Lentivirus vectors are effective for treatment of genetic disease. However, safety associated with vector related genotoxicity is of concern and currently available models are not reliably predictive of safety in humans. We have developed hInGeTox as the first human in vitro platform that uses induced pluripotent stem cells and their hepatocyte like cell derivatives to better understand vector-host interactions that relate vectors to their potential genotoxicity. Using lentiviral vectors carrying the eGFP expression cassette under SFFV promoter activity, that only differ by their LTR and SIN configuration, we characterised vector host interactions potentially implicated in genotoxicity. To do this, lentiviral infected cells were subjected to an array of assays and data from these was used for multi-omics analyses of vector effects on cells at early and late harvest time points. Data on the integration sites of lentiviral vectors in cancer genes and differential expression levels of these genes, showed that both vector configurations are capable of activating cancer genes. Through IS tracking in bulk infected cell populations, we also saw an increase in the viral sequence count in cancer genes present over time which were differentially regulated. RNASeq also showed each vector had potential to generate fusion transcripts with the human genome suggestive of gene splicing or vector mediated readthrough from the internal SFFV promoter. Initially, after infection, both vector configurations were associated with differential expression of genes associated cytokine production, however, after culturing over time there were differences in differential expression in cells infected by each LV. This was marked in particular by the expression of genes involved in the response to DNA damage in cells transduced by the SIN vector, suggesting effects likely to prevent tumour development, in contrast to the expression of genes involved in methylation, characteristic of tumour development, in cells transduced by the LTR vector. Both sets of lentiviral infected cells were also found associated with differential expression of MECOM and LMO2 genes known to be associated with clonal dominance, supporting their potential genotoxicity. Alignment of transcriptomic signatures from iPSC and HLC infected cultures with known cancer gene signatures showed the LTR vector with a higher cancer score than the SIN vector over time in iPSC and also in HLC, which further suggests higher genotoxic potential by the LTR configuration lentivirus. By application of hInGeTox to cells infected with LV at the pre-clinical stage of development, we hope that hInGeTox can act as a useful pre-clinical tool to identify lentivirus-host interactions that may be considered contributory to genotoxicity to improve safer lentiviral vector design for gene therapy.

Abstract Lentivirus vectors are effective for treatment of genetic disease and cancer, however, vector related insertional mutagenesis related genotoxicity is of concern and currently available safety models are not reliably predictive of safety in humans. We have developed hInGeTox as the first human in vitro platform that uses induced pluripotent stem cells and their hepatocyte like derivatives to further understand LV host interaction for vector safety evaluation and design. To characterise LV for genotoxic association, we used LTR and SIN configuration LV infected cells for a multi-omics analysis on data that included LV integration sites in cancer genes and their associated differential expression, clonal tracking of IS, novel vector/host fusion transcripts and methylated cancer genes with altered gene expression after infection. We present hInGeTox as a useful pre-clinical tool to identify lentivirus contributory factors mediating genotoxicity to use for improving LV design to provide gene therapy.

Hematopoietic stem cell gene therapy (GT) using a γ-retroviral vector (γ-RV) is an effective treatment for Severe Combined Immunodeficiency due to Adenosine Deaminase deficiency. Here, we describe a case of GT-related T-cell acute lymphoblastic leukemia (T-ALL) that developed 4.7 years after treatment. The patient underwent chemotherapy and haploidentical transplantation and is currently in remission. Blast cells contain a single vector insertion activating the LIM-only protein 2 (LMO2) proto-oncogene, confirmed by physical interaction, and low Adenosine Deaminase (ADA) activity resulting from methylation of viral promoter. The insertion is detected years before T-ALL in multiple lineages, suggesting that further hits occurred in a thymic progenitor. Blast cells contain known and novel somatic mutations as well as germline mutations which may have contributed to transformation. Before T-ALL onset, the insertion profile is similar to those of other ADA-deficient patients. The limited incidence of vector-related adverse events in ADA-deficiency compared to other γ-RV GT trials could be explained by differences in transgenes, background disease and patient's specific factors.

Background Allogeneic haematopoietic stem-cell transplantation is the standard treatment for bone marrow failure (BMF) in patients with Fanconi anaemia, but transplantation-associated complications such as an increased incidence of subsequent cancer are frequent. The aim of this study was to evaluate the safety and efficacy of the infusion of autologous gene-corrected haematopoietic stem cells as an alternative therapy for these patients. Methods This was an open-label, investigator-initiated phase 1/2 clinical trial (FANCOLEN-1) and long-term follow-up trial (up to 7 years post-treatment) in Spain. Mobilised peripheral blood (PB) CD34+ cells from nine patients with Fanconi anaemia-A in the early stages of BMF were transduced with a therapeutic FANCA-encoding lentiviral vector and re-infused without any cytotoxic conditioning treatment. The primary efficacy endpoint of FANCOLEN-1 was the engraftment of transduced cells, as defined by the detection of at least 01 therapeutic vector copies per nucleated cell of patient bone marrow (BM) or PB at the second year post-infusion, without this percentage having declined substantially over the previous year. The safety coprimary endpoint was adverse events during the 3 years after infusion. The completed open-label phase 1/2 and the ongoing long-term clinical trials are registered with ClinicalTrials.gov, NCT03157804; EudraCT, 2011-006100-12; and NCT04437771, respectively. Findings There were eight evaluable treated patients with Fanconi anaemia-A. Patients were recruited between Jan 7, 2016 and April 3, 2019. The primary endpoint was met in five of the eight evaluable patients (6250%). The median number of therapeutic vector copies per nucleated cell of patient BM and PB at the second year post-infusion was 018 (IQR 001-020) and 006 (001-019), respectively. No genotoxic events related to the gene therapy were observed. Most treatment-emergent adverse events (TEAEs) were non-serious and assessed as not related to therapeutic FANCA- encoding lentiviral vector. Nine serious adverse events (grade 3-4) were reported in six patients, one was considered related to medicinal product infusion, and all resolved without sequelae. Cytopenias and viral infections (common childhood illnesses) were the most frequently reported TEAEs. Interpretation These results show for the first time that haematopoietic gene therapy without genotoxic conditioning enables sustained engraftment and reversal of BMF progression in patients with Fanconi anaemia. Funding European Commission, Instituto de Salud Carlos III, and Rocket Pharmaceuticals. Copyright (c) 2024 Elsevier Ltd. All rights reserved, including those for text and data mining, AI training, and similar technologies.

Genotoxicity remains an unknown safety concern of gene therapy. Molecular techniques for determining the frequency and genomic localization of vector integration are central to understanding primarily integrating viral vectors (ie, retrovirus and lentivirus). Unlike these vectors, recombinant adeno-associated virus (rAAV) vectors integrate into host genomes at low frequencies. Nevertheless, the integration of rAAV sequences in oncogenic hotspots could theoretically lead to hepatocellular carcinoma (HCC). 1 This report describes the molecular characterization of the fi rst case of HCC complicating an rAAV gene therapy trial. Studies using rAAV in mice reported low integration levels into host chromosomal sequences associated with HCC. 2,3 Investigations suggested that HCC was driven by microRNA-341 dysregulation within the Rian locus, a hotspot for mouse genome integration. The Rian locus in mice has a human ortholog, the human long-coding RNA, MEG8 , which is overexpressed in some HCCs and may interact with microRNA-367-3p in the pathogenesis and progression of some HCCs. 4 Nevertheless, the microRNA-341 locus found to be susceptible to rAAV insertional mutagenesis in mice has no human homolog. 5 Studies using mouse models have previously been performed

Sickle cell disease (SCD) and transfusion-dependent β-thalassemia (TDT) are the most prevalent monogenic disorders worldwide. Trial HGB-205 ( NCT02151526 ) aimed at evaluating gene therapy by autologous CD34 + cells transduced ex vivo with lentiviral vector BB305 that encodes the anti-sickling β A-T87Q -globin expressed in the erythroid lineage. HGB-205 is a phase 1/2, open-label, single-arm, non-randomized interventional study of 2-year duration at a single center, followed by observation in long-term follow-up studies LTF-303 ( NCT02633943 ) and LTF-307 ( NCT04628585 ) for TDT and SCD, respectively. Inclusion and exclusion criteria were similar to those for allogeneic transplantation but restricted to patients lacking geno-identical, histocompatible donors. Four patients with TDT and three patients with SCD, ages 13–21 years, were treated after busulfan myeloablation 4.6–7.9 years ago, with a median follow-up of 4.5 years. Key primary endpoints included mortality, engraftment, replication-competent lentivirus and clonal dominance. No adverse events related to the drug product were observed. Clinical remission and remediation of biological hallmarks of the disease have been sustained in two of the three patients with SCD, and frequency of transfusions was reduced in the third. The patients with TDT are all transfusion free with improvement of dyserythropoiesis and iron overload.

BACKGROUND Betibeglogene autotemcel (beti-cel) gene therapy for transfusion-dependent beta-thalassemia contains autologous CD34+ hematopoietic stem cells and progenitor cells transduced with the BB305 lentiviral vector encoding the beta-globin (beta(A-)(T87Q)) gene. METHODS In this open-label, phase 3 study, we evaluated the efficacy and safety of beti-cel in adult and pediatric patients with transfusion-dependent beta-thalassemia and a non-beta(0)/beta(0) genotype. Patients underwent myeloablation with busulfan (with doses adjusted on the basis of pharmacokinetic analysis) and received beti-cel intravenously. The primary end point was transfusion independence (i.e., a weighted average hemoglobin level of >= 9 g per deciliter without red-cell transfusions for >= 12 months). RESULTS A total of 23 patients were enrolled and received treatment, with a median followup of 29.5 months (range, 13.0 to 48.2). Transfusion independence occurred in 20 of 22 patients who could be evaluated (91%), including 6 of 7 patients (86%) who were younger than 12 years of age. The average hemoglobin level during transfusion independence was 11.7 g per deciliter (range, 9.5 to 12.8). Twelve months after beti-cel infusion, the median level of gene therapy-derived adult hemoglobin (HbA) with a T87Q amino acid substitution (HbA(T87Q)) was 8.7 g per deciliter (range, 5.2 to 10.6) in patients who had transfusion independence. The safety profile of beti-cel was consistent with that of busulfan-based myeloablation. Four patients had at least one adverse event that was considered by the investigators to be related or possibly related to beti-cel; all events were nonserious except for thrombocytopenia (in 1 patient). No cases of cancer were observed. CONCLUSIONS Treatment with beti-cel resulted in a sustained HbA(T)(87)(Q) level and a total hemoglobin level that was high enough to enable transfusion independence in most patients with a non-beta(0)/beta(0) genotype, including those younger than 12 years of age.

lovo-cel (bb1111; LentiGlobin for sickle cell disease [SCD]) gene therapy (GT) comprises autologous transplantation of hematopoietic stem and progenitor cells transduced with the BB305 lentiviral vector encoding a modified β-globin gene (βA-T87Q ) to produce anti-sickling hemoglobin (HbAT87Q ). The efficacy and safety of lovo-cel for SCD are being evaluated in the ongoing phase 1/2 HGB-206 study (ClinicalTrials.gov: NCT02140554). The treatment process evolved over time, using learnings from outcomes in the initial patients to optimize lovo-cel's benefit-risk profile. Following modest expression of HbAT87Q in the initial patients (Group A, n = 7), alterations were made to the treatment process for patients subsequently enrolled in Group B (n = 2, patients B1 and B2), including improvements to cell collection and lovo-cel manufacturing. After 6 months, median Group A peripheral blood vector copy number (≥0.08 c/dg) and HbAT87Q levels (≥0.46 g/dL) were inadequate for substantial clinical effect but stable and sustained over 5.5 years; both markedly improved in Group B (patient B1: ≥0.53 c/dg and ≥2.69 g/dL; patient B2: ≥2.14 c/dg and ≥6.40 g/dL, respectively) and generated improved biologic and clinical efficacy in Group B, including higher total hemoglobin and decreased hemolysis. The safety of the lovo-cel for SCD treatment regimen largely reflected the known side effects of HSPC collection, busulfan conditioning regimen, and underlying SCD; acute myeloid leukemia was observed in two patients in Group A and deemed unlikely related to insertional oncogenesis. Changes made during development of the lovo-cel treatment process were associated with improved outcomes and provide lessons for future SCD GT studies.

Lentiviral vectors (LV) are attractive for permanent and effective gene therapy. However, integration into the host genome can cause insertional mutagenesis highlighting the importance of understanding of LV integration. Insertion site (IS) tethering is believed to involve cellular proteins such as PSIP1/LEDGF/p75, which binds to the virus pre-integration complexes (PICs) helping to target the virus genome. Transcription factors (TF) that bind both the vector LTR and host genome are also suspected influential to this. To determine the role of TF in the tethering process, we mapped predicted transcription factor binding sites (pTFBS) near to IS chosen by HIV-1 LV using a narrow 20 bp window in infected human induced pluripotent stem cells (iPSCs) and their hepatocyte-like cell (HLC) derivatives. We then aligned the pTFBS with these sequences found in the LTRs of native and self-inactivated LTRs. We found significant enrichment of these sequences for pTFBS essential to HIV-1 life cycle and virus survival. These same sites also appear in HIV-1 patient IS and in mice infected with HIV-1 based LV. This in silco data analysis suggests pTFBS present in the virus LTR and IS sites selected by HIV-1 LV are important to virus survival and propagation.

Protein-coding and non-coding genes like miRNAs tightly control hematopoietic differentiation programs. Although miRNAs are frequently located within introns of protein-coding genes, the molecular interplay between intronic miRNAs and their host genes is unclear. By genomic integration site mapping of gamma-retroviral vectors in genetically corrected peripheral blood from gene therapy patients, we identified the EVL/MIR342 gene locus as a hotspot for therapeutic vector insertions indicating its accessibility and expression in human hematopoietic stem and progenitor cells. We therefore asked if and how EVL and its intronic miRNA-342 regulate hematopoiesis. Here we demonstrate that overexpression (OE) of Evl in murine primary Lin− Sca1+ cKit+ cells drives lymphopoiesis whereas miR-342 OE increases myeloid colony formation in vitro and in vivo, going along with a profound upregulation of canonical pathways essential for B-cell development or myelopoietic functions upon Evl or miR-342 OE, respectively. Strikingly, miR-342 counteracts its host gene by targeting lymphoid signaling pathways, resulting in reduced pre-B-cell output. Moreover, EVL overexpression is associated with lymphoid leukemia in patients. In summary, our data show that one common gene locus regulates distinct hematopoietic differentiation programs depending on the gene product expressed, and that the balance between both may determine hematopoietic cell fate decision.

Abstract Background: The ongoing Phase 1/2 HGB-206 study (NCT02140554) of LentiGlobin for SCD (bb1111) GT uses a modified human β-globin gene that expresses an anti-sickling hemoglobin (HbA T87Q). The relationships between biological outcomes, clinical outcomes, and clonality in the initial cohort (Group A) and the cohort treated after substantial changes were made to the study protocol and manufacturing process to improve clinical benefit (Group C) are presented here. Methods: Patients (pts; ≥18 in Group A and ≥12-≤50 yrs in Group C) with SCD and recurrent severe vaso-occlusive events (VOEs), overt stroke, or tricuspid regurgitant jet velocity of >2.5 m/s, were enrolled. The initial protocol (cell collection and target busulfan dose) and manufacturing process in Group A was modified to improve cell dose, transduction efficiency, HbA T87Q expression, and clinical benefit. CD34+ cells (collected by bone marrow [BM] harvesting in Group A and plerixafor mobilization/apheresis in Group C) were transduced with BB305 lentiviral vector (LVV). LentiGlobin was infused after myeloablative busulfan conditioning. Transduction, SCD-related outcomes, clonality, and safety were assessed; data are median (min-max) unless otherwise stated. Results: As of 17 February 2021, there were 61.5 (55.5-66.1) months of follow-up post-LentiGlobin infusion in Group A (n=7) and 17.3 (3.7-37.6) months in Group C (n=35). After protocol and manufacturing modifications, median drug product vector copy number (DP VCN) and transduction efficiency were increased in Group C (3.7 c/dg with 80.3% transduced cells) compared with Group A (0.6 c/dg with 27.7% transduced cells). Peripheral blood (PB) VCN stabilized by Month 6 post-infusion and was sustained throughout follow up in both groups; however, the median PB VCN was correspondingly higher in Group C than in Group A (1.45 c/dg vs 0.09 c/dg). A higher DP VCN, %LVV+, and PB VCN in Group C generated increased HbA T87Q of 5.2 (2.6-8.8) g/dL (n=30) compared with HbA T87Q of 0.5 (0.1-1.8) g/dL (n=7) in Group A at Month 6. This was associated with near pancellular expression of HbA T87Q at ≥6 months post-infusion in Group C with a mean of 87% of red blood cells containing β A-T87Q by 18 months (n=14). Group C featured significantly higher median unique insertion sites (UIS) than Group A (p = 1.43 x 10 -12;Fig 1), consistent with increased polyclonality. Critically, median UIS also correlated strongly with PB VCN (Spearman rho = 0.97; Fig 1) and HbA T87Q at Month 6 post-infusion and was associated with improved clinical efficacy in Group C, with complete resolution of severe VOEs and near normal levels of key hemolysis markers. In Group C, the only treatment (tx) emergent serious adverse events (TESAEs) reported in >1 pt were abdominal pain, nausea, opioid withdrawal syndrome, and vomiting (n=2, 5.7% each). No events of malignancy were reported in Group C. One event of sudden death, considered unlikely related to LentiGlobin, occurred >18 months post-tx in a patient with significant baseline SCD-related cardiopulmonary disease. In Group A, the most common TESAE was sickle cell anemia with crisis (n=4, 57%). Two events of acute myeloid leukemia (AML) were reported in Group A pts at 3 and 5 years post-tx, both of which were considered unlikely related to the LVV. Both pts had classic AML driver mutations identified post-diagnosis. One pt died of AML and the second pt is receiving therapy for AML. The modifications made in Group C are anticipated to reduce risk of AML. To monitor safety, BM and PB will be screened for the presence of AML driver mutations prior to treatment, and patients already treated will have regular cytogenetic screening in addition to BB305 LVV integration site analysis. Summary: Alterations to the protocol and manufacturing process in HGB-206 resulted in improved cell dose, transduction efficiency, HbA T87Q expression, and clinical outcomes in Group C compared with Group A. Polyclonality was strongly correlated to PB VCN and HbA T87Q production, indicating that superior engraftment of LVV-transduced cells leads to favorable clinical outcomes. The safety profile post-LentiGlobin for all treated patients with SCD remains generally consistent with the risks of autologous stem cell transplant, myeloablative busulfan conditioning, and underlying SCD. Figure 1 Figure 1. Disclosures Thompson: Baxalta: Research Funding; Biomarin: Research Funding; bluebird bio, Inc.: Consultancy, Research Funding; Celgene/BMS: Consultancy, Research Funding; CRISPR Therapeutics: Research Funding; Vertex: Research Funding; Editas: Research Funding; Graphite Bio: Research Funding; Novartis: Research Funding; Agios: Consultancy; Beam: Consultancy; Global Blood Therapeutics: Current equity holder in publicly-traded company. Kwiatkowski: Bluebird Bio: Other: Consultancy Fees; Imara: Other: Consultancy Fees; Celgene: Honoraria; Silence Therapeutics: Honoraria; Agios: Honoraria; ApoPharma: Research Funding; Novartis: Research Funding; Bluebird Bio: Research Funding; Sangamo: Research Funding; Terumo BCT: Research Funding. Aygun: National Heart, Lung, Blood Institute: Research Funding; Global Blood Therapeutics: Consultancy; National Institute of Nursing Research: Research Funding; Patient Centered Outcomes Research Institute: Research Funding; bluebird bio, Inc.: Membership on an entity's Board of Directors or advisory committees, Research Funding. Schmidt: GeneWerk GmbH, Heidelberg, Germany: Current equity holder in publicly-traded company; German Cancer Research Center, Heidelberg, Germany: Current Employment. Pierciey: bluebird bio, Inc.: Current Employment, Current equity holder in publicly-traded company. Whitney: bluebird bio, Inc.: Current Employment, Current equity holder in publicly-traded company. Rogers: bluebird bio, Inc.: Current Employment, Current equity holder in publicly-traded company. Nnamani: bluebird bio, Inc.: Current Employment, Current equity holder in publicly-traded company. Foos: bluebird bio, Inc.: Current Employment, Current equity holder in publicly-traded company. Miller: bluebird bio, Inc.: Current Employment, Current equity holder in publicly-traded company. Zhang: bluebird bio, Inc.: Current Employment, Current equity holder in publicly-traded company. Lynch: bluebird bio, Inc.: Current Employment, Current equity holder in publicly-traded company. Walters: Vertex pharmaceuticals: Consultancy; Ensoma, Inc.: Consultancy; BioLabs, Inc: Consultancy; AllCells, Inc: Consultancy. Kanter: Fulcrum Therapeutics, Inc.: Consultancy; Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Forma: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Agios: Honoraria, Membership on an entity's Board of Directors or advisory committees; Beam: Honoraria, Membership on an entity's Board of Directors or advisory committees; Sanofi: Honoraria, Membership on an entity's Board of Directors or advisory committees; Graphite Bio: Consultancy; GuidePoint Global: Honoraria; Fulcrum Tx: Consultancy. Bonner: bluebird bio, Inc.: Current Employment, Current equity holder in publicly-traded company.