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Creation of de novo cryptic splicing for ALS and FTD precision medicine

Affiliations
  • 1UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK.
  • 2The Francis Crick Institute, London NW1 1AT, UK.
  • 3Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
  • 4Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
  • 5Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK.
  • 6UK Dementia Research Institute at King’s College London, London SE5 9RX, UK.
  • 7EGA-Institute for Women’s Health, University College London, London WC1E 6HX, UK.
  • 8MRC Prion Unit at UCL and UCL Institute of Prion Diseases, London W1W 7FF, UK.

Published on:

October 3, 2024

Abstract

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.