Integration Site Analysis in Gene Therapy Patients: Expectations and Reality.

Integration site (IS) analysis is one of the major tools for addressing the safety of gene therapy clinical protocols based on the use of integrating vectors. Over the past years, the study of viral insertions in gene therapy–treated patients has allowed identifying insertional mutagenesis events, evaluating the safety of new viral vector platforms and tracking the in vivo clonal dynamics of genetically engineered cell products. While gene therapy is progressively expanding its impact on a broader area of clinical applications, increasingly more accessible, faster, and more reliable safety readouts are required from IS analysis. Several actors, from researchers to clinicians, from regulatory agencies to private companies, have to interface to different degrees with the results of IS analysis while developing and evaluating gene therapy products based on retroviral vectors. This review is aimed at providing a brief overview of what the current state and the future is of these studies with a particular focu...

[1]  Luca Biasco,et al.  Integration profile of retroviral vector in gene therapy treated patients is cell-specific according to gene expression and chromatin conformation of target cell , 2011, EMBO molecular medicine.

[2]  L. Biasco,et al.  Current Approaches and Future Perspectives for In Vivo Clonal Tracking of Hematopoietic Cells. , 2016, Current gene therapy.

[3]  A. Fischer,et al.  Gene therapy of primary T cell immunodeficiencies. , 2013, Gene.

[4]  M. Lidonnici,et al.  Efficient Ex Vivo Engineering and Expansion of Highly Purified Human Hematopoietic Stem and Progenitor Cell Populations for Gene Therapy , 2017, Stem cell reports.

[5]  Bruce Aronow,et al.  Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in SCID-X1 gene therapy. , 2007, The Journal of clinical investigation.

[6]  F. Bushman,et al.  Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences , 2004, PLoS biology.

[7]  Davide Cittaro,et al.  Transcription Factor Binding Sites Are Genetic Determinants of Retroviral Integration in the Human Genome , 2009, PloS one.

[8]  David A. Williams.  Broadening the indications for hematopoietic stem cell genetic therapies. , 2013, Cell stem cell.

[9]  Christopher Baum,et al.  A modified γ-retrovirus vector for X-linked severe combined immunodeficiency. , 2014, The New England journal of medicine.

[10]  Allon M. Klein,et al.  Universal patterns of stem cell fate in cycling adult tissues , 2011, Development.

[11]  Luca Biasco,et al.  Multilineage hematopoietic reconstitution without clonal selection in ADA-SCID patients treated with stem cell gene therapy. , 2007, The Journal of clinical investigation.

[12]  Abigail Wacher,et al.  Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. , 2009, Blood.

[13]  Jérôme Larghero,et al.  Transfusion independence and HMGA2 activation after gene therapy of human β-thalassaemia , 2010, Nature.

[14]  Christine Kinnon,et al.  Gammaretrovirus-mediated correction of SCID-X1 is associated with skewed vector integration site distribution in vivo. , 2007, The Journal of clinical investigation.

[15]  Luigi Naldini,et al.  Gene therapy returns to centre stage , 2015, Nature.

[16]  A. Berns,et al.  Retroviral insertional mutagenesis: past, present and future , 2005, Oncogene.

[17]  Shawn M. Burgess,et al.  Transcription Start Regions in the Human Genome Are Favored Targets for MLV Integration , 2003, Science.

[18]  Hanno Glimm,et al.  High-resolution insertion-site analysis by linear amplification–mediated PCR (LAM-PCR) , 2007, Nature Methods.

[19]  C. Cancrini,et al.  In vivo tracking of T cells in humans unveils decade-long survival and activity of genetically modified T memory stem cells , 2015, Science Translational Medicine.

[20]  Jeffrey C. Miller,et al.  An unbiased genome-wide analysis of zinc-finger nuclease specificity , 2011, Nature Biotechnology.

[21]  Alessandro Aiuti,et al.  Hot spots of retroviral integration in human CD34+ hematopoietic cells. , 2007, Blood.

[22]  Jorge M Pacheco,et al.  Stochastic dynamics and the evolution of mutations in stem cells , 2011, BMC Biology.

[23]  Christof von Kalle,et al.  A serious adverse event after successful gene therapy for X-linked severe combined immunodeficiency. , 2003, The New England journal of medicine.

[24]  L. Biasco,et al.  Retroviral Integrations in Gene Therapy Trials , 2012, Molecular therapy : the journal of the American Society of Gene Therapy.

[25]  Crystal Mackall,et al.  Simplified process for the production of anti-CD19-CAR-engineered T cells. , 2013, Cytotherapy.

[26]  Yang Du,et al.  Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1 , 2006, Nature Medicine.

[27]  Luca Biasco,et al.  Lentiviral Hematopoietic Stem Cell Gene Therapy in Patients with Wiskott-Aldrich Syndrome , 2013, Science.

[28]  Luca Biasco,et al.  Comprehensive genomic access to vector integration in clinical gene therapy , 2009, Nature Medicine.

[29]  A. Schambach,et al.  Evaluating a ligation-mediated PCR and pyrosequencing method for the detection of clonal contribution in polyclonal retrovirally transduced samples. , 2013, Human gene therapy methods.

[30]  C. von Kalle,et al.  In Vivo Tracking of Human Hematopoiesis Reveals Patterns of Clonal Dynamics during Early and Steady-State Reconstitution Phases , 2016, Cell stem cell.

[31]  James M. Harris,et al.  Prostaglandin E2 enhances human cord blood stem cell xenotransplants and shows long-term safety in preclinical nonhuman primate transplant models. , 2011, Cell stem cell.

[32]  Michael Rothe,et al.  Gene Therapy for Wiskott-Aldrich Syndrome—Long-Term Efficacy and Genotoxicity , 2014, Science Translational Medicine.

[33]  L. Naldini,et al.  Whole transcriptome characterization of aberrant splicing events induced by lentiviral vector integrations. , 2012, The Journal of clinical investigation.

[34]  Cameron S. Osborne,et al.  LMO2-Associated Clonal T Cell Proliferation in Two Patients after Gene Therapy for SCID-X1 , 2003, Science.

[35]  Christof von Kalle,et al.  The genotoxic potential of retroviral vectors is strongly modulated by vector design and integration site selection in a mouse model of HSC gene therapy. , 2009, The Journal of clinical investigation.

[36]  F. Bushman,et al.  Decade-Long Safety and Function of Retroviral-Modified Chimeric Antigen Receptor T Cells , 2012, Science Translational Medicine.

[37]  J. Korlach,et al.  Length-Independent DNA Packing into Nanopore Zero-Mode Waveguides for Low-Input DNA Sequencing , 2017, Nature nanotechnology.

[38]  Anat Melamed,et al.  Estimating abundances of retroviral insertion sites from DNA fragment length data , 2012, Bioinform..

[39]  L. A. Panchenko,et al.  Non-random DNA fragmentation in next-generation sequencing , 2014, Scientific Reports.

[40]  N. Restifo,et al.  Moving T memory stem cells to the clinic. , 2013, Blood.

[41]  Stephan Wolf,et al.  Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing , 2010, Nature Protocols.

[42]  A. Schambach,et al.  Safety of gene therapy: new insights to a puzzling case. , 2014, Current gene therapy.

[43]  Frederic D. Bushman,et al.  Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial. , 2010, Blood.

[44]  Y. Fong,et al.  Acceptance and Access to Gene Editing: Science and Our Obligations to Mankind. , 2017, Molecular therapy : the journal of the American Society of Gene Therapy.

[45]  Hans Martin,et al.  Genomic instability and myelodysplasia with monosomy 7 consequent to EVI1 activation after gene therapy for chronic granulomatous disease , 2010, Nature Medicine.