Developing Precise Mitochondrial DNA Base Editors For Genome Therapy

About the project

About the Project Background Mutations in mitochondrial DNA (mtDNA) are the most common cause of inherited mitochondrial disease and are increasingly implicated in common age-related conditions including neurodegeneration. The multicopy, extra-nuclear nature of mtDNA makes conventional genome-editing strategies difficult to apply, and current treatments largely address symptoms rather than the underlying genetic defect. Recent mitochondrial base editors can directly modify mtDNA and have created a new route towards precision therapy, but improving their sequence specificity and minimising unwanted edits remain major challenges. This project forms an integral part of the recently established MRC Centre of Research Excellence in Mitochondrial Genome Therapeutics ( MRC CoRE-MitoGT ) established in collaboration with the Lily Foundation and LHON Collective . CoRE-MitoGT is an international consortium that aims to understand how mtDNA mutations cause disease and to develop therapies that target their root causes. The student will join the Minczuk lab , one of the core laboratories within CoRE-MitoGT, based at the Cambridge Institute for Medical Research . The project will contribute directly to the development of novel mtDNA editing tools and in vivo delivery methods, with a particular focus here on making mitochondrial base editors more precise. This work will be carried out in close collaboration with protein-engineering teams at the University of Manchester. The work will build on emerging cytosine and adenine mitochondrial base editors that can install or correct defined mtDNA variants without introducing double-strand DNA breaks. The student will combine editor design with systematic experimental testing to understand how deaminase choice, programmable DNA-binding domains, linker architecture and editing-window geometry determine activity and specificity. Priority disease variants will include mutations represented across CoRE-MitoGT models, such as those associated with LHON, MELAS and NARP/Leigh syndrome. Promising editors will be advanced from screening systems into disease-relevant cellular models, where on-target correction, bystander editing and mitochondrial and nuclear off-target effects can be assessed rigorously. The project will combine hypothesis-driven engineering with high-throughput approaches to: Discover and benchmark sequence-selective deaminases: Evaluate diverse cytosine- and adenine-modifying enzymes, including candidates emerging from genome mining, to define activity, sequence-context preferences and suitability for pathogenic mtDNA targets. Engineer next-generation mitochondrial base editors: Optimise deaminases, programmable DNA-binding domains and linkers using rational and computational design, together with directed-evolution approaches developed with collaborators in Manchester, to increase editing efficiency while reducing bystander activity. Develop quantitative screening and specificity assays: Establish scalable reporter, sequencing and biochemical workflows that allow rapid comparison of editor variants and direct measurement of desired versus unwanted editing across relevant sequence contexts. Validate lead editors in disease-relevant models: Test the most promising variants in heteroplasmic and homoplasmic cellular systems carrying pathogenic mtDNA mutations, quantify correction and functional rescue, and perform deep-sequencing-based assessment of mitochondrial and nuclear off-target activity. Findings from these approaches will be integrated with disease-model development and in vivo delivery work across CoRE-MitoGT. The strongest editor architectures will provide candidates for subsequent testing with viral and non-viral delivery platforms and in preclinical models, creating a direct path from molecular engineering to therapeutic evaluation. The overall goal is to develop mitochondrial base editors that combine high activity with substantially improved sequence specificity and minimal off-target effects . By defining the design principles that govern precise mtDNA editing, the project will help establish safer and more generalisable tools for correction of pathogenic mitochondrial mutations. Training and environment The project forms part of a major new collaborative research centre on mtDNA disease and gene-modifying therapy, with access to purpose-built disease models and a network of clinicians and researchers across the Cambridge Biomedical Campus and beyond. Hence, the student will join a large and interactive mitochondrial research community with access to state-of-the-art sequencing, imaging, cell engineering and mitochondrial phenotyping facilities, while also benefiting from close collaboration with the University of Manchester protein-engineering teams. The student can expect to receive technical training in molecular cloning and protein engineering, mammalian cell culture and mitochondrial targeting, mtDNA base editing, heteroplasmy quantification by ddPCR and sequencing, high-throughput screening, next-generation sequencing and bioinformatic analysis of on- and off-target editing, and mitochondrial functional assays. Depending on the precise evolution of the project, there will also be opportunities to gain experience in computational protein design and directed evolution. This combination will provide the experimental design, quantitative analysis and multidisciplinary skills required for an independent researcher. In addition, CoRE-MitoGT will provide an extensive programme of personal and professional training including ECR-focused events and development opportunities, as well as promoting best practice to enhance EDI and positive research culture.

Research areas