Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in SCID-X1 gene therapy - PubMed (original) (raw)
. 2007 Aug;117(8):2225-32.
doi: 10.1172/JCI31659.
Salima Hacein-Bey-Abina, Manfred Schmidt, Alexandrine Garrigue, Martijn H Brugman, Jingqiong Hu, Hanno Glimm, Gabor Gyapay, Bernard Prum, Christopher C Fraser, Nicolas Fischer, Kerstin Schwarzwaelder, Maria-Luise Siegler, Dick de Ridder, Karin Pike-Overzet, Steven J Howe, Adrian J Thrasher, Gerard Wagemaker, Ulrich Abel, Frank J T Staal, Eric Delabesse, Jean-Luc Villeval, Bruce Aronow, Christophe Hue, Claudia Prinz, Manuela Wissler, Chuck Klanke, Jean Weissenbach, Ian Alexander, Alain Fischer, Christof von Kalle, Marina Cavazzana-Calvo
Affiliations
- PMID: 17671652
- PMCID: PMC1934585
- DOI: 10.1172/JCI31659
Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in SCID-X1 gene therapy
Annette Deichmann et al. J Clin Invest. 2007 Aug.
Abstract
Recent reports have challenged the notion that retroviruses and retroviral vectors integrate randomly into the host genome. These reports pointed to a strong bias toward integration in and near gene coding regions and, for gammaretroviral vectors, around transcription start sites. Here, we report the results obtained from a large-scale mapping of 572 retroviral integration sites (RISs) isolated from cells of 9 patients with X-linked SCID (SCID-X1) treated with a retrovirus-based gene therapy protocol. Our data showed that two-thirds of insertions occurred in or very near to genes, of which more than half were highly expressed in CD34(+) progenitor cells. Strikingly, one-fourth of all integrations were clustered as common integration sites (CISs). The highly significant incidence of CISs in circulating T cells and the nature of their locations indicate that insertion in many gene loci has an influence on cell engraftment, survival, and proliferation. Beyond the observed cases of insertional mutagenesis in 3 patients, these data help to elucidate the relationship between vector insertion and long-term in vivo selection of transduced cells in human patients with SCID-X1.
Figures
Figure 1. RIS distribution analysis of engrafted cells.
(A) RIS distribution compared with chromosome size and gene content. The displayed chromosome distribution accounts for the double copy number of diploid autosomes. Black bars, size of chromosomes; gray bars, number of known genes; white bars, number of RISs. (B and C) Vector integration in and near RefSeq genes. RISs were preferentially found near the TSS (B) and within gene coding regions (C). Negative numbers denote the region upstream (Up) of a gene, positive numbers indicate the gene region downstream of the TSS (RefSeq gene) (B) or downstream (Down) of the gene (C). (C) The position of intragenic hits was mapped according to the percentage of overall gene length.
Figure 2. Comparison of pre- and posttransplant RIS distribution in Pt4.
(A) Percentage of RISs detected in the indicated gene regions. (B) Distribution of vector-targeted genes (including the surrounding 10-kbp genomic region) with respect to GO and CIS formation. The GO categories were chosen according to the most significantly overrepresented ones retrieved from engrafted cells from all patients. Black bars, pretransplantation samples of Pt4 (102 RISs); gray bars, posttransplantation samples of Pt4 (141 RISs).
Figure 3. Association between vector integration and gene expression.
(A and B) Number of RISs detected in engrafted cells (A) and in CD34+ cells prior to reinfusion (B) as a function of relative gene expression in stimulated peripheral blood CD34+ cells. For each gene, the probeset with the highest expression value was used. All 20,600 genes present on the array were sorted on expression and divided in 10 percentile categories according to their expression level, so that each category contains 10% of the genes. Values represent the average number of genes in each category based on 3 individual arrays (see Methods).
Comment in
- Retroviral integration and human gene therapy.
Bushman FD. Bushman FD. J Clin Invest. 2007 Aug;117(8):2083-6. doi: 10.1172/JCI32949. J Clin Invest. 2007. PMID: 17671645 Free PMC article.
Similar articles
- Retroviral integration and human gene therapy.
Bushman FD. Bushman FD. J Clin Invest. 2007 Aug;117(8):2083-6. doi: 10.1172/JCI32949. J Clin Invest. 2007. PMID: 17671645 Free PMC article. - Gammaretrovirus-mediated correction of SCID-X1 is associated with skewed vector integration site distribution in vivo.
Schwarzwaelder K, Howe SJ, Schmidt M, Brugman MH, Deichmann A, Glimm H, Schmidt S, Prinz C, Wissler M, King DJ, Zhang F, Parsley KL, Gilmour KC, Sinclair J, Bayford J, Peraj R, Pike-Overzet K, Staal FJ, de Ridder D, Kinnon C, Abel U, Wagemaker G, Gaspar HB, Thrasher AJ, von Kalle C. Schwarzwaelder K, et al. J Clin Invest. 2007 Aug;117(8):2241-9. doi: 10.1172/JCI31661. J Clin Invest. 2007. PMID: 17671654 Free PMC article. Clinical Trial. - Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial.
Wang GP, Berry CC, Malani N, Leboulch P, Fischer A, Hacein-Bey-Abina S, Cavazzana-Calvo M, Bushman FD. Wang GP, et al. Blood. 2010 Jun 3;115(22):4356-66. doi: 10.1182/blood-2009-12-257352. Epub 2010 Mar 12. Blood. 2010. PMID: 20228274 Free PMC article. Clinical Trial. - Gene Therapy for X-Linked Severe Combined Immunodeficiency: Where Do We Stand?
Cavazzana M, Six E, Lagresle-Peyrou C, André-Schmutz I, Hacein-Bey-Abina S. Cavazzana M, et al. Hum Gene Ther. 2016 Feb;27(2):108-16. doi: 10.1089/hum.2015.137. Hum Gene Ther. 2016. PMID: 26790362 Free PMC article. Review. - Stem cell gene transfer: insights into integration and hematopoiesis from primate genetic marking studies.
Dunbar CE. Dunbar CE. Ann N Y Acad Sci. 2005 Jun;1044:178-82. doi: 10.1196/annals.1349.023. Ann N Y Acad Sci. 2005. PMID: 15958711 Review.
Cited by
- The longitudinal kinetics of AAV5 vector integration profiles and evaluation of clonal expansion in mice.
Ismail AM, Witt E, Bouwman T, Clark W, Yates B, Franco M, Fong S. Ismail AM, et al. Mol Ther Methods Clin Dev. 2024 Jun 26;32(3):101294. doi: 10.1016/j.omtm.2024.101294. eCollection 2024 Sep 12. Mol Ther Methods Clin Dev. 2024. PMID: 39104575 Free PMC article. - Prenatal AAV9-GFP administration in fetal lambs results in transduction of female germ cells and maternal exposure to virus.
Borges B, Varthaliti A, Schwab M, Clarke MT, Pivetti C, Gupta N, Cadwell CR, Guibinga G, Phillips S, Del Rio T, Ozsolak F, Imai-Leonard D, Kong L, Laird DJ, Herzeg A, Sumner CJ, MacKenzie TC. Borges B, et al. Mol Ther Methods Clin Dev. 2024 May 4;32(2):101263. doi: 10.1016/j.omtm.2024.101263. eCollection 2024 Jun 13. Mol Ther Methods Clin Dev. 2024. PMID: 38827250 Free PMC article. - Embryo and fetal gene editing: Technical challenges and progress toward clinical applications.
Mattar CNZ, Chew WL, Lai PS. Mattar CNZ, et al. Mol Ther Methods Clin Dev. 2024 Mar 4;32(2):101229. doi: 10.1016/j.omtm.2024.101229. eCollection 2024 Jun 13. Mol Ther Methods Clin Dev. 2024. PMID: 38533521 Free PMC article. Review. - Partial correction of immunodeficiency by lentiviral vector gene therapy in mouse models carrying Rag1 hypomorphic mutations.
Castiello MC, Di Verniere M, Draghici E, Fontana E, Penna S, Sereni L, Zecchillo A, Minuta D, Uva P, Zahn M, Gil-Farina I, Annoni A, Iaia S, Ott de Bruin LM, Notarangelo LD, Pike-Overzet K, Staal FJT, Villa A, Capo V. Castiello MC, et al. Front Immunol. 2023 Nov 13;14:1268620. doi: 10.3389/fimmu.2023.1268620. eCollection 2023. Front Immunol. 2023. PMID: 38022635 Free PMC article. - Enhanced Biosafety of the Sleeping Beauty Transposon System by Using mRNA as Source of Transposase to Efficiently and Stably Transfect Retinal Pigment Epithelial Cells.
Harmening N, Johnen S, Izsvák Z, Ivics Z, Kropp M, Bascuas T, Walter P, Kreis A, Pajic B, Thumann G. Harmening N, et al. Biomolecules. 2023 Apr 7;13(4):658. doi: 10.3390/biom13040658. Biomolecules. 2023. PMID: 37189405 Free PMC article.
References
- Cavazzana-Calvo M., et al. Gene therapy of human severe combined immunodeficiency (SCID)-X1 disease. Science. 2000;288:669–672. - PubMed
- Aiuti A., et al. Correction of ADA-SCID by stem cell gene therapy combined with nonmyeloablative conditioning. Science. 2002;296:2410–2413. - PubMed
- Gaspar H.B., et al. Gene therapy of X-linked severe combined immunodeficiency by use of a pseudotyped gammaretroviral vector. Lancet. 2004;364:2181–2187. - PubMed
- Coffin, J.M., Hughes, S.H., and Varmus, H.E. 1997.Retroviruses . Cold Spring Harbor Laboratory Press. Plainview, New York, USA. 843 pp. - PubMed
- Moolten F.L., Cupples L.A. A model for predicting the risk of cancer consequent to retroviral gene therapy. Hum. Gene Ther. 1992;3:479–486. - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Medical