Mechanism of the DNA damage response in Huntington’s disease pathogenesis and relevance for therapeutics

Lead Research Organisation: University College London

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Technical Summary

The UK Dementia Research Institute (UK DRI) is an initiative funded by the Medical Research Council, Alzheimer's Society and Alzheimer's Research UK. Funding details for UK DRI programmes will be added in 2019.

Huntington’s disease (HD) is a fatal autosomal dominant neurodegenerative disease caused by a CAG repeat expansion. The repeat is unstable and prone to expansion with age in the most affected tissues, particularly the striatum, and the rate of this somatic instability (SI) correlates with disease course. However, the molecular mechanism underlying SI is not yet fully understood.
Our GWAS studies have identified genetic variation in DNA damage response (DDR) proteins such as FAN1 and MSH3 that modify the course of HD. We recently found that FAN1 protectively restrains CAG expansion in cell models, whereas MSH3 likely promotes expansion. We have demonstrated that genetic variation and reduced expression of MSH3 decreases somatic expansion, delays onset and slow progression in HD. We also showed that these HD genetic modifiers also influence the course of other repeat expansion diseases, such as the spinocerebellar ataxias (SCA) and myotonic dystrophy type 1 (DM1). In collaboration with Dr Thalassinos (UCL Institue of Structural Biology) we are investigating the effect of these variants on protein structure, and interactions using mass spectrometry. GWAS also implicate a wider network of DDR proteins, particularly those involved in mismatch repair (MMR) and known to be involved in SI in HD mouse models, such as EXO1, PCNA, MLH1, PMS2, LIG1 and MLH3. We hypothesise that expanded CAG repeats form abnormal secondary DNA structures that are recognised as lesions, prompting the DDR to attempt repair.
In cell models we are investigating how genetic variation in FAN1 and MSH3 influences somatic expansion. We developed human U20S cells stably expressing disease-modifying FAN1 variants and a pathogenic HTT exon 1, discovering that FAN1 restrains CAG expansion in a dose-dependent manner. We are currently investigating the functional interactions between FAN1 and mismatch repair (MMR) proteins such as MLH1 and MSH3.
We have generated several patient-derived lymphoblastoid and induced pluripotent stem cell (iPSC) lines that show robust CAG repeat expansion in culture, and used them to demonstrate that FAN1 knockdown in medium spiny neurons (MSN) accelerates repeat expansion. We are using CRISPR to introduce disease-modifying MSH3 and FAN1 variation, as well as knockouts of each gene, to investigate the mechanism by which they influence SI in MSNs. In collaboration with Dr Balmus (DRI Cambridge), we will dissect the specific roles of individual proteins in SI using a CRISPR screen for targeted deletion of DDR components in iPSCs and differentiated cortical neurons. The identified modifiers will be potential candidates for biomarkers and therapeutic targets for repeat expansion diseases. Finally, we are working with several industry partners to develop different approaches to targeting the DDR and in particular lowering MSH3 expression. MSH3 is a particularly attractive therapeutic target as its loss is well tolerated in vivo and will work with the Bates lab to explore the therapeutic potential of modulating DDR proteins in mouse models of HD.

Publications

10 25 50
 
Description CHDI Foundation grant: Mechanism of the DNA damage response in Huntington's disease pathogenesis
Amount £753,654 (GBP)
Organisation CHDI Foundation 
Sector Charity/Non Profit
Country United States
Start 05/2018 
End 05/2021
 
Description Mechanism of the DNA damage response in Huntington's disease pathogenesis
Amount £1,574,978 (GBP)
Funding ID A-15806 
Organisation CHDI Foundation 
Sector Charity/Non Profit
Country United States
Start 08/2020 
End 09/2022
 
Description Mechanism of the DNA damage response in Huntington's disease pathogenesis
Amount £398,581 (GBP)
Organisation CHDI Foundation 
Sector Charity/Non Profit
Country United States
Start 04/2021 
End 04/2023
 
Description NIHR BRC Grant - developing biomarkers of CAG repeat instability in patient CSF for HD therapeutic trials
Amount £25,000 (GBP)
Organisation NIHR Southampton Biomedical Research Centre 
Sector Academic/University
Country United Kingdom
Start 09/2021 
End 09/2022
 
Description TREAT-HD: targeting neurodegeneration in Huntington's disease
Amount £3,313,863 (GBP)
Funding ID 223082/Z/21/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2022 
End 12/2026
 
Description Wellcome Trust Multi-User Equipment grant (221521/Z/20/Z: Expanding the proteomics and establishing top-down capabilities for the UCL Mass Spectrometry Science Technology Platform. Co-applicant with Prof Thalassinos (principal investigator)
Amount £674,756 (GBP)
Funding ID 221521/Z/20/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start  
 
Title 125Q iPSC derived from a Huntington's disease patient 
Description Patient-derived iPSCs generated by Censo with 125 CAG repeats. These cells show somatic instability in culture. 
Type Of Material Cell line 
Year Produced 2018 
Provided To Others? No  
Impact The ability to study somatic instability in culture. 
 
Title Bioinformatics 
Description Analysis of genetic modifiers and transcriptomics 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact Publication in Nature Scientific Reports 
 
Title Cell models 
Description HEK, HeLa, SHSY5Y, U20S cells 
Type Of Material Cell line 
Provided To Others? No  
Impact Ongoing research into genetic modifiers 
 
Title Chromatin immunoprecipitation 
Description Protein-DNA interactions 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact Ongoing research into genetic modifiers 
 
Title DNA mismatch repair reporter assay 
Description DNA mismatch repair reporters 
Type Of Material Technology assay or reagent 
Year Produced 2021 
Provided To Others? No  
Impact N/a - to be shared with industrial partner 
 
Title Juvenile-onset Huntington's disease lymphoblastoid cell line with 130 CAG repeats 
Description Lymphoblastoid cell line which shows robust somatic expansion in culture 
Type Of Material Cell line 
Year Produced 2017 
Provided To Others? No  
Impact Under evaluation in the lab 
 
Title Long read sequencing on the PacBio and Oxford Nanopore platforms 
Description Long read sequencing on the PacBio and Oxford Nanopore platforms 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? No  
Impact Will be used for sequencing and repeat sizing. 
 
Title Molecular biology 
Description Genetic manipulation in various cell lines 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact Ongoing research in genetic modifiers 
 
Title Repeat expansion disease stem cells 
Description Two SCA3 (io33A and io34A) and a C9orf72 cell line (CS52). One Fragile X syndrome NPC line 
Type Of Material Cell line 
Year Produced 2019 
Provided To Others? No  
Impact Research into the DDR in stem cells 
 
Title iPSCs from repeat expansion diseases 
Description iPSC lines from SCA3 (x2), C9orf72 (x3) and FXS (x1) 
Type Of Material Cell line 
Year Produced 2019 
Provided To Others? No  
Impact No results yet 
 
Description ASO-mediated MSH3 knockdown (Ionis) 
Organisation Ionis Pharmaceuticals
Country United States 
Sector Private 
PI Contribution Testing the effect of ASO-mediated MSH3 knockdown on CAG expansion in 109 and 125 CAG iPSCs.
Collaborator Contribution Transfer of iPSC cells and intellectual input to research strategies
Impact N/a
Start Year 2019
 
Description Assessing effect of MSH3 repeat variation on MMR function (Toronto) 
Organisation The Hospital for Sick Children (SickKids)
Country Canada 
Sector Hospitals 
PI Contribution MMR function of patient-derived MSH3 protein will studied using in vitro slip-out repair assays in collaboration with the Hospital for Sick Children
Collaborator Contribution Culture cell lines and generate protein extracts used to assay for differences in DNA repair activity.
Impact None yet
Start Year 2021
 
Description Collaboration on DNA repair biology (Vertex) 
Organisation Vertex Pharmaceuticals
Country United States 
Sector Private 
PI Contribution Study design and all research work
Collaborator Contribution Provision of research funding. Strategic oversight and study design.
Impact 306. Goold R, Hamilton J, Menneteau T, Flower M, Bunting EL, Aldous SG, Porro A, Vicente JR, Allen ND, Wilkinson H, Bates GP, Sartori AA, Thalassinos K, Balmus G, Tabrizi SJ. FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's Disease. Cell Rep. 2021 Aug 31;36(9):109649. doi: 10.1016/j.celrep.2021.109649. Made Cell Reports' special preview and the front cover of the journal. Publications Bunting EL, Hamilton J, Tabrizi SJ. Polyglutamine diseases. Curr Opin Neurobiol. 2021 Sep 3;72:39-47. doi: 10.1016/j.conb.2021.07.001. [online ahead of print] Lange J, Wood-Kaczmar AW, Ali A, Farag S, Ghosh R, Parker J, Casey C, Uno Y, Kunugi A, Ferretti P, Andre R, Tabrizi SJ. Mislocalisation of nucleocytoplasmic transport proteins in human Huntington's disease PSC-derived striatal neurons. Frontiers in Cellular Neuroscience. 2021 Sep 29;15:742763. doi: 10.3389/fncel.2021.742763. eCollection 2021.
Start Year 2019
 
Description DNA Repair in HD (Wellcome Sanger Institute) 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Provisions of samples for analyses
Collaborator Contribution Genome sequencing expertise
Impact None yet
Start Year 2021
 
Description DNA repair in HD (Cambridge) 
Organisation University of Cambridge
Department Cambridge Neuroscience
Country United Kingdom 
Sector Academic/University 
PI Contribution Transfer of materials - iPSC lines which demonstrate somatic instability (SI) and controls, intellectual input for new grant application for CRISPR screen of DNA modifiers of SI. Developement of patent licensed to Adrestia Therapeutics.
Collaborator Contribution Develop high-throughput small molecule screen for modulators of repair activity and repeat expansion in HD iPSCs. Input into subsequent grant proposals and Developement of patent licensed to Adrestia Therapeutics.
Impact Publication: Goold R, Hamilton J, Menneteau T, Flower M, Bunting EL, Aldous SG, Porro A, Vicente JR, Allen ND, Wilkinson H, Bates GP, Sartori AA, Thalassinos K, Balmus G, Tabrizi SJ. FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's Disease. Cell Rep. 2021 Aug 31;36(9):109649. doi: 10.1016/j.celrep.2021.109649. Made Cell Reports' special preview and the front cover of the journal. Patent Patent on the FAN1-MLH1 interaction and structural analogs for the treatment of disease. Application number 2105484.6 - licensed to Adrestia Therapeutics. https://www.ucl.ac.uk/ion/news/2021/sep/new-mechanism-preventing-toxic-dna-lesions-opens-therapeutic-avenues-huntingtons
Start Year 2019
 
Description DNA repair in HD (Glasgow) 
Organisation University of Glasgow
Country United Kingdom 
Sector Academic/University 
PI Contribution Study design and leadership. Principal investigator on further funding applications
Collaborator Contribution Sensitive smool-pool PCR expertise
Impact Publications: Flower M, Lomeikaite V, Ciosi M, Cumming S, Morales F, Lo K, Moss D H, Jones L, Holmans P, the TRACK-HD Investigators, the OPTIMISTIC Consortium, Monckton DG, Tabrizi SJ. MSH3 modifies somatic instability and disease severity in Huntington's and myotonic dystrophy type 1. Brain. 2019 Jun 19. pii: awz115. doi: 10.1093/brain/awz115 Ciosi M, Maxwell A, Cumming SA, Hensman Moss DJ, Alshammari AM, Flower MD, Durr A, Leavitt BR, Roos RAC; TRACK-HD team; Enroll-HD team, Holmans P, Jones L, Langbehn DR, Kwak S, Tabrizi SJ, Monckton DG. A genetic association study of glutamine-encoding DNA sequence structures, somatic CAG expansion, and DNA repair gene variants, with Huntington disease clinical outcomes. EBioMedicine. 2019 Oct;48:568-580. doi: 10.1016/j.ebiom.2019.09.020. Epub 2019 Oct 10. Further funding: Wellcome Trust Collaborative Award (Ref 223082/Z/21/Z): £3,313,863. TREAT-HD: targeting neurodegeneration in Huntington's disease. Tabrizi (PI) Collaborator (Co-Applicant)
Start Year 2018
 
Description Generate iPSCs from HD patients with disease-associated FAN1 and MSH3 variation (Censo) 
Organisation Censo Biotechnologies
Country United Kingdom 
Sector Private 
PI Contribution Collection and provision of blood samples for iPSC generation. Investigating the mechanisms underlying Huntington's disease, including genetic modifiers and somatic instability
Collaborator Contribution Generate iPSC cells from human blood samples
Impact None yet
Start Year 2018
 
Description Investigating the role of FAN1 in DNA Repeat Expansion Disorders (Adrestia) 
Organisation Adrestia Therapeutics Ltd
Country United Kingdom 
Sector Private 
PI Contribution Design and execution of study demonstrating new mechanism that stops the progression of Huntington's disease in cells.
Collaborator Contribution Expertise to translate insights into therapies for HD and DNA repeat expansion disorders.
Impact None yet
Start Year 2021
 
Description Mechanism of the DNA damage response (Cardiff) 
Organisation Cardiff University
Department Division of Psychological Medicine and Clinical Neurosciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Study design, secured funding and research
Collaborator Contribution Intellectual input on study design
Impact Goold R, Hamilton J, Menneteau T, Flower M, Bunting EL, Aldous SG, Porro A, Vicente JR, Allen ND, Wilkinson H, Bates GP, Sartori AA, Thalassinos K, Balmus G, Tabrizi SJ. FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's Disease. Cell Rep. 2021 Aug 31;36(9):109649. doi: 10.1016/j.celrep.2021.109649. Made Cell Reports' special preview and the front cover of the journal.
Start Year 2018
 
Description Mechanism of the DNA damage response in Huntington's disease pathogenesis and relevance for therapeutics (UCL ISMB) 
Organisation University College London
Department Institute of Structural and Molecular Biology
Country United Kingdom 
Sector Academic/University 
PI Contribution Principal Investigator, and scientific design and leadership of research project,
Collaborator Contribution Co-Investigator, and scientific design and leadership of research project funded by CHDI Foundation
Impact Publication: Goold R, Hamilton J, Menneteau T, Flower M, Bunting EL, Aldous SG, Porro A, Vicente JR, Allen ND, Wilkinson H, Bates GP, Sartori AA, Thalassinos K, Balmus G, Tabrizi SJ. FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's Disease. Cell Rep. Further funding: 2018-2020 CHDI Foundation grant: £753,654. Mechanism of the DNA damage response in Huntington's disease pathogenesis 2020-2022 CHDI Foundation grant: £1,574,978. Mechanism of the DNA damage response in Huntington's disease pathogenesis
Start Year 2018
 
Description Mechanism of the DNA damage response in Huntington's disease pathogenesis and relevance for therapeutics (UCL IoN) 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Co-application for funding
Collaborator Contribution Co-application for funding
Impact Publications: Goold R, Flower M, Moss DH, Medway C, Wood-Kaczmar A, Andre R, Farshim P, Bates GP, Holmans P, Jones L, Tabrizi SJ. FAN1 modifies Huntington's disease progression by stabilising the expanded HTT CAG repeat. Human Molecular Genetics. 2019 Feb 15;28(4):650-661. Further funding: Wellcome Trust Collaborative Award (Ref 223082/Z/21/Z): £3,313,863. TREAT-HD: targeting neurodegeneration in Huntington's disease. Tabrizi (PI) Collaborator (Co-Applicant)
Start Year 2018
 
Description Phase 3 GENERATION HD1 HTT lowering clinical trial 
Organisation F. Hoffmann-La Roche AG
Country Global 
Sector Private 
PI Contribution We commenced a global phase 3 trial, GENERATION HD1 (NCT03761849), in September 2018. Roche partnered with IONIS in 2013 and acquired the drug in 2017 for $45m, renaming it RG6042. 90 sites are running in 18 countries, dosing 660 HD subjects with manifest disease, aged 25-65, bimonthly or 4 monthly, with 120 mg or placebo at a 3:1 ratio, for a total of 25 months, followed by an open label extension. This trial has the potential to measure a clinically meaningful improvement in disease progression. The primary outcome measure in the global study is cUHDRS27, whilst in the US only, the primary endpoint is TFC, a component of cUHDRS which also correlates with functional measures. Given our finding that HTT lowering may also reduce CAG expansion in cell and mouse models, as well as investigating the underlying mechanism in the lab, we are developing assays to measure repeat expansion in trial CSF.
Collaborator Contribution Clinical trial sponsors central to trial design and oversight
Impact Tabrizi SJ, Leavitt BR, Landwehrmeyer GB, Wild EJ, Saft C, Barker RA, Blair NF, Craufurd D, Priller J, Rickards H, Rosser A, Kordasiewicz HB, Czech C, Swayze EE, Norris DA, Baumann TF, Gerlach I, Schobel SA, Paz E, Smith AV, Bennett CF, Lane RM. Targeting Huntingtin Expression in Patients with Huntington's Disease. The New England Journal of Medicine. 2019 May doi: 10.1056/NEJMoa1900907
Start Year 2017
 
Description The transcription dependence of repeat expansion and the role of RNA:DNA R-loops (Oxford) 
Organisation University of Oxford
Department Oxford Hub
Country United Kingdom 
Sector Academic/University 
PI Contribution Strategic oversight and study design and execution
Collaborator Contribution Strategic oversight and study design and execution
Impact None as yet
Start Year 2020
 
Title Somatic instability analysis program 
Description Software for fragment analysis 
Type Of Technology Software 
Year Produced 2018 
Impact Standardises fragment analysis in this lab and for collaborators 
URL https://caginstability.ml
 
Description Filmed interview discussing genetic therapies for US television documentary 'The Gene' 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Filmed interview on genetic therapies for Huntington's disease for major US documentary series.
Year(s) Of Engagement Activity 2018
 
Description Interview for BBC Radio 4 Ingenious 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Prof Tabrizi inteviewed about Huntington's disease research for BBC Radio 4's Ingenious programme
Year(s) Of Engagement Activity 2021
URL https://www.bbc.co.uk/programmes/m000xzf5
 
Description Interview for BBC Radio 4 Inside Health 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Prof Sarah Tabrizi talking on BBC R4 about the challenges and opportunities of gene silencing treatments for Huntington's disease
Year(s) Of Engagement Activity 2021
URL https://www.bbc.co.uk/sounds/play/m0010p1p
 
Description Interview for BBC Radio 4 docmentary 'The Silence of the Genes' 
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 Media (as a channel to the public)
Results and Impact Interview on the ongoing Huntington's disease gene-lowering trials to promote research awareness for general public.
Year(s) Of Engagement Activity 2019
URL https://www.bbc.co.uk/sounds/play/m0009rhs
 
Description Interview on Huntigntons disease therapeutics with Nature Biotechnology 
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 Prof Tabrizi interview on Huntigntons disease therapeutics with Nature Biotechnology
Year(s) Of Engagement Activity 2021
URL https://www.nature.com/articles/s41587-021-00955-y?proof=tNature
 
Description Observer news article on Huntington diseae trials 03/03/2019 
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 Public/other audiences
Results and Impact Article on Huntington's disease therapies at current clinical trail. https://www.theguardian.com/science/2019/mar/03/huntingtons-disease-new-drug--families. Increased awareness of HD and generated interest in trial.
Year(s) Of Engagement Activity 2019
URL https://www.theguardian.com/science/2019/mar/03/huntingtons-disease-new-drug--families
 
Description Participated in filmed interview for Neuro Central and the Video Journal of Biomedicine 
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 Other audiences
Results and Impact Filmed interview regarding ongoing HD gene-lowering trials titled 'Genetic therapies for neurodegenerative diseases'.
Year(s) Of Engagement Activity 2019
URL https://www.neuro-central.com/2019/09/12/genetic-therapies-neurodegenerative-diseases-interview-sara...
 
Description Press conference at American Academy of Neurology Conference, Los Angeles following presentation of HTT lowering phase 1/2a clinical trial results. 
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 Press conference at American Academy of Neurology Conference following presentation of HTT lowering phase 1/2a clinical trial results. Conference generated questions from media an a plethora of subsequent scientific news articles
Year(s) Of Engagement Activity 2018
 
Description Press release for Cell Reports paper (August 2021) 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Press release for Cell Reports paper

Goold R, Hamilton J, Menneteau T, Flower M, Bunting EL, Aldous SG, Porro A, Vicente JR, Allen ND, Wilkinson H, Bates GP, Sartori AA, Thalassinos K,
Balmus G, Tabrizi SJ. FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's Disease. Cell Rep. 2021 Aug 31;36(9):109649. doi: 10.1016/j.celrep.2021.109649. Made Cell Reports' special preview and the front cover of the journal.

Received coverage in following media outlets

https://inews.co.uk/news/science/huntingtons-disease-treatment-breakthrough-1176576
https://www.dailymail.co.uk/wires/pa/article-9943895/New-study-pave-way-Huntington-s-disease-therapies.html
https://www.standard.co.uk/news/uk/ucl-university-of-cambridge-cambridge-b953105.html
https://www.msn.com/en-gb/news/other/new-study-could-pave-the-way-for-huntingtons-disease-therapies/ar-AANWtFn
Year(s) Of Engagement Activity 2021
URL https://www.ucl.ac.uk/news/2021/aug/new-mechanism-preventing-toxic-dna-lesions-opens-therapeutic-ave...
 
Description Press release for publication of New England Journal of Medicine paper 
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 Press release to accompany publication of results from the successful safety trial of a therapeutic for Huntington's disease. The release raised awareness of important research and resulted in enquiries to participate in research.
Year(s) Of Engagement Activity 2019
URL https://www.sciencedaily.com/releases/2019/05/190506150103.htm