Next Generation Gene Hunting in Amyotrophic Lateral Sclerosis

Lead Research Organisation: King's College London
Department Name: Clinical Neuroscience

Abstract

There are no effective treatments for amyotrophic lateral aclerosis (ALS) because so little is known about what causes it. In most instances ALS appears out of the blue (called sporadic ALS) but in 10% the disease runs in families (familial ALS) due to a single defective gene, passed down from generation to generation. Four genes are known to cause ALS (SOD1, TARDBP, FUS and ANG) but they account for only 25% of all familial and 7% of sporadic ALS patients. The cause of the disease in 90% of patients is unknown but a genetic basis is strongly implicated.

The ?Next Generation? of DNA technology has transformed what can be achieved in genetic research. The human genome mapping project published in 2000 one person?s entire genetic code. It took 15 years and cost #~300 million. This can now be done in 1 month for #~10,000. This grant application aims to harness the extraordinary power of these new research tools in a global gene hunting effort.

Only ~2% of the human genetic code provides the blueprint for making proteins (the building blocks of all cells). Mutations in these genes accounts for most human diseases. Revolutionary DNA capture methods mean that we can pull out the protein encoding 2% of genes for further analysis. Single molecule DNA sequencing allows us to read the spelling of millions of different DNA fragments and rapidly identify the disease-causing spelling mistakes.

We are focusing our most intensive sequencing on DNA from 100 families and comparisons made to healthy controls. Potential mutations will be then screened in DNA samples held by a global network of ALS researchers, ( 2,000 familial and 10,000 sporadic samples). For the 30% of genes that are not covered by DNA capture methods we will identify chromosomal regions that contain ancient mutations and target genes implicated in known pathological ALS pathways.

Screening of new ALS genes can be offered to at-risk families and sporadic patients who are worried about the risk to other family members. The gene mutations we identify can be introduced into cells and mice allowing us to study the harmful effects of ALS gene mutations. This will dramatically improve our understanding of the underlying disease mechanisms and develop drugs capable of arresting the disease process and even preventing it occurring in genetically susceptible individuals.

Technical Summary

Amyotrophic lateral sclerosis (ALS, also known as motor neurone disease) causes progressive paralysis and takes the lives of 1,200 people in the UK every year. There are no effective treatments and little is known about its causes. Most ALS is sporadic but in 10% it is clearly familial (FALS), due to a single gene mutation inherited in an autosomal dominant fashion. Clinically and pathologically, familial and sporadic ALS are indistinguishable and many cases of sporadic ALS may be caused by gene defects with low penetrance. Most genetic neurodegenerative disorders are due to mutations that cause a change in the amino acid sequence. Four genes known to cause ALS account for only 25% of familial and 7% of sporadic ALS. We aim to identify the remaining FALS genes in order to offer comprehensive counselling and gene testing to at-risk families and concerned individuals with apparently sporadic disease. This will dramatically improve our understanding of disease pathogenesis and significantly advance drug discovery.

Here we propose an unprecedented gene hunting effort using revolutionary techniques including DNA capture, deep resequencing and high-density SNP genotyping. Using an initial cohort of cultured lymphoblast lines from 100 FALS cases we will extract high quality DNA, RNA and protein. Using the Nimblegen 2.1m array we will capture ~180,000 exons (comprising ~70% of the human genome) for sequencing on the Solexa GAII. We will also perform high density SNP genotyping on the Illumina Quad650 arrays looking for ancient common founder mutations. Lastly we will target genes implicated in pathways implicated in ALS pathogenesis not represented in the Nimblegen arrays.

Our five criteria for prioritising variants are those that (i) change the amino acid sequence, (ii) segregate with disease within kindreds, (iii) affect multiple families, (iv) have multiple mutations in multiple families and (v) have a low mutation frequency in multiple control populations. Variants that meet these criteria will be confirmed by Sanger sequencing and compared to the controls in SNP databases. Genes with confirmed mutations will be screened in a second cohort of local familial (200) and sporadic cases (2,000). We will notify our FALS Network partners of the most promising genes (frequency 1%) and request screening in their FALS and SALS cohorts to determine their global frequency and ethnic variation. Having identified mutations with a high likelihood of pathogenicity we will test for toxicity in cell lines, primary neurons and simple animal models (embryonic chicken and zebrafish).

Publications

10 25 50

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Al-Chalabi A (2010) An estimate of amyotrophic lateral sclerosis heritability using twin data. in Journal of neurology, neurosurgery, and psychiatry

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Arnold ES (2013) ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43. in Proceedings of the National Academy of Sciences of the United States of America

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Balendra R (2014) Estimating clinical stage of amyotrophic lateral sclerosis from the ALS Functional Rating Scale. in Amyotrophic lateral sclerosis & frontotemporal degeneration

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Barker HV (2017) RNA Misprocessing in -Linked Neurodegeneration. in Frontiers in cellular neuroscience

 
Title YouTube educational video on ALS 
Description Educational video on ALS research available on YouTube 
Type Of Art Film/Video/Animation 
Year Produced 2018 
Impact Patient information and understanding about ALS and research 
URL https://www.youtube.com/watch?v=7KVSbwe7bHo
 
Description Association of British Neurologists Genetics Advisory Committee
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
 
Description Sumission to Parliamentary Science and Technology Committee
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
Impact Permitted the use of hybrid embryos in research in UK
 
Description King's Biomedical Sciences Institute PhD Studentship
Amount £100,000 (GBP)
Organisation King's College London 
Sector Academic/University
Country United Kingdom
Start 03/2014 
End 10/2017
 
Description MNDA studentship
Amount £87,502 (GBP)
Organisation Motor Neurone Disease Association (MND) 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2010 
End 09/2013
 
Description PhD Studentship
Amount £100,000 (GBP)
Organisation King's College London 
Department Psychiatry Research Trust
Sector Charity/Non Profit
Country United Kingdom
Start 11/2010 
End 11/2013
 
Description Programme Grant (MIROCALS)
Amount £387,723 (GBP)
Funding ID 633413 
Organisation European Commission 
Department Horizon 2020
Sector Public
Country European Union (EU)
Start 09/2015 
End 08/2019
 
Description Programme Grant FP7
Amount £666,323 (GBP)
Organisation Spanish National Research Council (CSIC) 
Sector Public
Country European Union (EU)
Start 12/2010 
End 12/2013
 
Description Research Grant (ALSoD)
Amount £40,000 (GBP)
Organisation Motor Neurone Disease Association (MND) 
Sector Charity/Non Profit
Country United Kingdom
Start 02/2017 
End 01/2020
 
Description Research Grant (ALSoD)
Amount £102,469 (GBP)
Organisation ALS Association 
Sector Charity/Non Profit
Country United States
Start 02/2017 
End 01/2020
 
Description Research Grant (ATXN2 penetrance)
Amount £134,207 (GBP)
Organisation Motor Neurone Disease Association (MND) 
Sector Charity/Non Profit
Country United Kingdom
Start 11/2015 
End 08/2019
 
Description Research Grant (HERV-K)
Amount £241,949 (GBP)
Organisation ALS Association 
Sector Charity/Non Profit
Country United States
Start 11/2017 
End 10/2019
 
Description Research Grant (JPND BRAIN-MEND)
Amount £2,044,052 (GBP)
Funding ID MR/R024804/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 02/2018 
End 01/2021
 
Description Research Grant Fellowship
Amount £265,000 (GBP)
Organisation Motor Neurone Disease Association (MND) 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2016 
End 02/2019
 
Description Studentship
Amount £250,000 (GBP)
Organisation British Society for the History of Science (BSHS) 
Department Darwin Trust of Edinburgh
Sector Academic/University
Country United Kingdom
Start 09/2014 
End 09/2017
 
Title Project MinE databrowser 
Description Summary statistics and output from the Project MinE whole genome sequencing consortium 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact Increased ability for researchers to identify ALS genes or interpret their own findings. Increased collaboration. 
URL http://databrowser.projectmine.com/
 
Description Exome sequencing in motor neuron disease: bioinformatic analyses and biological validation of novel variants 
Organisation Motor Neurone Disease Association (MND)
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution ALS research excellence
Collaborator Contribution financial
Impact Publication of new ALS genes
Start Year 2015
 
Description From ALS exomes to Functional assays: turning candidates into confirmed genes 
Organisation Medical Research Council (MRC)
Department Medical Research Foundation
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Scientific expertise on ALS pathogenesis
Collaborator Contribution financial support
Impact None yet as started 5 months ago
Start Year 2015
 
Description Generation and characterisation of induced pluripotent stem cells from ALS lymphoblasts to model disease pathogenesis and advance drug discovery 
Organisation Motor Neurone Disease Association (MND)
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Research excellence
Collaborator Contribution Financial and access to lymphoblast cell lines
Impact Nil yet as just started
Start Year 2015
 
Description Identification of compounds that enhance TDP43 clearance in ALS and FTD 
Organisation Eli Lilly & Company Ltd
Department Neuroscience Eli Lilly
Country United States 
Sector Private 
PI Contribution Identify therapeutic targets for drug discovery
Collaborator Contribution Expertise in drug discovery
Impact About to start
Start Year 2016
 
Description Investigating the role of autophagy and the UPS in TDP-ALS 
Organisation Motor Neurone Disease Association (MND)
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution ALS pathobiology
Collaborator Contribution Financial Support
Impact None
Start Year 2015
 
Description Vertex Pharmaceutical 
Organisation Vertex Pharmaceuticals
Country United States 
Sector Private 
PI Contribution Developing a cellular screening platform to identify small molecule correctors of the TDP-43 pathology
Collaborator Contribution Funding to develop Cellular assay for high throughout screening
Impact None so far
Start Year 2013
 
Title Lithium PRELUDE trial 
Description We have shown that Lithium carbonate, while ineffective in ALS as a whole, is effective in people with a poor prognosis genetic variant in the UNC13A gene (homozygosity for the CC genotype). We are now seeking funding for a trial of lithium in patients with ALS who carry this poor prognosis variant. This will be a precision medicine approach in ALS. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Initial development
Year Development Stage Completed 2019
Development Status Actively seeking support
Impact The initial findings have been published, and if the trial confirms the analysis, this will become a new treatment for ALS. 
URL https://www.ncbi.nlm.nih.gov/pubmed/28978660
 
Title ALSgenScanner 
Description ALSgeneScanner is a tool to allow neurologists to analyze whole genome sequence data for mutations specific to ALS and generates a detailed annotated report for each patient. 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact It has only just been released, but has had a good reception on social media platforms (Twitter in particular). 
URL https://www.tandfonline.com/doi/full/10.1080/21678421.2018.1562553
 
Title DNAscan 
Description A fast, computationally and memory efficient bioinformatics pipeline for the analysis of DNA next-generation-sequencing data 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Improved analysis pipeline for the international Project MinE whole genome sequencing consortium (http://www.projectmine.com) 
URL https://www.biorxiv.org/content/early/2018/02/18/267195
 
Description Alinda Fernandes gave Lewisham Health Lectures at Lewisham Library - Talk Title: Alzheimer's Disease and Dementia 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact The talk was received very good feedback and triggered a series of stimulating conversations
Year(s) Of Engagement Activity 2017
 
Description Alinda Fernandes poster presentation at MNDA Symposium Boston (2017) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The poster was presented to mainly scientists during the poster session which enabled new collaborations.
Year(s) Of Engagement Activity 2017
 
Description Ask the Experts Panel at International Symposium 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Patients, carers and/or patient groups
Results and Impact A live audience and online audience watched a presentation and then asked questions on ALS research
Year(s) Of Engagement Activity 2015
URL https://www.youtube.com/watch?v=U98WU4Zzu8s
 
Description Broadcast news items on new gene discoveries 
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 Interviews with BBC World (live TV interview), ITV News (recorded TV), Channel 5 News (recorded TV), BBC Radio London (live radio) and others. Example URL below
Year(s) Of Engagement Activity 2015,2016
URL https://twitter.com/ammaralchalabi/status/758321315698933760
 
Description Eva So Poster presentation at the Edmond J. Safra Memorial Lecture and Reception 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster presentation to the audience and interactive communication and discussion about research work. Event included presentation and talks highlighting the modern day approach to research in Parkinson's and other neurodegenerative diseases and the frontline advances being made by different researchers, followed by question and answer session with the audience and direct communication at the poster reception.
Year(s) Of Engagement Activity 2017
 
Description General research dissemination videos on YouTube 
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 Public/other audiences
Results and Impact Multiple videos on YouTube, responding to interviews on ALS research
Year(s) Of Engagement Activity 2014,2015,2016
URL https://www.youtube.com/results?search_query=ammar+al-chalabi+als
 
Description Graham Cocks Poster submission - Poster presentation on CRISPR work for the 4th Genome editing conference, Oxford (GEOX 2018) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation of a poster to international scientists.
Year(s) Of Engagement Activity 2018
 
Description Graham Cocks' participation 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact This involved guiding a group of MNDA donors through a tour of research undertaken here at the Wohl.
Year(s) Of Engagement Activity 2018
 
Description JNNP Podcast 
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 Professional Practitioners
Results and Impact I was interviewed for a podcast about our recent finding that genetic variants that increase ALS risk, also lower the age of onset. Our paper was Editor's Choice.
Year(s) Of Engagement Activity 2019
 
Description Jenny Greig Legacy fundraising event 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact People interested in supporting the MNDA came for a day of presentations to see the facility and the work that takes place here.
Year(s) Of Engagement Activity 2018
 
Description Jenny Greig poster presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster presentation at Stem Cell conference at Edinburgh University
Year(s) Of Engagement Activity 2017
 
Description Jenny Greig poster presentation at MNDA conference in Boston 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at MNDA conference in Boston
Year(s) Of Engagement Activity 2017
 
Description MND Genetics and Therapies 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Patients, carers and/or patient groups
Results and Impact Presentation on MND genetics and therapies to Palliative Health Care Professionals and members iof the public at a public centre
Year(s) Of Engagement Activity 2018
 
Description MNDA Legacy Event September 2018 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact The event was to educate the general public and those engaged with the MND Association about the research done that is funded by the MNDA, with the aim of increasing knowledge and encouraging a legacy to such research,
Year(s) Of Engagement Activity 2018
 
Description MNDA Legacy Event at King's College London 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Patients, carers and/or patient groups
Results and Impact Between 40 and 70 people attended each event, consisting of research presentations, a tour of the labs, and an Ask the Experts session. The events were to raise awareness of our research, to improve donations to the patient organisation (MNDA), and to improve public understanding of our clinical and research programme. Increased donations have been reported, and feedback shows a high demand for future events.
Year(s) Of Engagement Activity 2017,2018
 
Description MNDA information video on our research 
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 Public/other audiences
Results and Impact A YouTube video posted also on the Motor Neurone Disease Association website, describing our research.
Year(s) Of Engagement Activity 2016
URL https://youtu.be/tKz81aFVB04
 
Description MRC Centre Open Day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Primary Audience Participants in your research and patient groups
Results and Impact Our Open Day is for patients and carers with approximately 150 attendees. We organise 8 laboratory demonstrations presented by PhD students and postdoctoral researchers around which small groups (6-8 persons) circulate. We also have a group of about 12 sixth form students who perform a laboratory experiment. At the end of the day the sixth formers present their results to the who audience and this is followed by an "Any Questions" session with clinical and non-clinical experts answering questions from the visitors.

The Open Day has now been run on three occasions and each time has received universal acclaim from visitors. The report is also made available on our web site.
Year(s) Of Engagement Activity 2008
 
Description Many media interviews TV, Radio, Newspapers, Radio 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Primary Audience Public/other audiences
Results and Impact Many media interviews TV, Radio, Newspapers, Radio

Legislation modified
Year(s) Of Engagement Activity 2008
 
Description Multi-site Phosphorylation Assays for Tau Protein and their relevance to Alzheimer's disease and other neurological disorders 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Primary Audience Participants in your research and patient groups
Results and Impact Poster presentation at American Society of Mass Spectrometry conference

None
Year(s) Of Engagement Activity 2008
 
Description Patient and Carers meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Primary Audience Participants in your research and patient groups
Results and Impact Each meeting has 40-60 attendees and lasts 1.5 hours with talk and questions

Patients have come to our laboratory open day and are actively fundraising to create a studentship
Year(s) Of Engagement Activity 2006,2007,2008,2009,2010
 
Description Patient and Carers meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Primary Audience Participants in your research and patient groups
Results and Impact 40-60 Patients and Carers lasting 1.5 hours of talk and discussion

Members of the audience are fundraising for a studentship for my laboratory
Year(s) Of Engagement Activity 2006,2007,2008,2009,2010
 
Description Presented to Members of Parliament 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Primary Audience Policymakers/politicians
Results and Impact Presented to parliamentary parties

Legeislation changed
Year(s) Of Engagement Activity 2008
 
Description Public Lecture to Aotea Centre, Auckland New Zealand 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Lecture on motor neuron disease therapies to lay audience
Year(s) Of Engagement Activity 2018
 
Description Public lecture 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Public lecture on the genetics and biology of motor neuron disease
Year(s) Of Engagement Activity 2016
 
Description Public lecture on motor neuron disease research 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact I spoke at a dinner hosted by the MND Association for major donors at the Royal Institution
Year(s) Of Engagement Activity 2016
 
Description Review of Dementia Research Institute at King's 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Talk on the Dementia Research activity at Kings
Year(s) Of Engagement Activity 2018
 
Description School visit Peterborough 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Primary Audience Schools
Results and Impact Lectured to school students and informal chat

Enthusiastic discussion
Year(s) Of Engagement Activity 2006
 
Description Simon Topp's participation in MNDA fundraiser outreach - Promoting the research done at KCL in the field of Amyotrophic Lateral Sclerosis, to representatives from the UK's primary Motor Neurone Disease charity 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact A group of fundraisers (primarily consisting of spouses, children, and friends of patients) from the Motor Neurone Disease Association charity visited KCL and met with researchers in small groups, with the aim of discovering more about the research work done here on MND (Amyotrophic Lateral Sclerosis). I gave a 10 minute presentation to 8 groups in succession on the use of Whole Exome Sequencing to discover new genes causative for MND/ALS, and highlighted how KCL had been closely involved in the discovery of 10 of the 45 genes identified to date, averaging over one per year for the last 6 years. This event was recent and as yet there has been no formal feedback, but responses on the day were very positive.
Year(s) Of Engagement Activity 2018
 
Description Sleep and circadian rhythm disorder in Parkinson's Disease: association with hallucinations 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Primary Audience Participants in your research and patient groups
Results and Impact A world conference on sleep.

Received a citation award.
Year(s) Of Engagement Activity 2007
 
Description The Use of Mass Spectrometry for Multi-site Phosphorylation Assays for Tau Protein 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Primary Audience Participants in your research and patient groups
Results and Impact Poster presentation at International Conference on Alzheimer's Disease, Chicago

None
Year(s) Of Engagement Activity 2008