Comprehensive genomic access to vector integration in clinical gene therapy

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Richard Gabriel - , German Cancer Research Center (DKFZ) (Author)
  • Ralph Eckenberg - , Genomining (Author)
  • Anna Paruzynski - , German Cancer Research Center (DKFZ) (Author)
  • Cynthia C. Bartholomae - , German Cancer Research Center (DKFZ) (Author)
  • Ali Nowrouzi - , German Cancer Research Center (DKFZ) (Author)
  • Anne Arens - , German Cancer Research Center (DKFZ) (Author)
  • Steven J. Howe - , University College London (Author)
  • Alessandra Recchia - , University of Modena and Reggio Emilia (Author)
  • Claudia Cattoglio - , Vita-Salute San Raffaele University (Author)
  • Wei Wang - , German Cancer Research Center (DKFZ) (Author)
  • Katrin Faber - , German Cancer Research Center (DKFZ) (Author)
  • Kerstin Schwarzwaelder - , German Cancer Research Center (DKFZ) (Author)
  • Romy Kirsten - , German Cancer Research Center (DKFZ) (Author)
  • Annette Deichmann - , German Cancer Research Center (DKFZ) (Author)
  • Claudia R. Ball - , German Cancer Research Center, partner site Dresden, Environmental Monitoring and Endocrinology (Research Group), National Center for Tumor Diseases Dresden, National Center for Tumor Diseases (NCT) Heidelberg (Author)
  • Kamaljit S. Balaggan - , University College London (Author)
  • Rafael J. Yá̃ez-Mũoz - , Royal Holloway University of London (Author)
  • Robin R. Ali - , University College London (Author)
  • H. Bobby Gaspar - , Great Ormond Street Hospital for Children NHS Trust (Author)
  • Luca Biasco - , Telethon Foundation (Author)
  • Alessandro Aiuti - , Telethon Foundation, University of Rome Tor Vergata (Author)
  • Daniela Cesana - , Telethon Foundation (Author)
  • Eugenio Montini - , Telethon Foundation (Author)
  • Luigi Naldini - , Telethon Foundation (Author)
  • Odile Cohen-Haguenauer - , École normale supérieure Paris-Saclay, Hôpital Saint-Louis (Author)
  • Fulvio Mavilio - , University of Modena and Reggio Emilia, Vita-Salute San Raffaele University (Author)
  • Adrian J. Thrasher - , University College London, Great Ormond Street Hospital for Children NHS Trust (Author)
  • Hanno Glimm - , German Cancer Research Center, partner site Dresden, National Center for Tumor Diseases Dresden, National Center for Tumor Diseases (NCT) Heidelberg (Author)
  • Christof Von Kalle - , German Cancer Research Center (DKFZ), Cincinnati Children's Hospital Medical Center (Author)
  • William Saurin - , Genomining (Author)
  • Manfred Schmidt - , German Cancer Research Center (DKFZ) (Author)

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.

Details

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

External IDs

PubMed 19966782

Keywords