Foamy Virus Vectors Research Articles

The fourth central polypurine tract guides the synthesis of prototype foamy virus plus-strand DNA.

Foamy virus (FV) is a nonpathogenic retrovirus that has the potential to serve as a gene therapy vector. In retroviral replication, the central polypurine tract (cPPT) is used as a primer to synthesize plus-strand DNA. The cPPT is subsequently degraded to produce a single-stranded gap in the double-stranded viral DNA molecule. In the prototype foamy virus (PFV), four cPPT-like motifs have been previously identified, in which there is a gap with uncertain terminals. In this study, we determined the length of the PFV gap varying from 144 to 731bp. The 3' terminus of the cleavage sites is located between 6272bp and 6274bp from the first base of PFV genome, while the 5' terminus is located within a 465bp range. The start and terminal nucleotides of the gap are located on either side of the fourth cPPT element. Deletion, mutation, and replacement of the fourth cPPT with the Human immunodeficiency virus 1 (HIV-1) cPPT resulted in a significant reduction in modified PFV virions, indicating that the fourth cPPT ought to be the primer that guides the synthesis of PFV plus-strand DNA. These results improve the theoretical basis for understanding FVs replication and will help construct new FV vectors with simple genome sequences containing only the necessary cis elements.

Evidence for the in vivo safety of insulated foamy viral vectors.

Retroviral vector mediated stem cell gene therapy is a promising approach for the treatment of hematopoietic disorders. However, genotoxic side effects from integrated vector proviruses are a significant concern for the use of retroviral vectors in the clinic. Insulated foamy viral (FV) vectors are potentially safer retroviral vectors for hematopoietic stem cell gene therapy. We evaluated two newly identified human insulators, A1 and A2 for use in FV vectors. These insulators had moderate insulating capacity and higher titers than previously developed insulated FV vectors. The A1 insulated FV vector was chosen for comparison with the previously described 650cHS4 insulated FV vector in human cord blood CD34+ repopulating cells in an immunodeficient mouse model. To maximize the effects of the insulators on the safety of FV vectors, FV vectors containing a highly genotoxic spleen focus forming virus (SFFV) promoter was used to elicit differences in genotoxicity. In vivo, the A1 insulated FV vector showed an approximate 50% reduction in clonal dominance compared to either the 650cHS4 insulated or control FV vectors, although the transduction efficiency of the A1 insulated vector was higher. This data suggests that the A1 insulated FV vector is promising for future pre-clinical and clinical studies.

Rapid Expansion of Gene-Marked Lymphocytes in X-SCID Dogs after AMD3100+G-CSF-Based Hematopoietic Stem/Progenitor Cell Mobilization and Intravenous Injection of a Common γ-Chain Expressing Foamy Viral Vector

In both humans and canines, X-linked severe combined immunodeficiency disease (XSCID) is caused by mutations in the interleukin-2 receptor gamma chain gene (IL2RG) which results in a lack of response to common gamma-chain (gammaC) dependent cytokines and abnormal development of T and B lymphocytes, and natural killer (NK) cells. Death from infections usually occurs before 1 year of age unless allogeneic hematopoietic cell transplantation (HCT) is performed. While HCT is successful if an HLA-matched sibling donor is available, transplants from mismatched and unrelated donors are associated with greater morbidity and overall survival can be as low as 50%. To circumvent these complications, several clinical trials are testing the possibility of utilizing blood and marrow stem cells from the patient for ex vivo gene therapy to treat X-SCID. Although these trials show promising results, they require expensive GMP cell manufacturing that are not accessible to many patients, and may also necessitate low level of conditioning to improve engraftment of gene-corrected cells. With these limitations in mind, we have explored in vivo gene therapy as a treatment for X-SCID. We previously showed that foamy virus vectors (FVs), exhibit a potentially more favorable integration profile compared to lenti- and gamma-retroviral vectors. In vivo delivery of a gammaC-FV in dogs resulted in immune reconstitution with gene-corrected T cells in dogs but the treated animals still developed infections and had low levels of immunoglobulin levels. We hypothesized that an increased transduction of hematopoietic stem/progenitor cells in vivo might result in more rapid and sustained immune reconstitution. Thus, in the current study, we used cG-CSF and AMD3100 to mobilize hematopoietic stem/progenitor cells into the peripheral blood prior to in vivo injection with a FV expressing the gammaC gene driven by a PGK promoter (PGK-gammaC-FV). We mobilized two X-SCID dogs at ~3 weeks of age with 5ug/kg of cG-CSF bi-daily from day -4 to -1 prior to FV injection, and with 4mg/kg of AMD3100 on the morning of the injection with 4x10e8 IU of PGK-gammaC-FV. Our mobilization protocol resulted in a 10-fold increase in CD34+ cells in the peripheral blood of mobilized X-SCID dogs as compared to a unmobilized normal littermate control (Figure 1 A). Lymphocyte recovery and gene marking in the mobilized animals was significantly improved as compared to animals that were previously injected with similar doses of either PGK-gammaC-FV or EF1a-gammaC-FV but without mobilization. As illustrated in Figure 1B-C, lymphocyte counts expanded to ~3000 cells/uL with ~75% gene marking in the mobilized animals treated with PGK-gammC-FV within 30 days, as compared to <1500 cells/uL with <5% gene marking in unmobilized dogs treated with EF1a-gammaC-FV and to <1000 cells/uL with <50% gene marking in unmobilized dogs treated with PGK-gammaC-FV at all time points post-therapy. The expansion of CD3+ T-cells at 6 weeks post injection for the mobilized dogs was about 2700 cells/uL, as compared to <380 cells/uL in the PGK-gammaC-FV and <210 cells/uL in the EF1a-gammaC-FV unmobilized dogs. Notably, in human clinical trials, CD3 T cell counts were <250 cells/uL following transplantation with autologous CD34+ cells modified with EF1a-gammaC-SIN gamma-retrovirus (Hacein-Bey-Abina, NEJM, 2014). In conclusion, mobilization with cG-CSF and AMD3100 prior to in vivo injection of PGK-gammaC-FV substantially improved the lymphocyte expansion and immune reconstitution in X-SCID dogs and resulted in a higher level of gene marking in myeloid cells (about 1%) at one-month post injection than seen in our previous studies in unmobilized dogs. These results suggest remarkable potential for an accessible and portable approach for treatment of human X-SCID clinical trials using combination of hematopoietic stem/progenitor cells mobilization and in vivo foamy viral vector delivery. [Display omitted] [Display omitted] [Display omitted] DisclosuresAdair:Rocket Pharmaceuticals: Consultancy, Equity Ownership. Scharenberg:bluebird bio: Consultancy, Equity Ownership, Research Funding; Alpine Immune Sciences: Consultancy. Kiem:Rocket Pharmaceuticals: Consultancy, Equity Ownership, Research Funding.

Retargeted Foamy Virus Vectors Integrate Less Frequently Near Proto-oncogenes.

Retroviral gene therapy offers immense potential to treat many genetic diseases and has already shown efficacy in clinical trials. However, retroviral vector mediated genotoxicity remains a major challenge and clinically relevant approaches to reduce integration near genes and proto-oncogenes are needed. Foamy retroviral vectors have several advantages over gammaretroviral and lentiviral vectors including a potentially safer integration profile and a lower propensity to activate nearby genes. Here we successfully retargeted foamy retroviral vectors away from genes and into satellite regions enriched for trimethylated histone H3 at lysine 9 by modifying the foamy virus Gag and Pol proteins. Retargeted foamy retroviral vectors integrated near genes and proto-oncogenes less often (p < 0.001) than controls. Importantly, retargeted foamy retroviral vectors can be produced at high, clinically relevant titers (>107 transducing units/ml), and unlike other reported retargeting approaches engineered target cells are not needed to achieve retargeting. As proof of principle for use in the clinic we show efficient transduction and retargeting in human cord blood CD34+ cells. The modified Gag and Pol helper constructs we describe will allow any investigator to simply use these helper plasmids during vector production to retarget therapeutic foamy retroviral vectors.

Rapid and Efficient Stable Gene Transfer to Mesenchymal Stromal Cells Using a Modified Foamy Virus Vector.

Mesenchymal stromal cells (MSCs) hold great promise for regenerative medicine. Stable ex vivo gene transfer to MSCs could improve the outcome and scope of MSC therapy, but current vectors require multiple rounds of transduction, involve genotoxic viral promoters and/or the addition of cytotoxic cationic polymers in order to achieve efficient transduction. We describe a self-inactivating foamy virus vector (FVV), incorporating the simian macaque foamy virus envelope and using physiological promoters, which efficiently transduces murine MSCs (mMSCs) in a single-round. High and sustained expression of the transgene, whether GFP or the lysosomal enzyme, arylsulphatase A (ARSA), was achieved. Defining MSC characteristics (surface marker expression and differentiation potential), as well as long-term engraftment and distribution in the murine brain following intracerebroventricular delivery, are unaffected by FVV transduction. Similarly, greater than 95% of human MSCs (hMSCs) were stably transduced using the same vector, facilitating human application. This work describes the best stable gene transfer vector available for mMSCs and hMSCs.

687. Development of a Safe and Effective Combinatorial Foamy Virus Vector for HIV Gene Therapy

The Berlin patient and successes in retroviral hematopoietic stem cell (HSC) gene therapy suggest that gene therapy may provide a functional cure for HIV. However, retroviral-HSC gene therapy has resulted in serious adverse side effects due to vector mediated genotoxicity, including leukemia. Foamy virus (FV) vectors have a promising integration profile and may be safer than retroviral vectors. FV vectors also can efficiently deliver anti-HIV transgenes that can reduce the titer of HIV-1 based lentiviral vectors. We report a novel combinatorial anti-HIV FV vector that uses a housekeeping elongation factor 1 alpha (EF1α) promoter but still potently blocks HIV infection. We first evaluated the relative potency of various previously described anti-HIV transgenes, including the C46 fusion inhibitor, the F12-Vif derivative Chim3, lens epithelium derived growth factor-integrase binding domain (LIBD) and TRIM5α-CyclophilinA fusion (TCypA) in a FV vector background. We found that C46 was the most potent anti-HIV transgene, followed by TCypA and LEDGF-IBD. Next, we hypothesized that using a less-genotoxic internal promoter to drive the transgenes would reduce vector-mediated genotoxicity. Therefore, a direct comparison was made between the efficacy of housekeeping gene promoters (EF1α and Ubiquitin C; UbC) and a highly genotoxic SFFV promoter in expressing the C46 transgene and subsequently blocking HIV replication. We observed that C46 EF1α had ~2 to 4 fold higher anti-HIV effect than C46 driven by either SFFV or UbC promoters, respectively. Based on these results, we designed a novel combinatorial FV vector expressing three anti-HIV transgenes: C46, TcypA and LIBD. The gene cassette was driven by an EF1α promoter and also has mCherry as a reporter gene (FV-E C46TLmC-W). This vector can be produced at high titer, 1.4 × 107 transducing units/ml which is critical for clinical translation. This novel combinatorial anti-HIV FV vector showed a higher potency in blocking HIV replication than C46 alone at a late time point, 21 days post HIV infection (Figure 1Figure 1). An in vitro competitive survival advantage assay indicated that cells transduced with our novel combinatorial anti-HIV FV vectors are highly resistant to HIV infection compared to cells transduced with FV expressing a control EGFP reporter gene alone (FV-EG-W) (Figure 2Figure 2). Further studies will be focused on the efficacy of our novel combinatorial anti-HIV FV vector in human CD34+ cells transplanted in a mouse xenotransplant in vivo model. Our goal is to develop a safe and potent combinatorial FV vector for clinical studies.View Large Image | Download PowerPoint SlideView Large Image | Download PowerPoint Slide

285. Foamy Viral Vector Expressing Human CD18 Results in High Levels of Transduction and Multilineage Engraftment with CD18+ LAD-1 Cells in NSG Mice

Compared to other classes of retroviral vectors used for HSPC gene therapy, foamy viral vectors (FVV) have distinct advantages, including their non-pathogenicity, a safer integration profile, and a high-efficiency transduction of quiescent cells. Proof-of principle of its therapeutic safety and efficacy in HSPCs was provided with the correction of canine Leukocyte Adhesion Deficiency (CLAD). Dogs with CLAD and individuals with LAD type 1 (LAD-1) suffer from recurrent and life-threatening infections caused by mutations in the β2 integrin CD18 subunit. In this study, G-CSF-mobilized CD34+ HSPCs were isolated from a 19 YO male with severe LAD-1 due to homozygous deletions in CD18. CD34+ cells were transduced for 16 hours at MOI of 0, 5, 10, and 20 with a FVV expressing a human codon optimized CD18 transgene. Flow cytometry of CD34+ cells cultured for 3 days after transduction demonstrated CD18+ cell surface expression in 40-45% of cells. Thirty NSG mice were transplanted with CD18-FVV-transduced human LAD-1 HSPCs (~1.2 × 105 cells/mouse), and human cell engraftment was measured in murine BM 5 months after transplantation using flow cytometry. Human CD45+ cells were detected in all mice (average ~1%). Mice transplanted with mock-transduced (MOI=0) LAD-1 CD34+ cells showed a 3.4-fold, 2-fold and 1.4-fold lower engraftment compared to mice injected with CD34+ cells transduced with FVV at MOI 5 (p 0.05), respectively, suggesting a selective homing/engraftment or survival/proliferative advantage of CD18+ cells. The inverse relationship between engraftment levels and MOI correlated with a gradual decrease in cell survival with increasing MOI, most likely due to toxicity from DMSO (required for FVV cryopreservation) during transduction; cell viabilities of 91%, 84%, 82% and 69% were obtained at MOI 0, 5, 10 and 20, respectively, indicating that further increase in MOI would lead to increasing toxicity. High-level, clinically relevant gene marking levels were obtained; the percentages of human cells expressing CD18 in the murine BM 5 months post-transplantation were 36.0 ± 3.9%, 33.9 ± 5.1%, and 44.5 ± 1.6% at MOI 5, 10 and 20, respectively. Quantitative PCR analysis of vector integrants within engrafted human cells indicated a single integration event occurred in the majority of long-term repopulating HSPCs at all MOI tested. Flow cytometry-based lineage analysis of bone marrow from mice transplanted with FVV-transduced LAD-1 CD34+ cells revealed human CD18+ cells in all lineages, with a predominance in the CD13+ myeloid compartment (88.3 ± 4.5%) compared to other lineages, including CD20+ lymphoid (9.1 ± 3.9%), CD235a+ erythroid (0.2 ± 0.1%) and CD41+ megakaryocytic (0.6 ± 0.2%) lineages. Interestingly, human myeloid engraftment was superior in recipient mice engrafted with human CD18+ cells (81.5 ± 4.3%) compared to animals transplanted with non-transduced (CD18-) LAD-1 cells (65.3 ± 11.3%). Integration site analysis of engrafted human cells is ongoing. Thus, FVV-mediated transduction of human LAD-1 CD34+ cells leads to clinically significant levels of CD18 expression, supporting the use of this CD18-expressing FVV in a human clinical trial.

284. Long-Term Therapeutic Immune Reconstitution in XSCID Canine Model via In Vivo Foamy Virus Delivery of Common Gamma Chain

X-linked combined immunodeficiency disease (XSCID) is caused by mutation in the common gamma chain, γC (interleukin-2 receptor subunit gamma, IL2RG) in both humans and canines. It is characterized by the inability of T-cell development leading to absence of T-cells in peripheral blood, lack of T-cell mediated immune response, low IgA and IgG levels, and early infant mortality. In the 1990s, human XSCID clinical trials utilizing gamma-retroviral vectors to deliver the IL2RG gene caused leukemia in 5 out of 20 patients due to vector integration in or near proto-oncogenes. Recent studies showed Foamy virus based vectors as an excellent alternative for in vivo gene-therapy because it is non-pathogenic in humans while exhibiting increased serum stability and favorable integration pattern. Previously, we have demonstrated CD3+ T-cell reconstitution in the canine model via intravenous injection of foamy virus expressing human elongation factor-1 alpha promoter (Ef1α)-yC. Unfortunately, the treated animals contained a low number of gene corrected progenitors at a sub-therapeutic level. Here, we achieved long-term therapeutic immune-reconstitution by intravenous delivery of a human phosphoglycerate kinase promoter (Pgk)-mediated γC foamy viral vector into XSCID neonatal canines. Long-term (2 years) post-injection follow-up demonstrated therapeutic levels of CD3+ T-cell expansion. Within the T-cell population, gene correction with Pgk-γC stabilized at ~80%. We validated T-cell functionality by using spectratyping analysis, which exhibited a diverse repertoire of receptor gene rearrangement. Retroviral integration site analysis (RIS) indicated polyclonal contribution to the reconstituted T-cells. Immunoglobulin ELISA assays showed that IgA and IgG levels in peripheral blood are comparable to normal healthy controls. We immunized the gene-corrected canine recipients with bacteriophage ϕx174 and confirmed production of specific IgG antibodies, showing the ability for isotype switching in B-lymphocytes. Currently, the gene-corrected canines exhibit comparable health and physical attributes to normal controls. Furthermore, semen from the gene-corrected male canine was used via artificial insemination to produce a litter of viable offsprings. In summary, our data demonstrate that Pgk-γC foamy viral vector delivered long-term therapeutic gene correction in a large-animal model for XSCID gene therapy. Most importantly, these results indicate that in vivo Pgk-γC foamy vector administration is a viable option for long-term immune reconstitution in future XSCID human clinical trials.

683. Foamy Virus Gene Therapy Significantly Restores Lymphocyte Development and Function in SCID-X1 Mice

X-linked severe-combined immune deficiency (SCID-X1) results from inactivating mutations in the gene encoding the common gamma chain (γc), a cytokine receptor subunit required for lymphoid development and function. In humans, SCID-X1 is characterized by the absence of T cells and natural killer cells, non-functional B cells, and is fatal within the first year of life if left untreated. Although HLA matched allogenic stem cell transplants yield survival rates exceeding 90%, such donors are often unavailable. Thus, gene replacement therapy offers a promising alternative treatment for patients lacking suitable donors. Clinical trials using gamma-retroviral vectors demonstrated efficacy; however, adverse events highlighted the need for improved safety. While adverse events have been eliminated using SIN-gamma-retroviral vectors, we hypothesized that foamy viruses (FV) that lack native pathogenicity and boast an integration site profile much less focused on either active genes or promoter regions than lentiviruses or gamma-retroviruses might provide an improved and safer therapeutic platform. We determined whether a candidate clinical FV vector containing the human phosphoglycerate kinase 1 (PGK) promoter driving human γc expression could safely and effectively rescue lymphocyte development and function in SCID-X1 mice. Our promoter choice was based upon ongoing studies using FV vectors in parallel in a canine model of SCID-X1 where the PGK promoter outperforms the EF1α promoter currently in use in SIN-retro and lentiviral-based SCID-X1 clinical trials. We report here the combined results of 66 primary and 130 secondary transplant mice that demonstrate significant and sustained immune reconstitution. SCID-X1 mice were transplanted with 2×10^6 FV- or LV-transduced, or WT or SCID-X1 lineage negative HSCs. Animals were sacrificed at ~25 weeks post-transplant; bone marrow, spleen and thymus were collected for analysis and secondary recipients were also established. Primary FV gene therapy recipients showed significantly greater B and T lymphoid numbers compared to SCID-X1 controls, with output viral copy numbers of ~1-4 in all tissues. Splenocytes from primary treated animals proliferated in response to CD3/CD28 and also demonstrated γc dependent intracellular pSTAT signaling in response to IL-7 and IL-21. FV and LV gene therapy-treated mice displayed comparable lymphocyte reconstitution and output copy number. Secondary recipients revealed sustained partial rescue of lymphoid compartments and viral marking, indicating the transduction of long-term repopulating HSCs. RIS analysis demonstrated polyclonal marking in splenic lymphoid populations with 3508 unique FV and 2441 unique LV integrations detected (3 experiments/3 animals per experiment). Further, analysis of individual mice from a primary transplant experiment demonstrated polyclonal marking with 588-1060 and 651-895 unique integration sites in FV- and LV-treated animals, respectively. Analysis to determine detailed integration site profile and potential proximity to protooncogenes is ongoing. Together, these data suggest FV gene therapy may provide an effective alternative treatment option for SCID-X1.

6. Retargeted Foamy Virus Vectors Integrate Less Frequently Near Proto-Oncogenes

Hematopoietic stem cell gene therapy offers immense potential to treat many genetic diseases and has already shown efficacy in clinical trials. However, retroviral vector mediated gene dysregulation, known as genotoxicity, remains a major challenge and clinically relevant approaches to reduce integration near genes and proto-oncogenes are needed. The frequency at which a retroviral vector integrates near proto-oncogenes is a major factor in determining the safety of the vector. Here we describe a clinically relevant method to retarget foamy retroviral vector (FV) integration away from proto-oncogenes using modified Gag and Pol helper constructs. The chromatin binding site (CBS) of FV Gag was altered using a previously described triple alanine substitution mutation of RTY (Gag-RTY) shown to drastically reduce chromatin binding of the FV pre-integration complex. The modified FV Pol construct expresses chromobox protein homolog 1 fused to the C-terminus of integrase (CBX1-IN). CBX1 interacts with tri-methylated lysine 9 of histone H3 (H3K9me3) and is associated with gene sparse regions in the human genome. We hypothesized a modified FV expressing Gag-RTY and CBX1-IN would have an altered integration site profile and be retargeted to H3K9me3 regions and away from genes and proto-oncogenes. FV integration sites from modified and control FVs were compared in normal human fibroblasts and in CD34+ human cord blood cells. We observed retargeting of FV integration into H3K9me3 regions with the modified FV (Figure 1Figure 1). Importantly, retargeting FV integration significantly reduces the number of integration sites near proto-oncogene transcription start sites (Table 1Table 1). Retargeted FVs can be produced at clinically relevant titers (> 107 transducing units / ml), resulting in efficient transgene expression (75 % of control in CD34+ cells) with no evidence of vector silencing. Another published method to retarget lentiviral vector integration required using a modified cell line, which is not practical for clinical use. Our approach is cell line independent and the modified Gag and Pol helper constructs will allow an investigator to simply use these modified helper plasmids during vector production to retarget any therapeutic FV in any target cell. Retargeted FVs integrate less frequently near proto-oncogenes than gammaretroviral vectors and unmodified FVs, and may be the safest current option for hematopoietic stem cell gene therapy.Table 1Retargeted FV integrates further away from genes and proto-oncogenes than control FV.Percent of FV integration sites in human CD34*** cellsVectorTotal sitesIn RefSeq genes< 10 kb from TSS< 50 kb from proto-oncogene TSSControl FV421740.924.54.7Retargeted FV153430.6***12.5***2.2****statistically significant at p < 0.001 compared to control vector. FV, foamy retroviral vector; TSS, transcription start site.View Large Image | Download PowerPoint Slide

Prospects for Foamy Viral Vector Anti-HIV Gene Therapy.

Stem cell gene therapy approaches for Human Immunodeficiency Virus (HIV) infection have been explored in clinical trials and several anti-HIV genes delivered by retroviral vectors were shown to block HIV replication. However, gammaretroviral and lentiviral based retroviral vectors have limitations for delivery of anti-HIV genes into hematopoietic stem cells (HSC). Foamy virus vectors have several advantages including efficient delivery of transgenes into HSC in large animal models, and a potentially safer integration profile. This review focuses on novel anti-HIV transgenes and the potential of foamy virus vectors for HSC gene therapy of HIV.

Insulated Foamy Viral Vectors.

Retroviral vector-mediated gene therapy is promising, but genotoxicity has limited its use in the clinic. Genotoxicity is highly dependent on the retroviral vector used, and foamy viral (FV) vectors appear relatively safe. However, internal promoters may still potentially activate nearby genes. We developed insulated FV vectors, using four previously described insulators: a version of the well-studied chicken hypersensitivity site 4 insulator (650cHS4), two synthetic CCCTC-binding factor (CTCF)-based insulators, and an insulator based on the CCAAT box-binding transcription factor/nuclear factor I (7xCTF/NF1). We directly compared these insulators for enhancer-blocking activity, effect on FV vector titer, and fidelity of transfer to both proviral long terminal repeats. The synthetic CTCF-based insulators had the strongest insulating activity, but reduced titers significantly. The 7xCTF/NF1 insulator did not reduce titers but had weak insulating activity. The 650cHS4-insulated FV vector was identified as the overall most promising vector. Uninsulated and 650cHS4-insulated FV vectors were both significantly less genotoxic than gammaretroviral vectors. Integration sites were evaluated in cord blood CD34(+) cells and the 650cHS4-insulated FV vector had fewer hotspots compared with an uninsulated FV vector. These data suggest that insulated FV vectors are promising for hematopoietic stem cell gene therapy.

Production and purification of high-titer foamy virus vector for the treatment of leukocyte adhesion deficiency

Compared to other integrating viral vectors, foamy virus (FV) vectors have distinct advantages as a gene transfer tool, including their nonpathogenicity, the ability to carry larger transgene cassettes, and increased stability of virus particles due to DNA genome formation within the virions. Proof of principle of its therapeutic utility was provided with the correction of canine leukocyte adhesion deficiency using autologous CD34+ cells transduced with FV vector carrying the canine CD18 gene, demonstrating its long-term safety and efficacy. However, infectious titers of FV-human(h)CD18 were low and not suitable for manufacturing of clinical-grade product. Herein, we developed a scalable production and purification process that resulted in 60-fold higher FV-hCD18 titers from ~1.7 × 104 to 1.0 × 106 infectious units (IU)/ml. Process development improvements included use of polyethylenimine-based transfection, use of a codon-optimized gag, heparin affinity chromatography, tangential flow filtration, and ultracentrifugation, which reproducibly resulted in 5,000-fold concentrated and purified virus, an overall yield of 19 ± 3%, and final titers of 1–2 × 109 IU/ml. Highly concentrated vector allowed reduction of final dimethyl sulfoxide (DMSO) concentration, thereby avoiding DMSO-induced toxicity to CD34+ cells while maintaining high transduction efficiencies. This process development results in clinically relevant, high titer FV which can be scaled up for clinical grade production.

Pgk-Mediated Expression of Common Gamma Chain Is More Effective Than EF1a for Therapeutic Immune Reconstitution of X-SCID Dogs after In Vivo Gene Therapy with Foamy Virus Vector

In vivo gene therapy has several benefits over ex vivo hematopoietic stem cell gene therapy, including the correction of progenitor cells in their native environments, the portability of the treatment to the patient, and the ability to administer serial doses of therapeutic vector. Foamy viruses (FV) are ideal vectors for in vivo gene therapy because they are non-pathogenic in humans, they exhibit increased serum stability and they integrate into host genomes with a favorable integration pattern. We recently demonstrated that intravenous injection of a FV vector expressing the human common gamma chain (γC) under the constitutively active short elongation factor 1α (EF1α) promoter is sufficient to drive development of functional CD3+ lymphocytes in canine X-SCID (Burtner CR et al. Intravenous injection of a foamy virus vector to correct canine SCID-X1. Blood. 2014;123(23):3578-84). However, retroviral integration site analysis in that study indicated that T cell reconstitution occurred through the correction of a limited number of progenitors, possibly due to sub-therapeutic expression levels from the EF1α promoter. To address this issue, we are evaluating multiple parameters of vector design for in vivo gene therapy that include different promoters and different fluorophores.We performed a head-to-head comparison of two promoters, our previously used EF1α promoter and the human phosphoglycerate kinase (PGK) promoter, by simultaneously injecting three X-SCID pups with equal titers of two therapeutic, human γC-encoding FV vectors. These vectors expressed the fluorophores GFP or mCherry to allow for tracking of transduced cells. Each dog received between 3 and 4 x 108 infectious units of each FV vector. In all treated dogs, lymphocyte marking in the PGK arm reached 50% between day 60 and day 110 post-injection and continued to expand over time, while the EF1α arm peaked at day 42 and never expanded above 10% (Fig 1A). Interestingly, the expansion of T lymphocytes from gene-modified cells expressing γC under the PGK promoter appeared to preclude further development of T cells by the EF1α arm, suggesting competition within the expanding T cell niche. The development of total CD3+ T cells achieved therapeutic levels (1000 cells/μL of blood) in all three dogs between day 70 and day 130 post-treatment (Fig 1B). We further validated the functionality of these cells by showing that they express a diverse T cell receptor repertoire using spectratyping analysis. In addition, peripheral blood mononuclear cells from the treated animals could be activated in vitro by exposure to the mitogen Phytohemagglutinin A at a level comparable to normal cells. Immunization of the treated dogs with bacteriophage ΦX174 showed production of specific IgG antibodies, suggesting the ability of B lymphocytes to undergo isotype switching. Finally, retroviral integration site analysis revealed polyclonal contribution to the reconstituting T cells. In summary, our data suggest that the PGK promoter results in a robust and sustained correction of progenitor T cells in a relevant large-animal disease model for primary immunodeficiency. The outcome in dogs was substantially improved compared to our previous study using EF1α, where robust lymphocyte marking was achieved in only 2 of 5 dogs, and where clonal dominance was observed. Ongoing work will determine whether the superior performance of the PGK vector is due to higher γC expression in PGK vs. EF1α corrected cells. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Modified Genomic Sequencing PCR Using the MiSeq Platform to Identify Retroviral Integration Sites.

High-throughput mapping of retroviral vector integration sites (RIS) has become an invaluable tool to evaluate novel gene therapy vectors and to track clonal contribution in preclinical and clinical studies. Beard et al. (Methods Mol Biol 2014;1185:321-344) described an improved protocol developed for efficient capture, sequencing, and analysis of RIS that preserves gene-modified clonal contribution information. Here we describe adaptations to the previously published modified genomic sequencing PCR (MGS-PCR) protocol using the Illumina MiSeq paired-end sequencing platform. Lentiviral, gammaretroviral, and foamy virus vector integrations were analyzed. MGS-PCR using the MiSeq platform allows for the use of merged paired-end reads, which allows for efficient localization of RIS to published genomes.

533. A Clinically Relevant Approach for Retargeting Foamy Viral Vectors Into Heterochromatin

Retroviral (RV) vector mediated gene therapy offers immense potential for permanently treating a broad spectrum of genetic conditions and has shown efficacy in clinical trials. However, vector proviruses can dysregulate nearby host genes, referred to as genotoxicity, which can lead to oncogenic transformation. Studies on the integration profiles and the mechanisms responsible for targeting integration have been carried out, resulting in a better understanding of the safety of RV vectors. Integration is influenced by the pre-integration complex (PIC) and its interactions with host proteins. Retargeting RV vectors to safe locations in the genome is an important step in reducing potential genotoxic effects. Although the RV PIC and its interactions are poorly defined, studies have shown that it is possible to retarget RV vector integration. It has been demonstrated that lentiviral vector integration can be retargeted using artificial tethering factors. A modified cell line was produced that expressed lens epithelium–derived growth factor (LEDGF) fused to chromobox protein homolog 1 (CBX1) in place of the wild type LEDGF. The LEDGF-CBX1 fusion protein targeted lentiviral vector integration into methylated regions in the human genome. However, this strategy requires modifying a cell to express a fusion protein and is therefore not practical for clinical use. Other studies have also shown it is possible to retarget RV vector integration, but these studies resulted in reduced transgene expression or impaired vector titers. A clinically relevant method for retargeting integration to safer genomic locations is needed.Here we demonstrate an approach to retarget foamy viral (FV) vector integration into safer heterochromatic regions that does not require a modified cell line. Foamy viruses have a broad tropism, a large packaging capacity, and efficiently transduce hematopoietic stem cells, making them well suited for gene therapy. We describe a FV vector with a modified Pol which expresses an integrase-CBX1 (IN-CBX1) fusion protein and a modified Gag which expresses a mutated chromatin binding site (CBS) domain. CBX1 binds to trimethylated histone H3K9 (H3K9me3), so we hypothesized the IN-CBX1 fusion protein would target FV vector integration into heterochromatin. The integration sites of the modified FV vector (n = 1494) and the control FV vector were compared in normal human fibroblast cells. We analyzed the retargeting ability by comparing the integration sites to normal human fibroblast H3K9me3 ChIP-Seq data. Significant retargeting to H3K9me3 regions was observed with the modified FV vector (P 107 transducing units/ml). This study demonstrates that FV vectors can be efficiently retargeted using foamy integrase fusion proteins. Since this approach does not require engineering the target cells, it is promising for use in the clinic, including hematopoietic stem cell gene therapy.

461. Scale-Up and Manufacturing of High-Titer Foamy Virus Vector Containing Human CD18 for the Treatment of Leukocyte Adhesion Deficiency

Compared to other integrating viral vectors, foamy virus (FV) vectors have several distinct advantages as a gene transfer tool, including: the ability to carry larger expression cassettes, the increased stability due to a DNA genome formed in developing vector particles, and the random integration pattern without preference for promoter regions or active genes as is the case with gamma-retroviral and lentiviral vectors. In addition, the FV envelope has tropism for most cell types and is not associated with disease in humans. Combined, these properties make FV vectors the ideal candidate for gene therapy application. Proof of principle was provided by Bauer et al. (Nat. Med. 2008) showing cure of canine Leukocyte Adhesion Deficiency (LAD) using autologous CD34+ cells transduced with FV vector carrying the CD18 gene, without short or long-term adverse effects. Here we demonstrate the optimization of large scale manufacturing of FV vector carrying the human CD18 gene for the treatment of human LAD. As compared to the methods used in the canine LAD study, a 60-fold increase in FV-CD18 titer was observed using a combination of polyethylenimine (PEI) transfection and use of a codon-optimized gag, from approximately 1.70E+04 to 1.00E+06 Infectious Units/mL (IU/mL) on Raw 264.7 cells. An evaluation of purification strategies showed efficient vector purification and concentration of FV vector through a combination of heparin-affinity chromatography on the AKTA ready, a disposable fluid path chromatography unit, tangential flow filtration and ultracentrifugation, with an overall 5000-fold concentration and 20-30% recovery. This approach was compatible with large scale manufacturing in compliance with Good Manufacturing Practices (GMP). Although 5% DMSO is needed for optimal recovery of infectious FV vector from -80°C storage, highly concentrated vector can be diluted to reduce the DMSO concentration and toxicity to CD34+ cells, while maintaining effective transduction rates of up to 50%. This process is currently being finalized for clinical manufacturing in support of a Phase I trial for the treatment of LAD.Note: MN and DL equally contributed to this study.

532. Foamy Viral Vector Integration Sites in SCID-Repopulating Cells After MGMTP140K-Mediated In Vivo Selection

Foamy virus (FV) vectors are promising for hematopoietic stem cell (HSC) gene therapy but preclinical data on the clonal composition of FV vector transduced human repopulating cells is needed. Human CD34+ human cord blood cells were transduced with an FV vector encoding a methylguanine methyltransferase (MGMT) P140K transgene, transplanted into immunodeficient NOD/SCID IL2Rgnull (NSG) mice, and selected in vivo for gene-modified cells. The retroviral insertion site (RIS) profile of repopulating clones was examined using modified genomic sequencing PCR (MGS-PCR). We observed polyclonal repopulation with no evidence of clonal dominance even with the use of a strong internal spleen focus forming virus (SFFV) promoter known to be genotoxic. However we did observe that highly captured sites were found more often near proto-oncogenes than less frequently captured sites (Figure 1Figure 1). Our data supports the use of FV vectors with MGMTP140K for HSC gene therapy, but also suggests additional safety features should be developed and evaluated.Figure 1(a) Proximity of RIS to TSS of proto-oncogenes in Network of Cancer Genes 4.0 (NCG 4.0) cancer gene list (n = 2048). (b) Proportion of RIS within NCG 4.0 proto-oncogene transcripts or within 50 kb of a proto-oncogene TSS. In vivo low and in vivo high represent the lowest and highest thirds of RIS ranked by recovery frequency. Abbreviations: ns, not significant; RIS, retroviral insertion site; TSS, transcription start site.View Large Image | Download PowerPoint Slide

441. Direct Comparison of EF1α and PGK Promoters Reveals Superior Performance of the PGK Promoter for Expression of the Common Gamma Chain in a Canine Model of In Vivo Foamy Virus Gene Therapy for Severe Combined Immunodeficiency

Foamy viruses (FV) are ideal vectors for in vivo gene therapy because FV infection is non-pathogenic in people, FV are more resistant to serum inactivation than lentiviruses packaged with the vesicular stomatitis virus glycoprotein (VSV-G), and FV exhibit favorable proviral integration patterns compared to gammaretroviruses. In vivo gene therapy with a FV vector expressing the human common gamma chain (γC) under the short EF1α promoter results in a functional immune reconstitution in X-SCID dogs.

Tenth International Foamy Virus Conference 2014--achievements and perspectives.

For the past two decades, scientists from around the world, working on different aspects of foamy virus (FV) research, have gathered in different research institutions almost every two years to present their recent results in formal talks, to discuss their ongoing studies informally, and to initiate fruitful collaborations. In this report we review the 2014 anniversary conference to share the meeting summary with the virology community and hope to arouse interest by other researchers to join this exciting field. The topics covered included epidemiology, virus molecular biology, and immunology of FV infection in non-human primates, cattle, and humans with zoonotic FV infections, as well as recent findings on endogenous FVs. Several topics focused on virus replication and interactions between viral and cellular proteins. Use of FV in biomedical research was highlighted with presentations on using FV vectors for gene therapy and FV proteins as scaffold for vaccine antigen presentation. On behalf of the FV community, this report also includes a short tribute to commemorate Prof. Axel Rethwilm, one of the leading experts in the field of retrovirology and foamy viruses, who passed away 29 July 2014.