Skip to main content

Safety and Efficacy of Retroviral and Lentiviral Vectors for Gene Therapy

  • Chapter
  • First Online:

Abstract

In hematopoietic stem progenitor cell (HSPC) gene therapy (GT) applications for the treatment of genetic diseases, retroviral vectors (RVs) are used to efficiently transduce and integrate therapeutic genes in the genome of patient-derived HSPCs, which, upon reinfusion, reconstruct the entire hematopoietic system and restore the correct hematopoietic functions, or deliver the therapeutic factor to different tissues. However, in initial HSPC-GT clinical trials using early-generation γ-RVs, vector insertions near proto-oncogenes triggered their overexpression and induced leukemia in some of the transplanted patients. These unexpected adverse events have prompted the development of highly sensitive preclinical assays to test the genotoxic potential of different GT vector types and designs, and the development of powerful PCR-based techniques, combined with next generation sequencing (NGS) and bioinformatics analyses, have allowed to study integration sites (ISs) present in leukemic and dominant expanding cells, identify the genes targeted by insertions and to investigate the clonal composition of complex vector-marked cell populations. The positive safety data obtained from the testing in highly sensitive preclinical models and, successively, in clinical trials, of the more advanced lentiviral vectors (LVs) with self-inactivating (SIN) long terminal repeats (LTRs), have reduced the concerns related to insertional mutagenesis , encouraging the adoption of this vector platform in GT protocols for the treatment of many other diseases. Nevertheless, the evidences collected from genotoxicity assays and a β-thalassemia clinical trial, during which a vector-driven clonal dominance event has occurred, point to the fact that even SIN LVs insertions are not entirely neutral, and thus to the importance of a continuous effort to improve both the design of GT vectors, and the sensitivity of preclinical assays aimed at assessing their residual genotoxicity .

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  1. Karlsson S, Ooka A, Woods NB. Development of gene therapy for blood disorders by gene transfer into haematopoietic stem cells. Haemophilia: The Official Journal of the World Federation of Hemophilia. 2002;8:255–60.

    Article  CAS  Google Scholar 

  2. Williams DA, Lemischka IR, Nathan DG, Mulligan RC. Introduction of new genetic material into pluripotent haematopoietic stem cells of the mouse. Nature. 1984;310:476–80.

    Article  CAS  PubMed  Google Scholar 

  3. Hock RA, Miller AD. Retrovirus-mediated transfer and expression of drug resistance genes in human haematopoietic progenitor cells. Nature. 1986;320:275–7.

    Article  CAS  PubMed  Google Scholar 

  4. Naldini L. Ex vivo gene transfer and correction for cell-based therapies. Nat Rev Genet. 2011;12:301–15.

    Article  CAS  PubMed  Google Scholar 

  5. Blaese RM, Culver KW, Miller AD, Carter CS, Fleisher T, Clerici M, Shearer G, Chang L, Chiang Y, Tolstoshev P, Greenblatt JJ, Rosenberg SA, Klein H, Berger M, Mullen CA, Ramsey WJ, Muul L, Morgan RA, Anderson WF. T lymphocyte-directed gene therapy for ADA- SCID: initial trial results after 4 years. Science. 1995;270:475–80.

    Article  CAS  PubMed  Google Scholar 

  6. Kaufmann KB, Buning H, Galy A, Schambach A, Grez M. Gene therapy on the move. EMBO molecular medicine. 2013;5:1642–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Aiuti A, Vai S, Mortellaro A, Casorati G, Ficara F, Andolfi G, Ferrari G, Tabucchi A, Carlucci F, Ochs HD, Notarangelo LD, Roncarolo MG, Bordignon C. Immune reconstitution in ADA-SCID after PBL gene therapy and discontinuation of enzyme replacement. Nat Med. 2002;8:423–5.

    Article  CAS  PubMed  Google Scholar 

  8. Candotti F, Shaw KL, Muul L, Carbonaro D, Sokolic R, Choi C, Schurman SH, Garabedian E, Kesserwan C, Jagadeesh GJ, Fu PY, Gschweng E, Cooper A, Tisdale JF, Weinberg KI, Crooks GM, Kapoor N, Shah A, Abdel-Azim H, Yu XJ, Smogorzewska M, Wayne AS, Rosenblatt HM, Davis CM, Hanson C, Rishi RG, Wang X, Gjertson D, Yang OO, Balamurugan A, Bauer G, Ireland JA, Engel BC, Podsakoff GM, Hershfield MS, Blaese RM, Parkman R, Kohn DB. Gene therapy for adenosine deaminase-deficient severe combined immune deficiency: clinical comparison of retroviral vectors and treatment plans. Blood. 2012;120:3635–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Cicalese MP, Aiuti A. Clinical applications of gene therapy for primary immunodeficiencies. Hum Gene Ther. 2015;26:210–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Cicalese MP, Ferrua F, Castagnaro L, Pajno R, Barzaghi F, Giannelli S, Dionisio F, Brigida I, Bonopane M, Casiraghi M, Tabucchi A, Carlucci F, Grunebaum E, Adeli M, Bredius RG, Puck JM, Stepensky P, Tezcan I, Rolfe K, De Boever E, Reinhardt RR, Appleby J, Ciceri F, Roncarolo MG, Aiuti A. Update on the safety and efficacy of retroviral gene therapy for immunodeficiency due to adenosine deaminase deficiency. Blood;2016.

    Google Scholar 

  11. Gaspar HB, Cooray S, Gilmour KC, Parsley KL, Adams S, Howe SJ, Al Ghonaium A, Bayford J, Brown L, Davies EG, Kinnon C, Thrasher AJ. Long-term persistence of a polyclonal T cell repertoire after gene therapy for X-linked severe combined immunodeficiency. Sci Transl Med. 2011;3:97ra79.

    Google Scholar 

  12. Montiel-Equihua CA, Thrasher AJ, Gaspar HB. Gene therapy for severe combined immunodeficiency due to adenosine deaminase deficiency. Curr Gene Ther. 2012;12:57–65.

    Article  CAS  PubMed  Google Scholar 

  13. Gaspar HB, Parsley KL, Howe S, King D, Gilmour KC, Sinclair J, Brouns G, Schmidt M, Von Kalle C, Barington T, Jakobsen MA, Christensen HO, Al Ghonaium A, White HN, Smith JL, Levinsky RJ, Ali RR, Kinnon C, Thrasher AJ. Gene therapy of X-linked severe combined immunodeficiency by use of a pseudotyped gammaretroviral vector. The Lancet. 2004;364:2181–7.

    Article  CAS  Google Scholar 

  14. Hacein-Bey-Abina S, Le Deist F, Carlier F, Bouneaud C, Hue C, De Villartay JP, Thrasher AJ, Wulffraat N, Sorensen R, Dupuis-Girod S, Fischer A, Davies EG, Kuis W, Leiva L, Cavazzana-Calvo M. Sustained correction of X-linked severe combined immunodeficiency by ex vivo gene therapy. New Eng J Med. 2002;346:1185–93.

    Article  CAS  PubMed  Google Scholar 

  15. Bianchi M, Hakkim A, Brinkmann V, Siler U, Seger RA, Zychlinsky A, Reichenbach J. Restoration of NET formation by gene therapy in CGD controls aspergillosis. Blood. 2009;114:2619–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Kang EM, Choi U, Theobald N, Linton G, Long Priel DA, Kuhns D, Malech HL. Retrovirus gene therapy for X-linked chronic granulomatous disease can achieve stable long-term correction of oxidase activity in peripheral blood neutrophils. Blood. 2010;115:783–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Kang HJ, Bartholomae CC, Paruzynski A, Arens A, Kim S, Yu SS, Hong Y, Joo CW, Yoon NK, Rhim JW, Kim JG, Von Kalle C, Schmidt M, Kim S, Ahn HS. Retroviral gene therapy for X-linked chronic granulomatous disease: results from phase I/II trial. Mol Ther: The Journal of the American Society of Gene Therapy. 2011;19:2092–101.

    Article  CAS  Google Scholar 

  18. Ott MG, Schmidt M, Schwarzwaelder K, Stein S, Siler U, Koehl U, Glimm H, Kuhlcke K, Schilz A, Kunkel H, Naundorf S, Brinkmann A, Deichmann A, Fischer M, Ball C, Pilz I, Dunbar C, Du Y, Jenkins NA, Copeland NG, Luthi U, Hassan M, Thrasher AJ, Hoelzer D, von Kalle C, Seger R, Grez M. Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1. Nat Med. 2006;12:401–9.

    Article  CAS  PubMed  Google Scholar 

  19. Stein S, Ott MG, Schultze-Strasser S, Jauch A, Burwinkel B, Kinner A, Schmidt M, Kramer A, Schwable J, Glimm H, Koehl U, Preiss C, Ball C, Martin H, Gohring G, Schwarzwaelder K, Hofmann WK, Karakaya K, Tchatchou S, Yang R, Reinecke P, Kuhlcke K, Schlegelberger B, Thrasher AJ, Hoelzer D, Seger R, von Kalle C, Grez M. Genomic instability and myelodysplasia with monosomy 7 consequent to EVI1 activation after gene therapy for chronic granulomatous disease. Nat Med. 2010;16:198–204.

    Article  CAS  PubMed  Google Scholar 

  20. Bosticardo M, Ghosh A, Du Y, Jenkins NA, Copeland NG, Candotti F. Self-inactivating retroviral vector-mediated gene transfer induces oncogene activation and immortalization of primary murine bone marrow cells. Mol Ther: The Journal of the American Society of Gene Therapy. 2009;17:1910–8.

    Article  CAS  Google Scholar 

  21. Boztug K, Schmidt M, Schwarzer A, Banerjee PP, Diez IA, Dewey RA, Bohm M, Nowrouzi A, Ball CR, Glimm H, Naundorf S, Kuhlcke K, Blasczyk R, Kondratenko I, Marodi L, Orange JS, von Kalle C, Klein C. Stem-cell gene therapy for the Wiskott-Aldrich syndrome. New Eng J Med. 2010;363:1918–27.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Braun CJ, Boztug K, Paruzynski A, Witzel M, Schwarzer A, Rothe M, Modlich U, Beier R, Gohring G, Steinemann D, Fronza R, Ball CR, Haemmerle R, Naundorf S, Kuhlcke K, Rose M, Fraser C, Mathias L, Ferrari R, Abboud MR, Al-Herz W, Kondratenko I, Marodi L, Glimm H, Schlegelberger B, Schambach A, Albert MH, Schmidt M, von Kalle C, Klein C. Gene therapy for Wiskott-Aldrich syndrome–long-term efficacy and genotoxicity. Sci Transl Med. 2014;6:227ra233.

    Google Scholar 

  23. Mukherjee S, Thrasher AJ. Gene therapy for PIDs: progress, pitfalls and prospects. Gene. 2013;525:174–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Fischer A, Cavazzana-Calvo M. Gene therapy of inherited diseases. Lancet. 2008;371:2044–7.

    Article  PubMed  Google Scholar 

  25. Bousso P, Wahn V, Douagi I, Horneff G, Pannetier C, Le Deist F, Zepp F, Niehues T, Kourilsky P, Fischer A, de Saint Basile G. Diversity, functionality, and stability of the T cell repertoire derived in vivo from a single human T cell precursor. Proc Natl Acad Sci USA. 2000;97:274–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Chinen J, Davis J, De Ravin SS, Hay BN, Hsu AP, Linton GF, Naumann N, Nomicos EY, Silvin C, Ulrick J, Whiting-Theobald NL, Malech HL, Puck JM. Gene therapy improves immune function in preadolescents with X-linked severe combined immunodeficiency. Blood. 2007;110:67–73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Chatziandreou I, Siapati EK, Vassilopoulos G. Genetic correction of X-linked chronic granulomatous disease with novel foamy virus vectors. Exp Hematol. 2011;39:643–52.

    Article  CAS  PubMed  Google Scholar 

  28. Grez M, Reichenbach J, Schwable J, Seger R, Dinauer MC, Thrasher AJ. Gene therapy of chronic granulomatous disease: the engraftment dilemma. Mol Ther: The Journal of the American Society of Gene Therapy. 2011;19:28–35.

    Article  CAS  Google Scholar 

  29. Goebel WS, Dinauer MC. Gene therapy for chronic granulomatous disease. Acta Haematol. 2003;110:86–92.

    Article  CAS  PubMed  Google Scholar 

  30. Malech HL. Progress in gene therapy for chronic granulomatous disease. J Infect Dis. 1999;179(Suppl 2):S318–25.

    Article  CAS  PubMed  Google Scholar 

  31. Malech HL, Maples PB, Whiting-Theobald N, Linton GF, Sekhsaria S, Vowells SJ, Li F, Miller JA, DeCarlo E, Holland SM, Leitman SF, Carter CS, Butz RE, Read EJ, Fleisher TA, Schneiderman RD, Van Epps DE, Spratt SK, Maack CA, Rokovich JA, Cohen LK, Gallin JI. Prolonged production of NADPH oxidase-corrected granulocytes after gene therapy of chronic granulomatous disease. Proc Natl Acad Sci U S A. 1997;94:12133–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Candotti F. Gene transfer into hematopoietic stem cells as treatment for primary immunodeficiency diseases. Int J Hematol. 2014;99:383–92.

    Article  CAS  PubMed  Google Scholar 

  33. Hacein-Bey-Abina S, Garrigue A, Wang GP, Soulier J, Lim A, Morillon E, Clappier E, Caccavelli L, Delabesse E, Beldjord K, Asnafi V, MacIntyre E, Dal Cortivo L, Radford I, Brousse N, Sigaux F, Moshous D, Hauer J, Borkhardt A, Belohradsky BH, Wintergerst U, Velez MC, Leiva L, Sorensen R, Wulffraat N, Blanche S, Bushman FD, Fischer A, Cavazzana-Calvo M. Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1. J Clin Investig. 2008;118:3132–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Hacein-Bey-Abina S, von Kalle C, Schmidt M, Le Deist F, Wulffraat N, McIntyre E, Radford I, Villeval JL, Fraser CC, Cavazzana-Calvo M, Fischer A. A serious adverse event after successful gene therapy for X-linked severe combined immunodeficiency. New Eng J Med. 2003;348:255–6.

    Article  PubMed  Google Scholar 

  35. Woods NB, Muessig A, Schmidt M, Flygare J, Olsson K, Salmon P, Trono D, von Kalle C, Karlsson S. Lentiviral vector transduction of NOD/SCID repopulating cells results in multiple vector integrations per transduced cell: risk of insertional mutagenesis. Blood. 2003;101:1284–9.

    Article  CAS  PubMed  Google Scholar 

  36. Coffin JM, Stephen HH, Varmus HE. Retroviruses, Plainview, N.Y.; 1997.

    Google Scholar 

  37. Doorbar J. The papillomavirus life cycle. J Clin Virol: The Official Publication of the Pan American Society for Clinical Virology. 2005;32(Suppl 1):S7–15.

    Article  CAS  Google Scholar 

  38. Jonkers J, Berns A. Retroviral insertional mutagenesis as a strategy to identify cancer genes. Biochim Biophys Acta. 1996;1287:29–57.

    PubMed  Google Scholar 

  39. Uren AG, Kool J, Berns A, van Lohuizen M. Retroviral insertional mutagenesis: past, present and future. Oncogene. 2005;24:7656–72.

    Article  CAS  PubMed  Google Scholar 

  40. Coffin JM, Hughes SH, Varmus H. Retroviruses. N.Y. xv: Cold Spring Harbor Laboratory Press, Plainview; 1997 843 pp.

    Google Scholar 

  41. West AG, Fraser P. Remote control of gene transcription. Hum Mol Genet. 2005;14(Spec No 1):R101–111.

    Google Scholar 

  42. Hayward WS, Neel BG, Astrin SM. Activation of a cellular onc gene by promoter insertion in ALV-induced lymphoid leukosis. Nature. 1981;290:475–80.

    Article  CAS  PubMed  Google Scholar 

  43. Kool J, Berns A. High-throughput insertional mutagenesis screens in mice to identify oncogenic networks. Nat Rev Cancer. 2009;9:389–99.

    Article  CAS  PubMed  Google Scholar 

  44. Ranzani M, Annunziato S, Adams DJ, Montini E. Cancer gene discovery: exploiting insertional mutagenesis. Mol Cancer Res: MCR. 2013;11:1141–58.

    Article  CAS  PubMed  Google Scholar 

  45. Biffi A, Bartolomae CC, Cesana D, Cartier N, Aubourg P, Ranzani M, Cesani M, Benedicenti F, Plati T, Rubagotti E, Merella S, Capotondo A, Sgualdino J, Zanetti G, von Kalle C, Schmidt M, Naldini L, Montini E. Lentiviral vector common integration sites in preclinical models and a clinical trial reflect a benign integration bias and not oncogenic selection. Blood. 2011;117:5332–9.

    Article  CAS  PubMed  Google Scholar 

  46. Suzuki M, Ketterling MG, McCarty DR. Quantitative statistical analysis of cis-regulatory sequences in ABA/VP1- and CBF/DREB1-regulated genes of Arabidopsis. Plant Physiol. 2005;139:437–47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. de Ridder J, Uren A, Kool J, Reinders M, Wessels L. Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens. PLoS Comput Biol. 2006;2:e166.

    Article  PubMed  PubMed Central  Google Scholar 

  48. Sarver AL, Erdman J, Starr T, Largaespada DA, Silverstein KA. TAPDANCE: an automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data. BMC Bioinformatics. 2012;13:154. PMID: 22748055. doi: 10.1186/1471-2105-13-154.

  49. Abel U, Deichmann A, Bartholomae C, Schwarzwaelder K, Glimm H, Howe S, Thrasher A, Garrigue A, Hacein-Bey-Abina S, Cavazzana-Calvo M, Fischer A, Jaeger D, von Kalle C, Schmidt M. Real-time definition of non-randomness in the distribution of genomic events. PLoS ONE. 2007;2:e570.

    Article  PubMed  PubMed Central  Google Scholar 

  50. Berry CC, Ocwieja KE, Malani N, Bushman FD. Comparing DNA integration site clusters with scan statistics. Bioinformatics. 2014;30:1493–500.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Aiuti A, Biasco L, Scaramuzza S, Ferrua F, Cicalese MP, Baricordi C, Dionisio F, Calabria A, Giannelli S, Castiello MC, Bosticardo M, Evangelio C, Assanelli A, Casiraghi M, Di Nunzio S, Callegaro L, Benati C, Rizzardi P, Pellin D, Di Serio C, Schmidt M, Von Kalle C, Gardner J, Mehta N, Neduva V, Dow DJ, Galy A, Miniero R, Finocchi A, Metin A, Banerjee PP, Orange JS, Galimberti S, Valsecchi MG, Biffi A, Montini E, Villa A, Ciceri F, Roncarolo MG, Naldini L. Lentiviral hematopoietic stem cell gene therapy in patients with Wiskott-Aldrich syndrome. Science. 2013;341:1233151.

    Article  PubMed  PubMed Central  Google Scholar 

  52. Biffi A, Montini E, Lorioli L, Cesani M, Fumagalli F, Plati T, Baldoli C, Martino S, Calabria A, Canale S, Benedicenti F, Vallanti G, Biasco L, Leo S, Kabbara N, Zanetti G, Rizzo WB, Mehta NA, Cicalese MP, Casiraghi M, Boelens JJ, Del Carro U, Dow DJ, Schmidt M, Assanelli A, Neduva V, Di Serio C, Stupka E, Gardner J, von Kalle C, Bordignon C, Ciceri F, Rovelli A, Roncarolo MG, Aiuti A, Sessa M, Naldini L. Lentiviral hematopoietic stem cell gene therapy benefits metachromatic leukodystrophy. Science. 2013;341:1233158.

    Article  PubMed  Google Scholar 

  53. Kustikova OS, Baum C, Fehse B. Retroviral integration site analysis in hematopoietic stem cells. Methods Mol Biol. 2008;430:255–67.

    Article  CAS  PubMed  Google Scholar 

  54. Mueller PR, Wold B. In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science. 1989;246:780–6.

    Article  CAS  PubMed  Google Scholar 

  55. Harkey MA, Kaul R, Jacobs MA, Kurre P, Bovee D, Levy R, Blau CA. Multiarm high-throughput integration site detection: limitations of LAM-PCR technology and optimization for clonal analysis. Stem Cells Dev. 2007;16:381–92.

    Article  CAS  PubMed  Google Scholar 

  56. Schmidt M, Schwarzwaelder K, Bartholomae C, Zaoui K, Ball C, Pilz I, Braun S, Glimm H, von Kalle C. High-resolution insertion-site analysis by linear amplification-mediated PCR (LAM-PCR). Nat Methods. 2007;4:1051–7.

    Article  CAS  PubMed  Google Scholar 

  57. Schmidt M, Zickler P, Hoffmann G, Haas S, Wissler M, Muessig A, Tisdale JF, Kuramoto K, Andrews RG, Wu T, Kiem HP, Dunbar CE, von Kalle C. Polyclonal long-term repopulating stem cell clones in a primate model. Blood. 2002;100:2737–43.

    Article  CAS  PubMed  Google Scholar 

  58. Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. Estimating abundances of retroviral insertion sites from DNA fragment length data. Bioinformatics. 2012;28:755–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Biasco L, Baricordi C, Aiuti A. Retroviral integrations in gene therapy trials. Mol Ther: The Journal of the American Society of Gene Therapy. 2012;20:709–16.

    Article  CAS  Google Scholar 

  60. Wang GP, Berry CC, Malani N, Leboulch P, Fischer A, Hacein-Bey-Abina S, Cavazzana-Calvo M, Bushman FD. Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial. Blood. 2010;115:4356–66.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Gabriel R, Eckenberg R, Paruzynski A, Bartholomae CC, Nowrouzi A, Arens A, Howe SJ, Recchia A, Cattoglio C, Wang W, Faber K, Schwarzwaelder K, Kirsten R, Deichmann A, Ball CR, Balaggan KS, Yanez-Munoz RJ, Ali RR, Gaspar HB, Biasco L, Aiuti A, Cesana D, Montini E, Naldini L, Cohen-Haguenauer O, Mavilio F, Thrasher AJ, Glimm H, von Kalle C, Saurin W, Schmidt M. Comprehensive genomic access to vector integration in clinical gene therapy. Nat Med. 2009;15:1431–6.

    Article  CAS  PubMed  Google Scholar 

  62. Koudijs MJ, Klijn C, van der Weyden L, Kool J, ten Hoeve J, Sie D, Prasetyanti PR, Schut E, Kas S, Whipp T, Cuppen E, Wessels L, Adams DJ, Jonkers J. High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors. Genome Res. 2011;21:2181–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Gillet NA, Malani N, Melamed A, Gormley N, Carter R, Bentley D, Berry C, Bushman FD, Taylor GP, Bangham CR. The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones. Blood. 2011;117:3113–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Wu C, Jares A, Winkler T, Xie J, Metais JY, Dunbar CE. High efficiency restriction enzyme-free linear amplification-mediated polymerase chain reaction approach for tracking lentiviral integration sites does not abrogate retrieval bias. Hum Gene Ther. 2013;24:38–47.

    Article  CAS  PubMed  Google Scholar 

  65. Zhou S, Bonner MA, Wang YD, Rapp S, De Ravin SS, Malech HL, Sorrentino BP. Quantitative shearing linear amplification polymerase chain reaction: an improved method for quantifying lentiviral vector insertion sites in transplanted hematopoietic cell systems. Hum Gene Ther Methods. 2015;26:4–12.

    Article  CAS  PubMed  Google Scholar 

  66. Cavazzana-Calvo M, Payen E, Negre O, Wang G, Hehir K, Fusil F, Down J, Denaro M, Brady T, Westerman K, Cavallesco R, Gillet-Legrand B, Caccavelli L, Sgarra R, Maouche-Chretien L, Bernaudin F, Girot R, Dorazio R, Mulder GJ, Polack A, Bank A, Soulier J, Larghero J, Kabbara N, Dalle B, Gourmel B, Socie G, Chretien S, Cartier N, Aubourg P, Fischer A, Cornetta K, Galacteros F, Beuzard Y, Gluckman E, Bushman F, Hacein-Bey-Abina S, Leboulch P. Transfusion independence and HMGA2 activation after gene therapy of human beta-thalassaemia. Nature. 2010;467:318–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Firouzi S, Lopez Y, Suzuki Y, Nakai K, Sugano S, Yamochi T, Watanabe T. Development and validation of a new high-throughput method to investigate the clonality of HTLV-1-infected cells based on provirus integration sites. Genome Med. 2014;6:46.

    Article  PubMed  PubMed Central  Google Scholar 

  68. Biffi A, De Palma M, Quattrini A, Del Carro U, Amadio S, Visigalli I, Sessa M, Fasano S, Brambilla R, Marchesini S, Bordignon C, Naldini L. Correction of metachromatic leukodystrophy in the mouse model by transplantation of genetically modified hematopoietic stem cells. J Clin Invest. 2004;113:1118–29.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. De Palma M, Montini E, Santoni de Sio FR, Benedicenti F, Gentile A, Medico E, Naldini L. Promoter trapping reveals significant differences in integration site selection between MLV and HIV vectors in primary hematopoietic cells. Blood. 2005;105:2307–15.

    Article  PubMed  Google Scholar 

  70. Dupre L, Marangoni F, Scaramuzza S, Trifari S, Hernandez RJ, Aiuti A, Naldini L, Roncarolo MG. Efficacy of gene therapy for Wiskott-Aldrich syndrome using a WAS promoter/cDNA-containing lentiviral vector and nonlethal irradiation. Hum Gene Ther. 2006;17:303–13.

    Article  CAS  PubMed  Google Scholar 

  71. Lo M, Bloom ML, Imada K, Berg M, Bollenbacher JM, Bloom ET, Kelsall BL, Leonard WJ. Restoration of lymphoid populations in a murine model of X-linked severe combined immunodeficiency by a gene-therapy approach. Blood. 1999;94:3027–36.

    CAS  PubMed  Google Scholar 

  72. May C, Rivella S, Chadburn A, Sadelain M. Successful treatment of murine beta-thalassemia intermedia by transfer of the human beta-globin gene. Blood. 2002;99:1902–8.

    Article  CAS  PubMed  Google Scholar 

  73. Montini E, Cesana D. Genotoxicity assay for gene therapy vectors in tumor prone Cdkn2a(–)/(–) mice. Methods Enzymol. 2012;507:171–85.

    Article  CAS  PubMed  Google Scholar 

  74. Vigna E, Naldini L. Lentiviral vectors: excellent tools for experimental gene transfer and promising candidates for gene therapy. J Gene Med. 2000;2:308–16.

    Article  CAS  PubMed  Google Scholar 

  75. Bokhoven M, Stephen SL, Knight S, Gevers EF, Robinson IC, Takeuchi Y, Collins MK. Insertional gene activation by lentiviral and gammaretroviral vectors. J Virol. 2009;83:283–94.

    Article  CAS  PubMed  Google Scholar 

  76. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Du Y, Jenkins NA, Copeland NG. Insertional mutagenesis identifies genes that promote the immortalization of primary bone marrow progenitor cells. Blood. 2005;106:3932–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Arumugam PI, Higashimoto T, Urbinati F, Modlich U, Nestheide S, Xia P, Fox C, Corsinotti A, Baum C, Malik P. Genotoxic potential of lineage-specific lentivirus vectors carrying the beta-globin locus control region. Mol Ther: The Journal of the American Society of Gene Therapy. 2009;17:1929–37.

    Article  CAS  Google Scholar 

  79. Gaussin A, Modlich U, Bauche C, Niederlander NJ, Schambach A, Duros C, Artus A, Baum C, Cohen-Haguenauer O, Mermod N. CTF/NF1 transcription factors act as potent genetic insulators for integrating gene transfer vectors. Gene Ther. 2012;19:15–24.

    Article  CAS  PubMed  Google Scholar 

  80. Modlich U, Bohne J, Schmidt M, von Kalle C, Knoss S, Schambach A, Baum C. Cell-culture assays reveal the importance of retroviral vector design for insertional genotoxicity. Blood. 2006;108:2545–53.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Modlich U, Navarro S, Zychlinski D, Maetzig T, Knoess S, Brugman MH, Schambach A, Charrier S, Galy A, Thrasher AJ, Bueren J, Baum C. Insertional transformation of hematopoietic cells by self-inactivating lentiviral and gammaretroviral vectors. Mol Ther: The Journal of the American Society of Gene Therapy. 2009;17:1919–28.

    Article  CAS  Google Scholar 

  82. Schambach A, Zychlinski D, Ehrnstroem B, Baum C. Biosafety features of lentiviral vectors. Hum Gene Ther. 2013;24:132–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Zychlinski D, Schambach A, Modlich U, Maetzig T, Meyer J, Grassman E, Mishra A, Baum C. Physiological promoters reduce the genotoxic risk of integrating gene vectors. Mol Ther: The Journal of the American Society of Gene Therapy. 2008;16:718–25.

    Article  CAS  Google Scholar 

  84. Cesana D, Ranzani M, Volpin M, Bartholomae C, Duros C, Artus A, Merella S, Benedicenti F, Sergi Sergi L, Sanvito F, Brombin C, Nonis A, Serio CD, Doglioni C, von Kalle C, Schmidt M, Cohen-Haguenauer O, Naldini L, Montini E. Uncovering and dissecting the genotoxicity of self-inactivating lentiviral vectors in vivo. Mol Ther. 2014;22:774–85.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Cornils K, Bartholomae CC, Thielecke L, Lange C, Arens A, Glauche I, Mock U, Riecken K, Gerdes S, von Kalle C, Schmidt M, Roeder I, Fehse B. Comparative clonal analysis of reconstitution kinetics after transplantation of hematopoietic stem cells gene marked with a lentiviral SIN or a gamma-retroviral LTR vector. Exp Hematol. 2013;41(28–38):e23.

    Google Scholar 

  86. Hematti P, Hong BK, Ferguson C, Adler R, Hanawa H, Sellers S, Holt IE, Eckfeldt CE, Sharma Y, Schmidt M, von Kalle C, Persons DA, Billings EM, Verfaillie CM, Nienhuis AW, Wolfsberg TG, Dunbar CE, Calmels B. Distinct genomic integration of MLV and SIV vectors in primate hematopoietic stem and progenitor cells. PLoS Biol. 2004;2:e423.

    Article  PubMed  PubMed Central  Google Scholar 

  87. Kustikova O, Fehse B, Modlich U, Yang M, Dullmann J, Kamino K, von Neuhoff N, Schlegelberger B, Li Z, Baum C. Clonal dominance of hematopoietic stem cells triggered by retroviral gene marking. Science. 2005;308:1171–4.

    Article  CAS  PubMed  Google Scholar 

  88. Montini E, Cesana D, Schmidt M, Sanvito F, Bartholomae CC, Ranzani M, Benedicenti F, Sergi LS, Ambrosi A, Ponzoni M, Doglioni C, Di Serio C, von Kalle C, Naldini L. The genotoxic potential of retroviral vectors is strongly modulated by vector design and integration site selection in a mouse model of HSC gene therapy. J Clin Invest. 2009;119:964–75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Montini E, Cesana D, Schmidt M, Sanvito F, Ponzoni M, Bartholomae C, Sergi Sergi L, Benedicenti F, Ambrosi A, Di Serio C, Doglioni C, von Kalle C, Naldini L. Hematopoietic stem cell gene transfer in a tumor-prone mouse model uncovers low genotoxicity of lentiviral vector integration. Nat Biotechnol. 2006;24:687–96.

    Article  CAS  PubMed  Google Scholar 

  90. Nienhuis AW, Dunbar CE, Sorrentino BP. Genotoxicity of retroviral integration in hematopoietic cells. Mol Ther: The Journal of the American Society of Gene Therapy. 2006;13:1031–49.

    Article  CAS  Google Scholar 

  91. Li Z, Dullmann J, Schiedlmeier B, Schmidt M, von Kalle C, Meyer J, Forster M, Stocking C, Wahlers A, Frank O, Ostertag W, Kuhlcke K, Eckert HG, Fehse B, Baum C. Murine leukemia induced by retroviral gene marking. Science. 2002;296:497.

    Article  CAS  PubMed  Google Scholar 

  92. Beard BC, Dickerson D, Beebe K, Gooch C, Fletcher J, Okbinoglu T, Miller DG, Jacobs MA, Kaul R, Kiem HP, Trobridge GD. Comparison of HIV-derived lentiviral and MLV-based gammaretroviral vector integration sites in primate repopulating cells. Mol Ther: The Journal of the American Society of Gene Therapy. 2007;15:1356–65.

    Article  CAS  Google Scholar 

  93. Kiem HP, Sellers S, Thomasson B, Morris JC, Tisdale JF, Horn PA, Hematti P, Adler R, Kuramoto K, Calmels B, Bonifacino A, Hu J, von Kalle C, Schmidt M, Sorrentino B, Nienhuis A, Blau CA, Andrews RG, Donahue RE, Dunbar CE. Long-term clinical and molecular follow-up of large animals receiving retrovirally transduced stem and progenitor cells: no progression to clonal hematopoiesis or leukemia. Mol Ther: The Journal of the American Society of Gene Therapy. 2004;9:389–95.

    Article  CAS  Google Scholar 

  94. Serrano M, Lee H, Chin L, Cordon-Cardo C, Beach D, DePinho RA. Role of the INK4a locus in tumor suppression and cell mortality. Cell. 1996;85:27–37.

    Article  CAS  PubMed  Google Scholar 

  95. Liu M, Maurano MT, Wang H, Qi H, Song CZ, Navas PA, Emery DW, Stamatoyannopoulos JA, Stamatoyannopoulos G. Genomic discovery of potent chromatin insulators for human gene therapy. Nat Biotechnol. 2015;33:198–203.

    Article  PubMed  Google Scholar 

  96. Ambrosi A, Glad IK, Pellin D, Cattoglio C, Mavilio F, Di Serio C, Frigessi A. Estimated comparative integration hotspots identify different behaviors of retroviral gene transfer vectors. PLoS Comput Biol. 2011;7:e1002292.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Bushman F, Lewinski M, Ciuffi A, Barr S, Leipzig J, Hannenhalli S, Hoffmann C. Genome-wide analysis of retroviral DNA integration. Nat Rev Microbiol. 2005;3:848–58.

    Article  CAS  PubMed  Google Scholar 

  98. Bushman FD. Retroviral integration and human gene therapy. J Clin Investig. 2007;117:2083–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Cattoglio C, Facchini G, Sartori D, Antonelli A, Miccio A, Cassani B, Schmidt M, von Kalle C, Howe S, Thrasher AJ, Aiuti A, Ferrari G, Recchia A, Mavilio F. Hot spots of retroviral integration in human CD34+ hematopoietic cells. Blood. 2007;110:1770–8.

    Article  CAS  PubMed  Google Scholar 

  100. Cattoglio C, Pellin D, Rizzi E, Maruggi G, Corti G, Miselli F, Sartori D, Guffanti A, Di Serio C, Ambrosi A, De Bellis G, Mavilio F. High-definition mapping of retroviral integration sites identifies active regulatory elements in human multipotent hematopoietic progenitors. Blood. 2010;116:5507–17.

    Article  CAS  PubMed  Google Scholar 

  101. Mitchell RS, Beitzel BF, Schroder AR, Shinn P, Chen H, Berry CC, Ecker JR, Bushman FD. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol. 2004;2:E234.

    Article  PubMed  PubMed Central  Google Scholar 

  102. Schröder ARW, Shinn P, Chen H, Berry C, Ecker JR, Bushman F. HIV-1 integration in the human genome favors active genes and local hotspots. Cell. 2002;110:521–9.

    Article  PubMed  Google Scholar 

  103. Wu X, Li Y, Crise B, Burgess SM. Transcription start regions in the human genome are favored targets for MLV integration. Science. 2003;300:1749–51.

    Article  CAS  PubMed  Google Scholar 

  104. Craigie R, Bushman FD. Host factors in retroviral integration and the selection of integration target sites. Microbiol Spectr. 2014;2.

    Google Scholar 

  105. Modlich U, Kustikova OS, Schmidt M, Rudolph C, Meyer J, Li Z, Kamino K, von Neuhoff N, Schlegelberger B, Kuehlcke K, Bunting KD, Schmidt S, Deichmann A, von Kalle C, Fehse B, Baum C. Leukemias following retroviral transfer of multidrug resistance 1 (MDR1) are driven by combinatorial insertional mutagenesis. Blood. 2005;105(11):4235–46. PMID: 15713797.

    Google Scholar 

  106. Cartier N, Hacein-Bey-Abina S, Bartholomae CC, Bougneres P, Schmidt M, Kalle CV, Fischer A, Cavazzana-Calvo M, Aubourg P. Lentiviral hematopoietic cell gene therapy for X-linked adrenoleukodystrophy. Methods Enzymol. 2012;507:187–98.

    Article  CAS  PubMed  Google Scholar 

  107. Naldini L. Gene therapy returns to centre stage. Nature. 2015;526:351–60.

    Article  CAS  PubMed  Google Scholar 

  108. Cesana D, Sgualdino J, Rudilosso L, Merella S, Naldini L, Montini E. Whole transcriptome characterization of aberrant splicing events induced by lentiviral vector integrations. J Clin Invest. 2012;122:1667–76.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Eugenio Montini .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Cite this chapter

Cesana, D., Volpin, M., Serina Secanechia, Y.N., Montini, E. (2017). Safety and Efficacy of Retroviral and Lentiviral Vectors for Gene Therapy. In: Brunetti-Pierri, N. (eds) Safety and Efficacy of Gene-Based Therapeutics for Inherited Disorders. Springer, Cham. https://doi.org/10.1007/978-3-319-53457-2_2

Download citation

Publish with us

Policies and ethics