Human Gene Therapy

The Platform Vector-Gene Therapy (PaVe-GT) program is a National Institutes of Health (NIH) initiative that aims to develop adeno-associated virus (AAV) gene therapies for four monogenic rare diseases, two organic acidemias and two congenital myasthenic syndromes. PaVe-GT’s platform-based approach identifies and diminishes redundancies and applies efficiencies in preclinical, clinical, and regulatory activities. The program’s hypothesis is that implementing these efficiencies can accelerate clinical trial initiation. Based on its platform-centric experience and public-serving mission, the PaVe-GT program actively shares its scientific and regulatory learnings with the public to benefit the development of similar gene therapy products for rare diseases. PaVe-GT’s first investigational AAV gene therapy candidate is AAV serotype 9 human propionyl-CoA carboxylase alpha subunit (AAV9-hPCCA) for propionic acidemia caused by PCCA deficiency, which received initial feedback from the Food and Drug Administration (FDA) in an INitial Targeted Engagement for Regulatory Advice on CBER/Center for Drug Evaluation and Research (CDER) ProducTs (INTERACT) meeting. Upon further product development that took into consideration the FDA’s initial advice, the program obtained the Agency’s feedback in pre-investigational new drug (IND) (Type B) and Type C meetings. Here, we share our experience from these meetings, including strategy, preparation, pre- and post-meeting feedback from the FDA, and lessons learned during the AAV9-hPCCA regulatory process, which the program plans to apply across the PaVe-GT platform. Topics discussed in the regulatory meetings included animal model and efficacy studies, toxicology study plans, manufacturing of the investigational AAV product, and clinical trial design. The main lessons learned from the pre-IND and Type C meetings for AAV9-hPCCA are: (1) Pharmacology/Toxicology studies in a single rodent species are sufficient for filing an initial IND; (2) FDA feedback guides product quality improvements and early development of a quantitative potency assay; (3) use of biomarkers as potential surrogate endpoints in a future efficacy trial benefits from collection of data in the natural history study and the first-in-human Phase 1/2 study; and (4) evidence from the Phase 1/2 clinical trial could be leveraged to support a license application. Lightly redacted regulatory documents and comprehensive templates developed by the PaVe-GT team are available on the PaVe-GT website.

The adeno-associated virus (AAV) capsid variant known as “true type” (AAV-TT) is a capsid with enhanced central nervous system tropism and efficient retrograde transport across brain circuits. This property enables AAV-TT to transduce neurons in multiple regions projecting to the site of injection, as previously shown in rodent and sheep models. Such spreading offers the potential for broad therapeutic vector distribution to functionally connected brain areas via a single intraparenchymal administration. To assess the clinical potential of AAV-TT, we delivered a green fluorescent protein (GFP)-expressing AAV-TT vector into the left commissural putamen of two young adult Macaca fascicularis. For comparison, two additional animals received AAV9-GFP. Four weeks post-injection, animals were euthanized, and whole-brain transduction patterns were analyzed using a dedicated Aiforia^® deep learning-based image analysis algorithm to quantify GFP+ neurons. We observed GFP expression in structures known to innervate the injection site, consistent with retrograde transport. Both AAV-TT and AAV9 showed similar overall distribution patterns, but AAV-TT demonstrated modestly enhanced neuronal transduction efficiency compared with AAV9. This study provides the first direct comparison of AAV-TT and AAV9 in the adult nonhuman primate brain and positions AAV-TT as a promising tool for disease modeling and therapeutic interventions in neurodegenerative disorders targeting anatomically distributed neural circuits.

Hemophagocytic lymphohistiocytosis (HLH) is a life-threatening hyperinflammatory syndrome caused by genetic defects in cytotoxic lymphocyte function. Current therapies can control disease activity, but transplantation of allogeneic hematopoietic stem and progenitor cells (HSPCs) remains the only curative option and is associated with substantial risks. These limitations have accelerated development of genome editing approaches enabling precise correction of disease-causing mutations in autologous cells. Familial HLH (FHL) represents a compelling target for genome editing, but successful and safe clinical translation has remained challenging. Preclinical studies demonstrate that targeted editing of key genes, such as PRF1 and UNC13D, can restore cytotoxic function in HSPCs and T cells. Translation to the clinic, however, depends on multiple factors, including the choice of target cell population, the level of functional correction required, and gene-specific constraints such as locus complexity and regulation of gene expression. In this review, we synthesize current progress in genome editing for FHL and highlight critical biological and technical barriers to clinical implementation. We propose a conceptual framework for designing genome editing strategies tailored to FHL, emphasizing the alignment of editing platform, gene architecture, and cellular context to enable effective and clinically translatable therapies.

To treat patients affected with bestrophinopathies caused by mutations in the BEST1 gene, a recombinant adeno-associated virus vector (OPGx-BEST1 or rAAV2/2-VMD2-BEST1) is being developed. The vector construct includes the human BEST1 cDNA under control of the VMD2/BEST1 promoter and is packaged in an AAV2 capsid. This study evaluated the efficacy and toxicity of OPGx-BEST1 administered by subretinal injection in dogs that were homozygous mutant or compound heterozygotes for 3 naturally occurring mutations in BEST1. Twelve BEST1-mutant dogs were divided into 4 groups of 3 animals each, and they received in their left eye a subretinal injection of 0.15 mL of OPGx-BEST1 at 1 of 3 concentrations (9.5 × 10⁹ vector genome [vg]/mL; 3.0 × 10¹⁰ vg/mL; or 3.0 × 10¹¹ vg/mL) of OPGx-BEST1, resulting, respectively, in a low (1.4 × 10⁹ vg), high (4.5 × 10⁹ vg), and highest (4.5 × 10¹⁰ vg) dose or vehicle control. The right eyes were not injected. Subretinal injections were well tolerated and were not associated with any systemic or ocular toxicity. Electroretinography showed improved rod- and cone-mediated responses in eyes treated with OPGx-BEST1. Noninvasive retinal imaging by optical coherence tomography showed improved structural integrity with a reduction or prevention of appearance of vitelliform lesions and reversal of microdetachments in the retinal areas treated with OPGx-BEST1. These results support the use of OPGx-BEST1 in clinical studies with patients affected with bestrophinopathies and define the no-observed-adverse-effect level at 4.5 × 10¹⁰ vg/eye (0.15 mL, 3.0 × 10¹¹ vg/mL).

Recombinant adeno-associated virus (rAAV) vectors are widely used for gene therapeutics, yet their early effects on host chromatin remodeling and nuclear organization remain insufficiently characterized. In contrast, several DNA viruses are known to remodel host chromatin accessibility, for example, Herpes simplex virus type 1 (HSV-1) in mammalian cells and baculoviruses in insect systems. Here, we evaluated genome accessibility and nuclear organization of primary human fibroblast cells at 24 and 48 h after infection with wild-type AAV2, single-stranded (ss) and self-complementary rAAV2, as well as ssAAV2 and ssAAV-DJ in human lung carcinoma cells. Genome-wide assay for transposase-accessible chromatin using sequencing showed no detectable change in host chromatin accessibility at either time point. A DNase I digestion assay at five candidate loci supported this observation. Although host accessibility remained stable, immunofluorescence-based single-cell analyses uncovered modest changes in histone abundance, RNA polymerase II–associated signals, nuclear morphology, and the organization of liquid–liquid phase-separated nuclear compartments. These effects were generally mild in primary fibroblasts but showed greater dependence on vector type, cell cycle state, and transgene expression in carcinoma cells. Collectively, at the tested doses and times, AAV-based vectors did not remodel chromatin accessibility at scale and induced only small changes in polymerase-associated readouts and nuclear architecture. These data are consistent with limited nuclear perturbation under these conditions.

Cell and gene therapy (CGT) manufacturing has outpaced traditional chemistry, manufacturing, and controls frameworks, leaving a “black box” in vector quality control (QC). Legacy assays such as Sanger and short-read next-generation sequencing often fail to resolve complex structures including adeno-associated virus (AAV) inverted terminal repeats, lentiviral recombination, and mRNA poly(A) tails. Oxford Nanopore Technologies enables long-read, native single-molecule sequencing to access these attributes directly. This review summarizes nanopore sequencing across the CGT lifecycle. For plasmid DNA, it confirms full-length circular identity and reveals structural heterogeneity missed by restriction mapping. For viral vectors (AAV and lentivirus), it functions as an integrity assay to distinguish full genomes from truncations and to detect sequence-resolved impurities, including reverse-packaged plasmid backbones. For mRNA therapeutics, direct RNA sequencing profiles poly(A) tail length distributions and base modifications (e.g., m¹Ψ) in a single assay. We also discuss adaptive sampling for impurity enrichment and native epigenetic profiling of bacterial methylation. Finally, we assess limitations in accuracy and compliance and outline the regulatory path toward moving long-read sequencing from an orthogonal tool to a validated lot-release method. Overall, nanopore sequencing supports risk-based, high-resolution QC while reducing analytical turnaround time.

Adeno-associated virus (AAV) gene therapy is a promising therapeutic approach for both inherited and acquired disorders, yet its effectiveness is often limited by barriers that reduce target cell uptake and transgene expression. While body temperature is known to have a significant impact on viral infection, its controlled regulation for AAV gene therapy has been little explored. This article reviews therapeutic hyperthermia, carefully controlled mild heating, as a complementary strategy to improve delivery and expression. Evidence from cell and animal studies suggests that transient mild heating can increase blood flow and vessel permeability, promoting viral entry from the bloodstream into tissues. It can also trigger cellular stress responses that facilitate entry and downstream processing. Heating can also serve as an external switch when combined with heat-responsive genetic control systems, allowing gene expression to be activated only in the heated region. We summarize clinically used methods for delivering local, regional, and whole-body hyperthermia and discuss how spatially controlled heating could be integrated with AAV gene therapy workflows. We also highlight opportunities for clinical translation, key risks, and open questions, including thermal dose control, potential loss of viral particle stability with excessive heating, and the possibility of increased inflammatory or immune side effects.

Emerging evidence suggests CAR-NK cell therapy shows great promise in cancer treatment. ROBO1 is highly expressed in various cancer types, including glioblastoma, hepatocellular carcinoma, lung cancer, breast cancer, and uterine cancer. Our and other laboratories’ studies have shown that ROBO1 CAR-NK cells exhibit promising tumor therapeutic effects. However, the results still have some limitations. Cbl-b, an E3 ubiquitin ligase, has been reported to negatively regulate NK cell activation, homeostasis, and antitumor immunity. ¹ Therefore, we attempted to further enhance the antitumor activity of ROBO1 CAR-NK92 cells by knocking out Cbl-b using CRISPR/Cas9 gene-editing technology. In this study, we conjugated Cbl-b sgRNA with Cas9 protein to form ribonucleoprotein complexes, which were then delivered into ROBO1 CAR-NK92 and NK-92 cells (control cells) via electroporation. Through fluorescence-activated cell sorting, limiting dilution, and sequencing, we obtained monoclonal Cbl-b-knock-out (KO) cell lines. Both in vitro cytotoxicity assays and in vivo tumor xenograft experiments were conducted to examine whether Cbl-b knockout enhances the target cell killing and tumor suppression capacities of ROBO1 CAR-NK92 cells. In this study, monoclonal cell lines of ROBO1 CAR-NK92-Cbl-b-KO and NK92-Cbl-b-KO were successfully established. In vitro, at an effector-to-target (E:T) ratio of 0.1:1, ROBO1 CAR-NK92-Cbl-b-KO (50.55%) cells exhibited significantly higher cytolytic activity against ROBO1-positive T47D target cells after 3 h of coculture than ROBO1 CAR-NK92 (34.10%), NK92-Cbl-b-KO (22.22%), and parental NK-92 cells (3.28%). In vivo, tumor volume and weight measurements demonstrated that mice treated with ROBO1 CAR-NK92-Cbl-b-KO cells developed significantly smaller tumors than all control groups, achieving a tumor growth inhibition (TGI) rate of 32.45%, indicating enhanced antitumor efficacy conferred by Cbl-b knockout. In vitro and in vivo data confirmed that Cbl-b knockout potentiates the antitumor efficacy of ROBO1 CAR-NK92 cells. The overall cytotoxic capability ranked as follows: ROBO1 CAR-NK92-Cbl-b-KO > ROBO1 CAR-NK92 > NK92-Cbl-b-KO > NK-92.

Primary hyperoxaluria type 1 (PH1) is a rare autosomal recessive disorder that leads to kidney and liver failure. PH1 is caused by a mutation in the alanine glyoxylate aminotransferase (AGXT) gene, which encodes a key metabolic enzyme that converts glyoxylate to glycine in the liver. Inability to metabolize glyoxylate leads to oxalate overproduction, yielding insoluble calcium oxalate crystals; accumulation of these crystals leads to progressive organ failure. Here, we used a novel, minimally disruptive genome-editing approach to disrupt the mechanism of action of hydroxyacid oxidase 1 (HAO1), an upstream enzyme in the glyoxylate metabolic pathway. Successful gene editing and disruption of the HAO1 gene is expected to increase levels of glycolate, a harmless intermediate of the glycine metabolic pathway, thereby preventing the formation of calcium oxalate crystals. We intravenously administered an adeno-associated virus (AAV) vector expressing the M1HAO1 meganuclease to both wild-type and Agxt^−/− mice, a mouse model of PH1. We observed >30% editing of HAO1 in Agxt^−/− mice, correlating with a dose-dependent increase in serum glycolate levels. At the highest dose tested, urine glycolate levels increased by 79%, with a concomitant 75% decrease in urine oxalate levels. We also evaluated in vivo targeting in rhesus macaques injected with AAV expressing two different versions of the HAO1 meganuclease. Dose-dependent editing of hepatic DNA and RNA was achieved, and serum glycolate levels changed in a manner consistent with successful liver editing; additionally, the treatment was well tolerated. Our results indicate that AAV-delivered meganucleases can effectively target HAO1 in mice and nonhuman primates to achieve high levels of HAO1 gene editing. Moreover, increased glycolate levels in serum indicate that this intervention significantly impacts the HAO1-mediated glycolate-to-glyoxylate pathway. These data suggest that this approach may represent an effective treatment for PH1.

Comprehensive recombinant adeno-associated virus characterization is essential for establishing the knowledge base required to ensure clinical safety and efficacy, yet current long-read methods suffer from library preparation biases that obscure genome integrity. We present AviNP-seq, a blindspot-free nanopore sequencing framework utilizing one-end-sufficient ligation and Cas9–ribonucleoprotein (RNP) linearization to minimize terminal selection. Applied to a 1.5–6.5 kb panel, AviNP-seq delineates a sharp packaging cliff at 5.0–5.2 kb and reveals that sequence structure modulates integrity by 2–5× at fixed lengths. It unmasks covalent head-to-tail tandems in sub-3 kb vectors, detecting them with significantly higher sensitivity than PacBio HiFi. The Cas9–RNP step boosts ligation yield ∼7-fold, providing an unbiased assessment of genome integrity (≥95% inverted terminal repeat [ITR]-to-ITR). In addition, the assay quantifies plasmid impurities down to 0.05% with linear response. By integrating integrity mapping, tandem detection, and impurity profiling into a rapid (<36 h), low-input workflow, AviNP-seq provides a robust analytical tool to guide vector design and de-risk early-stage process development.

Site-specific integration of large genes in human primary stem cells remains a significant challenge in gene therapy, particularly for treating multiallelic diseases. Gene editing efficiency in primary stem cells is heavily influenced by the delivery strategy, which often faces issues with programmability, efficiency, and specificity. Here, we developed a dual-viral delivery system, targeted integration via virus-like particles and integrase-deficient lentivirus (TIVID). This system combines virus-like Cas9 edit particles for delivering Cas9/sgRNA ribonucleoprotein complexes and integrase-deficient lentiviral vectors for delivering HDR donor templates. The TIVID system achieves a knock-in efficiency of 65% ± 5% in human induced pluripotent stem cells (iPSCs). In erythroid progenitor HUDEP2 cells, TIVID mediates precise integration of a 7.1 kb HBB-GFP cassette (from cut site to cut site) at the AAVS1 locus with 20% efficiency and stable expression. Crucially, we demonstrate that TIVID overcomes stringent packaging constraints to deliver an approximately 6 kb full-length HBB therapeutic cassette into primary human CD34⁺ hematopoietic stem and progenitor cells. This platform achieved 5–10% targeted integration efficiency and preserved robust lineage-specific differentiation capacity, demonstrating its potential for treating β-thalassemia and other multiallelic disorders. In head-to-head comparisons, TIVID outperformed lentivirus-derived nanoparticles (∼50% vs. <10% at AAVS1 in K562 with M3814) and plasmid-based eePASSIGE in iPSCs (∼20% vs. ∼1.5%). Compared with traditional electroporation delivery, TIVID offers lower early cytotoxicity, promotes predominantly mono-allelic integration, and exhibits enhanced compatibility with primary stem cells. By decoupling nuclease and donor delivery, TIVID circumvents the payload constraints of single-vector systems and the toxicity of physical transfection, providing a robust ex vivo engineering platform for complex gene replacement therapies.

Mutations in the valosin-containing protein (VCP) gene lead to a hereditary type of inclusion body myositis (hIBM), in which sarcoplasmic and myonuclear inclusions with TAR DNA-binding protein 43 (TDP-43) pathology and mitochondrial abnormalities are observed in histological analysis. Pathophysiological conditions in the cell cause the protein quality control system to depend on the autophagy-lysosome pathway (ALP) for degradation of accumulated misfolded proteins and mitochondrial turnover. BCL2-associated athanogene 3 (BAG3) protein has a role in initiating the ALP. Our aim was to ameliorate disease processes resulting from mitochondrial abnormalities and misfolded protein aggregation by upregulating the ALP through overexpression of human BAG3 (hBAG3). The VCP-A232E mouse, a model for hIBM, received AAVrh74.tMCK.hBAG3 systemically at 3 months of age, and outcome measures, including functional, histological, and molecular studies, were assessed 9 months post-gene delivery. hBAG3 treatment improved treadmill running distance and rotarod duration, reduced the number of TDP-43-positive aggregates, and decreased the number of fibers showing abnormalities in mitochondrial enzyme histochemistry, compared with the untreated cohort. Moreover, hBAG3 gene therapy resulted in improvements in mitophagy and mitochondrial homeostasis observed as increased levels in mitophagy markers Parkin and Bnip3, mitochondria biogenesis marker Pgc1α and mitochondrial DNA-encoded subunits of complex IV, Cox1 and Cox3. In addition, the LC-II/I ratio increased, indicating increased autophagic flux. Our study presents evidence that the strategy of supporting the ALP system by overexpressing BAG3 has potential therapeutic use for myodegenerative conditions associated with abnormal protein aggregates and mitochondrial turnover.

Receptor engagement plays a key role in the cellular uptake, intracellular trafficking, and overall transduction efficiency of adeno-associated virus (AAV) vectors. Although heparan sulfate proteoglycan (HSPG) and α5ß1 integrin-binding motifs of the AAV serotype 2 (AAV2) capsid were mapped, it has remained incompletely understood how loss of these interactions affects AAV vector performance. Hence, we generated capsid variants harboring mutations at capsid residues responsible for HSPG binding (AAV2ΔHSPG), α5ß1 integrin binding (AAV2ΔIntegrin), or both (AAV2ΔHSPGΔIntegrin), and investigated the mutants systematically ex vivo and in vivo. While neither production nor packaging efficiency was affected, variants revealed distinct physicochemical alterations, including altered electrophoretic mobility and thermal stability. Ex vivo, loss of HSPG binding completely abolished transgene expression across various cell lines, whereas ablation of α5ß1 integrin binding lowered transduction efficiency. While cellular uptake was reduced for AAV2ΔIntegrin and almost eliminated for AAV2ΔHSPG and AAV2ΔHSPGΔIntegrin, mutants nevertheless reached the nuclear compartment, albeit with lower efficiency compared with AAV2. Strikingly, in vivo performance diverged sharply from ex vivo findings as we observed a substantially enhanced transduction in multiple non-hepatic tissues for AAV2ΔHSPG and AAV2ΔHSPGΔIntegrin in C57BL/6N albino and BALB/c mice, as well as a strong liver detargeting, while AAV2ΔIntegrin was non-infectious in vivo. These data uncover a fundamental dichotomy between ex vivo and in vivo determinants of AAV2 transduction and identify receptor-binding ablation, especially integrin binding, as a potential alternative to detarget AAV2 vectors for next-generation capsid engineering and tissue-specific retargeting.

Chimeric antigen receptor (CAR) T-cell therapy has transformed hematological cancer care, yet variability in efficacy, durability, and safety cannot be explained solely by antigen selection or patient factors. We propose that manufacturing platforms are active biological determinants of outcome. Viral vectors, used in all licensed products, provide stable genomic integration and durable expression but are limited by cost, cargo capacity, and centralized production. Nonviral strategies, including transposons, CRISPR knock-ins, and messenger RNA delivery, enable faster, less-expensive manufacturing with larger payloads, while introducing distinct safety and persistence profiles. This review presents a three-layer mechanistic framework that reframes manufacturing as biology: integration biology determines genomic risk and transgene stability; clonal fitness shapes persistence, dominance, and exhaustion; and epigenomic imprinting, influenced by gene transfer method, cytokines, and culture stress, preconfigures functional trajectories. Clinical observations link platform choice to immune recovery, where prolonged B-cell aplasia and delayed T-cell reconstitution contribute to infection-related nonrelapse mortality, and hematopoietic reserve at apheresis emerges as a practical predictor. Finally, manufacturing is positioned as the key to democratizing cell therapy. Decentralized, nonviral production aligned with regulatory standards may enable equitable access and transition CAR-T therapy from innovation to sustainable global care.

Oncolytic virotherapy harnesses genetically engineered viruses to selectively infect and lyse tumor cells while stimulating antitumor immunity through pro-inflammatory microenvironment activation. Celyvir represents a pioneering cell-based oncolytic therapy combining mesenchymal stromal cells (MSCs) as carriers of the human oncolytic adenovirus ICOVIR-5. Developed over two decades through collaborative efforts, Celyvir leverages the tumor-homing capacity of MSCs to enhance systemic delivery and therapeutic efficacy of oncolytic virotherapy against solid tumors. Preclinical and clinical studies, including compassionate use programs and phase I trials, have demonstrated Celyvir’s safety, feasibility, and potential efficacy. Mechanistic insights reveal that MSCs with a low pro-inflammatory profile and patients’ baseline immune competence correlate with improved responses. The evolution from autologous (Celyvir) to allogeneic MSC-based delivery (AloCelyvir) aims to overcome manufacturing delays and optimize clinical outcomes. This review summarizes the conceptual foundations, preclinical models, translational milestones, and ongoing clinical trials of Celyvir, illustrating its trajectory from bench to bedside as an improved oncolytic virotherapy modality.