Creation of de novo cryptic splicing for ALS and FTD precision medicine
Loss of function of the RNA-binding protein TDP-43 (TDP-LOF) is a hallmark of amyotrophic lateral sclerosis (ALS) and other neurodegenerative disorders. Here we describe TDP-REG, which exploits the specificity of cryptic splicing induced by TDP-LOF to drive protein expression when and where the disease process occurs. The SpliceNouveau algorithm combines deep learning with rational design to generate customizable cryptic splicing events within protein-coding sequences. We demonstrate that expression of TDP-REG reporters is tightly coupled to TDP-LOF in vitro and in vivo. TDP-REG enables genomic prime editing to ablate the UNC13A cryptic donor splice site specifically upon TDP-LOF. Finally, we design TDP-REG vectors encoding a TDP-43/Raver1 fusion protein that rescues key pathological cryptic splicing events, paving the way for the development of precision therapies for TDP43-related disorders.
Authors
- Puja R. Mehta (ORCID: https://orcid.org/0000-0002-0255-407X)
- Claire E. Le Pichon (ORCID: https://orcid.org/0000-0002-9274-3615)
- Matteo Zanovello (ORCID: https://orcid.org/0000-0003-3343-1547)
- Holly Digby (ORCID: https://orcid.org/0000-0003-1360-9686)
- Josette J Wlaschin (ORCID: https://orcid.org/0000-0003-1532-3905)
- Anna‐Leigh Brown (ORCID: https://orcid.org/0000-0003-1493-208X)
- Annalucia Darbey (ORCID: https://orcid.org/0000-0001-8541-5472)
- Juan Antinao Díaz (ORCID: https://orcid.org/0000-0001-7295-2738)
- Thomas J. Cunningham (ORCID: https://orcid.org/0000-0002-4751-3140)
- Rajvinder Karda (ORCID: https://orcid.org/0000-0001-9821-483X)
- Elizabeth Fisher (ORCID: https://orcid.org/0000-0003-2850-9936)
- Simone Barattucci (ORCID: https://orcid.org/0009-0006-8380-2931)
- Matthew J. Keuss (ORCID: https://orcid.org/0000-0002-2628-4115)
- Jernej Ule (ORCID: https://orcid.org/0000-0002-2452-4277)
- Oscar G. Wilkins (ORCID: https://orcid.org/0000-0002-3334-0568)
- Francesca Mattedi (ORCID: https://orcid.org/0000-0002-0306-5796)
- Rebecca L. Simkin (ORCID: https://orcid.org/0000-0001-8093-2139)
- Max Z. Y. J. Chien (ORCID: https://orcid.org/0009-0001-7731-605X)
- Peter Harley (ORCID: https://orcid.org/0000-0001-6689-0227)
- Lea Knez (ORCID: https://orcid.org/0009-0006-6555-9536)
- Eugeni Ryadnov (ORCID: https://orcid.org/0009-0003-9921-1755)
- Maria Pisliakova (ORCID: https://orcid.org/0009-0007-5157-5639)
- David Thompson (ORCID: https://orcid.org/0000-0002-2444-9844)
- Pietro Fratta (ORCID: https://orcid.org/0000-0002-8762-8188)
Institutions
- National Institutes of Health (US)
- Johns Hopkins University (US)
- King's College London (GB)
- The Francis Crick Institute (GB)
- Mary Lyon Centre at MRC Harwell (GB)
- UK Dementia Research Institute (GB)
- MRC Prion Unit (GB)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (US)
- National Hospital for Neurology and Neurosurgery (GB)
- University College London (GB)
Publication Details
- Journal
- Science
- Published
- 2024-10-03
- DOI
- https://doi.org/10.1126/science.adk2539
- Citations
- 28
- Primary Topic
- RNA Research and Splicing
- Type
- article
- Field-Weighted Citation Impact
- 6.55
Funders
- Wellcome Trust
- Francis Crick Institute
- LifeArc
- Target ALS
- Cancer Research UK
- Great Ormond Street Hospital Charity
- UK Dementia Research Institute
- National Institutes of Health
- Medical Research Council