Adeno-associated virus vector as a platform for gene therapy delivery

Evaluation of AAV vectors with tissue-specific or ubiquitous promoters in a mouse model of mucopolysaccharidosis type IVA

Mucopolysaccharidosis type IVA (MPS IVA) is caused by a deficiency of N-acetyl-galactosamine-6-sulfate sulfatase (GALNS), leading to the accumulation of keratan sulfate and chondroitin-6-sulfate and development of severe skeletal dysplasia. Enzyme replacement therapy and hematopoietic stem cell transplantation are current treatment options but have limited impact on bone lesions. In this study, we investigated adeno-associated virus (AAV)8 or AAV9 vectors with liver-specific thyroxine-binding globulin or liver-specific promoter-a modification of hAAT (LSPX), liver-muscle tandem (LMTP), liver-bone tandem (LBTP), and ubiquitous cytomegalovirus early enhancer/chicken β-actin (CAG) promoters in MPS IVA mice to compare therapeutic efficacy on biochemical markers and bone pathology. All vectors provided near- or supraphysiological levels of GALNS enzyme activity in plasma. Enzyme activities were also detected in various tissues, including bone. AAV9co-CAG, AAV9co-LMTP, and AAV9co-LBTP showed higher enzyme activities in the liver; however, AAV8co-CAG and AAV9co-LMTP have higher activities in most other tissues. All vectors normalized keratan sulfate levels in plasma, liver, and bone. Pathological analyses showed the reduction or complete absence of vacuolated cells in heart muscle and valves in all treated mice, while the AAV9co-LMTP vector most improved bone pathology. Overall, all studied vectors indicated a substantial improvement in biochemical parameters and pathology, and the AAV9co-LMTP vector demonstrated the best combined therapeutic efficacy.

Targeted spiral ganglion neuron degeneration in parvalbumin-Cre neonatal mice

The spiral ganglion neurons (SGNs) are the primary afferent neurons in the cochlea; damage to the SGNs leads to irreversible hearing impairment. Mouse models that allow selective SGN degeneration while sparing other cell types in the cochlea are lacking. Here, we investigated a genetic ablation method of the SGN using a Cre-responsive adeno-associated virus (AAV) vector expressing diphtheria toxin subunit-A (DTA). We microinjected AAV2-retro-FLEX-DTA-mCherry driven by the EF1a or hSYN promoter in neonatal parvalbumin-Cre (PVCre) and wild-type strains via the posterior semicircular canal. Apoptotic markers were observed in the degenerating SGNs as early as 3 days. After 1 week, we assessed the SGN cell density, revealing an average degeneration of 60% for AAV-DTA driven by the EF1a promoter and 61% for that driven by the hSYN promoter. By 1 month, injected ears demonstrated a nearly complete loss of SGN, while hair cell morphology was intact. The auditory brain stem response result showed significantly elevated threshold shifts at 1 month, while the distortion-product otoacoustic emissions function remained intact. Furthermore, we show that our method did not effectively ablate SGN in adult PVCre mice. We generated a neonatal mouse model with primary SGN degeneration in PVCre mice, mimicking auditory neuropathy phenotype using an AAV Cre-dependent expression of DTA.

Closing the gap: Nonviral TFAMoplex transfection boosted by bZIP domains compared to AAV-mediated transduction

The TFAMoplex is a nanoparticulate gene delivery system based on the mitochondrial transcription factor A (TFAM) protein, which can be engineered with various functional domains to enhance plasmid DNA transfection. In this study, we aimed at improving the TFAMoplex system by incorporating basic leucine zipper (bZIP) domains, derived from the cyclic AMP (cAMP)-responsive element-binding protein (CREB), which are known to bind DNA upon dimerization. Additionally, we screened bZIP domains of other proteins (i.e., transcription regulator protein BACH1, cyclic AMP-dependent transcription factor ATF-3, and basic leucine zipper transcriptional factor ATF-like BATF) under challenging transfection conditions, identifying the bZIP domain of BACH1, bZIPBACH1, as particularly effective in enhancing the TFAMoplex performance, reducing the half-maximal effective concentration by more than 2-fold. We show that bZIP domains facilitate interactions with the cell membrane as single proteins and thus increase the cell association of TFAMoplexes. Finally, we compared the optimized bZIPBACH1-TFAMoplex to adeno-associated viruses (AAVs) regarding in vitro transfection efficiency and transgene expression levels. While AAVs achieved higher transfection efficiency based on the number of transfected cells, both the original and improved TFAMoplex constructs surpassed AAVs in transgene expression per cell.

AAV-mediated GBA1 and GDNF rescue neurological defects in a murine model of neuronopathic Gaucher disease

Neuropathic Gaucher disease (nGD) is a life-threatening disease that progresses rapidly and is caused by a glucosylceramidase beta 1 (GBA1) mutation, which encodes the lysosomal hydrolase β-glucocerebrosidase (GCase). Nerve damage in nGD, associated with stunted growth and development, arises from the degeneration and death of nervous system cells, which is often irreversible. Approved therapies effectively reduce the substrate burden outside the central nervous system (CNS) through augmenting mutant enzyme activity with pharmacologic recombinant GCase or by inhibiting glucocerebroside synthesis. However, these therapies do not provide neuroprotection. In this study, we developed a novel double-gene therapy based on adeno-associated virus (AAV), AAV9-GBA1-GDNF, which stably expresses human GBA1 and glial derived neurotrophic factor (GDNF) over the long term. Pathological, molecular, and proteomic tests in the nGD model confirmed that the early stages of the disease are characterized by GBA1 deficiency, loss of neuronal function, and even neuronal death. After treatment with AAV9-GBA1-GDNF, the lifespan of nGD mice was extended, and weight, brain development, and motor ability were recovered. Additionally, GBA1 and GDNF additively prevented irreversible neuronal death by activating the AKT/GSK3β pathway. These findings offer potential therapeutic strategies for nGD and other neurodegenerative diseases associated with lysosomal dysfunction.

Non-viral, high throughput genetic engineering of primary immune cells using nanostraw-mediated transfection

Transfection of proteins, mRNA, and chimeric antigen receptor (CAR) transgenes into immune cells remains a critical bottleneck in cell manufacturing. Current methods, such as viruses and bulk electroporation, are hampered by low transfection efficiency, unintended transgene integration, and significant cell perturbation. The Nanostraw Electro-actuated Transfection (NExT) technology offers a solution by using high aspect-ratio nanostraws and localized electric fields to precisely deliver biomolecules into cells with minimal disruption. We demonstrate that NExT can deliver proteins, polysaccharides, and mRNA into primary human CD8+ and CD4+ T cells, and achieve CRISPR/Cas9 gene knockout of CXCR4 and TRAC in CD8+ T cells. We showcase NExT's versatility across a range of primary human immune cells, including CD4+ T cells, γδ-T cells, dendritic cells, NK cells, Treg cells, macrophages, and neutrophils. Finally, we developed a scalable, high-throughput multiwell NExT system capable of transfecting over 14 million cells and delivering diverse cargoes into multiple cell types from various donors simultaneously. This technology holds promise for streamlining high-throughput screening of allogeneic donors and reducing optimization costs for large-scale CAR-immune cell transfection.

Evaluation of AAV transduction efficiency via multiple delivery routes: Insights from peripheral and central nervous system analysis

This study evaluates the biodistribution and transduction efficiency of adeno-associated virus serotype 9 (AAV9) vectors administered via intracerebroventricular (ICV), intra-arterial (IA), and intravenous (IV) routes in a murine model. Quantitative assessments of green fluorescent protein (GFP) expression were conducted to compare transduction efficacy across central nervous system (CNS) and peripheral tissues. The results demonstrate that high-dose ICV administration resulted in robust GFP expressions in the hippocampus and fimbria, indicating effective CNS targeting. Conversely, when administered intravenously (IV), the distribution of the drug was more widespread, affecting peripheral organs such as the liver and lungs, with limited penetration of the CNS. IA delivery achieved a balanced distribution, facilitating moderate transduction in both CNS and peripheral tissues. These findings underscore the significance of selecting appropriate administration routes to optimize AAV-mediated gene delivery for specific therapeutic targets. The study also underscores the necessity for quantitative analyses to accurately assess transduction efficiencies, informing the development of targeted gene therapies for neurological disorders.

Chromatography in Downstream Processing of Recombinant Adeno-Associated Viruses: A Review of Current and Future Practises

Recombinant adeno-associated virus (rAAV) has emerged as an attractive gene delivery vector platform to treat both rare and pervasive diseases. With more and more rAAV-based therapies entering late-stage clinical trials and commercialization, there is an increasing pressure on the rAAV manufacturing process to accelerate drug development, account for larger trials, and commercially provide high doses. Still, many of the pre-clinical and clinical manufacturing processes are tied to outdated technologies, which results in substantial production expenses. Those processes face challenges including low productivity and difficult scalability, which limits its ability to provide for required dosages which in turn influences the accessibility of the drug. And as upstream efforts are expected to increase productivities, the downstream part needs to adapt with more scalable and efficient technologies. In this review, both traditional and novel rAAV downstream technologies are presented and discussed. Traditional rAAV downstream processes are based on density gradient ultracentrifugation and have been shown to effectively purify rAAVs with high yields and purities. However, those processes lack scalability and efficiency, which is why novel rAAV downstream processes based on column-chromatography have emerged as an attractive alternative and show potential for integration in continuous processes, following the principle of next-generation manufacturing.

Chronic motoneuronal activation enhanced axonal regeneration and functional recovery after brachial plexus injury

Background

Brachial plexus injury (BPI) leads to significant impairment of upper limb motor function, primarily due to progressive atrophy of denervated muscles resulting from the slow rate of axonal regeneration. Therefore, identifying strategies to accelerate axon extension is of critical importance.

Methods

In this study, we first established a mouse model of brachial plexus injury and employed chemogenetic approaches to specifically activate C6 spinal motoneurons. We then assessed axonal regeneration and motor function recovery in the injured mice through behavioral tests, morphological analyses, and electrophysiological detection.

Results

We found that the AAV9-hM3Dq virus efficiently transduced motoneurons, and CNO administration robustly activated mature hM3Dq+ motoneurons in vivo. Chronic chemogenetic activation significantly enhanced the regeneration of spinal motoneurons injured by ventral root crush, accelerated axon extension, and improved axonal remyelination, resulting in increased axon size. This activation also facilitated the formation of new neuromuscular junctions (NMJs) in adult motoneurons and reduced muscle atrophy. Furthermore, it promoted electrophysiological recovery of the motor unit and improved overall motor function.

Conclusion

Chemogenetic activation of adult motoneurons can robustly enhances axon growth and mediate better behavioral recovery. These findings highlight the therapeutic potential of chemogenetic neuronal activation in promoting functional recovery following nerve injury.

The translational potential of this article

We have established a chronic chemogenetic method to activate hM3Dq+ motor neurons after brachial plexus injury, which accelerates axonal regeneration and enhances functional recovery. This strategy holds promise as a clinical therapeutic approach for treating nervous system injuries.

State of the art in CAR-based therapy: In vivo CAR production as a revolution in cell-based cancer treatment

Chimeric antigen receptor (CAR) therapy has successfully treated relapsed/refractory hematological cancers. This strategy can effectively target tumor cells. However, despite positive outcomes in clinical applications, challenges remain to overcome. These hurdles pertain to the production of the drugs, solid tumor resistance, and side effects related to the treatment. Some cases have been missed during the drug preparation due to manufacturing issues, prolonged production times, and high costs. These challenges mainly arise from the in vitro manufacturing process, so reevaluating this process could minimize the number of missed patients. The immune cells are traditionally collected and sent to the laboratory; after several steps, the cells are modified to express the CAR gene before being injected back into the patient's body. During the in vivo method, the CAR gene is introduced to the immune cells inside the body. This allows for treatment to begin sooner, avoiding potential failures in drug preparation and the associated high costs. In this review, we will elaborate on the production and treatment process using in vivo CAR, examine the benefits and challenges of this approach, and ultimately present the available solutions for incorporating this treatment into clinical practice.

Combination of hydrophilic interaction liquid chromatography and top-down mass spectrometry for characterisation of adeno-associated virus capsid proteins

Adeno-associated virus (AAV) viral vector-based gene therapy is advancing rapidly, offering potential treatments for rare and severe diseases. The AAV capsid consists of a combination of three viral proteins (VPs), VP1, VP2, and VP3, ranging from 59 to 81 kDa and present at a theoretical bulk ratio of 1:1:10. This study employed hydrophilic interaction liquid chromatography (HILIC) and mass spectrometry (MS) to achieve robust separation and detailed characterisation of AAV9 capsid proteins. Advanced top-down MS approaches combining multiple fragmentation techniques (HCD, ETD, EThcD, and UVPD) were successfully applied, increasing the sequence coverage up to 40% for VP3 and confirming N-terminal acetylation on VP1 and VP3. The workflow demonstrated high reproducibility between injection duplicates and was subsequently applied to the characterisation of in-house produced biological replicates of AAV9 samples from HEK293 cells, showing consistent results across them. Analysis of AAV9 derived from Sf9 insect cells, a more complex sample due to higher levels of modification of the capsid VPs, further evidenced method versatility. Overall, this study highlights the potential of HILIC-MS and advanced top-down MS approaches for detailed characterisation of AAV capsid proteins.

Retina-directed gene therapy: Achievements and remaining challenges

Gene therapy is an innovative medical approach that offers new treatment options for congenital and acquired diseases by transferring, correcting, inactivating or regulating genes to supplement, replace or modify a gene function. The approval of voretigene neparvovec (Luxturna), a gene therapy for RPE65-associated retinopathy, has marked a milestone for the field of retinal gene therapy, but has also helped to accelerate the development of gene therapies for genetic diseases affecting other organs. Voretigene neparvovec is a vector based on adeno-associated virus (AAV) that delivers a functional copy of RPE65 to supplement the missing function of this gene. The AAV-based gene delivery has proven to be versatile and safe for the transfer of genetic material to retinal cells. However, challenges remain in treating additional inherited as well as acquired retinopathies with this technology. Despite the high level of activity in this field, no other AAV gene therapy for retinal diseases has been approved since voretigene neparvovec. Ongoing research focuses on overcoming the current restraints through innovative strategies like AAV capsid engineering, dual-AAV vector systems, or CRISPR/Cas-mediated genome editing. Additionally, AAV gene therapy is being explored for the treatment of complex acquired diseases like age-related macular degeneration (AMD) and diabetic retinopathy (DR) by targeting molecules involved in the pathobiology of the degenerative processes. This review outlines the current state of retinal gene therapy, highlighting ongoing challenges and future directions.

Harnessing Nanotechnology in HIV Therapy: Exploring Molecular Pathogenesis and Treatment Strategies with Special Reference to Chemotherapy and Immunotherapy

Human immunodeficiency virus (HIV) continues to be a global threat, contributing substantially to social and economic burdens worldwide. Synthetic ARV drugs are classified into six different classes viz NRTIs, NNRTIs, PIs, IIs, INSTIs, and FIs. Highly active anti-retroviral therapy (HAART) which is a combination of two or more ARV drugs from different classes is gaining immense popularity in the HIV therapy regimen due to its better therapeutic outcome. However, despite its successful endeavor in significant viral suppression, synthetic drugs are associated with numerous adverse effects. To mitigate this issue, scientists are exploring ARV agents derived from various natural sources like plants, and marine organisms that can exhibit potent anti-HIV activity with minimal side effects. Nevertheless, both synthetically and naturally derived ARV agents have failed to exhibit eradication of HIV from latent reservoirs. Henceforth, researchers are shifting their attention towards formulating a drug-encapsulated nano-delivery system to ensure a significant amount of drug delivery into these reservoirs. Additionally, the discovery of a novel HIV vaccine that can induce robust immune responses against multiple HIV strains and facilitate complete removal of the virus before the establishment of a latent reservoir is the need of an hour. Briefly, we discussed various synthetic and natural chemotherapeutic agents along with their specificity and limitations, different drug-delivery devices for ART, immunotherapy, vaccines, and lastly, challenges and strategies associated with vaccine development.

Structural characterization of antibody-responses following Zolgensma treatment for AAV capsid engineering to expand patient cohorts

Monoclonal antibodies are useful tools to dissect the neutralizing antibody response against the adeno-associated virus (AAV) capsids that are used as gene therapy delivery vectors. The presence of pre-existing neutralizing antibodies in large portions of the human population poses a significant challenge for AAV-mediated gene therapy, primarily targeting the capsid leading to vector inactivation and loss of treatment efficacy. This study structurally characterizes the interactions of 21 human-derived neutralizing antibodies from three patients treated with the AAV9 vector, Zolgensma®, utilizing high-resolution cryo-electron microscopy. The antibodies bound to the 2-fold depression or the 3-fold protrusions do not conform to the icosahedral symmetry of the capsid, thus requiring localized reconstructions. These complex structures provide unprecedented details of the mAbs binding interfaces, with many antibodies inducing structural perturbations of the capsid upon binding. Key surface capsid amino acid residues were identified facilitating the design of capsid variants with antibody escape phenotypes. These AAV9 capsid variants have the potential to expand the patient cohort to include those that were previously excluded due to their pre-existing neutralizing antibodies against the wtAAV9 capsid, and the possibly of further treatment to those requiring redosing.

The clinical safety landscape for ocular AAV gene therapies: A systematic review and meta-analysis

Adeno-associated virus (AAV) gene therapy is a promising approach for treating ocular monogenic or acquired diseases, though immunogenicity and safety remain critical considerations. We conducted a systematic review of 120 trials and 32 publications to assess immune responses across different delivery routes. Intravitreal administration was associated with higher rates of anterior uveitis (43.06% vs. 10.22%) and intermediate/posterior uveitis (40.36% vs. 6.18%) compared to subretinal delivery. Engineered AAV capsids, used exclusively in intravitreal studies, showed no significant difference in either type of uveitis incidence compared to natural serotypes. Prophylactic immunosuppression (PI) did not affect ocular or systemic immune responses in subretinal delivery, but significantly reduced systemic immune responses in intravitreal administration. These findings underscore the potential of PI to mitigate systemic immune responses in intravitreal AAV therapy. This review should help guide the choice of routes of administration and immunosuppression strategies, and highlights current trends in ocular AAV gene therapy.

On-Demand Regulation of Catalytic DNA Circuits Using Phosphorylated Charge Reversal Peptides

Catalytic DNA circuits have emerged as a powerful tool for high-performance biosensing application; however, the establishment of a safe and efficient in vivo delivery system remains a critical bottleneck. Peptides serve as attractive carriers due to their rich chemical diversity, excellent biocompatibility, high loading capacity, and specific binding ability, making them ideal candidates for the on-demand regulation of DNA circuits-yet remains largely unexplored. In this study, we developed a multifunctional enzyme-responsive peptide (ERP) for the efficient loading and specific intracellular delivery and release of catalytic circuitry probes through a phosphorylation-based charge reversal procedure. This ERP-programmed catalytic DNA circuit enables the precise, spatially controllable in vivo imaging of microRNA (miRNA). The multifunctional cationic peptide formed a stable nanocomplex with anionic DNA cargo via strong electrostatic interactions, thus protecting the DNA probes from degradation in biological environments. Moreover, with the ability to actively targeting tumor cells and facilitate endogenous phosphorylation-guided release of DNA probes, this multifunctional peptide could significantly reduce the nonspecific delivery of probes to healthy tissues, thereby minimizing unwanted off-site signal leakage. By the integration of cell-selective delivery and site-specific stimulation, this endogenously regulated and multiply guaranteed DNA circuit system paves a simple yet effective way for disease diagnosis.

Replicon RNA vaccines: design, delivery, and immunogenicity in infectious diseases and cancer

Replicon RNA (RepRNA) represents a cutting-edge technology in the field of vaccinology, fundamentally transforming vaccine design and development. This innovative approach facilitates the induction of robust immune responses against a range of infectious diseases and cancers. RepRNA vaccines leverage the inherent capabilities of RNA-dependent RNA polymerase associated with self-replicating repRNA, allowing for extreme replication within host cells. This process enhances antigen production and subsequently stimulates adaptive immunity. Additionally, the generation of double-stranded RNA during RNA replication can activate innate immune responses. Numerous studies have demonstrated that repRNA vaccines elicit potent humoral and cellular immune responses that are broader and more durable than those generated by conventional mRNA vaccines. These significant immune responses have been shown to provide protection in various models for infectious diseases and cancers. This article will explore the design and delivery of RepRNA vaccines, the mechanisms of immune activation, preclinical studies addressing infectious diseases and tumors, and related clinical trials that focus on safety and immunogenicity.

Compact transcription factor cassettes generate functional, engraftable motor neurons by direct conversion

Direct conversion generates patient-specific, disease-relevant cell types, such as neurons, that are rare, limited, or difficult to isolate from common and easily accessible cells, such as skin cells. However, low rates of direct conversion and complex protocols limit scalability and, thus, the potential of cell-fate conversion for biomedical applications. Here, we optimize the conversion protocol by examining process parameters, including transcript design; delivery via adeno-associated virus (AAV), retrovirus, and lentivirus; cell seeding density; and the impact of media conditions. Thus, we report a compact, portable conversion process that boosts proliferation and increases direct conversion of mouse fibroblasts to induced motor neurons (iMNs) to achieve high conversion rates of above 1,000%, corresponding to more than ten motor neurons yielded per cell seeded, which we achieve through expansion. Our optimized, direct conversion process generates functional motor neurons at scales relevant for cell therapies (>107 cells) that graft with the mouse central nervous system. High-efficiency, compact, direct conversion systems will support scaling to patient-specific, neural cell therapies.

Quantification and comparison of anti-AAV9 and anti-AAVrh74 antibodies in plasma and human milk: Implications for AAV-based gene therapy candidacy

BackgroundThe application of recombinant adeno associated virus (rAAV) in gene therapy is accepted as an effective strategy for the treatment of monogenic diseases. However, eligibility for such therapies is contingent upon the absence or minimal presence of antibodies against adeno-associated virus (AAV) capsid protein. While the passive transfer of maternal immunoglobulins in utero is well established, the potential impact of maternal antibodies transferred via breastfeeding remains less explored.ObjectiveThis study aims to quantify and compare the levels of anti-AAV9 and anti-AAVrh74 immunoglobulin G (IgG) and M (IgM) in both plasma and human milk from a group of healthy lactating mothers.MethodsIn this cross-sectional study, we analyzed plasma and human milk samples from healthy lactating mothers. We used an enzyme linked immunosorbent assay (ELISA) to determine the levels of circulating IgG and IgM antibodies against AAV9 and AAVrh74 capsids and compared their concentrations in the paired samples.ResultsThirty-one paired plasma and human milk samples were analyzed. The median age at participation was 34 years (range: 25-43), median duration of breastfeeding at the time of sample collection was 7.5 months (range:0.7-33), and median body mass index was 23 Kg/m2 (range: 19.7-35.4). Median anti-AAV9 IgG in plasma and human milk, were 183 U/mL (range: 29-7214) and 1 U/mL (range: 1-33), respectively. Median anti-AAVrh74 IgG, in plasma and human milk were 138 U/mL (range: 23-8725) and 1 U/mL (range: 1-27), respectively. The differences in anti-AAV9 and anti-AAVrh74 IgG levels between plasma and human milk were statistically significant (p < 0.0001). Additionally, a strong correlation (r: 0.97, p: < 0.0001) was observed between anti-AAV9 and anti-AAVrh74 IgG levels in plasma.ConclusionsThe levels of anti-AAV9 and anti-AAVrh74 antibodies in human milk are remarkably lower than those in plasma. Consequently, breastfeeding should not be restricted for term infants who are potential candidates for AAV-related gene therapy products.

Injectable polyplex-loaded glycol chitosan thermogel for efficient and safe inner ear gene delivery

Gene therapy has emerged as a promising approach for treating inner ear disorders, such as hearing loss and balance impairments, which require precise and efficient delivery mechanisms. This study introduces a dual-component delivery system combining RH-PAMAM G2 dendrimer-based polyplexes with hexanoyl glycol chitosan (HGC) thermogel to enhance gene delivery to the inner ear. The RH-PAMAM G2 dendrimers, modified with histidine and arginine, demonstrated high DNA binding affinity, low cytotoxicity, and effective cellular uptake, facilitating stable plasmid DNA (pDNA) transfection in HEI-OC1 auditory cells. Encapsulating these polyplexes within the HGC thermogel, an injectable and thermosensitive hydrogel, resulted in a supportive matrix that protects against premature clearance and provides sustained gene release upon intratympanic administration. In vivo studies in a mouse model confirmed substantial gene expression in the cochlear tissues, with widespread distribution in regions including the spiral ganglion and organ of Corti, compared to polyplexes alone. The HGC thermogel also exhibited favorable biocompatibility, with no observed inflammation or adverse effects in the middle ear tissues. This novel polyplex-HGC thermogel system demonstrates potential as a safe, efficient injectable gene delivery platform, offering a significant advance in gene therapy for inner ear disorders.

Engineering sialylated N-glycans on adeno-associated virus capsids for targeted gene delivery and therapeutic applications

Glycans with diverse biological functions have been extensively identified on enveloped viruses, whereas glycosylation on adeno-associated virus (AAV) serotypes remains poorly understood. Identifying potential glycosylation sites on AAVs could provide critical docking sites for rational engineering of AAV capsids, enabling targeted delivery of therapeutic genes. This study presents a strategy that integrates azido-monosaccharide metabolic incorporation, 1,2-diamino-4,5-methylenedioxybenzene-labeled sialic acid analysis, and mass spectrometry to identify N-glycosylation sites and glycoforms on AAVs. We identified sialylated N- oligosaccharides, particularly the conserved NNNS motif, on AAV2, AAV6, AAV7, and AAV9 capsids. These glycans play critical roles in maintaining capsid stability and enhancing resistance to neutralizing antibodies. Furthermore, we engineered an AAV vector with an azido-labeled terminal sialic acid, which was conjugated via click chemistry to cyclic Arg-Gly-Asp (RGD), a high-affinity ligand for integrin αvβ3, to generate an integrin-targeted delivery vehicle. This approach enabled the efficient delivery of c-Met-targeting shRNA in a glioma mouse model and facilitated CRISPR/Cas9-mediated SMOC2 knockout in a mouse model of kidney fibrosis using single-guide RNA (sgRNA). Our findings establish a foundation for creating editable AAV vectors through sialylated termini, thereby expanding their potential applications in basic research and therapeutic development.

A humanized Gs-coupled DREADD for circuit and behavior modulation

Designer receptors exclusively activated by designer drugs (DREADDs) play important roles in neuroscience research and show great promise for future clinical interventions in neurological diseases. The Gs-coupled DREADD, rM3Ds, modulates excitability in neuron subsets that are sensitive to downstream effectors of Gs protein. However, given the non-human nature of the rM3Ds backbone, risks about potential immunogenicity and tolerability exist when considering clinical translation. Here, we report the development of a whole sequence-humanized Gs-coupled DREADD, hM3Ds. We found that hM3Ds has a comparable DREADD ligand response profile to rM3Ds. We then selectively expressed hM3Ds in D1 medium spiny neurons (D1-MSNs) and found that hM3Ds was able to activate the D1-MSNs-mediated basal ganglia direct pathway and alleviate Parkinsonian phenotypes in a Parkinson's disease mouse model. In conclusion, this engineered humanized Gs-coupled DREADD is suitable as an effective, and likely safer, DREADD tool for both research and future clinical applications.

Gene regulation technologies for gene and cell therapy

Gene therapy stands at the forefront of medical innovation, offering unique potential to treat the underlying causes of genetic disorders and broadly enable regenerative medicine. However, unregulated production of therapeutic genes can lead to decreased clinical utility due to various complications. Thus, many technologies for controlled gene expression are under development, including regulated transgenes, modulation of endogenous genes to leverage native biological regulation, mapping and repurposing of transcriptional regulatory networks, and engineered systems that dynamically react to cell state changes. Transformative therapies enabled by advances in tissue-specific promoters, inducible systems, and targeted delivery have already entered clinical testing and demonstrated significantly improved specificity and efficacy. This review highlights next-generation technologies under development to expand the reach of gene therapies by enabling precise modulation of gene expression. These technologies, including epigenome editing, antisense oligonucleotides, RNA editing, transcription factor-mediated reprogramming, and synthetic genetic circuits, have the potential to provide powerful control over cellular functions. Despite these remarkable achievements, challenges remain in optimizing delivery, minimizing off-target effects, and addressing regulatory hurdles. However, the ongoing integration of biological insights with engineering innovations promises to expand the potential for gene therapy, offering hope for treating not only rare genetic disorders but also complex multifactorial diseases.

Distinct infectivity and neutralization antibody responses in the highly homologous AAV Go.1 and AAV5

Introduction

Goat-derived adeno-associated virus (AAV) vectors, such as AAV Go.1, represent a novel platform for gene therapy due to their unique origin and potential advantages in transduction efficiency and immune evasion. However, their therapeutic potential and biological properties remain underexplored.

Methods

In this study, we developed a recombinant AAV (rAAV) Go.1 by replacing the goat AAV rep gene with the standard AAV2-rep gene to improve packaging efficiency. We compared the transduction efficiency of rAAV Go.1 with that of AAV5, a closely related serotype with 95% genome similarity, both in vitro and in vivo. Additionally, we assessed immune evasion properties by evaluating resistance to neutralization using sera from rAAV5-immunized mice and human volunteers. To further enhance transduction efficiency, we introduced site-specific mutations in the VP1 unique (VP1u) region and VP1/2 common region.

Results

The rep gene modification led to a significantly higher packaging efficiency for rAAV Go.1 compared to the original goat AAV. rAAV Go.1 exhibited markedly higher transduction efficiency than AAV5 in both in vitro and in vivo models. Furthermore, rAAV Go.1 demonstrated a 4-fold increase in resistance to neutralization by sera from rAAV5-immunized mice. A study involving 20 healthy volunteers revealed that high-titer neutralizing antibodies had a more pronounced inhibitory effect on rAAV5 compared to rAAV Go.1. Mutagenesis studies identified key modifications that enhanced viral properties: K32R, K91R, and K122R mutations in the VP1u region significantly improved viral production, while K137R (VP1u) enhanced transduction efficiency in vitro and in vivo.

Discussion

Our findings highlight the potential of rAAV Go.1 as an improved gene therapy vector with superior transduction efficiency and enhanced immune evasion. The identified VP1 mutations further optimize viral properties, making rAAV Go.1 a promising candidate for future therapeutic applications.

Gene therapy shines light on congenital stationary night blindness for future cures

Congenital Stationary Night Blindness (CSNB) is a non-progressive hereditary eye disease that primarily affects the retinal signal processing, resulting in significantly reduced vision under low-light conditions. CSNB encompasses various subtypes, each with distinct genetic patterns and pathogenic genes. Over the past few decades, gene therapy for retinal genetic disorders has made substantial progress; however, effective clinical therapies for CSNB are yet to be discovered. With the continuous advancement of gene-therapy tools, there is potential for these methods to become effective treatments for CSNB. Nonetheless, challenges remain in the treatment of CSNB, including issues related to delivery vectors, therapeutic efficacy, and possible side effects. This article reviews the clinical diagnosis, pathogenesis, and associated mutated genes of CSNB, discusses existing animal models, and explores the application of gene therapy technologies in retinal genetic disorders, as well as the current state of research on gene therapy for CSNB.

Adeno-associated viral vector targeted evolution for neurofibromatosis gene delivery

Neurofibromatosis type 1 (NF1) is an inherited genetic disease resulting from pathogenic mutations in NF1 that drive tumor formation along peripheral nerves, leading to many functional consequences. Tumor removal or treatment often results in regrowth and/or nerve damage. Addressing NF1 pathogenic variations at the cellular level through gene therapy holds great potential for long-term treatment of patients with NF1. Adeno-associated viruses (AAVs) are broadly used gene delivery vehicles for gene therapies because of their low pathogenicity, ability to transduce nondividing cells, and potential for long-term gene expression. This article explores the landscape of AAV-mediated gene delivery strategies for NF1, discusses the challenges of efficient delivery to relevant cell types, and highlights the progress in vector design strategies.

Artificial Intelligence and Computational Biology in Gene Therapy: A Review

One of the trending fields in almost all areas of science and technology is artificial intelligence. Computational biology and artificial intelligence can help gene therapy in many steps including: gene identification, gene editing, vector design, development of new macromolecules and modeling of gene delivery. There are various tools used by computational biology and artificial intelligence in this field, such as genomics, transcriptomic and proteomics data analysis, machine learning algorithms and molecular interaction studies. These tools can introduce new gene targets, novel vectors, optimized experiment conditions, predict the outcomes and suggest the best solutions to avoid undesired immune responses following gene therapy treatment.

Mesenchymal Stem Cells Expressing Baculovirus-Engineered Brain-Derived Neurotrophic Factor Improve Peripheral Nerve Regeneration in a Rat Model

BACKGROUND

Peripheral nerve injuries are a major clinical challenge because of their complex nature and limited regenerative capacity. This study aimed to improve peripheral nerve regeneration using Wharton's jelly mesenchymal stem cells (WJ-MSCs) engineered to express brain-derived neurotrophic factor (BDNF) via a baculovirus (BV) vector. The cells were evaluated for efficacy when seeded into acellular nerve grafts (ANGs) in a rat sciatic nerve defect model.

METHODS

WJ-MSCs were transfected with recombinant BV to upregulate BDNF expression. Conditioned medium (CM) from these cells was utilized to treat Schwann cells (SCs), and the impact on myelination-related markers, including KROX20, myelin basic protein (MBP), glial fibrillary acidic protein (GFAP), and S100 calcium-binding protein β (S100β), and the activation of the mammalian target of rapamycin (mTOR)/ protein kinase B (AKT)/p38 signaling pathways were evaluated. In vivo, BDNF-expressing WJ-MSCs were seeded into ANGs and implanted into a rat sciatic nerve defect model. Functional recovery was evaluated via video gait analysis, isometric tetanic force measurement, muscle weight evaluation, ankle contracture angle measurement, and histological analysis using toluidine blue staining.

RESULTS

BDNF expression was significantly upregulated in WJ-MSCs post-transfection. BDNF-MSC CM substantially promoted the expression of myelination markers in SCs and activated the mTOR/AKT/p38 signaling pathway. In the rat model, seeding of ANGs with BDNF-expressing WJ-MSCs resulted in improved functional outcomes, including enhanced toe-off angles, increased isometric tetanic force, greater muscle weight recovery, and a higher total number of myelinated axons compared with controls.

CONCLUSION

WJ-MSCs engineered to express BDNF significantly enhanced peripheral nerve regeneration when utilized in conjunction with ANGs. These findings indicate BDNF-expressing WJ-MSCs are a promising therapeutic approach for treating peripheral nerve injuries.

AAV-mediated expression of proneural factors stimulates neurogenesis from adult Müller glia in vivo

The lack of regeneration in the human central nervous system (CNS) has major health implications. To address this, we previously used transgenic mouse models to show that neurogenesis can be stimulated in the adult mammalian retina by driving regeneration programs that other species activate following injury. Expression of specific proneural factors in adult Müller glia causes them to re-enter the cell cycle and give rise to new neurons following retinal injury. To bring this strategy closer to clinical application, we now show that neurogenesis can also be stimulated when delivering these transcription factors to Müller glia using adeno-associated viral (AAV) vectors. AAV-mediated neurogenesis phenocopies the neurogenesis we observed from transgenic animals, with different proneural factor combinations giving rise to distinct neuronal subtypes in vivo. Vector-borne neurons are morphologically, transcriptomically and physiologically similar to bipolar and amacrine/ganglion-like neurons. These results represent a key step forward in developing a cellular reprogramming approach for regenerative medicine in the CNS.

Advances in AAV capsid engineering: Integrating rational design, directed evolution and machine learning

Adeno-associated virus (AAV) has emerged as a highly promising vector for human gene therapy due to its favorable safety profile, versatility, and ability to transduce a wide range of tissues. However, natural AAV serotypes have shortcomings, including suboptimal transduction efficiency, pre-existing immunity, and a lack of tissue specificity, that hinder their therapeutic potential. To address these challenges, significant efforts are being applied to engineer novel AAV capsids. Rational design leverages structural insights to enhance capsid properties, directed evolution enables unbiased selection of superior variants, and machine learning accelerates discovery by computational analysis of high-throughput screening results to enable predictive algorithms. These strategies have yielded novel capsids with improved transduction efficiency, reduced immunogenicity, and enhanced tissue targeting. Future advances that continue to integrate such multi-disciplinary approaches will further drive the clinical translation of AAV-based therapies.

Targeted degradation of α-Synuclein using an evolved botulinum toxin protease

There is considerable interest in the targeted degradation of proteins implicated in human disease. The use of sequence-specific proteases for this purpose is severely limited by the difficulty in engineering the numerous enzyme-substrate interactions required to yield highly selective proteases while maintaining catalytic activity. Herein, we report a strategy to evolve a protease for the programmed degradation of α-Synuclein, a presynaptic protein closely linked to Parkinson's disease. Our structure-guided evolution campaign uses the protease from botulinum neurotoxin and showcases the stepwise change of specificity from its native substrate SNAP25 to the selective degradation of α-Synuclein. The protease's selectivity is further demonstrated in human cells where near complete degradation of overexpressed human α-Synuclein is observed with no significant effects on cell proliferation. This stepwise strategy may serve as a general approach to evolve highly selective proteases targeting dysregulated proteins.

Is Duchenne gene therapy a suitable treatment despite its immunogenic class effect?

INTRODUCTION

Duchenne muscular dystrophy (DMD) is a severe X-linked disorder characterized by progressive muscle weakness and eventual death due to cardiomyopathy or respiratory complications. Currently, there is no cure for DMD, with standard treatments primarily focusing on symptom management. Using immunosuppressive measures and optimized vector designs allows for gene therapies to better address the genetic cause of the disease.

AREAS COVERED

This review evaluates the efficacy and safety of emerging DMD gene therapies as of 2024. It also discusses the potential of utrophin upregulation, gene editing, and truncated dystrophin as therapeutic strategies. It highlights safety concerns associated with these therapies, including adverse events and patient deaths. A comprehensive overview of developments covers topics such as CRISPR-Cas9 therapies, micro-dystrophin, and the potential delivery of full-length dystrophin.

EXPERT OPINION

The FDA's recent approval of delandistrogene moxeparvovec (Elevidys) underscores the promise of gene replacement therapies for DMD patients. Understanding the mechanisms behind the adverse effects and excluding patients with specific pathogenic variants may enhance the safety profiles of these therapies. CRISPR/Cas9 therapies, while promising, face significant regulatory and safety challenges that hinder their clinical application. Optimal DMD therapies should target both skeletal and cardiac muscles to be effective.

2024 VCP International Conference: Exploring multi-disciplinary approaches from basic science of valosin containing protein, an AAA+ ATPase protein, to the therapeutic advancement for VCP-associated multisystem proteinopathy

Valosin-containing protein (VCP/p97) is a ubiquitously expressed AAA+ ATPase associated with numerous protein-protein interactions and critical cellular functions including protein degradation and clearance, mitochondrial homeostasis, DNA repair and replication, cell cycle regulation, endoplasmic reticulum-associated degradation, and lysosomal functions including autophagy and apoptosis. Autosomal-dominant missense mutations in the VCP gene may result in VCP-associated multisystem proteinopathy (VCP-MSP), a rare degenerative disorder linked to heterogeneous phenotypes including inclusion body myopathy (IBM) with Paget's disease of bone (PDB) and frontotemporal dementia (FTD) or IBMPFD, amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), parkinsonism, Charcot-Marie Tooth disease (CMT), and spastic paraplegia. The complexity of VCP-MSP makes collaboration among stakeholders essential and necessitates a multi-disciplinary approach. The 2024 VCP International Conference was hosted at Caltech between February 22 and 25. Co-organized by Cure VCP Disease and Dr. Tsui-Fen Chou, the meeting aimed to center the patient as a research partner, harmonize diverse stakeholder engagement, and bridge the gap between basic and clinical neuroscience as it relates to VCP-MSP. Over 100 multi-disciplinary experts attended, ranging from basic scientists to clinicians to patient advocates. Attendees discussed genetics and clinical presentation, cellular and molecular mechanisms underlying disease, therapeutic approaches, and strategies for future VCP research. The conference included three roundtable discussions, 29 scientific presentations, 32 scientific posters, nine patient and caregiver posters, and a closing discussion forum. The following conference proceedings summarize these sessions, highlighting both the identified gaps in knowledge and the significant strides made towards understanding and treating VCP diseases.

Protein Carrier Adeno-Associated Virus

Adeno-associated virus (AAV) has emerged as a leading platform for gene therapy, enabling the delivery of therapeutic DNA to target cells. However, the potential of AAV to deliver protein payloads has been unexplored. In this study, we engineered a protein carrier AAV (pcAAV) to package and deliver proteins by inserting binding domains on the interior capsid surface. These binding domains mediate the packaging of specific target proteins through interaction with cognate peptides or protein tags during the capsid assembly process. We demonstrate the packaging of multiple proteins, including green fluorescent protein, Streptococcus pyogenes Cas9, Cre recombinase, and the engineered peroxidase APEX2. Packaging efficiency is modulated by the binding domain insertion site, the viral protein isoform containing the binding domain, and the subcellular localization of the target protein. We show that pcAAV can enter cells and deliver the protein payload and that enzymes retain their activity after packaging. Importantly, this protein packaging capability can be translated to multiple AAV serotypes. Our work establishes AAV as a protein delivery vehicle, significantly expanding the utility of this viral vector for biomedical applications.

The deLIVERed promises of gene therapy: Past, present, and future of liver-directed gene therapy

Gene therapy has revolutionized modern medicine by offering innovative treatments for genetic and acquired diseases. The liver has been and continues as a prime target for in vivo gene therapy due to its essential biological functions, vascular access to the major target cell (hepatocytes), and relatively immunotolerant environment. Adeno-associated virus (AAV) vectors have become the cornerstone of liver-directed therapies, demonstrating remarkable success in conditions such as hemophilia A and B, with US Food and Drug Administration (FDA)-approved therapies like etranacogene dezaparvovec, Beqvez, and Roctavian marking milestones in the field. Despite these advances, challenges persist, including vector immunogenicity, species-specific barriers, and high manufacturing costs. Innovative strategies, such as capsid engineering, immune modulation, and novel delivery systems, are continuing to address these issues in expanding the scope of therapeutic applications. Some of the challenges with many new therapies result in the discordance between preclinical success and translation into humans. The advent of various genome-editing tools to repair genomic mutations or insert therapeutic DNAs into precise locations in the genome further enhances the potential for a single-dose medicine that will offer durable life-long therapeutic treatments. As advancements accelerate, liver-targeted gene therapy is poised to continue to transform the treatment landscape for both genetic and acquired disorders, for which unmet challenges remain.

Specific and efficient RNA A-to-I editing through cleavage of an ADAR inhibitor

RNA editing can be a promising therapeutic approach. However, ectopic expression of RNA editing enzymes has been shown to trigger off-target editing. Here we identified adenosine deaminase acting on RNA (ADAR) inhibitors (ADIs) that suppress the activity of the fused ADAR2 deamination domain (ADAR2DD). Using these specific ADIs, we develop an RNA transformer adenosine base editor (RtABE) with high specificity. Fusing ADI to ADAR2DD, RtABE remains inactive until it binds to its target site. After binding to the target site, ADI is cleaved from ADAR2DD, and RtABE becomes active. RtABE can induce efficient editing in broad sequence contexts, including UAN, AAN, CAN and GAN. Using an adeno-associated virus for delivery of RtABE enables therapeutic RNA correction and restoration of α-L-iduronidase activity in Hurler syndrome mice with no substantial off-target editing. RtABE is a specific and efficient RNA editing system with a broad scope that may be a better alternative to existing RNA editing tools.

TRIM15 drives chondrocyte senescence and osteoarthritis progression

Osteoarthritis (OA) is a prevalent joint disease characterized by pain, disability, and loss of physical function, posing a challenge to public health. However, molecular mechanisms of OA pathogenesis have not been fully described. We report that tripartite motif containing 15 (TRIM15) is a regulator in chondrocyte senescence and OA. Our study revealed heightened expression of TRIM15 in chondrocytes of senescent cartilage from patients with OA and in aged wild-type mice. Using gain- and loss-of-function studies, we found that TRIM15 facilitated human chondrocyte senescence. Conditional deletion of Trim15 in mouse chondrocytes severely impaired skeletal growth, partially because of impaired embryonic chondrocyte senescence. Compared with conditionally knocked out Col2a1-CreERT2/Trim15flox/flox mice, Trim15flox/flox control mice exhibited accelerated OA phenotypes, increased senescence markers, and senescence-associated secretory phenotype during aging. Mechanistically, TRIM15 bound with yes-associated protein (YAP) and mediated K48-linked YAP ubiquitination at K254, which interrupted the interaction between YAP and angiomotin, leading to enhanced YAP nuclear translocation. Dysregulation of TRIM15-YAP and transcriptional coactivator with PDZ-binding motif (TAZ) signaling promoted OA progression in both the surgery-induced and natural aging-induced mouse OA model. Intra-articular injection of adeno-associated virus 5 (AAV5)-Trim15 shRNA decelerated OA progression in mice. In particular, YAP and TAZ protein amounts were increased in chondrocytes of patients with OA. Our preclinical results demonstrated that the AAV5-TRIM15 shRNA treatment protected human OA explants against degeneration through inhibiting chondrocyte senescence. Together, our findings underscore the potential of targeting TRIM15 in reshaping the aging cartilage microenvironment and suggest a promising therapeutic avenue for OA.

Hearing restoration through hair cell regeneration: A review of recent advancements and current limitations

Hearing loss is extremely common, yet limited treatment options are available to restore hearing, and those that are available provide incomplete recovery of hearing detection. For patients who are born with normal hearing, the most common cause of hearing loss is the loss of the sensory hair cells located in the cochlea of the inner ear. Non-mammals, including birds, fish, and amphibians, naturally regenerate new hair cells after damage and this natural process results in functional recovery. While some limited hair cell regeneration also occurs in the immature cochlea of mice, the mature mammalian cochlea does not naturally produce replacement hair cells, and thus hearing loss is permanent. Since the late 1980s, researchers have been investigating mechanisms to convert supporting cells, the cells that remain once hair cells have been killed, into new replacement hair cells. Here we review the current status of hair cell regeneration in the adult cochlea, highlighting recent achievements, as well as challenges that have yet to be resolved.

Mechanism of LncRNA-MiRNA in Renal Intrinsic Cells of Diabetic Kidney Disease and Potential Therapeutic Direction

The occurrence of diabetic kidney disease (DKD), a critical microvascular issue in diabetes, is progressively on the rise. In recent years, long noncoding RNAs (lncRNAs) have garnered considerable attention as a novel and critical layer of biological regulation. Our knowledge regarding the roles and underlying mechanisms of lncRNAs in various diseases, including DKD, continues to evolve. Similarly, microRNAs (miRNAs), which are small noncoding RNAs, have been recognized as crucial contributors to cellular processes and disease pathogenesis. Emerging studies have highlighted the complex interactions between lncRNAs and miRNAs, particularly in the context of DKD, underscoring their importance in complex human diseases. Renal intrinsic cell damage is an important cause of inducing DKD. Persistent high glucose stimulation leads to remodeling of renal intrinsic cells and a cascade of pathological changes. This article aims to review recent literature on the lncRNAs-mediated regulation of miRNAs affecting renal intrinsic cells in DKD and to propose novel molecular-level therapeutic strategies for DKD. Through in-depth investigation of this dynamic molecular interaction, we can gain a profound understanding of the potential mechanisms underlying diabetic nephropathy, potentially identifying new targets for therapeutic intervention and paving the way for personalized and effective treatments.

Advances in Optogenetics and Thermogenetics for Control of Non-Neuronal Cells and Tissues in Biomedical Research

Optogenetics and chemogenetics are relatively new biomedical technologies that emerged 20 years ago and have been evolving rapidly since then. This has been made possible by the combined use of genetic engineering, optics, and electrophysiology. With the development of optogenetics and thermogenetics, the molecular tools for cellular control are continuously being optimized, studied, and modified, expanding both their applications and their biomedical uses. The most notable changes have occurred in the basic life sciences, especially in neurobiology and the activation of neurons to control behavior. Currently, these methods of activation have gone far beyond neurobiology and are being used in cardiovascular research, for potential cancer therapy, to control metabolism, etc. In this review, we provide brief information on the types of molecular tools for optogenetic and thermogenetic methods─microbial rhodopsins and proteins of the TRP superfamily─and also consider their applications in the field of activation of non-neuronal tissues and mammalian cells. We also consider the potential of these technologies and the prospects for the use of optogenetics and thermogenetics in biomedical research.

Targeted gene silencing in mouse testicular Sertoli and Leydig cells using adeno-associated virus vectors

ABSTRACT

Researchers commonly use cyclization recombination enzyme/locus of X-over P1 (Cre/loxP) technology-based conditional gene knockouts of model mice to investigate the functional roles of genes of interest in Sertoli and Leydig cells within the testis. However, the shortcomings of these genetic tools include high costs, lengthy experimental periods, and limited accessibility for researchers. Therefore, exploring alternative gene silencing techniques is of great practical value. In this study, we employed adeno-associated virus (AAV) as a vector for gene silencing in Sertoli and Leydig cells. Our findings demonstrated that AAV serotypes 1, 8, and 9 exhibited high infection efficiency in both types of testis cells. Importantly, we discovered that all three AAV serotypes exhibited exquisite specificity in targeting Sertoli cells via tubular injection while demonstrating remarkable selectivity in targeting Leydig cells via interstitial injection. We achieved cell-specific knockouts of the steroidogenic acute regulatory (Star) and luteinizing hormone/human chorionic gonadotropin receptor (Lhcgr) genes in Leydig cells, but not in Sertoli cells, using AAV9-single guide RNA (sgRNA)-mediated gene editing in Rosa26-LSL-Cas9 mice. Knockdown of androgen receptor (Ar) gene expression in Sertoli cells of wild-type mice was achieved via tubular injection of AAV9-short hairpin RNA (shRNA)-mediated targeting. Our findings offer technical approaches for investigating gene function in Sertoli and Leydig cells through AAV9-mediated gene silencing.

Spatial genomics of AAV vectors reveals mechanism of transcriptional crosstalk that enables targeted delivery of large genetic cargo

Cell-type-specific regulatory elements such as enhancers can direct expression of recombinant adeno-associated viruses (AAVs) to specific cell types, but this approach is limited by the relatively small packaging capacity of AAVs. In this study, we used spatial genomics to show that transcriptional crosstalk between individual AAV genomes provides a general method for cell-type-specific expression of large cargo by separating distally acting regulatory elements into a second AAV genome. We identified and profiled transcriptional crosstalk in AAV genomes carrying 11 different enhancers active in mouse brain. We developed spatial genomics methods to identify and localize AAV genomes and their concatemeric forms in cultured cells and in tissue, and we demonstrate here that transcriptional crosstalk is dependent upon concatemer formation. Finally, we leveraged transcriptional crosstalk to drive expression of a 3.2-kb Cas9 cargo in a cell-type-specific manner with systemically administered engineered AAVs, and we demonstrate AAV-delivered, minimally invasive, cell-type-specific gene editing in wild-type mice that recapitulates known disease phenotypes.

Correcting a patient-specific Rhodopsin mutation with adenine base editor in a mouse model

Genome editing offers a great promise to treating human genetic diseases. To assess genome-editing-mediated therapeutic effects in vivo, an animal model is indispensable. The genomic disparities between mice and humans often impede the direct clinical application of genome-editing-mediated treatments using conventional mouse models. Thus, the generation of a mouse model with a humanized genomic segment containing a patient-specific mutation is highly sought after for translational research. In this study, we successfully developed a knockin mouse model for autosomal-dominant retinitis pigmentosa (adRP), designated as hT17M knockin, which incorporates a 75-nucleotide DNA segment with the T17M mutation (Rhodopsin-c.C50T; p.T17M). This model demonstrated significant reductions in electroretinogram amplitudes and exhibited disruptions in retinal structure. Subsequently, we administered an adeno-associated virus vectors carrying an adenine base editor (ABE) and a single-guide RNA specifically targeting the T17M mutation, achieving a peak correction rate of 39.7% at the RNA level and significantly improving retinal function in ABE-injected mice. These findings underscore that the hT17M knockin mouse model recapitulates the clinical features of adRP patients and exhibits therapeutic effects with ABE-mediated treatments. It offers a promising avenue for the development of gene-editing therapies for RP.

Therapeutic potential of AAV2-shmTOR gene therapy in reducing retinal inflammation and preserving endothelial Integrity in age-related macular degeneration

Age-related macular degeneration (AMD) is a prevalent retinal disorder that leads to central vision loss, mainly due to chronic inflammation. Tumor necrosis factor-alpha (TNF-α) is a critical mediator of inflammatory responses within the retinal environment. This study has investigated TNF-α's influence on inflammatory cytokine production and endothelial barrier integrity in human microglial (HMC3) and endothelial (HUVEC) cells. We found that TNF-α significantly elevated the expression and secretion of interleukin-6 (IL-6) and interleukin-1β (IL-1β) in HMC3 cells and disrupted endothelial tight junctions in HUVECs, as evidenced by weakened ZO-1 staining and compromised barrier function. To mitigate these effects and further investigate the in vitro mechanism of actions in CRG-01's in vivo therapeutic efficacy of anti-inflammation, we employed AAV2-shmTOR, CRG-01, as the candidate for therapeutic vector targeting the mammalian target of the rapamycin (mTOR) pathway. TNF-α-induced IL-6, IL-1β, and NF-κB signaling in HMC3 cells were significantly reduced by AAV2-shmTOR treatment, which may present a promising avenue for the fight against AMD. It also effectively preserved endothelial tight junction integrity in TNF-α-treated HUVECs, providing reassurance about its effectiveness. Furthermore, the supernatant medium collected from AAV2-shmTOR-treated HMC3 cells decreased oxidative stress, protein oxidation, and cytotoxicity in ARPE retinal pigment epithelial cells. These results strongly suggested that CRG-01, the candidate therapeutic vector of AAV2-shmTOR, may have a therapeutic potential to treat AMD-related retinal inflammation.

Encapsulation of a Single-Stranded Form of DNA Impurities into the Capsid of a Recombinant Adeno-Associated Virus

Recombinant adeno-associated viruses (rAAVs) are widely used viral vectors in human gene therapy. However, DNA impurities, such as plasmid DNA and host cell DNA, remain a significant quality control concern for final products. Our study examined purified rAAV1-ZsGreen1, rAAV2-ZsGreen1, rAAV5-ZsGreen1, and rAAV6-ZsGreen1 samples and found that they contained 0.69-3.27% DNA impurities derived from three plasmids, as detected by droplet digital PCR. These plasmid-derived impurities primarily consisted of those derived from the pAAV plasmid (≥98.88%), with small amounts of pRC1, pRC2mi342, pRC5, or pRC6 (≤0.91%), and pHelper (≤0.21%) plasmids. To determine the DNA strand form of these impurities within the capsids, we used two different DNases with distinct substrate specificities. The extracted DNA impurities from the rAAV samples exhibited high sensitivity to nuclease P1 but not to lambda exonuclease. Similarly, host cell DNA encapsulated within the capsids revealed similar sensitivities to the nucleases. These findings indicate that DNA impurities derived from the plasmids and host cell DNA are encapsulated into rAAV capsids as single-stranded DNA, likely through a mechanism similar to that of the rAAV genome.

Preclinical development of genome editing to treat Duchenne muscular dystrophy by exon skipping

Duchenne muscular dystrophy (DMD) is caused by loss-of-function mutations to the gene encoding dystrophin. Restoring the reading frame of dystrophin by removing internal out-of-frame exons may address symptoms of DMD. Therefore, the principle of exon skipping has been at the center stage in drug development for Duchenne muscular dystrophy (DMD) over the past two decades. Antisense oligonucleotides (AONs) have proven effective in modulating splicing sites for exon skipping, resulting in the FDA approval of several drugs using this technique in recent years. However, due to the temporary nature of AON, researchers are actively exploring genome editing as a potential long-term, single-administration treatment. The advancements in genome-editing technology over the last decade have boosted this transition. While no clinical trials for exon skipping in DMD via genome editing have been conducted as of this writing, preclinical studies show encouraging results. This review describes the preclinical landscape of genome editing for exon skipping in DMD treatment. Along with highlighting the adaptability of genome editing in exon skipping, this review also describes delivery challenges and outlines future research directions that could set a new stage for enhanced therapeutic development in DMD.

Perfusion-Based Production of rAAV via an Intensified Transient Transfection Process

Increasing demand for recombinant adeno-associated virus (rAAV)-based gene therapies necessitates increased manufacturing production. Transient transfection of mammalian cells remains the most commonly used method to produce clinical-grade rAAVs due to its ease of implementation. However, transient transfection processes are often characterized by suboptimal yields and low fractions of full-to-total capsids, both of which contribute to the high cost of goods of many rAAV-based gene therapies. Our previously developed mechanistic model for rAAV2/5 production indicated that the inadequate capsid filling is due to a temporal misalignment between viral DNA replication and capsid synthesis within the cells and the repression of later phase capsid formation by Rep proteins. We experimentally validated this prediction and showed that performing multiple, time-separated doses of plasmid increases the production of rAAV. In this study, we use the insights generated by our mechanistic model to develop an intensified process for rAAV production that combines perfusion with high cell density re-transfection. We demonstrate that performing multiple, time-separated doses at high cell density boosts both cell-specific and volumetric productivity and improves plasmid utilization when compared to a single bolus at standard operating conditions. Our results establish a new paradigm for continuously manufacturing rAAV via transient transfection that improves productivity and reduces manufacturing costs.

An enhancer-AAV toolbox to target and manipulate distinct interneuron subtypes

In recent years, we and others have identified a number of enhancers that, when incorporated into rAAV vectors, can restrict the transgene expression to particular neuronal populations. Yet, viral tools to access and manipulate specific neuronal subtypes are still limited. Here, we performed systematic analysis of single cell genomic data to identify enhancer candidates for each of the telencephalic interneuron subtypes. We established a set of enhancer-AAV tools that are highly specific for distinct cortical interneuron populations and striatal cholinergic interneurons. These enhancers, when used in the context of different effectors, can target (fluorescent proteins), observe activity (GCaMP) and manipulate (opto-genetics) specific neuronal subtypes. We also validated our enhancer-AAV tools across species. Thus, we provide the field with a powerful set of tools to study neural circuits and functions and to develop precise and targeted therapy.

The combination of rAAV pseudo-lipid nanoparticle and triamcinolone acetonide enables multi-administration to liver

The multi-administration of recombinant adeno-associated virus (rAAV) is limited largely by immunological barriers. Herein, a novel strategy, named rAAV pseudo-lipid nanoparticle combined with triamcinolone acetonide (LNP-rAAV + TAC), has been described in mice. We showed successful but low efficient triple trafficking by LNP-rAAV2 carrying EGFP, human factor IX (hFIX), and luciferase (luc), due to its encapsulation characteristic. Additionally, sustained TAC treatment, which dose-dependently downregulated the anti-rAAV2 antibodies, permitted rAAV2 re-administration at dosages of ≥45 mg/kg/3 days. Furthermore, to improve the efficiency and safety, LNP-rAAV + TAC was evaluated, using LNP-rAAV2 carrying EGFP, hFIX, and luc co-treating with 45 mg/kg/3 days TAC before and after treatment with LNP-rAAV2 injections. Notable neutralizing antibody reductions of 37.8-fold and 12.7-fold were observed by the combinatorial strategy compared with the independent LNP encapsulation and TAC treatment approaches. The plasma hFIX protein was enhanced to 15.1 μg/mL and the liver bioluminescence was elevated to 1.4 × 108 p/s/cm2/sr following the second and third administrations, with weaker levels in LNP encapsulation (1.9 μg/mL, 2.1 × 104 p/s/cm2/sr) and TAC treatment (3.0 μg/mL, 6.1 × 104 p/s/cm2/sr) groups. Thus, this combination strategy is an attractive candidate for enabling multi-dosing of rAAV vector and warrants further study on the underlying mechanism.

Polo-like kinase inhibitors increase AAV production by halting cell cycle progression

Recombinant adeno-associated viruses (rAAVs) are commonly used in gene therapy for preclinical research and therapeutic applications. Despite the clinical efficacy of rAAVs, their manufacturing involves challenges in productivity and quality, leading to limited availability. In this study, we aimed to identify compounds that increase the capacity of cells to produce AAV9 with a high-throughput small-molecule screening strategy. With the Arrayed Targeted Library for AAV Screening platform, we screened a library of 3,300 small molecules and identified several targets, including cell cycle modulators, G protein-coupled receptor modulators, histone deacetylate inhibitors, Janus kinase inhibitors, and metabolic modulators. Most notably, we identified Polo-like kinase isoform 1 (PLK1) inhibitors as enhancers of adeno-associated virus (AAV) production. Inhibiting PLK1 with HMN-214 increased AAV production, which was largely consistent across HEK293 cell lines, vector payloads, and capsid serotypes. Using cell cycle and RNA-sequencing analysis, we showed that PLK1 inhibition halts cells in the G2/M phase and blocks their exit from the M to G1 phase. These findings support that inhibiting PLK1 may enhance AAV production and could be used to develop more cost-effective methods to manufacture AAV for gene therapies.