Functional Guy’s and St Thomas’ NHS Foundation Trust and King’s College London’s comprehensive Genomics Biomedical Research Centre Workshop
10-12 February 2016 Introduction
Functional Genomics Workshop
10-12 th February 2016 St Thomas’ Hospital Governors’ Hall King’s College London London, UK
Aims of the workshop • To highlight new advances in understanding the functional impact of genetic variation in immune mediated inflammatory and related diseases. • To provide delegates with an experimental framework for investigating the functional basis of genetic variation. • To provide opportunities for investigators and their collaborators to network in this field of research.
Organising Committee Tim Vyse (KCL) Lars Klareskog (Karolinska Institute) Tom Huizinga (Leiden University Medical Centre) Jane Worthington (Manchester University) Frank Nestlé (KCL) Richard Trembath (KCL) Andrew Cope (KCL)
Workshop Sponsors
BTCURE EU IMI Programme NIHR/Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London Workshop programme Keynote Lectures: 45mins Plenary Talks: 25mins + 5min discussion Abstract presentations: 10mins Day 1 : Wednesday 10 th February (including discussion)
12:30 Registration opens in Governor’s Hall, St Thomas’ Hospital
13:50 Welcome and Opening Remarks
14:00 - 15:30: Session 1 – Rheumatoid Arthritis (Chair: Jane Worthington)
Plenary 1 Soumya Raychaudhuri (Harvard Medical School, Boston, US): Using human genetics to define molecular mechanisms of rheumatoid arthritis Plenary 2 Fina Kurreeman (Leiden University Medical Centre, The Netherlands): Novel ncRNA in the TRAF1-C5 region associated with Rheumatoid arthritis Plenary 3 Andrew Cope (Kings College London, UK): PTPN22 links integrin-mediated adhesion with autoimmunity
15:30 - 16:00 Tea break with poster viewing
16:00 - 17:30: Session 2 – Genetics of the immune response (Chair: Kerrin Small)
Plenary 4 Frank Nestlé (Kings College London, UK) : Genetic Architecture of the Human Immune System Selected abstract presentations (10 min each, including discussion)
A1. Sylvie Grandemange (INSERM, Paris, France): NLRP1 mutations cause autoinflammatory diseases in human: implication of the NLRP1 inflammasome? A2. Elena Lopez-Isac (CSIC, Madrid, Spain): Interrogating the common genetic background for systemic sclerosis and rheumatoid arthritis through a cross-disease meta-analysis of Genome-wide Association Studies. Plenary 5 Julian Knight (University of Oxford, UK) : eQTL mapping of induced innate immune response
17:30 - 18:15: Session 3 – Keynote Lecture (Chair: Tim Vyse)
Speaker: Manolis Dermitzakis (University of Geneva, Switzerland) : Population and personal genomics to reveal disease biology
End of Day 1 Scientific sessions
18:30 – 21:00 Welcome Reception in Central Hall, St Thomas’ Hospital
1 Workshop programme
Day 2: Thursday 11 th February
MORNING SESSION
08:30 – 10:30: Session 4 – Functional genomics of mucosal and epithelial immunity (Chair: Graham Lord)
Plenary 6 Daniel Graham (Broad Institute, Boston, USA): Coping with stress in mucosal tissues Plenary 7 Holm Uhlig (University of Oxford, UK): The genetic landscape of monogenic forms of inflammatory bowel disease Plenary 8 Anne Bowcock (Imperial College, London, UK): Role of CARD14 in psoriasis pathogenesis Plenary 9 Linde Meyaard (University Medical Centre, Utrecht, The Netherlands): A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the immune checkpoint gene SIRL-1 10:30 - 11:00 Coffee break with poster viewing
11:00 - 13:00: Session 5 – Novel approaches, technologies and tools – I (Chair: Richard Trembath)
Plenary 10 Richard Trembath (Kings College London, UK) : Sequencing in a specific population for recessive variants Plenary 11 Trevor Lawley (Sanger Institute, Cambridge, UK) : Levels of genomic and functional diversity in the human intestinal microbiota Plenary 12 Alka Saxena (NIHR-BRC at Guy’s and St Thomas’ NHS Foundation Trust, London, UK) : Single cell technologies Selected abstract presentations (10 min each, including discussion)
A3. Eric Schordan (FIRALIS SAS, Huningue, France): miRNA profiling using HTG-Edgeseq platform predicts response to anti-TNF therapy in rheumatoid arthritis α A4. Chris Odhams (King’s College London, UK): Discovering SLE candidate genes and mechanisms by eQTL analysis using RNA-Seq. A5. Angela Hodges (King’s College London, UK): AD-associated TREM2 variants lead to fewer microglia expressing HLA-DP, DQ, DR in the hippocampus of post-mortem human brains 13:00 - 14:00 Lunch with posters
2 Day 2: Thursday 11 th February
AFTERNOON SESSION
14:00 – 16:00: Session 6 – Whole organism models to dissect gene function – I (Chair: Lars Klareskog)
Plenary 13 David Rawlings (Seattle Children’s Hospital, Washington, US): Altered B cell signaling orchestrates loss of tolerance and systemic autoimmunity Plenary 14 Stephen McMahon (King’s College London, UK): Pain – why does it hurt so much? Plenary 15 George Kollias (Alexander Fleming Institute, Athens, Greece): Mesenchymal causalities in chronic inflammation Selected abstract presentations (10 min each, including discussion) A6. Miranda Houtman (Karolinska Institute, Solna, Sweden): Investigation of the associated PTPN2 locus in rheumatoid arthritis: importance of long non-coding RNA A7. Olfa Khalifa (INSERM, Paris, France): New genes in the X chromosome associated with Rheumatoid Arthritis A8. Klementy Shchetynsky (Karolinska Institute, Solna, Sweden): Discovery of new candidate genes for rheumatoid arthritis by integration of genetic association data with expression pathway analysis 16:00 - 16:30 Tea break
16:30 - 18:00: Session 7 – Novel approaches, technologies and tools – II (Chair: Frank Nestlé)
Plenary 16 Nicholas Luscombe (Francis Crick Institute, London, UK) : Using hiCLIP to identify long-range loops in RNAs Plenary 17 Aviv Madar (Cornell University, New York, USA) : Computational biology as applied to hypersensitivity DNase analysis Plenary 18 Phil de Jager (Harvard Medical School, Boston, USA) : eQTL analyses and systems biology in MS and dementia
End of Day 2 Scientific session s
Speakers Dinner (Meeting in the Park Plaza Westminster Bridge hotel lobby at 7:45pm)
Free evening for all other delegates
3 Workshop programme
Day 3: Friday 12 th February
MORNING SESSION
09:00 – 11:00: Session 8 – Autoimmunity - I (Chair: Deborah Cunninghame-Graham)
Plenary 19 David Morris (Kings College London, UK): Genes, ancestry and prevalence in SLE Plenary 20 Kim Simpfendorfer (Feinstein Institute, New York, USA): Investigating immune endophenotypes in healthy human carriers of autoimmune disease-associated risk haplotypes in BLK and TNIP1 Plenary 21 Ward Wakeland (University of Texas Southwestern, Dallas, US): A genomic analysis of susceptibility to systemic autoimmunity Plenary 22 Gil McVean University of Oxford, UK): Dissecting the structure and phenotypic consequences of HLA genomic variation 11:00 - 11:30 Coffee break
11:30 - 13:00: Session 9 - Whole organism models to dissect gene function – II (Chair: Andrew Cope)
Plenary 23 Marc Dionne (Imperial College London, UK) : Infections and immune responses in Drosophila Plenary 24 Chrissy Hammond (Bristol University, UK) : Using zebrafish to unpick the interactions between biomechanics and genes in making, shaping and maintaining a joint Plenary 25 Rikard Holmdahl (Karolinksa Institute, Sweden) : Positioning and analysis of the major genes controlling arthritis in rats 13:00 - 14:00 Lunch with posters AFTERNOON SESSION
14:00 – 15:00: Session 10 – Autoimmunity – II (Chair: Tim Vyse)
Plenary 26 Stephen Sawcer (University of Cambridge, UK): Making progress in MS Selected abstract presentations (10 min each, including discussion)
A9. Michelle Krishnan (King’s College London, UK): Investigation of biological pathways involved in brain development in preterm neonates using a multivariate phenotype and sparse regression A10. Gisela Orozco (University of Manchester, UK): Capture Hi-C reveals a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23
15:00 - 15:45: Session 11 - Keynote Lecture (Tim Vyse)
Speaker: John Todd (University of Cambridge, UK) : Type I Diabetes Closing remarks and Depart
4 Soumya Raychaudhuri Session 1 Divisions of Genetics & Rheumatology Day 1: Wednesday Brigham & Women's Hospital 10 th February Harvard Medical School Boston USA
Using human genetics to define molecular mechanisms of rheumatoid arthritis
Dr. Raychaudhuri is an Associate Professor at Harvard Medical School and at Brigham and Women’s Hospital. He is also appointed as an Associate Member at the Broad Institute and a Professor in Genetics at the University of Manchester. He matriculated into the Stanford University NIH funded MST program in 1997 after completing degrees in mathematics and biophysics at the University at Buffalo. In 2004, he completed both his medical training and his doctoral training in biomedical informatics under Russ Altman. After completing his clinical training in Internal Medicine, he joined the rheumatology fellowship training program in 2006, and concurrently completed his postdoctoral fellowship training under Mark Daly at the Broad Institute. Since starting his own group in 2010 at Harvard Medical School and Brigham and Women’s Hospital, his lab has focused on finding and fine-mapping disease alleles in rheumatoid arthritis (with a particular interest in the HLA region), age related macular degeneration and other diseases. He has also been devising integrative statistical genetics strategies to identify causal variation by taking advantage of large-scale epigenetic data. He is the current Systems Biology Group Director for the NIH funded Accelerating Medical Progress (AMP) program in rheumatoid arthritis and systemic lupus erythematosus. He has published over 100 papers in peer-reviewed journals including Nature Genetics, Nature, Science, and the PNAS.
Key references: a. Hu X, Kim H, Stahl E, Plenge R, Daly M, Raychaudhuri S . Integrating Autoimmune Risk Loci with Gene Expression Data Identifies Specific Pathogenic Immune Cell Subsets. American Journal of Human Genetics . 89:496–50, 2011. PMC3188838. b. Trynka, G, Sandor C, Han B, Xu H, Stranger B, Liu X, Raychaudhuri S . Identifying critical cell-types to fine-map complex trait variants with chromatin marks. Nature Genetics . 45:124-130, 2013 PMC3826950. c. Stahl, EA, Wegmann D, Trynka G, Guitierrez J, Do R, Voight BF, et al… Raychaudhuri S# , and Plenge RM#. Bayesian inference reveals the hidden polygenic architecture of common disease. Nature Genetics . 44:483–489, 2012. PMC in Progress. d. Raychaudhuri S* , Sandor C, Stahl EA, et al… de Bakker PIW*. Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Nature Genetics . 44:291-6, 2012. PMC3288335. e. Hu X, Deutsch AJ, Lenz TL, Onengut-Gumuscu S, Han B, Chen W-M, Howson JMM, Todd JA, de Bakker PIW, Rich SS, Raychaudhuri S . Additive and interaction effects at three key amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes genetic risk. Nature Genetics. 47(8):898-905. PMC in Progress. f. Lenz TL*, Deutsch AJ*, Han B, Hu X, et al … de Bakker PIW*, Raychaudhuri S* . Widespread non-additive and interaction effects within the HLA modulate the risk of autoimmune diseases. Nature Genetics . 47(9):1085-90. PMC in Progress. g. Seddon JM*, Yu Y, Miller EC, Reynolds R, Tan PL, Gowrisankar S, Goldstein JI, Triebwasser M, Anderson HE, Zerbib J, Kavanagh D, Souied E, Katsanis N, Daly MJ, Atkinson JP, and Raychaudhuri S* . Rare variants in CFI, C3 and C9 are associated with high risk of advanced age- related macular degeneration. Nature Genetics . 45:1366-70, 2013. PMC3902040.
5 6 Fina Kurreeman Session 1 Leiden University Medical Centre Day 1: Wednesday th The Netherlands 10 February
Novel ncRNA in the TRAF1-C5 region associated with Rheumatoid arthritis
Dr Fina Kurreeman is assistant professor at Leiden University Medical Center. She graduated from her PhD in 2009 (Cum Laude) following the discovery of the third genetic risk factor associated with rheumatoid arthritis. She spent three years doing her post-doctoral training in the lab of Dr Robert Plenge at Harvard Medical School and at the broad institute of MIT and Harvard. During this time, she implemented largescale NGS techniques to discover the role of genetic variation in human disease, in particular rheumatoid arthritis. This work led to several important publications in American Journal of Human genetics (main author) and several papers in Nature genetics (co-author). She has contributed to the discovery of >100 genetic regions linked with Rheumatoid Arthritis. Dr Kurreeman is the recipient of several prestigious National and European Grants and is regularly invited by consortia and conferences to give lectures (BTCURE, EULAR).
Dr. Fina Kurreeman’s research currently focuses on (i) Understanding how genetic variation results in functional changes relevant in disease (ii) Understanding the role of specific cells in chronic activation (iii) the possible role of microbes in disease. Her main interest is to leverage genomics techniques to help unravel novel mechanisms underlying disease pathogenesis.
7 Andrew Cope Session 1 Academic Rheumatology Day 1: Wednesday th Kings College London, UK 10 February
PTPN22 links integrin-mediated adhesion with autoimmunity
Andrew Cope graduated in Medicine from the University of London with first class honours. After training in general internal medicine at Northwick Park Hospital, The National Hospital for Nervous Diseases and the Royal Brompton Hospital, he trained in rheumatology with Professor Sir Ravinder Maini and Dr. Barbara Ansell CBE. In 1990, he was awarded a Wellcome Trust Clinical Training Fellowship, studying for a PhD in Cytokine Biology with Professor Sir Marc Feldmann at the Kennedy Institute of Rheumatology. Following a postdoctoral fellowship with Professor Hugh McDevitt at Stanford University, California, studying transgenic models of autoimmunity, he returned to the Kennedy Institute to set up his own laboratory. In 2005 Andrew Cope was appointed Reader in Molecular Medicine at the Kennedy Institute of Rheumatology, and in 2008 was recruited to the Arthritis Research UK Chair in Rheumatology at King’s College London. He is currently Head of the Academic Department of Rheumatology and Associate Director of the King’s Clinical Trials Unit, and has been Lead for the NIHR Biomedical Research Centre’s School for Translational and Experimental Medicine (STEM) at Guy’s and St Thomas NHS Foundation Trust since 2012. His clinical research interests revolve around aspects of inflammatory arthritis, including very early inflammatory arthritis and disease remission states. Research in the Cope lab is focused around two key themes: the biology of T cell activation and differentiation in the context of chronic inflammatory diseases, such as rheumatoid arthritis, with an emphasis on antigen receptor signal transduction and cell migration; understanding how allelic variants of immunologically important genes contribute to autoimmune disease pathogenesis. The Cope lab is housed in the Centre for Molecular and Cellular Biology of Inflammation (CMCBI) on the Guy’s Campus, Faculty of Life Sciences and Medicine, King’s College London.
8 Frank Nestlé Session 2 Division of Genetics and Molecular Medicine Day 1: Wednesday th St Johns Institute of Dermatology 10 February Kings College London, UK
Genetic Architecture of the Human Immune System
Professor Frank O Nestlé holds the post of Mary Dunhill Chair of Cutaneous Medicine and Immunotherapy at St. John’s Institute of Dermatology, King’s College London. He is a Non Executive Director at Guy’s and St. Thomas’ Hospital and a member of the Biomedical Research Centre (BRC) Executive. He is also Director of the Federation of Clinical Immunology Society (FOCIS) Centre of Excellence King’s College London. Professor Nestle is a National Institute for Health Research (NIHR) Senior Investigator and a Fellow of the Academy of Medical Sciences (FMedSci). His main research interests include the pathogenesis and immunotherapy of inflammatory skin disease and skin cancer. He has given over 350 scientific lectures at national and international conferences. He was a Visiting Professor at the Mayo Clinic, Yale Medical School and Rockefeller University. He is a member of numerous national and international societies and is currently President of the Federation of Clinical Immunology Societies (FOCIS). He has published over 200 scientific articles in publications such as Nature, Nature Medicine, Cell, New England Journal of Medicine, Journal of Experimental Medicine and Lancet. He has received numerous awards including the Alfred Marchionini Research Award at the 20th World Congress of Dermatology and the American Skin Association Achievement Award at the Tricontinental Meeting of the Societies of Investigative Dermatology. Despite recent discoveries of genetic variants associated with autoimmunity and infection, genetic control of the human immune system during homeostasis is poorly understood. We undertook a comprehensive immunophenotyping approach, analysing 78,000 immune traits in 669 female twins. From the top 151 heritable traits (up to 96% heritable), we used replicated GWAS to obtain 297 SNP associations at 11 genetic loci, explaining up to 36% of the variation of 19 traits. We found multiple associations with canonical traits of all major immune cell subsets and uncovered insights into genetic control for regulatory T cells. This data set also revealed traits associated with loci known to confer autoimmune susceptibility, providing mechanistic hypotheses linking immune traits with the etiology of disease. Our data establish a bioresource that links genetic control elements associated with normal immune traits to common autoimmune and infectious diseases,providing a shortcut to identifying potential mechanisms of immune-related diseases.
9 10 Abstracts
A1 Sylvie Grandemange : NLRP1 mutations A2 Elena Lopez-Isac : Interrogating the cause autoinflammatory diseases in human: common genetic background for systemic implication of the NLRP1 inflammasome? sclerosis and rheumatoid arthritis through a Authors: cross-disease meta-analysis of Genome-wide Sylvie Grandemange 1-2 , Elodie Sanchez 2-3 , Pascale Louis- Association Studies. Plence 2, Cécile Rittore 1-2 , John C Reed 4 , Florence Authors: Apparailly 2, Isabelle Touitou 1-2-5 , David Geneviève 2-3 . Elena López-Isac 1* , Shervin Assassi 2, Carmen Pilar Simeón 3, Affiliation: Patricia Carreira 4, Norberto Ortego-Centeno 5, the Spanish 1. Laboratoire des maladies rares et auto- Scleroderma Group, Benjamín Fernández-Gutiérrez 7, inflammatoires, Hôpital Arnaud de Villeneuve, Miguel A González-Gay 8, Lorenzo Beretta 9, Claudio CHRU Montpellier, France Lunardi 10 , Gianluca Moroncini 11 , Armando Gabrielli 11 , Torsten Witte 12 , Nicolas Hunzelmann 13 , Jörg H.W. Distler 14 , 2. INSERM U1183, Institute of regenerative medicine Gabriella Riekemasten 15 , Annete H van der Helm-van Mil 22 , and biotherapy, Montpellier, France Jeska de Vries-Bouwstra 16 , Cesar Magro 16 , Alexandre E. 3. Département de Génétique médicale, Hôpital Voskuyl 17 , Madelon C Vonk 18 , Øyvind Molberg 19 , Tony Arnaud de Villeneuve, CHRU Montpellier, France Merriman 20 , Roger Hesselstrand 21 ,Annika Nordin 22 , Leonid Padyukov 22 , Ariane Herrick 23 , Steve Eyre 23 , Bobby PC 4. Sanford-Burnham Medical Research Institute, Koeleman 24 , Christopher P. Denton 25 , Carmen Fonseca 25 , La Jolla, CA. United-States Timothy RDJ Radstake 26 , Jane Worthington 23 , Maureen D. 5. University of Montpellier Mayes 2, Javier Martín 1 Abstract text: Affiliation: Inflammation is a vital and complex process in response to 1. Institute of Parasitology and Biomedicine López-Neyra, diverse tissue damaging stimuli such as trauma, injury and IPBLN-CSIC, PTS Granada, Granada, Spain. pathogen. NLRP1, NLRP3 and NLRC4 belonging to the 2. The University of Texas Health Science Center–Houston, intracellular proteins Nod like receptor family, are capable Houston, USA. of sensing the inflammatory inducers and trigger the 3. Department of Internal Medicine, Valle de Hebrón assembly of a large complex called the inflammasome. By Hospital, Barcelona, Spain. inducing the caspase-1 activation, inflammasome plays a 4. Department of Rheumatology, 12 de Octubre University crucial role in the release of IL-1 and IL-18, two critical Hospital, Madrid, Spain. cytokines of the initial steps of inβflammatory responses. 5. Department of Internal Medicine, Clinic University Whereas mutations in NLRP3 and NLRC4 have been Hospital, Granada, Spain. linked to two rare monogenic systemic autoinflammatory 7. Rheumatology Service, Hospital Clínico San Carlos, diseases (SAIDs), several polymorphisms in the NLRP1 gene Madrid, Spain. have been associated extensively to an increased risk of 8. Health Research Institute of Santiago de Compostela autoimmune disorders (e.g. vitiligo, psoriasis, type 1 (IDIS), Division of Rheumatology, Clinical University diabetes, and rheumatoid arthritis). We identified for the Hospital of Santiago de Compostela, Spain. first time two distinct NLRP1 mutations in patients 9. Referral Center for Systemic Autoimmune Diseases, displaying a novel SAID combining autoinflammation and Fondazione IRCCS Ca' Granda Ospedale Maggiore autoimmunity. The aim of our study was to unravel how Policlinico di Milano, Milan Italy. mutation in NLRP1 impaired its function and triggered 10. Department of Medicine, Università degli Studi di autoinflammation. Verona, Verona, Italy. Peripheral blood mononuclear cells from patients were 11. Clinica Medica, Department of Clinical and Molecular analyzed to identify the immunologic components involved Science, Università Politecnica delle Marche and in these novel diseases, using flow cytometry and ex vivo Ospedali Riuniti, Ancona, Italy. NLRP1 inflammasome stimulation. The pathogenic effect of 12. Department of Clinical Immunology, Hannover Medical the NLRP1 mutations in inflammation was investigated School, Hannover, Germany. using in vitro functional assays in transfected HEK293T. 13. Department of Dermatology, University of Cologne, The level of caspase-1, IL-18 and IL-1 in serum Cologne, Germany. samples from patients was increased as cβompared to 14. Department of Internal Medicine, Institute for Clinical controls and unaffected parents. Moreover, patient’s cells Immunology, University of Erlangen-Nuremberg, displayed constitutive production of IL-1 . Functional Erlangen, Germany. studies in HEK293T revealed that the NLRβP1 mutations 15. Clinic of Rheumatology, University of Lübeck, Lübeck , resulted in a constitutive activation of the NLRP1 Germany inflammasome. 16. Department of Rheumatology, Leiden University We demonstrated for the first time that two mutations Medical Center, Leiden, The Netherlands. in the NLRP1 gene are involved in autoinflammation in 17. Department of Rheumatology, VU University Medical human. We named this disease NAIAD, for NLRP1- Center, Amsterdam, The Netherlands. associated autoinflammation arthritis and dyskeratosis. Our data, combined to the literature, highlight the pleomorphic roles of NLRP1 in inflammation and immunity. continued overleaf
11 Abstracts
A2
Affiliation (continued)
18. Department of Rheumatology, Radboud University RA loci identified IRF4 as a novel shared risk factor for these -12 Nijmegen Medical Center, Nijmegen, The Netherlands. two rheumatic conditions (P combined = 3.29 x 10 ). In 19. Rheumatology Unit, Oslo University Hospital addition, the analysis of the biological connection across Rikshospitalet and Institute of Clinical Medicine, known SSc-RA shared loci pointed to the type I interferon University of Oslo, Oslo, Norway. and the interleukin 12 signaling pathways as the main 20. Department of Biochemistry, University of Otago, common etiopathogenic factors. New Zealand. Conclusions : The present study has identified a novel shared 21. Department of Rheumatology, Lund University, Lund, locus, IRF4, for SSc and RA and highlighted the usefulness of Sweden. inter-disease GWAS meta-analysis in the identification of 22. Rheumatology Unit, Department of Medicine, common risk loci. With this study, we provide additional Karolinska University Hospital, Karolinska Institutet, genetic evidence for the IFN signature described for SSc and Stockholm, Sweden. RA patients. 23. Centre for Musculoskeletal Research and NIHR Manchester Musculoskeletal Biomedical Research Unit, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK. 24. Section Complex Genetics, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands. 25. Centre for Rheumatology, Royal Free and University College Medical School, London, United Kingdom. 26. Department of Rheumatology & Clinical Immunology, Laboratory of Translational Immunology, department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands.
Abstract text: Background : Systemic sclerosis (SSc) and rheumatoid arthritis (RA) are two autoimmune diseases that share clinical and immunological features: Both are rheumatic connective tissue disorders, characterized by an exacerbated inflammatory response, deregulation of innate and adaptive immunity, including autoantibody production, and systemic complications. To date, several shared SSc-RA loci have been identified independently, pointing to a common genetic background underlying these two autoimmune processes. Aim : To systematically identify new common SSc-RA loci through a cross-disease meta-GWAS strategy. Methods : We performed a meta-analysis combining GWAS datasets of SSc and RA using a strategy that allowed identification of loci with both same-direction and opposing- direction allelic effects. The top single-nucleotide polymorphisms (SNPs) showing a P-value < 5 x 10 -6 in the cross-disease meta-analysis and nominal significance in the association study for each disease separately were followed- up in independent SSc and RA case-control cohorts. In total, this study comprises 8,830 SSc patients, 16,870 RA patients and 43,393 controls. Results : The cross-disease meta-analysis of the GWAS datasets identified several SNPs from different genomic regions showing a P-value < 5 x 10 -6 and nominal association in the disease-specific GWAS scan. These loci included several genomic regions not previously reported as shared loci, besides risk factors associated with both diseases in previous studies. The follow-up of the putatively new SSc-
12 Julian Knight Session 2 Nuffield Department of Medicine Day 1: Wednesday th Wellcome Trust Centre for Human Genetics 10 February University of Oxford UK eQTL mapping of induced innate immune response
Julian Knight trained as a clinician scientist, studying Medicine at the University of Cambridge and the University of Edinburgh before completing his DPhil at the University of Oxford at the Weatherall Institute of Molecular Medicine in 1998. He developed his research interest in the functional genomics of immunity working in Oxford at the Wellcome Trust Centre for Human Genetics (WTCHG) and at Harvard University in the Department of Molecular and Cellular Biology. Since 2005 he has worked at the WTCHG as a Principal Investigator and as an Honorary Consultant Physician at the Oxford University Hospitals NHS Trust. The core interest of the lab’s research is how genetic variation between individuals modulates genes critical to mounting an appropriate immune and inflammatory response and may contribute to susceptibility to autoimmune and infectious disease (http://www.well.ox.ac.uk/knight-j).
13 Manolis Dermitzakis Session 3 Department of Genetic Medicine and Development Day 1: Wednesday th University of Geneva Medical School 10 February Switzerland
Population and personal genomics to reveal disease biology
Emmanouil (Manolis) Dermitzakis is currently a Professor of Genetics in the Department of Genetic Medicine and Development of the University of Geneva Medical School. He is a member of the executive board of the Institute of Genetics and Genomics in Geneva (iGE3), a member of the Swiss Institute of Bioinformatics and adjunct faculty member of the Biomedical Research Foundation of the Academy of Athens. He obtained his B.Sc. in 1995 and M.Sc. in 1997 in Biology from the University of Crete (Greece) and his PhD in 2001 from the Pennsylvania State University in the USA, studying the evolutionary biology and population genetics of regulatory DNA in mammals and Drosophila. His post-doctoral work was at the University of Geneva Medical School, focusing on comparative genome analysis and the functional characterization of conserved non-genic elements. He, previously, was an Investigator and Senior Investigator at the Wellcome Trust Sanger Institute in Cambridge from 2004 to 2009. He was elected an EMBO member in 2014 and has also been named Highly Cited Researcher by ISI in 2014 and 2015. He currently serves as the president of the Executive Board of the World Hellenic Biomedical Association (2014-2015). His current research focuses on the genetic and molecular basis of human disease. He has had leading roles in big international projects such as ENCODE (ENCyclopedia Of Dna Elements), Mouse Genome Sequencing Consortium, International HapMap project, 1000genome and GTEx. He has served as an editor for the journals Science, PLoS Genetics and eLife.
14 Daniel Graham Session 4 Broad Institute Day 2: Thursday th Boston 11 February USA
Population and personal genomics to reveal disease biology
Daniel Graham is a principal investigator at the Broad Institute and faculty member at the Massachusetts General Hospital of Harvard Medical School. He received his PhD in immunology from the Mayo Clinic College of Medicine and completed postdoctoral training at Washington University School of Medicine in St. Louis. His work leverages insights gleaned from human genetics to identify key pathways underlying inflammatory bowel disease (IBD). His research adopts multidisciplinary approaches comprised of (1) functional genetic screens to place genes in immune pathways, (2) multi’omic platforms for deep mechanistic characterization of gene function, (3) developing mouse models to discern gene function in the context of complex pathological responses in vivo, and (4) identification of novel targets for therapeutic development. Collectively, his work has contributed to the understanding of inflammatory signal transduction pathways that elicit innate effector mechanisms (oxidative burst, natural cytotoxicity) and acquisition of adaptive immunity (antigen presentation, T cell differentiation). Ongoing efforts aim to shed light on the coordinated interactions between the innate and adaptive immune systems within the gut mucosa.
15 Holm Uhlig Session 4 Nuffield Department of Medicine Day 2: Thursday th Experimental Medicine Division 11 February University of Oxford UK
The genetic landscape of monogenic forms of inflammatory bowel disease
Holm Uhlig is an Associate Professor and Honorary Consultant in Paediatric Gastroenterology, Children’s Hospital Oxford and the Translational Gastroenterology Unit, University of Oxford. He completed medical residency in pediatrics and pediatric gastroenterology at the University of Leipzig (Germany) and obtained a DPhil in mucosal immunology at the Sir William Dunn School of Pathology in Oxford (UK). Holm investigates rare monogenic disorders that are associated with very early onset of inflammatory bowel disease. Holm contributed to the functional characterisation of several genetic defects that can cause intestinal inflammation. He investigates patients by whole exome sequencing translating genetic information and immunologic understanding into individualised patient care.
16 Anne Bowcock Session 4 National Heart and Lung Institute Day 2: Thursday th Imperial College London 11 February UK
Role of CARD14 in psoriasis pathogenesis
Anne Bowcock is Professor and Chair in Cancer Genomics at Imperial College London. She obtained a PhD from the University of Witwatersrand in South Africa and was a postdoctoral fellow at Stanford University working with Professor Luigi Cavalli-Sforza. She held faculty positions at the University of Texas Southwestern Medical Center at Dallas and Washington University School of Medicine in Saint Louis. Among her research achievements are demonstrating the use of DNA markers in reconstructing human evolution, identifying proteins interacting with the early onset breast cancer gene BRCA1 and identifying a gene commonly mutated in highly metastatic uveal melanoma. She has studied the genetics of psoriasis and psoriatic arthritis for over twenty years and her recent achievements in this field have been in identifying a familiar form of psoriasis and psoriatic arthritis and functional consequences of the disease causing mutations. She is also searching for additional rare and highly penetrant genetic changes that lead to psoriasis and psoriatic arthritis, their role in disease susceptibility and ways of combatting their effects.
17 Linde Meyaard Session 4 Department of Immunology, Day 2: Thursday University Medical Centre Utrecht 11 th February The Netherlands
A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the immune checkpoint gene SIRL-1
Linde Meyaard finished her undergraduate studies in Biomedical Sciences at Leiden University in 1990. She subsequently studied T cell function in HIV-1 infection at Sanquin in Amsterdam with Prof. Frank Miedema, where she graduated in 1995 (Cum Laude). She started studying immune inhibitory receptors at DNAX research institute in Palo Alto, CA in the laboratory of Prof Lewis Lanier and Joseph Phillips, where she cloned the inhibitory receptor LAIR-1. Upon return to the Netherlands she continued her work on LAIR-1 initially as a post-doc with Prof Hans Clevers and later as an independent group leader at the University Medical Center in Utrecht. She was the first to identify collagens and collagen-like proteins as the natural ligands for LAIR-1. She extended her research towards other inhibitory receptors that are able to control collateral damage by the immune system and discovered SIRL-1 as a novel inhibitory receptor able to regulate the function of neutrophils and monocytes. Currently, she focuses on studying the control of immune- mediated collateral tissue damage through inhibitory receptors. She introduced mouse models in her lab, which allowed her to establish an essential role for CD200R in the control of sex-biased immune- mediated damage upon viral infections. Furthermore, she formed a translational research team with clinician Prof Louis Bont, studying regulation of neutrophilic airway inflammation and the potential to therapeutically exploit inhibitory receptors. Meyaard was appointed full Professor of Immune Regulation in Utrecht in 2007. Her work is supported by several prestigious grants, such as a fellowship of the Royal Dutch Academy of Sciences (1999-2001) and personal grants from the Dutch society for Scientific Research (2001, 2002 and 2015) and by grants from the Dutch Arthritis Foundation, Dutch Cancer Society, AICR and others. In addition, the growing global interest in targeting inhibitory receptors therapeutically resulted in consultancies, collaborations and invitations for seminars in pharmaceutical companies opening up possibilities for clinical application of her work. Professor Meyaard serves on multiple scientific boards of and was secretary general of the Dutch Society of Immunology from 2008-2014.
18 19 Richard Trembath Session 5 Division of Genetics & Molecular Medicine Day 2: Thursday th King’s College London 11 February UK
Sequencing in a specific population for recessive variants
Professor Trembath trained in Medicine at Guy's Hospital Medical School, undertook postgraduate studies in genetics at the Institute of Child Health in London and moved to the University of Leicester in 1992, being appointed to the Foundation Chair of Medical Genetics in Leicester in 1998, before moving to King’s in the summer of 2005 where he held the role of Head of Division of Genetics & Molecular Medicine and as the founding Director of the National Institute for Health Research Comprehensive Biomedical Research Centre in association with Guy's & St Thomas' NHS Foundation Trust. Professor Trembath moved to QMUL in 2011 where he held the position of Vice-Principal for Health and Executive Dean of the Barts and The London School of Medicine and Dentistry. In this role Professor Trembath led a major period of change, strengthening cross faculty working, developing models of support for development of the early stages of academic careers, driving forward QMUL new Life Sciences Initiative and partnership working at scale, as an Executive and Board member of the academic health science centre, UCL Partners. He is Fellow of the Academy of Medical Sciences and a former Senior Investigator for the National Institute of Health Research. Professor Trembath's research interests include the identification and characterisation of genes and the molecular pathways underlying a range of human common and rare disorders. Working with colleagues at the University of Cambridge and the Wellcome Trust Sanger Institute, he is the Principal investigator and Co-Director of a major population genomics programme, known as East London Genes and Health.
20 Trevor Lawley Session 5 Trevor Lawley Day 2: Thursday th Sanger Institute 11 February Cambridge UK
Levels of Genomic and Functional Diversity in the Human Intestinal Microbiota
Trevor's research investigates the mechanisms that underlie how micro- organisms on mucosal surfaces (gut, nasopharnyx, uro-gential tract) interact with their host during periods of health and disease. In particular he seeks to develop novel ways to treat diseases that are associated with unwanted imbalances in the micro-organism communities. Trevor uses high-throughput genome sequencing to investigate the microbial communities contained on and within host organisms that are associated with health and disease. He uses clinical samples and mouse models to identify the pathogen and host factors that are linked to disease and infectivity. Trevor obtained his PhD from the University of Alberta, Canada, where he studied the mechanisms that pathogenic bacteria use to disseminate antibiotic resistance genes. Dr Diane Taylor and Dr Laura Frost were his supervisors. His PhD thesis culminated in 2004 with him receiving the 'Gold Award' (Graduate Student of the Year) from the Canadian Society of Microbiologists. After his PhD Trevor was awarded a Canadian Institutes of Health Research post-doctoral fellowship to work in the Laboratory of Professor Stanley Falkow and Dr Denise Monack at Stanford University, USA, where he studied the impact of antibiotic treatment on Salmonella disease and transmission. In 2007 Trevor received a Royal Society of London Award - sponsored by Professor Gordon Dougan - to start a research programme on Clostridium difficile disease and transmission within the Microbial Pathogenesis group at the Wellcome Trust Sanger Institute. In 2010, Trevor was appointed as a Career Development Fellow in the Sanger Institute Faculty and was promoted to Group Leader in 2014. He receives funding from the Medical Research Council.
21 22 Alka Saxena Session 5 NIHR-BRC at Guy’s and St Thomas’ NHS Foundation Trust Day 2: Thursday th London 11 February UK
Single cell technologies
Dr Alka Saxena studied medicine at Shivaji University in India and after 7 years of clinical practice, completed her PhD at the Murdoch Children’s Research Institute at the University of Melbourne in Australia. Alka then went on to work on monogenic disorders, first on Duchenne Muscular Dystrophy at the Australian Neuromuscular Research Institute in Perth, Australia as a Muscular Dystrophy Association (MDA) Research Fellow and later on Rett Syndrome as an NH& MRC postdoctoral Research Fellow at the University of Western Australia, where she received the Barry Marshall Award for her work, before becoming an Assistant Professor. Alka continued her work on Rett Syndrome through Advanced Genomics Technologies at the RIKEN Omics Science Centre in Japan as an international JSPS research Fellow, where she also participated in the FANTOM 5 project, learned new methods for next generation sequencing of RNAs and studied promoters, non-coding RNAs, small RNAs, piRNAs and iPS cells in the context of human disease. At RIKEN, Alka developed special skills for generating and sequencing RNA libraries from miniscule amounts of input RNA. Alka relocated to the UK in 2013, where she is the Head of the Genomics Research Platform at the BRC at Guy's and St Thomas' NHS Foundation Trust and an Honorary Senior Research Fellow at King’s College London. In this role, Alka and her team are not only providing more than 15 different types of library preparation and sequencing services but also pushing the boundaries of science through technology development for Single Cell Genomics.
Peer reviewed recent publications: 1. Kaudewitz D, Skroblin P, Bender LH, Barwari T, Willeit P, Pechlaner R, Sunderland NP, Willeit W, Morton A, Armstrong PC, Chan MV, Lu R, Yin X, Gracio F, Dudek D, Langley S, Zampetaki A, de Rinaldis E, Ye S, Warner T, Saxena A , Kiechl S, Storey R, Mayr M, Association of MicroRNAs and YRNAs with platelet function , Circ Res 2015 Dec 8 Epub 2. Lennartsson A, Arner E, Fagiolini M, Saxena A , Andersson R, Takahashi H, Noro Y, Sng J, Sandelin A, Hensch TK, Carninci P; Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors , Epigenetics Chromatin 2015 14;8:55. Epub 2015 Dec 14. 3. Arner E et al Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells , Science 2015 Feb 12;347(6225):1010-4. Epub 2015 Feb 12. 4. Francescatto M, Vitezic M, Heutink P, Saxena A ; Brain-specific noncoding RNAs are likely to originate in repeats and may play a role in up- regulating genes in cis. Int J Biochem Cell Biol 2014 Sep 30;54:331-7. Epub 2014 Jun 30. 5. Vitezic M, Bertin N, Andersson R, Lipovich L, Kawaji H, Lassmann T, Sandelin A, Heutink P, Goldowitz D, Ha T, Zhang P, Patrizi A, Fagiolini M, Forrest ARR, Carninci P, Saxena A , CAGE-defined promoter regions of the genes implicated in Rett Syndrome BMC Genomics 2014 24;15:1177. Epub 2014 Dec 24. 6. Fort A, Hashimoto K, Yamada D, Salimullah M, Keya CA, Saxena A , Bonetti A, Voineagu I, Bertin N, Kratz A, Noro Y, Wong C, Hoon M, Andersson R, Sandelin A, Suzuki H, Wei C, Koseki H, Hasegawa Y, Forrest ARR & Carninci P, Deep transcriptome profiling of mammalian stem cells supports a key regulatory role for retrotransposon in pluripotency maintenance , Nat Genet 2014 Jun 28;46(6):558-66. Epub 2014 Apr 28. 7. Forrest ARR, et al A promoter-level mammalian expression atlas , Nature 2014 Mar;507(7493):462-70 8. Durand S, Patrizi S, Quast K, Hachigian L, Pavlyuk R, Saxena A , Carninci P, Hensch TK and Fagiolini M; NMDA Receptor Regulation Prevents Regression of Visual Cortical Function in the Absence of Mecp2 , Neuron 2012, 76(6) 1078-1090 9. Saxena A* , Tang D and Carninci P; piRNAs warrant investigation in Rett Syndrome: an Omics perspective ; Disease Markers 2012, 10.3233/DMA-2012-0932, *corresponding author 10. Francia S, Michelini F, Saxena A , Viviana A, Tang D, Dobreva M, Mione M, Carninci P and d'Adda di Fagagna F; DICER and DROSHA RNA products control the DNA damage response ; Nature, 2012, doi:10.1038/nature 11179
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23 Session 5
Day 2: Thursday 11th February
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11. Saxena A* , Wagatsuma A*, Noro Y, Kuji T, Watahiki A, Gurnot C, Fagiolini M, Hensch T and Carninci P; Trehalose-enhanced isolation of specific neuron sub-types from adult mouse brain , BioTechniques, 2012, (*shared first authorship) 12. Cernilogar F, Onoratti MC, O’ Kothe G, Burroughs A, Parsi KM, Breiling A, lo Sardo F, Saxena A , Miyoshi K, Siomi H, Siomi M, Carninci P, Gilmour D, Corona D, and Orlando V; Chromatin associated RNAi components control transcriptional regulation in Drosophila , Nature 2011 doi: 10.1038/nature10492 13. Saxena A and Carninci P, Long Non coding RNA modifies Chromatin ; Bioessays 2011, DOI: 10.1002/bies.201100084 14. Saxena A and Carninci P; Whole transcriptome analysis: What are we still missing? 2010; Advanced Reviews, WIRES; Systems Biology and Medicine, Pubmed id:21197667; Doi 10.1002/wbsm.135
24 Abstracts
A3 Eric Schordan : miRNA profiling using A4 Chris Odhams : Discovering SLE HTG-Edgeseq platform predicts response to candidate genes and mechanisms by eQTL anti-TNF therapy in rheumatoid arthritis analysis using RNA-Seq Authors α Authors E. Schordan, G. Bilger, M. Coq, S. Danilin, M. Chris Odhams, Deborah Cunninghame Graham, David Schumacher, H. Firat. Morris, Andrea Cortini, Tim Vyse . Affiliation Affiliation Firalis SAS, Huningue, France King’s College London Department of Medical & Molecular Genetics Abstract text Abstract text Millions of patients suffering Rheumatoid Arthritis (RA) are treated with agents inhibiting TNF- , however, Background : Integration of expression quantitative trait response rate is low (30 to 40%) and nαo tool exists to loci (eQTL) mapping with Genome-wide association studies predict the treatment response. Using the HTG-Edgeseq (GWAS) allow for the functional interpretation of disease platform, an innovative combination of nuclease susceptibility loci by prioritizing candidate genes and protection assay and next generation sequencing, we refining causal variants. The majority of existing studies identified sets of miRNAs that discriminate responders implement 3 targeted microarrays to profile gene ′ from non-responders to anti TNF- therapy. expression and are thus limited in their ability to accurately Sixty-seven patients diagnosedα with RA, eligible for quantify transcriptional output and target the full array of treatment with 1st line anti-TNF and for whom DMARD expressed isoforms. Large eQTL mapping studies using therapy had failed were enrolledα in the study. Twelve to RNA-Sequencing (RNA-Seq) are now accessible and have 14 weeks after anti-TNF therapy, patients were the potential to reveal novel disease-associated eQTLs and categorized as respondeαrs or non-responders based on the accompanying pathogenic mechanism. DAS28 index. Patients’ miRNA profile was established Aims & Methods : In this study we functionally annotate from 15µl of plasma using HTG-Edgeseq Whole SLE associated loci through integration of cis-eQTL data Transcriptome Assay (WTA) miRNA panel (2256 miRNA). derived from microarray and RNA-Seq experiments in LCLs Results were normalized based on the median of the and whole blood with results from the largest current sample and Random forest was used as the classification GWAS in SLE to compare the ability of both quantification model. For 8 patients, miRNA were also analyzed with methods to discover eQTLs. We consider only eQTLs that the qPCR Exiqon miRNA panel V4 to determine HTG- show evidence of a shared causal variant between disease Edgeseq accuracy. Method reproductibility was assessed and eQTL signal by applying a conditional and by analyzing 4 times an independent sample on different colocalisation analysis pipeline. sites, with different instruments/days/operators. Results obtained from both HTG-Edgeseq and qPCR Results : We detect eight SLE candidate causal cis-eQTLs methods showed an overall correlation of 0.63 for the using microarray (modulating expression of twelve 341 miRNA common between those 2 kits, and eGenes), eleven using gene-level RNA-Seq (nineteen correlations factors between the 4 independent eGenes), and fourteen using exon-level RNA-Seq (thirty- experiments ranged from 0.993 to 0.999. Statistical four eGenes); demonstrating the benefits of increased analysis of patients’ miRNA profile identified 2 panels of accuracy and resolution in eQTL detection. We provide a 6 and 52 miRNAs with significant predictive power to detailed example of annotation of novel susceptibility discriminate responders from non-responders (sensitivity locus, 2q34, which appeared quiescent using microarray was 0.898 and 0.918, and AUC 0.773 and 0.824 analysis but with RNA-Seq unearthed a putative causal respectively). splicing mechanism (replicated with qPCR) in IKZF2, a T-reg In conclusion, miRNA profiling in RA patients using restricted transcription factor. HTG-EdgeSeq allowed us to build 2 predictive models for Discussion : We have emphasised the need to employ response to anti-TNF- drugs. Moreover, we showed that RNA-Seq to increase elucidation of GWAS results and, in HTG-Edgeseq platformα offers accurate and sensitive RNA doing so, have pointed to targeted follow-up studies. We expression measurement. Its low sample input shall increase our understanding of the genetic control of requirement and compatibility with all biological material gene and isoform expression in the genetic architecture of makes it an invaluable tool for biomarkers discovery. complex disease once RNA-Seq eQTL cohorts become available across a wider range of ex vivo cell types and conditions.
25 Abstracts
A5 Angela Hodges : AD-associated TREM2 variants lead to fewer microglia expressing HLA-DP, DQ, DR in the hippocampus of post- mortem human brains Authors: Yau Mun Lim 1, Anaelle Dumas 1, Andrew King 1, Claire Troakes 1, Christina Murray 2 Kuang Lin 1, Safa Al-Sarraj 1, Lawrence Sivakumar 1, Tammaryn Lashley 2, and Angela Hodges 1 Affiliation: 1 King's College London, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK 2 University College London, Institute of Neurology, London, WC1N 3BG, UK Abstract text: Recent research revealed the triggering receptor expressed on myeloid cells 2 (TREM2) gene is a risk gene for Alzheimer’s disease (AD) and related dementias. Gene variants appear to cause a loss-of-function of normal TREM2 function. TREM2 is crucial for the functioning of microglia, the cells that mediate immune function and respond to damage in the brain. We set out to investigate the effects of TREM2 variants in post-mortem human brain sections by labelling microglia with the established microglial markers CD68 and Iba-1 (proteins involved in phagocytosis, a process of internalising debris and unwanted substances) and HLA-DP, DQ, DR (henceforth called HLA, a set of proteins involved in recognising misfolded and pathogenic proteins and thus appearing to mediate adaptive immune responses in the brain. We compared the abundance of microglia with the different markers in the CA1 and CA4 hippocampal regions between AD cases with suspected pathogenic TREM2 variants (TREM2+) and AD and Control cases without TREM2 variants (TREM2-). AD/TREM2+ cases were found to have significantly fewer HLA-stained microglia, marginally lower CD68-stained microglia but no difference in Iba-1-stained microglia compared to AD/TREM2- cases. Our results suggest that TREM2 variants inhibit the activation of resident resting microglia but not the overall number of microglia as we did not detect differences between Iba-1-stained microglia in AD/TREM2+, AD/TREM2- and Control/TREM2- groups. This may lead to the inability of microglia to respond appropriately to pathology that arise in AD and thus result in a susceptibility for individuals with TREM2 variants to develop AD.
26 David Rawlings Session 6 Division of immunology Day 2: Thursday th Seattle Children’s Hospital 11 February Washington USA
Altered B cell signaling orchestrates loss of tolerance and systemic autoimmunity
Dr. David Rawlings is Chief of the Division of Immunology at Seattle Children’s Hospital, the major Pacific Northwest referral center for immunodeficiency patients; and Director for Center for Immunity and Immunotherapies (CIIT) at Seattle Children's Research Institute (SCRI) pursuing translational research focused on human immune disorders. He co-directed the NIH roadmap-supported, Northwest Genome Engineering Consortium (NGEC) and currently co-directs the Seattle Children’s Program for Cell and Gene Therapy (PCGT). His primary research has focused on altered immune cell function leading to immunodeficiency, autoimmunity or lymphoid malignancies, and the development of gene therapy or gene repair for these disorders.
27 Stephen McMahon Session 6 Sherrington Professor of Physiology, King's College London Day 2: Thursday th and Director, London Pain Consortium UK 11 February
Pain – why does it hurt so much?
Stephen McMahon is Sherrington Professor of Physiology at King’s College London, and Director of the London Pain Consortium. He is a neuroscientist who trained with Patrick Wall in the 1980s. He is principally interested in somatosensory systems and actively engaged in work ranging from molecular biology to electrophysiology to human psychophysical studies. He has published more than 290 original research articles, many highly rated (H-index 92) and is co-editor of the Textbook of Pain. His work has been published in leading scientific journals including, Nature, Nature Medicine, Science, Nature Neuroscience, Cell, Neuron and Brain.He is the holder of a Wellcome Trust Senior Investigator Award and a Fellow of the Academy of Medical Sciences. His major interest is in pain mechanisms. He was the principal investigator on a major grant from the Wellcome Trust in 2002 to establish the London Pain Consortium (LPC), of which he is the Scientific Director. Further funding from the Wellcome Trust, in the form of a 5 year Strategic Award, in May 2008, on which he was again the principal investigator, supported further research activity and a 4-year PhD training programme. He is the principal investigator on a recent Strategic award (awarded 2014) from the Wellcome Trust entitled “Defining pain circuitry in health and disease”. He is also the academic lead of an EU consortium, Europain, which is a private- public partnership funded under the Innovative Medicines Initiative (IMI) scheme. This brings together a large group of academic scientists working in Europe with a group of pharmaceutical companies with an interest in analgesic drug development. Europain receives €6m support from the EU and €13.5m from industry and is undertaking precompetitive clinical and preclinical research aimed at improving understanding and treatment of chronic pain. Both of these collaborations (the London Pain Consortium and Europain) involve a series of interlinked and mutually supportive programmes of experimental research, underpinned and supported by a coordinated training and bioinformatics facility. There are considerable synergies between the programmes. About half of the research activity is focused on the study of pain in preclinical models, with the major aims of: identifying novel pain mediators; elucidating the peripheral and central nervous system changes contributing to pain; improving and refining animal models of pain and the measurement of pain in these models. The other half of the research activity explores pain mechanisms in humans, with the major aims of: establishing and validating mechanism-based pain models in human volunteers; finding objective measures of spontaneous pain; collecting detailed phenotypic data on chronic pain patients; and determining psychosocial, genetic and clinical risk factors for development of chronic pain .
28 29 George Kollias Session 6 Alexander Fleming Biomedical Sciences Research Centre Day 2: Thursday th Athens 11 February Greece
Mesenchymal causalities in chronic inflammation
George Kollias is a full member of the Academy of Athens, Professor of Experimental Physiology at the Medical School of the University of Athens and Director of the Immunology Division at the Biomedical Sciences Research Center "Alexander Fleming", where he served as President and Scientific director from 2002-2010. In 2005 he founded the first CRO- biotech spin-off of BSRC Fleming, Biomedcode Hellas SA. Professor Kollias has pioneered genetic approaches to study the function of cytokine signaling, with specific focus on Tumor Necrosis Factor (TNF), in animal models of human diseases. His lab is highly cited for a series of discoveries on molecular and cellular mechanisms driving chronic inflammation and autoimmunity and for proof of principle studies that provided the preclinical rationale and drove the development of the first biological anti-TNF therapies for rheumatoid arthritis in the clinic. His laboratory is supported by several competitive grants from the European Commission and National sources, as well as by the pharmaceutical industry. He was recently granted an Advanced ERC grant to study the role of mesenchymal cells in tissue homeostasis and pathophysiology. In 2014, he was awarded the Carol-Nachman Award for Rheumatology.
30 Abstracts
A6 Miranda Houtman : Investigation of the A7 Olfa Khalifa : New genes in the X associated PTPN2 locus in rheumatoid chromosome associated with Rheumatoid arthritis: importance of long non-coding RNA Arthritis Authors Authors M. Houtman, K. Shchetynsky & L. Padyukov Olfa KHALIFA 1,2 , Isabelle Duroux-Richard 1, Nathalie BALANDRAUD 3,4 , Nathalie LAMBERT 3, Isabelle AUGER 3, Affiliation Jean ROUDIER 3,4 , Audrey SÉNÉCHAL 5, David Rheumatology Unit, Department of Medicine Solna, GENEVIÈVE 1,2,6 , Christophe PICARD 7, Gérard LEFRANC 2,8 , Karolinska Institute and Karolinska University Hospital, Isabelle TOUITOU 1,2,9 , Bakridine M'MADI MRENDA 10 , Stockholm, Sweden Etienne PARDOUX 10 , Anne-laure GAGEZ 11 , Yves-Marie Abstract text PERS 1,2,12 , Christian JORGENSEN 1,2,12 , Touhami MAHJOUB 13 and Florence APPARAILLY 1,2 Background : Rheumatoid arthritis (RA) is a common chronic autoimmune disorder that has a strong genetic Affiliation component. Over 100 risk loci have been confirmed in 1 Inserm, U1183, Institute for Regenerative Medicine genome-wide association studies and the major risk and Biotherapies, CHU Saint Eloi, 80 Avenue Augustin factor are the HLA-DRB1 shared epitope (SE) alleles. Fliche, 34295 Montpellier cedex 5, France Outside the HLA-DRB1 region, one of the recently identified candidate genes for RA is protein tyrosine 2 University of Montpellier, Boulevard Henri IV, 34090 phosphatase non-receptor type 2 ( PTPN2) . However, the Montpellier, France functional consequences of genetic variations in the 3 Inserm UMRs 1097, Aix-Marseille University, Marseille, PTPN2 region remain undefined. We aimed to France understand the functional mechanisms that connect variations in the PTPN2 region with the risk of RA 4 APHM, Rhumatology department, Marseille, France development. 5 Inserm, U1051, University Hospital Saint Eloi, Institute Methods : We conducted an association study in the for Neurosciences Montpellier, France RACI cohort (6573 seropositive RA cases and 15870 6 Department of Clinical Genetics, University Hospital of controls), computed gene-gene interactions using Montpellier, France attributable proportion for SE alleles with 11 SNPs in the PTPN2 region, analyzed DNA methylation data (354 7 Aix-Marseille Université, CNRS, EFS, ADES UMR 7268, seropositive RA cases and 337 controls), and performed 13916, Marseille, France RNA expression analysis for PTPN2 and genes in its close 8 Laboratoire d'Immuno Génétique Moléculaire, UPR proximity in samples from 179 RA patients and 175 1142 CNRS, Institute of Human Genetics, Montpellier, healthy controls. France Results : The interaction analysis between SNPs within 9 Department of Molecular Genetics, University Hospital PTPN2 and SE alleles pointed to the RA-associated SNP of Montpellier, France rs657555 (meta-analysis in RACI cohort, p = 3.35e-06; OR = 1.1352; Q = 0.3993). The expression of total 10 Aix-Marseille University, CNRS, Centrale Marseille, I2M, PTPN2 and PTPN2 splice variants, did not vary UMR 7373 13453 Marseille, France significantly in individuals with different rs657555 11 CNRS UMR 5235, Université de Montpellier, genotypes. In addition, the expression of other protein- Montpellier, France coding genes from the locus within 1 Mb from rs657555 were not different in relation to genotypes in our and 12 Clinical department for Osteoarticular diseases and publicly available data. We detected that the rs657555 Biotherapy, University Hospital, Lapeyronie, 34295 risk allele is strongly associated with changes in DNA Montpellier, France. methylation at four CpG sites 7 kb downstream of PTPN2 13 Laboratory of Human Genome and Multifactorial and with changes in expression of the long non-coding diseases, University of Monastir, Faculty of Pharmacy, RNA LOC100996324. Monastir, Tunisie. Conclusion : These results provide a new insight into the Abstract text mechanism driving the increased RA risk at the PTPN2 region and suggest LOC100996324 for future studies Objective : Among risk genes associated with rheumatoid of RA. arthritis (RA) susceptibility, the Xq28 region was the first reported and is thus of importance given the female predominance of the disease. The X chromosome is also encoding sixty-seven micro-RNAs (miRNA). Here, we aimed at investigating the association between 3 gene polymorphisms (rs13397, rs1059702 and rs1059703) and 12 miRNAs in the X chromosome in Tunisian and French population.
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31 Abstracts Continued
Methods : A case–control study of 408 RA women and A8 Klementy Shchetynsky : Discovery of New 471 healthy age-matched women was conducted in Candidate Genes for Rheumatoid Arthritis by Tunisian and French subjects. The genotype distribution, Integration of Genetic Association Data with haplotype analysis, and linkage disequilibrium (LD) were analyzed using Bayesian statistical method, PLINK 1.07 and Expression Pathway Analysis Haploview 4.2 softwares, respectively. Total RNA was Authors: extracted from PBMC (Peripheral blood mononuclear cell) K Shchetynsky, LM Diaz-Gallo, L Folkersen, AH Hensvold, AI of 20 RA patients, as well as sex- and age-matched Catrina, L Berg, L Klareskog, L Padyukov controls. miRNAs expression levels were quantified using RT-qPCR. Affiliation: Rheumatology Unit, Department of Medicine, Karolinska Results : The TMEM187 rs13397 G and IRAK1 rs1059703 Institutet/Karolinska University Hospital, Stockholm, T major alleles were significantly increased in RA patients Sweden compared with controls in both Tunisian and French women. The two variants were in strong LD in the Abstract text: Tunisian, but not in the French cohort. The GTC haplotype Combining data from genetic association studies with displayed a protective effect against RA, while the ATC, gene expression analysis may help us to expand our GCC and GTT haplotypes conferred significant risk for RA understanding of genetic background of rheumatoid in the French population. All the 4 detected haplotypes arthritis (RA). We performed RNA-seq based expression displayed however neutral effect in the Tunisian analysis of 377 genes from previously-verified RA- population. Analyses of 12 miRNAs expression levels are associated loci in blood cells from 5 newly diagnosed, non- ongoing. treated RA patients, 7 patients with treated RA and 12 Conclusion : These data further support the involvement of healthy controls. Our focus was on differentially expressed X chromosome in RA susceptibility, evidencing however genes sharing a similar expression pattern in the RA sub- ethnicities differences. groups. 11 qualifying genes were selected for pathway analysis and grouped into 2 functional protein networks, containing 29 and 27 additional “connector” molecules. The expression of genes, corresponding to connector molecules was then also tested in our RNA-seq data. ERBB2, TP53 and THOP1 showed similar expression difference in both treated and non-treated RA patients and additional nine genes were differentially expressed in at least one patient’s group compared to healthy control group. ERBB2, TP53 and THOP1 expression profile was successfully replicated in RNA-seq data from peripheral blood mononuclear cells from healthy controls and non- treated RA patients in an independent material. In summary, an integration of RNA-seq data with findings from association studies, and consequent pathway analysis implicate new candidate genes, ERBB2, TP53, and THOP1 in the pathogenesis of RA.
32 Nicholas Luscombe Session 7 Cancer Research UK London Research Institute Day 2: Thursday th University College London 11 February UK
Using hiCLIP to identify long-range loops in RNAs
Following a degree in Natural Sciences at Jesus College, University of Cambridge (1993-1996), Nick studied for a Ph.D. with Janet Thornton at UCL (1996-2000) on the basis for specificity of DNA-binding proteins. He then moved to Yale University, USA, as an Anna Fuller Postdoctoral Fellow with Mark Gerstein (2000-2005), where he shifted research focus to genomics with a particular emphasis on yeast transcriptional regulation. He was a Group Leader at the EMBL-European Bioinformatics Institute (2005- 2012) in Cambridge and built a computational biology laboratory with an emphasis on genomics and gene regulation. During this time, he joined the Okinawa Institute of Science & Technology as an Adjunct Faculty to establish a small group focused on developmental regulation (2011-present). He recently returned to UCL as a Chair in Computational Biology in the UCL Genetics Institute and holds a joint appointment as a Senior Group Leader at the Cancer Research UK London Research Institute. His laboratory joined the Francis Crick Institute in 2015.
33 Aviv Madar Session 7 Department of Biological Statistics and Computational Biology Day 2: Thursday th Cornell University 11 February New York USA
High-resolution maps of regulatory DNA cell-type activity profiles improve the discovery of risk alleles for autoimmune diseases and their interpretability
Dr Aviv Madar is a computational biologist with a broad background encompassing engineering, biology, mathematics, statistics, and computer science. He is currently a postdoc jointly advised by Prof. Alon Keinan (Department of Biological Statistics and Computational Biology) and Prof. Andrew Clark (Department of Molecular Biology and Genetics) laboratories, at Cornell University. During his Ph.D., Aviv contributed to the field of cellular network inference and quantitative model building in systems biology. For example, Statistical methods he developed were selected as best performers in two consecutive international DREAM network inference competitions (2008 and 2009). Building upon his Ph.D. work, Aviv developed a data-integrative network inference pipeline that was used to characterize a high-accuracy regulatory network of T helper-17 cell differentiation in mice, a key T cell contributor to multiple autoimmune diseases (Cell, 2012). His current work is aimed at leveraging the growing volume and accuracy of regulatory annotation of the human genome toward detecting and interpreting non-coding sequence variants that contribute to complex traits, focusing on autoimmune diseases.
34 Phil de Jager Session 7 Brigham & Women's Hospital Day 2: Thursday th Harvard Medical School 11 February Boston USA eQTL analyses and systems biology in MS and dementia
Dr. Philip De Jager is an Associate Professor of Neurology at Harvard Medical School and Director of the Program in Translational NeuroPsychiatric Genomics within the Ann Romney Center for Neurologic Diseases in the Department of Neurology at Brigham and Women’s Hospital. He is the first incumbent of the Steven R. and Kathleen P. Haley Distinguished Chair for the Neurosciences. He is a practicing clinical neuroimmunologist.
The goal of Dr. De Jager’s work as a clinician-scientist is to apply modern methods of neuroimmunology, statistical genetics and computational biology to first delineate and then intervene in the sequence of events leading from health to neurodegenerative diseases.
35 David Morris Session 8 Genetics and Modular Medicine Day 3: Friday th King’s College London 12 February UK
Genes, ancestry and prevalence in SLE
David’s work involves statistical analysis of genetic data arising from Lupus studies. He has extensive experience in association studies, quantitative trait analysis, copy number variation analysis and genetic imputation (SNPs and HLA genotype). He gained experience in DNA expression analysis and Bayesian Statistics during his PhD which was entitled ‘Bayesian Analysis of Microarray data’. During this time he worked closely with the industrial sponsor Pfizer. He is joint first author of the largest ever genome wide association study (GWAS) on SLE, which has increased the number of associated loci by 50%. He led the statistical analysis of the current GWAS, a large MHC meta-analysis, a sub-phenotype analyses of SLE European data and a large collaboration with two Chinese groups for a meta-analysis of GWAS data across populations. He also has experience in modelling biological processes with multistate capture- recapture methods applied to a brown Trout population.
36 Kim Simpfendorfer Session 8 The Feinstein Institute for Medical Research Day 3: Friday New York 12 th February USA
Investigating immune endophenotypes in healthy human carriers of autoimmune disease- associated risk haplotypes in BLK and TNIP1
Kim Simpfendorfer is an Institute Scientist at the Feinstein Institute for Medical Research. Prior to joining the Feinstein Institute as a post-doctoral fellow in Peter Gregersen’s group in 2010, Kim completed her PhD in the Department of Microbiology and Immunology at the University of Melbourne, studying the contribution of mucosal antibodies to susceptibility to type I diabetes in the Non-Obese Diabetic mouse model (1) . Additionally, Kim was involved in research into the innate immune defense against Salmonella Typhimurium infection as well as pathogen transmission (2) . Since joining The Feinstein Institute for Medical Research, Dr. Simpfendorfer’s research has focused on the functional analysis of immune-related genes associated with human autoimmune disease, including lupus and rheumatoid arthritis (3, 4, 5, 6) . Her research has contributed to understanding how autoimmune risk alleles influence the functional diversity of cells in the human immune system, particularly human B cells. Her work has emphasized the value of defining endophenotypes in healthy human carriers of specific risk genes, including BLK, TNIP1 and PTPN22 . In addition to fundamental insights into autoimmune pathogenesis, her work may lead to improved diagnostic criteria for personalized medicine and potentially identifying healthy patients at risk of developing autoimmunity.
Peer reviewed recent publications - see overleaf: (1) Simpfendorfer KR , Strugnell RA, Brodnicki TC, Wijburg OLC. 2015. “Hitchhiking” genomic intervals in pIgR-deficient NOD mice confirm and localize Idd5.4 , a susceptibility locus for autoimmune diabetes. PlosOne (2) Wijburg OL, Uren TK, Simpfendorfer K , Johansen FE, Brandtzaeg P, Strugnell RA. 2006. Innate secretory antibodies protect against natural Salmonella typhimurium infection. Journal of Experimental Medicine (3) Simpfendorfer KR , Olsson LM, Manjarrez Orduno N, Khalili H, Simeone AM, Katz MS, Lee AT, Diamond B, Gregersen PK. 2012. The autoimmunity-associated BLK haplotype exhibits cis-regulatory effects on mRNA and protein expression that are prominently observed in B cells early in development. Human Molecular Genetics (4) Simpfendorfer KR , Armstead BE, Shih A, Li W, Curran M, Manjarrez-Orduño N, Lee AT, Diamond B and Gregersen PK. 2015. Autoimmune disease associated haplotypes of BLK exhibit lowered thresholds for B-cell activation and expansion of immunoglobulin class switched B- cells. Accepted at Arthritis & Rheumatology (5) Gregersen PK, Klein G, Keogh M, Kern M, DeFranco M, Simpfendorfer KR , Kim SJ, Diamond B. 2015. The Genotype and Phenotype (GaP) registry: a living biobank for the analysis of quantitative traits. Immunologic Research (6) Gregersen PK, Kosoy R, Lee AT, Lamb J, Sussman J, McKee D, Simpfendorfer KR , Pirskanen-Matell R, Piehl F, Pan-Hammarstrom Q, Verschuuren JJ, Titulaer MJ, Niks EH, Marx A, Strobel P, Tackenberg B, Putz M, Maniaol A, Elsais A, Tallaksen C, Harbo HF, Lie BA, Raychaudhuri S, de Bakker PI, Melms A, Garchon HJ, Willcox N, Hammarstrom L, Seldin MF. 2012. Risk for myasthenia gravis maps to a (151) Pro-->Ala change in TNIP1 and to human leukocyte antigen-B*08. Annals of Neurology
37 38 Ward Wakeland Session 8 The University of Texas Southwestern Medical Center Day 3: Friday Dallas 12 th February USA
A genomic analysis of susceptibility to systemic autoimmunity
Edward K. Wakeland, Ph.D., an internationally recognized immunologist, has been a faculty member at UT Southwestern Medical Center since 1998 and Chair of the Department of Immunology since 2007. An expert on the genetic basis for susceptibility to autoimmune disease, Dr. Wakeland’s labs have made significant advances in the study of lupus, a chronic, debilitating disease that affects more than a million Americans. Among his many professional activities, he is a past Chair of the Genetics Initiative Planning Committee, Alliance for Lupus Research , and a past member of the American Cancer Society's National Scientific Advisory Committee for Immunology. Dr. Wakeland has been an invited speaker at dozens of meetings and workshops around the world and is the author of more than 175 published scientific papers. He currently serves on the editorial boards or review boards of several leading immunology publications, including Current Opinion in Immunology and the Journal of Immunology . An experienced educator, Dr. Wakeland has mentored nearly 50 doctoral students and postdoctoral fellows now serving in various capacities at academic institutions and research facilities in the United States, Europe, and Asia. In addition to leading the Department of Immunology, Dr. Wakeland is also Director of the Walter M. and Helen D. Bader Center for Research on Arthritis and Autoimmune Diseases at UT Southwestern, as well as Director of the Genomics Core Facility.
39 Gil McVean Session 8 The University of Texas Southwestern Medical Center Day 3: Friday th Dallas 12 February USA
Dissecting the structure and phenotypic consequences of HLA genomic variation
Gil McVean is Professor of Statistical Genetics at the University of Oxford and Acting Director of Oxford’s Big Data Institute within the Li Ka Shing Centre for Health Information and Discovery. After an undergraduate training in Zoology, he worked in Cambridge and Edinburgh on evolutionary genetics before joining Oxford in 2000. His research focuses on understanding the molecular and evolutionary processes that shape genetic variation in populations and the relationship between genetic variation and phenotype. He has made contributions to our understanding of areas including recombination hotspots, historical patterns of natural selection, the male mutation rate, human genetic variation, the role of HLA in complex disease and genealogical processes. He has played a leading role in the HapMap and 1000 Genomes Projects and currently works on organisms from HIV to malaria.
40 Marc Dionne Session 9 MRC Centre for Molecular Bacteriology and Infection Day 3: Friday Imperial College London 12 th February UK
Dissecting the structure and phenotypic consequences of HLA genomic variation
Marc did his undergraduate degree at Yale University in Mathematics and Physics. He then went on to do a PhD at the University of California, Berkeley, under the supervision of Professor Richard Harland, where he did developmental genetics on mice. After his PhD, Marc moved to a postdoctoral position at Stanford University, where he worked in the laboratory of Professor David Schneider to develop systems to analyse the host genetic contribution to bacterial infections using Drosophila melanogaster as a model host. Marc moved to King’s College London to begin his own group in 2007; they have continued this work, with a focus on the interaction of bacterial pathogenesis with host metabolic regulation. The group have developed ways to integrate in vivo functional screening with computational functional predictions to reveal new mechanisms of immune-metabolic interaction and pathology driven by infection and inflammation. In 2015, Marc moved his laboratory to the Department of Life Sciences and the MRC Centre for Molecular Bacteriology and Infection at Imperial College London.
41 Chrissy Hammond Session 9 School of Physiology and Pharmacology Day 3: Friday th University of Bristol 12 February UK
Using zebrafish to unpick the interactions between biomechanics and genes in making, shaping and maintaining a joint
After studying Biochemistry at the University of Oxford, Chrissy swapped fields into Developmental Biology for her PhD in Simon Hughes’ lab at King’s College London. Her PhD was studying the origins of the dermomyotome, during which she developed an enduring love of zebrafish. After a short stint as postdoc at the Royal Veterinary College working on chick skeletal development, she was awarded an EMBO fellowship to identify novel genes controlling bone development in Stefan Schulte-Merker’s lab at the Hubrecht Institute in the Netherlands. After 3 years in the flatlands, she attempted to put her work on muscle, cartilage and bone together and was awarded an Arthritis Research UK fellowship to study joint development in zebrafish. Her lab now focuses on understanding the interaction between genes and biomechanics using zebrafish as a model organism.
42 Rikard Holmdahl Session 9 Department of Medical Biochemistry and Biophysics (MBB) Day 3: Friday Division of Medical Inflammation Research 12 th February Karolinska Institute Sweden
Positioning and analysis of the major genes controlling arthritis in rats
PhD 1985, MD 1987, professor Lund university 19932008, guest professor at Finnish Academy Turku 1987-2011 and Southern medical university, Guangzhou 2011-, professor Karolinska Institutet 2008- Member of the Nobel Assembly. Member of the governmental advisory board for gene technology in Sweden Receiver of the Swedish Göran Gustafsson prize (1994), the European Descartes prize (2002), the Nordic SalusAnsvar prize (2003) and the Nordic Anders Jahre prize (2015) Main supervisor for 37 PhD and assistant supervisor for additional 11. Publication summary : 536 publications (436 peer reviewed original articles, 60 peer reviewed overviews, 26 books/book chapters, 12 patents, 1 thesis, 1 popular press) + more than 300 abstracts/conference proceedingsThomson: 16917 citations, h-index 70. Google Scholar: 22293 citations, h-index 81 Some key research achievements: • The identification of the major gene associated with animal models for rheumatoid arthritis (Aq) and its human functional homologue (DRB1*0401) using humanized mice • The identification of a glycopeptide within the type II collagen molecule as binding DR4 and Aq and being a major T cell recognition peptide in CIA and RA • The identification of the major gene regions associated with disease in mouse and rat models for MS and RA • The cloning of the Ncf1 gene responsible for a major locus associated with arthritis (Pia4) and thereby discovery of a new pathway for how oxidative radicals regulate the adaptive immune system • Demonstration of pathogenicity and molecular interaction of antibodies specific for citrullinated proteins, of critical importance in rheumatoid arthritis Currently he is leading a research laboratory (Medical Inflammation research) (www.inflam.mbb.ki.se) with a focus on complex genetics and immunology of chronic inflammatory diseases. The main emphasis is on autoimmune diseases, using models for arthritis as a prototype disease. Identified genes are investigated through their molecular pathogenic pathway and therapy is developed with the aim to transfer the knowledge into clinical use.
Key references: 1. Vingsbo-Lundberg C, Nordquist N, Olofsson P, Sundvall M, Saxne T, Pettersson U, Holmdahl R : Genetic control of arthritis onset, severity and chronicity in a model for rheumatoid arthritis in rats. Nature Genetics 20, 401-404. 1998. 2. Olofsson P, Holmberg J, Tordsson J, Lu S, Åkerström B, Holmdahl R : Positional identification of Ncf1 as a gene that regulates arthritis severity in rats. Nature Genetics 33, 25-32. 2003. 3. Gelderman KA, Hultqvist M, Holmberg J, Olofsson P, Holmdahl R : T cell surface redox levels determine T cell reactivity and arthritis susceptibility. Proc Natl Acad Sci U S A ; 103, 12831-6, 2006. 4. Rintisch, C., Ameri, J., Olofsson, P., Luthman, H. and Holmdahl, R. , Positional identification of the V lambda gene and its association with rheumatoid factor production and eosinophilic inflammation in rats. P roc Natl Acad Sci U S A 2008. 105:14005-10.
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43 Session 9
Day 3: Friday 12 th February
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5. Kraaij, M. D., Savage, N. D. L., van der Kooij, S. W., Koekkoek, K., Wang, J., van den Berg, J. M., Ottenhoff, T. H. M., Kuijpers, T. W., Holmdahl, R. , van Kooten, C., and Gelderman, K. A., Induction of regulatory T cells by macrophages is dependent on ROS generated by the NADPH-oxidase. Proc Natl Acad Sci U S A 2010;107(41):17686-91. 6. Hultqvist, M., Sareila, O., Vilhardt, F., Norin, U., Olsson, L. M., Olofsson, P., Hellman, U. and Holmdahl, R ., Positioning of a Polymorphic Quantitative Trait Nucleotide in the Ncf1 Gene Controlling Oxidative Burst Response and Arthritis Severity in Rats. Antioxid Redox Signal 2011;14(12):2373-83. 7. Tuncel J, Haag S, Carlsén S, Yau ACY, Lu S, Burkhardt H and Holmdahl R. MHC class II-restricted Response to Collagen type XI regulates the Chronic development of Arthritis in rats. Arthritis Rheum . 2012 Mar 5. 8. Schiavone S, Jaquet V, Sorce S, Dubois-Dauphin M, Hultqvist M, Bäckdahl L, Holmdahl R , Colaianna M, Trabace L and Krause KH. NADPH oxidase elevations in pyramidal neurons drive psychosocial stress-induced neuropathology. Transl Psych 2012;2:e111. 9. Bäckdahl L, Ekman D, Jagodic M, Olsson T, Holmdahl R : Identification of candidate risk gene variations by whole-genome sequence of four rat strains commonly used in inflammation research. BMC Genomics . 2014;15:391. 10. Tuncel J, Haag S, Yau ACY, Norin U, Baud A, Lönnblom E, Maratou K, Ytterberg J, Ekman D, Thordardottir S, Johannesson M, Gillett A, Stridh P, Jagodic M, Olsson T, Fernández-Teruel A, Zubarev RA, Mott R, Aitman TJ, Flint J and Holmdahl R : Natural Polymorphisms in Tap2 Influence Negative Selection and CD4:CD8 Lineage Commitment in the Rat. PLoS Genet . 2014 Feb 20;10(2):e1004151. doi: 10.1371/journal.pgen.1004151. PMID: 24586191 11. Haag S, Jonatan Tuncel J, Thordardottir S, Mason DE, Yau ACY, Dobritzsch D, Bäcklund J, Peters EC, Holmdahl R : Positional identification of RT1-B (HLA-DQ) as susceptibility locus for autoimmune arthritis. J Immunol 2015 Mar 15;194(6):2539–50. 12. Holmdahl R , Sareila O, Olsson L, Bäckdahl L, Wing K: Ncf1 polymorphism reveals oxidative regulation of autoimmune chronic inflammation, Immunol Rev 2015 (in press)
44 Stephen Sawcer Session 10 Department of Clinical Neurosciences Day 3: Friday th University of Cambridge 12 February UK
Making progress in MS
Stephen Sawcer is Professor of Neurological Genetics at the University of Cambridge and an Honorary Consultant Neurologist at Addenbrooke's Hospital. He completed a BSc in Physics at Liverpool University and went to medical school (MB ChB) at Birmingham University. After completing MRCP in 1991 he undertook Neurology specialist training in Manchester and Cambridge and became FRCP in 2010. His PhD (A linkage genome screen in multiple sclerosis, 1997) was undertaken at the University of Cambridge, supervised by Professor Alastair Compston and Professor Peter Goodfellow and examined by Professor Martin Bobrow and Professor Kay Davies. Professor Sawcer has worked on the genetics of multiple sclerosis for more than 20 years with a main focus on genomewide approaches. He is a member of the International Multiple Sclerosis Genetics Consortium (IMSGC) and the Wellcome Trust Case Control Consortium (WTCCC). Key MS genetics references a) IMSGC. (2005) A high-density screen for linkage in multiple sclerosis. Am J Hum Genet 77, 454-67. b) IMSGC (2007) Risk Alleles for Multiple Sclerosis Identified by a Genomewide Study. N Engl J Med 357, 851-62. c) IMSGC and WTCCC2. (2011) Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature 476, 214-9. d) IMSGC. (2013) Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat Genet 45, 1353-60.
45 Abstracts
A9 Michelle Krishnan : Investigation of Conclusions biological pathways involved in brain Biological pathways associated with a quantitative multivariate imaging endophenotype of prematurity suggest development in preterm neonates using a an important role for lipid metabolism. FADS2 might be multivariate phenotype and sparse regression driving pathway selection as it is a member of two highly Authors ranked, relatively small pathways involving lipid metabolism. Michelle L Krishnan 1, James Boardman 2, Matt Silver 3, Gareth Ball 1, Serena Counsell 1, Andrew J Walley 4, A David [1] Silver, M., Janousova E., Hua X., Thompson, P.M., Montana, Edwards 1, Giovanni Montana 5 G.: Identification of gene pathways implicated in Alzheimer's disease using longitudinal imaging phenotypes with sparse Affiliation regression. Neuroimage, 63(3): 1681-1694 (2012) 1 Centre for the Developing Brain, King’s College London; [2] Boardman, J.P., Walley, A., Ball, G., Takousis, P., Krishnan, 2 3 Neonatology, Royal Infirmary of Edinburgh; London M.L., Hughes-Carre, L., Aljabar, P., Serag, A., King, C., 4 School of Hygiene and tropical Medicine; Institute of Merchant, N., Srinivasan, L., Froguel, P., Hajnal, J., Rueckert, Medical & Biomedical Education (IMBE), St. George's D., Counsell, S., Edwards, A.D.: Common Genetic Variants 5 University of London; Department of Biomedical and Risk of Brain Injury After Preterm Birth. Pediatrics, Engineering, King's College London 133(6): e1655-e1663 (2014) Abstract text Background The incidence of preterm birth is increasing, with a high proportion of survivors experiencing adverse motor, cognitive and psychiatric sequelae. Diffusion tensor imaging (DTI) provides measures of white matter microstructure that are correlated with neurodevelopmental outcome and highly heritable. Joint modelling of multivariate imaging and genetic data, using prior biological knowledge of functional pathways, increases power to detect associations in complex disease. We aim to identify biological pathways through which premature birth impacts the microstructure of white matter in neonates. Methods 3-Tesla MR images and saliva were acquired for 72 preterm infants (mean gestational age (GA) 28+4 weeks, mean postmenstrual age (PMA) at scan 40+3 weeks). FA maps were constructed from 15-direction DTI, and Tract Based Spatial Statistics was used to obtain a group white matter skeleton varying with degree of prematurity, adjusting for PMA and GA at scan. Salivary DNA was extracted and genotyped using Illumina HumanOmniExpress-12 arrays. Pathways sparse reduced- rank regression (PsRRR) [1] was used to jointly model the voxel-wise effects of genome- wide SNPs grouped into 186 KEGG pathways. Results Lipid pathways were significantly over-represented in the top ranking pathways adjusted for PMA (p ≤0.005) and the empirical selection frequency of the most highly ranked lipid pathway (peroxisome proliferator-activated receptor (PPAR) signaling) increased from 0.09 to 0.2 with adjustment for GA. The highest ranked pathways have corresponding low selection probabilities in the null model. Two of the top three pathways (PPAR metabolism and alpha-linoleic acid metabolism) include the gene fatty acid desaturase (FADS2), which has been recently associated with changes in brain microstructure in a candidate study with this cohort [2].
46 Abstracts
A10 Gisela Orozco : Capture Hi-C reveals a In conclusion, we have compelling evidence that the novel causal gene, IL20RA, in the autoimmune risk variant, rs6927172, is within a complex gene regulatory region, involving IL20RA, TNFAIP3 and regulatory pan-autoimmune genetic susceptibility elements, such as lncRNAs. These results show that CHi-C can region 6q23 help identify GWAS causal genes and suggest novel therapeutic Authors targets; indeed, anti-IL-20 monoclonal antibody therapy has Amanda McGovern 1, Stefan Schoenfelder 2, Paul Martin 1, recently been shown to be effective in the treatment of Jonathan Massey 1, Kate Duffus 1, Darren Plant 3, Arthur G rheumatoid arthritis. Pratt 4, Amy E Anderson 4, John D Isaacs 4, Julie Diboll 4, Nishanthi Thalayasingam 4, Caroline Ospelt 5, Peter Fraser 2, Anne Barton 1,3 , Jane Worthington 1,3 , Stephen Eyre 1, Gisela Orozco 1 Affiliation 1 Arthritis Research UK Centre for Genetics and Genomics. Centre for Musculoskeletal Research. Institute of Inflammation and Repair. Faculty of Medical and Human Sciences. Manchester Academic Health Science Centre. The University of Manchester. Stopford Building. Oxford Road. M13 9PT Manchester, UK. 2 Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, UK. 3 NIHR Manchester Musculoskeletal BRU, Manchester Academic Health Sciences Centre, Central Manchester Foundation Trust, Manchester, UK. 4 Institute of Cellular Medicine (Musculoskeletal Research Group), Newcastle University, Newcastle upon Tyne, NE2 4HH, UK. 5 Center of Experimental Rheumatology Department of Rheumatology, University Hospital of Zurich, Wagistrasse 14, CH-8952 Schlieren, Switzerland. Abstract text The majority of genetic variants that predispose to complex diseases map to non-coding enhancer regions, which may regulate transcription through long-range interactions with their target genes. The 6q23 locus is associated with a number of autoimmune diseases. Associated SNPs lie a large distance from any gene. The aim of this work was to identify causal disease genes at the locus by studying long range chromatin interactions using capture Hi-C in T and B cell lines. The disease intergenic region and all promoters within 500kb of associated SNPs were targeted. The disease associated intergenic SNPs interacted with IL20RA, IFNGR1 and lncRNAs downstream of TNFAIP3. IL20RA interacts with these lncRNAs and the promoter of TNFAIP3. TNFAIP3 also demonstrated interactions with the same lncRNAs. The lead SNP in the 6q23 region is in tight LD with eight other SNPs. The most plausible causal SNP seems to be rs6927172, as it maps to an enhancer in B and T cells, is in a DNase hypersensitivity cluster and shows transcription factor binding. We used human primary T cell gene expression data to examine expression eQTLs. The risk allele was associated with an increased expression of IL20RA . LCLs carrying the risk allele of rs6927172 showed a higher frequency of interactions between this SNP and IL20RA. Chromatin immunoprecipitation demonstrated enriched binding of chromatin marks of active enhancers (H3K4me1 and H3K27ac) and the transcription factor NF B to rs6927172 risk allele in Jurkat cells. κ
47 John Todd Session 11 Cambridge Institute for Medical Research Day 3: Friday University of Cambridge 12 th February UK
Type I Diabetes
John Todd FRS, FMedSci, FRCP Hons, PhD is Professor of Medical Genetics at Cambridge University, Director of the JDRF/Wellcome Trust Diabetes and Inflammation Laboratory (DIL) in the University’s Cambridge Institute for Medical Research and a Senior Investigator of the National Institute for Health Research. Todd researches type 1 diabetes (T1D) genetics and disease mechanisms with an aim of clinical intervention. Previously, Todd was Professor of Human Genetics at Oxford University and a Wellcome Trust Principal Research Fellow. Todd helped pioneer genome-wide genetic studies, first in mice and then in humans. He then went on to study the associations between mapped genomic disease-associated regions and phenotypes by founding and deploying the Cambridge BioResource. His research in genetics and diabetes has received several awards and prizes. In the latest phase of his research, to translate basic genetic and immunological knowledge to treatment and prevention, the DIL has now completed its first mechanistic, statistically adaptive, drug dose-finding trial in T1D patients, establishing new and effective methods of trial design, governance, conduct and patient recruitment. The DIL has a major role in training and mentoring others in patient/people-based research, promoting data/sample access and sharing, and can advise other laboratories and industrial partners in immunotherapeutics and experimental medicine. Todd has supervised 29 PhD students with five in progress. h-index 89, total citations 33,681 (Nov 2014).
48 Posters
P1 Aggelos Banos : Transcriptome Analysis P2 Elena Carnero-Montero : Epigenome- of Hematopoietic Stem Cells (HSCs) in wide analysis of myeloid:lymphoid ratios in Systemic Lupus Erythematosus (SLE) whole blood Authors Authors Banos A. 1* , Grigoriou M. 1, Verginis P. 1, Pavlidis P. 2, Bertsias Elena Carnero-Montoro 1, Vivek Naranbhai 2, Ben Fairfax 2, G. 3, Boumpas DT. 1,4 Tim D. Spector 1, Jordana T. Bell 1 Affiliation Affiliation 1. Biomedical Research Foundation of the Academy of 1Department of Twin Research and Genetic Epidemiology, Athens, Athens, Greece King’s College London, London, United Kingdom; 2. Institute of Molecular Biology and Biotechnology 2 Wellcome Trust Centre for Human Genetics, Nuffield (IMBB), Foundation of Research and Technology-Hellas, Department of Medicine, University of Oxford, Oxford, Heraklion, Crete, Greece United Kingdom 3. Medical School, University of Crete, Heraklion, Greece 4. Joint Academic Rheumatology Program, Medical Abstract text School, National and Kapodistrian University of Athens, Athens, Greece Recent studies have shown that peripheral blood monocyte:lymphocyte (ML) and neutrophils:lymphocyte (NL) ratios are better predictors of cellular transcriptional Abstract text profiles and of infectious, cardiovascular and malignant Hematopoietic Stem Cells (HSCs) give rise to all blood cell diseases than peripheral blood leukocyte subset counts on lineages, which have been implicated in the pathogenesis of their own. Functional genomic studies of myeloid:lymphoid Systemic Lupus Erythematosus (SLE). We reasoned that the ratios can add important insights into the biology of white fundamental immune aberrations in SLE –genetic or blood cells and the mechanisms behind immune responses. epigenetic- may be more facile to be traced back to the HSC Because the methylome of different white blood cell types population. is unique and is related to cell origin and function, we HSCs were isolated from either healthy C57/BL6 or hypothesized that ML and NL ratios may be linked to NZBxNZW/F1 lupus prone mice bone marrow (n=15±5). The changes in DNA methylation profiles that can explain some selection markers used are Lin-Sca-1+c-Kit+ for LSK of the observed transcriptional and physiological changes. compartment, including both long and short term HSCs. We tested whether myeloid-lymphoid ratios associate Flow cytometry cell sorting of the aforementioned with DNA methylation at CpG sites assayed by 450K populations was utilized for enumeration, RNA extraction and Illumina Infinium methylation array in 877 whole blood cell cultures. Finally, paired-end RNA-sequencing analysis was samples from female participants in TwinsUK. We performed with HiSeq 2000 platform. calculated myeloid-lymphoid ratios using cell proportions We identified significantly increased frequencies ( ~3% predicted by the DNA methylation age calculator and pre-diseased vs ~5% diseased, p<0.05) as well as absolute adjusted the analysis for family structure, smoking, age, numbers (80-100×10 3 pre-diseased vs 100-150×10 3 batch effects, and predicted cell proportions. We used diseased, p<0.05) of HSCs in the BM of lupus NZBxNZW/F1 granulocyte proportion as a surrogate measure of mice with established disease as compared to young pre- neutrophils. diseased NZBxNZW/F1 or control C57/BL6 mice. Bone Our preliminary genome-wide results show that ML and marrow populations such as hematopoietic stem progenitors NL ratios are associated with DNA hypomethylation effects cells (HSPCs), lymphoid and myeloid lineages differed in at 770 and 219 CpG sites respectively, after Bonferroni and homogeneity depending upon either age or disease, genomic inflation correction. Interestingly, multiple key suggesting alterations in HSC potential under inflammatory immune-, cancer- and transcriptional-related pathways are conditions. Accordingly, serum from F1 young mice significantly enriched in hypomethylated genes. These promoted healthy HSCs to proliferation and skewed their include leukocyte extravasation signaling, NF-kB activation differentiation towards to myeloid lineage. Transcriptome by viruses and integrin signaling for ML, and cell cycle analysis by RNA-seq of HSCs from lupus mice revealed various regulation and apoptosis-, ceramida- and HIPPO-signaling differentially expressed genes (DEGs) (FC>1.5, q<0.05) in pathways for NL. We also found significant enrichment for diseased lupus mice compared to pre-diseased. DEGs show hypomethylated genes to be under transcriptional control enrichment in transcription factors involved in hematopoiesis of ID3, mir-17-5p, TGFB1, TNF, CD3 and actin . (Arid3a, Runx2), regulation of immune responses during Altogether our findings suggest that DNA methylation inflammation and autoimmune diseases (Irf4, Maf) and HSC dynamics could explain previous associations found function and homeostasis (Cxcl2, Vegfa, Fbxw7). between myeloid-lymphoid ratios, transcriptional changes These data provide initial insights in the fundamental and immune responses; and show the potential of DNA changes and the molecular identity of HSCs in lupus within methylation profiling to identify new genes involved in the inflammatory milieu of the disease, regulated by a pathological outcomes and develop new predictive complex transcriptional network. markers.
49 Posters
P3 Lingyan Chen : Genetic Risk and Gene P4 Fiona Clarke : The protein tyrosine Expression in Systemic Lupus Erythematosus phosphatase PTPN22 negatively regulates Fc Authors receptor signalling in dendritic cells Lingyan Chen, David L Morris, and Timothy J Vyse Authors Fiona Clarke, Cristina Sanchez-Blanco and Andrew Cope Affiliation King’s College London Affiliation Academic Department of Rheumatology, Centre for Abstract text Molecular and Cellular Biology of Inflammation, Faculty of Life Sciences and Medicine, King’s College London, United Systemic lupus erythematosus (SLE) is a chronic Kingdom autoimmune disease with marked clinical heterogeneity. The genetic basis of SLE remains largely undetermined due Abstract text to its complexity, involving multiple genetic and environmental factors. Although genome-wide association PTPN22 is a non-receptor tyrosine phosphatase, expressed studies (GWAS) have identified many common risk variants in hematopoietic cells. A single nucleotide polymorphism in underlying susceptibility to SLE, there is scant and often the gene confers an arginine to a tryptophan substitution conflicting information on how these variants modify at position 620 of the human protein. This is associated normal lymphocyte signalling and predispose to with an enhanced susceptibility to multiple autoimmune autoimmunity. diseases including type 1 diabetes and rheumatoid arthritis. The promising findings from the largest European SLE PTPN22 dephosphorylates Src family kinases and Syk GWAS and trans-ancestry meta-analysis of Chinese and and is known to negatively regulate T cell receptor (TCR) European GWAS (in review) provide an opportunity to signalling. Despite also being expressed in other immune explain the genetics of SLE. eQTL mapping, which cell types, its role in these cells has been less well studied. integrates the genetic variants and the gene expression This project aims to investigate the role of PTPN22 in Fc phenotype, may functionally annotate GWAS signals, thus receptor (Fc R) signalling in dendritic cells (DCs). We γ providing evidence for further causality inference. My study hypothesise γthat PTPN22 dampens down Fc R signalling as aims to use genome-wide gene expression datasets on its targets Src family kinases and Syk are dowγnstream of the multiple ex vivo cell types from microarray or exon-array receptors. In addition, the majority of the autoimmune sources to identify if the SLE associated variants are cis- or diseases associated with the variant protein have an trans- eQTLs and infer the underlying causal genes. In autoantibody component. Fc Rs recognise the Fc regions addition, joint analysis across populations/tissues in the of IgGs and are expressed onγ most innate immune cells. current available datasets applying a Bayesian Framework The immune system utilises both activating and inhibitory (eQTLBMA) is performed to get higher statistical power, as Fc Rs to modulate its response to foreign antigens. The well as formally estimate the best models of combinations boγund IgGs crosslink the activating Fc Rs, leading to of subgroups. downstream signalling, resulting in DCγ maturation, cytokine production and antigen presentation. Using bone marrow derived dendritic cells (BMDCs) from wild type (WT) and PTPN22 -/- mice, we have found that PTPN22 is dispensable for binding and uptake of ovalbumin:anti-ovalbumin immune complexes (ICs) via Fc Rs. However, PTPN22 -/- BMDCs stimulated with ovγalbumin ICs upregulate MHCII and costimulatory molecules CD80 and CD86 to a greater extent than WT BMDCs. These cells also secrete higher levels of IL-12/23p40 after IC stimulation. When these IC-pulsed PTPN22 -/- BMDCs are cocultured with ovalbumin-specific WT CD4 + T cells, they cause enhanced T cell proliferation and augmented secretion of IL-17. These results suggest that PTPN22 negatively regulates signalling downstream of Fc Rs in dendritic cells. γ
50 Posters
P5 Georgina Cornish : PTPN22 negatively P6 Kate Duffus : Characterising the causal regulates effector T cell migration. mechanism at the 5q11 suceptibility locus Authors associated with rheumatoid arthritis Georgina Cornish 1, Garth L. Burn 1, Rose Zamoyska 2, Lena Authors M. Svensson 3 and Andrew P. Cope 1. Kate McAllister 1, Gisela Orozco1 Stephen Eyre 1 Affiliation Affiliation 1Academic Department of Rheumatology, Centre for 1Arthritis Research UK Centre for Genetics and Genomics, Molecular and Cellular Biology of Inflammation, Faculty of University of Manchester Life Sciences and Medicine, King’s College London, United Kingdom. 2Institute of Immunology and Infection Abstract text Research, Centre for Immunity, Infection and Evolution, Introduction University of Edinburgh, Edinburgh, United Rheumatoid arthritis (RA) has a strong genetic component Kingdom. 3Department of Experimental Medical Science, with over 100 loci associated with disease suceptibility, Lund University, Lund, Sweden. however for the majority the causal genes and mechanism Abstract text remain unknown. The third strongest association in RA lies intronic to the ANKRD55 gene, on chromosome 5q11. The PTPN22/Lyp is a protein phosphatase known to negatively objective was to further characterise the 5q11 risk locus regulate Src-family kinases Lck and Zap-70 down stream of T using genetic, bioinformatic and functional approaches. cell receptor signaling. These src kinases also signal downstream of affinity matured LFA-1 integrin. This study Methods aimed to investigate PTPN22 driven regulation of Lck and Genetic fine mapping of 60 single nucleotide Zap-70 on engagement of LFA-1 with ligand ICAM-1 during polymorphisms (SNPs) was carried out at the 5q11 locus in T cell migration. LFA-1 is a 2 integrin highly expressed on 11,475 cases and 15,870 controls. Bioinformatic tools lymphocytes and is thoughβt to mediate effector T cell trans- were used to prioritise SNPs based on their regulatory endothelial cell migration from the blood stream into potential. Prioritised SNPs were then correlated with inflamed tissue. The Lyp-R620W mutation is known to effect expression of nearby genes in whole blood (n=67), CD4+ phosphatase activity of PTPN22 and is associated with (n=185) and CD8+ T cell subsets (n=23). Additionally in multiple autoimmune diseases including Rheumatoid B and T cell lines capture Hi-C, in order to identify long- Arthritis, Graves disease, Type1 Diabetes and Lupus. Our range DNA interactions and chromatin results show that loss of PTPN22/Lyp expression, or immunoprecipitation (ChIP) for histone markers of expression of the autoimmune disease associated Lyp- enhancers was carried out. R620W mutant is associated with hyper-phosphorylation of Results Lck and Zap-70, increased T cell motility and integrin- Fine-mapping refined the association at the 5q11 locus to mediated adhesion under static and shear flow conditions. rs71624119 (p = 5.59E-20). Bioinformatic prioritisation These data suggest loss of PTPN22 function differentially implicated 2 SNPs, rs10065637 and rs6859219 with regulates integrin signaling in T lymphocytes. strong evidence of regulatory potential. The risk SNPs correlated with expression of ANKRD55 in whole blood (p =3.85E-05) and both ANKRD55 (p = 6.21E-11) and IL6ST (p = 6.54E-04) in CD4 +. Preliminary capture Hi-C data in T and B cell lines identified that the disease-associated SNPs physically interact with the promoters of both ANKRD55 and IL6ST . ChIP data was suggestive of enrichment for the histone marks of enhancer activity, H3K4me1 and H3K27ac. Conclusion The 5q11 locus contains multiple gene candidates for causality, however preliminary findings implicate the SNPs are located in an intronic enhancer element strongly regulating expression of ANKRD55 , and to a lesser extent IL6ST in CD4+ T cells. It is crucial to further dissect the functional mechanism at this locus in order to illuminate novel pathways and therapeutic targets in disease.
51 Posters
P7 Isabelle Duroux-Richard : Microrna in Systemic Lupus Erythematosus Authors Duroux-Richard I 1,2 , Cuenca J 3, Ponsolles C 1,2 , Roubert C 4, Jorgensen C 1,2,5 , Figueroa F 3, Khoury M 3, Apparailly F 1,2,5 Affiliation 1 INSERM, U1183, University Hospital Saint Eloi, 80 rue Augustin Fliche, 34295 Montpellier, France 2 University of Medicine, Boulevard Henri IV, 34090 Montpellier, France 3 University de Los Andes, Las condes, San carlos de Apoquindo 2200, 73000 Santiago, Chile 4 Exploratory Unit, Sanofi R & D, 371 rue du professeur J. Blayac, 34184 Montpellier, France 5 Clinical department for osteoarticular diseases, University hospital Lapeyronie, 371 Avenue Gaston Giraud, 34295 Montpellier, France Abstract text Several micro(mi)RNAs have been related to B cell differentiation and functions, known to participate in the pathogenesis of systemic lupus erythematosus (SLE). However, a common miRNA signature has not emerged in SLE, since published arrays from patients exhibit variable patterns due to variability in genetic background, severity and type of disease, as well as to the limitation of performing gene expression studies in unfractionated, heterogeneous cell populations. Here, we aimed at identifying a miRNA-based signature of disease severity in a population unexplored so far using purified B cells. Blood samples were obtained from healthy controls (HC) with no history of autoimmune diseases and SLE patients with or without severe lupus nephritis (LN), and ethnic homogeneity for chilean population. Naive and memory B cells were sorted using CD27 surface marker. The genome- wide miRNA expression study was perfomed using the TaqMan ® Human MicroRNA Array Cards v3.0 (Applied Biosystems). TLDA analyses of naive and memory B cells from HC and 2 subsets of SLE patients revealed two categories of miRNA-based signatures. The first signature represents miRNAs with potential as diagnostic biomarkers : 11 miRNAs discriminating all SLE patients from HC, and 8 miARNs discriminating patient subsets (SLE versus SLE-LN). Clustering analyses of TLDA datasets evidenced that the main differences in miRNA expression profilings between SLE patients were between naive and memory B cells, independently of disease severity. Among these, we found miR-223 that was previously reported as deregulated in SLE, as well as in other autoimmune disorders and B cell leukemia. Array data were further validated on individual samples (n=6). Overall, the present work identified two types of miRNA-based signatures in circulating B cells isolated from Chilean SLE patients, providing promising biomarkers in molecular diagnostics for disease severity as well as potential new targets for therapeutic intervention in SLE.
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