MRC Strategic Award to establish an International Centre for Genomic Medicine in Neuromuscular Diseases

Lead Research Organisation: University College London
Department Name: Institute of Neurology

Abstract

Neuromuscular Diseases (NMD) affect at least 17 million children and adults globally. They cause either premature death or are chronic diseases causing lifelong disability with economic impact. They include many different disorders affecting muscle and nerve function and account for ~20% of all non-infectious neurological diseases. Examples include muscular dystrophies, congenital myopathies, neuropathies, motor neuron diseases, muscle channelopathies and mitochondrial diseases. Advances in genetics have improved our ability to diagnose patients in the UK, and this has resulted in improved patient care and enabled clinical trials. However the benefits of genetic advances have not been realised in Official Development Assistance (ODA) defined Lower and Middle Income Countries (LMICs), partly because of a lack of neurologists trained specifically in genomic NMD medicine.

NMDs are commonly genetic and are inherited. Identifying genetic pathways and applying genetic testing has led to some of the most important advances in disease understanding alongside patient management plans and the development of new therapies. Many of the key interventions involve the inexpensive practical applications of widely available medical technology (e.g. low-cost off-licence medication, targeted vaccination, cardiac monitoring and respiratory care), but their application is contingent on making a precise diagnosis. For example, a precise genetic diagnosis can lead to a personalised and often simple management plan following established care guidelines that includes basic screening for known complications (e.g. cardiac, respiratory, gastroenterological and metabolic) and often simple interventions that improve health outcomes - interventions that could be implemented easily in LMICs providing an accurate genetic diagnosis is made. In the UK, a muscle biopsy has been the mainstay in the investigation algorithm in many patients, but this requires a specialist laboratory equipped for frozen section analysis with a growing panel of diagnostic antibodies. However, recent advances in genomics provide the opportunity to diagnose with high precision based on a DNA sample and clinical data collected remotely.

Our central objective is to build ethnically diverse cohorts of children and adults with NMDs and undertake genomic analysis to find known and identify new disease genes. We will increase the number of patients with a precise genetic diagnosis to both improve patient care and to increase knowledge on the comparative genetic architecture of NMDs across four continents.

This is a brand new transcontinental programme led by UK professors at UCL, Newcastle and Cambridge Universities. The research programme will train a new generation of academic doctors, generate the world's largest cohort of 15,000 ethnically diverse NMD patients and will investigate the causative genes. We will work with five LMIC clinical and academic centres in: India, Turkey, South Africa, Zambia and Brazil. The trained doctors will be the future clinical academic leaders to undertake research and improve NMD patient care in these countries. The fellows will already be fully trained in neurology and will spend a year in the UK for specialist training in NMD genomic medicine and spend three years in their country building NMD patient cohorts that will be assessed in detail clinically and will undergo full genetic analysis to achieve a precise diagnosis and optimise patient management. All data produced will be anonymised and shared by all researchers. Importantly, we have access to several thousand ethnically matched control DNAs already and will build this control resource further, complementing those available through the Genomics England 100,000 genomes project, the NIHR BioResource and international collaborative resources. We will train a new generation of NMD doctors who will pursue their research career in their own country, discover new genes and improve patient care.

Technical Summary

We will train a new group of clinical academic fellows to ultimately benefit patients in each partner LMIC. Fellows will be trained to build a cohort of 15,000 Neuromuscular disease (NMD) patients for deep phenotyping and comprehensive genotyping, we will:

(i) Establish an easy to use platform for deep clinical phenotyping and sharing of genome data/results between all project members. We will adopt the pseudo-anonymised, secure and cloud based RD-Connect platform (http://rd-connect.eu/), that uses PhenoTips (https://phenotips.org/) and Human Phenotype Ontology (HPO) (http://human-phenotypeontology.github.io/) terminology. This freely available software platform will be used for each patient/family, entered on secure iPAD locally. This platform allows future collaboration with European and International rare disease initiatives. We will also adopt Open-Clinica for natural history of disease, and later therapeutic trials. This approach ensures cross compatibility with national (GEL, NIHR BioResource) and international efforts (RD-connect).
(ii) Establish a common laboratory framework for high quality DNA extraction from blood, logged and stored in the cloud database following guidelines of UK accredited diagnostic laboratories.
(iii) Establish common genetic screening platform across laboratories, based on a tiering genetic analysis system hierarchy we developed and tested in the UK. This accounts for the molecular test complexity, number of genes and analysis requirements.
(iv) Train fellows in core bioinformatics skills and basic genetic laboratory techniques to ensure an equal skill set in each LMIC.
(v) Employ integrated genomic-phenotype cloud based platform for effective interpretation and gene discovery.

We will identify known and new disease genes, and assess comparative genetic architecture across 4 continents. This will improve understanding of phenotypic variability, disease progression and disease mechanisms, and build "trial ready" cohorts.

Planned Impact

The mission is to create a transcontinental genomics research and capacity building partnership between the UK & India, Turkey, South Africa, Zambia and Brazil. The beneficiaries include:
1) Patients and patient organisations
2) Basic and clinical scientists in neurology, neuroscience and genetics
3) Policy and guidelines
4) Pharmaceutical industry
There are particular challenges faced in the field of NMD which apply across stakeholder groups, and impact in all challenge areas will be achieved through our outputs. Patients and the patient organisations face uncertain access to diagnosis and care, have limited access to clinical trials and the majority are without effective therapies. The clinical and academic groups who work with NMD require resources and know-how to underpin delivery of care and translational research. The policy-makers determine care delivery, and need information on which to base health recommendations. Industrial partners frequently lack knowledge in the disease areas and perceive that the field lacks "trial readiness". By targeting the needs of these distinct stakeholder groups, we will provide outputs which will promote health in this patient group, as well as promoting UK international research competitiveness. Strong relationships are already in place to ensure that impact can be maximised. These include:
1) Key roles for our PIs in national/international patient organisations
2) Strong involvement of our patients and patient organisations in research design and oversight
3) Leading roles of our PIs in host clinical/academic organisations
4) Existing relationships in key areas of liaison with policy makers involved in rare disease public health decision making in UK and LMICs
5) Many links to industry (as detailed in Pathway to Impact)

PATIENTS AND PATIENT ORGANISATIONS: They will benefit from precise genetic diagnosis and cohort stratification enabling trial ready cohorts for the experimental medicine studies and increased trial activity, aimed at defining better therapeutic strategies. Improved diagnostics and treatments will ultimately impact on health, quality of life and societal benefit via greater participation of this patient group in their communities.

CLINICIANS AND ACADEMICS: The clinical and academic groups working with NMD require resources and know-how to deliver care and genomic translational research effectively. Underpinning the experimental medicine potential will be the development of international stratified genetic cohorts, enabling personalised medicine and a much larger group of patients to contribute to experimental clinical studies and access standardised procedures for care and assessment internationally. Training LMIC fellows in genomic medicine will benefit the local academic community and increase research in NMD and benefit patients through more expert clinical care, accurate genetic diagnosis and through "trial ready" cohorts.

POLICY AND GUIDELINES: Policy makers in LMICs who determine care delivery in this area need information on which to base health recommendations. Detailed understanding of prevalence and population specific genetic variations in NMD cohorts, and the important insights these data will provide to NMD patients globally, will aid healthcare policy development. These data will also facilitate development of national and international diagnostic and management guidelines. Policy makers will have access to clearer and more harmonised guidance on the management of these patient groups which can be applied to healthcare planning.

INDUSTRY: Stratified cohorts, research know-how, and a strategic programme of preclinical research provide a conducive environment for increased industry engagement with the presence of trial expertise and ready access to rare patients. We will identify targets for new areas of industrial exploitation.

Publications

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100,000 Genomes Project Pilot Investigators (2021) 100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care - Preliminary Report. in The New England journal of medicine

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Averdunk L (2021) The recurrent missense mutation p.(Arg367Trp) in YARS1 causes a distinct neurodevelopmental phenotype. in Journal of molecular medicine (Berlin, Germany)

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Barp A (2023) Anti-HMGCR myopathy: barriers to prompt recognition. in Practical neurology

 
Description A Lily Precision Diagnostic Service - Accelerating the Introduction of Advanced Diagnostics for Mitochondrial Patients in the NHS
Amount £644,882 (GBP)
Organisation The Lily Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2023 
End 02/2027
 
Description BRC3
Amount £25,000 (GBP)
Organisation University College Hospital 
Sector Hospitals
Country United Kingdom
Start 01/2022 
End 09/2022
 
Description Indian Council of Medical Research (ICMR) research grant to All India Institute of Medical Sciences (Delhi): Identification of the Genetic architecture of Facioscapulohumeral muscular dystrophy in India
Amount ₹836,422,659 (INR)
Organisation Indian Council of Medical Research (ICMR) 
Sector Public
Country India
Start 05/2023 
End 06/2026
 
Description Investigating the role of cardiolipin metabolism in mitochondrial DNA replication and mitochondrial division
Amount £1,083,602 (GBP)
Funding ID MR/S002065/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 02/2024
 
Description Joint Seed Fund Call
Amount £5,000 (GBP)
Organisation University College London 
Sector Academic/University
Country United Kingdom
Start 01/2022 
End 07/2022
 
Description MitoCluster Consortium : An Integrated Phenotyping and Mouse Model Generation Platform for Mitochondrial Disease and Dysfunction
Amount £2,933,088 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 03/2023 
End 02/2029
 
Description Neuromuscular Clinical Trial Coordinator
Amount £56,294 (GBP)
Organisation National Brain Appeal 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2019 
End 11/2020
 
Description Neuromuscular Disease Theme 3
Amount £257,408 (GBP)
Organisation University College Hospital 
Sector Hospitals
Country United Kingdom
Start 03/2020 
End 05/2022
 
Description Neuromuscular Research Manager
Amount £200,312 (GBP)
Organisation National Brain Appeal 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2019 
End 05/2024
 
Description TransNAT: Transforming delivery, safety, and efficacy of nucleic acid therapeutics; from intracellular uptake to targeting brain, heart and muscle
Amount £1,777,003 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 09/2022 
End 09/2025
 
Description UCL:AIIMS Intramural award: The first investigation of the genetic causes of Facioscapulohumeral muscular dystrophy (FSHD) in the Indian population
Amount £10,000 (GBP)
Funding ID UCL:AIIMS collaborative seed funding awards (Global Engagement) 
Organisation University College London 
Sector Academic/University
Country United Kingdom
Start 03/2022 
End 06/2023
 
Title Quadruple immunofluoresence images of skeletal muscle biopsies from patients with the mtDNA m.3243A>G variant 
Description Fluorescent images of 10µm transverse muscle sections from patients carrying the pathogenic m.3243A>G mtDNA variant, captured by automated scanning at 20× magnification using Zen 2011 (blue edition) software and Zeiss Axio imager MI microscope. Exposure times across all sections for each experimental batch were maintained. Muscle sections were stained using a 'Quantitative quadruple immunohistochemistry' technique, designed to capture expression profiles of proteins belonging to oxidative phosphorylation (OXPHOS) complexes. 'OXPHOS' sections were labelled with antibodies detecting subunits of mitochondrial complex I (NDUFB8) and complex IV (COX-1), a mitochondrial mass marker (mitochondrial porin; VDAC1) and laminin, followed by incubation with secondary antibodies (Alexa Fluor 488, 546, biotinylated IgG1 and 750) and subsequently with streptavidin 647. Alongside each sample, a no-primary control section (NPC; labelled only for laminin) was processed. This resource contains .iaf, .jpg and .png files from OXPHOS and NPC sections from 17 patients (P01-P17) and five controls (C01-C05). It also contains PDFs for 10 sections for which single fibre molecular genetic data are available at https://github.com/CnrLwlss/Ahmed_2022 File naming convention: b : where n=2 or 4 and refers to the batch that the samples were processed in. Some samples have been processed twice, in two separate batches. P01-P17 : Sections from m.3243A>G patients C01-C05 : Non-disease controls NPC : Non-primary control - sections labelled only with laminin OXPHOS : Sections labelled for OXPHOS complexes ch1 : MTCO1 (Complex IV; 488nm) ch2 : VDAC (Porin; 546nm) ch3 : NDUFB8 (Complex I; 647nm) ch4 : Laminin (750nm) 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
URL https://data.ncl.ac.uk/articles/dataset/Quadruple_immunofluoresence_images_of_skeletal_muscle_biopsi...
 
Description Titinopathy and Nebulin myopathy collaboration between ICGNMD & Folkhälsan Research Center, Helsinki 
Organisation Folkhalsan Research Centre
Country Finland 
Sector Charity/Non Profit 
PI Contribution ICGNMD collaborates with the Professor Bjarne Udd and Dr Marco Savarese to discuss relevance of mutations in the Titin gene present in the ICGNMD cohort, and with Professor Vilma Lehtokari, Professor Carina Wallgren and Dr Katarina Pelin to discuss mutations in the Nebulin gene.
Collaborator Contribution ICGNMD provides anonymised genetic and clinical data and discusses the significance of Titin and Nebulin gene variants with the team in Helsinki, who have specialist expertise.
Impact The collaboration is new so there are no formal outputs yet.
Start Year 2023