Research
Genomics and epigenomics of megakaryocytes and platelet traits
Background
I lead the NHS Blood and Transplant (NHSBT) research group in the Department of Haematology. The group’s program of research in megakaryocyte and platelet biology and genomics is one of the largest in Europe and focuses primarily on the relationship between sequence variation in genes transcribed in megakaryocytes, and the function of platelets. The group's work can be divided into the following areas:
Platelet Biology & Genomics
Platelets are the second most abundant cell in the blood and are produced by fragmentation of megakaryocytes that reside in the bone marrow. Platelets play a vital role in maintaining the integrity of blood vessel walls and respond to signals of vascular damage by aggregating and enhancing plasma coagulation.
Individuals with reduced platelet count or function have bleeding tendencies, whereas those with elevated values are at greater risk of heart attack and stroke. Individual variation in platelet function, count, and volume is to a large extent inherited and therefore stable over time. The main aim of our research is to identify genetic sequence variants that regulate these parameters, thus highlighting genes required for platelet production and thereby linked to cardiovascular diseases.
To support this endeavour we have established the Cambridge Platelet Function Cohort (PFC) from the Cambridge BioResource. The platelet function of almost 1,000 volunteers in this cohort has been characterised so far.
Platelet RNA samples from donors representing the full range of functional responses have also been applied to whole-genome expression arrays, and analysis of this microarray data identified 63 transcript levels that correlated with variation in platelet functional response.
One bottleneck to understanding the genetic controls of platelet function is the development of suitable testing systems. We are developing new ways of measuring platelet activity by a combination of microfluidics and image processing technology.
Overall we believe that by studying sequence variation in human platelet genes, we will add to knowledge of megakaryopoiesis, platelet formation and the quality of platelet transfusions, as well as to pathways targeted by current or future antiplatelet therapy.
Clinical Bioinformatics, Statistical Genetics and Genomics
Our team applies statistical and computational methods to discover new genes and molecular mechanisms that control platelet life and function in health and disease.
We translate this knowledge into the clinic by developing comprehensive and cost effective DNA tests to improve the diagnosis of inherited bleeding and platelet disorders.
Finally we integrate our findings from the gene discovery efforts and from various genome annotation assays to define the networks of protein-protein interactions and of gene regulation that underpin the lineage commitment and maturation of blood progenitors along the platelet lineage.
Our main projects are:
Thrombogenomics: Streamlining the genetic diagnosis of inherited bleeding and thrombotic disorders under the umbrella of the International Society of Thrombosis and Haemostasis.
BRIDGE: Exome and whole genome sequencing to identify the genetic basis of rare diseases with emphasis on cardiovascular disorders.
Genetics of haematological traits: Discovering new gene functions through genome wide association studies of blood indices and elucidating the molecular mechanisms by which sequence variation alters these traits.
BLUEPRINT: We functionally annotate the genomes of all human blood cells and progenitors. Our group focuses on the platelet lineage and its progenitors.
Integration: This knowledge is integrated to improve our understanding of gene regulation and networks.
NIHR BioResource for Rare Disease
Our team is responsible for the enrollment of participants with a rare disease; to form a BioResource for Rare Diseases.
A rare disease is defined as a condition which has an incidence of less than 5 in 10,000 individuals of the UK population, and thus affects ~3% of the population.
The aims of the BioResource for Rare Diseases are:
- To reduce the delay in ascertaining a genetic diagnosis for inherited and acquired genetic disorders (including rare cancers), where the genotype causing phenotype is known, by developing NGST-based diagnostic tests covering NHS diagnostically-important genes; such projects can include translational projects on e.g. a subset of diagnostic genes;
- To determine the genetic basis of Inherited Rare Diseases, including rare cancers for which the causative locus has hitherto not been identified, but which have potential wider relevance for the common diseases that are the focus of Biomedical Research Centres/Units (BRC/BRU)-funded translational and experimental medicine research.
Recruitment is via participating BRC/BRU/hospitals with specialist interest in rare diseases, and currently the main focus of our study fall into the themes: infection and immunity, rare cancers, neuroscience and cardiovascular disease. Our active studies are:
Bleeding and Platelet Diseases (BPD) The immediate purpose of this study is to identify the genetic basis of hitherto unresolved bleeding and platelet disorders by exome-sequencing.
Pulmonary Arterial Hypertension (PAH) The discovery of the range of genetic mutations underlying PAH will provide a more complete picture of the cause of this disease and identify rational targets for new drugs. It will also pave the way towards prevention strategies for this disease and of the prediction of prognosis based on a genetic classification of PAH.
Primary Immune Disorders (PID) This study focuses on genetic causes of severe immune disorders, also known as Primary ImmunoDeficiencies with the largest category being CVID, but it may also include the “extreme phenotype” of premature and severe autoimmunity.
Specialist Pathology: Evaluating Exomes in Diagnostics (SPEED) to develop more affordable DNA-based tests for the diagnosis of rare diseases for which the gene is known.
Steroid Resistant Nephrotic Syndrome (SRNS) This study will focus on genetic causes Steroid Resistant Nephrotic Syndrome.
Blueprint
The team spearhead the healthy samples collection for the European consortium, Blueprint by making use of the NIHR Cambridge Bioresource volunteers. The aim of this consortium is to generate reference epigenomes for all the cell types present in the blood as part of the International Human Epigenome Consortium.
Additionally, we apply next generation sequencing methods to further our understanding of megakaryocytes and platelet biology.
Our main projects are:
Comparative Transcription Network Biology: Megakaryocyte and neuronal cells make shared usage of several transcription factors and we aim to dissect the mechanisms that lead to different developmental outcomes.
GWAS functional follow-up: Recent genome wide association studies of blood indices has led to the discovery of several genes involved in megakaryopoiesis and erythropoiesis. We are using cellular biology and next generation sequencing based techniques to elucidate the function of these genes.
Nuclear Architecture and common variants: We are mapping regulatory regions and their target genes in a variety of haemopoietic cell types.
INTERVAL
The INTERVAL study is a randomised controlled trial in up to 50,000 whole-blood donors recruited at 25 NHS Blood and Transplant donation centres across England. Participants will be randomised to give blood either at their usual donation intervals or more frequently over two years.
Current practice is to invite men and women to give whole blood every 12 and 16 weeks, respectively. During this study, men will be randomised to donate every 12, 10 or 8 weeks and women every 16, 14 or 12 weeks. At the end of the study, we will compare the amount of blood donated and assessments of well-being between the different study groups.
The study’s main objectives are to determine:
- The optimum interval between donations, for men and women, that maximizes blood supply without unacceptably increasing iron deficiency and its potential complications
- Whether blood donation intervals can be tailored to donors on the basis of demographic, haematological, genetic and lifestyle factors.
During the course of the study, additional blood samples will be taken for a full blood count and storage of plasma, serum and DNA. These will be used to measure biomarkers as well as genetic factors. Online questionnaires regarding health, lifestyle and cognitive function will also be collected. A subset of participants will take part in a study of the impact of donation interval on physical activity levels.
Funding
We are funded by the British Heart Foundation, European Commission, The Evelyn Trust, National Institute of Health Research, NHS Blood and Transplant and the Wellcome Trust.
Publications
Recent publications are listed on PubMed.
A dominant gain-of-function mutation in universal tyrosine kinase SRC causes thrombocytopenia, myelofibrosis, bleeding, and bone pathologies. Turro E, Greene D, Wijgaerts A, Thys C, Lentaigne C, Bariana TK, Westbury SK, Kelly AM, Selleslag D, Stephens JC, Papadia S, Simeoni I, Penkett CJ, Ashford S, Attwood A, Austin S, Bakchoul T, Collins P, Deevi SV, Favier R, Kostadima M, Lambert MP, Mathias M, Millar CM, Peerlinck K, Perry DJ, Schulman S, Whitehorn D, Wittevrongel C; BRIDGE-BPD Consortium, De Maeyer M, Rendon A, Gomez K, Erber WN, Mumford AD, Nurden P, Stirrups K, Bradley JR, Lucy Raymond F, Laffan MA, Van Geet C, Richardson S, Freson K, Ouwehand WH. Sci Transl Med. 2016 Mar 2;8(328):328ra30. doi: 10.1126/scitranslmed.aad7666.
A gain-of-function variant in DIAPH1 causes dominant macrothrombocytopenia and hearing loss. Stritt S, Nurden P, Turro E, Greene D, Jansen SB, Westbury SK, Petersen R, Astle WJ, Marlin S, Bariana TK, Kostadima M, Lentaigne C, Maiwald S, Papadia S, Kelly AM, Stephens JC, Penkett CJ, Ashford S, Tuna S, Austin S, Bakchoul T, Collins P, Favier R, Lambert MP, Mathias M, Millar CM, Mapeta R, Perry DJ, Schulman S, Simeoni I, Thys C, Consortium BB, Gomez K, Erber WN, Stirrups K, Rendon A, Bradley JR, van Geet C, Raymond FL, Laffan MA, Nurden AT, Nieswandt B, Richardson S, Freson K, Ouwehand WH, Mumford AD. Blood. 2016 Feb 24. pii: blood-2015-10-675629.
Use of a novel floxed mouse to characterise the cellular source of plasma coagulation FXIII-A. Griffin K, Simpson K, Beckers C, Brown J, Vacher J, Ouwehand W, Alexander W, Pease R, Grant P. Lancet. 2015 Feb 26;385 Suppl 1:S39.
A multicenter validation of recombinant β3 integrin-coupled beads to detect human platelet antigen-1 alloantibodies in 498 cases of fetomaternal alloimmune thrombocytopenia. Chong W, Turro E, Metcalfe P, Yusuf R, Mérieux Y, Rigal D, Porcelijn L, Huiskes E, Lucas G, Bendukidze N, Green A, Fontão-Wendel R, Husebekk A, Dixey J, Guest A, Mushens R, Ouwehand WH, Navarrete CV. Transfusion. 2015 Nov;55(11):2742-51.
Runs of Homozygosity: Association with Coronary Artery Disease and Gene Expression in Monocytes and Macrophages. Christofidou P, Nelson CP, Nikpay M, Qu L, Li M, Loley C, Debiec R, Braund PS, Denniff M, Charchar FJ, Arjo AR, Trégouët DA, Goodall AH, Cambien F, Ouwehand WH, Roberts R, Schunkert H, Hengstenberg C, Reilly MP, Erdmann J, McPherson R, König IR, Thompson JR, Samani NJ, Tomaszewski M. Am J Hum Genet. 2015 Aug 6;97(2):228-37.
Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders. Westbury SK, Turro E, Greene D, Lentaigne C, Kelly AM, Bariana TK, Simeoni I, Pillois X, Attwood A, Austin S, Jansen SB, Bakchoul T, Crisp-Hihn A, Erber WN, Favier R, Foad N, Gattens M, Jolley JD, Liesner R, Meacham S, Millar CM, Nurden AT, Peerlinck K, Perry DJ, Poudel P, Schulman S, Schulze H, Stephens JC, Furie B, Robinson PN, van Geet C, Rendon A, Gomez K, Laffan MA, Lambert MP, Nurden P, Ouwehand WH, Richardson S, Mumford AD, Freson K; BRIDGE-BPD Consortium. Genome Med. 2015 Apr 9;7(1):36.
A rare variant in MCF2L identified using exclusion linkage in a pedigree with premature atherosclerosis. Maiwald S, Motazacker MM, van Capelleveen JC, Sivapalaratnam S, van der Wal AC, van der Loos C, Kastelein JJ, Ouwehand WH, Hovingh GK, Trip MD, van Buul JD, Dallinga-Thie GM. Eur J Hum Genet. 2015 Apr 22.
Genetically determined height and coronary artery disease. Nelson CP, Hamby SE, Saleheen D, Hopewell JC, Zeng L, Assimes TL, Kanoni S, Willenborg C, Burgess S, Amouyel P, Anand S, Blankenberg S, Boehm BO, Clarke RJ, Collins R, Dedoussis G, Farrall M, Franks PW, Groop L, Hall AS, Hamsten A, Hengstenberg C, Hovingh GK, Ingelsson E, Kathiresan S, Kee F, König IR, Kooner J, Lehtimäki T, März W, McPherson R, Metspalu A, Nieminen MS, O'Donnell CJ, Palmer CN, Peters A, Perola M, Reilly MP, Ripatti S, Roberts R, Salomaa V, Shah SH, Schreiber S, Siegbahn A, Thorsteinsdottir U, Veronesi G, Wareham N, Willer CJ, Zalloua PA, Erdmann J, Deloukas P, Watkins H, Schunkert H, Danesh J, Thompson JR, Samani NJ; CARDIoGRAM+C4D Consortium. N Engl J Med. 2015 Apr 23;372(17):1608-18.
αIIbβ3 variants defined by next-generation sequencing: predicting variants likely to cause Glanzmann thrombasthenia. Buitrago L, Rendon A, Liang Y, Simeoni I, Negri A; ThromboGenomics Consortium, Filizola M, Ouwehand WH, Coller BS. Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):E1898-907.
Genetic studies of body mass index yield new insights for obesity biology. Locke AE, Kahali B, Berndt SI, Justice AE, Pers TH,..., Barroso I, North KE, Ingelsson E, Hirschhorn JN, Loos RJ, Speliotes EK. Nature. 2015 Feb 12;518(7538):197-206.
New genetic loci link adipose and insulin biology to body fat distribution. Shungin D, Winkler TW, Croteau-Chonka DC, Ferreira T, Locke AE,..., Heid IM, Loos RJ, Cupples LA, Morris AP, Lindgren CM, Mohlke KL.Nature. 2015 Feb 12;518(7538):187-96.
