Genomics of Brain Disorders 18 - 20 March 2020 ABSTRACT BOOK ABSTRACT 2020 CONFERENCES COURSES Evolutionary Systems Biology LABORATORY COURSES LECTURE/DISCUSSION COURSES 12-14 February Genomics and Clinical Microbiology Clinical Genomics: Fundamentals of Optimmunize: Improving the beneficial 19-24 January Variant Interpretation in Clinical Practice effects of vaccines NEW Genomics and Clinical Virology 29-31 January 19-21 February 23–28 February Genomic Practice for Genetic Counsellors Single Cell Biology Genetic Engineering of Mammalian 3-5 February 11-13 March Stem Cells Practical Aspects of Small Molecule Genomics of Brain Disorders 15–27 March Drug Discovery 18-20 March Next Generation Sequencing 21-26 June Genomics of Rare Diseases 20–27 April Evolutionary Biology and Ecology 25-27 March Low Input Epigenomics NEW of Cancer Proteomics in Cell Biology and 12-20 May 29 June-3 July Disease Mechanisms RNA Transcriptomics Science Policy: Improving the 30 March-1 April 17-26 June Uptake of Research into UK Policy Longitudinal Studies Single Cell Technologies and Analysis 19-21 August 20-22 April 24-31 July Genomics for Dermatology Nursing, Genomics and Healthcare NEW Molecular Pathology and 25-27 November 27-29 April Diagnosis of Cancer OVERSEAS COURSES Antimicrobial Resistance - Genome 22-27 November Next Generation Big Data and Emerging Technologies Derivation and Culture of Human 4-6 May Sequencing Bioinformatics Induced Pluripotent Stem Cells (hiPSCs) 19-24 January (Chile) Curating the Clinical Genome 14-18 December 20-22 May 9-14 February (Malaysia) Healthy Ageing COMPUTATIONAL COURSES Molecular Approaches to Clinical 27-29 May Mathematical Models for Infectious Microbiology in Africa 21-27 March (The Gambia) Genomic Epidemiology of Malaria Disease Dynamics 7-10 June 24 February-6 March Genomics and Epidemiological Surveillance of Bacterial Pathogens Virus Genomics and Evolution Fungal Pathogen Genomics 19-24 April (Paraguay) 15-17 June 11-16 May Reproducibility, Replicability and Trust Summer School in Bioinformatics Working with Pathogen Genomes in Science NEW 22-26 June 10-15 May (Vietnam) 9-11 September Systems Biology: From Large Viral Genomics and Bioinformatics Genome Informatics Datasets to Biological Insight 7-12 June (Uruguay) 14-17 September 6-10 July Antimicrobial Resistance of CRISPR and beyond: perturbations at Genetic Analysis of Mendelian Bacterial Pathogens scale to understand genomes and Complex Disorders 27 September-3 October (Kenya) 15-21 July 23-25 September Malaria Experimental Genetics Proteomics Bioinformatics Genomic Imprinting - from Biology 8-13 November (The Gambia) to Disease NEW 26-31 July 28-30 September Genetic Analysis of Practical Aspects of Drug Discovery Exploring Human Host-Microbiome Population-based Association Studies 29 November-4 December (Uruguay) Interactions in Health and Disease 21-25 September 21-23 October Working with Protozoan Parasite ONLINE COURSES Database Resources Bacterial Genomes - 4 courses 4-9 October Genetic Counselling - 1 course Next Generation Please see our website for more details Sequencing Bioinformatics and scheduling of online courses 18-24 October Computational Systems Biology for Complex Human Disease NEW 6-11 December
@ACSCevents wellcomegenomecampus.org/coursesandconferences
WGC_Courses_and_Conferences_2020-Abstract-Books(Blue-FullColour)december2019.indd 1 03/12/2019 11:08:04 Name:
Genomics of Brain Disorders 2020
Wellcome Genome Campus Conference Centre, Hinxton, Cambridge, UK 18-20 March 2020
Scientific Programme Committee:
Kristen Brennand Icahn School of Medicine at Mount Sinai, USA
Alison Goate Icahn School of Medicine at Mount Sinai, USA
Michael Owen Cardiff University, UK
Mina Ryten UCL, UK
Tweet about it: #GBD20
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Scientific Programme Committee
Kristen Brennand Alison Goate Icahn School of Medicine at Mount Sinai, USA Icahn School of Medicine at Mount Sinai, USA
Michael Owen Mina Ryten Cardiff University, UK UCL, UK
Wellcome Genome Campus Scientific Conferences Team:
Jemma Hume Nicole Schatlowski Conference and Events Scientific Programme Organiser Officer
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Dear colleague,
I would like to offer you a warm welcome to Genomics of Brain Disorders 2020. I hope you will find the talks interesting and stimulating, and find opportunities for meeting colleagues, making new connections and form new and exciting collaborations throughout your time here with us.
The conference is organised by Wellcome Genome Campus Advanced Courses and Scientific Conferences (ACSC), which is run on a not-for-profit basis, funded by the Wellcome Trust. ACSC funds, develop and deliver training and conferences that span basic research, cutting-edge biomedicine, and the application of genomics in healthcare. Our scientific programme committees, speakers and instructors are world-renowned scientists and clinicians. We run ~60 events each year attracting up to 3,500 people, from ~130 countries to the Campus.
Our programme includes a range of conferences and laboratory-, computational - and discussion- based courses, providing hands-on training in the latest biomedical techniques for research scientists, clinicians and healthcare professionals. We also organise invitation-only retreats for high-level discussion on emerging science, technologies and strategic direction for select groups and policy makers. To enable everyone to benefit from the revolution in genomic medicine, we have recently introduced an online courses programme to provide training across the globe for free. To find out more about our programme, please visit: https://coursesandconferences.wellcomegenomecampus.org/
We also have a strong commitment to equality, diversity and inclusion across the programme. We provide funding to support childcare, or extra costs for dependants, while attending a conference or course. There is also a family room for parents, to accommodate feeding and napping. Delegates can stay involved in the conference, as the talks will be live-streamed into this room. To further promote a culture of inclusion and equal representation at our conferences, we ensure that 50% or our programme committees, session chairs and invited speakers are women. We also work with our programme committees to invite speakers from a range of countries. To read more about our policies, please visit: https://coursesandconferences.wellcomegenomecampus.org/about-us/policies/
The conference team are here to help this meeting run smoothly, and at least one member will be at the registration desk between sessions, so please do come and speak with us if you have any queries.
Finally, enjoy the conference.
Best wishes,
Dr Rebecca Twells Head of Advanced Courses and Scientific Conferences [email protected]
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General Information
Conference Badges Please wear your name badge at all times to promote networking and to assist staff in identifying you.
Scientific Session Protocol Photography, audio or video recording of the scientific sessions, including poster session is not permitted.
Social Media Policy To encourage the open communication of science, we would like to support the use of social media at this year’s conference. Please use the conference hashtag #GBD20. You will be notified at the start of a talk if a speaker does not wish their talk to be open. For posters, please check with the presenter to obtain permission.
Internet Access Wifi access instructions: Join the ‘ConferenceGuest’ network Enter your name and email address to register Click ‘continue’ – this will provide a few minutes of wifi access and send an email to the registered email address Open the registration email, follow the link ‘click here’ and confirm the address is valid Enjoy seven days’ free internet access! Repeat these steps on up to 5 devices to link them to your registered email address
Presentations Please provide an electronic copy of your talk to a member of the AV team who will be based in the meeting room.
Poster Sessions Posters will be displayed throughout the conference. Please display your poster in the Conference Centre on arrival. There will be two poster sessions during the conference.
Odd number poster assignments will be presenting in poster session 1, which takes place on Wednesday, 18 March at 18:00 – 19:30.
Even number poster assignments will be presenting in poster session 2, which takes place on Thursday, 19 March at 18:00 – 19:30.
The page number of your abstract in the abstract book indicates your assigned poster board number. An index of poster numbers appears in the back of this book.
Conference Meals and Social Events Lunch and dinner will be served in the Hall, apart from on Lunch on Wednesday, 18 March when it will be served in the Conference Centre alongside registration. Please refer to the conference programme in this book as times will vary based on the daily scientific presentations. Please note there are no lunch or dinner facilities available outside of the conference times.
All conference meals and social events are for registered delegates. Please inform the conference organiser if you are unable to attend the conference dinner.
The Hall Bar (cash bar) will be open from 19:00 – 23:00 each day.
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Dietary Requirements If you have advised us of any dietary requirements, you will find a coloured dot on your badge. Please make yourself known to the catering team and they will assist you with your meal request.
If you have a gluten or nut allergy, we are unable to guarantee the non-presence of gluten or nuts in dishes, even if they are not used as a direct ingredient. This is due to gluten and nut ingredients being used in the kitchen.
For Wellcome Genome Campus Conference Centre Guests Check in If you are staying on site at the Wellcome Genome Campus Conference Centre, you may check into your bedroom from 14:00. The Conference Centre reception is open 24 hours.
Breakfast Your breakfast will be served in the Hall restaurant from 07:30 – 09:00.
Telephone If you are staying on-site and would like to use the telephone in your room, you will need to contact the Reception desk (Ext. 5000) to have your phone line activated – they will require your credit card details to do so.
Departures You must vacate your room by 10:00 on the day of your departure. Please ask at reception for assistance with luggage storage in the Conference Centre.
Taxis Please find a list of local taxi numbers on our website. The conference centre reception will also be happy to book a taxi on your behalf.
Return Ground Transport Complimentary departure transport from the Conference Centre has been arranged on Friday, 20 March at the following times:
12:45 to Stansted and Heathrow airports. 13:00 to Cambridge train station and city centre (Downing Street).
A sign-up sheet will be available at the conference registration desk from 15:20 on Wednesday, 18 March until Thursday, 19 March. Please note that places are limited and will be allocated on a first come first served basis.
Please allow a 30-40 minute journey time to both Cambridge and Stansted Airport, and two and a half hours to Heathrow.
Messages and Miscellaneous Lockers are located outside the Conference Centre toilets and are free of charge.
All messages will be available for collection from the registration desk in the Conference Centre.
A variety of toiletry and stationery items are available for purchase at the Conference Centre reception. Cards for our self-service laundry are also available.
Certificate of Attendance A certificate of attendance can be provided. Please request one from the conference organiser based at the registration desk.
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Contact numbers Wellcome Genome Campus Conference Centre – 01223 495000 (or Ext. 5000) Wellcome Genome Campus Conference Organiser (Jemma) – 07473934631
If you have any queries or comments, please do not hesitate to contact a member of staff who will be pleased to help you.
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Conference Summary
Wednesday, 10 March 11:45 – 13:00 Registration with buffet lunch 13:00 – 13:10 Welcome and introduction 13:10 – 14:10 Keynote lecture Michael Owen, Cardiff University, UK 14:10 – 15:35 Session 1: Systems Biology 15:35 – 15:50 Afternoon tea 15:50 – 17:20 Session 2: Modelling disease 17:20 – 18:00 Lightning Talks 18:00 – 19:30 Drinks reception and poster session 1 (odd numbers) 19:30 Dinner
Thursday, 19 March 09:00 – 10:30 Session 3: Tools 10:30 – 11:00 Morning coffee 11:00 – 12:30 Session 4: Population studies 12:30 – 14:00 Lunch 14:00 – 15:30 Session 5: Genetic architecture 15:45 – 16:15 Afternoon tea 16:15 – 17:30 Session 6: Delivery of genomic results 17:30 – 18:00 Drinks reception and poster session 2 (even numbers) 19:30 Dinner
Friday, 20 March 09:00 – 10:00 Keynote lecture: Naomi Wray, University of Queensland, Australia 10:00 – 10:30 Morning coffee 10:30 – 12:30 Session 7: Using genomics to drive therapeutics 12:30 – 12:40 Closing remarks 12:40 Lunch 12:45 Coach departs to London Heathrow airport via London Stansted airport 13:00 Coach departs to Cambridge train station and city centre (Downing Street)
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Hold your own meeting at the Wellcome Genome Campus Conference Centre
The Conference Centre hosts hundreds of one-day and residential meetings for biomedical sector clients each year, and offers preferential rates to organisers from this sector.
Facilities: • 300-seat auditorium with all the latest • On-site accommodation: 134 modern and audiovisual capabilities comfortable bedrooms • 8 distinctive meeting rooms with flexible • Outdoor space for team building activities set-up options for groups of 2-120 people and BBQs in summer • Large naturally-lit exhibition space with bar • Complimentary parking for 180 cars and • 300-seat restaurant bike rack We would love to welcome you and your delegates to our venue at the heart of life-changing science.
We chose the conference facility for the beautiful surrounds, the professionalism of the staff, the high quality of the venue itself and the“ amazing wow factor. Health Enterprise East Innovation” Showcase
To enquire or to book a show round please call the Sales team on 01223 495123 or email [email protected] www.wellcomegenomecampus.org/conferencecentre
WGC CC abstract book ad final.indd 1 12/12/2019 15:26 Conference Sponsors
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Genomics of Brain Disorders
Wellcome Genome Campus Conference Centre, Hinxton, Cambridge
18 – 20 March 2020
Lectures to be held in the Francis Crick Auditorium Lunch and dinner to be held in the Hall Restaurant Poster sessions to be held in the Conference Centre
Spoken presentations - If you are an invited speaker, or your abstract has been selected for a spoken presentation, please give an electronic version of your talk to the AV technician.
Poster presentations – If your abstract has been selected for a poster, please display this in the Conference Centre on arrival.
Conference programme
Wednesday, 18 March
11:45-13:00 Registration with lunch
13:00-13:10 Welcome and introductions Alison Goate
13:10-14:10 Keynote lecture The nature of schizophrenia Michael Owen Cardiff University, UK Chair: Alison Goate
14:10-15:35 Session 1: Systems Biology Chair: Alison Goate
14:10 CRISPR-based functional genomics for brain diseases Martin Kampmann University of California, San Francisco, USA
14:50 The role of neuroinflammation in Parkinson’s disease Caleb Webber University of Oxford, UK
15:20 Genetic Identification of Cell Types Underlying Brain Complex Traits Yields Novel Insights Into the Etiology of Parkinson’s Disease Nathan Skene Imperial College London, UK
15:35-15:50 Afternoon Tea
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15:50-17:20 Session 2: Modelling disease Chair: Kristen Brennand
15:50 A Collaborative Study of Tauopathy in 3D from the Tau Consortium Stem Cell Group Sally Temple Neural Stem Cell Institute, USA
16:20 Understanding the contribution of cortical interneuron dysfunction in schizophrenia Beatriz Rico Kings College London, UK
16:50 Population-scale profiling of dopaminergic neuron development Julie Jerber Wellcome Sanger Institute, UK
17:05 The effects of the 15q11.2 BP1-BP2 copy number variant on white matter microstructure Ana Silva Cardiff University, UK
17:20-18:00 Lightning talks Chair: Michael Owen
18:00-19:30 Poster session 1 (odd numbers) with drinks reception
19:30 Buffet dinner
19:30 Cash bar
Thursday, 19 March
09:00-10:30 Session 3: Tools (single cells, proteomics, metabolomics, spacial transcriptomics) Chair: Kristen Brennand
09:00 Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction Anat Kreimer UC Berkeley, USA
09.30 In vivo Perturb-seq: Study gene function at scale in developing tissues Xin Jin Harvard University, USA
10.00 Cell type and cortex-specific RNA editing in single human neurons informs neuropsychiatric disorders Melanie Bahlo Walter and Eliza Hall Institute, Australia
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10.15 Dysregulation of splicing in human brain from individuals with Lewy body disease informs disease mechanisms Regina Reynolds University College London, UK
10:30-11:00 Morning coffee
11:00-12:30 Session 4: Population Studies Chair: Michael Owen
11:00 Mendelian randomization combining GWAS and eQTL data reveals genetic determinants of complex and clinical traits Eleonora Porcu University of Lausanne, Switzerland
11:30 Genetic risk loci and polygenic architecture of ADHD Ditte Demontis Aarhus University, Denmark
12:00 Gene-environment interaction study suggests significant interaction between gestational age at birth and genetic risk for psychiatric disease on cognition at age four Harriet Cullen Kings College London, UK
12:15 Investigating Causality of Environmental and Lifestyle Risk Factors Associated with Parkinson's Disease: A Mendelian Randomization Study Carmen Domínguez Brigham and Women's Hospital, USA
12:30-14:00 Lunch
14:00-15:45 Session 5: Genetic Architecture Chair: Michael Owen
14:00 The genetic architecture of Parkinson’s disease Andy Singleton NIH, USA
14:30 How might the genetic contribution to major depressive disorder inform diagnosis, course and treatment? Cathryn Lewis Kings College London, UK
15:00 Analysis of neurodevelopmental de novo risk alleles in schizophrenia Elliott Rees Cardiff University, UK
15:15 Exploring the phenome-wide consequences of Anorexia Nervosa associated genes Jessica Johnson Icahn School of Medicine at Mount Sinai, USA
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15:30 Human-lineage-specific genomic elements are present at high density within genes implicated in neurodegenerative diseases and are enriched for heritability of intelligence Zhongbo Chen UCL Institute of Neurology, UK
15:45-16:15 Afternoon tea
16:15-17:30 Session 6: Delivery of genomic results Chair: Mina Ryten
16:15 Your DNA Your Say: global public attitudes towards genomic data sharing Anna Middleton Wellcome Genome Campus, UK
16:45 Title TBC Tonu Esko University of Tartu Pärnu College, Estonia
17.15 Results of genetic testing in adult patients with psychiatric disorders and intellectual disability or cognitive regression Anneke Kievit Erasmus MC Rotterdam, The Netherlands
17:30-18:00 Lightning talks Chair: Alison Goate
18:00-19:30 Poster session 2 (even numbers) with drinks reception
19:30 prompt Silver service conference dinner
19:30 Cash Bar
Friday, 20 March
09:00-10:00 Keynote lecture Will genetic risk prediction be useful in psychiatry and neurology? Naomi Wray University of Queensland, Australia Chair: Mina Ryten
10:00-10:30 Morning coffee
10:30-12:30 Session 7: Using genomics to drive therapeutics Chair: Mina Ryten
10:30 Stress granules as therapeutic targets in neurodegeneration Stefan Aigner UC San Diego School of Medicine, USA
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11:00 Using human genetics to discover new medicines Jeff Barrett Genomics plc, UK
11:30 Genome-wide meta-analysis, fine-mapping, and integrative prioritization identify new Alzheimer’s disease risk genes Jeremy Schwartzentruber EBML-EBI, UK
11:45 Discussion
12:30 Closing remarks Michael Owen
12:40 Lunch
12:45 Coaches depart to Heathrow Airport via Stansted Airport
13:00 Coaches depart to Cambridge Train Station and Cambridge City Centre
The following abstracts should not be cited in bibliographies. Materials contained herein should be treated as personal communication and should be cited as such only with consent of the author.
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Spoken Presentations
The Nature of Schizophrenia. Michael J Owen
MRC Centre for Neuropsychiatric Genetics and Genomics, and Division of Psychological Medicine and Clinical Neurosciences, Cardiff University. Schizophrenia is a severe and frequently disabling psychiatric condition that is highly heritable. Multiple environmental risk factors have also been implicated including a number that impact on the developing brain. Recent genomic studies have begun to reveal the complex and highly polygenic genetic architecture of schizophrenia and to identify specific risk alleles across the frequency spectrum. Despite this complexity, and the fact that much of the genetic risk remains unaccounted for, the emerging picture is instructive in several ways. First, extensive pleiotropy with other psychiatric disorders reminds us that current syndromic diagnostic categories do not define biologically distinct disorders and that mechanistic and aetiological research will require different approaches to phenotype definition. Second, the pattern of pleiotropic relationships with other conditions supports the view that schizophrenia is fundamentally a neurodevelopmental disorder and that there is a continuum of outcomes from disrupted brain development, which includes not just schizophrenia but also childhood neurodevelopmental disorders, such as intellectual disability, autism and attention-deficit- hyperactivity- disorder. Third, the genes implicated in schizophrenia converge onto sets of plausible biological processes. In particular, the data point to synaptic function and implicate mechanisms involved in plasticity that are important in development and in learning and cognition. While these are almost certainly not the only processes involved, they provide robust entry points for clinical and basic neuroscience research. Finally, genomic findings are beginning to solve the evolutionary puzzle of how a heritable disorder that is associated with quite markedly reduced reproductive success is maintained in the population.
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CRISPR-based functional genomics for brain diseases Martin Kampmann University of California, San Francisco, USA Human genes associated with brain-related diseases are being discovered at an accelerating pace. A major challenge is the identification of the mechanisms through which these genes act, and of potential therapeutic strategies. To elucidate such mechanisms in human cells, we established a CRISPR-based platform for genetic screening in human iPSC-derived neurons, astrocytes and microglia. Our approach relies on CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa), in which a catalytically dead version of the bacterial Cas9 protein recruits transcriptional repressors or activators, respectively, to endogenous genes to control their expression, as directed by a small guide RNA (sgRNA). Complex libraries of sgRNAs enable us to conduct genome-wide or focused loss-of-function and gain-of-function screens. Such screens uncover molecular players for phenotypes based on survival, stress resistance, fluorescent phenotypes, high-content imaging and single-cell RNA-Seq. To uncover disease mechanisms and therapeutic targets, we are conducting genetic modifier screens for disease-relevant cellular phenotypes in patient-derived neurons and glia with familial mutations and isogenic controls. In a genome- wide screen, we have uncovered genes that modulate the formation of disease-associated aggregates of tau in neurons with a tauopathy-linked mutation (MAPT V337M). CRISPRi/a can also be used to model and functionally evaluate disease-associated changes in gene expression, such as those caused by eQTLs, haploinsufficiency, or disease states of brain cells. We will discuss an application to Alzheimer’s Disease-associated genes in microglia.
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The role of neuroinflammation in Parkinson’s disease Caleb Webber UK Dementia Research Institute @Cardiff, UK The role of neuroinflammation in Parkinson’s disease has been the subject of growing interest, particularly given the prominent role in other neurodegenerative diseases. Here, I will present results identifying the specific cell types within the Substantia nigra through which the common genetic risk of Parkinson’s likely manifests. I will then turn to several deeply and longitudinally phenotyped Parkinson’s cohorts and derive a small number of universal continuous axes of patient phenotypic variation. These phenotypic axes reveal that the genetic variation influencing PD progression appears quite distinct to that which influences PD risk. These new results propose that disease prevention and disease modification may require very different strategies.
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Genetic Identification of Cell Types Underlying Brain Complex Traits Yields Novel Insights Into the Etiology of Parkinson’s Disease
Nathan Skene†, Julien Bryois1†, Nathan G.Skene2,3,4†, Thomas Folkmann Hansen5,6,7, LisetteKogelman5, Hunna J.Watson8,Zijing Liu4,Eating Disorders Working Group of the Psychiatric Genomics Consortium, International Headache Genetics Consortium, 23andMeResearch Team9,Leo Brueggeman10, Gerome Breen11,12, CynthiaM.Bulik1,8,13, Ernest Arenas2, Jens Hjerling-Leffler2*,Patrick F.Sullivan1,14* († = co-first authors)
1 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177 Stockholm, Sweden 2 Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden 3 UCL Institute of Neurology, Queen Square, London, UK 4 Division of Brain Sciences, Department of Medicine, Imperial College, London, UK 5 Danish Headache Center, Dept. of Neurology, Copenhagen University Hospital, Glostrup, Denmar 6 Institute of Biological Psychiatry, Copenhagen University Hospital MHC Sct. Hans, Roskilde, Denmark 7 Novo Nordic Foundations Center for Protein Research, Copenhagen University, Denmark. 8 Department of Psychiatry, University of North Carolina at Chapel Hill, North Carolina, US 9 23andMe, Inc., Mountain View, CA, 94041, USA 10 epartment of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa. 11 nstitute of Psychiatry, MRC Social, Genetic andDevelopmental Psychiatry Centre, King’s College London, UK 12 ational Institute for Health Research Biomedical Research Centre, South London and Maudsley National Health Service Trust, London, UK 13 epartment of Nutrition, University of North Carolina, Chapel Hill, NC, 27599-7264, USA 14 Departments of Genetics, University of North Carolina, Chapel Hill, NC, 27599-7264, USA
Genome-wide association studies (GWAS) have discovered hundreds of loci associated withcomplexbrain disorders, and provide the best current insights into the etiology of these idiopathic traits. However, it remains unclear in which cell types thesevariants are active, which is essential for understanding etiology and subsequent experimental modeling. Here we integrate GWAS results with single-cell transcriptomic data from the entire mouse nervous system to systematically identify cell types underlying psychiatric disorders, neurological diseases, and brain complex traits. We show that psychiatric disorders are predominantly associated with cortical and hippocampal excitatory neurons, as well as medium spiny neurons from the striatum. Cognitive traits were generally associated with similar cell types but their associations were driven by different genes. Neurological diseases were associated with different cell types, which is consistent with other lines of evidence. Notably, we found that Parkinson's disease is not only genetically associated with cholinergic and monoaminergic neurons (which include dopaminergic neurons fromthe substantia nigra) but also with neurons from the enteric system and oligodendrocytes. Using post-mortem brain transcriptomic data, we confirmed alterations in these cells, even at the earliest stages of disease progression. Our study provides an important framework for understanding the cellular basis of complex brain maladies,and reveals an unexpected role of oligodendrocytes in Parkinson's disease.
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A Collaborative Study of Tauopathy in 3D from the Tau Consortium Stem Cell Group Sally Temple PhD Scientific Director, Neural Stem Cell Institute, One Discovery Prive, Rensselaer NY 12144 Identifying early cellular and molecular changes associated with tauopathies could provide novel targets for early intervention to slow disease progression. Tauopathies are associated with synapse loss, neuronal and glial cell death, tau aggregation, and tau hyperphosphorylation, but which pathways lead to these neurodegenerative events are not fully resolved. Working with several clinical centers participating in longitudinal studies of families carrying MAPT mutations that are associated with frontotemporal dementia (FTD), we have helped establish an extensive collection of iPSC lines and isogenic controls. Our goal is to characterize the impact of these mutations by creating 3D models of human forebrain, then broadly phenotyping the organoids to understand the timecourse of development of mutation- associated changes. We established large-scale 3D cerebral cortical organoid production at our core facility Neuracell and shipped thousands of organoids covering several MAPT mutations with isogenic controls in triplicate to six labs engaged in the Tau Consortium that are specialized in different aspects of tau biology. By centralizing organoid production, findings from each lab can be compiled and compared, providing opportunities for independent data reproduction and data complementation. Using studies examining tau proteaforms, isoforms, turnover, histology, as well as transcriptomic approaches and live imaging, we have demonstrated phenotypic changes associated with neurodegenerative disease and changes that may contribute to early phases of the disease process.
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Understanding the contribution of cortical interneuron dysfunction in schizophrenia
Beatriz Rico King's College London, UK
The pathophysiology of schizophrenia remains poorly understood, but defects in cortical interneurons -primarily in Parvalbumin-expressing (PV+) interneurons- are among the most replicated neuropathological findings. In addition, functional studies in humans have shown gamma oscillatory activity is abnormal in schizophrenia patients. We have shown that reducing the normal complement of excitatory synapses received by PV+ interneurons through the specific deletion of the tyrosine kinase receptor ErbB4 from these cells in a genetic mouse model also increases cortical excitability, impairs gamma oscillations and disrupts cognitive function. This later finding sparked a recent series of studies that confirmed that ErbB4 also seems to be required for the maturation of excitatory synapses onto PV+ interneurons in primates. Consistently, changes in ERBB4 splicing have been associated with a reduction in the number of excitatory synapses received by PV+ interneurons in schizophrenia patients. Collectively, these findings suggest that the disruption of excitatory inputs to PV+ interneurons is a plausible pathological mechanism in schizophrenia. Since work in rodents have demonstrated that PV+ interneurons are required for gamma oscillations, these findings reinforce the notion that PV+ interneurons are central to the disease process in schizophrenia.
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Population-scale profiling of dopaminergic neuron development
Julie Jerber1, 2, Julie Jerber1,2, Daniel Seaton3, Anna Cuomo3, Natsuhiko Kumasaka2, James Haldane2, Juliette Steer2, Daniel Pearce2, Madeline Lancaster4, Marc Jan Bonder3, Edward Mountjoy1, Florian Merkle5, Oliver Stegle6,7, Daniel Gaffney2
1 Open Targets, Wellcome Genome Campus, Hinxton, UK 2 Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK 3 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK 4 MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom. 5 WT-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK 6 European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany 7 Division of Computational Genomics and Systems Genetic, German Cancer Research Center, 69120 Heidelberg, Germany One of the biggest challenges in biology is to identify molecular and cellular mechanisms that contribute to human disease. They are often cell type specific and in the case of common genetic disorders also influenced by lifestyle, environmental exposure, and genetic factors. IPS cell lines are a promising system for modelling the function of human genetic variation as they provide a controlled experimental platform in cell types relevant to the studied trait. However, complex IPS cell differentiation protocols in particular have been challenging to scale to the size required to allow for passing the effects of common genetic variants. Here, we address this using a high-throughput system with a multiplexed design, where lines from different donors are pooled at the iPSCs stage and differentiated to a neuronal dopaminergic fate, the cell type preferentially lost in Parkinson disease. We profile over 1 million cells from 215 IPS cell lines across three differentiation stages and following stimulation with rotenone using single-cell RNA sequencing. We first show that cells generated within the modelled disease process are highly heterogeneous and we confidently identified 8 major cell types. We found that cell line differentiation outcomes are highly variable between cell lines but consistent across repeated differentiations of the same line including in other neuronal protocols. This suggests that much of the variability in differentiation outcomes is due to cell line intrinsic factors rather than batch to batch differentiation variability. We identify robust molecular markers in pluripotent cells that can be used to predict neuronal cell fate. Furthermore, we mapped thousands of expression quantitative trait loci (eQTLs) that influence expression dynamically during differentiation, allowing us to quantify the effects of disease risk alleles on gene expression, across multiple cell types, time points, and stress conditions. Our work will guide future efforts to develop iPSC-based approaches to model and treat neuronal disorders and provide a unique resource for assessing the effect of common genetic variants in different states of neuronal development.
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The effects of the 15q11.2 BP1-BP2 copy number variant on white matter microstructure
Ana Silva1, Josephine E. Haddon1, Simon Trent1, Yasir Ahmed Syed1, Magnus O Ulfarsson2, Hreinn Stefansson2, Omar Gustafsson2, G Bragi Walters2, David E. J. Linden1, Michael J. Owen1, Jeremy Hall1, Lawrence S. Wilkinson1
1-Neuroscience and Mental Health Research Institute, Hadyn Ellis Building, Cathays, Cardiff, CF24 4HQ 2-deCODE genetics/Amgen, Sturlugata 8, IS-101 Reykjavik, Iceland
Altered white matter has been consistently reported in neurodevelopmental disorders. A key question is whether genetic risk variants that are associated with neurodevelopmental disorders, are also associated with white matter changes. The 15q11.2 BP1-BP2 copy number variant (CNV) has been associated with several neurodevelopmental disorders, including autism spectrum disorders and schizophrenia. Our aim is to identify cellular changes underlying white matter effects at this chromosomal region. To this end, we first used diffusion tensor imaging (DTI) to explore the impact of 15q11.2 BP1-BP2 CNV on white matter microstructure. Clinically healthy deletion (n=30) and duplication (n=27) carriers were compared to controls (n=19) with no neuropsychiatric CNVs, recruited from a large genotyped population sample from Iceland. This study showed a reciprocal effect of 15q11.2 BP1-BP2 CNV dosage on white matter microstructure. In unpublished findings, we have confirmed this phenotype in a bigger and more genetically diverse population using UK Biobank data (n=54 deletion and n=55 duplication carriers, and n=15663 controls). The cytoplasmic FMR1 interacting protein 1 (CYFIP1), a gene in this region, is involved in two complexes, known to regulate actin cytoskeleton dynamics and protein translation - mechanisms that are crucial in white matter dynamics. To investigate the possible contribution of CYFIP1 to the phenotype seen in 15q11.2 BP1-BP2 deletion carriers, we created a novel CRISPR-engineered Cyfip1-heterozygous (Cyfip1+/-) rat model. Using DTI (n=12 wild-type (WT) and 12 Cyfip1+/- rats), we revealed widespread white matter abnormalities in Cyfip1+/- rats. To investigate the cellular nature of these changes we used transmission electron microscopy (TEM) in a new cohort (n=5 WT and 4 Cyfip1+/- rats). These analyses revealed a thinning of the myelin sheath in the corpus callosum, where no differences were found in the number of unmyelinated and myelinated axons, nor in axon diameter. Immunofluorescence techniques further revealed a reduction of mature oligodendrocytes, the specific cell-type that produces myelin, in Cyfip1+/- rats. We then used cell culture to look at the specific effects of Cyfip1 haploinsufficiency on oligodendrocyte function. Mature oligodendrocytes, generated from Cyfip1+/- neonatal pups, showed an aberrant intracellular distribution of myelin basic protein (MBP), a key protein in myelination. Forthcoming experiments, using in-situ hybridisation to target MBP mRNA, will allow us to investigate how Cyfip1 affects MBP distribution in oligodendrocytes.
These findings suggest that Cyfip1 haploinsufficiency affects myelination, providing insight into the contribution made by low dosage of CYFIP1 to the 15q11.2 BP1-BP2 deletion phenotype.
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Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction
Anat Kreimer UC Berkeley and UCSF, USA
Epigenomic regulation and lineage-specific gene expression act in concert to drive cellular differentiation, but the temporal interplay between these processes is largely unknown. Using neural induction from human pluripotent stem cells (hPSCs) as a paradigm, we interrogated these dynamics by performing RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and assay for transposase accessible chromatin using sequencing (ATAC-seq) at seven time points during early neural differentiation. We found that changes in DNA accessibility precede H3K27ac, which is followed by gene expression changes. Using massively parallel reporter assays (MPRAs) to test the activity of 2,464 candidate regulatory sequences at all seven time points, we show that many of these sequences have temporal activity patterns that correlate with their respective cell-endogenous gene expression and chromatin changes. A prioritization method incorporating all genomic and MPRA data further identified key transcription factors involved in driving neural fate. These results provide a comprehensive resource of genes and regulatory elements that orchestrate neural induction and illuminate temporal frameworks during differentiation.
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In vivo Perturb-seq: Study gene function at scale in developing tissues
Xin Jin Harvard University, USA
The thousands of disease risk genes and loci identified through human genetic studies far outstrip our current capacity to systematically study their functions. I will discuss our attempt to develop a scalable genetic screen approach, in vivo Perturb-Seq, and apply this method to the functional evaluation of 35 autism spectrum disorder (ASD) de novo loss-of-function risk genes. Using CRISPR-Cas9, we introduced frameshift mutations in these risk genes in pools, within the developing brain in utero, and then performed single-cell RNA-Seq in the postnatal brain. We identified recurrent and cell type-specific gene signatures from both neuronal and glial cell classes that are affected by genetic perturbations, and pointed at elements of both convergent and divergent cellular effects across many ASD risk genes. In vivo Perturb-Seq pilots a systems genetics approach to investigate at scale how diverse mutations affect cell types and states in the developing brain, and can be used in various in vivo and in vitro model organisms and systems.
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Cell type and cortex-specific RNA editing in single human neurons informs neuropsychiatric disorders
Melanie Bahlo, Brendan Robert E. Ansell 1 , Simon N. Thomas 1 , Jacob E. Munro 1 , Saskia Freytag 2 , Melanie Bahlo 1.
1. The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia. 2. Molecular Medicine Division, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
Conversion of adenosine to inosine in RNA by ADAR enzymes occurs at thousands of sites in the human transcriptome and is essential for healthy brain development. This process, known as 'RNA editing', is dysregulated in many neuropsychiatric diseases, but is little understood at the level of individual neurons. We examined full-length nuclear transcriptomes of 3,055 neurons from six cortical regions of a neurotypical post-mortem female donor and identified 40,861 high-confidence edited sites. The majority of sites were located within Alu repeats in introns or 3' UTRs and were present in previously published RNA editing databases. We identified 15,784 putative novel RNA editing sites, 30% of which were also detectable in independently generated neuronal transcriptomes from unrelated donors. The strongest correlates of global editing rates were expression levels of small nucleolar RNAs from the SNORD115 and SNORD116 cluster (15q11), known to modulate serotonin receptor processing and to colocalize with ADAR2, one of three known RNA editing enzymes in humans. As expected, expression of DNA and RNA binding proteins were negatively associated with editing. We present evidence for dysregulated RNA editing in six rare genetic conditions; and report 117 differentially edited sites between cortical regions and neuronal subtypes. These results provide spatial and neurophenotypic context for 1,871 and 998 sites that are differentially edited in the brains of 24 schizophrenic and autistic patients respectively and a reference for future studies of RNA editing in single brain cells from these cohorts.
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Dysregulation of splicing in human brain from individuals with Lewy body disease informs disease mechanisms
Regina H Reynolds, Rahel Feleke, Amy Smith, Bension Tilley, John Hardy, Paul Matthews, Steve Gentleman, David Owen, Michael Johnson, Prashant Srivastava, Mina Ryten
1. Department of Neurodegenerative Disease, University College London 2. Department of Brain Sciences, Imperial College London 3. UK Dementia Research Institute at Imperial College London 4. UK Dementia Research Institute at University College London 5. National Heart & Lung Institute, Imperial College London
Dysregulation of splicing is an important contributor to complex disease risk, with evidence to suggest that it may harbour more disease risk than variation in expression. Nevertheless, splicing remains understudied in many complex disorders, including the Lewy body diseases (Parkinson's disease (PD), Parkinson's disease dementia (PDD) and dementia with Lewy bodies (DLB)), which together affect an estimated 6% of the population over 65 and for which no disease-modifying therapies exist. To address this gap, we applied bulk-tissue and single-nucleus RNA-sequencing to anterior cingulate cortex samples derived from 28 individuals, including healthy controls, PD, PDD and DLB cases (n = 7 per group). This pairing permitted identification of major cell-type classes, including less prevalent cell types such as endothelial cells; estimation of bulk-tissue cell-type abundances, which are known to change in disease; and finally, in-depth splicing analyses. We found significant increases in the proportions of non-neuronal cell types, including endothelial cells, microglia, oligodendrocyte precursor cells and pericytes, across most disease groups. In addition, we found that differential splicing was more robust to changes in cell-type abundance, with a loss of only 25% of differentially spliced intron clusters (found in at least one disease group) post correction, compared to a loss of 98% of differentially expressed genes. Of those intron clusters found differentially spliced, they overlapped genes that were primarily enriched in non-neuronal cell types, such as oligodendrocytes. Furthermore, we found that 24% of genes associated with PD (mendelian and sporadic) intersected with one or more differentially spliced intron clusters. These results demonstrate the importance of splicing in Lewy body diseases, particularly in non-neuronal cell types.
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MENDELIAN RANDOMIZATION INTEGRATING GWAS AND EQTL DATA REVEALS GENETIC DETERMINANTS OF COMPLEX AND CLINICAL TRAITS
Eleonora PORCU1,2, Kaido LEPIK2,3,4, Sina RUEGER2,3, eQTLGen Consortium, Federico A. SANTONI5, Alexandre REYMOND1, Zoltán KUTALIK2,3
1 Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
2 Swiss Institute of Bioinformatics, Lausanne Switzerland
3 Institute of Social and Preventive Medicine, CHUV and University of Lausanne, Switzerland
4 Institute of Computer Science, University of Tartu, Tartu, Estonia
5 Endocrine, Diabetes, and Metabolism Service, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne 1011, Switzerland
Correspondence to: [email protected]
Interpretation of GWAS results is challenging, as most of the associated variants fall into regulatory regions and overlap with expression-QTLs (eQTLs), indicating their potential involvement in gene expression regulation.
To address this challenge, we propose an advanced transcriptome-wide summary statistics- based Mendelian Randomization approach (called TWMR) that uses multiple SNPs jointly as instruments and multiple gene expression traits as exposures, simultaneously. When applied to 43 human phenotypes it uncovered 2,369 genes whose blood expression is putatively associated with at least one phenotype resulting in 3,913 gene-trait associations; of note, 36% of them had no genome-wide significant SNP nearby in previous GWAS analysis. Using independent association summary statistics (UKBiobank), we confirmed that the majority of these loci were missed by conventional GWAS due to power issues. Noteworthy among these novel links is educational attainment-associated BSCL2, known to carry mutations leading to a mendelian form of encephalopathy. We similarly unraveled novel pleiotropic causal effects suggestive of mechanistic connections, e.g. the shared genetic effects of GSDMB in rheumatoid arthritis, ulcerative colitis and Crohn's disease. We then explored whether sex-specific eQTLs lead to sex-specific complex trait association and conversely if sex-specific trait associations were due to sex-specific eQTLs or sex- specific causal effects. In summary, our advanced Mendelian Randomization unlocks hidden value from published GWAS through higher power in detecting associations. It better accounts for pleiotropy and unravels new biological mechanisms underlying complex and clinical traits.
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Genetic risk loci and polygenic architecture of ADHD
Ditte Demontis, 23andMe Research Team, the iPSYCH-Broad Consortium
Attention-deficit hyperactivity disorder (ADHD) is a highly heritable childhood psychiatric disorder affecting 5% of school-age children and 3% of adults. In our recent genome-wide association study (GWAS) meta-analysis of 20,183 ADHD cases and 35,191 controls we identified 12 genome-wide significant risk loci for ADHD, which revealed new and exciting information about the biology of the disorder.
Here we will present results from our updated GWAS meta-analysis of ADHD including 25,000 clinically ascertained and 96,000 self-reported ADHD cases and 900,000 controls. We identified 85 genome-wide significant loci implicating new interesting genes informing about the biological mechanisms involved in ADHD.
While increasing sample size for ADHD highlights new risk loci for general ADHD risk, heterogeneity exist in the ADHD phenotype, and genetic analyses of more homogenous case groups could reveal further insight into the genetic architecture of the disorder. Not all children diagnosed with ADHD will demonstrate symptoms as adults as approximately two third will continue to experience ADHD symptoms during adulthood referred to as persistent ADHD, while some individuals are not diagnosed with ADHD before adulthood. However, the extent to which the genetic architecture differs depending on age at first diagnosis is not known. Here we will also report results from a comprehensive analysis of the genetic architecture of childhood, persistent and late diagnosed ADHD in the Danish iPSYCH cohort. We identified significant increased polygenic risk load for ADHD risk variants in individuals with persistent ADHD compared to childhood and late diagnosed ADHD. Genetic correlation analyses demonstrated several interesting differences among the groups including lower genetic correlation with ADHD symptoms (impulsivity and inattention) for late diagnosed ADHD than observed for childhood and persistent ADHD. This suggests that late diagnosis to some extent is caused by biological factors that predispose late diagnosed individuals to be less inattentive and less impulsive compared to childhood ADHD. Overall our results suggest that the polygenic architecture of childhood, persistent and late diagnosed ADHD to some extent differ.
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Gene-environment interaction study suggests significant interaction between gestational age at birth and genetic risk for psychiatric disease on cognition at age four
Harriet Cullen (1), Saskia Selzam (2), Robert Plomin (2), A David Edward (1)
(1) Centre for the Developing Brain, Kings College, London, SE1 7EH, United Kingdom, (2) Institute of Psychiatry, Psychology and Neuroscience, Kings College London, SE5 8AF, United Kingdom,
Genome-wide association studies have identified many genetic variants associated with an increased risk of psychiatric disease. However, how these genetic effects are modulated by the environmental stress of preterm birth has not been investigated. Here, we test for an interaction effect between psychiatric polygenic risk and gestational age at birth (GA) on cognition at age four.
Our sample comprises 4934 unrelated individuals from the longitudinal Twins Early Development Study. 2066 of these individuals were born at less than 37 weeks gestation and 562 were born at less than 34 weeks gestation, (normal term gestation is 37 weeks or more). Genome-wide polygenic scores (GPSs) were calculated for each individual for five different psychiatric pathologies: Schizophrenia, Bipolar Disorder, Major Depressive Disorder, Attention Deficit Hyperactivity Disorder and Autism Spectrum Disorder using the software LDpred.
We used linear regression modelling to estimate the interaction effect between psychiatric GPS and GA on cognitive outcome for each of the five psychiatric disorders. Each model was adjusted for the covariates: gender, social economic status, ten ancestry principle components and genotype chip and plate. Interaction terms between GA and GPS and the covariates gender and social economic status were additionally included in the model to control for possible confounding. P-values lower than the significance level alpha = 0.05/5 = 0.01 were considered significant to account for the family-wise error rate using the Bonferroni method (five psychiatric disorders examined).
We found a significant interaction effect between Schizophrenia GPS and GA (beta= 0.038, se= 0.014, p= 0.0068) and Bipolar Disorder GPS and GA (beta = 0.039, se= 0.014, p = 0.0052) on cognitive outcome. Individuals with greater genetic risk for Schizophrenia or Bipolar Disorder are more vulnerable to the environmental stress of preterm birth, as assessed by cognition at four. Better understanding of gene-environment interactions will inform more effective risk-reducing interventions in the future.
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Investigating Causality of Environmental and Lifestyle Risk Factors Associated with Parkinson's Disease: A Mendelian Randomization Study.
Carmen Domínguez-Baleón(1), Miguel E. Rentería(2), Xianjun Dong(1), Clemens Scherzer(1)
(1) Neurogenomics Laboratory and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA. (2)Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, QLD 4006, Australia
1. Objective Epidemiological studies have been useful in determining associations between environmental factors and Parkinson's disease (PD), but causality of potentially protective or risk factors still remains to be established. The aim of this project is to determine the causal relationship between 6 traits related to 3 phenotypes of interest (Smoking, Alcohol drinking and Years of education) and Parkinson's disease using a Mendelian Randomization approach.
2. Methods Two-sample MR was undertaken using genome-wide association studies (GWAs) summary statistics data. Inverse-variance weighted (IVW) and GSMR methods were implemented to obtain the causal estimates between each of the 6 exposures and PD, while MR-Egger and MRPRESSO methods were used to test for pleiotropy. Heterogeneity between variants was evaluated using Cochran's Q and I2 statistic, and further verified by funnel plots.
3. Results Alcohol drinking, measured by drinks per week, shows a protective effect over PD (OR = 0.78; 95% CI 0.66-0.9; p=0.000), in which the variant rs1229984 on the Alcohol dehydrogenase 1B (ADH1B) locus, known to be involved in alcohol dependence, is driving this association. Individuals who are current smokers have a lower risk of PD when compared to former smokers (OR = 0.52; 95% CI 0.044-1; p=0.008), although pleiotropy may be underlying this effect. In the case of years of education, contrasting results were obtained by different methods, IVW showed a positive association (OR= 1.29; 95% CI 1.07- 1.51; p=0.023) while MR-Egger a negative association (OR=0.29; 95% CI -0.75-1.33; p=0.02), making it difficult to derive any conclusion about the causal effect of years of education over PD.
4. Conclusions Mendelian Randomization results show that Alcohol drinking has a protective effect over PD risk, with the novel finding that ADH1B might be driving this association, although the mechanism behind it remains to be studied. On the other hand, MR supports the hypothesis of smoking being a protective factor, but only in the case of current smokers being compared to former smokers. Lastly, the causal effect of years of education over PD could not be determined.
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The genetic architecture of Parkinson’s disease
Andrew Singleton National Institute on Aging
Over the last twenty years our understanding of the genetic basis of Parkinson’s disease has evolved considerably. In this talk I will discuss the most recent progress in this regard, highlighting the results of work aimed at identifying novel risk loci and understanding the genetic basis of disease related traits. I will highlight the most immediate downstream interpretations of these data, related to functional consequences of risk variability and the use of existing data to place genetics in the appropriate cellular context. In addition to using genetic data to understand etiology I will discuss the application of genetics to informing risk prediction and the use of multi-modal data in predicting progression. Lastly I will discuss the future path for genetic investigation in Parkinson’s disease, highlighting the planned work of the Global Parkinson’s Genetics Program.
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How might the genetic contribution to major depressive disorder inform diagnosis, course and treatment? Cathryn Lewis, for the Psychiatric Genomics Consortium Major Depressive Disorder Working group. More than 300 million people suffer from depression worldwide. The disorder comprises 7.5% of all years lived with disability in 2015, and it is the main contributor to deaths by suicide, yet our understanding of its pathophysiology is weak. Genetic studies of depression have been challenging to perform because of the high life-time risk (~15%) and the low heritability (~40%), but recent studies have started to identify associated variants in genome- wide association studies. In this talk I will describe our current knowledge of the genomic underpinnings of major depressive disorder (MDD) and show how these findings have increased our understanding of the disorder as a brain disease. Our recent Psychiatric Genomics Consortium (PGC) studies of MDD have identified 44 associated loci [Wray et al., 2018], expanding to 102 loci with a broadening of the criteria used to define MDD cases [Howard et al. 2019]. These successful studies required 100k – 250k depression cases to be analysed, demonstrating the highly polygenic nature of depression. The PGC results show that with a sufficiently large sample size, the genomic underpinnings of depression can be identified, but the results also raise intriguing questions of diagnostic specificity. For example, how does the genetics of MDD as a clinical disorder overlap with depression symptoms at a population level? Is the heterogeneity of depression partially genetically determined? And could genetics help us improve treatment response in depression? My talk will address these and other questions.
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Analysis of neurodevelopmental de novo risk alleles in schizophrenia
Elliott Rees, Andrew Pocklington, George Kirov, Peter Holmans, James Walters, Michael Owen, Michael O’Donovan
MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
Background Exome sequencing studies have identified de novo variants in individual genes, such as SETD1A and SLC6A1, as important risk factors for schizophrenia. More broadly, de novo variants in schizophrenia are enriched among genes associated with early-onset neurodevelopmental disorders, such as developmental disorders (DD) and autism spectrum disorders (ASD). However, the size of published de novo studies and the low per-base mutation rate has precluded researchers from testing whether the same de novo alleles confer risk to both schizophrenia and DD/ASD or whether different alleles confer risk in the two groups of disorders. In the current study, we used de novo data from a large DD study (31K trios) and 6,430 ASD trios to evaluate whether specific DD/ASD de novo alleles were enriched for de novo variants in 3,444 schizophrenia trios. We hypothesised that DD/ASD de novo alleles would be associated with schizophrenia only in genes associated with neurodevelopmental disorders (n=299 genes). Methods The expected number of DD/ASD de novo alleles in 3,444 schizophrenia trios was estimated using tri-nucleotide mutation rates. A Poisson Exact test was used to compare observed and expected rates of de novo variation. The burden of DD/ASD de novo alleles in schizophrenia was also evaluated using exome-sequencing data from 4,079 cases and 5,712 controls. Results In the 3,444 schizophrenia trios, nonsynonymous DD/ASD de novo alleles were significantly enriched among 299 neurodevelopmental disorder genes (7 observed, 0.98 expected; P=7.5 x 10-5). No enrichment was observed for nonsynonymous DD/ASD de novo alleles in the remaining 19,568 genes (8 observed, 7.27 expected; P = 0.7). An enrichment of DD/ASD de novo alleles in the 299 neurodevelopmental disorder genes was observed for both missense (4 observed, 0.7 expected, P = 0.006) and LoF (3 observed, 0.29 expected, P=0.0032) alleles. The rate of LoF ASD/DD de novo alleles was significantly greater in independent schizophrenia cases compared with population matched controls (P=0.0039; odds ratio (95% CI) = 8.3 (1.9-78.2)). Discussion Previous research has shown rare CNVs associated with DD/ASD also increase risk for schizophrenia. We exploited data from as large exome-sequencing study of DD to extend these findings to coding de novo variants, by showing pathogenic de novo alleles are also shared between DD/ASD and schizophrenia. Our work identifies specific alleles in NOTCH1, SLC6A1, SCN2A, CSNK2A1, AUTS2, NF1 and KMT2D as novel risk factors for schizophrenia, and provides further support for a shared genetic basis between DD/ASD and schizophrenia.
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Exploring the phenome-wide consequences of Anorexia Nervosa associated genes
Jessica Johnson, MPH (1), Amanda Dobbyn, PhD (1); Alanna C. Cote (1); Weiqing Wang (1); Liam Cotter (1); Alex Charney, PhD, MD (1,2) ; PGC-ED; Eli Stahl (1), PhD; Cynthia M. Bulik (3,4), PhD, Laura M. Huckins, PhD (1,2)
(1) Pamela Sklar Division of Psychiatric Genetics, Icahn School of Medicine at Mount Sinai, NYC, NY, USA; (2) James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA (3) Department of Psychiatry, University of North Carolina at Chapel Hill, NC, USA (4) Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
Background: Anorexia nervosa (AN) is a complex psychiatric disorder and, despite the severity of the disease, little is known about its etiology. The Eating Disorders Working Group of the Psychiatric Genomics Consortium (PGC-ED) recently published the largest GWAS of AN (NCases = 16,992), which identified 8 genome-wide significant loci. Patient symptomatology, GWAS, TI, and microbiota studies suggest brain- and gastrointestinal AN-etiology. Therefore, we applied transcriptomic imputation (TI) methods to translate PGC-ED GWAS findings into higher-order biology (genetically regulated gene expression, GReX), and performed PheWAS using Mount Sinai BioMe data to test the clinical consequences of aberrant expression of these genes.
Methods: We performed TI using S-PrediXcan on the latest PGC-ED GWAS summary statistics across 50 tissues (GTEx; CMC; DGN predictor models), and tested for association with AN case-control status (Bonferroni-corrected threshold: pExperiment<3.75e-08; ptissue<1.88e-06). For ptissue significant genes, we imputed GReX in the Mount Sinai BioMe Biobank (N=31,633), and ran a PheWAS testing for association with 1,700 clinical outcomes (including phecodes, OBGYN, medical history, allergies, and vital signs; self-reported family history and socio-behavioural factors). Analyses were run separately across six ancestry-defined cohorts and meta-analysed using an inverse-variance approach in METAL. We required at least 10 instances of a diagnosis per cohort for inclusion.
Results: We identified 2 loci reaching experiment-wide significance (pExperiment<3.75e-08), and a further 10 reaching tissue-specific significance (ptissue<1.88e-06). These include what is, to our knowledge, the first MHC association for AN (CLIC1-Tibial Nerve, p=1.47e-06). Our S-PrediXcan identified 47 unique genes for PheWAS follow-up. These were associated with phecodes for gastrointestinal and autoimmune disorders, (type 1 diabetes, peptic ulcer, and celiac disease; p<1.06x10-6); alcohol abuse and tobacco use (SEMA3F-DLPFC, p=1.35e-24; ARIH2-Amygdala, p=3.84e-38); endophenotypes of AN such as irregular menstruation (ASB3-Esophagus_mucosa, p=1.35e-05), and anthropometric phenotypes including adult lifetime highest and lowest weight (USP19-DLPFC, 2.18e-04 ;CLIC1-Spleen, 8.76e-05, respectively).
Discussion and Future Work: Translating GWAS findings into tissue-specific gene expression can elucidate biological mechanisms and functional pathways to disease etiology. Future work will focus on fine-mapping AN-GReX loci to disentangle these gene-tissue signals and identify specific pathways contributing to AN symptomatology. PheWAS allows us to study the clinical consequences of AN-GReX. We find that AN-genes are independently associated with commonly comorbid traits and AN-endophenotypes, even among individuals who do not have the disease itself. Future work will probe the tissue- and sex-specificity of our PheWAS associations, and the clinical impact of these genes conditioned on healthy and unhealthy psychiatric and BMI phenotypes.
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Human-lineage-specific genomic elements are present at high density within genes implicated in neurodegenerative diseases and are enriched for heritability of intelligence
Zhongbo Chen (1), David Zhang(1), Regina H. Reynolds (1), John Hardy (1), Juan Botía (1, 2), Sarah Gagliano (3), Mina Ryten (1)
1. Department of Neurodegenerative Diseases, Queen Square Institute of Neurology, University College London, UK, WC1N 3BG 2. Departamento de Ingeniería de la Información y las Comunicaciones. Universidad de Murcia, 30100, Murcia, Spain 3. Center for Statistical Genetics and Department of Biostatistics, University of Michigan, Ann Arbor, 48109-2029, Michigan, USA
While telencephalization has had obvious advantages for Homo sapiens, this process may also have predisposed humans to specific neurological and psychiatric diseases. This view is supported by the observation that some common forms of neurodegeneration, including Alzheimer's and Parkinson's diseases do not occur in other species, including aged non- human primates, indicating that these may be exclusively human conditions. This suggests that knowledge of the genomic features specific to the human lineage may provide insights into a range of brain-related diseases.
In this study, we leverage high-depth whole genome sequencing data and improved conservation metrics to generate a combined annotation to simultaneously identify regions that are relatively depleted for genetic variation (constrained regions) and have low conservation (non-conserved regions) across primates at ten base pair resolution. We propose that these regions, which we term constrained-non-conserved regions (CNCRs), have been subject to human-specific purifying selection and are enriched for brain-specific elements and related risk loci for nervous system diseases.
We find that CNCRs are significantly enriched within long non-coding RNAs but are relatively depleted from protein coding genes. Furthermore, we find that CNCR enrichment is a feature of genes with known central nervous system-specific functions and that CNCRs are enriched for per-SNP heritability of complex human-specific phenotypes, namely intelligence (stratified linkage disequilibrium score coefficient p-value = 1.4 x 10-3). We specifically identify CNCR enrichment in genes already implicated in neurological disease, including SOD1, NKX6-2 and APOE. Focusing on the latter, we identify high CNCR density within intron-3 of APOE and provide additional support for an APOE intron-3 retaining transcript, which is not currently within annotation, but which has been previously reported to regulate neuronal APOE. We confirm the existence of this transcript using targeted reverse transcription-PCR and oligonucleotide probe pull-down of polyA-selected RNA extracted from human hippocampal tissue. Finally, using publicly-available short-read RNA- sequencing data, we quantify the intron-3 retention event across human brain tissues, disease states, and APOE-allele status.
Thus, we generate a robust and highly-granular annotation that provides evidence for the importance of human-lineage-specific sequences in brain development and complex neurological phenotypes with implications for disease modelling and interpretation of non- coding variants in genetic association studies.
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Your DNA Your Say: global public attitudes towards genomic data sharing Anna Middleton Head of Society and Ethics Research, Wellcome Genome Campus, Cambridge Public acceptance is critical for sharing of genomic data at scale. This presentation examines how acceptance of data sharing pertains to the perceived similarities and differences between DNA and other forms of personal data. It explores the perceptions of a global public audience (n = 36,268) from 22 low, middle and high income countries in 15 languages towards willingness to donate DNA and medical information for research. First we examine how the willingness to donate one’s DNA and health data is correlated to an individual’s familiarity with genomics. Familiarity relates to knowledge, but is broader in terms of capturing individuals’ experience with and exposure to genetics and genomics, whether through popular culture or through personal encounters with genetic research or genetic medicine. We then consider the extent to which willingness to donate DNA and health data is correlated to participants viewing DNA as being distinct or different from other forms of information about an individual and their health. We conclude with recommendations for the delivery of genomic medicine. More information can be gained from www.wgc.org.uk/ethicsa
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Tonu Esko University of Tartu Pärnu College, Estonia
Abstract unavailable at the time of printing
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Results of genetic testing in adult patients with psychiatric disorders and intellectual disability or cognitive regression
Anneke J.A. Kievit (1), Merel W. de Vries (2), Femke A.T. de Vries (1), Marjon A. van Slegenhorst (1), Steven A. Kushner (2)
Department of Clinical Genetics (1), Department of Psychiatry (2), ErasmusMC Rotterdam, the Netherlands
Introduction There is a strong genetic component underlying the risk for developing psychiatric disorders, but the genetic architecture is complex. Highly penetrant genetic variations are rare, but recent findings suggest an increased prevalence of pathogenic variants in phenotypically-defined high risk subgroups of patients with psychatric disease. We recently demonstrated that pathogenic copy number variations are present in nearly a quarter of patients with syndromic forms of psychiatric disorder, most prominently associated with facial dysmorphisms, congenital malformations and intellectual disability. Patients and methods We studied a cohort of 100 adult outpatients with intellectual disability or cognitive regression and psychiatric disorders, who were referred by neurologists, psychiatrists, intelectual disability physicians and general practitioners for diagnostic testing and genetic counseling. Written informed consent was obtained from each patient or their legal representative. We performed clinical genetic testing, including metabolic screening, SNP-array and if these tests were negative, whole exome sequencing, in addition to dysmorphological- and neurological examination, and comprehensive medical record review. Results We will present the clinical findings of the patients and the results of genetic testing, with a diagnostic yield of more than 50%. In particular, we will highlight several pathogenic or likely pathogenic findings, including variants in CHD8, SETD1B, MYT1L, MAGEL2, and NBEA, as well as several copy number variations with established associations to psychiatric disorders. Conclusion Our findings confirm a broad spectrum of rare genetic variation in association with psychiatric disorders, for which the diagnostic yield of genetic testing in patients with psychiatric disorders co-morbid with intellectual disability or cognitive regression is particularly high. We also discuss the importance of obtaining a genetic diagnosis for optimizing clinical care and genetic counseling of patients and relatives.
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Will genetic risk prediction be useful in psychiatry and neurology? Naomi R Wray Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia The last decade has demonstrated that common diseases, including common psychiatric and common neurological diseases, are polygenic. In spite of this complexity, it is now possible to use genetic data to make a predictor of risk of disease. The so-called polygenic risk scores (PRS) can be calculated for many diseases from a single saliva or blood sample using genotyping technologies that are inexpensive (< $100/per person). These risk scores, by definition, are far from accurate. By definition, firstly because the genetic contribution to complex disease risk only explains part of the risk, and second because the risk scores can only track part of the genetic contribution. Despite these limitations, studies are already taking shape to evaluate the utility of PRS in clinical practice for diseases where lifestyle risk predictors and population screening already exist (e.g. heart disease, eye disease and cancers). While public acceptance of PRS is expected to be more challenging for disorders of the brain than other common diseases, clinical applications of PRS to psychiatric and neurological disorders are already under discussion. Moreover, commercial genotyping is now available to the public from a number of private companies at low cost by mailing off a spit sample. Once an individual has received their genome-wide information and perhaps commercial PRS, it is simple to upload the genotype data into online calculators and download PRS scores for many common disorders. Hence, a patient (or parent of a patient) attending a consultation may come armed with their own, commercially derived PRS – are these useful or not? I will review some of the underlying PRS methodology considering their applications in examples of disorders of the brain, since there is not a one-size-fits-all solution. At face value, the utility of PRS can seem underwhelming. A “glass half-empty” perspective is understandable, because fortunately there is no genetic determinism for complex disease, and it is important not to oversell or overhype the contribution PRS can make. However, I will encourage a “glass half-full” perspective. For decades, researchers have tried to identify biomarkers for psychiatric and neurological disorders that could be “the” diagnostic test akin to the fasting blood sugar test for diabetes or electrocardiogram for heart arrhythmia. Perhaps for the first time in psychiatric and neurological applications, PRS provide a strong foundation on which to build more accurate evidence-based risk predictors, as used routinely in other complex diseases.
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Stefan Aigner University of California, San Diego, USA
Abstract unavailable at time of printing.
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Using human genetics to discover new medicines
Jeff Barrett Genomics plc, UK
Assimilation and analysis of masses of biomedical data is transforming our understanding of human biology. Genomic data is a key to inferring processes that initiate and shape disease progression. It can be used to help develop safe, and specific interventions, and to identify individuals who would potentially benefit most from them. We have assembled, harmonized and imputed >15,000 GWAS summary statistics datasets on molecular and cellular phenotypes, biomarkers, physiological and cognitive quantitative traits, and disease outcomes. We have used a model-based clustering method in a non-parametric Bayesian framework to simultaneously analyse all of these data, and identify groups of traits that share the same causal variant at a given location in the genome (i.e. ‘colocalize’).
I will describe how we use this powerful joint analysis to discover new genetic risk factors, identify causal variants, and reveal shared biology. These insights help us prioritise new potential drug targets. By precisely defining which studies are affected by which variants we learn more about mechanisms, additional indications, biomarkers, and safety risks. I will also describe how we are integrating additional functional data and rare variant sequencing data to complement our approach.
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Genome-wide meta-analysis, fine-mapping, and integrative prioritization identify new Alzheimer’s disease risk genes
Jeremy Schwartzentruber, Sarah Cooper, Jimmy Liu, Inigo Barrio-Hernandez, Erica Bello, Natsuhiko Kumasaka, Toby Johnson, Karol Estrada, Daniel J. Gaffney, Pedro Beltrao, Andrew Bassett
1. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Genome Campus, Cambridge, UK 2. Open Targets, Wellcome Genome Campus, Cambridge, UK 3. Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK 4. Biogen, Cambridge, MA, 02142, USA 5. Target Sciences-R&D, GSK Medicines Research Centre, Stevenage, UK 6. BioMarin Pharmaceutical, San Rafael, CA 94901, USA 7. Genomics Plc, Oxford, OX1 1JD, UK
Genome-wide association studies (GWAS) have discovered numerous genomic loci associated with Alzheimer's disease (AD), yet the causal genes and variants remain incompletely identified. We performed an updated genome-wide AD meta-analysis, which identified 37 risk loci, including novel associations near genes CCDC6, TSPAN14, NCK2, and SPRED2. Using three SNP-level fine-mapping methods, we identified 21 SNPs with greater than 50% probability each of being causally involved in AD risk, and others strongly suggested by functional annotation. We followed this with colocalisation analyses across 109 gene expression quantitative trait loci (eQTL) datasets, and prioritization of genes using protein interaction networks and tissue-specific expression. Combining this information into a quantitative score, we find that evidence converges on likely causal genes, including the above four genes, and those at previously discovered AD loci including BIN1, APH1B, PTK2B, PILRA, and CASS4.
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Poster Presentations
The molecular mechanism underlying EHMT1 regulation of REST in neurodevelopment via suppression of miRNAs-dependent REST
Mouhamed Alsaqati, Adrian Harwood
Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, CF24 4HQ, UK
Disrupted epigenetic regulation is a feature of a number of neurodevelopment disorders (NDDs). EHMT1 silences gene expression via catalysing dimethylation of histone H3 lysine 9 (H3K9me2). Haploinsufficiency of EHMT1 gene causes Kleefstra Syndrome (KS), a NDD characterized by delayed psychomotor development, variable intellectual disability and mild dysmorphic features. REST/NRSF is a transcription factor, which represses neuronal gene transcription in non-neuronal cells. While the epigenetic roles of both EHMT1 and REST/NRSF are well established, the interplay between these genes during neurodevelopment is poorly understood. The aim of the current study is to investigate the influence of altering EHMT1 activity on the expression of REST/NRSF and the neurodevelopment using human iPSCs-derived neuronal models. hiPSs line was used for all experiments. hiPSCs were differentiated into cortical neurons following a protocol adapted from Chambers et al. 2009. The level of REST was determined by immunoblotting using appropriate specific antibody (Abcam). Levels of the neuronal markers and REST-target genes were quantified by RT-qPCR (Qiagen). EHMT1 activity was modulated by UNC0638, a histone methyltransferase (HMT) inhibitor, or by RNA-guided CRISPR/Cas9. Chromatin immunoprecipitation (ChIP)-qRT-PCR was performed with three targets within REST promoter and three around REST-regulated miRNAs transcription start sites (TSSs). High-throughput miRNA sequencing was performed to determine the differentially expressed miRNAs in EHMT1-/+ cells. In hiPSCs, suppression of EHMT1 activity down-regulated the expression of REST protein. During neuron differentiation, knocking-down EHMT1 activity was associated with a reduction in the expression of REST, an elevation in the expression of lineage-specific REST-target genes and an accelerated neuronal differentiation. When EHMT1 activity was suppressed, we detected a significant elevation in the expression of a number of miRNAs- regulated REST. ChIP-qRT-PCR analysis showed that whilst regions around REST promoter were not modified by H3k9me2, REST-regulated miRNA regions were occupied by H3k9me2. In EHMT1 knocked-down iPSCs-derived neurons, overexpressing REST reduced the levels of REST-target genes as well as the neuronal markers. The current data provide the first demonstration of a novel mechanism linking the phenotype observed in EHMT1-/+ to the reduction in the expression of REST protein in these cells. EHMT1 regulates REST via a mechanism involving suppression of REST-regulated miRNAs, rather than REST being a direct target gene of EHMT1. A number of EHMT1-/+- associated phenotypes are rescued by overexpressing REST, indicating the involvement of REST as a key element in this pathway. This approach may be applied to rescue the cellular phenotype in KS patient cells.
P1
Childhood trauma in psychosis: effects at the epigenetic level
Solveig Brunstad, Tatiana Polushina, Anne-Kristin Stavrum, Vidar Steen, Ingrid Melle, Stephanie Le Hellard
(1) NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (2) Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway (3) NORMENT, KG Jebsen Center for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Norway
Exposure to psychological trauma is a strong risk factor for developing psychosis. Childhood trauma (CT) is one of the best-studied factors, that has a strong link to an increased risk for developing a psychotic disorder.
Besides the impact on mental state and behaviour in the exposed individuals, it has been suggested that CT can affect the biology of the individuals and thought these biological mechanisms induce behavioural and psychological consequences. Epigenetic modification is one possible mechanism in response to traumatic events. Various studies showed that epigenetic modifications could occur in response to different type of trauma and stress. Recent studies support that exposure to trauma in childhood is associated with specific epigenetic modifications in those that develop a psychiatric disorder.
In our study, we address how epigenetic modifications (DNA methylation) can be implicated in psychotic disorders (bipolar disorders and schizophrenia), and how these modifications can be modulated by exposure to childhood trauma. We hypothesize that exposure to CT affects the DNA at the epigenetic level and that these modifications contribute to increasing the individual risk to develop a psychotic disorder later in life.
P2
Multiplexing brain organoids: longitudinal dissection at single cell resolution of developmental traits. N. Caporale, M.T. Rigoli, D. Castaldi, E.C. Villa, C. Cheroni, A. López-Tobón, S. Trattaro, E. Tenderini and G. Testa Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, 20139 Milan, Italy Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy Center for Neurogenomics, Human Technopole
Current neuropsychiatric research has the aim to map disease dynamics at molecular and single cell resolution, to unravel the complex interplay of polygenic and environmental causality. Emerging epidemiological studies are scaling up the measurements of human exposures. In parallel, human experimental models, such as brain organoids, allow multi- omics profiling of neurodevelopment, thus pushing towards the elucidation of gene- environment interactions in the human setting. However, there is still the need to functionally integrate disease dynamics through the experimental tractability of human genetic diversity across patterns of exposures. Here we address this need for endocrine disrupting chemicals (EDC), which accumulating evidence has associated to a major impact on human health. Despite their ubiquitous presence, the impact of similar EDC exposures varies substantially among individuals, pointing to a major genetic contribution to such vulnerability, thus making it a paradigmatic case for advancing the potential of induced pluripotent stem cells (iPSC)- derived brain organoids. Here we provide proof of principle for dissecting the disruptive events triggered by EDC on the physiological neurodevelopmental trajectories captured in 3D across multiple genetic backgrounds. Specifically, to tackle the limitations associated to technical variability, high costs and workload needed to differentiate organoids from multiple lines, we optimized two multiplexing strategies. In the first approach, which we term downstream multiplexing, we mixed brain organoid samples just before library preparation, increasing cost- effectiveness while reducing variability across libraries and sequencing runs. In the second approach, which we term upstream multiplexing, different pluripotent stem cell lines were mixed during organoid generation, yielding chimeric models that overcome also culture- associated variability. We used a bioinformatic pipeline that uses single nucleotide polymorphisms to deconvolute the identity of multiplexed lines and proved its applicability in both downstream and upstream settings. Along with the observation that such chimeric brain organoids preserve the morphological organization and transcriptomics signatures benchmarked in the individual lines-derived ones, we propose a new analytical framework, which we named eDTL (expression Developmental Trait Loci) to correlate the impact of genomic variants and/or environmental insults to the developmental trajectory analysed by single cell pseudotime. Our work establishes the feasibility of using organoids multiplexing and single cell transcriptomics for the simultaneous, cost-effective interrogation of the impact of real-life EDC exposures across different genotypes.
P3
Interrogating Parkinson’s disease associated mutations at single cell resolution
Elaine Guo Yan Chew 1,2, Yue Jing Heng 1,2, Michelle Lian 2, Moses Tandiono 2, Emma Thompson 3, Stefania Policicchio 3, Jonathan Mill 3,4, Richard Reynolds 5, Jia Nee Foo 1,2
1 -- Human Genetics, Genome Institute of Singapore, Singapore; 2 -- Genetics and Genomics of Neurological Diseases, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; 3 -- University of Exeter Medical School, University of Exeter, Exeter, UK; 4 -- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; 5 -- Division of Brain Sciences, Faculty of Medicine, Imperial College London, UK
Parkinson's disease (PD) is a common neurodegenerative movement disorder resulting from dopaminergic neuronal loss in the substantia nigra. As known germline PD variants only account for <10% of PD cases and explain a small percentage of PD risk, sporadic PD cases may be attributed to somatic mutations within brains of affected individuals. We aim to uncover potentially causative PD somatic mutations in post-mortem substantia nigra pars compacta (SNpc) tissues from sporadic PD patients with single cell DNA sequencing. We evaluated single NeuN+ nuclei isolation methods involving flow cytometry, microfluidics- based platforms such as Fluidigm C1 chips, and droplet-based platforms such as 10x Genomics Chromium for single cell genome partitioning. The flow cytometry based nuclei isolation method yielded the highest single nuclei recovery. We proceeded with whole genome library construction from flow cytometry isolated single nuclei and sequenced 15 single nuclei from the first brain sample as our first pilot dataset. Single nuclei were sequenced to mean coverage of 9.97x, with at least 5x coverage in approximately 43% of bases within autosomal chromosomes. We utilized the LiRA package for single nucleotide variation (SNV) calling and proceeded with identifying potential somatic SNV (sSNV) within each single nuclei. We observed 0-62 potential sSNV per single nuclei with a median of 1 sSNV found per single nuclei. We also identified 2 recurring sSNV in two nuclei each that were localized to non-coding regions. We utilized the CBS-based Gingko package for copy number variation (CNV) calling with fixed genomic windows from 50kb-1Mb and found genomic window of 500kb to be most suitable for the majority of single nuclei (9 out of 15 single nuclei). Copy number (CN) loss was more common than gain, with CN loss and gain between 1.2Mb-102.5Mb and 2.5Mb-180.5Mb in size, respectively. We identified 12 and 2 overlapping regions of CN loss and gain, respectively, which were not present in the bulk sample and are potentially somatic. We demonstrated both somatic SNV and CNV identification in our pilot PD patient SNpc. The potential application of this methodology for the identification of somatic variants in larger number of single nuclei across multiple patients is cost-prohibitive and inefficient. Existing high-throughput single cell DNA sequencing methods are challenging to apply on frozen postmortem tissues. Until suitable methods arise, high coverage bulk DNA sequencing approaches followed by targeted validation of potential PD-associated causative somatic mutations is the most feasible approach for identifying somatic variants in the brain.
P4
Association of Complement factor H Y402H in Pakistani major depressive patients
Mahnoor Ejaz, Aisha Hashmi, Maleeha Azam, Raheel Qamar
COMSATS University Islamabad Pakistan
Major Depressive Disorder (MDD) is a complex psychiatric condition which affects the neurovegetative functions leading to cognitive dysfunction, and is known to be the fourth leading cause of mental illness globally. A number of molecular mechanisms have been shown to be involved in MDD, of which Complement Factor H (CFH), an immune-regulatory gene controls the alternative pathway of complement cascade, preventing the lysis of healthy cells during a microbial attack. CFH genetic polymorphisms are known to possess risk for development of neurodegenerative and psychiatric disorders. In the current case- control association study CFH rs1061170 (Y402H) was screened in 118 MDD subjects and 150 controls and was genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Statistical analysis of CFH Y402H revealed no association under both the dominant/ recessive model, with risk allele C being at a higher frequency in controls than cases but showing no involvement of this SNP with MDD. Further, the gender wise comparison also revealed no significant association of Y402H in male and female gender with development of MDD. Serum profiling of MDD patients was done using ELISA which revealed that the CFH serum levels were significantly lower in patients with MDD compared to the control group. Homozygous CC risk genotype CFH levels were significantly lower in MDD patients compared to heterozygous CT and reference homozygous TT genotype showing a plausible CFH deficiency in individuals with depression. This is the first genetic study based on determining the role of CFH Y402H polymorphism in the manifestation of MDD in Pakistani population, where we found no association of this SNP with MDD possibly due to lower sample size or genetic heterogeneity within the Pakistani population, but the decreased CFH protein expression indicates that it has a role in development of Major depression.
P5
The real-world diagnostic and clinical utility of whole exome sequencing in a broad range of neurological disorders
Dhamidhu Eratne, Amy Schneider, Haloom Rafehi, Dennis Velakoulis, Patrick Kwan, Michael Fahey, Richard Leventer, Melanie Bahlo, Elly Lynch, Melissa Martyn, Sebastian Lunke, Belinda Chong, Dean Phelan, Elle Uebergang, Belinda Creighton, Heather Chalinor, Kirsty West, Adrienne Sexton, Yael Prawer, Yana Smagarinski, Anne Harbison, Anna Jarmolowicz, Nikki Gelfand, Tamar Saks, Tianxin Pan, Saul Mullen, Zornitza Stark, Ilias Goranitis, Zanfina A Delaney, Danny Liew, Clara L Gaff, Martin B Delatycki, Samuel F Berkovic
Melbourne Genomics & University of Melbourne, Melbourne, Australia
Aim: Complex neurologic and neurodegenerative disorders are often associated with diagnostic uncertainty and delay; this adds to stress and negative impacts on patients, families and the healthcare system. Our study aimed to investigate the utility of whole exome sequencing (WES) on diagnostic rate as well as wider impacts on clinical management, psychosocial and health economics outcomes.
Methods: We aimed to recruit patients from Victoria, Australia, with a range of neurologic disorders with onset less than 60 years (ataxia, dystonia, spastic paraplegia, Parkinson's disease, motor neurone disease, dementia and complex/not-otherwise-specified disease) via genetics clinics, where they would receive genetic counselling and follow up. Whole exome sequencing was performed with targeted analysis of specific genes for each condition. The primary outcome was the diagnostic rate in the entire cohort. Secondary outcomes were diagnostic rates in diagnostic subgroups, impacts of results (e.g. changes in management, psychological and social impacts for patients and families), and cost-effectiveness analyses.
Results: 247 patients were prospectively referred between August 2017 to September 2018. Of 206 potentially eligible patients, 161 were recruited with a median age of 52 years. 32 (20%) received a molecular diagnosis, 23 (14%) were uncertain (e.g. variant of uncertain significance; 17/23 (74%) of these deemed strong candidate/likely cause), and 106 (66%) were negative. Diagnostic rates were highest in spastic paraparesis (10/25, 40%), complex/not-otherwise-specified disease (9/38, 24%), ataxia (6/28, 21%), followed by Parkinson's disease (2/19, 11%), dementia (2/22, 9%), dystonia (2, 24%) and motor neurone disease (1/5, 20%). Impacts on management included relief with ending diagnostic odysseys, improving precision of genetic counselling, genetic testing options for family, more precise management plans referrals to specific services and supports, and often for patients looking in hindsight at many years of uncertainty, multiple opinions and investigations and so on, and the potential impact had they had a molecular diagnosis much earlier.
Conclusion: The success of recruitment reflects great interest and demand for genetic testing in complex neurologic disorders. Our findings are very encouraging, demonstrating a diagnostic rate of over 20%, which is consistent with emerging literature. Ongoing analysis of genomic, clinical management, psychosocial and health economic data will be presented and will help establish the place, promises and challenges of wider implementation of genomics in neurologic disorders.
P6
Leveraging transcriptomics to understand differential nuclear-mitochondrial correlation profiles across CNS regions
Aine Fairbrother-Browne, Aminah T Ali, Regina H Reynolds, Alan Hodgkinson, Mina Ryten
University College London, King's College London
Mitochondrial dysfunction contributes to the pathogenesis of many neurodegenerative diseases (ND) as mitochondria serve essential roles in neuronal function. The mitochondrial genome encodes a small number of core respiratory chain proteins, whereas the vast majority of these proteins, as well as proteins involved in key mitochondrial processes such as mtDNA transcription, are encoded by the nuclear genome. In light of this, this work aims to first establish a profile of nuclear-mitochondrial relationships in normal brain tissue, focusing on CNS regional differences. We will then test whether these relationships become perturbed under neurodegenerative disease states.
Using publicly available bulk RNA-seq data from the GTEx Consortium, we analysed gene expression correlations between nuclear genes expressed in all CNS regions (15,001) and protein-encoding mitochondrial genes (13) for each of the 12 available tissues (mean N=89). To understand what drives differential nuclear-mitochondrial correlation profiles across CNS regions, we investigated: 1) which nuclear-mitochondrial gene pairs showed strong correlations within each brain region, 2) which cell type markers were enriched in highly correlated nuclear-mitochondrial gene pairs, and 3) whether there were nuclear- mitochondrial gene pairs with highly variable or highly consistent regional correlations.
We observed that the distribution of nuclear-mitochondrial correlation values is CNS region- specific. While this might suggest specialised nuclear-mitochondrial interaction profiles in CNS regions, it is more likely to reflect regional differences in cell-specific densities. To evidence this, we found that within CNS regions, and most significantly within the basal ganglia, astrocytic marker genes were overrepresented in positively correlated nuclear- mitochondrial gene pairs, whereas neuronal marker genes were overrepresented in negative pairs.
Gene ontology analysis of nuclear genes with high or low variance in nuclear-mitochondrial correlations across the CNS supported this finding. There was enrichment for OXPHOS and mRNA processing terms amongst low variance nuclear-mitochondrial pairs. However, enriched terms amongst high variance nuclear-mitochondrial pairs were largely synaptic, and specifically post-synaptic. This indicates that there are region-specific nuclear- mitochondrial interactions within post-synaptic pathways.
Overall, we find that CNS regions exhibit unique nuclear-mitochondrial correlation profiles and that are driven by region-specific cell type composition.
P7
Molecular Neuropathology of HACE1-Deficiency
Fell C. W.1, 2 , Kokotović T.1, 2 , Lenartowicz E.1 , Nagy V.1, 2 1. Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), Vienna, Austria 2. Research Centre for Molecular Medicine (CeMM), Vienna, Austria
HACE1, encoding the HECT Domain and Ankyrin Repeat Containing E3 Ubiquitin Protein Ligase 1, has been of interest to biomedical research groups for its role in cancer, heart function and inflammation. Surprisingly, mutations in HACE1 have recently been shown to cause a rare autosomal recessive neurodevelopmental syndrome called Spastic Paraplegia and Psychomotor Retardation with or without Seizures (SPPRS; OMIM #616756). SPPRS is marked by global delay of developmental milestones, most prominent of which are intellectual disability (ID), hypotonia and ataxia. Magnetic resonance imaging (MRI) findings were variable among patients, but included enlarged ventricles, hypoplastic corpus callosum and atrophy of the cerebrum and brain stem. Guided by patient clinical descriptions, our group performed detailed phenotypic analyses of Hace1-deficient mice and SPPRS patient fibroblasts and uncovered surprising new roles for HACE1 in both human and mouse brain development. In the present study, we show that HACE1 KO primary neurons show significant morphological disturbances as well as increased intra-cellular ROS and DNA damage, which has significant implications in the pathology of this disorder. Furthermore, these findings are conserved in cell line model of the disorder, permitting ongoing high-throughput chemical screening assays for rescue of mutant phenotypes.
P8
Blood-based miRNA panel for diagnostics of Alzheimer’s disease (AD)
Aleksandra Fesiuk, Katarzyna Laskowska-Kaszub, Urszula Wojda
Laboratory of Preclinical Testing of Higher Standard, Neurobiology Center, Nencki Institute of Experimental Biology, Warsaw
Alzheimer's disease (AD) is a progressive and chronic neurodegenerative disorder and the most common cause of age-related dementias. According to the latest statistics, number of people suffering from AD is constantly increasing. It has been reported that in 2018 almost 50 million people were affected by AD-related dementia worldwide and this number is thought to increase to 152 million by 2050. That is why Alzheimer's disease is considered to be one of the biggest health concerns in modern society. The most studied molecular mechanisms involved in AD pathology are formation of β- amyloid plaques and neurofibrillary tangles (NFTs) which cause synapse degeneration and neuronal death. That leads to the most common AD symptoms like memory loss, speech difficulties and behavioural and neuropsychiatric changes. Current clinical diagnosis of AD is based on dementia assessment by neuropsychological tests and can be supported by analysis of brain biomarkers by imaging methods (amyloid-PET, MRI, SPECT) and by assays in cerebrospinal fluid of such AD biomarkers as amyloid-β, tau and phospho-tau protein. However, these methods require professional and expensive equipment or are invasive and not adjusted for screening of many patients. For those reasons a diagnostic method based on biomarkers in blood is highly needful. Blood microRNA (miRNA) profiling in AD is an innovative and promising area of research conductive to understanding the causes and mechanisms of the disease and development of easily accessible biomarkers of the disease. Our research aims at development of a new diagnostic method of AD based on dysregulated miRNA in human plasma which we have identified in our previous studies (Oncotarget 2017, PMID: 28179587, Ageing Research Reviews 2019, PMID: 30391753). Here we applied RT- qPCR for studying levels of the reported miRNA in plasma derived from the two newly recruited groups of subjects: 40 patients suffering from AD and 20 healthy individuals. The AD diagnostics was based on neuropsychological assessment and was confirmed by positive CSF AD biomarkers. The obtained data showed significant differences for all investigated miRNAs in their plasma levels in AD patients versus control subjects. These results confirm chosen miRNAs as promising non-invasive diagnostic biomarkers for AD. This research was supported by the European Union's H2020 research and innovation programme under the FETOPEN grant no 737390 (ArrestAD), and by the Polish National Science Centre grant OPUS 2018/29/B/NZ7/02757.
P9
Improving gene annotation to support better genetic diagnosis Adam Frankish1, J.M. Mudge1, J.M. Gonzalez1, T.J. Hunt1, The GENCODE consortium 1,2,3,4,5,6,7 1 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom. 2 University of California, Santa Cruz, California 95064, USA; 3 Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; 4 Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland; 5 Centre for Genomic Regulation (CRG) and UPF, 08003 Barcelona, Catalonia, Spain; 6 Yale University, New Haven, Connecticut 06520-8047, USA; 7 Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain;
The accurate identification and structural and functional annotation of genes and transcripts in the human genome is fundamental for high quality analysis for genome biology and clinical genomics. Gene annotation that is incorrect or incomplete impacts downstream analysis and introduces potentially significant false positive and false negative errors. As part of the GENCODE project, we are responsible for producing detailed reference annotation of all human protein-coding genes, pseudogenes, long non-coding RNAs and small RNAs. The emergence of long transcriptomic sequencing methods such as PacBio ISOseq and ONT promises to massively increase the length and depth of the data that supports gene annotation. Indeed, in a recent study we re-annotated 191 genes predominantly implicated in Early Infantile Epileptic Encephalopathies (EIEE) using this data and added 3,567 novel alternatively-spliced transcripts, raising the total to 5,381 compared to 559 RefSeq NM_ transcripts at the same loci. The updated annotation identified 1390 novel exons and 577 novel splice sites in existing exons which together add ~365kb to the genomic coverage of gene annotation. While this study was a fully manual effort, this does not scale to larger data volumes and gene numbers. We have developed a workflow taking alignments of reads from long transcriptomic sequencing experiments. Alignments are quality filtered and merged, introns confirmed with RNAseq and the resulting transcripts clustered into models and filtered for novelty, then confirmed by manual assessment so as not to compromise the quality of the GENCODE geneset. Novel lncRNA loci generated by this method (TAGENE) have been added to the GENCODE geneset (available from GENCODE 31) and the workflow is being used to add alternatively spliced transcripts to protein coding genes. We are piloting this method on a list of 500 genes associated with childhood-onset epilepsy, brain malformations and hereditary neuropathy.
P10
The genetics of depression in samples with East Asian ancestry
Olga Giannakopoulou, Kuang Lin, Arden Moscati, Niamh Mullins, Ruth Loos, Murray Stein, Robert Ursano, Robin Walters, Cathryn Lewis, Karoline Kuchenbaecker
Olga Giannakopoulou, Division of Psychiatry, University College of London, London, W1T 7NF, UK. Kuang Lin, Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, U.K. Arden Moscati, The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Niamh Mullins, MRC Social, Genetic and Developmental Psychiatry Centre, King’s College London, London, UK. Ruth Loos, The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Murray Stein, Department of Family Medicine & Public Health, University of California San Diego, La Jolla, California; Department of Psychiatry, University of California San Diego, La Jolla, California Robert Ursano, Department of Psychiatry, Uniformed Services University, Bethesda, Maryland. Robin Walters, Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, U.K. Cathryn Lewis, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK. Karoline Kuchenbaecker, Division of Psychiatry, University College of London, London, W1T 7NF, UK; UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
Most of previous genome-wide association studies (GWAS) of depression have been limited to individuals of European ancestry, raising questions about the transferability of findings across populations. We have undertaken a large effort to study genetics of depression in non-European populations. The relatively high prevalence rates of depression in the general population has allowed us to build the Ancestrally Diverse (AnDi) resource, supported by the PGC MDD Group, using existing biobanks and cohort studies. As part of this project, we have performed the largest GWAS in samples with East Asian ancestry to date (11,400 cases, 79,531 controls), combining data from two studies conducted in China (CONVERGE and China Kadoorie Biobank,CKB) with other US and UK studies with East Asian samples. We used a mix of measures to define depression, including structured questionnaires/interviews and health records. We performed a fixed-effect meta-analysis of the available studies (N=8,034,117 markers). A variant at 7p21.2, intronic in the AGMO gene (minor allele frequency (MAF)=0.34) was associated with depression at significance level P<5x10-8 (per-allele odds ratio (OR)=1.103, standard error (SE)=0.02). The minor allele (MAF=0.26) of a variant at locus 1p36.12 (OR=1.101,SE=0.02) was associated with increased risk of depression at a suggestive threshold of P<10-6. We created credible sets comprising the lead variant and those in linkage disequilibrium with it (r2>=0.6) at each locus. None of these variants were associated with risk of depression in European-ancestry studies (P>0.05) even though the lead variants were also common in this group (MAF>0.05). We explored evidence for reproducibility of established depression loci from European-discovery studies in the East Asian samples. A trans-ethnic colocalization method (TEColoc) did not provide evidence for transferability of any of the depression signals across populations. To assess if the genetic risk factors for depression across the genome are shared between East Asian and European populations, we estimated the trans-ethnic genetic correlation with the largest European-ancestry GWAS (Wray et al., 2018). The results were similar for the two largest East Asian studies (rg=0.40,SE=0.08 for CONVERGE and rg=0.54,SE=0.16 for CKB). The results of our study reveal a novel genetic association with depression that is specific to samples with East Asian ancestry. We found llittle evidence for reproducibility of depression loci across populations. The trans-ethnic genetic correlation between East Asian and European-ancestry studies was considerably lower than estimates for other psychiatric traits (e.g., rg=0.98 for schizophrenia). These findings highlight the need to increase the diversity of genetic studies for depression.
P11
Transcriptome-wide association studies (TWAS) in Alzheimer's disease.
Janet Harwood, Ganna Leonenko, Rebecca Sims and Peter Holmans
MRC Centre for Neuropsychiatric Genetics & Genomics, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ.
Alzheimer's disease (AD) accounts for 60-70% of the dementias, affecting 50 million people worldwide. Multiple recent powerful collaborative genome-wide association studies (GWAS) have identified more than 40 gene loci that are implicated in AD. The strongest genetic risk factor for AD is being a carrier of the E4 allele of the APOE gene. However, there is significant evidence that there is a polygenic component in AD that is independent of the APOE locus. Since AD is polygenic, this makes deciphering the functional relevance of the associated loci and defining the mechanisms underpinning disease aetiology challenging. Gene-set analysis (GSA) has shown that genes implicated in AD are involved in multiple diverse biological pathways such as the immune response, cholesterol metabolism, amyloid protein processing and APP metabolism. However, the specific mechanisms involved in AD- related changes in gene regulation have not yet been identified. Here we draw together the results of GWAS using functional analysis methods to understand the molecular basis of the associations. Linking together genetic information with changes in gene expression will provide an insight into the mis-regulation of genes implicated in AD. Methods have been developed to test the association between changes in cell/tissue-specific gene expression and disease by predicting functional/molecular phenotypes into GWAS. We will present our current results generated from transcriptome-wide association studies (TWAS) that correlate gene expression and genetic changes in AD. To begin to investigate the biological mechanisms involved in inflammation in the AD brain, we have integrated published expression and genetic data from naïve and induced CD14+ monocytes to study genetically controlled gene expression in monocytes at different stages of differentiation. Using TWAS we have identified a significant correlation between a change in the direction of gene expression of LACTB2 and AD risk. LACTB2, a mitochondrial endoribonuclease, is a novel candidate gene for AD. This result will be replicated and validated using biological assays.
P12
Preliminary findings from DRAGON-DATA: A large psychiatric cross-disorder genotype/phenotype resource
Leon Hubbard & Amy Lynham, Sarah Knott, Antonio Pardiñas, Michael Owen, Jeremy Hall and James Walters
MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University
Background and aims: Large scale integration of clinical, environmental, genomic and other biological data across psychiatric disorders will lead to better understanding, improved classification and development of novel therapeutic strategies. We have developed DRAGON-DATA, a large cross-disorder psychiatric genotype/phenotype resource comprised of 14 adult and child/adolescent cohorts collected at the MRC Centre for Neuropsychiatric Genetics and Genomics at Cardiff University. Across cohorts, diagnoses include but are not limited to schizophrenia, bipolar disorder (BP), major depressive disorder (MDD), attention deficit hyperactivity disorder and post-traumatic stress disorder. In total we have phenotype and genotype data on over 40,000 individuals.
Phenotyping: cohorts used a range of different clinical interviews, rating scales and questionnaires. Most studies in the Centre used similar protocols so there were commonalities in the measures they employed. In keeping with our project aim, we focused on variables that would be applicable to cross-disorder research and were measured in at least half of the cohorts. These variables were then subject to vigorous data cleaning and harmonisation.
Genotyping: We developed an automated pipeline to perform genotype quality control for each cohort. Genotype imputation was performed using the Michigan Imputation Server and samples underwent additional post-imputation quality control. Separately, we developed a pipeline for copy number variant (CNV) calling for each cohort where raw intensity data was available. As cohorts used a variety of genotyping platforms, initially we are restricting analyses to large known neurodevelopmental risk CNVs that can be reliably called across genotype platforms.
Analysis plan: This resource is under active development and will enable us to address diverse cross-disorder questions. We will present preliminary results of two studies we are currently undertaking. First, we plan to investigate depressive symptoms across disorders to identify possible shared risk factors including depression polygenic risk, childhood abuse, substance abuse, physical health, and measures of disability. Second, we will identify rates of neurodevelopmental risk CNVs across psychiatric disorders and assess whether individuals who carry such CNVs have an earlier age of onset than non-neurodevelopmental CNV carriers regardless of diagnosis.
P13
The Gut Microbiome Contributes to Schizophrenia
Xiancang Ma2, Huijue Jia1, Ruijin Guo1, Feng Zhu2, Yanmei Ju1, Wei Wang2, Qi Wang1, Qingyan Ma2, Karsten Kristiansen1
1BGI-Shenzhen, 518083, Shenzhen, China; 2Department of Psychiatry, The First Affiliated Hospital of Xi’an Jiaotong University, 277 Yanta West Road, 710061, Xi’an, China
Although schizophrenia is known to have a high heritability, it is not clear whether the gut microbiome could nonetheless play a role. Here we provide metagenomic shotgun data for schizophrenia, and demonstrate that transplantation of feces from medication-free patients could lead to schizophrenia-like behaviors and dysregulated kynurenine metabolism in mice pretreated with antibiotics, providing a convenient mouse model for schizophrenia. From the Metagenome-wide Association Study (MWAS), we establish a disease classifier based on the patients' fecal microbiome. Interestingly, the patient-enriched Streptococcus vestibularis could be singly applied to microbiota-eradicated mice to cause symptoms in social functioning, while the bacterium scarcely colonized the mice when the fecal community was transplanted as a whole. Besides, we identified gender-specific M-GWAS (Metagenome- Genome-wide Assocation Studies) hits, including a male-only association between Acidaminococcus and rs4650205 at NEGR1-LINC01360 , both implicated with schizophrenia. Our findings illustrate the value in combining cohort studies with animal models for a complete picture, and indicate that microbiome samples should be considered in genetic studies of psychiatric and neurological disorders.
In addition, we welcome neuropsychiatric cohorts to join the Million Microbiome of Humans Project (MMHP). https://en.mgitech.cn/news/114/, Email: [email protected]
P14
What’s next in autism genomics? Sharing research progress, potential and opportunities for public involvement
Lorna Lopez, Michael Foley, Sarah Bowman, Louise Gallagher
Department of Psychiatry, Trinity Centre for Health Sciences, Trinity College Dublin, Ireland (LML, LG). Health Research Board-Irish Research Council IGNITE Programme, Trinity College Dublin, Ireland (MF, SB).
Genomics is a key feature in the future of healthcare with significant benefits including the development of personalised medicine acceleration of discoveries in diagnoses and treatments. While the progress of genomics is exciting, there are key challenges including genomic literacy, public patient engagement (PPE) and data-complexity. The future success of genomics in healthcare depends on building trust in the technology, trust in the evidence- base and trust in the genomic professionals about how data will be used. It is crucial therefore that research participants have their voice heard in this conversation. To address this need, Trinity College Dublin's Autism Research Group sought the support of specialists who advance PPE in health engaged research - HRB-IRC Ignite Team, to run an interactive and informative event for research participants. The event was hosted in Trinity College Dublin, in an integrated academic and primary-care centre. This was a unique, comfortable, accessible venue and in view of the Dublin mountains - an ideal setting to spark conversation. Those who had previously participated in our research studies, whatever their background, were invited to learn, chat and contribute in an informal setting with genomic and autism researchers. We introduced genomics - a key component of future healthcare - in autism, shared current knowledge on the research landscape, and facilitated a conversation between two key groups - researchers and families affected by autism - through a Conversation Café. We included an open discussion on the challenges, the opportunities and the potential use of genomics to drive therapeutics. A key aspect of the event was recording the event, the creative output and media engagement that embodied the essence of the event https://www.tcd.ie/ttmi/AutismGenomics/ The benefit for the participants was an understanding of autism genomics (89% felt more confident in having a conversation on autism genomics research), a connection with researchers (91% felt importance of chatting with researchers) and a voice to shape future research questions (89% felt that their voice was heard on the day). The impact on health- research was a subsequent interest in public involvement in research (90% more excited to take part in research), the training of a research group that embraces engagement and the generation of knowledge to establish the meaningful ways to continue the conversation (100% participants felt this event was useful to start a community conversation). Meaningful PPE is a key ingredient for scientists and clinicians to ensure the success of genomics to drive therapeutics.
P15
UniProtKB and Neurodegenerative Diseases: Towards a deeper understanding of underlying mechanisms
Yvonne C. Lussi1, Elena Speretta1, Kate Warner1, Michele Magrane1, Sandra Orchard1 and UniProt Consortium1,2,3
1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK 2SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland. 3Protein Information Resource, Georgetown University, Washington DC and University of Delaware, USA
Neurodegenerative diseases are a heterogeneous group of disorders that are characterized by the progressive degeneration of the structure and function of the central or peripheral nervous systems. This causes problems with mental functioning (called dementias), or movement (called ataxias). Although treatments may help relieve some of the physical or mental symptoms associated with neurodegenerative diseases, there is currently no way to slow disease progression and no known cures. In order to find treatments for these incurable and debilitating disorders, it is crucial to understand the underlying mechanisms that lead to disease development and identify the genetic variants that are associated with the disease. In this context, UniProtKB aims to link genetic and medical information to protein sequences and associated biological knowledge to improve our understanding of disease development. By focusing our curation efforts on proteins involved in neurodegenerative diseases, we hope to shed light on the mechanisms leading to these devastating diseases. We focus on a thorough review of available information on sequence variants and associated neurodegenerative disease information linking to specialized databases, as well as collecting literature information on the normal function of proteins associated with the disease. The information on variants together with variant functional description, protein molecular function, structural data and protein-protein interactions should help researchers in the field of neurodegeneration, clinicians and biomedical researchers to gain a global view on the relation between variant and disease and help in elucidating disease mechanism. As part of the curation efforts, we will identify and annotate orthologs of those proteins in other model organisms including mouse, rat and the fruit fly Drosophila melanogaster. D.melanogaster is an excellent model system to study neurological diseases and is widely used in the research community. Collecting information on the function of these orthologous proteins will greatly improve our understanding of protein function in humans. To further facilitate retrieval of disease-specific information, we will follow previous efforts at UniProKB which focused on the annotation of information on proteins and protein variants involved in Alzheimer disease. These efforts included the development of the Disease Portal, which is a disease-centric entry point into UniProtKB, supporting the navigation through information available on Alzheimer disease and which will be launching this year. The aim will be to expand the information exhibited on the Disease Portal to additional neurodegenerative diseases.
P16
Genes influenced by MEF2C contribute to neurodevelopmental disease via gene expression changes that affect multiple types of cortical excitatory neurons
Dr Derek Morris, Donna Cosgrove, Laura Whitton, Laura Fahey, Pilib Ó Broin, Gary Donohoe
National University of Ireland Galway
Myocyte enhancer factor 2 C (MEF2C) is an important transcription factor during neurodevelopment. Mutation or deletion of MEF2C causes intellectual disability (ID) and common variants within MEF2C are associated with cognitive function and schizophrenia risk. We investigated if genes influenced by MEF2C during neurodevelopment are enriched for genes associated with neurodevelopmental phenotypes, and if this can be leveraged to identify biological mechanisms and individual brain cell types affected. We used a set of 1,052 genes that were differentially expressed in the adult mouse brain following early embryonic deletion of Mef2c in excitatory cortical neurons. Using GWAS data, we found these differentially expressed genes (DEGs) to be enriched for genes associated with schizophrenia, intelligence and educational attainment but not autism spectrum disorder (ASD). Using sequencing data from trios studies, we found these DEGs to be enriched for genes containing de novo mutations reported in ASD and ID, but not schizophrenia. Using single cell RNA-seq data, we identified that a number of different excitatory glutamatergic neurons in the cortex were enriched for these DEGs including deep layer pyramidal cells and cells in the retrosplenial cortex, entorhinal cortex and subiculum. These data indicate that genes influenced by MEF2C during neurodevelopment contribute to cognitive function and risk of neurodevelopmental disorders. Within excitatory neurons, common SNPs in these genes contribute to cognition and SZ risk via an effect on synaptic function based on gene ontology analysis. In contrast, rare mutations contribute to earlier onset ASD and ID via an effect on cell morphogenesis.
P17
Investigating functional and genetic interactions underlying schizophrenia in 22q11.2 Deletion Syndrome
Aine Moylett, Professor Nigel Williams and Professor Meng Li
NMHRI, MRC Centre for Neuropsychiatric Genetics and Genomics
22q11.2 Deletion Syndrome (22q11.2DS) is a genetic disorder caused by a hemizygous deletion in the long arm of chromosome 22 at region 11.2. 22q11.2DS is the highest known genetic risk factor associated with schizophrenia (SCZ) and is estimated to be present in 0.3-2% of all schizophrenia patients, however how this deletion confers such risk remains largely unknown. In this project, we are proposing that multiple genes spanned by the deletion at 22q11.2 are acting, potentially through epistatic interactions or converging on similar pathways in neurodevelopment. This coordinated disruption leads to increased risk for neuropsychiatric disorders.
A potential SCZ candidate gene from within the 22q11.2 locus is DGCR8. DGCR8 plays a role in microRNA biogenesis, which are involved in gene expression regulation. DGCR8's role in gene regulation makes it an initial candidate for epistatic interactions contributing to SCZ risk. To identify genes at the 22q11.2 locus that functionally or genetically interact with DGCR8, a literature review focusing on loss-of-function intolerant genes and gene expression correlation analysis of RNA sequencing data from fetal brain tissue was performed. As a result, DGCR8, HIRA and ZDHHC8 were selected as candidate genes to be investigated in cortical differentiation of human embryonic stem cells.
Using a lentiviral based CRISPR/Cas9 method, investigation of knockout/happloinsuffiency of DGCR8 has been investigated in two ways; at the embryonic stem cell stage to generate a clonal knockout cell line and at the neuroprogenitor cell (NPC) stage. Prior generation of DGCR8 homozygous and heterozygous KO lines revealed a CNV deletion on chromosome 17, encompassing the Tp53 gene. Elevated Tp53 is known to restrict differentiation potential of microRNA deficient stem cells, indicating this mutation would be advantageous for cell survival in DGCR8 deficient cells. A DGCR8 heterozygous knockout line has been generated using an alternative CRISPR/Cas9 method and different parental cell-line to see if the same CNV occurs. No CNV was found encompassing the Tp53 gene, however DGCR8 protein levels remained unaltered, indicating an underlying compensatory mechanism and the importance of DGCR8 in stem cells. At the neuroprogenitor stage, preliminary data indicates alterations in neuronal markers, such as TBR1, further work is required to elucidate the role of DGCR8 in cortical differentiation.
Investigation of DGCR8, HIRA and ZDHHC8 is going to be explored by conducting RNA sequencing on infected NPCs with guide RNAs targeting each gene respectively. This will establish disrupted pathways to indicate the underlying mechanisms conferring the schizophrenia risk in 22q11.2DS.
P18
Characterisation of DNA Variants from Whole Genome Sequence Data of Monozygotic Twins Discordant for Psychiatric Disorder
Cathal Ormond, Elizabeth Heron1, Niamh Ryan1, Viktoria Johansson2, Anna Hedman2, PGC, Christina Hultman2, Michael Gill1, Patrick F. Sullivan2, Aiden Corvin1
1: Dept. of Psychiatry, Trinity College Dublin; 2: Dept. of Medical Epidemiology and Biostatistics, Karolinska Institutet
Despite the high heritability of the major psychotic disorders, concordance rates between monozygotic (MZ) twins are not complete. For example, concordance for schizophrenia is estimated to be 50%. One explanation for the discordance between MZ twins is that both individuals share a common genetic risk which alone is insufficient to be causal for the phenotype, but rare, post-zygotic variation present in one twin modifies the disease burden for that individual, increasing their disease risk. Previous research has implicated a spectrum of DNA variant classes as contributing towards psychiatric illnesses, including: common single nucleotide polymorphisms (SNPs), de novo variation and rare, high odds ratio copy number variation (CNVs). To investigate the hypothesis that post-zygotic variation is implicated in phenotypic discordance, we investigated a cohort of 17 pairs of MZ twins discordant for major psychosis (seven bipolar disorder, six schizoaffective disorder, five major depressive disorder, four schizophrenia and 12 unaffected individuals) using whole genome sequencing (WGS). This allowed us to investigate variants of different types, frequency and function across the genome. Using a stringent filtering approach, we have identified 40 rare, putatively deleterious SNVs in 34 unique genes, that were present in an affected twin only. We have applied an in-house CNV calling pipeline to the WGS data, consisting of a consensus of four separate calling algorithms to maximize detection ability. The called variants were screened against a list of CNVs with a known association with psychiatric illness; however, none of these variants were identified in this cohort. Using a rigorous filtering method we next filtered out variants which were known to be common or had no predicted pathogenic evidence from public databases. This strategy identified 65 rare CNVs present in affected individuals only, of which 36 CNVs overlapped gene regions. Further work is required to identify supportive independent evidence for the pathogenicity of specific loci. WGS is a powerful technique that allows the generation of a comprehensive profile of genetic variation that may contribute towards phenotypic risk. In the largest reported study of MZ twins discordant for disorders, we have shown that this approach can provide useful insights into the genetic aetiology of psychiatric illness.
P19
DLG2 regulates neurogenic transcriptional programmes disrupted in complex neurodevelopmental disorders
Andrew Pocklington 1, Daniel D’Andrea 1, Bret Sanders 2, Elliott Rees 1, Michael Owen 1&2, Jenny Shin 2
1 MRC Centre for Neuropsychiatric Genetics and Genomics,Cardiff University, Cardiff CF24 4HQ, UK 2 Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff CF24 4HQ, UK
Disorders such as severe neurodevelopmental delay (NDD), autism (ASD), schizophrenia (SZ) and attention deficit hyperactivity disorder (ADHD) are widely understood to have a major neurodevelopmental component. However, the specific processes contributing to disease aetiology - the relevant phase(s) of development, cell-types and aspects of cellular function - remain elusive.
Mutations at the DLG2 locus have been identified in individuals with schizophrenia and autism. DLG2 encodes a MAGUK scaffold protein with a well-studied role in postsynaptic signal transduction at mature excitatory synapses. Studying cortical excitatory neuron differentiation from human embryonic stem cells we uncovered significant dysregulation of early corticoneurogenesis in DLG2-/- compared to wildtype control lines, with genes down- regulated in DLG2-/- cultures during this period also being enriched for common SZ risk variants (see companion abstract by Shin). Further parsing this association, we uncovered distinct gene expression programs active during early excitatory corticoneurogenesis that are enriched for schizophrenia genetic risk. These programs largely captured SZ common variant association in genes intolerant to loss-of-function mutations (LoFi genes), localising risk factors to roughly one third of LoFi genes and providing a clear biological context for their action. Genetic risk factors contributing to NDD, ASD and ADHD were also found to converge on the same cascade of neurogenic transcriptional programs.
It has been proposed that adult and childhood disorders lie on an aetiological and neurodevelopmental continuum: the more severe the disorder the greater the contribution from rare, damaging mutations and the earlier their developmental impact. Our data support this model and ground it in developmental neurobiology, embedding genetic risk for multiple disorders in a common pathophysiological framework.
P20
Gene expression imputation across multiple tissue types provides insight into frontotemporal dementia and its clinical subtypes
Lianne Maria Reus, International FTD-Genomics Consortium (IFGC), Yolande Pijnenburg, Roel Ophoff
LMR, YALP: Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands. RO: Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California. Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California. Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, California.
Background: The genetic etiology of frontotemporal dementia (FTD) is poorly understood. To identify genes whose expression levels associate with FTD, we performed a transcriptome- wide association studies (TWAS), by integrating FTD genome-wide association study (GWAS) summary statistics with cis gene expression data from multiple tissue types including brain structures and other tissue types. Methods: We used GWAS summary statistics on FTD (meta-FTD, n=2,340 cases, n=7,252 controls) and FTD clinical subtypes separately (behavioral variant FTD, bvFTD n=1,337 cases, n=2,754 controls; semantic dementia, SD n=308 cases, n= 616 controls; progressive non-fluent aphasia, PNFA n=269 cases, n=538 controls, FTD with motor neuron disease, FTD-MND n=200 cases, n=400 controls) from IFGC, and 53 cis eQTL tissue type panels (n=12,205 from five consortia). The TWAS was performed using FUSION software. Significance was assessed using a 5% false discovery rate threshold (p<0.05). Results: We identified 73 significant gene-tissue associations for meta-FTD, representing 44 (40 non-major histocompatibility complex genes) unique genes in 34 tissue types. Most genes (n=36, 81.8%) showed a significant association in only one tissue type - with the majority in the dorsolateral prefrontal cortex (DLPFC) (n=19, 26.0%). Eight genes reached transcriptome-wide significance across multiple tissue types. Top hits with supporting evidence from colocalization analysis included SEC22B on chromosome 1 (thyroid PFDR=2.28x10-3), TRGV5P on chromosome 17 (cells transformed fibroblasts PFDR= 2.39x10-3), ZNF302 on chromosome 19 (DLPFC splicing data PFDR=5.80x10-8, and multiple genes on inversion polymorphism 17.q21.31 (min PFDR= 1.83x10-26). The TWAS on FTD clinical separately showed that RAB38 on chromosome 11 was differentially expressed in bvFTD in eight different non-brain tissue types. For SD, PNFA and FTD-MND, no significant transcriptome-wide associations were observed. Conclusions: We identified genes with differential expression in FTD, with both tissue- specific patterns and genic associations across several tissue types. This study helps identifying which FTD risk loci identified in GWAS studies contribute to pathology.
P21
Identity by Descent analysis of a large Tourette’s syndrome pedigree
Niamh Ryan, Cathal Ormond[1], Yi-Chieh Chang[2], Carol A. Mathews[2], PGC, Michael Gill[1], Elizabeth Heron[1], Aiden Corvin[1]
[1] Trinity College Dublin, [2] University of Florida
Tourette Syndrome (TS) is a substantially heritable neuropsychiatric disorder (h2 0.6-0.8) (Mataix-Cols et al., 2015). While a large part of the heritability of TS can be attributed to common variation, rare variants are also predicted to play a role (Davis et al., 2013). Whole genome sequencing (WGS) data from large, densely affected pedigrees can be used to study the full spectrum of genetic variations contributing to disease aetiology within a more homogenous genetic background.
We report data from a large pedigree densely affected by TS and co-morbid psychiatric disorders (>500 individuals) from an isolated Costa Rican population. The pedigree spans 11 generations and shares ancestry from six founder couples. We generated WGS data from 19 individuals separated by at least 12 meiotic steps for an identity-by-descent (IBD) analysis to identify regions of genome inherited from common ancestors. Sixteen of the selected individuals had TS (nine of these had co-morbid ADHD diagnoses), of the remaining two individuals, one had OCD, one had ADHD and one was identified as unaffected.
Pairwise IBD analysis was performed using the refined-IBD algorithm (Browning and Browning, 2013). Clusters of individuals sharing haplotypes IBD were identified using the efficient multiple-IBD (EMI) algorithm (Qian, Browning & Browning, 2014). ). Over 450 multi- haplotype IBD clusters (three or more haplotypes) were identified, of which more than 30 IBD clusters were found to be shared across four or more haplotypes. These multi-haplotype IBD clusters were further subset to identify haplotypes shared by individuals descended from the same founder pair.
The amount of expected IBD sharing between related individuals can be calculated. For example, while a pair of fifth cousins (separated by 12 meiotic steps) usually have no detectable IBD sharing, when they do, it tends to be composed of a single segment of mean length 8.3 cM (Browning & Browning, 2012). Multiple individuals separated by 12 or more meiotic steps sharing the same region IBD is increasingly improbable and therefore more noteworthy. Based on these estimations, we have identified several haplotypes in this extended pedigree with a greater than expected amount of IBD sharing: one ~800Kb haplotype on chromosome 3 shared by seven individuals, as well as several regions >10 Mb in length shared between three or more individuals. We will present data on the presence and frequency of these haplotypes in the wider Costa Rican population and report on putative pathogenic mutations identified at these loci.
P22
Familial Parkinson’s disease mutations induce global epigenomic dysregulation in human dopaminergic neurons.
Samantha L. Schaffner (1), Isabel Paiva (2), Diana Lazaro (2), Tiago F. Outeiro (2,3,4), and Michael S. Kobor (1,5)
1. Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia,Vancouver, BC, Canada 2. Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Goettingen, 37073, Goettingen, Germany 3. CEDOC – Chronic Diseases Research Center, Faculdade de Ciencias Medicas, Universidade Nova de Lisboa, Lisboa, Portugal 4. Max Planck Institute for Experimental Medicine, 37075 Goettingen, Germany 5. Human Early Learning Partnership, University of British Columbia, Vancouver, BC, Canada
Introduction: Parkinson's disease (PD) is the second most common neurodegenerative disorder, affecting 1% of the population over age 60. Determination of individual risk for PD remains challenging due to heterogeneity in onset, symptoms, and pathology. The alpha- synuclein (SNCA) gene contributes to PD pathology as a major component of protein aggregates, and also regulates synaptic transmission and neuronal health, which may influence PD symptoms. SNCA multiplications leading to overexpression and SNCA mutations such as the A30P variant are associated with rare familial cases of PD, while SNCA single nucleotide polymorphisms may contribute to sporadic PD risk. However, familial PD variants are not fully penetrant, and genetic and environmental contributions to both forms of PD are not completely understood. Epigenetic patterns - including DNA methylation (DNAm) and DNA hydroxymethylation (DNAhm) - are altered by both genes and environment and may mediate human disease outcomes. In this study, we characterized the influence of SNCA variants on DNAm and DNAhm patterns in human dopaminergic neurons in order to understand potential epigenomic underpinnings of PD.
Methods: We assessed genome-wide DNAm and DNAhm in wild type human dopaminergic neurons, dopaminergic neurons overexpressing wild type human SNCA, and dopaminergic neurons overexpressing A30P SNCA at >850,000 cytosine-guanine (CpG) sites using the Illumina MethylationEPIC BeadChip array. We additionally examined the transcriptome of each group by RNA-seq. Results: SNCA overexpression and A30P SNCA mutation each induced DNAm changes at thousands of sites genome-wide, including 4,613 CpGs which were affected in both genotypes. We also found differential DNAhm at hundreds of sites, including 15 affected in both genotypes. Differentially methylated sites in wild type SNCA overexpressing cells were significantly enriched for glutamate receptor signaling functions. Both genotypes also showed differential DNAm, differential DNAhm, and differential expression of genes involved in glutamate and NOTCH signaling, while A30P cells displayed epigenomic and transcriptomic dysregulation of genes involved in PDGF signaling. Significance: Our results indicate that SNCA genetic variants have a significant impact on the epigenome of dopaminergic neurons, influencing pathways related to neuronal development, synaptic function, and signaling. The impacts of SNCA multiplication and mutation reach beyond protein aggregation and may contribute to widespread neuronal dysfunction and impaired neuronal health. Future studies will assess the ability of environmental factors to compound or reverse these epigenomic changes, with implications for personalized strategies for PD prevention and treatment.
P23
Synaptic protein DLG2 has a novel role in early neurogenesis regulating expression of genes harbouring schizophrenia risk variants
Jenny Shin1, Bret Sanders1, Daniel D’Andrea2, Mark Collins3, Tom Steward4, Ying Zhu1, Michael Owen1,2, Derek Blake2, Daniel Whitcomb4, Andrew Pocklington2
1 Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff CF24 4HQ, UK 2 MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff CF24 4HQ, UK 3 Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK 4 Bristol Medical School, University of Bristol, Bristol BS1 3NY, UK
Discs large homolog 2 (DLG2) is a membrane associated guanylate kinase with an established role as a scaffold protein in the postsynaptic density (PSD) where it regulates receptor clustering and signal transduction, contributing to higher cognition. Recurrent de novo deletions of DLG2 have been identified in schizophrenic individuals. Although DLG2 mRNA expression has been reported in human embryonic brain and human embryonic stem cell (hESC)-derived neural precursors (NPCs), its functional role during neural development and its relevance to schizophrenia aetiology has yet to be studied. To this end, DLG2 knockout (KO) hESCs generated using CRIPSR/Cas9 together with isogenic wildtype hESCs were used to recapitulate the early human cortical development in vitro. RNA-seq analysis revealed many protein-coding genes to be differentially expressed in DLG2 KO cells across developmental stages peaking during early neurogenesis, long before PSD formation. In the absence of DLG2, NPCs displayed increased proliferation and adhesion to extracellular matrix proteins. Genes down-regulated in DLG2 KO cells following cell-cycle exit were enriched for schizophrenia common risk variants. Schizophrenia risk was distributed across genes known to play a role in neuronal growth, migration and active properties. In line with this, neurons lacking DLG2 showed reduced migration, delayed expression of known markers of deep cortical layer identity (TBR1 and CTIP2), a simplified morphology and immature AP firing. In this study we uncover a major role for the scaffold protein DLG2 in corticoneurogenesis, providing an unexpected link between neurodevelopmental and mature synaptic signalling deficits contributing to schizophrenia. Precise timing is crucial during brain development, where the correct dendritic morphology, axonal length and electrical properties are required for normal cortical and subcortical circuit formation. Consequently, even transient perturbation of neurogenesis may have a profound impact on fine-grained neuronal wiring, network function and ultimately perception, cognition and behaviour.
P24
One by one: single cell resolution illuminates disease pathogenesis in organoid models of neuropsychiatric disorders Giuseppe Testa, A. López-Tobón, R. Shyti, N. Caporale, S. Trattaro, E.C. Villa, C. Cheroni, P.L. Germain, E. Tenderini, F. Troglio et al. Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, 20139 Milan, Italy Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy Center for Neurogenomics, Human Technopole
Single cell omics has enabled the construction of cell diversity atlases with unparallel resolution. We harness the synergy between this newly available resource and the most advanced protocols to differentiate patient-derived brain organoids in order to study the molecular mechanisms underlying neuropsychiatric disorders. We are particularly focused in syndromes resulting from copy number variations at the Williams-Beuren syndrome critical region (WBSCR, 7q11.23). Deletion of the WBSCR causes Williams-Beuren syndrome (WBS), characterized by hypersociability, anxiety and intellectual disability, while duplication give rise to 7q duplication syndrome (7Dup) with severe impairments in language, anxiety and autism spectrum disorder (ASD). Despite the well-established genetic underpinnings of these disorders, effective treatments are unavailable. Our results in patient-derived neurons and cortical brain organoids uncovered opposite dynamics of neuronal maturation with accelerated maturation in 7Dup and decelerated in WBS, mirrored by opposite defects of neuronal intrinsic excitability. Single cell transcriptome dissection confirmed this asymmetry and revealed the presence of divergent neural trajectories, resulting in differences in the relative abundance of specific sub populations across conditions. Our previous work in patient-derived iPSC and neural progenitors showed that GTF2I associates with LSD1 to suppress expression of genes involved in neuronal function, whereas inhibition of LSD1 restored gene expression balance. Knockdown of GTF2I in 7Dup organoids rescued neuronal maturation rate to control levels, suggesting that its key role in transcriptional regulation downstream of the WBSCR remains throughout neurodevelopment. Finally, we used mouse models with duplication of GTF2I and demonstrated that GTF2I dosage imbalance is enough to recapitulate the ASD-like phenotype in the three-chambered sociability apparatus. Remarkably, semi-chronic administration of an irreversible LSD1 inhibitor was able to rescue this ASD-like phenotype. These findings suggest that GTF2I-LSD1 axis play a critical role in social behavior and cognition by controlling the timing of cortical maturation and represent a key insight into the mechanistic dissection of a paradigmatic genomic cause of a neuropsychiatric disorder, with implications for the potential discovery of new therapeutic routes.
P25
Cell Type Specific Selective Vulnerability to Pathological Tau
Emir Turkes, Karen E. Duff PhD
UK Dementia Research Institute at University College London
Background: Region-specific neuronal subpopulations known to be selectively vulnerable to Tau pathology, as characterized in our previous work (Fu et al., 2019), were identified across several public single-nucleus RNA sequencing datasets from non-diseased human in order to derive putative properties and mechanisms that drive vulnerability. Methods: We analyzed datasets from the Allen Brain Institute (Hodge et al., 2019), Broad Institute (Habib et al., 2017), and Polo group (Grubman et al., 2019). After QC, dimensionality reduction, and clustering, vulnerable and invulnerable neuronal subpopulations were identified using anatomical metadata and marker genes. Differential expression between subpopulations were performed using the Wilcoxon test, while differential pathway analysis was carried out using the GSVA algorithm. Results: We were able to identify putative subpopulations across a range of presumed vulnerability as defined by classical pathological staging. Several themes emerge from differential pathway analysis of these subpopulations in various comparisons, including those related to vesicle-mediated exocytosis activity and synaptic plasticity. Following further assessment of the association of these pathways with selective vulnerability, pathways will be systematically screened in a model system measuring Tau aggregation. Conclusion: Extensive pathway analysis of neuronal subpopulations selectively vulnerable to Tau pathology in human single-nucleus RNA sequencing data reveal significant heterogeneity between neurons that may be responsible for driving pathology.
P26
Associations of mitochondrial genomic variation with Progressive supranuclear palsy, Corticobasal degeneration, and neuropathological tau lesions
Rebecca R. Valentino, Ph.D.1, Nikoleta Tamvaka1, Michael G. Heckman, M.S.3, Patrick W. Johnson, B.S.3, Alexandra I. Beasley, M.Sc.1, Ronald L. Walton, B.Sc.1, Shunsuke Koga, M.D.1, Ryan J. Uitti, M.D.2, Zbigniew K. Wszolek, M.D.2, Dennis W. Dickson, M.D.1, Owen A. Ross, Ph.D.1,4
¹Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA 2Department of Neurology, Mayo Clinic, Jacksonville, FL 32224, USA 3Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL 32224, USA 4Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL 32224, USA
Progressive supranuclear palsy (PSP) and Corticobasal degeneration (CBD) are rare, sporadic, and progressive neurodegenerative diseases which are characterised as primary four-repeat tauopathies. Both diseases are age-related and have overlapping clinical symptoms to each other and other neurodegenerative diseases such as Parkinson’s disease (PD) and Alzheimer’s disease (AD). Mitochondrial health influences ageing and neurodegenerative disease development and mitochondrial DNA (mtDNA) background has been associated with PD and AD; however no study has characterised mtDNA variation in PSP or CBD, or its contribution to severity of neuropathological tau lesions. Utilising three independent and unrelated cohorts from European descent, associations of mtDNA haplogroups with risk of PSP, risk of CBD, age of PSP onset, PSP disease duration, and semi- quantitative neuropathological tau pathology measures for neurofibrillary tangles (NFT), neuropil threads (NT), tufted astrocytes, and oligodendroglial coiled bodies in both PSP and CBD were evaluated in a case-control manner. Cohorts consisted of 1020 (42.5% male) neurologically-healthy controls, 1140 (54.1% male) pathologically-confirmed PSP cases, and 199 (51.4% male) pathologically-confirmed CBD cases. Median age at death was 75 and 70 years in PSP and CBD patients respectively. For controls, median age at blood collection was 79 years. All samples were genotyped for 39 unique mtDNA SNPs using iPlex Gold chemistry and Sequenom MassARRAY technology. mtDNA haplogroups were then defined to mitochondrial phylogeny and association tests were performed using multivariable logistic regression models that were adjusted for age and sex. After adjustment for multiple testing, we observed a significantly increased risk of CBD for individuals with a mtDNA sub-haplogroup H4 background (OR=4.49, P=0.001) and a decreased severity of NT tau pathology in PSP cases with a mtDNA haplogroup HV/HV0a background (P=0.0023). Haplogroup T background also suggested to decrease NFT pathology (P=0.009) whilst a mtDNA haplogroup W background suggested to increase disease duration in PSP cases (P=0.003). mtDNA background did not suggest to influence tau pathology severity in CBD. This is the first study to investigate the role mitochondrial genomic variation has on disease risk and tau lesion severity in large cohorts of pathologically-confirmed cases of PSP and CBD.
P27
Identification of DNA methylation associated with antipsychotic and lithium treatment
Jonelle Villar, Anne-Kristin Stavrum, Stéphanie Le Hellard, Ingrid Melle, Tatiana Polushina, Ole Andreassen
Dept. of Clinical Science, Haukeland University Hospital, University of Bergen, Division of Mental Health and Addiction, Oslo University Hospital, University of Oslo, Norwegian Centre for Mental Disorders (NORMENT)
Background: Antipsychotic medications used to treat Schizophrenia (SCZ) and Bipolar Disorder (BPD) are the most commonly prescribed drugs for symptom alleviation, despite the severity of side effects which often challenge patient compliance. It is also well documented that antipsychotic drugs induce epigenetic modifications, particularly, alterations of methylation patterns at CpG sites. These alterations are known to alter gene expression, although a complete understanding of the relationship between gene expression and pathways in successful treatment is still unknown. In addition, differentially methylated regions (DMRs) identified in SCZ and BPD may contribute to the highly heritable nature of these disorders, as well as to drug response (Ovenden et al., 2018). In the current study, whole-genome methylation genotyping was performed to identify differential methylation induced by antipsychotic and mood stabilizing drugs. We aimed to identify the common effect of these drugs on DNA methylation (DNAm), and sought to isolate the specific effect of monotherapy with an antipsychotic or mood stabilizing drug. Method: Patients being treated for psychosis were recruited through the TOP project (Thematically Organised Psychosis, Oslo, Norway). Methylation data derived from blood samples was assessed genome-wide using the Illumina 850K EPIC array. The analysis will be performed in three parts: 1) To evaluate the common effect of antipsychotic drugs on DNA methylation, 2) To isolate the specific effect of monotherapy treatment on DNAm with either Olanzapine (Zyprexa), Quetiapine (Seroquel), Aripiprazole (Abilify), or Risperidal (Risperidone), 3) To evaluate the specific effect of lithium monotherapy on DNAm. The statistical model will be corrected for gender, smoking, cell-type composition, age, and non- correlated principle components. Time of blood draw will be evaluated in the model for possible confounding by oscillating modified cytosines (Oh et al, 2019), as well as recent evidence of the correlation between BMI and severe mental disorders (Bahrami et al, 2020). Results: Analysis of the data, including verification in an independent sample is expected to be finished in March 2020. Discussion: Given the chronic nature of SCZ and BPD, it is essential to alleviate the burden of symptoms and characteristic drug side-effects. A further priority must be the early identification of individuals at risk for psychotic disorders. Our motivation, therefore, is to annotate the CpGs and differentially methylated regions (DMRs) induced by psychotropic drug adherence in patients with psychosis. Knowledge of these DMRs may eventually contribute towards personalized treatment; indeed, a desired proposal towards a new standard of care in psychiatry.
P28
Alterations in psychiatric risk gene CACNA1C affect neuronal differentiation of human iPS cells
Gemma Wilkinson, Jeremy Hall, Adrian Harwood
NMHRI, Cardiff University
Many common gene variants confer increased risk of psychiatric diseases. One of the variants repeatedly linked to psychiatric disorders is CACNA1C, which encodes the pore- forming ɑ1 subunit of the L-type voltage gated calcium channel Cav1.2. These variations occur in the non-coding region of CACNA1C and have been shown to alter Cav1.2 expression. Additionally, exonic mutations in CACNA1C cause Timothy Syndrome, a multi- system disorder associated with Autism Spectrum Disorder and Developmental Delay. Understanding how alterations in CACNA1C affect neuronal development and function may help discover the pathways that lead to disease. Homozygous CACNA1C knockout lines were generated in human iPS cells using CRISPR Cas9. Knockout of CACNA1C was verified by minION sequencing and qRT-PCR. A patient line containing a point mutation in CACNA1C was also obtained. Both these lines were differentiated into cortical neurons using a dual-SMAD inhibition protocol. RNA and protein samples were taken at regular time points to identify the role of CACNA1C throughout neuronal differentiation. qRT-PCR results showed alterations in the expression of markers of neuronal differentiation, such as increased expression of FoxG1, which has also been implicated in Autism Spectrum Disorder. Changes to the phosphorylation of downstream signalling molecules Erk1/2 and CREB was seen via Western Blot at various time points in the differentiation. These results suggest that CACNA1C plays a role in neuronal development and points to possible pathways that can be targeted in the patient cells. Future work aims to identify the functional affect that alterations in CACNA1C will have on neuronal signalling using multi-electrode arrays to measure network activity.
P29
Phenotypic and genetic associations between anhedonia and brain structure in UK Biobank
Xingxing Zhu, Breda Cullen, Joey Ward, Rona Strawbridge, Laura Lyall, Daniel Smith
Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
Background: Anhedonia, the reduced ability to experience pleasure, is a prominent common symptom across different psychiatric disorders such as major depressive disorder and schizophrenia. Previous neuroimaging studies have reported associations between anhedonia and significant differences in grey and white matter structure, however findings are inconsistent, which is likely due to small sample sizes. Furthermore, existing studies have mainly focused on populations with diagnoses of mental illness. Therefore, the present study seeks to explore the associations between brain structure, anhedonia and its genetic risk in a large general sample. Methods: In UK Biobank, we examined associations of frequency of recent anhedonia (data field 2060, assessed at imaging visit) with subcortical volumes and white matter integrity in 18,053 participants with complete data and no diagnosis of developmental or neurological disorder or mental illness. Regression models were used to test associations of anhedonia with brain structural phenotypes. Age, age2, sex and estimated intra-cranial volume were controlled for in the models. All p-values were FDR-corrected. Preliminary Results: Significant associations were observed between anhedonia and reduced volume of total grey matter (β= -0.006, pcorrected = 0.033), nucelus accumbens (β= -0.030, pcorrected <0.001), thalamus (β= -0.019, pcorrected <0.001). Regarding white matter integrity, anhedonia was positively associated with mean diffusivity in the superior thalamic radiation (β= 0.048, pcorrected = 0.03), and the association with fractional anisotropy of the posterior thalamic radiation (β = -0.047 pcorrected = 0.060) trended to significance. These findings are consistent with previous reports, and with associations using a polygenic risk score for anhedonia recently published by our group (Ward et al, 2019, Trans Psych). Conclusions: Our findings demonstrate that anhedonia is associated with alterations in grey and white matter structure in a population without mental illness, especially the reward processing-related brain structures, similar to previously reported associations. These results would contribute to a better understanding of anhedonia and mental illness. Work is ongoing* to expand upon these findings to explore potential causality of the associations. *likely to be completed prior to the Genomics of Brain disorders meeting
P30
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P32
Delegate List Zhongbo Chen UCL Stefan Aigner [email protected] University of California, San Diego [email protected] Zhongbo Chen UCL Institute of Neurology Mouhamed Alsaqati [email protected] Cardiff University [email protected] Elaine Chew Nanyang Technological University Alexander Arguello [email protected] National Institute of Mental Health [email protected] Louisa Christie Cerevance Melanie Bahlo [email protected] Walter and Eliza Hall Institute [email protected] Nicholas Clare Synthego Jeffrey Barrett [email protected] Genomics plc [email protected] Justin Cooper 10x Genomics Dominik Biezonski [email protected] New York Genome Center [email protected] Harriet Cullen Centre for the Developing Brain, King's Amrita Bobok College Gedeon Richter Plc [email protected] [email protected] David Curtis Lorenzo Bomba UCL Genetics Institute Biomarin [email protected] [email protected] Daniel D Andrea Kristen Brennand Cardiff University Icahn School of Medicine at Mount Sinai [email protected] [email protected] Maria Dalby Solveig Brunstad Lundbeck AS/Karolinska Institute University of Bergen [email protected] [email protected] Sterre de Boer Nicolò Caporale Alzheimercentrum Amsterdam Human Technopole [email protected] [email protected] Samuel Demharter Tom Chambers Lundbeck Cardiff University [email protected] [email protected]
Ditte Demontis Lynsey Hall Aarhus University Cardiff University [email protected] [email protected]
Carmen Domínguez Anne Marja Hammar Brigham and Women's Hospital TAMK [email protected] [email protected]
Laura Donker Kaat Adrian Harwood Erasmus MC Cardiff University [email protected] [email protected]
Mahnoor Ejaz Janet Harwood Atta Ur Rahman School of Applied Cardiff University Biosciences, National University of Sciences [email protected] and Technology [email protected] Iiris Hovatta University of Helsinki Dhamidhu Eratne [email protected] University of Melbourne [email protected] Leon Hubbard Cardiff University Karol Estrada [email protected] BioMarin Pharmaceuticals [email protected] Laura Huckins Pamela Sklar Division of Psychiatric Genomics Aine Fairbrother Browne [email protected] UCL [email protected] Charlotte Jacob VIB UAntwerpen Christopher Fell [email protected] LBI-RUD [email protected] Julie Jerber Sanger Institute Aleksandra Fesiuk [email protected] Nencki Institute of Experimental Biology [email protected] Huijue Jia BGI Research, BGI-Shenzhen Adam Frankish [email protected] EMBL-EBI [email protected] Xin Jin Harvard University Olga Giannakopoulou [email protected] University College London [email protected] SAMUEL JOBBINS CARDIFF UNIVERSITY Alison Goate [email protected] Icahn School of Medicine [email protected]
Jessica Johnson Peter Maycox Icahn School of Medicine at Mount Sinai Takeda [email protected] [email protected]
Martin Kampmann Roderick McInnes UCSF Lady Davis Institute [email protected] [email protected]
Anneke Kievit Anna Middleton Erasmus MC Rotterdam Wellcome Genome Campus [email protected] [email protected]
Laura Kleckner Derek Morris Cardiff University Nat. Uni. of Ireland, Galway [email protected] [email protected]
Anat Kreimer Aine Moylett UC Berkeley and UCSF Cardiff University [email protected] [email protected]
Anne Krogh Noehr Graham Murray University of Copenhagen University of Cambridge [email protected] [email protected]
Jonathan LeBowitz Victor Neduva BioMarin Pharmaceutical, Inc. MSD [email protected] [email protected]
Cathryn Lewis Cathal Ormond King's College London Trinity College Dublin [email protected] [email protected]
Nan Li Michael Owen University of Sheffield Cardiff Universtiy [email protected] [email protected]
Lorna Lopez Noemí Pallas Bazarra Trinity College Dublin King's College London [email protected] [email protected]
Ashley Lu Robert Pearsall VIB & KU Leuven NHS LANARKSHIRE [email protected] [email protected]
Yvonne Lussi Yolande Pijnenburg EMBL-EBI Amsterdam UMC [email protected] [email protected]
Andrew Pocklington Natasha Sangha Cardiff University University of Glasgow [email protected] [email protected]
Eleonora Porcu Faezeh Sarayloo University of Lausanne McGill University [email protected] [email protected]
Geraint Price Samantha Schaffner Imperial College London University of British Columbia [email protected] [email protected]
David Pulford Jeremy Schwartzentruber GlaxoSmithKline EMBL-EBI [email protected] [email protected]
Bobbie RaySannerud Jenny Shin DNV GL Cardiff University [email protected] [email protected]
Elliott Rees Muhammad Shoaib Cardiff University Kings College London [email protected] [email protected]
Alastair Reith Ana Silva GlaxoSmithKline Pharmaceuticals R&D Cardiff University [email protected] [email protected]
Lianne Reus Andrew Singleton Alzheimer Centre Amsterdam National Institute on Aging [email protected] [email protected]
Regina H Reynolds Nathan Skene University College London Imperial College London [email protected] [email protected]
Beatriz Rico Anne Kristin Stavrum King's College London University of Bergen [email protected] [email protected]
Niamh Ryan Vasanta Subramanian Trinity College Dublin University of Bath [email protected] [email protected]
Mina Ryten Rachana Tank University College London University of Glasgow [email protected] [email protected]
Eden Teferedegn Gemma Wilkinson Ege University Cardiff University [email protected] [email protected]
Sally Temple Jan Witkowski Neural Stem Cell Institute Cold Spring Harbor Laboratory [email protected] [email protected]
Giuseppe Testa Naomi Wray Human Technopole The University of Queensland [email protected] [email protected]
Nicky Thrupp ChunFang Xu KU Leuven GSK [email protected] [email protected]
Emir Turkes Karen Yu UK DRI at UCL BioMarin Pharmaceutical [email protected] [email protected]
Cora Vacher Xingxing Zhu Illumina University of Glasgow [email protected] [email protected]
Rebecca Valentino Mayo Clinic [email protected]
Heidi Valtatie Tampere of university of applied sciences [email protected]
Jonelle Villar University of Bergen [email protected]
Caleb Webber UK Dementia Research Institute @Cardiff [email protected]
Catherine Widnall Cardiff University [email protected]
Lawrence Wilkinson Cardiff University [email protected]
Index
Aigner, S S51 Lewis, C S35 Alsaqati, M P1 Lopez, L P15 Lussi, Y P16 Bahlo, M S21 Barrett, J S53 Middleton, A S43 Brunstad, S P2 Morris, D P17 Moylett, A P18 Caporale, N P3 Chen, Z S41 Ormond, C P19 Chew, E P4 Owen, M S1 Cullen, H S29 Pocklington, A P20 Demontis, D S27 Porcu, E S25 Domínguez, C S31 Rees, E S37 Ejaz, M P5 Reus, L P21 Eratne, D P6 Reynolds, R.H S23 Esko, T S45 Rico, B S11 Ryan, N P22 Fairbrother Browne, A P7 Fell, C P8 Schaffner, S P23 Fesiuk, A P9 Schwartzentruber, J S55 Frankish, A P10 Shin, J P24 Silva, A S15 Giannakopoulou, O P11 Singleton, A S33 Skene, N S7 Harwood, J P12 Hubbard, L P13 Temple, S S9 Testa, G P25 Jia, H P14 Turkes, E P26 Jerber, J S13 Jin, X S19 Valentino, R P27 Johnson, J S39 Villar, J P28
Kampmann, M S3 Webber, C S5 Kievit, A S47 Wilkinson, G P29 Kreimer, A S17 Wray, N S49
Zhu, X P30 To Hinxton Village (Vehicle access via main exit to site) Willow Court (A&B) B = 230-243 330-343 Mulberry Court (C) A = 244-259 201-229 344-361 301-329 401-406 A B
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Disabled Tennis Court Conference Centre Training Suite Reception Francis Crick Auditorium James Watson Pavilion Rosalind Franklin Pavilion Hinxton Hall Loft Room 1 and 2 Pompeiian Room Library Room Green Room Restaurant Lounges/Bar Bedrooms 362-367/407-410
Hinxton Hall
Conference Centre
EMBL - EBI The Sulston Laboratories
West Pavilion
The Cairns Pavilion The Data Centre RSF
Wet
Labs The Morgan Building Morgan The
Reception
Fire Assembly Point Designated Smoking Area EBI South @ACSCevents Wellcome Genome Campus Courses and Conferences wellcomegenomecampus.org /coursesandconferences