Developing a Precision RNA Editing Platform for Therapeutic Applications

Academic Supervisors: Prof. Carlo Rinaldi; Prof. Stephan Sanders

Project summary

RNA editing is a natural and widespread post-transcriptional modification in mammalian cells, primarily involving adenosine to inosine (A-to-I) conversions mediated by ADAR enzymes, and cytosine to uridine (C-to-U) conversions facilitated by APOBECs. These modifications are crucial for regulating gene expression, splicing, and other cellular processes. Recent developments in programmable RNA editing, especially those leveraging ADARs, have opened new possibilities for correcting pathogenic mutations with high specificity and reversibility, offering advantages over permanent DNA editing approaches.

Current therapeutic RNA editing strategies focus on delivery of recombinant enzymes and guide RNAs or use of highly chemically modified antisense oligonucleotides (ASO); while demonstrating proof-of-concept in correcting disease-causing mutations in vivo, they face challenges such as low efficacy, hurdles with the delivery of large payloads, and off-target effects. These limitations highlight the need for more effective, targeted delivery systems to unlock the full therapeutic potential of RNA editing.

Combining the precision of ASOs with the targeted delivery capabilities of ASO conjugates, here we aim to develop a new class of therapeutics with high specificity, safety and potency which has the potential to open up hundreds of therapeutic targets.

Lay project summary

This project aims to develop a new class of targeted therapies by harnessing the natural and essential-to-life process of RNA editing, which allows cells to modify gene messages after they are made. Here we plan to conjugate novel moieties with antisense oligonucleotides to precisely direct editing tools to specific RNA targets. This approach could correct disease-causing mutations with high accuracy and reversibility, offering a safer alternative to permanent DNA editing. It has the potential to treat a wide range of conditions, including those currently untreatable by existing therapies, especially genetic disorders caused by missense mutations. The modular design of the three elements of this approach (molecular conjugate, antisense oligonucleotide sequence, and the linker in between) allows for customization to target different diseases, opening new avenues in precision medicine. Additionally, this platform is poised to generate valuable patents and drive innovation in RNA therapeutics. Integrated with the MRC CoRE in Therapeutic Genomics, this work will benefit from access to a broad spectrum of genetic targets, accelerating the development of effective treatments for rare and complex diseases.

Project Objectives

1. Mining available databases (e.g., ClinVar, Genomics England) to identify disease-causing mutations that are amenable to RNA editing
2. Conjugate antisense oligonucleotides with moieties targeting endogenous RNA editors to identify the most effective combinations
3. Test ASO conjugates in reporter cell lines and disease models (iPSC-derived neurons)

1. Deliver lead ASO conjugates in mice (optional)

Research Methodologies

1. Molecular Cloning and Protein Engineering: Designing and constructing expression vectors
2. Engineering and optimizing linker sequences and protein modifications
3. Protein expression, purification, and characterization (e.g., ELISA)
4. Nucleic Acid Synthesis and Modification
5. Cell Culture and Transfection
6. RNA Editing and Gene Expression Analysis (i.e., RT-PCR, and sequencing to assess editing outcomes)
7. Bioinformatics & Data Analysis (i.e., Analysing sequencing data for editing efficiency and off-target effects).

Potential Project Impact

This project has the potential to create a new class of highly specific, safe, and reversible RNA-based therapeutics. By harnessing antisense oligonucleotide conjugates, it could enable the correction or modulation of a wide range of genetic disorders, including those that are currently not amenable to standard ASO therapy. Additionally, the project holds significant potential for intellectual property generation, with opportunities to develop novel patents that can propel further commercialization and clinical translation.

Proposed Project Timelines

Year 1: Concept Development & Design

• Conduct literature review on RNA editing and oligonucleotides conjugates
• Establish protocols for protein expression, purification, and binding
• Begin preliminary in vitro studies

Year 2: Optimization & In Vitro Validation

• Develop and test ASO conjugates
• Assess RNA editing efficiency and specificity in mammalian cell models

Year 3: Preclinical Evaluation & In Vivo Studies

• Select lead conjugates
• Evaluate therapeutic efficacy in relevant disease models
• Refine delivery methods

Year 4: Validation, Translation & Preparation for Clinical Development

• Confirm therapeutic benefits and safety in in vivo studies
• Prepare detailed data for publication

Project Risks & Mitigations

A potential risk is delays in developing or optimizing high-affinity moieties against endogenous RNA editors, which could impact project timelines. To mitigate this, the candidate will focus on characterizing and optimizing an existing strategy already generated in the Rinaldi lab in the last year, allowing the project to progress. Regular reviews and flexible project planning will ensure timely adjustments, minimizing the impact of unforeseen delays and maintaining steady progress toward project goals.

Training Opportunities

During the first Year of the DPhil, the candidate will have the opportunity to gain insight into the process of protein generation by visiting the dedicated Discovery Platform at the Rosalind Franklin Institute, in Harwell (Oxfordshire), with whom this project will be developed in collaboration.

Opportunities for student participation in Public and Patient Involvement and Engagement (PPIE)

Once a disease suitable for this RNA editing technology has been identified, we will actively liaise with affected family groups and patient organizations. We plan to organize activities such as informational sessions, workshops, and public engagement events to explain the therapeutic strategy, its potential benefits, and the research process. This collaboration aims to foster understanding, gather feedback, and build trust with the community. Engaging patients and families early will also help tailor the research to real-world needs, ensuring that the development of this innovative therapy aligns with patient priorities and expectations.

Studentship code: MRCCoRETG2025003

Funding Notes

Long-term funding obtained

Application Deadline

12 noon, Tuesday 2nd December 2025

Enquiries

mrccoretg@paediatrics.ox.ac.uk

Please read these guidance notes for detail on how to apply

Click here to apply: IPP login screen (ox.ac.uk)

For more information on DPhil in Paediatrics: DPhil in Paediatrics | University of Oxford

For more information about our MRC-Oxford Doctoral Training Programme see: https://www.medsci.ox.ac.uk/study/graduateschool/mrcdtp