Comprehensive genomic access to vector integration in clinical gene therapy

Richard Gabriel, Ralph Eckenberg, Anna Paruzynski, Cynthia C. Bartholomae, Ali Nowrouzi, Anne Arens, Steven J. Howe, Alessandra Recchia, Claudia Cattoglio, Wei Wang, Katrin Faber, Kerstin Schwarzwaelder, Romy Kirsten, Annette Deichmann, Claudia R. Ball, Kamaljit S. Balaggan, Rafael J. Yá̃ez-Mũoz, Robin R. Ali, H. Bobby Gaspar, Luca BiascoAlessandro Aiuti, Daniela Cesana, Eugenio Montini, Luigi Naldini, Odile Cohen-Haguenauer, Fulvio Mavilio, Adrian J. Thrasher, Hanno Glimm, Christof Von Kalle, William Saurin, Manfred Schmidt

Research output: Contribution to journalArticle

131 Citations (Scopus)

Abstract

Retroviral vectors have induced subtle clonal skewing in many gene therapy patients and severe clonal proliferation and leukemia in some of them, emphasizing the need for comprehensive integration site analyses to assess the biosafety and genomic pharmacokinetics of vectors and clonal fate of gene-modified cells in vivo. Integration site analyses such as linear amplification-mediated PCR (LAM-PCR) require a restriction digest generating unevenly small fragments of the genome. Here we show that each restriction motif allows for identification of only a fraction of all genomic integrants, hampering the understanding and prediction of biological consequences after vector insertion. We developed a model to define genomic access to the viral integration site that provides optimal restriction motif combinations and minimizes the percentage of nonaccessible insertion loci. We introduce a new nonrestrictive LAM-PCR approach that has superior capabilities for comprehensive unbiased integration site retrieval in preclinical and clinical samples independent of restriction motifs and amplification inefficiency.

Original languageEnglish
Pages (from-to)1431-1436
Number of pages6
JournalNature Medicine
Volume15
Issue number12
DOIs
Publication statusPublished - Dec 2009

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Gene therapy
Genetic Therapy
Virus Integration
Amplification
Polymerase Chain Reaction
Leukemia
Pharmacokinetics
Genes
Genome

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Gabriel, R., Eckenberg, R., Paruzynski, A., Bartholomae, C. C., Nowrouzi, A., Arens, A., ... Schmidt, M. (2009). Comprehensive genomic access to vector integration in clinical gene therapy. Nature Medicine, 15(12), 1431-1436. https://doi.org/10.1038/nm.2057

Comprehensive genomic access to vector integration in clinical gene therapy. / Gabriel, Richard; Eckenberg, Ralph; Paruzynski, Anna; Bartholomae, Cynthia C.; Nowrouzi, Ali; Arens, Anne; Howe, Steven J.; Recchia, Alessandra; Cattoglio, Claudia; Wang, Wei; Faber, Katrin; Schwarzwaelder, Kerstin; Kirsten, Romy; Deichmann, Annette; Ball, Claudia R.; Balaggan, Kamaljit S.; Yá̃ez-Mũoz, Rafael J.; Ali, Robin R.; Gaspar, H. Bobby; Biasco, Luca; Aiuti, Alessandro; Cesana, Daniela; Montini, Eugenio; Naldini, Luigi; Cohen-Haguenauer, Odile; Mavilio, Fulvio; Thrasher, Adrian J.; Glimm, Hanno; Von Kalle, Christof; Saurin, William; Schmidt, Manfred.

In: Nature Medicine, Vol. 15, No. 12, 12.2009, p. 1431-1436.

Research output: Contribution to journalArticle

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, Yá̃ez-Mũoz, 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 2009, 'Comprehensive genomic access to vector integration in clinical gene therapy', Nature Medicine, vol. 15, no. 12, pp. 1431-1436. https://doi.org/10.1038/nm.2057
Gabriel R, Eckenberg R, Paruzynski A, Bartholomae CC, Nowrouzi A, Arens A et al. Comprehensive genomic access to vector integration in clinical gene therapy. Nature Medicine. 2009 Dec;15(12):1431-1436. https://doi.org/10.1038/nm.2057
Gabriel, Richard ; Eckenberg, Ralph ; Paruzynski, Anna ; Bartholomae, Cynthia C. ; Nowrouzi, Ali ; Arens, Anne ; Howe, Steven J. ; Recchia, Alessandra ; Cattoglio, Claudia ; Wang, Wei ; Faber, Katrin ; Schwarzwaelder, Kerstin ; Kirsten, Romy ; Deichmann, Annette ; Ball, Claudia R. ; Balaggan, Kamaljit S. ; Yá̃ez-Mũoz, Rafael J. ; Ali, Robin R. ; Gaspar, H. Bobby ; Biasco, Luca ; Aiuti, Alessandro ; Cesana, Daniela ; Montini, Eugenio ; Naldini, Luigi ; Cohen-Haguenauer, Odile ; Mavilio, Fulvio ; Thrasher, Adrian J. ; Glimm, Hanno ; Von Kalle, Christof ; Saurin, William ; Schmidt, Manfred. / Comprehensive genomic access to vector integration in clinical gene therapy. In: Nature Medicine. 2009 ; Vol. 15, No. 12. pp. 1431-1436.
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