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Mucopolysaccharidosis type I (MPS-I) is a severe genetic disease caused by a deficiency of the alpha-L-iduronidase (IDUA) enzyme. Ex vivo hematopoietic stem cell (HSC) gene therapy is a promising therapeutic approach for MPS-I, as demonstrated by preclinical studies performed in naive MPS-I mice. However, after enzyme replacement therapy (ERT), several MPS-I patients develop anti-IDUA immunity that may jeopardize ex vivo gene therapy efficacy. Here we treat MPS-I mice with an artificial immunization protocol to mimic the ERT effect in patients, and we demonstrate that IDUA-corrected HSC engraftment is impaired in pre-immunized animals by IDUA-specific CD8+ T cells spared by pre-transplant irradiation. Conversely, humoral anti-IDUA immunity does not impact on IDUA-corrected HSC engraftment. The inclusion of lympho-depleting agents in pre-transplant conditioning of pre-immunized hosts allowes rescue of IDUA-corrected HSC engraftment, which is proportional to CD8+ T cell eradication. Overall, these data demonstrate the relevance of pre-existing anti-transgene T cell immunity on ex vivo HSC gene therapy, and they suggest the application of tailored immune-depleting treatments, as well as a deeper immunological characterization of patients, to safeguard the therapeutic effects of ex vivo HSC gene therapy in immunocompetent hosts., MPS-I patients receiving enzyme replacement therapy develop an anti-IDUA immune response that may affect ex vivo gene therapy. Squeri et al. show, in the MPS-I murine model, that pre-existing IDUA-specific CD8+ T cell response impairs LV-transduced HSC engraftment and that the efficacy of ex vivo gene therapy is rescued by lympho-depleting drugs.

Improving hematopoietic stem and progenitor cell (HSPC) permissiveness to HIV-derived lentiviral vectors (LVs) remains a challenge for the field of gene therapy as high vector doses and prolonged ex vivo culture are still required to achieve clinically relevant transduction levels. We report here that Cyclosporin A (CsA) and Rapamycin (Rapa) significantly improve LV gene transfer in human and murine HSPC. Both compounds increased LV but not gammaretroviral transduction and acted independently of calcineurin and autophagy. Improved gene transfer was achieved across all CD34(+) subpopulations, including in long-term SCID repopulating cells. Effects of CsA were specific of HSPC and opposite to its known impact on HIV replication. Mutating the Cyclophilin A binding pocket of the viral capsid (CA) further improved transduction in combination with CsA. Tracking of the LV genome fate revealed that CsA relieves a CA-dependent early block and increases integration, while Rapa acts early in LV infection independently of the viral CA. In agreement, only Rapa was able to improve transduction by an integrase-defective LV harboring wild-type CA. Overall, our findings pave the way for more efficient and sustainable LV gene therapy in human HSPCs and shed light on the multiple innate barriers specifically hampering LV transduction in these cells.

The high transduction efficiency of lentiviral vectors in a wide variety of cells makes them an ideal tool for forward genetics screenings addressing issues of cancer research. Although molecular targeted therapies have provided significant advances in tumor treatment, relapses often occur by the expansion of tumor cell clones carrying mutations that confer resistance. Identification of the culprits of anticancer drug resistance is fundamental for the achievement of long-term response. Here, we developed a new lentiviral vector-based insertional mutagenesis screening to identify genes that confer resistance to clinically relevant targeted anticancer therapies. By applying this genome-wide approach to cell lines representing two subtypes of HER2(+) breast cancer, we identified 62 candidate lapatinib resistance genes. We validated the top ranking genes, i.e., PIK3CA and PIK3CB, by showing that their forced expression confers resistance to lapatinib in vitro and found that their mutation/overexpression is associated to poor prognosis in human breast tumors. Then, we successfully applied this approach to the identification of erlotinib resistance genes in pancreatic cancer, thus showing the intrinsic versatility of the approach. The acquired knowledge can help identifying combinations of targeted drugs to overcome the occurrence of resistance, thus opening new horizons for more effective treatment of tumors.

Lentiviral vectors with self-inactivating (SIN) long terminal repeats (LTRs) are promising for safe and sustained transgene expression in dividing as well as quiescent cells. As genome organization and transcription substantially differs between actively dividing and postmitotic cells in vivo, we hypothesized that genomic vector integration preferences might be distinct between these biological states. We performed integration site (IS) analyses on mouse dividing cells (fibroblasts and hematopoietic progenitor cells (HPCs)) transduced ex vivo and postmitotic cells (eye and brain) transduced in vivo. As expected, integration in dividing cells occurred preferably into gene coding regions. In contrast, postmitotic cells showed a close to random frequency of integration into genes and gene spare long interspersed nuclear elements (LINE). Our studies on the potential mechanisms responsible for the detected differences of lentiviral integration suggest that the lowered expression level of Psip1 reduce the integration frequency in vivo into gene coding regions in postmitotic cells. The motif TGGAA might represent one of the factors for preferred lentiviral integration into mouse and rat Satellite DNA. These observations are highly relevant for the correct assessment of preclinical biosafety studies, indicating that lentiviral vectors are well suited for safe and effective clinical gene transfer into postmitotic tissues.

The objective to use gene therapy to provide sustained, therapeutic levels of factor VIII (FVIII) for hemophilia A is compromised by the emergence of inhibitory antibodies that prevent FVIII from performing its essential function as a cofactor for factor IX (FIX). FVIII appears to be more immunogenic than FIX and an immune response is associated more frequently with FVIII than FIX gene therapy strategies. We have evaluated a modified lentiviral delivery strategy that facilitates liver-restricted transgene expression and prevents off-target expression in hematopoietic cells by incorporating microRNA (miRNA) target sequences. In contrast to outcomes using this strategy to deliver FIX, this modified delivery strategy was in and of itself insufficient to prevent an anti-FVIII immune response in treated hemophilia A mice. However, pseudotyping the lentivirus with the GP64 envelope glycoprotein, in conjunction with a liver-restricted promoter and a miRNA-regulated FVIII transgene resulted in sustained, therapeutic levels of FVIII. These modifications to the lentiviral delivery system effectively restricted FVIII transgene expression to the liver. Plasma levels of FVIII could be increased to around 9% that of normal levels when macrophages were depleted prior to treating the hemophilia A mice with the modified lentiviral FVIII delivery system.

Mucopolysaccharidosis type I (MPS I) is a lysosomal storage disease characterized by mutations to the α-L-iduronidase (IDUA) gene resulting in inactivation of the IDUA enzyme. The loss of IDUA protein results in the progressive accumulation of glycosaminoglycans within the lysosomes resulting in severe, multi-organ system pathology. Gene replacement strategies have relied on the use of viral or nonviral gene delivery systems. Drawbacks to these include laborious production procedures, poor efficacy due to plasmid-borne gene silencing, and the risk of insertional mutagenesis. This report demonstrates the efficacy of a nonintegrating, minicircle (MC) DNA vector that is resistant to epigenetic gene silencing in vivo. To achieve sustained expression of the immunogenic IDUA protein we investigated the use of a tissue-specific promoter in conjunction with microRNA target sequences. The inclusion of microRNA target sequences resulted in a slight improvement in long-term expression compared to their absence. However, immune modulation by costimulatory blockade was required and permitted for IDUA expression in MPS I mice that resulted in the biochemical correction of pathology in all of the organs analyzed. MC gene delivery combined with costimulatory pathway blockade maximizes safety, efficacy, and sustained gene expression and is a new approach in the treatment of lysosomal storage disease.

Survival rates after allogeneic hematopoietic cell transplantation (HCT) for Fanconi anemia (FA) have increased dramatically since 2000. However, the use of autologous stem cell gene therapy, whereby the patient's own blood stem cells are modified to express the wild-type gene product, could potentially avoid the early and late complications of allogeneic HCT. Over the last decades, gene therapy has experienced a high degree of optimism interrupted by periods of diminished expectation. Optimism stems from recent examples of successful gene correction in several congenital immunodeficiencies, whereas diminished expectations come from the realization that gene therapy will not be free of side effects. The goal of the 1st International Fanconi Anemia Gene Therapy Working Group Meeting was to determine the optimal strategy for moving stem cell gene therapy into clinical trials for individuals with FA. To this end, key investigators examined vector design, transduction method, criteria for large-scale clinical-grade vector manufacture, hematopoietic cell preparation, and eligibility criteria for FA patients most likely to benefit. The report summarizes the roadmap for the development of gene therapy for FA.

MicroRNAs are essential regulators of normal and malignant hematopoiesis. miRNAs are relevant for gene therapy, since they can be exploited to fine-tune the expression profile of vector constructs or to alter viral tropism (GentnerN Chiriaco et al, 2014; Escobar et al, 2014) and described the function of miR-126 in HSC where it regulates the balance between quiescence and self-renewal (Lechman et al, 2012). We here report a novel role for miR-126 in the induction and maintenance of high-grade B cell malignancies. By ectopically expressing miR-126 in transplanted BM cells, we observed that up to 60% of mice (n=71) developed B cell malignancies. LV insertion site (IS) analysis revealed that all tumors were monoclonal. We then tracked back leukemic clone to different hematopoietic lineages prospectively purified from the mice 2-6 months before disease onset. IS sharing between normal lineages and leukemic clone suggests stem or multipotent progenitor cell as origin for most tumors. Importantly, we show that miR-126 is the direct cause of genesis and maintenance of leukemia, since leukemogenesis is abolished when miRNA expression is inhibited by doxycycline (doxy) using a tetracycline-repressible miR-126 cassette, and established symptomatic leukemia completely regresses when miR-126 is switched off by doxy through induction of apoptosis. Transcriptional profiling indicated that miR-126 regulates multiple genes in p53 pathway both in murine blasts and in normal human CD34+ cells. Previous work suggested expression of miR-126 in acute lymphoblastic leukemia (ALL) and germinal center lymphoma. To further establish the relevance of miR-126 in human disease, we measured miR-126 expression in blasts from 16 adult patients with ALL. miR-126 was highly expressed in most studied ALL cases (Phil+: n=11, Phil-: n=5), at similar levels as CD34+ cells. We then down-regulated miR-126 in primary blasts from human B-ALL patients (n=5), and we observed increased apoptosis and impaired engraftment in xenograft models after primary and secondary transplantation (miR-126/KD: n=32 mice; Ctrl: n=37 mice), demonstrating the relevance of miR-126 in human B-ALL. In conclusion, we present a novel spontaneous mouse model for high grade B cell malignancies which are addicted to miR-126 expression, provide insight into the dynamic process of leukemogenesis by clonal IS tracking and unveil key tumor signaling pathways controlled by miR-126. Down-regulation of miR-126 could be exploited as therapeutic strategy in ALL, since it would deplete leukemic cells while expanding normal HSC, two ways to restore normal hematopoieis.

Recent studies suggest that hematopoietic stem cells (HSC) can sense foreign nucleic acids and pathogen-associated molecular patterns (PAMPs). Exposure to lentiviral vectors (LV) upon gene transfer may thus trigger acute host responses in HSC that could potentially impact on their biological properties, although no comprehensive studies are available to date. We have performed a high throughput RNA-Seq analysis on human cord-blood (CB)-derived CD34+ hematopoietic stem and progenitor cells (HSPC) exposed to research- or clinical-grade VSV-g pseudotyped (SIN) LV at a high multiplicity of infection, matching current clinical vector dose requirements. As controls, cells were exposed to non-transducing Env-less, genome-less or heat inactivated control vectors or kept in culture untreated. RNA was extracted at different times early after transduction, processed and ran in Illumina HiSeq2000. Analysis of Differential Expression in Time Course was performed using LIMMA R/BioConductor library. Key pathways were assessed by Term Enrichment Analysis considering KEGG pathways and Gene Ontology Biological processes. Transduction with both research-and clinical-grade LV significantly triggered DNA damage and apoptosis-related responses. In particular, p53 signaling was among the most significantly altered pathways (p

Despite the remarkable clinical results of chimeric antigen receptor (CAR) T-cell immunotherapy in B-cell tumors, its long-term success is limited by the emergence of CD19-loss tumor escape variants. We have developed a CD28-endocostimulated CD44v6 CAR for the targeting of multiple tumors, including acute myeloid leukemia (AML), multiple myeloma and epithelial cancers. Besides its widespread tumor expression, the appeal of CD44v6 as a CAR target stems from its non-redundant role in tumor progression and absent expression on hematopoietic stem cells (HSCs).

Lentiviral (LV)-based hematopoietic stem and progenitor cell (HSPC) gene therapy is becoming a promising alternative to allogeneic stem cell transplantation for curing genetic diseases. To potentially improve the efficacy, safety and economic sustainability of HSPC transduction, we reasoned to genetically manipulate only the more potent CD34+CD38- HSPC, thereby improving HSPC maintenance in culture in the absence of differentiating cells and downscaling the cell therapy product by a factor of ten without compromising long-term engraftment. This approach would also decrease the total load of vector integration infused in the patients, thus improving its overall safety.First, we determined the engraftment kinetics of CD34+ mobilized peripheral blood (mPB) subpopulations over a 24wk xenotransplantation period. We sorted CD34+ mPB into 4 fractions with increasing expression levels of CD38 and marked each fraction with a specific fluorescent protein allowing to track the population of origin driving hematopoietic reconstitution. Differentially labeled fractions were mixed, and various combinations of CD38-, CD38int and CD38hi HSPC were injected into NSG mice (2 exp, n=30). Almost all long-term repopulating capacity (>90%) was contained within CD34+CD38- cells, and these cells took over hematopoiesis by 9wks. Instead, early reconstitution was mainly driven by CD34+CD38int progenitor cells.In the prospect of a clinical translation, we then modeled the co-administration of gene-modified CD34+CD38- mPB cells with uncultured CD34+CD38int/+ supporter cells aimed to drive fast hematopoietic recovery (3 exp, n=38). Repopulation by gene-modified CD34+CD38- cells was slower (15wks) and incomplete ( 5 wks and re-established long-term (24wks) gene marking up to 85%, thus allowing to benefit from prompt hematopoietic recovery driven by transiently repopulating CD38int/+ supporter cells.Last, we optimized LV transduction in the framework of an improved culture protocol. Exposing CD34+ or CD34+CD38- mPB cells to prostaglandin E2 (PGE2) increased transduction efficiency 1.5-2.5x, allowing to markedly reduce pre-stimulation and LV exposure times better preserving HSC functions. Importantly, the higher gene-transfer efficiency was maintained for up to 24 wks following xenotransplantation (n=33), suggesting that PGE2 facilitated LV transduction in long-term HSC.In summary, these results support the clinical development of novel HSPC gene therapy protocols based on the modification of highly purified HSC subsets, with the prospect to improve the efficacy, safety and feasibility of future ex vivo gene therapy studies.

Lentiviral vectors (LVs) are attractive vehicles for liver-directed gene therapy by virtue of their ability to stably integrate in the genome of target cells and the lack of pre-existing immunity against vector components in most humans. Over the past years, we have developed a LV platform that can achieve stable transgene expression in the liver, induce transgene-specific immune tolerance and establish correction of hemophilia in mouse models upon systemic administration. This LV is designed to stringently target transgene expression to hepatocytes through transcriptional and microRNA-mediated regulation. We then investigated the efficacy and safety profile of portal vein administration of LVs expressing wild-type, codon-optimized (c.o.) or c.o. and hyperactive factor IX (FIX) in a canine model of hemophilia B. We produced large-scale batches of LVs qualified for in vivo administration and treated adult hemophilia B dog by portal vein administration. We observed long-term stable reconstitution of canine FIX activity up to 1% of normal and significant amelioration of the clinical phenotype in 3 treated dogs (>9 years cumulative follow up). LV infusion was associated with transient signs of inflammation and mild hepatotoxicity, which could be abrogated by pretreatment with anti-inflammatory drugs. There was no detectable long-term toxicity or development of FIX inhibitors. In the perspective of clinical translation and to increase therapeutic efficacy, we next treated an 11-kg, hemophilia B dog by peripheral vein administration of LVs expressing the c.o. and hyperactive canine FIX at a 5-fold higher dose than those previously administered. At the current follow-up (3 months after gene therapy) FIX activity is 6-9% of normal. Intravenous LV administration, coupled with a 1-day anti-inflammatory and anti-histamine pre-treatment, induced mild and selflimiting leukopenia and elevation of aminotransferases. Treatment of more hemophilia B dogs is underway to confirm and extend these results. Overall, our studies, which suggest comparable efficacy of LV by both portal and peripheral vein administration, position LV-mediated liver gene therapy for further pre-clinical development and clinical translation. LVs may thus complement other available vectors to address some of the outstanding challenges posed by liver gene therapy of hemophilia and conceivably other diseases.

Type 1 diabetes (T1D) is an autoimmune disease resulting in complete destruction of insulin-producing pancreatic β cells. In T1D in human and in the non-obese diabetic (NOD) mouse, the spontaneous murine model of T1D, auto-reactive T cells target islet-associated antigens. Induction of antigen (Ag)-specific tolerance could cure Type 1 Diabetes (T1D) but it has not been achieved yet. We previously showed that lentiviral vector (LV)-mediated gene expression in hepatocytes induces active tolerance toward the encoded-Ag. Systemic administration of a single dose of Integrase competent (IC) or integrase defective (ID) LV.ET.InsB9-23.142T, enabling stable and transient expression of InsB9-23 in hepatocytes, respectively, arrests β cell destruction in NOD mice at advanced pre-diabetic stage by generating InsB9-23-specific FoxP3+ T regulatory cells (Tregs). In the present study we tested the efficacy of hepatocytes-directed LV.ET. InsB9-23.142T gene transfer in protecting from disease progression at later stages and in reversing T1D.Treatment with LV.ET.InsB9-23.142T in NOD mice with glucose levels ranging from 200mg/mL to 250mg/mL blocked T1D progression in only 27% of the mice. Co-expression of the late auto-Ags-derived epitopes GAD206-220 and IGRP195-214 in hepatocytes did not improve the efficacy of LV.ET.InsB9-23.142T treatment. LV.ET.InsB9-23.142T treatment in diabetic NOD mice with blood glucose levels ranging from 250mg/mL to 300mg/mL did not result in reversion to normoglycemic levels in any of the treated mice.We next combined InsB9-23 gene transfer with anti-CD3 monoclonal antibody (mAb) treatment. Treatment with anti-CD3 mAb at optimal doses is able per se to reverse T1D in NOD mice. Therefore, we tested decreasing doses of anti-CD3 mAb in diabetic NOD mice with blood glucose levels ranging from 250mg/mL to 300mg/mL to identify the sub-optimal dose unable to revert T1D. We found that a single administration of anti-CD3 mAb at 5μg instead of 10μg results was not effective. This sub-optimal dose of anti-CD3 mAb (1X 5μg) was administered together with LV.ET.InsB9-23.142T to NOD mice with blood glucose levels ranging from 250mg/mL to 300mg/mL. Results showed T1D reversal in 75% of ICLV-treated and 40% of the IDLV-treated mice. These data indicate that the LV.ET. InsB9-23.142T treatment combined with sub-optimal anti-CD3 mAb treatment is able to reverse overt diabetes.

There are several diseases whereby the goal of gene therapy is to silence rather than replace a gene function. Paradigmatic examples are diseases caused by a dominant negative mutation or those in which silencing of a host gene confers resistance to a pathogen or compensates the function of the missing gene. Yet, gene silencing can be used to enhance efficacy of cell therapy and for biotechnological applications. Until now, two technologies have been used to silence gene expression, namely RNA interference with short harping RNAs (shRNA) and gene disruption with Artificial Nucleases (ANs). Although some promising pre-clinical and clinical data have been already obtained, the low efficiency of knock-down with shRNA and of biallelic disruption with ANs may limit efficacy of these treatments, especially when residual gene activity can exert a biological function. To overcome this issue, we have developed a novel modality of gene silencing that exploits endogenous epigenetic mechanisms to convey robust and heritable states of repression at the desired target gene. We have generated Artificial Transcriptional Repressors (ATRs), chimeric proteins containing a custom-made DNA binding domain fused to the effector domain of a chromatinmodifying enzyme involved in silencing of Endogenous RetroViruses (ERVs). By performing iterative rounds of selection in human cell lines and primary cells engineered to report for synergistic activity of candidate effector domains, we identified a combination of 3 domains that, when transiently co-assembled on the promoter of the reporter cassette, fully abrogated transgene expression in up to 90% of treated cells. Importantly, silencing was maintained for more than 250 days in cultured cell lines, was resistant to in vitro differentiation or metabolic activation of primary cells, and was confined to the reporter cassette. Silencing was associated with high levels of de novo DNA methylation at the targeted locus and was dependent on this epigenetic mark for its propagation. Finally, transient transfection of 3 ATRs targeted to the promoter region of the Beta-2-microglobulin (B2M) gene resulted in the loss of surface expression of B2M and, consequently, of the MHC-I molecules in up to 80% of treated cells. This phenotype was associated with a switch in the epigenetic and transcriptional state of the constitutively active B2M gene, which became highly decorated with DNA methylation and deprived of RNA PolII and of its transcript. Of note, silencing was resistant to IFN-γ treatment, a potent B2M inducer. Overall, these data provide the first demonstration of efficient and stable silencing of an endogenous gene upon transient delivery of ATRs. This result was made possible by repurposing the machinery involved in silencing of ERVs, which instructs self-sustaining repressive epigenetic states on the gene of interest. While silencing of B2M might be used to generate universally transplantable allogeneic cells, our hit-and-run strategy provides a powerful new alternative to conventional gene silencing for the treatment of several diseases. (LN & AL co-authorship)

Targeted genome editing by artificial nucleases has brought the goal of gene correction within the reach of gene therapy. A candidate disease for HSPC gene correction is SCID-X1, because gene therapy with early generation integrating vectors showed robust clinical efficacy even from few corrected cells but also the occurrence of adverse events due to insertional mutagenesis and unregulated transgene expression. We recently reported a strategy that enabled targeted integration of a corrective cDNA into the IL2RG gene in 6% of human HSPC with high specificity. Gene corrected HSPC generated polyclonal lymphoid cells that express the IL2RG protein and have a selective growth advantage over those carrying disruptive IL2RG mutations (Genovese, Nature, 2014). Here, to model SCID-X1 disease correction, we developed a mouse model carrying the IL2RG human gene including a common disease-causing mutation in place of the murine Il2rg gene, allowing to use the same reagents utilized for gene correction of human cells. These mice have impairment in lymphoid development which phenocopies that reported for Il2rg-/- mice. To assess the minimal level of corrected HSPC required to achieve immune reconstitution we first performed competitive transplants with wild-type (WT) and Il2rg-/- HSPC and found that 1% of WT cells are sufficient to reconstitute at least in part the T and B cell compartments. We then developed a protocol to obtain gene correction in murine Lin- HSPC based on the delivery of donor DNA template by IDLVs followed by transfection of ZFN mRNAs. This protocol was associated with high on-target nuclease activity (40%) and a mean of 6% transgene integration by HDR, but also with high levels of acute cytotoxicity (65% cell loss). The surviving cells remained capable of expansion in culture and preserved their clonogenic potential. Importantly, upon transplant into lethally irradiated mice, only the gene corrected cells were able to generate lymphoid lineages (B and T cells), showing a clear selective advantage over un-corrected cells. These data indicate functional correction of the IL2RG gene by our strategy. Yet, measuring percentage of correction within myeloid cells at long-term we found that it was almost undetectable. Despite the lack of HSC marking, gene corrected lymphoid cells stably persisted in the mice up to 7 months post transplantation within all the hematopoietic organs. Furthermore, upon challenging the transplanted mice with a murine pathogen (LCMV Arm.) we observed viral-specific γIFN production by CD8+ gene corrected cells at a similar extent as for WT mice, proving in vivo the functionality of corrected T cells. These results suggest that our protocol achieves biologically relevant levels of gene correction in progenitors that sustain long-term lymphopoiesis but is limited in multipotent HSC. Ongoing studies aim to improve murine HSC gene targeting and to compare safety and efficacy of gene correction vs gene replacement in our disease model.

Mutations in the IL2RG gene may result in X-linked severe combined immunodeficiency (X-SCID), an immunodeficiency disorder in which the body produces very few T cells and natural killer cells, resulting in premature death due to opportunistic infections. At present, allogeneic hematopoietic stem cell transplant (HSCT) is the standard of care and results in full immune reconstitution if engraftment is successful. However, the search for a compatible donor is not always successful and transplantation from a non MHC-identical donor carries the risk of graft-versus-host disease. An autologous HSCT containing a replaced or corrected IL2RG gene would avoid these risks.Previous autologous gene therapy for X-SCID successfully treated the disease but relied on early generation gene replacement retroviral vectors and resulted in insertional oncogenesis and leukemia development in some treated subjects. Here we report a gene correction approach to X-SCID gene therapy involving targeted integration (TI) of a corrective IL2RG donor DNA cassette (cDNA from exons 2-8) into intron 1 of the IL2RG gene. This strategy has the advantage of retaining the endogenous IL2RG promoter and enhancer and allows treatment of patients with almost all X-SCID causing IL2RG mutations (excluding only those affecting the gene upstream of intron 1). Using engineered zinc-finger nucleases (ZFNs) delivered as mRNA and IL2RG donor DNA delivered as adeno-associated virus (AAV) to CD34+ human hematopoietic stem and progenitor cells (HSPCs) cultured ex vivo, we have achieved TI of the corrective IL2RG donor in up to 25% of alleles. These cells differentiate normally in vitro and retain consistent levels of TI in both erythroid and myeloid lineages. IL2RG mRNA expression was successfully restored in an IL2RG knockout model human cell line, validating this strategy. Coupled with the strong, intrinsic in vivo selection for cells with IL2RG activity, our data are a promising advance towards an autologous HSPC-based gene therapy for the treatment of X-SCID.

Regulation of gene expression represents a long-sought goal of gene therapy. However, most viral vectors pose constraints on the incorporation of drug-dependent transcriptional regulatory systems. Here, by optimizing the design of self-regulating lentiviral vectors based on the tetracycline system, we have been able to overcome the limitations of previously reported constructs and to reach both robust expression and efficient regulation from a single vector. The improved performance allows us to report for the first time effective long-term in vivo regulation of a human clotting Factor IX (hF.IX) transgene upon systemic administration of a single vector to SCID mice. We showed that hF.IX expression in the plasma could be expressed to therapeutically significant concentrations, adjusted to different set levels by varying the tetracycline dose, rapidly turned off and on, and completely recovered after each treatment cycle. The new vector design was versatile, as it successfully incorporated a tissue-specific promoter that selectively targeted regulated expression to hepatocytes. Robust transgene expression in the systemic circulation coupled to the ability to switch off and even adjust the expression level may open the way to safer gene-based delivery of therapeutics.

Gene silencing holds great promise for the treatment of several diseases and can be exploited to investigate gene function and activity of the regulatory genome. Here, we develop a novel modality of gene silencing that exploits epigenetics to achieve stable and highly efficient repression of target genes. To this end, we generated Artificial Transcriptional Repressors (ATRs), chimeric proteins containing a custom-made DNA binding domain fused to the effector domain of chromatin-modifying enzymes involved in silencing process of Endogenous RetroViruses (ERVs). By performing iterative rounds of selection in cells engineered to report for synergistic activity of candidate effector domains, we identified a combination of 3 domains (namely KRAB, DNMT3A and DNMT3L) that, when transiently co-assembled on the promoter of the reporter cassette, recreate a powerful embryonic-specific repressive complex capable of inducing full and long-term (>150 days) silencing of transgene expression in up to 90% of the cells. The ATR-induced silencing was cell type and locus independent, and resistant to metabolic activation of the cells. Importantly, these findings were holding true also for endogenous genes embedded in their natural chromatin context, as shown for the highly and ubiquitously expressed B2M gene. Here, transient co-delivery of TALE-based ATRs resulted in loss of surface expression of B2M and, consequently, of the MHC-I molecules in up to 80% of the cells. This phenotype was associated with a drastic switch in the epigenetic and transcriptional state of the constitutively active B2M promoter, which become highly decorated with de novo DNA methylation and deprived of RNAP II. Importantly, silencing was sharply confined to the targeted gene and resistant to INF-γ, a potent natural activator of B2M. We further extended these studies by showing that our silencing approach is portable to the CRISPR/dCas9 DNA binding technology. In this setting, comparable levels of B2M silencing (up to 80%) were achieved using either pools or even individual sgRNAs coupled to dCas9-based ATRs. Yet, adoption of this technology allowed performing simultaneous, highly efficient multiplex gene silencing within the same cell, as shown for B2M, IFNAR1 and VEGFA. Finally, we assessed resistance of the silenced gene to activity of potent artificial transcription activators and chromatin remodelers, and found that only targeted DNA demethylation was able to reawaken the silent gene. This allowed performing iterative cycles of silencing and reactivation of the same gene in the same cell population. Overall, these data provide the first demonstration of efficient and stable epigenetic silencing of endogenous genes upon transient delivery of ATRs. This was accomplished by repurposing the ERVs silencing machinery, which instructs self-sustaining repressive epigenetic states to the target gene. While silencing of B2M might be used to generate universally transplantable allogeneic cells, our hit-and-run strategy provides a powerful new alternative to conventional gene silencing for both basic and translational research.

A novel strategy of targeted gene correction of the interleukin-2 receptor common gamma chain (IL2RG) gene for the treatment of X-linked Severe Combined Immunodeficiency (SCID-X1) is achieved by the combination of a pair of IL2RG-specific Zinc Finger Nucleases (ZFN) and the correct-gene template DNA delivered by integration-defective lentiviral vector (IDLV).The transient expression of the ZFN pair targeting the disease-causing gene is obtained by the electroporation of the two corresponding mRNAs, produced by in vitro transcription starting from plasmid DNA template. A major limitation of the mRNA transcribed in vitro is the presence of residual contaminants such as short RNAs and double stranded (ds)RNAs that may affect the function and spectrophotometric quantification of the product hampering therefore the delivery of high quality and precise amount of mRNA to target cells. Moreover, dsRNA contaminants represent a possible risk in terms of immunogenicity of the product, leading to activation of unwanted innate immune response with consequent reduction/abrogation of mRNA translation as well as potential alteration of the properties of the transfected cells. To improve nuclease expression while decreasing cellular innate response to mRNA transfection we combined different strategies: (i) inclusion of UTRs and polyA tails in the DNA template used for mRNA production; (ii) use of modified nucleotides during mRNA production and (iii) purification of the mRNAs by dHPLC with a reverse phase column made of non-porous matrix consisting of polystyrene-divinylbenzene copolymer beads alkylated with C-18 chains (Transgenomic, LTD.). In particular, the purification of in vitro transcribed mRNAs by means of dHPLC has been shown to strongly improve the translation of mRNA and significantly reduce the contaminant presence thus preventing innate immunity and eventually increasing modified cells persistence in vivo. We have developed feasible and reproducible, small and large scale mRNA production and downstream purification processes of the ZFN pairs obtaining accurate RNA quantification and reduced risk of immunogenicity. The full process achieved a 60% yield, loading with a 500µg RNA for each run with a single clean chromatographic peak. Furthermore, the level of residual organic solvent (i.e. Acetonitrile) used in the purification process is compatible with that applicable into clinic. The highly translatable non-immunogenic dHPLC-purified mRNA can be delivered without toxicity and represents a powerful and safe tool for the application of gene therapy protocols.

A major challenge in gene therapy is to achieve efficient transduction of hematopoietic stem cells (HSC). It has previously been shown that lentiviral vectors (LV) transduce efficiently human cord blood-derived NOD/SCID mouse repopulating cells (SRC). Here we studied the effect of cytokines during the short ex vivo incubation with vector. Although SRC transduction was efficient without stimulation, the presence of cytokines significantly improved it. The treatment did not affect the engraftment level or the SRC frequency, but seemed to enhance SRC susceptibility to LV. SRC transduced in both conditions repopulated primary and secondary recipients, maintaining stable multi-lineage transgene expression. Using linear amplification-mediated PCR, we then analyzed vector integration in the bone marrow and CFC of the engrafted mice to monitor the clonal activity of the transduced SRC in vivo. We showed polyclonal engraftment, multi-lineage differentiation, and propagation to secondary recipients of individual SRC. We observed multiple integrations in most clones. These results provide the first formal demonstration that primitive human HSC with self-renewal and multi-lineage repopulation capacities were transduced by LV. Our findings are relevant for the design of clinical protocols that exploit this system to reach significant engraftment by genetically modified HSC in the absence of in vivo selection or strong conditioning regimens.

We developed a panel of lentiviral vectors that displayed tetracycline-regulated transgene expression over two orders of magnitude in bulk, non-selected populations of transduced cells in vitro and in vivo. The robust expression and homogeneous response indicated that most transduced vector genomes were transcription competent and responsive to regulation, providing the lentiviral vector with a novel competitive advantage for gene transfer. After ex vivo transduction and transplantation of cord blood CD34+ cells into NOD/SCID mice, reporter gene expression could be switched "on" and "off" in human hematopoietic cells in vivo for prolonged times, proving integration of the regulated expression system into long-term repopulating cells. By vector injection into established tumor grafts, we achieved efficient delivery and quantitative regulation of transgene expression in vivo. By these approaches, gene function studies can now be performed in in vivo models of human hematopoiesis and cancer. In the future, regulated lentiviral vectors will improve the safety and efficacy of gene therapy.

Gene therapy with ex vivo-transduced hematopoietic stem/progenitor cells may represent a valid therapeutic option for monogenic immunohematological disorders such as Wiskott-Aldrich syndrome (WAS), a primary immunodeficiency associated with thrombocytopenia. We evaluated the preclinical safety and efficacy of human CD34(+) cells transduced with lentiviral vectors (LV) encoding WAS protein (WASp). We first set up and validated a transduction protocol for CD34(+) cells derived from bone marrow (BM) or mobilized peripheral blood (MPB) using a clinical grade, highly purified LV. Robust transduction of progenitor cells was obtained in normal donors and WAS patients' cells, without evidence of toxicity. To study biodistribution of human cells and exclude vector release in vivo, LV-transduced CD34(+) cells were transplanted in immunodeficient mice, showing a normal engraftment and differentiation ability towards transduced lymphoid and myeloid cells in hematopoietic tissues. Vector mobilization to host cells and transmission to germline cells of the LV were excluded by different molecular assays. Analysis of vector integrations showed polyclonal integration patterns in vitro and in human engrafted cells in vivo. In summary, this work establishes the preclinical safety and efficacy of human CD34(+) cells gene therapy for the treatment of WAS.

Gene targeting is rapidly progressing thanks to the development of improved nucleases and donor constructs, and represents a new gene therapy-based strategy for the treatment of inherited diseases, such as Fanconi anemia (FA). Because FA can be generated by multiple mutations in up to 19 different genes, we focused our interests in the insertion of therapeutic FA genes in safe harbor loci, since this approach could serve as a platform for treating all FA subtypes and pathogenic mutations. In previous studies we demonstrated the feasibility of correcting the phenotype of hematopoietic progenitors through the genome editing and reprogramming of fibroblasts from FA patients. Because of the limited repopulating properties so far reported for iPSC-derived hematopoietic precursor cells, here we aimed to investigate the possibility of conducting a similar gene targeting approach using human primary CD34+ cells. In a first set of experiments we investigated the efficiency of targeting the AAVS1 locus in cord blood HSPCs. Pre-stimulated CD34+ cells were transduced with integrase-defective lentiviral vectors (IDLV) encoding an EGFP reporter gene under the control of the PGK promoter, flanked by sequences homologous to the AAVS1 target site. The cells were then nucleofected with AAVS1 -specific ZFN mRNAs. The average targeting efficiencies ranged from 10-20% both in in vitro cultured cells and NSG mice-repopulating cells. In subsequent experiments, the EGFP reporter gene was replaced by the hFANCA therapeutic gene. Gene targeting experiments conducted in lymphoblast cell lines and primary CD34+ cells from FA-A patients reverted the characteristic hypersensitivity of FA cells to mitomycin C (MMC), and also restored the formation of FANCD2 foci after DNA damage, evidencing the phenotypic correction of these cells. Our data confirm the efficacy of AAVS1-gene targeting in hHSPCs and demonstrate the feasibility of conducting these approaches in primary CD34+ cells from FA patients.

Ex vivo gene addition into CD34+ hematopoietic stem and progenitor cells (HSPC) followed by autologous transplantation has proven a safe and efficacious therapy for immunodeficiencies, storage diseases and hemoglobinopathies. According to xenograft models and population size estimates of vector-marked cells in gene therapy-treated patients, less than 0.01% of infused CD34+ cells drive long-term (LT) repopulation. Advances in clinical-grade cell sorting technology may make HSC-enriched CD34+ subpopulations accessible for gene therapy, with advantages in terms of lentiviral vector (LV) cost, safety (lowering of integration load) and, potentially, efficacy. By differentially marking mobilized peripheral blood (mPB) CD34 subpopulations distinguished by increasing levels of CD38 expression in order to quantitatively assess their hematopoietic output in an NSG xenograft model over 6 months, we previously mapped most (>90%) LT repopulating capacity to CD34+CD38- cells (lowest 10% CD38 staining), while CD34+CD38int cells drove short-term (ST) reconstitution during the first 2 months after transplantation. We now characterize these subpopulations in terms of CD90 expression, a marker, which has been used in conjunction with CD34 for HSC purification in past clinical trials. CD34+ mPB cells were sorted into CD38-90+ (5% of CD34+), CD38-90- (5%), CD38+90+ (30%) and CD38+90- (60%) fractions and exhaustively transduced with GFP-, OFP-, BFP- and mCherry-expressing LVs, respectively. Differentially marked subfractions were pooled maintaining their original proportions and transplanted into NSG mice. ST engraftment mainly came from CD38+ cells, with equal contribution from the CD90+ and CD90- compartment. LT engraftment was almost exclusively derived from CD34+CD38- cells, of which 70% came from CD90+ and 30% from CD90- cells. Hence, CD34+CD38- is a more sensitive and specific marker combination than CD34+CD90+ to purify LT-HSC. CD34+CD38- cells can be purified by a sequential bead-based selection (CD34 selection of CD38-depleted cells) potentially applicable to clinical practice. We show that CD34+CD38- cells can be efficiently transduced with clinical grade LVs using shortened ex vivo manipulation protocols, reaching similar gene marking levels as with the standard protocol currently used in clinical trials that comprises a double dose of LV. Transduction was stable for at least 5 months when serially measured in xenotransplanted mice, and mice showed multi-lineage hematopoiesis indistinguishable from CD34+ grafts. Based on these results, we are aiming towards clinical development of a new gene therapy protocol based on CD34+CD38-HSPC efficiently transduced with minimum ex vivo culture time (

Wiskott-Aldrich Syndrome (WAS) is a severe X-linked primary immunodeficiency characterized by micro-thrombocytopenia, eczema and increased risk of infections, autoimmunity and tumors. Allogeneic hematopoietic stem cell (HSC) transplantation is a recognized curative treatment for WAS, but when a matched donor is not available, administration of WAS gene-corrected autologous HSCs represents a valid alternative therapeutic approach. Since alterations of WAS protein (WASp)-deficient B lymphocytes contribute to immunodeficiency and autoimmunity in WAS, we followed the B cell reconstitution in 4 WAS patients treated by lentiviral vector-gene therapy (GT) after a reduced-intensity conditioning regimen combined with anti-CD20 administration. We analyzed the B cell subset distribution in the bone marrow and peripheral blood by flow cytometry and the autoantibody profile by a high-throughput autoantigen microarray platform before and after GT. Lentiviral vector-transduced progenitor cells were able to repopulate the B cell compartment with a normal distribution of transitional, naive and memory B cells. The reduction in the proportion of autoimmune-associated CD21low B cells and in the plasma levels of B cell-activating factor was associated with the decreased autoantibody production in WAS patients after GT. Then, we evaluated the functionality of B cell tolerance checkpoints by testing the reactivity of recombinant antibodies isolated from single B cells. Before GT, we found a decreased frequency of autoreactive new emigrant/transitional B cells in WAS patients, suggesting a hyperfunctional central B cell checkpoint in the absence of WASp. In contrast, high frequency of polyreactive and Hep2 reactive clones were found in mature naive B cells of WAS patients, indicating a defective peripheral B cell checkpoint. Both central and peripheral B cell tolerance checkpoints were restored after GT, further supporting the qualitative efficacy of this treatment. In conclusion, WASp plays an important role in the regulation of B cell homeostasis and in the establishment of B cell tolerance in humans and lentiviral-mediated GT is able to ameliorate the functionality of B cell compartment contributing to the clinical and immunological improvement in WAS patients.

Lentiviral vectors (LVs) are attractive vehicles for liver-directed gene therapy by virtue of their ability to stably integrate in the genome of target cells and the low prevalence of pre-existing immunity against HIV in humans. Over the past years, we have developed a LV platform that can achieve stable transgene expression in the liver, induce transgene-specific immune tolerance and establish correction of hemophilia in mouse models upon systemic administration. This LV is designed to stringently target transgene expression to hepatocytes through transcriptional and microRNA-mediated regulation. We then investigated the efficacy and safety profile of portal vein administration of LVs expressing canine factor IX (FIX) in a canine model of hemophilia B. We produced large-scale batches of LVs qualified for in vivo administration and treated adult hemophilia B dog by portal vein administration. We observed long-term stable reconstitution of canine FIX activity up to 1% of normal and significant amelioration of the clinical phenotype in 3 treated dogs with 6, 3.5 and 2.5 years of follow up. LV infusion was associated with transient signs of inflammatory response and mild hepatotoxicity, which could be abrogated by pretreatment with anti-inflammatory drugs. There was no detectable long-term toxicity or development of FIX inhibitors. In the perspective of clinical translation and to increase therapeutic efficacy, we next treated two 10-kg hemophilia B dogs by peripheral vein administration of LVs expressing a codon-optimized and hyperfunctional canine FIX at a 5-fold higher dose than those previously administered. Intravenous LV administration was well tolerated with mild and self-limiting elevation of aminotransferases in one dog. In the dog that reached more than 1 year of follow up FIX activity ranged between 4-8% of normal. Treatment of two more dogs at a higher dose is underway. Overall, our studies position LV-mediated liver gene therapy for further pre-clinical development and clinical translation. LVs may thus complement other available vectors to address some of the outstanding challenges posed by liver gene therapy of hemophilia and conceivably other diseases.

Lentiviral vectors (LVs) represent efficient and versatile vehicles for gene therapy. Current manufacturing of clinical-grade LVs mostly relies on transient transfection of plasmids expressing the multiple vector components. This method is labor and cost intensive and becomes challenging when facing the need of scale-up and standardization. The development of stable LV producer cell lines will greatly facilitate overcoming these hurdles. We have generated an inducible LV packaging cell line, carrying the genes encoding for third-generation vector components stably integrated in the genome under the control of tetracycline-regulated promoters. These LV packaging cells are stable in culture even after single-cell cloning and can be scaled up to large volumes. In order to minimize the immunogenicity of LVs for in vivo administration, we set out to remove the highly polymorphic class-I major histocompatibility complexes (MHC-I) expressed on LV packaging cells and incorporated in the LV envelope. We performed genetic disruption of the β-2 microglobulin (B2M) gene, a required component for the assembly and trafficking of all MHC-I to the plasma membrane in LV producer cells, exploiting the RNA-guided Cas9 nuclease. The resulting B2M-negative cells were devoid of surface-exposed MHC-I and produced MHC-free LVs. These LVs retain their infectivity on all tested cells in vitro and efficiently transduced the mouse liver upon intravenous administration. Strikingly, the MHC-free LVs showed significantly reduced immunogenicity in a T-cell activation assay performed on human primary T cells co-cultured with syngeneic monocytes exposed to LV, from several (n=7) healthy donors. To reproducibly generate LV-producer cell lines from these cells, we insert the LV genome of interest in the AAVS1 locus, chosen for robust expression, exploiting engineered nucleases and homology-directed repair. By this strategy, we have obtained several independent producer cell lines for LVs that express marker or therapeutic genes and are devoid of plasmid DNA contamination. LVs produced by these cells reproducibly show titer and infectivity within the lower bound range of standard optimized transient transfection, and effectively transduce relevant target cells, such as hematopoietic stem/progenitor cells and T cells ex vivo and the mouse liver in vivo. Overall, we provide evidence that rationally designed targeted genome engineering can be used to improve the yield, quality, safety and sustainability of LV production for clinical use.

Background: Despite the remarkable clinical results of CD19 CAR-T cells in B-cell leukemias, their long-term efficacy is limited by the emergence of CD19-loss escape variants. Moreover, whether the cytokine release syndrome (CRS) is necessary for durable remissions is a matter of debate. Currently available xenograft models in NSG mice are not suited for studying the antitumor effects of CAR-T cells beyond 3-4 weeks, because of xenograft-versus-host disease (X-GVHD). Moreover, since NSG mice lack functional myeloid cells, the CRS does not develop. Aim: To verify whether the CRS contributes to the antileukemic effects of CAR in an innovative xenotolerant mouse model.Results: NSG mice triple transgenic for human IL-3, GM-CSF and SCF (NSG-3GS) were sub-lethally irradiated and injected intra-liver with human HSCs soon after birth, enabling an accelerated and better balanced lympho-hematopoietic reconstitution compared with NSG mice. Reconstituting human T cells were single CD4+/CD8+ T cells, representing all memory sub-populations. After ex vivo isolation and activation with CD3/CD28-beads and IL-7/IL-15, NSG-3GS T cells were transduced with a CD44v6 CAR, retaining an early-differentiated (stem-cell/central-memory) phenotype and full antitumor functionality against acute myeloid leukemia (AML). NSG-3GS-derived CD44v6 CAR T cells were subsequently infused in tumor-bearing secondary recipients previously humanized with autologous HSCs. CAR-T cells persisted in vivo for at least 6 months and mediated durable leukemia remissions (P

Upon gene therapy (GT) for adenosine deaminase (ADA) deficient-SCID and Wiskott-Aldrich Syndrome (WAS), gene-corrected hematopoietic stem/progenitor cells (HSPC) generated a stable genetically engineered hematopoietic system where each vector-marked cell is univocally barcoded by a vector integration site (IS). To study the dynamics of human hematopoietic system, we collected by LAM-PCR+Illumina sequencing 28.539.414 sequence reads corresponding to 89.373 IS tagging clones belonging to 13 different cell types purified from the bone marrow and the peripheral blood of 4 WAS patients up to 48 months after GT. We firstly identified identical IS shared among CD34+ progenitors, and mature Myeloid/Lymphoid cells as markers of the real-time clonal output of vector-marked HSPC clones in vivo. We unraveled the nature and timing of short, intermediate and long term HSPC output showing that CD34+ clones active at 3-6 months after GT are not detectable at later follow up. Distinct waves of HSPC diversity were observed during the first 6-9 months after GT reaching a homeostatic equilibrium only by 12 months. By unsupervised clustering of IS similarities among lineages we unveiled diverse HSPC output towards lymphoid, myeloid and megakaryo-erythroid cells showing hints of a NK cells origin distinct from T and B cells. We exploited IS similarities to infere and test hematopoietic hierarchies by combining conditional probability distributions and static/dynamic graphical models of dependencies. We also estimated by mark-recapture approaches that just few thousands clones (1185-2884) are responsible for the long-term maintenance of the whole genetically engineered hematopoietic system. The ongoing analyses on IS collected from 7 distinct CD34+ subtypes isolated from GT patients will further increase HSPC tracking resolution. To evaluate the preservation of activity by transplanted HSPC we exploited data derived from the IS-based tracking of 4.845 clones in ADA-SCID patients performed for up to 6 years after GT. We showed that identical IS are consistently detected at multiple lineages level even several years after GT. Strikingly, by semi-quantitative PCRs on specific vector-genome junctions we tracked a fluctuating but consistent output of marked HSPC over a period of 5 years without the manifestation of clonal quiescence phases. Since gamma-retroviral vector used in this GT trial actively transduce only replicating cells, this provide the first evidence that HSPC, awaken from dormancy in vitro, can still retain in vivo long-term activity. Overall our work constitute the first molecular tracking of hematopoietic system in humans. The information gathered are crucial for the design of therapeutic approaches for a broad spectrum of hematological diseases and tumors.

Chromatin insulators (CI) have been proposed as safety features to increase the safety of self-inactivating (SIN) lentiviral vectors (LV) for gene therapy applications.By taking advantage of an in vivo genotoxicity assay based on the systemic injection of LVs in newborn tumor-prone Cdkn2a-/- mice we were able to measure vector-induced genotoxicity as an accelerated tumor onset that was proportional to the genotoxic potential of the tested LV. Importantly, we took advantage of integration sites (IS) analysis to qualitatively characterize CI that were shown by other in vitro and ex vivo studies to function as insulators. Recently we showed for the first time that a CAAT-box binding Nuclear factor 1 (CTF/NF1)-based CI, when cloned in the LTRs of a SIN.LV with a strong SFFV enhancer-promoter in internal position, significantly reduced the frequency of tumors harboring integrations activating Map3k8 oncogene accompanied by a marked skewing towards tumors harboring inactivating insertions targeting Pten.Here by using this stringent in vivo genotoxicity assay and IS analysis in tumors we expanded our studies towards other CI sequences whose function is regulated by the binding of the CCCTC-binding factor (CTCF), the best characterized insulator protein in vertebrates.Each CTCF-based insulating cassette was cloned in the LTRs of a LV construct containing the SFFV promoter in internal position (CTCF.SIN.LVs) and injected in Cdkn2a-/- mice. Interestingly, mice treated with some of the CTCF.SIN.LVs tested displayed an increased median survival time (ranging from 193.5 to 214 days) compared to mice treated with the uninsulated parental SIN.LV (186 days). Importantly, our preliminary IS analysis in tumors (881 IS) showed that two CTCF.SIN.LVs did not target Map3k8 oncogene while Pten was often disrupted by exonic insertions, an escape genotoxicity mechanism on which CI cannot act.These data confirm that the inclusion of two novel CTCF-based CIs of human origin completely abrogated the formation of tumors caused by enhancer-mediated activation of an oncogene in vivo.The ability of these two new insulator elements to block the crosstalk between powerful vector enhancers and cellular regulatory elements increase the safety of SIN LVs and justify their prompt adoption in future gene therapy applications.

Lentiviral vectors (LVs) represent efficient and versatile vehicles for gene therapy. The manufacturing of clinical-grade LVs relies on transient transfection of vector components. This method is labor and cost intensive and becomes challenging when facing the need of scale-up and standardization. The development of stable LV producer cell lines will greatly facilitate overcoming these hurdles. We have generated an inducible LV packaging cell line, carrying the genes encoding for third-generation vector components stably integrated in the genome under the control of tetracycline-regulated promoters. In order to minimize the immunogenicity of LVs for in vivo administration, we set out to remove the highly polymorphic and antigenic class-I major histocompatibility complex (MHC-I) expressed on LV packaging cells and subsequently incorporated on the LV envelope. We performed genetic disruption of the β-2 microglobulin (B2M) gene, a required component for the assembly and trafficking of the MHC-I to the plasma membrane in LV producer cells, exploiting the RNA-guided Cas9 nuclease. We generated B2M-negative cells devoid of surface-exposed MHC-I, which retain the ability to produce LVs. In order to insert the LV genome of interest in the packaging cell line, we performed site-specific integration in predetermined loci of the genome of these cells, chosen for robust expression, exploiting artificial nucleases and homology-directed repair. In several independent iterations of this process, we generated producer cell lines both for LV expressing marker genes and a therapeutic gene, i.e. coagulation factor IX (FIX), the gene mutated in hemophilia B. We show that these LV producer cells are stable in culture and can produce several liters of LV-containing conditioned medium. These LVs have comparable or only slightly lower infectious titer and specific infectivity than LVs produced by state-of-the-art transient transfection process and can transduce therapeutically relevant target cells, such as hematopoietic stem/progenitor cells and T lymphocytes to high efficiency. Moreover, we intravenously administered FIX-expressing LVs produced by the cell line to hemophilia B mice and established therapeutic levels of circulating FIX. These data indicate that site-specific integration is an efficient, rapid and reproducible method to generate LV producer cells, starting from a universal stable inducible LV packaging cell line. Overall, we provide evidence that rationally designed targeted genome engineering can be used to improve the quality, safety and sustainability of LV production for clinical use.

We recently described a lineage of proangiogenic monocytes implicated in tumor angiogenesis. These cells, identified by expression of the angiopoietin receptor (Tie2-Expressing Monocytes, TEMs), are selectively recruited to tumors and promote angiogenesis in a paracrine manner by interacting with locally derived endothelial cells (De Palma et al., Cancer Cell, 2005).

Metachromatic Leukodystrophy (MLD) is a demyelinating lysosomal storage disorder with an urgent medical need. We previously showed that transplantation of lentiviral vector- transduced Hematopoietic Stem Cells (HSC) targets therapeutic genes to the CNS and PNS and prevents functional and pathological manifestations of MLD in the mouse model, when applied at early pre-symptomatic stage (Biffi A. et al., JCI 2004). We now report that the HSC-based approach can also correct already established neurologic functional deficits and neuronal damage when applied to symptomatic animals. These new data, considering the poor or null outcome of hematopoietic stem cell transplant on symptomatic patients, provide a strong rationale for testing gene therapy in MLD patients. To this regard, we showed that the degree of efficacy of gene therapy is dependent on the levels of enzyme activity in HSC and in target organs, thus strengthening the concept that the major advantage of gene therapy might be related to the possibility to express the functional enzyme largely above normal donor's levels in HSC and in their progeny. As far as the mechanism of disease correction and the biodistribution of the functional enzyme are concerned, we demonstrated the role of gene corrected, ARSA over-expressing microglia as unique and efficacious source of bioavailable enzyme in the brain. Further, we provided a long-sought proof of the direct in vivo occurrence of active enzyme secretion by HSC- derived microglia and of enzyme transfer to other neural and non-neural cells in the brain. Interestingly, by establishing a sustained hepatic source of ARSA in chimeric mice harboring ARSA over-expressing hepatocytes from transgenic donors, we failed to deliver the enzyme to the CNS. These new findings highlight the role of microglia as exclusive source of bioavailable enzyme to the brain, and most importantly challenge the potential efficacy of newly developed enzyme replacement strategies for CNS targeting in lysosomal disorders. Finally, the detection of ARSA in the peripheral nervous system of treated mice underlines, together with correction of PNS neurophysiological and histopathological abnormalities, underlines the relevance of this approach in targeting not only the CNS, but also the widespread distributed PNS network, whose involvement is critical for patient's prognosis.

X-linked severe combined immunodeficiency (X-SCID), a fatal disorder caused by mutations in the IL2R|[gamma]| gene, has been treated by retroviral vector (RV) mediated gene replacement in hematopoietic stem cells (HSC). A crucial factor for the success of this approach was the selective growth advantage of gene-modified cells, which allowed lymphoid repopulation from a small number of transduced HSC. Unfortunately, leukemia developed in a fraction of treated patients and its origin was linked to RV insertional mutagenesis.

We have shown previously that human genome editing can be performed at high efficiency using designed zinc finger nucleases (ZFNs). ZFNs can be engineered to generate a double-strand break at a specific chromosomal location both in transformed and primary human cells. These breaks are repaired by the cell's own DNA repair machinery, and when a homologous extrachromosomal donor molecule is provided, a homology-directed repair process leads to highly efficient transfer of single-base-pair changes into the chromosome (Urnov et al. Nature 435: 646). ZFNs can be engineered to target virtually any chromosomal location (Pabo et al., Ann. Rev. Biochem. 70: 313), and function robustly in human hematopoietic stem cells, hence such localized gene modification may potentially be useful in the correction and treatment of certain monogenic diseases. Here we show that ZFNs can also be used for the preciseinsertion of a novel sequence into a pre-determined location in the human genome. Remarkably, this novel sequence can constitute a short patch sequence or several kilobases of one or more transgenes. We have observed ZFN-driven targeted integration into endogenous chromosomal loci in human cells of entire open reading frames and promoter-transcription units at a frequency of 5% in the absence of any selection. We also show the use of this process to disrupt with high efficiency an endogenous chromosomal locus with a selectable marker ORF. Finally, we describe our work on using ZFN-driven integration to insert a therapeutically-relevant transgene into a |[ldquo]|safe-harbor|[rdquo]| locus in the human genome, potentially avoiding the problem of insertional mutagenesis. Hence, the homology-directed repair process invoked by the ZFNs can be used to carry out high-efficiency targeted integration to potentially improve the safety and efficacy of gene therapy.

Immune responses against genetically modified cells represents a major obstacle to the success of gene therapy. Cellular and humoral immune responses to vector-associated and transgene-derived proteins lead to prompt elimination of transgene expressing cells abrogating the benefits of gene transfer. Several strategies have been used to limit immune response following gene transfer, including immunosuppression and the use of different routes of administration.

Wiskott-Aldrich syndrome (WAS) is a severe X-linked immunodeficiency characterized by recurrent infections, thrombocytopenia, eczema and increased risk of autoimmune disorders and lymphomas. Hematopoietic stem cell (HSC) transplantation from HLA-identical sibling donors is a resolutive treatment, but it is available only for a minority of patients. Transplantation of genetically corrected autologous HSC could represent an alternative treatment, potentially applicable to all patients. In a murine model of WAS (WAS|[minus]|/|[minus]|), we recently demonstrated correction of the T cell defect 4 months after lentiviral vector-mediated gene therapy [Dupr|[eacute]|, Marangoni, et al. Hum Gene Ther. 2006, 17]. The aim of the present study was to investigate the long-term efficacy and safety of our gene therapy approach in WAS|[minus]|/|[minus]| mice.

Top of pageAbstract We have recently shown that in order to attain therapeutic efficacy by HSC gene therapy for Metachromatic Leukodystrophy (MLD), Arylsulfatase A (ARSA) over-expression in HSC and their progeny is required. The recent identification of Sulfatase Modifying Factor 1 (SUMF1) as a common activator of sulfatases and a rate-limiting factor in the biological activation of these enzymes, raises concerns for possible adverse effects of enzyme over-expression within certain cell type (Cosma M.P. et al., Cell 2003). In fact, over-expression of one type of sulfatase may lead to reduced activity of other sulfatases by a competitive interaction with their common activator. In order to assess the safety of ARSA over-expression in vivo we generated transgenic mice over-expressing the ARSA gene by lentiviral vectors (LV). Pups were genotyped for the presence of the LV backbone by PCR, and screened for vector content (expressed in LV copies per cell, CpC) and ARSA activity. Transgenic mice bearing multiple LV copies (up to 30CpC) and expressing ARSA at high levels were bred to generate a high expressor colony. In mice of the first 5 generations, we detected over-expression of ARSA up to 30 fold above wild type syngenic controls at the level of all tested tissues (liver, kidney, brain, bone marrow). Immunofluorescence and confocal microscopy showed the tagged enzyme widely expressed in these tissues, within different cell types, and correctly sorted to the lysosomal compartment. Despite these supra-physiological conditions, these mice, which have been monitored for survival, body weight, hematopoietic and neurological functions (behavioral and neurophysiological studies), showed no sign of toxicity in the 5 to 6 generations already bred. These data demonstrate the absence of major toxicity or detrimental effects related to ARSA over-expression. We then evaluated the activity of several other SUMF1-dependet sulfatases (Arylsulfatases C, D and E, of Sulfamidase and Iduronate 2-sulfatase) in the blood and tissue samples of ARSA transgenic mice. No significant differences were documented between transgenic mice and syngenic controls, suggesting that either SUMF1 could be inducible upon over-expression of one of the sulfatases, or that other molecules, such as the newly identified SUMF2, could play a compensatory role in sulfatases activation.

The initial interaction with host tissues of systemically administered viral vectors is a critical event for stable gene transfer. It is now well established that injection of adenoviral vectors leads to an inflammatory response, mediated by elevations in IL-6 and TNF|[alpha]|. This response triggers the adaptive immune response, and leads to anti-vector and transgene immunity.

Adenosine deaminase (ADA) deficiency is a severe combined immunodeficiency (SCID) characterized by systemic toxicity and profoundly impaired lymphoid cell development and functions due to the accumulation of purine metabolites. ADA-deficient (ADA KO) mice die within 3 weeks of age due to metabolic toxicity and can be rescued by enzyme replacement therapy with PEG-ADA. The aim of our study was to investigate the efficacy of gene therapy (GT) in comparison to bone marrow transplantation (BMT) in the ADA KO mouse model. A SIN HIV-1-based lentiviral vector encoding human ADA cDNA under the control of PGK promoter was constructed. ADA KO mice were maintained short-term on PEG-ADA and then transplanted, after non-myeloablative conditioning either with WT BM cells or with ADA KO BM cells transduced ex vivo. We first showed that BMT with donor WT cells rescued mice from lethality, restored T-cell and B-cell counts in the peripheral blood and led to normal proliferation after T or B cells specific stimulation. Similarly, GT with transduced BM cells rescued ADA KO mice from lethality and restored their growth to normal levels. Quantitative PCR for donor cells (Y chromosome in sex-mismatched transplant) and vector-positive cells showed the presence of ADA transduced cells in the peripheral circulation of transplanted ADA KO mice (30|[ndash]|40% 5 months post-GT). Two months after GT, ADA activity in red blood cells reached normal levels and dAXP toxic metabolites decreased to undetectable levels. GT resulted in normal lymphoid differentiation in primary and secondary lymphoid organs, as well as restoration of T-cell and B-cell in vitro proliferative responses after stimulation with anti-CD3/anti-CD28 and anti-IgM antibody, respectively. Finally, serum levels of IgM and IgG were comparable between GT and BMT mice. These studies demonstrate that lentiviral-mediated ADA gene transfer associated with non-myeloablative conditioning corrects both the metabolic and the immunological defects in the ADA KO animal model. We are currently evaluating the long-term safety related to the use of hematopoietic stem/progenitor cells transduced with lentiviral vectors.

Wiskott-Aldrich syndrome (WAS) is a X-linked primary immunodeficiency with a median survival of 14 years of age due to infections, severe hemorrhage, and lymphomas. Transplantation of hematopoietic stem cells (HSC) from HLA-identical sibling donors is a resolutive treatment, but is available for a minority of patients. Transplantation of genetically corrected autologous HSC could represent an alternative treatment applicable to all patients. We investigated the efficacy and safety of WAS gene transfer with HIV-based lentiviral vectors using untransformed T cells from WAS patients and HSC.

Stable gene replacement by in vivo administration of lentiviral vectors (LV) has important therapeutic applications. However, successful gene therapy is often limited by the immune response to the transgene products, which leads to the clearance of transduced cells. Induction of tolerance to a transgene is highly desirable for successful gene therapy trials. We developed a model in which immunocompetent B6 mice were injected with LV expressing GFP under the CMV promoter (LV-GFP). Peak of GFP expression was detected two weeks after injection and a rapid decrease thereafter. Infiltration of CD8+ T cells was observed in the liver two weeks after LV-GFP injection. GFP-specific IFN-g production by splenic CD8+ T cells derived from LV-GFP injected mice was detected by ELISPOT assay starting from the first week until fifteen weeks post injection. Anti-GFP Abs were also present two weeks after injection and gradually decreased over time. Overall these data indicate that immunocompetent mice injected with LV-GFP develop an Ag-specific CD8+ T cell response that leads to clearance of the transgene expressing cells. CD4+CD25+ T regulatory (Tr) cells play a key role in peripheral tolerance and they have been extensively characterized in preclinical models of T cell mediated diseases. In the present model we investigated whether Tr cells could prevent GFP clearance in vivo. B6 mice were co-injected with LV-GFP and Tr cells isolated from syngeneic wt mice (wt Tr). Clearance of GFP expressing cells and anti-GFP immune response was unmodified in LV-GFP+ wt Tr cells co-injected mice, suggesting that injection of wt Tr cells and consequent increase in the Tr cells pool did not protect from the immune response to the transgene. To investigate whether CD4+CD25+ Tr cells need to be GFP specific in order to modulate the anti-GFP immune response, B6 mice were co-injected with LV-GFP and GFP expressing cells obtained from splenocytes of GFP-Tg mice (GFP Tg cells). Interestingly, transfer of GFP Tg cells was able to down-modulate expansion of splenic GFP-specific CD8+ T cells. Since the GFP Tg cells comprise of both CD4+CD25+ Tr (13,5%) and GFP Tg antigen presenting cells (GFP Tg APC) we next investigated the respective role of these two cell populations. We first co-injected mice with LV-GFP and highly purified GFP Tg Tr (99,1%). As with the administration of wt Tr cells, the transfer of highly purified GFP Tg Tr cells did not modulate the immune response to GFP in vivo. On the contrary, the co-administration of LV GFP and highly purified GFP Tg APC significantly modulated both the cellular and humoral anti-GFP immune responses. These results demonstrate that APC isolated from GFP tolerant mice can reduce the immune response to GFP when transferred in vivo. We hypothesize that after LV-GFP injection the transgene expressing GFP Tg APC activate the endogenous CD4+CD25+ Tr in the absence of danger signals leading to down regulation of the anti-GFP response. Transgene presentation by APC is therefore crucial to trigger an immune-regulatory response mediated by CD4+CD25+ Tr cells.

In mouse, retroviral infection triggers leukemias by activation of cellular proto-oncogenes. This is usually mediated by promoter/enhancer sequences in the proviral LTR that recruit ubiquitous and/or cell type-specific transcription factors, and up-regulate expression of flanking genes, up to 300 Kb away from the integration site, and independently of orientation. Unfortunately, Retroviral Vectors (RV) used in gene therapy also triggered unwanted oncogenesis, indicating that the risk of RV insertional mutagenesis had been underestimated, and raising concerns for their further use in gene therapy. In addition RV, Lentiviral (LV) and Adeno-Associated vectors have the tendency to integrate in the proximity of expressed genes. Thus, these safety concerns apply to all integrative vectors, in particular to the closely related LV that have been proposed as improved versions of RV for several applications. The actual frequency and extent of transcriptional de-regulation occurring at randomly picked retroviral integration sites is currently unknown. In fact, integration sites retrieved from tumors are likely the result of in vivo selection for proto-oncogene activation, and it has proven very difficult to estimate the frequency of such events in unselected target cells. This information is critical to properly assess the insertional mutagenesis risk of each vector. Thus, we embarked in testing and comparing the effect of non-selected RV and LV integration on the expression of flanking genes. We generated three panels of hematopoietic cell clones, each carrying a single insertion of either a conventional RV expressing GFP from the LTR, a self inactivating (SIN)-RV expressing GFP from an internal PGK promoter, and a third-generation SIN-LV expressing GFP from the same PGK promoter. For each vector, we isolated 150 clones, and retrieved genomic DNA flanking the proviral insertion in 50 of them by linear amplification-mediated PCR. So far, sequence analysis has allowed in silico mapping of 40 single integrations. Even if our study requires a relatively small sample size, it is apparent that integration site selection differed between RV and LV; RV integrated within regions of lower gene density with respect to LV; 66% of RV insertions were intergenic, while 83 % of LV insertions were intragenic; 50% of RV insertions were found between 0.5–5kb from the closest transcription start site, as compared to only 5% of LV insertions. We then selected all the genes (SeqRef database) contained in a 600 kb interval centered on each integration site (344 up to now). We are currently comparing their relative expression levels in all cell clones by microarray technology, using custom-made microchips spotted with the selected sequences, and probing with total cDNA obtained from each clone and a pool of control untransduced ones. This analysis will indicate the frequency and extent of transcriptional perturbation around RV and LV integration. We expect to find significant differences between each vector, according to its viral origin and design. If so, our data will be critical to estimate the relative risk of oncogene activation in gene therapy applications.

HIV-derived pseudotyped lentiviral vectors are potent vectors for the transfer of potentially therapeutic genes into the brain. However, the efficiency of LV-mediated gene transfer into the brain has not been examined in detail. Further, nothing is known on the effects of the systemic priming of an anti-lentiviral immune response on transgene expression and inflammation in the brain. The self-inactivating pRRLsin.cPPT.CMV.Wpre, and pRRLsin.cPPT.ALB.Wpre constructs were used to generate VSV-pseudotyped LV stocks expressing either GFP (LV-GFP) or human FIX (LV-hFIX). Titers for LV-GFP were determined on HeLa and mouse liver (MLP29) cells and were approx. 5 × 109 to 2 × 1010 transducing units (TU)/ml with 100–400 ug HIV-1 p24/ml. To study the innate inflammatory responses to LV vectors in the CNS, LV-GFP was injected into the striatum at doses of 1 × 102−1 × 107 TU. Transduced cells could be found at all doses, and transgene expression increased up to the highest dose. Even at the highest dose, there was no statistically significant increase in the influx of either activated macrophages or CD8+-T cells. To analyze the effects of the systemic anti-LV immunization on gene expression in the CNS, LV-GFP was injected into the striatum, followed 30 days later, by the systemic immunization with either LV-GFP or LV-FIX, or the injection of saline. The effectiveness of the immune responses were determined by the presence of anti-envelope and anti-transgene antibodies by ELISA. In animals immunized against LV-FIX or injected with saline, there was no changes in the number of immunoreactive cells in the brain. However, in animals immunized against LV-GFP, there was a 30–50% reduction in the number of immunoreactive neurons. Concomitantly, there was a highly significant increase in the number of CD8+ T-cells in the brains of animals immunized with LV-GFP, but not those immunized with LV-FIX. This indicates that LV-injected into the brain cause minimal activation of the CNS innate inflammatory response. However, in the presence of a systemic anti-transgene immune response, activated lymphocytes can enter the brain and contribute to a down-regulation of LV-encoded transgene expression. Since LV-derived vectors do not express any vector proteins, immunization against a LV vector expressing a different transgene did not cause brain inflammation or down-regulation of CNS transgene expression. In conclusion, a systemic anti-transgene immune response can down-regulate gene expression from a LV vector in the CNS.

MLD and GLD are inborn lipidosis caused by the deficiency of the lysosomal enzymes arylsulfatase A (ARSA) and galactocerebrosidase (GALC). They are characterized by storage of undegraded sulfatides in the CNS and PNS, leading to progressive demyelination and early death. Using Lentiviral Vectors (LV), we efficiently transduced Hematopoietic Stem Cells (HSC) ex vivo and evaluated the potential of their progeny to target therapeutic genes to the CNS and PNS of transplanted mice, and correct MLD and GLD phenotypes in the mouse models. We proved extensive transgene expression in the CNS and PNS of transplanted mice due to progressive turnover of microglia and endoneurial macrophages by HSC-derived cells. Recruitment of these cells was consistently observed independently from the conditioning protocol, and it was faster and more robust in MLD and GLD mice. By transplanting HSC transduced with the ARSA gene, we reconstituted enzyme activity in the hematopoietic system of MLD mice at supranormal levels and prevented all mayor disease manifestations. Transplanted mice were completely protected from the development of motor conduction impairment (normalization of motor conduction velocity and F wave latency, and of central conduction time), of learning and coordination deficits (normalization of the performance at rotarod test), and of neuropathological abnormalities (prevention of sulfatide accumulation and demyelination in CNS and PNS) typical of the disease. Remarkably, ex vivo gene therapy had a significantly better therapeutic impact than wild-type HSC transplantation on all examined parameters, highlighting the crucial role of enzyme over-expression and indicating the likely occurrence of in vivo cross-correction. Confocal analysis of the CNS of treated mice showed the presence of tagged ARSA enzyme within the lysosomes both of the transduced HSC-derived microglia cells and of resident neurons, demonstrating in vivo enzyme transfer and, most likely, cross-correction. To further evaluate the therapeutic impact of this approach we challenged it with the acute and devastating evolution of GLD in the mouse model. Neonate GLD mice were transplanted with HSC transduced with the GALC gene, supplemented with accessory Sca1- cells to reduce short-term toxicity of conditioning. We observed a dramatic improvement in survival of transplanted mice, which reached an average of 135 days, as compared to 40 days of untreated GLD mice and 80 days of mice transplanted with wild type bone marrow, providing striking evidence, in another disease setting, of the therapeutic advantage of ex vivo gene therapy versus allogeneic BMT. We observed a significant improvement in the GLD phenotype (absence of leg palsy and delayed, minor twitching) and prevention of mayor histopathological signs of the disease (demyelination, axonal loss). Overall, these results demonstrate that transplantation of LV-transduced autologous HSC represents a new, potentially efficacious therapeutic strategy for MLD, GLD and possibly other neurodegenerative disorders.