Targeted Base Editing with VLP Delivery: Blocking Cellular Repair Enzymes to Maximize In Vivo Base Correction Efficiency
Background
Safe Gene Delivery Technology Overcoming Cellular Barriers
Base editing, a technology that modifies DNA without cleaving the double helix, represents a new paradigm in the treatment of genetic diseases. In particular, cytosine base editors (CBEs), which convert cytosine (C) to thymine (T), hold the key to treating various genetic disorders. However, the safe and efficient delivery of these editors to target cells has been a long-standing challenge.
Existing viral or lipid nanoparticle (LNP) methods carry the risk of genomic insertion and off-target mutations. As an alternative, virus-like particles (VLPs), which function temporarily and then disappear, have emerged.
However, in vivo cytosine editing using VLPs has been inefficient due to cellular repair mechanisms that interfere with the editing process. When a CBE converts cytosine to uracil (U), uracil DNA glycosylase (UDG) immediately reverses the modification. Due to the transient nature of VLPs, conventional uracil DNA glycosylase inhibitors (UGIs) are insufficient to control the cell's robust repair mechanisms.
Key Findings
Development of 'tBE-VLP4' to Inhibit Repair Enzymes
Professor Jia Chen of ShanghaiTech University, in collaboration with Professors Li Yang and Jiaxu Hong of Fudan University, addressed this issue by blocking cellular repair enzymes. Their key tool, designed to prevent the risk of genetic dysfunction, is the 'Transformer Base Editor' (tBE). The tBE has a unique switch-like mechanism that is activated only when bound to the target DNA sequence.
In the process of incorporating the tBE into VLPs, the researchers developed 'tBE-VLP4,' which features a stereoscopically designed UGI binding method. This structure allows the UGI within the VLP to more strongly inhibit intracellular UDG. By overcoming the interference of repair enzymes, the uracil intermediate converted by the deaminase is preserved, enabling precise conversion of the target base to thymine.
The results of animal model experiments were also noteworthy. Single administration targeting the proprotein convertase subtilisin/kexin type 9 (Pcsk9) gene, which is involved in the development of hyperlipidemia, resulted in an average base editing efficiency of 46.0%. Consequently, the concentration of PCSK9 protein and total cholesterol levels in the mice's serum were significantly reduced.
Visible therapeutic effects were also observed in a mouse model of hereditary tyrosinemia type I (HT1), a life-threatening metabolic disorder. Targeting the 4-hydroxyphenylpyruvate dioxygenase (Hpd) gene, which causes the accumulation of toxic substances, resulted in a maximum correction rate of 64.2% in liver tissue, halting the rapid weight loss and significantly improving overall survival.
The potential as a therapeutic agent for ophthalmic diseases is also highly regarded. Targeting the vascular endothelial growth factor A (Vegfa) gene in retinal pigment epithelial cells and administering it subretinally resulted in a correction efficiency of 24.2%. In particular, whole-genome and transcriptome analysis revealed no off-target gene mutations or unwanted RNA modifications, indicating excellent safety.
Significance and Prospects
A New Horizon for Safe Gene Therapy: Process Optimization is Key for Commercialization
This achievement is considered to have enhanced the potential for practical application of non-viral vectors, VLPs. It overcomes the limitations of existing LNP methods, which are limited to liver tissue, and demonstrates that precise gene editing is possible even in delicate tissues such as the eye. Because VLPs do not leave a trace in the genome and act only for a short period, concerns about cell toxicity due to long-term expression are also eliminated.
However, to advance to actual therapeutic commercialization, it is essential to establish a standardized production process that yields high-purity VLP particles with uniform quality. This is because it is necessary to control the technology to ensure that a uniform amount of therapeutic substance is loaded per particle. In the future, research on VLP surface glycoprotein engineering will also be necessary to expand the scope to various target organs other than the liver, such as the lungs and muscles.
Nature Biotechnology, Published online: 10 July 2026; doi:10.1038/s41587-026-03227-9In vivo cytosine base editing is made efficient with potent glycosylase inhibition.
This platform presents realistic clinical application scenarios in areas where existing gene therapies have been difficult to access, such as the retina and liver. For example, in patients with hereditary hypercholesterolemia, instead of repeated LNP administrations or virus-based vector therapies with the risk of side effects, a single administration of tBE-VLP4 via systemic injection can safely knock out the Pcsk9 gene in liver cells, potentially eliminating the need for lifelong cholesterol management. Patients with macular degeneration can also benefit from subretinal injection therapy to regulate Vegfa gene expression, reducing the inflammation and neovascularization side effects associated with long-term expression of existing gene therapies. If high-purity production can be achieved, this could become a standard treatment for safe and effective treatment of rare metabolic and sensory genetic diseases.