Strong viral enhancers in gammaretrovirus vectors have caused cellular proto-oncogene activation and leukemia, necessitating the use of cellular promoters in "enhancerless" self-inactivating integrating vectors. However, cellular promoters result in relatively low transgene expression, often leading to inadequate disease phenotype correction. Vectors derived from foamy virus, a nonpathogenic retrovirus, show higher preference for nongenic integrations than gammaretroviruses/lentiviruses and preferential integration near transcriptional start sites, like gammaretroviruses. We found that strong viral enhancers/promoters placed in foamy viral vectors caused extremely low immortalization of primary mouse hematopoietic stem/progenitor cells compared to analogous gammaretrovirus/lentivirus vectors carrying the same enhancers/promoters, an effect not explained solely by foamy virus' modest insertional site preference for nongenic regions compared to gammaretrovirus/lentivirus vectors. Using CRISPR/Cas9-mediated targeted insertion of analogous proviral sequences into the gene and then measuring expression, we demonstrate a sequence-specific effect of foamy virus, independent of insertional bias, contributing to reduced genotoxicity. We show that this effect is mediated by a 36-bp insulator located in the foamy virus long terminal repeat (LTR) that has high-affinity binding to the CCCTC-binding factor. Using our LMO2 activation assay, expression was significantly increased when this insulator was removed from foamy virus and significantly reduced when the insulator was inserted into the lentiviral LTR. Our results elucidate a mechanism underlying the low genotoxicity of foamy virus, identify a novel insulator, and support the use of foamy virus as a vector for gene therapy, especially when strong enhancers/promoters are required. Understanding the genotoxic potential of viral vectors is important in designing safe and efficacious vectors for gene therapy. Self-inactivating vectors devoid of viral long-terminal-repeat enhancers have proven safe; however, transgene expression from cellular promoters is often insufficient for full phenotypic correction. Foamy virus is an attractive vector for gene therapy. We found foamy virus vectors to be remarkably less genotoxic, well below what was expected from their integration site preferences. We demonstrate that the foamy virus long terminal repeats contain an insulator element that binds CCCTC-binding factor and reduces its insertional genotoxicity. Our study elucidates a mechanism behind the low genotoxic potential of foamy virus, identifies a unique insulator, and supports the use of foamy virus as a vector for gene therapy.

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.

Baculoviruses are commonly used for recombinant protein and vaccine production. Baculoviruses are nonpathogenic to vertebrates, have a large packaging capacity, display broad host and cell type tropism, infect both dividing and nondividing cells, and do not elicit strong immune or allergic responses in vivo. Hence, their use as gene delivery vehicles has become increasingly popular in recent years. Moreover, baculovirus vectors carrying mammalian regulatory elements can efficiently transduce and express transgenes in mammalian cells. Based on the finding that heparan sulfate, which is structurally similar to heparin, is an attachment receptor for baculovirus, we developed a novel scalable baculovirus purification method using heparin-affinity chromatography. Baculovirus supernatants were loaded onto a POROS heparin column, washed to remove unbound materials, and eluted with 1.5 mol/l NaCl, which yielded a recovery of purified baculovirus of 85%. After ultracentrifugation, baculovirus titers increased from 200- to 700-fold with overall yields of 26–29%. We further show that baculovirus particles were infectious, normal in morphology and size, despite high-salt elution and shear forces used during purification and concentration. Our chromatography-based purification method is scalable and, together with ultracentrifugation and/or tangential flow filtration, will be suitable for large-scale manufacturing of baculovirus stocks for protein and vaccine production and in gene therapy applications.

sequencing (NGS) technology. However, success of this approach depends on low prevalence of circulating antibodies against common AAV serotypes such as AAV2 and AAV9 because these serotypes serve as internal reference controls in this system. Therefore, it is essential to investigate the prevalence of neutralizing antibodies against various serotypes in cats for applying the AAV Barcode-Seq to preclinical studies and ultimately for successful translation of AAV vector-mediated gene therapy approaches into the veterinary clinic. Here we report the results of the initial screening of 30 cat serum samples obtained from the Liberty Research Inc. cat colony for the presence of antibodies against a total of 11 different AAV serotypes (AAV1 through 11). Such a study is imperative because a vaccine against feline panleukopenia virus (FPV), a feline parvovirus, is widely used to immunize cats and all the cats to be used for our study will have received that vaccine. In the study, serum samples were incubated in ELISA plates coated with serotype-specific particles followed by addition of an HRP-conjugated anti-cat IgG antibody. Anti-FPV antibody titers were determined by a hemagglutination inhibition test (Cornell University, Animal Health Diagnostic Center). The results showed that the majority of the 30 cats did not harbor any detectable antibodies against AAV1,

Strong viral enhancers in γ-retrovirus vectors (GV) have caused cellular proto-oncogene activation and leukemia in gene therapy trials, necessitating the use of cellular promoters in enhancer-less integrating vectors. However, data is now emerging that inadequate transgene expression from cellular promoters may limit successful correction. Vectors derived from foamy virus (FV), a nonpathogenic retrovirus, have a higher preference for non-genic integrations than GV/lentiviral vectors (LV), and may be less genotoxic. We constructed GV, LV and FV driven either by the spleen focus forming virus (SFFV) or the murine stem cell virus (MSCV) enhancer/promoters, all driving eGFP expression, and compared their relative genotoxicity using an in vitro immortalization assay on primary hematopoietic stem/progenitor cells (HSPC). In this assay, integration near a protooncogene/gene promoting cell proliferation results in quantifiable HSPC immortalization. Strong viral enhancer/promoters from SFFV or MSCV in FV caused a remarkably low immortalization of HSPC compared to analogous LV or GV: compared to the immortalization frequency of HSPC with the SFFV-GV in this assay, SFFV-LV and MSCV-LV had 12- and 14-fold lower immortalization frequency, while the SFFV-FV and MSCV-FV showed a 155- and 414-fold lower immortalization frequency, respectively. Immortalized clones had multiple (3-10) integrated copies. Integration site analysis of FV immortalized clones revealed a majority of integrants in non-gene regions; those in genic regions targeted cell proliferation or proto-oncogenes, as previously reported. FV has been previously reported to have 2-fold higher insertions in non-genic regions and higher, but nearly half the propensity to target promoters compared to GV. However, this remarkably reduced genotoxicity with FV was not explained by the integration pattern. We therefore hypothesized that FV backbone may contain sequences that have an enhancer blocking/insulator effect. Studies on chromatin insulators have shown that enhancer-blocking property of insulators is mediated via binding of CTCF to its consensus sequences within the insulator. Indeed, an in silico analysis for CCCTC-binding factor (CTCF) binding sites in the vector backbone sequences showed more predicted CTCF binding sites in the FV than in GV or LV (26, 8, and 6, respectively). To functionally validate the enhancer-blocking effect of the FV backbone and ensure that only effects of the vector backbone would be measured, without the confounding influence of integration site or the enhancer/promoter/transgene, we inserted SFFV-GV, SFFV-LV and SFFV-FV into a clinically relevant proto-oncogene, LMO2, using CRISPR/Cas9, and assessed LMO2 expression. LMO2 upregulation has previously resulted in leukemias in the X-linked severe combined immune-deficiency and Wiscott-Aldrich syndrome (WAS) GV-mediated gene transfer trials; notably SFFV-GV was used in the WAS trial and caused leukemias in 8 of 10 patients from insertional oncogenesis. HeLa cells were transfected with the proviral donor plasmids and the guide-RNA/spCas9 plasmids and GFP+ cells sorted and cloned. Nearly all clones derived had one intact LMO2 allele, while the other alleles had GV/LV/FV proviral insertions. We next assessed LMO2 mRNA and protein expression in these clones. We found a minimal increase in LMO2 mRNA expression with SFFV-FV, in sharp contrast to significantly increased LMO2 expression with SFFV-GV and SFFV-LV by qRT-PCR (Figure 1A). Overall, the SFFV enhancer in GV demonstrated the greatest fold-increase in LMO2 expression (median increase of 280+/-23-fold over unmodified HeLa cells), followed by the SFFV enhancer in LV (median 200+/-27-fold increase). However, the same SFFV enhancer in FV only showed a 45+/-7-fold median increase in expression. Western blot analysis for LMO2 protein expression in three clones for each vector showed no detectable LMO2 expression in SFFV-FV clones, which was similar to baseline in mock (non-targeted) HeLa cells (Figure 1B). However, significantly higher LMO2 protein was detectable in GV and LV clones. Hence, the remarkably low genotoxic potential of FV, even those carrying strong viral enhancers appears to be, in large part, from an insulator property of FV sequences, making FV ideal for situations where high transgene expression, necessitating strong enhancers is required for a therapeutic effect. Disclosures No relevant conflicts of interest to declare.