The CRISPR/Cas9 genome editing methodology as a weapon against human viruses

Discovery Medicine

Volumn 19, Issue 105, 2015, Pages 255-262

  White, Martyn K ^a   Hu, Wenhui ^a   Khalili, Kamel ^a  

^a TEMPLE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRISPR ASSOCIATED PROTEIN; PROTEIN P53; VIRUS PROTEIN; ANTIVIRUS AGENT; GUIDE RNA;

ARTICLE; CELL CYCLE PROGRESSION; CELL METABOLISM; CELL PROLIFERATION; CRISPR CAS SYSTEM; EPSTEIN BARR VIRUS; GENETIC TRANSFECTION; HEPATITIS B VIRUS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN PAPILLOMAVIRUS TYPE 16; HUMAN PAPILLOMAVIRUS TYPE 18; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN EXPRESSION; RNA EDITING; VIRUS INFECTION; VIRUS TRANSMISSION; ANIMAL; BACTERIUM; FEMALE; GENETICS; GENOME; HELA CELL LINE; OPEN READING FRAME; PAPILLOMAVIRIDAE; VIRUS DISEASES;

ANIMALS; ANTIVIRAL AGENTS; BACTERIA; CRISPR-CAS SYSTEMS; FEMALE; GENOME; HELA CELLS; HEPATITIS B VIRUS; HERPESVIRUS 4, HUMAN; HIV-1; HUMANS; OPEN READING FRAMES; PAPILLOMAVIRIDAE; RNA EDITING; RNA, GUIDE; VIRUS DISEASES;

EID: 84940495894     PISSN: 15396509     EISSN: 19447930     Source Type: Journal    
DOI: None     Document Type: Article

References (68)

1. Abbot SD, Rowe M, Cadwallader K, Ricksten A, Gordon J, Wang F, Rymo L, Rickinson AB. Epstein-Barr virus nuclear antigen 2 induces expression of the virus-encoded latent membrane protein. J Virol 64(5):2126-2134, 1990.
2. Adams A, Lindahl T. Epstein-Barr virus genomes with properties of circular DNA molecules in carrier cells. Proc Natl Acad Sci U S A 72:1477-1481, 1975.
3. Baer R, Bankier AT, Biggin MD, Deininger PL, Farrell PJ, Gibson TJ, Hatfull G, Hudson GS, Satchwell SC, Seguin C, Tuffnell PS, Barrell BG. 1984. DNA sequence and expression of the B95-8 Epstein-Barr virus genome. Nature 310(5974):207-211.
4. Beaudenon S, Huibregtse JM. HPV E6, E6AP and cervical cancer. BMC Biochem 9(Suppl 1):S4, 2008.
5. Bhaya D, Davison M, Barrangou R. CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet 45:273-997, 2011.
6. Campos SK, Barry MA. Current advances and future challenges in Adenoviral vector biology and targeting. Curr Gene Ther 7(3):189-204, 2007.
7. Chang Y, Cesarman E, Pessin MS, Lee F, Culpepper J, Knowles DM, Moore PS. Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi's sarcoma. Science 266(5192):1865-1869, 1994.
8. Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S, Kim JS. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 24(1):132-141, 2014.
9. Dane DS, Cameron CH, Briggs M. Virus-like particles in serum of patients with Australia-antigen-associated hepatitis. Lancet 1(7649):695-698, 1970.
10. Danos O, Katinka M, Yaniv M. Human papillomavirus 1a complete DNA sequence: a novel type of genome organization among papovaviridae. EMBO J 1(2):231-236, 1982.
11. Doudna JA, Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346(6213):1258096, 2014.
12. Diao J, Garces R, Richardson CD. X protein of hepatitis B virus modulates cytokine and growth factor related signal transduction pathways during the course of viral infections and hepatocarcinogenesis. Cytokine Growth Factor Rev 12(2-3):189-205, 2001.
13. Ebina H, Misawa N, Kanemura Y, Koyanagi Y. Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus. Sci Rep 3:2510, 2013.
14. Feitelson MA, Zhu M, Duan LX, London WT. Hepatitis B x antigen and p53 are associated in vitro and in liver tissues from patients with primary hepatocellular carcinoma. Oncogene 8(5):1109-1117, 1993.
15. Felsani A, Mileo AM, Paggi MG. Retinoblastoma family proteins as key targets of the small DNA virus oncoproteins. Oncogene 25(38):5277-5285, 2006.
16. Feng H, Taylor JL, Benos PV, Newton R, Waddell K, Lucas SB, Chang Y, Moore PS. Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma. J Virol 81:11332-11340, 2007.
17. Gaj T, Guo J, Kato Y, Sirk SJ, Barbas CF. Targeted gene knockout by direct delivery of zinc-finger nuclease proteins. Nat Methods 9(8):805-807, 2012.
18. Gaj T, Gersbach CA, Barbas CF 3rd. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31(7):397-405, 2013.
19. Gardner SD, Field AM, Coleman DV, Hulme B. New human papovavirus (B.K.) isolated from urine after renal transplantation. Lancet 1(7712):1253-1257, 1971.
20. Guilinger JP, Thompson DB, Liu DR. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol 32(6):577-582, 2014.
21. Hamid NA, Brown C, Gaston K. The regulation of cell proliferation by the papillomavirus early proteins. Cell Mol Life Sci 66(10):1700-1717, 2009.
22. Henle G, Henle W, Clifford P, Diehl V, Kafuko GW, Kirya BG, Klein G, Morrow RH, Munube GM, Pike P, Tukei PM, Ziegler JL. Antibodies to Epstein-Barr virus in Burkitt's lymphoma and control groups. J Natl Cancer Inst 43(5):1147-1157, 1969.
23. Howes R, Schofield C. Genome engineering using Adeno-Associated Virus (AAV). Methods Mol Biol 1239:75-103, 2015.
24. Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157(6):1262-1278, 2014.
25. Hu W, Kaminski R, Yang F, Zhang Y, Cosentino L, Li F, Luo B, Alvarez-Carbonell D, Garcia-Mesa Y, Karn J, Mo X, Khalili K. RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection. Proc Natl Acad Sci U S A 111(31):11461-11466, 2014a.
26. Hu Z, Yu L, Zhu D, Ding W, Wang X, Zhang C, Wang L, Jiang X, Shen H, He D, Li K, Xi L, Ma D, Wang H. Disruption of HPV16-E7 by CRISPR/Cas system induces apoptosis and growth inhibition in HPV16 positive human cervical cancer cells. Biomed Res Int 2014:612823, 2014b.
27. Kennedy EM, Kornepati AV, Goldstein M, Bogerd HP, Poling BC, Whisnant AW, Kastan MB, Cullen BR. Inactivation of the human papillomavirus E6 or E7 gene in cervical carcinoma cells by using a bacterial CRISPR/Cas RNA-guided endonuclease. J Virol 88(20):11965-11972, 2014.
28. Kennedy EM, Bassit LC, Mueller H, Kornepati AV, Bogerd HP, Nie T, Chatterjee P, Javanbakht H, Schinazi RF, Cullen BR. Suppression of hepatitis B virus DNA accumulation in chronically infected cells using a bacterial CRISPR/Cas RNA-guided DNA endonuclease. Virology 476:196-205, 2015.
29. Kennedy EM, Cullen BR. Bacterial CRISPR/Cas DNA endonucleases: A revolutionary technology that could dramatically impact viral research and treatment. Virology, in press, 2015.
30. Kew MC. Hepatitis B virus x protein in the pathogenesis of hepatitis B virus-induced hepatocellular carcinoma. J. Gastroenterol Hepatol 26(Suppl 1):144-152, 2011.
31. Khalili K, Gordon J, Kaminski R, Cosentino L, Hu W. Genome editing strategies: potential tools for eradicating HIV-1/AIDS. J Neurovirol, in press, 2015.
32. Kim YG, Li L, Chandrasegaran S. Insertion and deletion mutants of FokI restriction endonuclease. J Biol Chem 269(50):31978-31982, 1994.
33. Lemon SM, Hutt LM, Shaw JE, Li JL, Pagano JS. Replication of EBV in epithelial cells during infectious mononucleosis. Nature 268(5617):268-270, 1977.
34. Liao HK, Gu Y, Diaz A, Marlett J, Takahashi Y, Li M, Suzuki K, Xu R, Hishida T, Chang CJ, Esteban CR, Young J, Izpisua Belmonte JC. Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells. Nat Commun 6:6413, 2015.
35. Lin SR, Yang HC, Kuo YT, Liu CJ, Yang TY, Sung KC, Lin YY, Wang HY, Wang CC, Shen YC, Wu FY, Kao JH, Chen DS, Chen PJ. The CRISPR/Cas9 System Facilitates Clearance of the Intrahepatic HBV Templates In Vivo. Mol Ther Nucleic Acids 3:e186, 2014.
36. Liu KC, Lin BS, Gao AD, Ma HY, Zhao M, Zhang R, Yan HH, Yi XF, Lin SJ, Que JW, Lan XP. Integrase-deficient lentivirus: opportunities and challenges for human gene therapy. Curr Gene Ther 14(5):352-364, 2014.
37. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 31(9):833-838, 2013a.
38. Mali P, Esvelt KM, Church GM. Cas9 as a versatile tool for engineering biology. Nat Methods 10(10):957-963, 2013b.
39. Manjunath N, Yi G, Dang Y, Shankar P. Newer gene editing technologies toward HIV gene therapy. Viruses 5(11):2748-2766, 2013.
40. Marquitz AR, Raab-Traub N. The role of miRNAs and EBV BARTs in NPC. Semin Cancer Biol 22(2):166-172, 2012.
41. Munger K, Baldwin A, Edwards KM, Hayakawa H, Nguyen CL, Owens M, Grace M, Huh K. Mechanisms of human papillomavirus-induced oncogenesis. J Virol 78(21):11451-11460, 2004.
42. Padgett BL, Zu Rhein GM, Walker DL, Eckroade RJ, Dessel BH. Cultivation of papova-like virus from human brain with progressive multifocal leukoencephalopathy. Lancet 1(7712):1257-1260, 1971.
43. Pagano JS. Epstein-Barr virus: the first human tumor virus and its role in cancer. Proc Assoc Am Physicians 111(6):573-580, 1999.
44. Platt RJ, Chen S, Zhou Y, Yim MJ, Swiech L, Kempton HR, Dahlman JE, Parnas O, Eisenhaure TM, Jovanovic M, Graham DB, Jhunjhunwala S, Heidenreich M, Xavier RJ, Langer R, Anderson DG, Hacohen N, Regev A, Feng G, Sharp PA, Zhang F. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 159(2):440-455, 2014.
45. Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y, Zhang F. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154(6):1380-1389, 2013a.
46. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc 8(11):2281-2308, 2013b.
47. Rawlins DR, Milman G, Hayward SD, Hayward GS. Sequence-specific DNA binding of the Epstein-Barr virus nuclear antigen (EBNA-1) to clustered sites in the plasmid maintenance region. Cell 42(3):859-868, 1985.
48. Robinson WS, Clayton DA, Greenman RL. DNA of a human hepatitis B virus candidate. J Virol 14(2):384-391, 1974.
49. Rothe M, Modlich U, Schambach A. Biosafety challenges for use of lentiviral vectors in gene therapy. Curr Gene Ther 13(6):453-468, 2013.
50. Rowe M, Lear AL, Croom-Carter D, Davies AH, Rickinson AB. Three pathways of Epstein-Barr virus gene activation from EBNA1-positive latency in B lymphocytes. J Virol 66(1):122-131, 1992.
51. Seeger C, Sohn JA. Targeting Hepatitis B Virus with CRISPR/Cas9. Mol Ther Nucleic Acids 3:e216, 2014.
52. Senís E, Fatouros C, Große S, Wiedtke E, Niopek D, Mueller AK, Börner K, Grimm D. CRISPR/Cas9-mediated genome engineering: an adeno-associated viral (AAV) vector toolbox. Biotechnol J 9(11):1402-1412, 2014.
53. Shen B, Zhang W, Zhang J, Zhou J, Wang J, Chen L, Wang L, Hodgkins A, Iyer V, Huang X, Skarnes WC. Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat Methods 11(4):399-402, 2014.
54. Stone D, Kiem HP, Jerome KR. Targeted gene disruption to cure HIV. Curr Opin HIV AIDS 8(3):217-223, 2013.
55. Swiech L, Heidenreich M, Banerjee A, Habib N, Li Y, Trombetta J, Sur M, Zhang F. In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9. Nat Biotechnol 33(1):102-106, 2015.
56. Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ, Joung JK. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol 32(6):569-576, 2014.
57. Veres A, Gosis BS, Ding Q, Collins R, Ragavendran A, Brand H, Erdin S, Cowan CA, Talkowski ME, Musunuru K. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell 15(1):27-30, 2014.
58. Wakisaka N, Pagano JS. Epstein-Barr virus induces invasion and metastasis factors. Anticancer Res 23(3A):2133-2138, 2003.
59. Wang J, Quake SR. RNA-guided endonuclease provides a therapeutic strategy to cure latent herpesviridae infection. Proc Natl Acad Sci U S A 111(36):13157-13162, 2014
60. Wang W, Ye C, Liu J, Zhang D, Kimata JT, Zhou P. CCR5 gene disruption via lentiviral vectors expressing Cas9 and single guided RNA renders cells resistant to HIV-1 infection. PLoS One 9(12):e115987, 2014.
61. White MK, Pagano JS, Khalili K. Viruses and human cancers: a long road of discovery of molecular paradigms. Clin Microbiol Rev 27(3):463-481, 2014.
62. Wright DA, Li T, Yang B, Spalding MH. TALEN-mediated genome editing: prospects and perspectives. Biochem J 462(1):15-24, 2014.
63. Yang L, Grishin D, Wang G, Aach J, Zhang CZ, Chari R, Homsy J, Cai X, Zhao Y, Fan JB, Seidman C, Seidman J, Pu W, Church G. 2014. Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells. Nat Commun 5:5507, 2014.
64. Yuen KS, Chan CP, Wong NH, Ho CH, Ho TH, Lei T, Deng W, Tsao SW, Chen H, Kok KH, Jin DY. CRISPR/Cas9-mediated genome editing of Epstein-Barr virus in human cells. J Gen Virol 96(3):626-636, 2015.
65. Zhen S, Hua L, Liu YH, Gao LC, Fu J, Wan DY, Dong LH, Song HF, Gao X. Harnessing the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated Cas9 system to disrupt the hepatitis B virus. Gene Ther, in press, 2015.
66. Zetsche B, Volz SE, Zhang F. A split-Cas9 architecture for inducible genome editing and transcription modulation. Nat Biotechnol 33(2):139-142, 2015.
67. Zhu W, Lei R, Le Duff Y, Li J, Guo F, Wainberg MA, Liang C. The CRISPR/Cas9 system inactivates latent HIV-1 proviral DNA. Retrovirology 12(1):22, 2015.
68. Zur Hausen H. Infections causing human cancer. Wiley, Wilmington, DE, USA, 2006.