An siRNA Screen Identifies the U2 snRNP Spliceosome as a Host Restriction Factor for Recombinant Adeno-associated Viruses

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Mammalian cells have developed diverse innate/intrinsic immune strategies to counteract viral infections. Post-entry infection steps of a single-strand DNA virus, adeno-associated virus (AAV), are subject to such restrictions. Here, we screened an siRNA library to identify a novel cellular factor involved in AAV restriction. We found PHF5A, a component of the U2 snRNP mRNA splicing factor, blocks expression from recombinant AAV vectors. Disruption of PHF5A expression specifically enhanced AAV vector performance. Moreover, genetic and pharmacological inhibition of other U2 snRNP proteins, but not spliceosome proteins involved in other splicing steps, strongly increased transgene expression from AAV vectors. Further study demonstrated that U2 snRNP proteins recognize incoming AAV capsids to mediate this cellular restriction at the step after second-strand synthesis. In summary, we identify the U2 snRNP spliceosome complex as novel host factors that effectively restrict recombinant AAV vectors. Considering frequent reorganization of host splicing machinery in DNA virus infections, it is conceivable that U2 snRNP plays a role as a broad spectrum antiviral factor and helper viruses have evolved to counteract this restriction through sequestration of snRNP proteins.

Vyšlo v časopise: An siRNA Screen Identifies the U2 snRNP Spliceosome as a Host Restriction Factor for Recombinant Adeno-associated Viruses. PLoS Pathog 11(8): e32767. doi:10.1371/journal.ppat.1005082
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1005082

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1. Bridge E, Xia DX, Carmo-Fonseca M, Cardinali B, Lamond AI, et al. (1995) Dynamic organization of splicing factors in adenovirus-infected cells. J Virol 69: 281–290. 7983720

2. Burch AD, Weller SK (2004) Nuclear sequestration of cellular chaperone and proteasomal machinery during herpes simplex virus type 1 infection. J Virol 78: 7175–7185. 15194794

3. Geoffroy MC, Salvetti A (2005) Helper functions required for wild type and recombinant adeno-associated virus growth. Current gene therapy 5: 265–271. 15975004

4. Xiao PJ, Samulski RJ (2012) Cytoplasmic trafficking, endosomal escape, and perinuclear accumulation of adeno-associated virus type 2 particles are facilitated by microtubule network. J Virol 86: 10462–10473. doi: 10.1128/JVI.00935-12 22811523

5. Venkatakrishnan B, Yarbrough J, Domsic J, Bennett A, Bothner B, et al. (2013) Structure and dynamics of adeno-associated virus serotype 1 VP1-unique N-terminal domain and its role in capsid trafficking. J Virol 87: 4974–4984. doi: 10.1128/JVI.02524-12 23427155

6. Bartlett JS, Wilcher R, Samulski RJ (2000) Infectious entry pathway of adeno-associated virus and adeno-associated virus vectors. J Virol 74: 2777–2785. 10684294

7. Thomas CE, Storm TA, Huang Z, Kay MA (2004) Rapid uncoating of vector genomes is the key to efficient liver transduction with pseudotyped adeno-associated virus vectors. J Virol 78: 3110–3122. 14990730

8. Ferrari FK, Samulski T, Shenk T, Samulski RJ (1996) Second-strand synthesis is a rate-limiting step for efficient transduction by recombinant adeno-associated virus vectors. J Virol 70: 3227–3234. 8627803

9. Fisher KJ, Gao GP, Weitzman MD, DeMatteo R, Burda JF, et al. (1996) Transduction with recombinant adeno-associated virus for gene therapy is limited by leading-strand synthesis. J Virol 70: 520–532. 8523565

10. Douar AM, Poulard K, Stockholm D, Danos O (2001) Intracellular trafficking of adeno-associated virus vectors: routing to the late endosomal compartment and proteasome degradation. J Virol 75: 1824–1833. 11160681

11. Mitchell AM, Samulski RJ (2013) Mechanistic insights into the enhancement of adeno-associated virus transduction by proteasome inhibitors. J Virol 87: 13035–13041. doi: 10.1128/JVI.01826-13 24027330

12. Nonnenmacher M, Weber T (2012) Intracellular transport of recombinant adeno-associated virus vectors. Gene Ther 19: 649–658. doi: 10.1038/gt.2012.6 22357511

13. Qing K, Hansen J, Weigel-Kelley KA, Tan M, Zhou S, et al. (2001) Adeno-associated virus type 2-mediated gene transfer: role of cellular FKBP52 protein in transgene expression. J Virol 75: 8968–8976. 11533160

14. Schwartz RA, Palacios JA, Cassell GD, Adam S, Giacca M, et al. (2007) The Mre11/Rad50/Nbs1 complex limits adeno-associated virus transduction and replication. J Virol 81: 12936–12945. 17898048

15. Lentz TB, Samulski RJ (2015) Insight into the mechanism of inhibition of adeno-associated virus by the Mre11/Rad50/Nbs1 complex. J Virol 89: 181–194. doi: 10.1128/JVI.01990-14 25320294

16. Chen H, Lilley CE, Yu Q, Lee DV, Chou J, et al. (2006) APOBEC3A is a potent inhibitor of adeno-associated virus and retrotransposons. Current biology: CB 16: 480–485. 16527742

17. Mitchell AM, Hirsch ML, Li C, Samulski RJ (2014) Promyelocytic leukemia protein is a cell-intrinsic factor inhibiting parvovirus DNA replication. J Virol 88: 925–936. doi: 10.1128/JVI.02922-13 24198403

18. Asokan A, Schaffer DV, Samulski RJ (2012) The AAV vector toolkit: poised at the clinical crossroads. Molecular therapy: the journal of the American Society of Gene Therapy 20: 699–708.

19. Asokan A, Conway JC, Phillips JL, Li C, Hegge J, et al. (2010) Reengineering a receptor footprint of adeno-associated virus enables selective and systemic gene transfer to muscle. Nat Biotechnol 28: 79–82. doi: 10.1038/nbt.1599 20037580

20. Grimm D, Lee JS, Wang L, Desai T, Akache B, et al. (2008) In vitro and in vivo gene therapy vector evolution via multispecies interbreeding and retargeting of adeno-associated viruses. J Virol 82: 5887–5911. doi: 10.1128/JVI.00254-08 18400866

21. Lisowski L, Dane AP, Chu K, Zhang Y, Cunningham SC, et al. (2014) Selection and evaluation of clinically relevant AAV variants in a xenograft liver model. Nature 506: 382–386. doi: 10.1038/nature12875 24390344

22. Adachi K, Enoki T, Kawano Y, Veraz M, Nakai H (2014) Drawing a high-resolution functional map of adeno-associated virus capsid by massively parallel sequencing. Nature communications 5: 3075. doi: 10.1038/ncomms4075 24435020

23. Yang L, Jiang J, Drouin LM, Agbandje-McKenna M, Chen C, et al. (2009) A myocardium tropic adeno-associated virus (AAV) evolved by DNA shuffling and in vivo selection. Proc Natl Acad Sci U S A 106: 3946–3951. doi: 10.1073/pnas.0813207106 19234115

24. Cataliotti A, Tonne JM, Bellavia D, Martin FL, Oehler EA, et al. (2011) Long-term cardiac pro-B-type natriuretic peptide gene delivery prevents the development of hypertensive heart disease in spontaneously hypertensive rats. Circulation 123: 1297–1305. doi: 10.1161/CIRCULATIONAHA.110.981720 21403100

25. Takeda S, Takahashi M, Mizukami H, Kobayashi E, Takeuchi K, et al. (2004) Successful gene transfer using adeno-associated virus vectors into the kidney: comparison among adeno-associated virus serotype 1–5 vectors in vitro and in vivo. Nephron Experimental nephrology 96: e119–126. 15122061

26. Ashtari M, Cyckowski LL, Monroe JF, Marshall KA, Chung DC, et al. (2011) The human visual cortex responds to gene therapy-mediated recovery of retinal function. J Clin Invest 121: 2160–2168. doi: 10.1172/JCI57377 21606598

27. Nathwani AC, Rosales C, McIntosh J, Rastegarlari G, Nathwani D, et al. (2011) Long-term safety and efficacy following systemic administration of a self-complementary AAV vector encoding human FIX pseudotyped with serotype 5 and 8 capsid proteins. Molecular therapy: the journal of the American Society of Gene Therapy 19: 876–885.

28. Bowles DE, McPhee SW, Li C, Gray SJ, Samulski JJ, et al. (2012) Phase 1 gene therapy for Duchenne muscular dystrophy using a translational optimized AAV vector. Molecular therapy: the journal of the American Society of Gene Therapy 20: 443–455.

29. Zsebo K, Yaroshinsky A, Rudy JJ, Wagner K, Greenberg B, et al. (2014) Long-term effects of AAV1/SERCA2a gene transfer in patients with severe heart failure: analysis of recurrent cardiovascular events and mortality. Circ Res 114: 101–108. doi: 10.1161/CIRCRESAHA.113.302421 24065463

30. Smith BK, Collins SW, Conlon TJ, Mah CS, Lawson LA, et al. (2013) Phase I/II trial of adeno-associated virus-mediated alpha-glucosidase gene therapy to the diaphragm for chronic respiratory failure in Pompe disease: initial safety and ventilatory outcomes. Hum Gene Ther 24: 630–640. doi: 10.1089/hum.2012.250 23570273

31. Grieger JC, Samulski RJ (2012) Adeno-associated virus vectorology, manufacturing, and clinical applications. Methods in enzymology 507: 229–254. doi: 10.1016/B978-0-12-386509-0.00012-0 22365777

32. Mingozzi F, High KA (2013) Immune responses to AAV vectors: overcoming barriers to successful gene therapy. Blood 122: 23–36. doi: 10.1182/blood-2013-01-306647 23596044

33. Deyle DR, Russell DW (2009) Adeno-associated virus vector integration. Current opinion in molecular therapeutics 11: 442–447. 19649989

34. Hubert CG, Bradley RK, Ding Y, Toledo CM, Herman J, et al. (2013) Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A. Genes & development 27: 1032–1045.

35. Wang Q, Rymond BC (2003) Rds3p is required for stable U2 snRNP recruitment to the splicing apparatus. Molecular and cellular biology 23: 7339–7349. 14517302

36. Rzymski T, Grzmil P, Meinhardt A, Wolf S, Burfeind P (2008) PHF5A represents a bridge protein between splicing proteins and ATP-dependent helicases and is differentially expressed during mouse spermatogenesis. Cytogenetic and genome research 121: 232–244. doi: 10.1159/000138890 18758164

37. Osman S, Albert BJ, Wang Y, Li M, Czaicki NL, et al. (2011) Structural requirements for the antiproliferative activity of pre-mRNA splicing inhibitor FR901464. Chemistry 17: 895–904. doi: 10.1002/chem.201002402 21226105

38. Schneider-Poetsch T, Usui T, Kaida D, Yoshida M (2010) Garbled messages and corrupted translations. Nature chemical biology 6: 189–198. 20154667

39. Kronenberg S, Bottcher B, von der Lieth CW, Bleker S, Kleinschmidt JA (2005) A conformational change in the adeno-associated virus type 2 capsid leads to the exposure of hidden VP1 N termini. J Virol 79: 5296–5303. 15827144

40. Horowitz ED, Rahman KS, Bower BD, Dismuke DJ, Falvo MR, et al. (2013) Biophysical and ultrastructural characterization of adeno-associated virus capsid uncoating and genome release. J Virol 87: 2994–3002. doi: 10.1128/JVI.03017-12 23269804

41. Sebastian S, Luban J (2005) TRIM5alpha selectively binds a restriction-sensitive retroviral capsid. Retrovirology 2: 40. 15967037

42. Osman S, Waud WR, Gorman GS, Day BW, Koide K (2011) Evaluation of FR901464 analogues in vitro and in vivo. MedChemComm 2: 38.

43. Russell DW, Alexander IE, Miller AD (1995) DNA synthesis and topoisomerase inhibitors increase transduction by adeno-associated virus vectors. Proc Natl Acad Sci U S A 92: 5719–5723. 7777575

44. Zentilin L, Marcello A, Giacca M (2001) Involvement of cellular double-stranded DNA break binding proteins in processing of the recombinant adeno-associated virus genome. J Virol 75: 12279–12287. 11711618

45. Zhou C, Yang Q, Trempe JP (1999) Enhancement of UV-induced cytotoxicity by the adeno-associated virus replication proteins. Biochimica et biophysica acta 1444: 371–383. 10095060

46. Mah C, Qing K, Khuntirat B, Ponnazhagan S, Wang XS, et al. (1998) Adeno-associated virus type 2-mediated gene transfer: role of epidermal growth factor receptor protein tyrosine kinase in transgene expression. J Virol 72: 9835–9843. 9811719

47. Ju XD, Lou SQ, Wang WG, Peng JQ, Tian H (2004) Effect of hydroxyurea and etoposide on transduction of human bone marrow mesenchymal stem and progenitor cell by adeno-associated virus vectors. Acta pharmacologica Sinica 25: 196–202. 14769209

48. Zhong L, Zhao W, Wu J, Li B, Zolotukhin S, et al. (2007) A dual role of EGFR protein tyrosine kinase signaling in ubiquitination of AAV2 capsids and viral second-strand DNA synthesis. Molecular therapy: the journal of the American Society of Gene Therapy 15: 1323–1330.

49. Johnson JS, Li C, DiPrimio N, Weinberg MS, McCown TJ, et al. (2010) Mutagenesis of adeno-associated virus type 2 capsid protein VP1 uncovers new roles for basic amino acids in trafficking and cell-specific transduction. J Virol 84: 8888–8902. doi: 10.1128/JVI.00687-10 20573820

50. Salganik M, Aydemir F, Nam HJ, McKenna R, Agbandje-McKenna M, et al. (2014) Adeno-associated virus capsid proteins may play a role in transcription and second-strand synthesis of recombinant genomes. J Virol 88: 1071–1079. doi: 10.1128/JVI.02093-13 24198419

51. Isono K, Mizutani-Koseki Y, Komori T, Schmidt-Zachmann MS, Koseki H (2005) Mammalian polycomb-mediated repression of Hox genes requires the essential spliceosomal protein Sf3b1. Genes & development 19: 536–541.

52. Convertini P, Shen M, Potter PM, Palacios G, Lagisetti C, et al. (2014) Sudemycin E influences alternative splicing and changes chromatin modifications. Nucleic acids research 42: 4947–4961. doi: 10.1093/nar/gku151 24623796

53. Heo K, Kim B, Kim K, Choi J, Kim H, et al. (2007) Isolation and characterization of proteins associated with histone H3 tails in vivo. J Biol Chem 282: 15476–15483. 17403666

54. Akusjarvi G, Stevenin J (2003) Remodelling of the host cell RNA splicing machinery during an adenovirus infection. Current topics in microbiology and immunology 272: 253–286. 12747553

55. Aspegren A, Rabino C, Bridge E (1998) Organization of splicing factors in adenovirus-infected cells reflects changes in gene expression during the early to late phase transition. Exp Cell Res 245: 203–213. 9828117

56. Phelan A, Carmo-Fonseca M, McLaughlan J, Lamond AI, Clements JB (1993) A herpes simplex virus type 1 immediate-early gene product, IE63, regulates small nuclear ribonucleoprotein distribution. Proc Natl Acad Sci U S A 90: 9056–9060. 8415652

57. Bryant HE, Wadd SE, Lamond AI, Silverstein SJ, Clements JB (2001) Herpes simplex virus IE63 (ICP27) protein interacts with spliceosome-associated protein 145 and inhibits splicing prior to the first catalytic step. J Virol 75: 4376–4385. 11287586

58. Gao Y, Vogt A, Forsyth CJ, Koide K (2013) Comparison of splicing factor 3b inhibitors in human cells. Chembiochem: a European journal of chemical biology 14: 49–52. doi: 10.1002/cbic.201200558 23172726

59. Zmuda EJ, Powell CA, Hai T (2011) A method for murine islet isolation and subcapsular kidney transplantation. Journal of visualized experiments: JoVE.

60. Sielaff TD, Hu MY, Rao S, Groehler K, Olson D, et al. (1995) A technique for porcine hepatocyte harvest and description of differentiated metabolic functions in static culture. Transplantation 59: 1459–1463. 7770934

61. Tonne JM, Sakuma T, Deeds MC, Munoz-Gomez M, Barry MA, et al. (2013) Global gene expression profiling of pancreatic islets in mice during streptozotocin-induced beta-cell damage and pancreatic Glp-1 gene therapy. Disease models & mechanisms 6: 1236–1245.

62. McCarty DM, Monahan PE, Samulski RJ (2001) Self-complementary recombinant adeno-associated virus (scAAV) vectors promote efficient transduction independently of DNA synthesis. Gene Ther 8: 1248–1254. 11509958

63. Ohmine S, Sakuma R, Sakuma T, Thatava T, Solis GP, et al. (2010) Cytoplasmic body component TRIM5{alpha} requires lipid-enriched microdomains for efficient HIV-1 restriction. J Biol Chem 285: 34508–34517. doi: 10.1074/jbc.M110.158188 20810659

64. Tonne JM, Campbell JM, Cataliotti A, Ohmine S, Thatava T, et al. (2011) Secretion of glycosylated pro-B-type natriuretic peptide from normal cardiomyocytes. Clin Chem 57: 864–873. doi: 10.1373/clinchem.2010.157438 21482747