Development of antisense oligonucleotide and base editing therapeutics for neurodevelopmental haploinsufficiency disorders

Academic Supervisors: Dr. Thomas Roberts, Prof. Matthew P.A Wood

Project summary

Neurodevelopmental disorders constitute a group of diseases in which the normal development of the nervous system is disrupted and for which treatment options are currently very limited. As such, neurodevelopmental disorders constitute a major unmet and neglected clinical need. Many neurodevelopmental disorders are caused by low levels of expression of the disease-causing gene (i.e. haploinsufficiency) and so gene activation strategies are desirable.

This proposal aims to generate therapeutics that can activate gene expression at the level of translation in order to treat or manage specific neurodevelopmental disorders by compensating for haploinsufficiency. We have identified upstream open reading frames (uORFs) as gene regulatory elements that are possible targets for therapeutic intervention. uORFs act to repress the translation of their associated protein coding sequences, and so disrupting their function can lead to targeted protein upregulation. Importantly, many genes associated with neurodevelopmental disorders contain predicted uORF sequences. More than 10 such targetable neurodevelopmental genes have been identified in initial computational screens, and the Therapeutic Genomics Centre will expand this list. Here we propose to experimentally validate these targets, and then screen molecular medicine drugs intended to upregulate them. We will utilise both antisense oligonucleotide and CRISPR-Cas9 base editing approaches for targeted uORF disruption. The proposed work has the potential to identify lead candidate molecules for multiple currently untreatable neurodevelopmental diseases.

Lay project summary

This proposal aims to develop molecular medicines for the treatment of genetic neurodevelopmental disorders. The work entails a primarily wet lab approach through which neurodevelopmental disease genes are validated, followed by initial drug screening to select lead molecules. The proposed work builds on state-of-the-art methods, technologies, and know-how generated in the Roberts group. The work is highly competitive as there are relatively few technologies that can specifically activate gene expression, and there is little (or nothing) effective that can currently be done to treat neurodevelopmental disease patients. If successful, this work has the potential to form the basis of multiple drug development programmes. This project is aimed at an experimentalist with an interest in the development of modular and scalable technologies for high throughput drug development.

Project Objectives

1. Experimental validation of target transcripts with upregulation potential and confirmation of target transcript expression in human brain tissue.
2. Selection of ASO or CRISPR base editing as appropriate for each disease indication and initial screening of candidate molecules.
3. Optimisation of lead candidate molecules for 3-5 target disease indications.
4. Proof-of-concept protein upregulation in iPSC-derived cortical neurons (and in vivo mouse brain – depending on human-mouse sequence conservation).
5. Development of scalable/high throughput approaches for target validation and compound screening.

Research Methodologies

The student will be trained in basic Python skills for bioinformatics applications. The student will also receive training in mammalian cells culture, animal experimentation, recombinant DNA technology, and gene expression analysis. There is also the opportunity for the student to learn oligonucleotide synthesis techniques. By the end of the DPhil the student will be adept in the design of splice switching oligonucleotides and CRISPR-Cas9 guide strategies.

Potential Project Impact

This project has the potential to generate new molecular medicines for the treatment of neurodevelopmental disorders. A clear path for intellectual property rights protection and commercialisation is in place throughout-licencing.

This project will also result in the training of a scientist who will have both wet and dry lab expertise in important scientific growth areas.

Proposed Project Timelines

Year 1: TARGET FINDING/VALIDATION - Completion of target indication finding exercise using combined target prediction (in-house bioinformatics tools) combined with confirmation of RNA transcript isoform expression in relevant target tissue/brain regions, and commercial analyses (incidence/prevalence, clinical trial readiness assessment, established endpoints etc.). Putative targets will be validated using plasmid DNA deletion report constructs. Initial work to identify either ASO or CRISPR base editing strategies will be performed. This aim builds on extensive preliminary data.

Year 2: LEAD OPTIMISATION - Optimisation of ASO and CRISPR guides RNA will be undertaken with an emphasis on finding the most effective molecules that can induce endogenous protein upregulation. Assay development will be an important element of this stage. Off-target effects will also be carefully investigated.

Year 3: PRECLINIAL DEVELOPMENT/TRANSLATABILITY - Proof-of-content demonstration of protein upregulation using human iPSC-derived cortical neurons and, where possible, healthy mice by ICV injection. Functional assessments of restored protein will be performed where appropriate.

Year 4: FINALISATION - Completion of outstanding experimental work, preparation of manuscripts/patents. Compile thesis.

Project Risks & Mitigations

There are multiple criteria which can result in target de-prioritisation (e.g., high missense to protein truncating variant ratio, low incidence/prevalence, unclear molecular biology/pathomechanism, competition from existing pharmacology/novel drug development programmes in progress etc.). As such, ‘casting a wide net’ for targets minimises the risk of failure at the early stages as there are multiple ‘shots on goal’ with this project. Initial indication finding has identified multiple potential novel targets, and there are several ‘high value’ established targets (e.g., SCN1A, SLC6A1, SCN2A) which are worth pursuing regardless. There are also multiple modalities available (i.e., ASO and CRISPR) such that if one approach is unsuccessful, effort can be directed towards another modality. We have so far demonstrated proof-of-concept endogenous protein upregulation using both uORF-targeting splice switching and CRISPR-Cas9 base editing strategies.

Training Opportunities

Internships/training opportunities are available through Oxford-external CoRE member labs with world leading drug delivery expertise and extensive experience with ICV injections (Prof EL Andaloussi) and with potential industrial partners (Orfonyx Bio).

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

• Patient Engagement - Patient engagement will depend on which disease indications are ultimately selected for drug development. There are a number of patient organisations associated with specific neurodevelopmental disorders. We aim to approach these at the earliest appropriate opportunity (once preliminary data has been acquired). We envisage opportunities to share our findings with these communities, gain feedback, and ideally work towards establishing a network of clinical trial-suitable patients.
• Public Engagement - The work described in this proposal is ideally suited for public engagement events whereby the drug development process can be communicated to school-age children. We aim to participate in public engagement events in Oxford (e.g., IF-Oxford) by running a stall with posters aimed at school children of various ages, and hands-on activities illustrating concepts like complementary base pairing, RNA splicing, and haploinsufficiency.

Studentship code: MRCTGCORE2025002

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