:10.1126/science.1232033 (2013).
48. Jiang, J. & Luo, G. Cell culture-adaptive mutations promote viral protein-protein interactions and morphogenesis of infectious hepatitis C virus. J Virol 86, 8987-8997 (2012).
49. Qian, L. et al. Bidirectional effect of Wnt signaling antagonist DKK1 on the modulation of anthrax toxin uptake. Science China. Life sciences 57, 469-481 (2014).
50. Reed, L. J. & Muench, H. A simple method of estimating fifty percent endpoints. Am. J. Epidemiol. 27, 493-497 (1938).
51. Lindenbach, B. D. et al. Complete replication of hepatitis C virus in cell culture. Science 309, 623-626 (2005).