RNA-protein complexes in health and disease and their therapeutic targeting

Lead Research Organisation: University of Sheffield
Department Name: Neurosciences

Abstract

All cells contain a variety of large, microscopically visible complexes made of RNA and protein - ribonucleoprotein (RNP) granules. Increased concentration of molecules within RNP granules makes them very efficient biochemical "microreactors". RNP granules transact cellular functions in a very dynamic fashion and can act as highly accurate sensors of changes in the cell environment. Recent exciting breakthroughs in RNP granule research established these structures as the key organising principle of a living cell. Given the fundamental activities carried out by RNP granules, it is unsurprising that even small changes in their structure lead to fatal human diseases such as neurodegenerative disorders. Restoring RNP granule balance in cells by targeting their components and regulatory factors is therefore an attractive therapeutic strategy that can be transformative for many diseases.

My recent research suggested that RNP granules that are physically separated in cells (e.g. those localised in the cell nucleus and those in the cytoplasm) are connected into a network. It also suggested that the entire network becomes affected in disease states, such as the fatal and currently incurable neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). This finding not only established a new biological concept of signal propagation in cells but also suggested that components of the RNP granule network, including RNAs, represent promising points for therapeutic intervention. Until recently, targeting RNA with small molecule drugs has been seen as problematic, because of the structural flexibility of this molecule. However, it is becoming increasingly appreciated that the discovery of biologically active small molecule drugs acting on RNA/RNA-protein complexes can be successfully driven by a specific drug discovery approach called "phenotypic assay" and informed by complex motifs in the RNA structure.

My proposal aims to improve our knowledge of how RNP granule network is regulated, why this regulation collapses in disease states and how it can be restored using therapeutic small molecules. This will be achieved via: 1) structural and functional interrogation of the role for the RNP granule network in the normal cell physiology and pathophysiology of two representative neurodegenerative disorders, ALS and FTD; and 2) identification and follow-up of novel RNA drug targets for the above diseases using small molecule drugs.

I will lead this innovative programme building upon my previous experience in RNP granule and neurodegenerative disease research; access to the skills and toolkit of the collaborator network and Cardiff neuroscience community; input from the co-investigator who is a drug discovery expert; strategic placement within a drug discovery centre; and bespoke training and personal development program.

Overall, my research will provide new knowledge of how cells exploit interconnected RNP granules to survive and thrive and how abnormal metabolism of RNP granules can be corrected for the benefit of human health.
 
Description This programme of research commenced ~6 months ago. Over this period of time, a number of essential tools have been developed/established in the lab that should ensure smooth project progression (including optogenetic tools for modeling neurodegeneration-linked phase separation in cultured cells; in vitro aggregation assays for neurodegeneration linked RNA-binding proteins; cellular assays for high-content studies of RNP granules). Novel phenotypes and mechanistic insights for the role of post-translational protein modifications (methylation in particular) in nuclear RNP granule separation/autonomy have been discovered. Novel molecular targets (RNAs and proteins) for motor neuron disease have been identified (e.g. RNA methylation pathway). More in-depth studies of these findings are currently under way.
Exploitation Route Not applicable as still very early stage of the project.
Sectors Education,Pharmaceuticals and Medical Biotechnology

 
Description NEAT1 isoforms in the regulation of cellular glucose metabolism downstream TDP-43 dysfunction in ALS
Amount £114,917 (GBP)
Organisation Motor Neurone Disease Association (MND) 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2023 
End 03/2027
 
Title Optogenetics tools for manipulation of ALS-linked proteins in living cells 
Description A panel of genetic constructs for light-driven phase separation/aggregation of ALS-linked proteins (RNA-binding proteins FUS, NONO, TDP-43; and C9ORF72 dipeptide repeat proteins) has been generated and characterised. 
Type Of Material Technology assay or reagent 
Year Produced 2022 
Provided To Others? No  
Impact These plasmids will be highly instrumental for experiments with spatial and temporal control of physiological and pathological phase separation. After publication, these plasmids will be shared with other researchers via Addgene. 
 
Description RNA tracking in live cells using novel chemical probes 
Organisation Ohio State University
Country United States 
Sector Academic/University 
PI Contribution The collaboration is with Prof Dennis Bong whose team is providing non-commercial fluorescent chemical probes for labeling RNA (NEAT1 and C9ORF72) in living cells. These probes are highly complementary to the proposal aims and will allow efficient characterisation of small molecules from project screens in cellular systems. We are providing molecular cloning (plasmid generation) and cell biology expertise within this project.
Collaborator Contribution The collaboration is with Prof Dennis Bong whose team is providing non-commercial fluorescent chemical probes for labeling RNA (NEAT1 and C9ORF72) in living cells. These probes are highly complementary to the proposal aims and will allow efficient characterisation of small molecules from project screens in cellular systems. We are providing molecular cloning (plasmid generation) and cell biology expertise within this project.
Impact None yet, in progress
Start Year 2022
 
Description Global MND Awareness Day 2022 'Thank you' video (SITraN) 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Patients, carers and/or patient groups
Results and Impact Participated in the video "Thank you" clip, together MNDA-funded PIs, and also a mass SITraN " thank you" on the Global MND Awareness Day 2022.
Year(s) Of Engagement Activity 2022
URL https://www.mndassociation.org/about-us/who-we-are/mnd-awareness-day/
 
Description MND Symposium interview 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Symposium Blogathon: The interview involved answering questions about my research and views on the MND Symposium experience and expectations. It was used in a series of small clips before the event an then after the Symposium.
Year(s) Of Engagement Activity 2022
URL https://symposium.mndassociation.org/symposium-blogathon/