Molecular Therapy Methods & Clinical Development

Adeno-associated viruses (AAVs) are popular gene therapy vectors, but AAVs can cause toxicity. This is particularly evident following expression of some transgenes, e.g. GFP, in the retinal pigment epithelium (RPE), which leads to loss of RPE cells and photoreceptors. Here, we sought to unravel the toxicity mechanism(s). Several transgenes, self and non-self, were tested for toxicity, with no clear correlation for this variable. RPE RNA-sequencing revealed upregulation of translational processes, cell stress, cytokine release, antiviral responses, and leukocyte infiltration pathways. Toxicity-inducing pathways were explored for causality by injecting toxic AAVs into mice deficient for intrinsic, innate, or adaptive immune pathways. The CHOP KO partially alleviated toxicity for RPE but not photoreceptors, whereas the type I interferon receptor KO partially alleviated toxicity for photoreceptors but not RPE. In situ hybridization of interferon pathway transcripts (IFNB1, IFNAR1) revealed that the RPE and retina can produce and potentially respond to interferon. These data suggest that transgene-induced cell stress responses in the RPE lead to RPE cell death, while interferon signaling contributes to the death of photoreceptors.

Cystic fibrosis (CF) is the most common monogenic lung disease and results from mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). There have been over 2000 variants identified in patients that result in loss of function of the CFTR protein leading to systemic disease and respiratory failure in adolescence. While some variants encode proteins with residual activity that can be corrected or potentiated by CFTR modulators, at least 10% of CF individuals cannot tolerate the modulators or have nonsense mutations which fail to make any protein. For all people with CF, a mutation agnostic gene replacement strategy could provide a cure for CF lung disease. Here, we propose using a systemic route of administration to deliver a functional CFTR minigene cargo with a lung tropic AAV capsid. This would serve to reach multiple organs, most importantly the lung epithelium, and would provide a functional CFTR transgene that could be expressed in any cell type with a ubiquitous promoter. To achieve this, we generated the smallest CFTR minigene tested in an AAV delivery to date. We demonstrate its expression and function following transfection in cell-based assays and restoration of function in primary CF airway cells after viral delivery. Furthermore, we identify an AAV capsid that can transduce alveolar and airway epithelium with systemic delivery in non-human primates. These data provide tools for delivering a functional CFTR minigene that fits within the packaging capacity of an AAV and demonstrate lung transduction with an AAV following systemic delivery in a large animal model. This strategy first and foremost can reach target airway cells by circumventing the strong mucosal barrier in CF airways but may also provide a method by which to restore CFTR function in additional CF affected organs.

Mutations in the Eyes Shut Homolog (EYS) gene are a leading cause of autosomal recessive retinitis pigmentosa, a progressive retinal degenerative disease for which no effective treatment currently exists. However, the large size of the EYS coding sequence ([~]9.4 kb) exceeds the packaging limit of adeno-associated virus (AAV) vectors, posing a major barrier to gene replacement therapy. To address this challenge, we developed a tripartite AAV vector system that enables delivery and reconstitution of the full-length EYS gene using a Cre-lox-based unidirectional DNA recombination strategy, Uni-STAR (Uni-directional and Site-specific Transgene Assembly by Recombination). The system consists of three AAV constructs carrying discrete EYS segments flanked by engineered, non-compatible lox sites that drive ordered and unidirectional recombination in target cells. We validated this system in vitro by demonstrating successful reconstitution and expression of full-length EYS protein in HEK293T cells. In vivo, subretinal co-injection of the three AAV vectors into mouse eyes led to precise reconstitution and expression of full-length EYS protein in the retina. These findings establish the feasibility of using a tripartite AAV system to deliver the complete EYS gene and provide a foundation for future therapeutic development targeting EYS-associated retinal degenerations.

Sandhoff Disease (SD), a fatal neurodegenerative disorder, is caused by the absence of {beta}-hexosaminidase (Hex) and subsequent accumulation of GM2 ganglioside in lysosomes. Previous studies have led to adeno-associated virus (AAV) gene therapy for children with GM2 gangliosidosis in both expanded access and Phase I/II clinical trials via intracranial and/or cerebrospinal fluid-based delivery. The current study investigated intravenous (IV) gene therapy of SD cats, treated at one month of age with a bicistronic AAV vector. While untreated SD cats lived to 4.3{+/-}0.2 months, cats treated with low and high doses lived to 8.3{+/-}1.2 and 12.4{+/-}2.7 months, respectively. In-life assessments revealed clear clinical benefit of AAV treatment, with the most dramatic improvement seen in the reduction of overt full-body tremors. Cerebrospinal fluid levels of aspartate aminotransferase (AST) and lactate dehydrogenase (LDH) were decreased, indicating a reduction of cell damage within the central nervous system. Magnetic resonance imaging (MRI) and spectroscopy (MRS) acquired on a 7 Tesla scanner indicated that structural pathology and metabolite abnormalities are partially normalized by AAV treatment. Dose-dependent reduction of GM2 ganglioside storage and increases in Hex activity were most substantial in the caudal regions of the brain and in the spinal cord. Immunohistochemistry revealed reduction in neuroinflammatory cell populations and partial correction of myelin deficits. These results support the dose-dependent efficacy of AAV delivered IV for significant restoration of clinical metrics and Hex function in a feline model of SD. One Sentence SummaryIntravenous administration of AAV gene therapy is safe and efficacious in a feline model of Sandhoff disease.

Microglia are critical innate immune cells of the brain. In vivo targeting of microglia using gene-delivery systems is crucial for studying brain physiology and developing gene therapies for neurodegenerative diseases and other brain disorders such as NeuroAIDS. Historically, microglia have been extremely resistant to transduction by viral vectors, including adeno-associated virus (AAV) vectors. Recently, there has been some progress demonstrating the feasibility and potential of using AAV to transduce microglia after direct intraparenchymal vector injection. Data suggests that combining specific AAV capsids with microglia-specific gene expression cassettes to reduce neuron off-targeting will be key. However, no groups have developed AAV capsids for microglia transduction after intracerebroventricular (ICV) injection. The ICV route of administration has advantages such as increased brain biodistribution while avoiding issues related to systemic injection. Here, we performed an in vivo selection using an AAV peptide display library that enables recovery of capsids that mediate transgene expression in microglia. Using this approach, we identified a capsid, MC5, which mediated enhanced transduction of microglia after ICV injection compared to AAV9. Furthermore, MC5 enhanced both the efficiency (85%) and specificity (93%) of transduction compared to a recently described evolved AAV9 capsid for microglia targeting after direct injection into the brain parenchyma. Exploration of the use of MC5 in a mouse models of Alzheimers disease revealed transduced microglia surrounding and within plaques. Overall, our results demonstrate that the MC5 capsid is a useful gene transfer tool to target microglia in vivo by direct and ICV routes of administration.

BackgroundLocal gene therapies, including in vivo genome editing, are highly anticipated for the treatment of genetic diseases in skin, especially the epidermis. While the adeno-associated virus (AAV) is a potent vector for in vivo gene delivery, the lack of efficient gene delivery methods has limited its clinical applications. ObjectiveTo optimize the AAV gene delivery system with higher gene delivery efficiency and specificity for epidermis and keratinocytes (KCs), using AAV capsid and promoter engineering technologies. MethodsAAV variants with mutations in residues reported to be critical to determine the tropism of AAV2 for KCs were generated by site-directed mutagenesis of AAVDJ. The infection efficiency and specificity for KCs of these variants were compared with those of previously reported AAVs considered to be suitable for gene delivery to KCs in vitro and in vivo. Additionally, we generated an epidermis-specific promoter using the most recent short-core promoter and compared its specificity with existing promoters. ResultsA novel AAVDJ variant capsid termed AAVDJK2 was superior to the existing AAVs in terms of gene transduction efficiency and specificity for epidermis and KCs in vitro and in vivo. A novel tissue-specific promoter, termed the K14 SCP3 promoter, was superior to the existing promoters in terms of gene transduction efficiency and specificity for KCs. ConclusionThe combination of the AAVDJK2 capsid and K14 SCP3 promoter improves gene delivery to epidermis in vivo and KCs in vitro. The novel AAV system may benefit experimental research and development of new epidermis-targeted gene therapies.

Adeno-associated viruses (AAVs) have emerged as powerful tools for delivery of genes to a variety of cell types including pancreatic endocrine cells. Currently, AAV serotype 8 (AAV8) is the main AAV vector employed for infecting pancreatic cells for transgene transfer. We aimed to address whether alternative serotypes (AAV2, AAV6, and AAV9) commonly used for gene transfer can be effective in transducing pancreatic cells efficiently. We also screened the additives heparin and neuraminidase to further understand the interaction between the individual AAV types included in this work and the cells for optimal infection. Murine pancreatic {beta}-cells and -cells as well as fibroblasts were infected with AAV serotypes 2, 6, and 9 carrying the transgene for enhanced green fluorescent protein (eGFP). AAV2 outperformed AAV9 in transducing pancreatic cells, while AAV6 induced cytotoxicity. Both AAV2 and AAV9 displayed slightly higher tropism for -cells than for {beta}-cells. Compared to the pancreatic cells, the fraction of GFP-expressing cells at various multiplicities of infection was consistently lower for fibroblasts. Incubation of AAV2 with heparin prior to transduction failed to induce any GFP expression in {beta}-cells, indicating that the primary site used for initial interaction with pancreatic cells are heparan sulfate proteoglycans. Treatment of {beta}-cells with neuraminidase prior to AAV9 infection appeared to improve the number of GFP-positive cells, but the increase was not statistically significant. These findings expand the repertoire of available serotypes for AAV-mediated delivery of transgenes to pancreatic endocrine cells and may contribute to gene therapy strategies for pancreas pathologies.

The efficacy of adeno-associated virus (AAV)-mediated systemic gene therapy for central nervous system (CNS) diseases is often limited by the blood-brain barrier (BBB). This study systematically evaluated the tissue distribution of three BBB-crossing AAV capsid variants (PHP.eB, CNSRCV300, and BI-hTFR1) following intravenous injection in mice, using either a constitutive promoter (CAG) or a neuron-specific promoter (hSyn) to drive EGFP reporter expression. Compared with AAV9, both PHP.eB and CNSRCV300 demonstrated significantly enhanced BBB penetration and brain transduction efficiency. While the use of the hSyn promoter led to reduced transgene expression in the brain compared with the CAG promoter, and substantially decreased visible reporter expression in peripheral organs, viral deposition in the liver could still be detected via immunohistochemistry. Overall, CNSRCV300 exhibited the most favorable balance between brain-targeting efficiency and biosafety, highlighting its potential as a promising delivery vector. In summary, both the capsid and promoter jointly influence AAV-mediated expression in vivo, and although cell type-specific promoters can reduce off-target expression, residual viral deposition in non-target tissues remains a potential safety concern.

Viral vector technologies based on adeno-associated virus (AAV) have demonstrated promising ability to deliver genetic cargo to a range of organs in vivo, with several novel candidates showing clinical efficacy in human trials over the past decade. However, naturally occurring AAV serotypes are limited in their ability to target skeletal muscle, an important gene therapy target for many neuromuscular disorders. This means that high doses of AAV are often required to achieve therapeutically effective doses in muscle. To overcome this, novel AAV vector capsids have been engineered by inserting targeting peptides into the AAV9 capsid variable region VIII (VRIII) to achieve greater muscle transduction efficiency. Here we describe investigation of a newly reported capsid, called MyoAAV1A combined with clinically validated muscle-specific promoters. We profiled the efficiency of in vivo delivery to murine skeletal muscle and found that the optimal combination of MyoAAV1A capsid with MHCK7 promoter maintains transgene expression in skeletal muscle, and reduces expression in off-target tissues, particularly the liver. This highlights a promising capsid-promoter combination to progress in further preclinical research for skeletal muscle gene therapy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/605568v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@10bbe78org.highwire.dtl.DTLVardef@5e2e0org.highwire.dtl.DTLVardef@71f4a7org.highwire.dtl.DTLVardef@1750d81_HPS_FORMAT_FIGEXP M_FIG C_FIG

Although adeno-associated virus (AAV) has enjoyed enormous success as a delivery modality for gene therapy, it continues to suffer from the high prevalence of preexisting neutralizing antibodies in human populations, limiting who can receive potentially life-saving treatments. In this regard, AAV therapies generally also must be administered as a single dose since neutralizing antibodies develop in patients who receive the virus. Strategies for circumventing these issues remain limited. As a novel solution, we employed SpyTag-SpyCatcher molecular glue technology to facilitate packaging of AAVs inside of recombinant protein vault nanoparticles. Vaults are endogenous particles produced by mammalian cells. We therefore hypothesized that they may shield packaged molecules from neutralizing antibodies. Vaults have previously been utilized to deliver drugs and proteins into cells, but our study represents the first time anyone has packaged an entire virus inside of a vault. We showed that our vaultAAV (VAAV) delivery vehicle transduces cells in the presence of anti-AAV neutralizing serum. VAAV is positioned as a new gene therapy delivery platform with potential to overcome the neutralizing antibody problem and perhaps even allow administration of multiple doses, expanding the scope of AAV treatments.

Autosomal recessive thymidine kinase 2 (TK2) mutations causes TK2 deficiency, which typically manifests as a progressive and fatal mitochondrial myopathy in infants and children. Treatment with deoxycytidine and thymidine ameliorates mitochondrial defects and extends lifespan of Tk2 knock-in mouse (TK2-/-); however, efficacy is limited by age- and tissue-dependent expression of the cytosolic enzymes Tk1 and Dck. Thus, therapies aimed at systemic restoration of TK2 activity are needed. Here, we demonstrate that delivery of human TK2 cDNA to Tk2-/- mice using AAV9 efficiently rescued Tk2 activity in all the tissues tested except kidney, delayed disease onset, and increased lifespan. Sequential treatment of Tk2-/- mice with AAV9 first followed by AAV2 at different ages allowed us to reduce the viral dose while further prolonging the lifespan. Furthermore, addition of deoxycytidine and deoxythymidine supplementation to AAV9 + AAV2 treated Tk2-/- mice dramatically improved mtDNA copy numbers in liver and kidney, animal growth, and lifespan. These data indicate that combined pharmacological and gene therapies may be highly efficacious for human TK2 deficiency.

Recombinant adeno-associated viral (rAAV) vectors are a potent tool, but their clinical application is restricted by insufficient target tissue transduction and liver toxicity. We employed a novel two-step engineering strategy to create novel rAAV capsids with global tissue de-targeting, then produced strong tissue-specific expression by adding a peptide sequence. We created a novel capsid, AAV.Zero1, with globally de-targeted transduction by loop swapping domains from AAV9 into AAV2. Making an R585A substitution (AAV.Zero2) re-targeted tissues but deleting residues 585-587 (AAV.Zero3) abrogated transduction. Inserting a myogenic peptide into AAV.Zero3 produced a novel capsid (AAV.eM) with strong muscle-specific transgene expression while maintaining minimal off-target expression, including in liver, which was conserved in two mouse strains and non-human primates. AAV.eM showed similar expression as the leading myotropic vector MyoAAV.4A but had a more favorable safety profile. Importantly, AAV.eM was able to functionally rescue a mouse model of Duchenne Muscular Dystrophy following systemic delivery of a micro-dystrophin gene. Thus, AAV.eM is an improved myotropic rAAV capsid that de-targets other tissues, especially the liver, and proof-of-concept for a platform to create capsids with specific properties that translate across species by addition of peptides onto low transduction backbones.

Systemic administration of adeno-associated virus (AAV) vectors for spinal cord gene therapy has challenges including toxicity at high doses and pre-existing immunity that reduces efficacy. Intrathecal delivery of AAV vectors into the cerebral spinal fluid (CSF) can avoid many of the issues of systemic delivery, although achieving broad distribution of the vector and transgene expression throughout the spinal cord is challenging and vector entry to the periphery occurs, sometimes initiating hepatotoxicity. Here we performed two rounds of in vivo biopanning in non-human primates (NHPs) with an AAV9 peptide display library injected intrathecally and performed insert sequencing on DNA isolated from either whole tissue (conventional selection), isolated nuclei, or nuclei from transgene-expressing cells. A subsequent barcoded pool of candidates and AAV9 was compared at the DNA (biodistribution) and RNA (expression) level in spinal cord and liver of intrathecally injected NHPs. Most of the candidates displayed enhanced biodistribution compared to AAV9 at all levels of spinal cord ranging from 2 to 265-fold. Nuclear isolation or expression-based selection yielded 4 of 7 candidate capsids with enhanced transgene expression in spinal cord (up to 2.4-fold), while no capsid obtained by conventional selection achieved that level. Furthermore, several capsids displayed lower biodistribution to the liver of up to 1,250-fold, compared to AAV9, providing a remarkable on target/off target biodistribution ratio. These capsids may have potential for gene therapy programs directed at the spinal cord and the selection method described here should be useful in clinically relevant large animal models.

To facilitate the translation of NF1 exon 17 skipping as a mutation-specific therapy for Neurofibromatosis type 1 into in vivo testing, we have continued to develop more efficient antisense oligonucleotides (ASOs), humanized mouse models, and explored multiple delivery platforms including an adeno-associated virus (AAV)-U7-SnRNA vector approach. We evaluated both biodistribution and exon skipping efficacy of a U7-SnRNA targeting NF1 exon 17 with an SFFV-driven cassette containing T2A-linked Luciferase (Luc) and eGFP packaged in AAV-9, AAV-F and AAV-B1 capsids. We show that AAV-F is superior to AAV-9 and AAV-B1 for mouse brain delivery based on DNA transduction, GFP expression, and luciferase activity, but AAV-B1 delivers 2-4 fold more to sciatic nerve (SCN). In terms of exon skipping, AAV-F appears to induce the most skipping in liver and optic nerve (ON), while AAV-B1 mediates highest skipping in the liver, SCN, and ON. The identification of AAV serotypes that allow efficient transduction and delivery of transgenes to the mouse CNS and PNS is impactful for preclinical research in murine models of other diseases. Furthermore, this is both the first report of NF1 exon skipping efficacy in vivo and the first successful application of an U7-SnRNA for the restoration of functional neurofibromin for NF1.

Recently approved adeno-associated viral (AAV) vectors for liver monogenic diseases hemophilia A and B are exemplifying the success of liver-directed viral gene therapy. In parallel, additional strategies are rapidly emerging to overcome some inherent AAV limitations, such as non-persistence of episomal transgene in rapidly growing liver and immune response. Integrating lentiviral vectors and non-viral lipid nanoparticles encapsulating mRNA (LNP-mRNA) are rapidly being developed, currently at preclinical and clinical stages respectively. Macrophages are first effector cells of the innate immune response triggered by gene therapy vectors. Macrophage uptake and activation following administration of viral gene therapy and LNPs has been reported. In this study, we assessed the biodistribution of AAV, lentiviral and LNP-mRNA gene therapy following inhibition of tissue macrophages by clodronate liposomes in neonatal and juvenile mice. Juvenile clodronate-treated mice showed significant increase of lentiviral-transduced hepatocytes, and increasing trend of transduction was shown in neonatally-injected mice. In contrast, AAV- and LNP-mRNA-treated neonatal and juvenile animals did not show significant increase of liver biodistribution following clodronate administration. These findings will have translational application for liver-targeting gene therapy programmes.

Heat Shock Protein 90 (HSP90) is a critical molecular chaperone that exists as two cytosolic paralogs, HSP90 and HSP90{beta}, which share high sequence identity but may perform non-redundant functions in vivo. Loss of HSP90 in mice results in progressive rod photoreceptor degeneration despite normal retinal development and expression of HSP90{beta}. To investigate whether HSP90{beta} can substitute for HSP90 in photoreceptors, we generated adeno-associated virus (AAV) vectors expressing HA-tagged HSP90 or HSP90{beta} under the control of a short rhodopsin promoter. In Hsp90 -/- mice, subretinal delivery of AAV-Hsp90aa1 (HSP90) restored rod function and prevented photoreceptor degeneration, as measured by electroretinography (ERG). In contrast, AAV-mediated expression of HSP90{beta} failed to rescue rod function despite comparable expression levels. Overexpression of either paralog in wild-type mice had no adverse effects on retinal function. These findings reveal a paralog-specific and intrinsic requirement for HSP90 in rod photoreceptors, demonstrating that HSP90{beta} cannot compensate for its loss despite structural similarity.

In vivo gene delivery to tissues using adeno-associated vector (AAVs) has revolutionized the field of gene therapy. Yet, while sensorineural hearing loss is one of the most common sensory disorders worldwide, gene therapy applied to the human inner ear is still in its infancy. Recent advances in the development recombinant AAVs have significantly improved their cell tropism and transduction efficiency across diverse inner ear cell types to a level that renders this tool valuable for conditionally manipulating gene expression in the context of developmental biology studies of the mouse inner ear. Here, we describe a protocol for in utero micro-injection of AAVs into the embryonic inner ear, using the AAV-PHP.eB and AAV-DJ serotypes that respectively target the sensory hair cells and the supporting cells of the auditory sensory epithelium. We also aimed to standardize procedures for imaging acquisition and image analysis to foster research reproducibility and allow accurate comparisons between studies. We find that AAV-PHP.eB and AAV-DJ provide efficient and reliable tools for conditional gene expression targeting cochlear sensory and supporting cells in the mouse inner ear, from late embryonic stages on.

Adeno-associated virus (AAV) gene therapies have achieved some clinical success, with multiple products reaching regulatory approval. Encapsulation of AAV vectors within engineered extracellular vesicles (EVs) is an emerging strategy which could help overcome challenges including pre-existing anti-capsid immunity and the need for controlling targeting and tropism. To guide the development of EV-AAV technologies, we developed an assay for quantifying and controlling for the contribution of pseudotransduction to evaluations of EV-AAV-mediated transduction. We developed an AAV vector that switches its transgene output from one reporter to another when acted upon by Cre recombinase expressed in a recipient cell. Using this platform, we investigated EV-AAV transduction as a function of various engineered EV surface modifications. For actively endocytic cells (HEK293FTs), modifications that enhance EV uptake and membrane fusion influence pseudotransduction but not true transduction. Conversely, in less endocytic Jurkat T cells, modifications enhancing EV uptake enhanced both pseudotransduction and true transduction. These conclusions held across two AAV serotypes. Our results provide new insight into prior reports and suggest that effects of enhancing uptake and membrane fusion of EV-AAV vectors are recipient cell type-specific. The methods developed here unambiguously dissect EV-AAV transduction mechanisms and can guide future bioengineering of EV-AAV vectors.

The liver is a prime target for in vivo gene therapies using recombinant adeno-associated viral vectors (rAAV). Multiple clinical trials have been undertaken for this target in the past 15 years, however we are still to see market approval of the first liver-targeted AAV-based gene therapy. Inefficient expression of the therapeutic transgene, vector-induced liver toxicity and capsid, and/or transgene-mediated immune responses reported at high vector doses are the main challenges to date. One of the contributing factors to the insufficient clinical outcomes, despite highly encouraging preclinical data, is the lack of robust, biologically- and clinically-predictive preclinical models. To this end, this study reports findings of a functional evaluation of six AAV vectors in twelve preclinical models of the human liver, with the aim to uncover which model is the most relevant for the selection of AAV capsid variant for safe and efficient transgene delivery to primary human hepatocytes. The results, generated by studies in models ranging from immortalized cells, iPSC-derived and primary hepatocytes, and primary human hepatic organoids to in vivo models, increased our understanding of the strengths and weaknesses of each system. This should allow the development of novel gene therapies targeting the human liver.

The use of adeno-associated viral vectors for delivery of genetic information into the mammalian CNS remains popular but producing highly purified vectors for in vivo applications requires a significant investment of resources and time that can impede the development and testing of AAV vectors for experimentation. To address this issue, we have developed a simplified AAV packaging protocol that does not require large capital equipment (ultracentrifugation or chromatography machines) yet still produces virus in quantities that are sufficient for testing AAV prototypes in the rodent CNS. This protocol is serotype agnostic, and has been successful with AAV1, AAV9, AAV-DJ, and rAAV2-retro. Intracranial injection of AAV-EF1a-GFP-KASH into rats demonstrated that our "small scale" AAV preps produce patterns of transgene expression and inflammation that are similar to those produced by the same AAV vector purified by affinity column chromatography. Our protocol allows for multiple vectors to be packaged and processed in parallel, making it ideal for testing multiple variants, constructs, and prototypes simultaneously.