Preclinical modeling highlights the therapeutic potential of hematopoietic stem cell gene editing for correction of SCID-X1

Preclinical studies establish the conditions for safe and effective correction of SCID-X1 by targeted gene editing of hematopoietic stem cells. Gene correction, one step at a time Although gene therapy has been proposed for a variety of genetic disorders, including severe combined immunodeficiency, it has not yet found routine use in the clinic, in part because of potential complications. To help pave the way for safer translation of such gene therapy, Schiroli et al. studied potential approaches to it in mouse models of severe combined immunodeficiency. The authors systematically analyzed the outcomes of using different approaches to conditioning, different numbers of gene-edited cells, different techniques for editing the faulty gene, and other aspects of the technology to find the safest and most effective method. Targeted genome editing in hematopoietic stem/progenitor cells (HSPCs) is an attractive strategy for treating immunohematological diseases. However, the limited efficiency of homology-directed editing in primitive HSPCs constrains the yield of corrected cells and might affect the feasibility and safety of clinical translation. These concerns need to be addressed in stringent preclinical models and overcome by developing more efficient editing methods. We generated a humanized X-linked severe combined immunodeficiency (SCID-X1) mouse model and evaluated the efficacy and safety of hematopoietic reconstitution from limited input of functional HSPCs, establishing thresholds for full correction upon different types of conditioning. Unexpectedly, conditioning before HSPC infusion was required to protect the mice from lymphoma developing when transplanting small numbers of progenitors. We then designed a one-size-fits-all IL2RG (interleukin-2 receptor common γ-chain) gene correction strategy and, using the same reagents suitable for correction of human HSPC, validated the edited human gene in the disease model in vivo, providing evidence of targeted gene editing in mouse HSPCs and demonstrating the functionality of the IL2RG-edited lymphoid progeny. Finally, we optimized editing reagents and protocol for human HSPCs and attained the threshold of IL2RG editing in long-term repopulating cells predicted to safely rescue the disease, using clinically relevant HSPC sources and highly specific zinc finger nucleases or CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9). Overall, our work establishes the rationale and guiding principles for clinical translation of SCID-X1 gene editing and provides a framework for developing gene correction for other diseases.

[1]  M. Cavazzana‐Calvo,et al.  A self-inactivating lentiviral vector for SCID-X1 gene therapy that does not activate LMO2 expression in human T cells. , 2010, Blood.

[2]  Luigi Naldini,et al.  Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery , 2007, Nature Biotechnology.

[3]  D. Prows,et al.  Stem Cell-Specific Mechanisms Ensure Genomic Fidelity within HSCs and upon Aging of HSCs. , 2015, Cell reports.

[4]  W. Leonard,et al.  Defective lymphoid development in mice lacking expression of the common cytokine receptor gamma chain. , 1995, Immunity.

[5]  E. Rebar,et al.  Long-term multilineage engraftment of autologous genome-edited hematopoietic stem cells in nonhuman primates. , 2016, Blood.

[6]  L. Naldini,et al.  Lentiviral-mediated gene therapy leads to improvement of B-cell functionality in a murine model of Wiskott-Aldrich syndrome. , 2011, The Journal of allergy and clinical immunology.

[7]  C. Di Serio,et al.  Brain conditioning is instrumental for successful microglia reconstitution following hematopoietic stem cell transplantation , 2012, Proceedings of the National Academy of Sciences.

[8]  W. Leonard,et al.  Restoration of lymphoid populations in a murine model of X-linked severe combined immunodeficiency by a gene-therapy approach. , 1999, Blood.

[9]  Hojun Li,et al.  In vivo genome editing restores hemostasis in a mouse model of hemophilia , 2011, Nature.

[10]  D. Scadden,et al.  Non-genotoxic conditioning for hematopoietic stem cell transplantation using a hematopoietic-cell-specific internalizing immunotoxin , 2016, Nature Biotechnology.

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

[12]  Pachai Natarajan,et al.  CRISPR-Cas9 gene repair of hematopoietic stem cells from patients with X-linked chronic granulomatous disease , 2017, Science Translational Medicine.

[13]  A. Fischer,et al.  Lymphoid development in mice with a targeted deletion of the interleukin 2 receptor gamma chain. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Margherita Neri,et al.  Site-specific integration and tailoring of cassette design for sustainable gene transfer , 2011, Nature Methods.

[15]  D. Weissman,et al.  Generating the optimal mRNA for therapy: HPLC purification eliminates immune activation and improves translation of nucleoside-modified, protein-encoding mRNA , 2011, Nucleic acids research.

[16]  L. Notarangelo,et al.  Transplantation outcomes for severe combined immunodeficiency, 2000-2009. , 2014, The New England journal of medicine.

[17]  A. Schambach,et al.  A Differentiation Checkpoint Limits Hematopoietic Stem Cell Self-Renewal in Response to DNA Damage , 2014 .

[18]  Volker Rasche,et al.  Cell competition is a tumour suppressor mechanism in the thymus , 2014, Nature.

[19]  H. Kim,et al.  A guide to genome engineering with programmable nucleases , 2014, Nature Reviews Genetics.

[20]  A. Bhandoola,et al.  Chemokine treatment rescues profound T-lineage progenitor homing defect after bone marrow transplant conditioning in mice. , 2014, Blood.

[21]  Margaret A Goodell,et al.  Highly Efficient Genome Editing of Murine and Human Hematopoietic Progenitor Cells by CRISPR/Cas9. , 2016, Cell reports.

[22]  Claus V. Hallwirth,et al.  Limiting Thymic Precursor Supply Increases the Risk of Lymphoid Malignancy in Murine X-Linked Severe Combined Immunodeficiency , 2016, Molecular therapy. Nucleic acids.

[23]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[24]  L. Notarangelo,et al.  Lentiviral hematopoietic stem cell gene therapy for X-linked severe combined immunodeficiency , 2016, Science Translational Medicine.

[25]  Yong Huang,et al.  Promoterless gene targeting without nucleases ameliorates haemophilia B in mice , 2014, Nature.

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

[27]  J. Puck,et al.  Mutation analysis of IL2RG in human X-linked severe combined immunodeficiency. , 1997, Blood.

[28]  H. Ochs,et al.  Targeted gene editing restores regulated CD40L function in X-linked hyper-IgM syndrome. , 2016, Blood.

[29]  M. Katsuki,et al.  Modulation of hematopoiesis in mice with a truncated mutant of the interleukin-2 receptor gamma chain. , 1996, Blood.

[30]  Martin J. Aryee,et al.  GUIDE-Seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases , 2014, Nature Biotechnology.

[31]  Sruthi Mantri,et al.  CRISPR/Cas9 β-globin gene targeting in human haematopoietic stem cells , 2016, Nature.

[32]  Eli J. Fine,et al.  DNA targeting specificity of RNA-guided Cas9 nucleases , 2013, Nature Biotechnology.

[33]  F. Chisari,et al.  Platelets prevent IFN-α/β-induced lethal hemorrhage promoting CTL-dependent clearance of lymphocytic choriomeningitis virus , 2008, Proceedings of the National Academy of Sciences.

[34]  A. Fischer,et al.  Sustained correction of X-linked severe combined immunodeficiency by ex vivo gene therapy. , 2002, The New England journal of medicine.

[35]  T. Fleisher Transplantation Outcomes for Severe Combined Immunodeficiency 2000–2009 , 2015, Pediatrics.

[36]  J. Doudna,et al.  The new frontier of genome engineering with CRISPR-Cas9 , 2014, Science.

[37]  Mason A. Israel,et al.  Lin−Sca1+Kit− Bone Marrow Cells Contain Early Lymphoid-Committed Precursors That Are Distinct from Common Lymphoid Progenitors1 , 2008, The Journal of Immunology.

[38]  F. Bushman,et al.  Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1. , 2008, The Journal of clinical investigation.

[39]  Lei Zhang,et al.  Editing T cell specificity towards leukemia by zinc finger nucleases and lentiviral gene transfer , 2012, Nature Medicine.

[40]  Benjamin L. Oakes,et al.  Multi-reporter selection for the design of active and more specific zinc-finger nucleases for genome editing , 2016, Nature Communications.

[41]  Robert Langer,et al.  CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling , 2014, Cell.

[42]  M. van der Burg,et al.  Targeted Genome Editing in Human Repopulating Hematopoietic Stem Cells , 2014, Nature.

[43]  M. Warr,et al.  Hematopoietic stem cell quiescence promotes error-prone DNA repair and mutagenesis. , 2010, Cell stem cell.

[44]  Castle Raley,et al.  Targeted Gene Addition to a Safe Harbor locus in human CD34+ Hematopoietic Stem Cells for Correction of X-linked Chronic Granulomatous Disease , 2016, Nature Biotechnology.