Self-inactivating Gammaretroviral Vectors Research Articles

Long-Term Outcome of Gene Therapy for X-Linked Severe Combined Immunodeficiency (SCID-X1) Using an Enhancer-Deleted Self-Inactivating Gammaretroviral Vector

Long-Term Outcome of Gene Therapy for X-Linked Severe Combined Immunodeficiency (SCID-X1) Using an Enhancer-Deleted Self-Inactivating Gammaretroviral Vector

Immune Reconstitution and Preliminary Safety Analysis Of 9 Patients Treated With Somatic Gene Therapy For X-Linked Severe Combined Immunodeficiency (SCID-X1) With a Self-Inactivating Gammaretroviral Vector

▪X-linked severe combined immunodeficiency (SCID-X1) is a fatal genetic disease currently treated with hematopoietic stem cell transplantation. Previous gene therapy trials using a MLV-based gammaretroviral vector expressing the IL-2 receptor gamma chain (γc) controlled by the viral long-terminal repeat (LTR) induced T cell reconstitution in 18 of 20 boys with SCID-X1, but also resulted in insertional oncogenesis in 5 of 20, leading to leukemia, with 4 of the 5 demonstrating insertion at the LMO2 locus (Trial 1). We tested whether a self-inactivating (SIN) gammaretroviral vector, pSRS11.EFS.IL2RG.pre*, derived by removing the MLV LTR U3 (enhancer/promoter) region and driving expression of γc by an intronless elongation factor 1α (EF1-α) promoter, would promote T cell reconstitution in boys with X-SCID with an improved safety profile (Trial 2). Pre-clinical studies showed a lack of clonal skewing in primary and secondary transplant recipient mice in vivo and lack of insertions in either Lmo2 or Evi1 in these mice. The primary endpoints of the study are: 1. immune recovery defined as CD3+ T cell count >300/microliter and restoration of proliferation to phytohemagglutinin (PHA); and 2. Lack of insertional oncogenesis.To date 9 boys with SCID-X1 age 3.9 to 10.5 months were enrolled with 5-32 months follow-up on the current trial. All received bone marrow derived CD34+ cells transduced with the pSRS11.EFS.IL2RG.pre* vector, infused without conditioning. Transduction was performed at each site with one of two common protocols and the same GMP-produced vector supernatant. Transduction efficiency of infused CD34+ cells ranged from 0.25-2.92 vector copy number (VCN). One patient with a low initial transduction underwent a repeat procedure 1 month after infusion of the first product. Overall survival is excellent with 8 out of 9 patients alive and well; 1 patient died of overwhelming adenoviral infection, present at study entry, at 4 months prior to full reconstitution with genetically modified T cells. Excluding 1 patient with high level maternal engraftment who is unevaluable with regard to T cell number, 5 of 7 (71%) achieved CD3+ T cell count >300/microliter. The 2 patients who did not achieve T cell count >300/microliter received CD34+ cells with the lowest vector copy number (VCN). An early rise in CD16/56+ NK cells was also associated with T cell recovery. Of 8 surviving patients, 7 of 8 (87.5%) had PHA stimulation index >15 at or before 6 months (n=8; median 85.5; range 0.2-224); the patient who had no functional recovery received mismatched allogeneic cord blood transplant. At last follow-up, the remaining 7 patients have evidence of γc transgene expression in T cells, naïve T cell generation, and normal diversity. They are free of SCID related infections and humoral immune evaluation is ongoing.We compared the early immune recovery and peripheral blood insertion site analysis between 6 evaluable subjects on Trial 2 with the 20 subjects enrolled on the previous trials of MLV-based γc vector. The CD3+ T cell count at 6 months for Trial 2 (n=6; median 548/microliter; range 87-3960) does not appear to be lower than for Trial 1 (n=19; median 1755/microliter; range 200-4759; p=0.14 in 2-sided Wilcoxon rank sum test). However, we recognize that this test is underpowered, and results are preliminary. Because the latency time to leukemic events in the previous trial was long (33-60 months), we compared insertion sites as a surrogate measure of safety. Insertional activation of growth controlling genes has been demonstrated to be associated in some murine models with clonal skewing during in vitro expansion and in vivo reconstitution. Therefore, we hypothesized that removal of the transcription factor binding site-rich LTR U3 enhancer regions would change the insertion pattern detected in peripheral blood after transplantation away from the 5' ends of genes important for cell proliferation or persistence. Whereas in Trial 1, LMO2, EVI1 and other lymphoid proto-oncogenes showed prominent clusters of integration sites post-transplantation, these locations were not significant clusters in the second trial (p<10-4; comparison of n=19 Trial 1 versus n=6 Trial 2). Thus, we show promising early data that a modified gammaretroviral vector retains efficacy in treatment of SCID-X1 and is likely to have an improved safety profile. Disclosures:Off Label Use: Off-label use of CliniMACS device for purification of CD34+ bone marrow cells. Baum:Transatlantic Gene Therapy Consortium: Patents & Royalties.

Gene therapy for primary immunodeficiencies: current status and future prospects.

Gene therapy using autologous haematopoietic stem cells offers a valuable treatment option for patients with primary immunodeficiencies who do not have access to an HLA-matched donor, although such treatments have not been without their problems. This review details gene therapy trials for X-linked and adenosine deaminase (ADA)-deficient severe combined immunodeficiency (SCID), Wiskott-Aldrich syndrome (WAS) and chronic granulomatous disease (CGD). X-linked SCID was chosen for gene therapy because of previous 'natural' genetic correction through a reversion event in a single lymphoid precursor, demonstrating limited thymopoiesis and restricted T-lymphocyte receptor repertoire, showing selective advantage of progenitors possessing the wild-type gene. In early studies, patients were treated with long terminal repeats-intact gamma-retroviral vectors, without additional chemotherapy. Early results demonstrated gene-transduced cells, sustained thymopoiesis, and a diverse T-lymphocyte repertoire with normal function. Serious adverse effects were subsequently reported in 5 of 20 patients, with T-lymphocyte leukaemia developing, secondary to the viral vector integrating adjacent to a known oncogene. New trials using self-inactivating gamma-retroviral vectors are progressing. Trials for ADA-SCID using gamma-retroviral vectors have been successful, with no similar serious adverse effects reported; trials using lentiviral vectors are in progress. Patients with WAS and CGD treated with early gamma-retroviral vectors have developed similar lymphoproliferative adverse effects to those seen in X-SCID--current trials are using new-generation vectors. Targeted gene insertion using homologous recombination of corrected gene sequences by cellular DNA repair pathways following targeted DNA breakage will improve efficacy and safety of gene therapy. A number of new techniques are discussed.

From Bench to Bedside: Preclinical Evaluation of a Self-Inactivating Gammaretroviral Vector for the Gene Therapy of X-linked Chronic Granulomatous Disease

Chronic granulomatous disease (CGD) is a primary immunodeficiency characterized by impaired antimicrobial activity in phagocytic cells. As a monogenic disease affecting the hematopoietic system, CGD is amenable to gene therapy. Indeed in a phase I/II clinical trial, we demonstrated a transient resolution of bacterial and fungal infections. However, the therapeutic benefit was compromised by the occurrence of clonal dominance and malignant transformation demanding alternative vectors with equal efficacy but safety-improved features. In this work we have developed and tested a self-inactivating (SIN) gammaretroviral vector (SINfes.gp91s) containing a codon-optimized transgene (gp91(phox)) under the transcriptional control of a myeloid promoter for the gene therapy of the X-linked form of CGD (X-CGD). Gene-corrected cells protected X-CGD mice from Aspergillus fumigatus challenge at low vector copy numbers. Moreover, the SINfes.gp91s vector generates substantial amounts of superoxide in human cells transplanted into immunodeficient mice. In vitro genotoxicity assays and longitudinal high-throughput integration site analysis in transplanted mice comprising primary and secondary animals for 11 months revealed a safe integration site profile with no signs of clonal dominance.

Critical Variables affecting clinical-grade production of the self-inactivating gamma-retroviral vector for the treatment of X-linked severe combined immunodeficiency

Patients with X-linked severe combined immunodeficiency (SCID-X1) were successfully cured following gene therapy with a gamma-retroviral vector (gRV) expressing the common gamma chain of the interleukin-2 receptor (IL2RG). However, 5 of 20 patients developed leukemia from activation of cellular proto-oncogenes by viral enhancers in the long-terminal repeats (LTR) of the integrated vector. These events prompted the design of a gRV vector with self-inactivating (SIN) LTRs to enhance vector safety. Herein we report on the production of a clinical-grade SIN IL2RG gRV pseudotyped with the Gibbon Ape Leukemia Virus envelope for a new gene therapy trial for SCID-X1, and highlight variables that were found to be critical for transfection-based large-scale SIN gRV production. Successful clinical production required careful selection of culture medium without pre-added glutamine, reduced exposure of packaging cells to cell-dissociation enzyme, and presence of cations in wash buffer. The clinical vector was high titer; transduced 68-70% normal human CD34(+) cells, as determined by colony-forming unit assays and by xenotransplantation in immunodeficient NOD.CB17-Prkdc(scid)/J (nonobese diabetic/severe combined immunodeficiency (NOD/SCID)) and NOD.Cg-Prkdc(scid) Il2rg(tm1Wjl)/SzJ (NOD/SCID gamma (NSG))) mice; and resulted in the production of T cells in vitro from human SCID-X1 CD34(+) cells. The vector was certified and released for the treatment of SCID-X1 in a multi-center international phase I/II trial.

Gene therapy for Fanconi anemia: one step closer to the clinic.

Game-changing trends in biomedical science usually start as daring, visionary ideas that struggle through the confusion of trials and experiments, experience a crisis at the collision of an expectant public and disbelieving colleagues, and—if successful—finally emerge as widely accepted new standards (Evans, 2011). The gene therapy field has followed this sequence and, in the teens of the twenty-first century, seems to be emerging as a realistic new therapy for genetic disorders of hematopoiesis, such as congenital immunodeficiencies and bone marrow failure syndromes (Naldini, 2011; Sheridan, 2011). Fanconi anemia (FA) is a prototypical inherited bone marrow failure disorder characterized by aplastic anemia and a dramatically increased risk of hematological and solid malignancies. FA is due to defects in one of at least 15 genes that encode the proteins involved in the cellular response to DNA damage and the maintenance of genomic integrity. More than half of the reported cases of FA are due to FANCA gene mutations. FANCA protein is a member of a ‘‘functional core complex’’ (formed with seven other proteins) that is essential in the DNA damage response. A lack of core complex results in a phenotype characterized by bone marrow failure, myelodysplasia, leukemia, and other cancers (D’Andrea, 2010). With support from the FA Research Fund and Fanconi Hope Charitable Trust, two dozen scientists and clinicians convened in Barcelona on November 22, 2011 for the second meeting of the FA Gene Therapy International Work Group. This International Work Group, chaired by Jakub Tolar (University of Minnesota, Minneapolis, MN), has been established with the goal of coordinating the best available knowledge in gene therapy with the best format of clinical trial for FA. The first meeting, a year ago in London, brought together researchers from fields that rarely interact. The objective of that meeting was to establish an open platform whereby teams initiating gene therapy trials in FA, institutions that already have strong track records in gene therapy, and groups that are developing novel strategies in genome modification could be brought together. We found common ground in our efforts to accelerate the transition of gene therapy research into clinical trials for patients with FA. The initial FA gene therapy platform was outlined as follows: FANCA gene delivered by third-generation lentiviral vector pseudotyped with vesicular stomatitis virus (VSV-G); short transduction without prolonged prestimulation with growth factors; and exclusion of individuals who have a human leukocyte antigen-matched sibling donor, an abnormal karyotype, or a serious infection (Tolar et al., 2011). The particular focus of this year’s event was to synthesize the data to inform the impending clinical trials and make the future iterations of FA gene therapy trials possible. Hematopoietic stem cell gene therapy has the potential to transform conventional therapy for FA, which for decades has involved transfusion support, anabolic steroids, and hematopoietic cell transplantation (HCT). Androgens can

SIN Retroviral Vectors Expressing COL7A1 Under Human Promoters for Ex Vivo Gene Therapy of Recessive Dystrophic Epidermolysis Bullosa

Recessive dystrophic epidermolysis bullosa (RDEB) is caused by loss-of-function mutations in COL7A1 encoding type VII collagen which forms key structures (anchoring fibrils) for dermal-epidermal adherence. Patients suffer since birth from skin blistering, and develop severe local and systemic complications resulting in poor prognosis. We lack a specific treatment for RDEB, but ex vivo gene transfer to epidermal stem cells shows a therapeutic potential. To minimize the risk of oncogenic events, we have developed new minimal self-inactivating (SIN) retroviral vectors in which the COL7A1 complementary DNA (cDNA) is under the control of the human elongation factor 1alpha (EF1alpha) or COL7A1 promoters. We show efficient ex vivo genetic correction of primary RDEB keratinocytes and fibroblasts without antibiotic selection, and use either of these genetically corrected cells to generate human skin equivalents (SEs) which were grafted onto immunodeficient mice. We achieved long-term expression of recombinant type VII collagen with restored dermal-epidermal adherence and anchoring fibril formation, demonstrating in vivo functional correction. In few cases, rearranged proviruses were detected, which were probably generated during the retrotranscription process. Despite this observation which should be taken under consideration for clinical application, this preclinical study paves the way for a therapy based on grafting the most severely affected skin areas of patients with fully autologous SEs genetically corrected using a SIN COL7A1 retroviral vector.

A new PG13-based packaging cell line for stable production of clinical-grade self-inactivating γ-retroviral vectors using targeted integration

The clinical application of self-inactivating (SIN) retroviral vectors has been hampered by the lack of reliable and efficient vector production technologies. To enable production of SIN gamma-retroviral vectors from stable producer clones, a new PG13-based packaging cell, known as PG368, was developed. Viral vector expression constructs can be reliably inserted at a predefined genomic locus of PG368 packaging cells by an Flp-recombinase-mediated targeted cassette exchange (RMCE) reaction. A new, carefully designed vector-targeting construct, pEMTAR-1, eliminated the co-packaging of the selectable marker gene used for the identification of successful recombination at the predefined genomic locus and thus, improved the safety of the production system. Selected clones produced vector supernatants at consistent titers. The targeted insertion of therapeutically relevant SIN vectors for chronic granulomatous disease and X-linked severe combined immunodeficiency into PG368 cells results in stable titers within the range necessary for clinical application. The production of retroviral SIN vectors from stable clinical-grade producer cells is feasible and will contribute to the safe production and application of SIN gamma-retroviral vectors for clinical trials.

Correction of murine hemophilia A following nonmyeloablative transplantation of hematopoietic stem cells engineered to encode an enhanced human factor VIII variant using a safety-augmented retroviral vector

AbstractInsertional mutagenesis by retroviral vectors is a major impediment to the clinical application of hematopoietic stem cell gene transfer for the treatment of hematologic disorders. We recently developed an insulated self-inactivating gammaretroviral vector, RMSinOFB, which uses a novel enhancer-blocking element that significantly decreases genotoxicity of retroviral integration. In this study, we used the RMSinOFB vector to evaluate the efficacy of a newly bioengineered factor VIII (fVIII) variant (efVIII)—containing a combination of A1 domain point mutations (L303E/F309S) and an extended partial B domain for improved secretion plus A2 domain mutations (R484A/R489A/P492A) for reduced immunogenicity—toward successful treatment of murine hemophilia A. In cell lines, efVIII was secreted at up to 6-fold higher levels than an L303E/F309S A1 domain–only fVIII variant (sfVIIIΔB). Most important, when compared with a conventional gammaretroviral vector expressing sfVIIIΔB, lower doses of RMSin-efVIII-OFB–transduced hematopoietic stem cells were needed to generate comparable curative fVIII levels in hemophilia A BALB/c mice after reduced-intensity total body irradiation or nonmyeloablative chemotherapy conditioning regimens. These data suggest that the safety-augmented RMSin-efVIII-OFB platform represents an encouraging step in the development of a clinically appropriate gene addition therapy for hemophilia A.

Production of High Titer cGMP-Grade SIN Gamma-Retroviral Vectors by Transfection in a Closed System Bioreactor

The need for gamma-retroviral vectors with self-inactivating (SIN) long terminal repeats for clinical trials has prompted a shift in the method with which large scale GMP-grade vectors are produced, from the use of stable producer lines to transient transfection-based techniques. The main challenge of instituting this methodology was to develop SIN retrovirus vectors that produced high amounts of genomic vector RNA in packaging cells, and to design scalable processes for closed system culture, transfection and virus harvest. Using improved expression plasmids, the Vector Production Facility, an academic GMP manufacturing laboratory that is part of the Translational Cores at Cincinnati Children's Hospital, has developed such a method based on the Wave Bioreactor® production platform. In brief, cells from a certified 293T master cell bank are expanded, mixed with transfection reagents, and pumped into a 2, 10 or 20 Liter Wave Cell Bag containing FibraCel® discs. Cells are cultured in DMEM with GlutaMax® and 10% FBS at 37°C, 5% CO2 at a rocking speed of 22 rpm and 6° angle. At 16–20 hrs post-transfection, the media is changed; virus is harvested at 12-hour intervals, filtered through a leukocyte reduction filter, aliquoted into Cryocyte freezing containers, and frozen at or below −70°C. Several processing parameters, including the confluency of cells harvested prior to transfection, the timing of transfection, the amount of plasmid DNA, exposure of cells to PBS/TrypLESelect, and the timing of the media change post-transfection affected vector titer. Mixing cells with plasmid and transfection mixture prior to seeding onto FibraCel, as compared to transfecting cells 1-day post-seeding (as is standard when using tissue culture plastic) increased the titer from 104 to 4 × 105 IU/mL. Similarly, increasing the amount of plasmid DNA per mL from 4.6 to 9.2 μg doubled the titer in the Wave, while it reduced titer by 20–40% in tissue culture flasks (Fig. 1). Using an optimized protocol, six cGMP-grade SIN gamma-retroviral vectors have now been produced in support of the FDA's National Toxicology Program (NTP), with unconcentrated vector titers ranging from 1 × 106 to as high as 4 × 107 IU/mL. Using similar processing, we have produced a large scale SIN gamma-retroviral vector (GALV pseudotyped) for an international X-linked SCID trial with average unconcentrated titers of 106 IU/mL in all viral harvests. In summary, the process developed at the Cincinnati Children's Hospital Vector Production Facility allows for large scale closed-system production of high-titer retroviral vectors for clinical trials using transient transfection. [Display omitted]

Combinatorial incorporation of enhancer-blocking components of the chicken beta-globin 5'HS4 and human T-cell receptor alpha/delta BEAD-1 insulators in self-inactivating retroviral vectors reduces their genotoxic potential.

Insertional mutagenesis by retroviral vectors has emerged as a serious impediment to the widespread application of hematopoietic stem cell gene transfer for the treatment of hematologic diseases. Here we report the development of a 77-base pair element, FII/BEAD-A (FB), which contains the minimal enhancer-blocking components of the chicken beta-globin 5'HS4 insulator and a homologous region from the human T-cell receptor alpha/delta BEAD-1 insulator. With a new flow cytometry-based assay, we show that the FB element is as effective in enhancer-blocking activity as the prototypical 1.2-kilobase 5'HS4 insulator fragment. When incorporated into the residual U3 region of the 3' long terminal repeat (LTR) of a self-inactivating (SIN) gammaretroviral vector, the FB element was stably transferred to the 5' LTR during reverse transcription, flanking the integrated transgene expression cassette. Notably, using a recently established in vitro insertional mutagenesis assay involving primary murine hematopoietic cells, we found that SIN gammaretroviral vectors, as well as SIN lentiviral vectors, containing the FB element exhibited greatly reduced transforming potential-to background levels under the experimental conditions used-compared with their unshielded counterparts. These results suggest that the FB element-mediated enhancer-blocking modification is a promising approach to dramatically improve the safety of retroviral vectors for therapeutic gene transfer.

Reciprocal Relationship between O6-Methylguanine-DNA Methyltransferase P140K Expression Level and Chemoprotection of Hematopoietic Stem Cells

Retroviral-mediated delivery of the P140K mutant O(6)-methylguanine-DNA methyltransferase (MGMT(P140K)) into hematopoietic stem cells (HSC) has been proposed as a means to protect against dose-limiting myelosuppressive toxicity ensuing from chemotherapy combining O(6)-alkylating agents (e.g., temozolomide) with pseudosubstrate inhibitors (such as O(6)-benzylguanine) of endogenous MGMT. Because detoxification of O(6)-alkylguanine adducts by MGMT is stoichiometric, it has been suggested that higher levels of MGMT will afford better protection to gene-modified HSC. However, accomplishing this goal would potentially be in conflict with current efforts in the gene therapy field, which aim to incorporate weaker enhancer elements to avoid insertional mutagenesis. Using a panel of self-inactivating gamma-retroviral vectors that express a range of MGMT(P140K) activity, we show that MGMT(P140K) expression by weaker cellular promoter/enhancers is sufficient for in vivo protection/selection following treatment with O(6)-benzylguanine/temozolomide. Conversely, the highest level of MGMT(P140K) activity did not promote efficient in vivo protection despite mediating detoxification of O(6)-alkylguanine adducts. Moreover, very high expression of MGMT(P140K) was associated with a competitive repopulation defect in HSC. Mechanistically, we show a defect in cellular proliferation associated with elevated expression of MGMT(P140K), but not wild-type MGMT. This proliferation defect correlated with increased localization of MGMT(P140K) to the nucleus/chromatin. These data show that very high expression of MGMT(P140K) has a deleterious effect on cellular proliferation, engraftment, and chemoprotection. These studies have direct translational relevance to ongoing clinical gene therapy studies using MGMT(P140K), whereas the novel mechanistic findings are relevant to the basic understanding of DNA repair by MGMT.

Self-inactivating Gammaretroviral Vectors for Gene Therapy of X-linked Severe Combined Immunodeficiency

Gene therapy for X-linked severe combined immunodeficiency (SCID-X1) has proven highly effective for long-term restoration of immunity in human subjects. However, the development of lymphoproliferative complications due to dysregulated proto-oncogene expression has underlined the necessity for developing safer vector systems. To reduce the potential for insertional mutagenesis, we have evaluated the efficacy of self-inactivating (SIN) gammaretroviral vectors in cellular and in vivo models of SCID-X1. Vectors incorporating an internal human elongation factor-1alpha regulatory element were capable of fully restoring the lymphoid differentiation potential of gammac-deficient lineage negative cells. Multilineage lymphoid reconstitution of a murine model was achieved at a similar level to that achieved by a conventional long-terminal repeat (LTR)-regulated vector used in previous clinical trials. Functional proliferative responses to mitogenic stimuli were also restored, and serum immunoglobulin levels were normalized. The reduced mutagenic potential conferred by SIN vector configurations and alternative non-LTR-based regulatory elements, together with proven efficacy in correction of cellular defects provides an important platform for development of the next phase of clinical trials for SCID-X1.