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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 In the reporting period, we continued refining our understanding of the crosstalk between TDP-43 and FUS in biomolecular condensates. In particular, several new project partners have been brought onboard (see partnerships), which enabled detailed analysis of molecular interactions between TDP-43 and FUS using in vitro reconstitution of condensates and coarse-grained simulations. As a result, the manuscript in revision has been significantly enhanced and extended (currently under assessment).The crosstalk between paraspeckles and another biomolecular condensate, TDP-43 de novo nuclear granules, has been characterised (manuscript published in Cell Reports). Optogenetic models have been transferred to the neuronal system using lentiviral expression. Follow-up funding has been secured for further development of optogenetic platforms of protein aggregation in ALS/FTD (grant from ARUK and MRC DiMeN studentship). Furthermore, significant translational funding has been secured for the development of NEAT1 targeting small molecules (My name'5 Doddie Foundation Advancing Treatment Award), that will support hit-to-lead optimisation. Translational partnerships are currently being explored with LifeArc, Ono Pharma and other companies, both for NEAT1/paraspeckles, TDP-43 and other molecular targets. New PhD students have been recruited to the group, who will continue the development of the individual aims of this project (paraspeckle/TDP-43 crosstalk; FUS regulation in health and disease; optogenetic modeling of ALS pathology; differential role of NEAT1 isoforms).
Exploitation Route 1. Novel tools. Optogenetic constructs have been deposited at Addgene (already requested by several labs) and are freely available. ImmuCon assay is now used in collaborative projects.

2. Research findings have been disseminated at several scientific conferences (national and international) and departmental seminars, including via oral talks by the PI and PDRAs working on this grant:
1) School of Life Sciences seminar series, University of Dundee (March 7, 2024) - PI
2) 2nd Paraspeckle conference (Perth, Australia, Oct 2024): TDP-43 in paraspeckle regulation (oral talk) - PI
3) Translation UK (Surrey, July 2024) - oral talk, PDRA
4) Sheffield Nucleic Acids Institute seminar series (Sheffield, June 2024) - oral talk, PDRA
5) 11th annual FTD UK conference (Cambridge, May 2024) - invited talk, PDRA
6) RNA Biology of the Nervous System (London, Dec 2024) - invited talk, PI

3. Establishing the UK-wide network on biomolecular condensates. The PI was part of the core group of 25 group leaders who attended the inaugural (in-person, 2-day) meeting for this Network in January 2025. She is now working to establish a group led by UKRI Future Leader Fellows involved in the condensate-applicable research (FLF-CAR; application for FLF Plus Funds submitted). FLF-CAR will contribute to a number of Network activities, including the annual symposium, PI retreat and ECR summer school organisation. This will engage new scientists, including ECRs, into condensate research.
Sectors Education

Manufacturing

including Industrial Biotechology

Pharmaceuticals and Medical Biotechnology

URL https://www.ts-lab.co.uk/
 
Description 1. Pharmaceuticals/drug discovery. The work within this project has generated new drug discovery tools, including optogenetic models and an in vitro condensate platform amenable to drug screening, as well as novel small tool molecules. These outputs has attracted the interest of biopharma companies and are well positioned to generate impact in the drug discovery space in the future. 2. Education. This project has yielded an impact in the educational sector, via the ability of the project staff to contribute to the training of undergraduate and postgraduate students. 3. Biotechnology. In the long-term, the discoveries of this project should contribute to the field of synthetic biology and biotechnology (synthetic/engineered condensates as tunable bioreactors).
First Year Of Impact 2024
Sector Education,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description Deciphering the C9ORF72-DPR aggregation using optogenetic and in vitro analyses of modifiers
Amount £129,782 (GBP)
Funding ID Shelkovnikova/Oct24/2402-792 
Organisation Motor Neurone Disease Association (MND) 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2026 
End 08/2029
 
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 09/2023 
End 03/2027
 
Description Optogenetic modeling of a hallmark neurodegeneration pathology for mechanistic research and drug discovery
Amount £120,000 (GBP)
Organisation MRC Doctoral Training Program 
Sector Academic/University
Country United Kingdom
Start 09/2024 
End 09/2028
 
Description Optogenetic modelling of C9ORF72 DPR pathology in neurons for FTD/ALS research and drug discovery
Amount £67,000 (GBP)
Funding ID ARUK-PPG2023B-007 
Organisation Alzheimer's Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2024 
End 03/2026
 
Description Small molecule hit optimisation for lncRNA NEAT1_2 - a molecular target for neuroprotection in (sporadic) ALS
Amount £376,528 (GBP)
Funding ID MN5DF/ATAEoI24/100002 
Organisation My Name'5 Doddie Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2025 
End 08/2028
 
Description Small molecule modulators of lncRNA NEAT1_2: A novel approach to enhancing the endogenous neuroprotective response in amyotrophic lateral sclerosis
Amount £183,000 (GBP)
Funding ID MC_PC_MR/W031647/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 03/2022 
End 03/2023
 
Description Unravelling the structure and regulation of prototypical membraneless organelles paraspeckles
Amount £44,094 (GBP)
Funding ID BB/X018393/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 05/2023 
End 06/2025
 
Title Human iPSCs with NEAT1 isoform knockout 
Description Hman iPS cell lines with selective knockout of NEAT1_2 isoform (NEAT1_2 KO) and selective knockout of NEAT1_1 isoform (NEAT1_2 PAS mutant) have been generated and characterised. 
Type Of Material Cell line 
Year Produced 2023 
Provided To Others? No  
Impact These cell lines will be critical for establishing the role of NEAT1 isoforms in differentiation (neurodevelopment) and in the CNS cell types, including under stress conditions. 
 
Title ImmuCon: in vitro condensate reconstitution for high-resolution imaging 
Description ImmCon is an in vitro assay using purified protein for reconstitution of biomolecular condensates and analysis of various factors that affect them. 
Type Of Material Technology assay or reagent 
Year Produced 2023 
Provided To Others? Yes  
Impact ImmuCon has been used across several studies, including those with collaborators, and has provided valuable insights into TDP-43 and FUS regulation. 
URL https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4721338
 
Title In vitro assay for measuring small molecule binding to RNA using FIDA: Flow Induced Dispersion Analysis 
Description Assay was developed for NEAT1 binders validaiton using the recently developed Fida technology. 
Type Of Material Technology assay or reagent 
Year Produced 2024 
Provided To Others? No  
Impact This assay is being used for compound validation from the MRC/AZ screen of NEAT1 modulators. It will be used in the new grant application for hit-to-lead compound optimisation activities. 
 
Title Optogenetic tools for researching and 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. These constructs have been made available though a non-profit repository Addgene. 
Type Of Material Technology assay or reagent 
Year Produced 2024 
Provided To Others? Yes  
Impact These plasmids will be highly instrumental for experiments with spatial and temporal control of physiological and pathological phase separation and now accessible to any researcher via Addgene. 
URL https://www.addgene.org/Tatyana_Shelkovnikova/
 
Description Analysis of biomolecular condensate dynamics using single molecule imaging 
Organisation University of Sheffield
Department Sheffield Institute for Translational Neuroscience (SITraN)
Country United Kingdom 
Sector Academic/University 
PI Contribution This a new collaboration with Dr Alison Twelvetrees. Using her bespoke TIRF imaging setup and protocols, protein dynamics within condensates will be measured in living cells.
Collaborator Contribution Bespoke imaging setup and relevant protocols for condensate labeling and data analysis.
Impact N/A
Start Year 2023
 
Description Identification of compounds selectively binding NEAT1_2 as templates for new drugs 
Organisation Cardiff University
Department School of Biosciences
Country United Kingdom 
Sector Academic/University 
PI Contribution This is a collaborative effort between the Medicines Discovery Institute early projects team and my team. We developed a panel of HTS-compatible assays for the identification of NEAT1_2 small molecules binders.
Collaborator Contribution MDI team provides screening and chemistry expertise and support within this collaboration (HTS library assembly, initial assessment and triage of hits). Once promising hits are identified, hit-to-lead optimisation activities will be started.
Impact Manuscript s published resource/methods paper) Results presented at conferences (RNA UK 2022; ENCALS meeting 2020) Follow-on funding obtained (Welsh Government grant, MRC/AZ Centre for Lead Discovery) Hit compounds identified and binding confirmed in vitro
Start Year 2019
 
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 Regulation of FUS splicing 
Organisation Goethe University Frankfurt
Country Germany 
Sector Academic/University 
PI Contribution This partnership led to a new FUS autoregulation mechanism described. My team has uncovered the ability of FUS intron 7 to drive RNA condensation and its potential to be used as a therapeutic agent in ALS-FUS.
Collaborator Contribution Eugene Makeyev's group provided access to a new technology - HyPro-MS, that allows characterising proteomes/interactomes of nuclear bodies and individual RNA species. Michaela Muller-McNicoll provided guidance with experimental design and interpretation (expert in regulation of RNA via intron retention)
Impact BioRxiv preprint: https://www.biorxiv.org/content/10.1101/2025.02.01.633781v1
Start Year 2023
 
Description Regulation of FUS splicing 
Organisation King's College London
Department MRC Centre for Developmental Neurobiology
Country United Kingdom 
Sector Academic/University 
PI Contribution This partnership led to a new FUS autoregulation mechanism described. My team has uncovered the ability of FUS intron 7 to drive RNA condensation and its potential to be used as a therapeutic agent in ALS-FUS.
Collaborator Contribution Eugene Makeyev's group provided access to a new technology - HyPro-MS, that allows characterising proteomes/interactomes of nuclear bodies and individual RNA species. Michaela Muller-McNicoll provided guidance with experimental design and interpretation (expert in regulation of RNA via intron retention)
Impact BioRxiv preprint: https://www.biorxiv.org/content/10.1101/2025.02.01.633781v1
Start Year 2023
 
Description Structural variation in NEAT1 in ALS 
Organisation Murdoch University
Country Australia 
Sector Academic/University 
PI Contribution Structural variation in NEAT1_2 was established as potentially contributing to ALS via modulation of TDP-43 binding under stress, in cellular models. This is a collaboration within Sheffield and with external partners. In Sheffield, it is collaboration with Dr J Cooper-Knock and Dr Jenny Lord, as well as Prof Ivana Barbaric. Other partners included Project MinE (Joke van Vugt) and Murdoch University (Ianthe Pitout and Sue Fletcher).
Collaborator Contribution Project MinE database was used for the analysis of NEAT1_2 UG repeat association with ALS severity (ExpansionHunter), with post-analysis done by Dr Cooper-Knock and validation cohort data provided by collaborators at Murdoch University. Subsequently, collaborations were established with Jenny Lord at SITraN (rare diseases informatics) and Ivana Barbaric (neural differentiation) at TUoS School of Biosciences, to examine possible contribution of the developmental component in ALS through impact on NEAT1 expression.
Impact Preprint is published; manuscript in review
Start Year 2023
 
Description Structural variation in NEAT1 in ALS 
Organisation Project MinE
Sector Charity/Non Profit 
PI Contribution Structural variation in NEAT1_2 was established as potentially contributing to ALS via modulation of TDP-43 binding under stress, in cellular models. This is a collaboration within Sheffield and with external partners. In Sheffield, it is collaboration with Dr J Cooper-Knock and Dr Jenny Lord, as well as Prof Ivana Barbaric. Other partners included Project MinE (Joke van Vugt) and Murdoch University (Ianthe Pitout and Sue Fletcher).
Collaborator Contribution Project MinE database was used for the analysis of NEAT1_2 UG repeat association with ALS severity (ExpansionHunter), with post-analysis done by Dr Cooper-Knock and validation cohort data provided by collaborators at Murdoch University. Subsequently, collaborations were established with Jenny Lord at SITraN (rare diseases informatics) and Ivana Barbaric (neural differentiation) at TUoS School of Biosciences, to examine possible contribution of the developmental component in ALS through impact on NEAT1 expression.
Impact Preprint is published; manuscript in review
Start Year 2023
 
Description TDP-43 and FUS condensation in health and disease 
Organisation University of Essex
Country United Kingdom 
PI Contribution This collaboration allowed elucidating the patterns and mechanisms of TDP-43 (co-)condensation. My team has uncovered the disruptive role for TDP-43 on FUS condensation / phase separation, using paraspeckles as models.
Collaborator Contribution Gareth Wright (Essex) provided purified TDP-43 protein fragments and structural biology expertise (AlphaFold predictions). Mark Driver/Patrick Onck (Groningen) performed coarse-grained simulations of TDP-43 - FUS co-condensation.
Impact Manuscript under review
Start Year 2024
 
Description TDP-43 and FUS condensation in health and disease 
Organisation University of Groningen
Country Netherlands 
Sector Academic/University 
PI Contribution This collaboration allowed elucidating the patterns and mechanisms of TDP-43 (co-)condensation. My team has uncovered the disruptive role for TDP-43 on FUS condensation / phase separation, using paraspeckles as models.
Collaborator Contribution Gareth Wright (Essex) provided purified TDP-43 protein fragments and structural biology expertise (AlphaFold predictions). Mark Driver/Patrick Onck (Groningen) performed coarse-grained simulations of TDP-43 - FUS co-condensation.
Impact Manuscript under review
Start Year 2024
 
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 Association Soak A Scientist 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Soak A Scientist is an annual engagement and fundraising initiative co-organised by SITraN and the South Yorkshire branch of the MND Association. Members of the team attended and helped run the event.
Year(s) Of Engagement Activity 2023
 
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/
 
Description SITraN Open Day 2024 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Patients, carers and/or patient groups
Results and Impact SITraN open day that hosted ~100 patients, carers and charity representatives. My group run two stations with hands-on experience (microscopy and molecular biology) - ~6 groups of 5-6 people took part. This was the first open day since the pandemic and was a great success with significant interest from all targeted groups.
Year(s) Of Engagement Activity 2024