Project ID iCASE2023_07

ThemeNS-MH

Co Supervisor 1A Institute of Psychiatry, Psychology & Neuroscience School of Neuroscience Basic and Clinical Neuroscience UK Dementia Research Institute at KCLWebsite

Co Supervisor 1B Faculty of Life Sciences & Medicine School of Basic & Medical Biosciences Centre for Gene Therapy and Regenerative MedicineWebsite

Combining systems biology and bioengineering to evaluate the efficacy of new ALS therapies

The global research into therapeutics for neurodegenerative diseases is rapidly generating new candidate therapeutic approaches, especially new small molecules and gene therapy vectors. However, the bottleneck in translating these to clinical trials is the need to examine the efficacy and specificity of these candidate therapies in a human system that mimics the neuromuscular environment that is affected in ALS. For this purpose, this project will combine several approaches that are rarely employed together: transcriptomics, systems and computational biology with microfabrication-based solutions to model patient-derived neuromuscular circuits. Induced pluripotent stem cells (iPSCs) from ALS patients containing a mutation in an RNA-binding proteins along with CRISPR-corrected isogenic controls will be used to generate the circuits, and transcriptomic methods to study protein-RNA networks with crosslinking and immunoprecipitation (iCLIP) and their effects on mRNA translation with ribosome profiling (Ribo-seq) followed by advanced computational modelling. Thereby the project will comprehensively characterize the capacity of therapies to decrease the mutation-driven transcriptomic perturbations in protein-RNA networks, while also assessing the potentially unintentional side-effects of therapies on the transcriptome.

The project will integrate expertise from three partners. The Ule lab that developed iCLIP, established a highly sensitive Ribo-seq and associated computational software, and keeps developing it further and integrating with functional transcriptomics. The Lieberam group established a compartmented co-culture system composed of motor neurons, glia and myofibers directly derived iPSCs. The commercial partner Goodwright is a software SME that is focused on developing new platforms for analysis of sequencing data and its visual interpretation, integration and management.

One representative publication from each co-supervisor:

Hallegger M, Chakrabarti AM, Lee FCY, Lee BL, Amalietti AG, Odeh HM, Copley KE, Rubien JD, Portz B, Kuret K, Huppertz I, Rau F, Patani R, Fawzi NL, Shorter J, Luscombe NM, Ule J. (2021) TDP-43 condensation properties specify its RNA-binding and regulatory repertoire, Cell. 2021 Sep 2;184(18):4680-4696.e22.

Harley, P., Neves, G., Riccio, F., Machado, C.B., Cheesbrough, A., R’Bibo, L., Burrone, J., and Lieberam, I. (2022). Pathogenic TDP-43 Disrupts Axon Initial Segment Structure and Neuronal Excitability in a Human iPSC Model of ALS. bioRxiv 2022.05.16.492186