NIHRDataInsights/HRCSData huggingface dataset:
Title: Unravelling key regulators of thrombopoiesis using a novel RNA based clonal and molecular approaches
Funder: Wellcome Trust

Abstract: Platelets are anuclear cells originating from functionally heterogeneous population of haematopoietic stem cells (HSC). The existence of a distinct HSC subtype exclusively supporting long-term platelet production (LT-PP) has been recently demonstrated[1,2]. Decreased platelet counts are common in cancer patients and aged individuals, while direct platelet transfusion has a high risk of adverse reactions. An alternative therapy could rely on donor-independent platelet sources. However, such studies are hampered by lack of quantitative lineage tracing methods in platelets, which (if available) could pinpoint the cell of origin and its molecular characterization. Such a tool could significantly help in development of improved protocols for platelet production from specific subpopulations of cells and testing chemical agents affecting this process. In this context I propose to use a novel, RNA-based cellular barcoding approach to: 1. Characterize the HSC and progenitors most efficiently producing platelets in vivo through barcode retrieval from RNA in platelets, progenitors, and HSC 2. To identify key signalling pathways enhancing efficient thrombopoiesis in vivo. 3. Perform a functional screen of a small molecule library in order to modulate these key pathways in iPSC-derived MKs to maximize ex vivo platelet output.

Lay abstract: Platelets are small but important blood cells: they stop bleeding at sites of injury, and counter infections by providing a physical barrier to the outside world. Cancer patients frequently have decreased platelet levels due to side effects of chemotherapy, and low platelet levels are also seen in elderly individuals. The result is a potentially life-threatening increase in infections and bleeding problems. Our most effective treatment for this condition is transfusion with donor platelets, but this procedure is risky and some patients respond poorly. My research will improve our understanding of the cells that normally produce platelets, with the goal to increase platelet production. I will use a novel tracking system allowing me to characterize the cells that give rise to platelets. The results from this study will allow us to identify drugs that can efficiently stimulate platelet production, first in cells grown in the lab, and ultimately directly in patients.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: BLOOD;CANCER AND NEOPLASMS
Title: Role of the haematopoietic stem cell niche in pre-leukemic clonal haematopoiesis and myelodysplatic syndromes
Funder: Wellcome Trust

Abstract: Myelodysplastic syndromes (MDS) are prototype pre-leukemic conditions that initiate in haematopoietic stem cells (HSC). These are characterized by clonal HSC expansion, inefficient production of mature blood cells and a higher propensity to progress to acute myelogenous leukaemia. Multiple studies suggest that MDS-HSCs are highly dependent on the bone marrow niche. It is possible that leukemic stem cells exploit the normal remodelling capacity of the niche to create a self-reinforcing leukemic environment, thereby favouring leukaemia development. However the molecular mechanisms involved in this process are still largely unknown. This project aims at identifying the signalling networks involved in the bidirectional crosstalk between MDS-HSCs and specific niche cells, and how this contributes to MDS pathogenesis in both mouse and human. A multidisciplinary approach will be used, combining transcriptomic analysis of niche cells and HSCs, 3D-imaging of the bone marrow and computational modelling. I will investigate which essential interactions between MDS-HSCs and their niches are responsible for their competitive advantage over normal HSCs. These studies have the goal of ultimately disrupting these interactions as a novel therapeutic avenue for MDS, a disease that currently has very few treatment options.

Lay abstract: Haematopoietic stem cells (HSC) sustain the production of blood cells throughout life and are located within the bone marrow, where other cell types (forming the so-called niche) support and regulate their function. Myelodysplastic syndromes (MDS) are pre-leukemic conditions that initiate with the acquisition of mutations in HSCs, which confer a competitive advantage over healthy HSCs. MDS is characterized by the accumulation of dysfunctional HSCs, inefficient production of blood cells and a higher risk to develop full-blown leukaemia. There are currently no effective treatments for MDS. Importantly, MDS-HSCs are highly dependent on the niche where they reside but it is still largely unknown exactly how. Targeting the MDS-HSC niche constitutes a novel and rather unexplored therapeutic avenue. This project aims at identifying the niche and the mechanisms by which it confers advantage to MDS-HSCs, with the goal of designing new therapies for MDS.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: BLOOD;CANCER AND NEOPLASMS
Title: Genetic identification and functional dissection of the cellular interactome of haematopoietic stem cells and leukaemic stem cells
Funder: Medical Research Council

Abstract: Haematopoietic stem cells (HSCs) sustain life-long haematopoiesis and reside in specialized niches in the bone marrow (BM), which support their functions. Leukaemogenesis leads to the emergence of leukaemic stem cells (LSCs). LSCs exploit and transform the BM niche into a pathological niche. The precise cellular components of the BM niches that sustain the functions of HSCs and/or LSCs remain poorly defined due to technical limitations. Previous studies delineating these niche cells employed either genetic-deletion of critical factors from candidate cells, high-resolution imaging, or single-cell profiling of BM cells. These studies lack the full specificity or resolution to capture the small number of niche cells of unknown phenotype in physical contact with the rare stem cells. Therefore, alternative methodologies are needed to precisely define BM niches and their functions. To tackle this, I propose a direct genetic approach to fluorescently label, isolate and explore the niche cells in cell-to-cell contact with HSCs and/or LSCs. I have generated a new genetic tool (Yin&Yang mice) which employs orthogonal signaling pathways to fluorescently label cells in physical contact to HSCs and/or LSCs. These putative-niche cells will be prospectively isolated and transcriptionally profiled at a single-cell resolution to define their identity and illuminate novel regulators of HSCs and LSCs function. The microenvironment that supports HSC expansion during infancy, the effect of ageing on HSC-niches and the differences with LSC-niches will be investigated. Taken together, this research will provide multiple means to 1) expand HSC in vitro to improve BM transplantation, to model blood diseases ex vivo and to perfect gene therapy techniques; and 2) to generate novel therapeutic strategies to treat BM failure and leukaemias.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.2 CELLULAR AND GENE THERAPIES
Health categories: BLOOD;CANCER AND NEOPLASMS;INFLAMMATORY AND IMMUNE SYSTEM
Title: 2010 Doctoral Fellowships: Effect of a polyphenol-rich diet on vascular and platelet function: a randomised controlled trial
Funder: Health and Social Care Research and Development Division (HSC R&D) of Public Health Agency, Northern Ireland

Abstract: We have previously shown that increasing fruit and vegetable intake in patients with mild hypertension improves microvascular function which was assessed using a method that has been shown to be significantly correlated with improved coronary event-free survival and also to independently predict cardiovascular mortality. This beneficial effect may have been, at least partly, owing to the high poiyphenol content of fruit and vegetables. We hypothesise that a further increase in overall poiyphenol dietary intake could result in additional improvements in microvascular function. This study will assess the effect of a diet rich in polyphenol-rich foods on microvascular function in patients with mild hypertension. A total of 110 subjects with mild hypertension will be recruited and randomised to follow a low poiyphenol diet, or to consume 6 portions of fruit and vegetable (to include 1 portion of berries) and 1 portion of dark chocolate daily for 8 weeks. Vascular and platelet function measures will be assessed before and after the intervention period. At the start and end of the intervention period, markers of vascular function, cardiovascular risk and dietary compliance will be assessed, including clinical (microvascular function, blood pressure, platelet function) and biochemical measures (lipids, C-Reactive Protein, Plasminogen Activator Inhibitor-1, vitamin C, carotenoids, polyphenols, and flavonoids). This study will provide important data of clinical and public health relevance on the effect of a polyphenol-rich diet on vascular and platelet function.


Research activity codes: 6.7 PHYSICAL
Health categories: BLOOD;CARDIOVASCULAR
Title: Novel Cardiac MRI techniques for the diagnosis of coronary artery disease compared to PET imaging and Invasive Coronary Angiography.
Funder: Medical Research Council

Abstract: Routine coronary angiography alone cannot detect significant coronary artery disease (CAD) unless further invasive measurements are performed. Measurement of myocardial blood flow (MBF) with imaging tests for detection of CAD improves diagnostic accuracy, adds incremental independent prognostic value and provides utility for clinical decision-making. PET is the gold standard to measure MBF, although not widely available, expensive and uses ionising radiation. We have developed novel automated MBF techniques with CMR. Hybrid PET-MR imaging allows simultaneous PET and CMR acquisition to overcome confounders from previous studies. AIMS 1. To validate novel CMR techniques against the non-invasive gold standard of PET for measurement of MBF. 2. To validate novel CMR techniques against the invasive gold standard coronary angiography. HYPOTHESES 1. MBF measured with novel CMR agrees and correlates strongly with the non-invasive gold standard PET. 2. MBF measurement with novel CMR techniques is superior to conventional visual CMR analysis for the detection of CAD and in clinical decision-making. 3. Non-invasive novel CMR techniques can detect significant CAD on invasive coronary angiography with a high precision. METHODS 1. 10 healthy volunteers will undergo a cardiac PET-MR study for method development and optimisation of the clinical protocol. 2. 77 patients with suspected CAD listed for coronary angiography will undergo a PET-MR scan. PET and CMR perfusion data will be acquired during adenosine stress and at rest. MBF with CMR will be compared against the gold standard for measurement of MBF with PET. MBF measured with novel CMR methods will be compared with invasive FFR data to detect flow-limiting CAD. IMPACT Validation of a robust CMR tool to measure MBF and detect significant CAD will lead to translation for routine clinical care for enhanced diagnosis, added clinical value and utility for enhanced clinical decision-making for patient benefit.


Research activity codes: 4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: BLOOD;CARDIOVASCULAR
Title: The response of lower limb deep vein thrombosis to anticoagulation therapy: resolution, recurrence and post thrombotic syndrome.
Funder: Health Education England

Abstract: Deep vein thrombosis (DVT) is a blood clot in one of the deep veins, usually in the leg. DVT can cause long term symptoms of pain and swelling which is called post thrombotic syndrome (PTS) and those that have had a DVT are more likely to get another one in the future. This study will follow-up DVT patients over a two year period to determine how quickly their clots resolve, whether they re-occur, and how often PTS develops. The study will look for risk factors that could predict which individuals are most at risk of further DVT or PTS.

Lay abstract: Deep vein thrombosis (DVT) is a blood clot in one of the deep veins, usually in the leg. DVT can cause long term symptoms of pain and swelling which is called post thrombotic syndrome (PTS) and those that have had a DVT are more likely to get another one in the future. This study will follow-up DVT patients over a two year period to determine how quickly their clots resolve, whether they re-occur, and how often PTS develops. The study will look for risk factors that could predict which individuals are most at risk of further DVT or PTS.

Research activity codes: 3.1 PRIMARY PREVENTION INTERVENTIONS TO MODIFY BEHAVIOURS OR PROMOTE WELL-BEING;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: BLOOD;CARDIOVASCULAR
Title: Biogenesis and bioengineering of human platelets
Funder: Wellcome Trust

Abstract: Platelets are essential for haemostasis and play critical roles in innate immunity, angiogenesis and tissue repair. They are derived from megakaryocytes, each of which generates several thousand platelets. A major goal is to generate platelets in vitro, to address shortage of platelet supply for transfusion, and to enable fundamental discovery of gene function. To date, however, only very small numbers (approximately 10 per megakaryocyte) of platelets can be made in vitro. We propose a step change using novel in vitrosystems, to increase generation efficiency by 1-2 orders of magnitude. We will use two in vitrosystems (mouse lung vasculature and microcirculation microfluidics) using forward-programmed iPSC-derived megakaryocytes. Our new data show that passage of megakaryocytes through lung vasculature ‘educates’ them to undergo a sequence of changes: reversible deformation, enucleation and abscission to release platelets. We aim to understand the detailed biology of these processes using CRISPR-edited megakaryocytes. We also show we can make human platelets in our novel microfluidic system and will optimize this to bioengineer large quantities of cells, by learning from the biology of the ex vivolung preparation. This is potentially transformative for fundamental understanding of human platelets and megakaryocytes, and for their bioengineering for clinical uses.

Lay abstract: Platelets are small cells in the blood that are essential to stop us bleeding. There are many reasons for low platelet levels, such as trauma, major surgery or chemotherapy. In these cases it will be vital to receive additional platelets by transfusion. The supply of compatible platelets for transfusion is precarious, and there is substantial effort to make these cells outside the body, ‘in vitro’. Unfortunately, at present, we are able only to make very small quantities in vitro. We have developed a new way to make these cells in vitro, from their parent cell the megakaryocyte. This proposal aims to understand the process of platelet generation, using two vascular model systems and megakaryocytes that we have manufactured from stem cells. We will optimize our systems to enable scaling up for clinical use. This is potentially transformative for fundamental understanding and for bioengineering cells for clinical use.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: BLOOD;CARDIOVASCULAR
Title: Using proteomic approaches to investigate the role of plasma and urine biomarkers for disease stratification in childhood Hypertrophic Cardiomyopathy
Funder: LifeArc

Abstract: Hypertrophic cardiomyopathy (HCM) causes thickening of the heart muscle and is associated with sudden death in young people. Current treatments aim to manage symptoms, screen relatives and prevent complications – including sudden death, heart failure and stroke. However, we currently do not have any treatments targeting the underlying molecular processes or preventing the development of the disease in at-risk individuals. To develop such therapies, we have to understand the early features of the condition and how it progresses over time. We need simple, non-invasive tests to achieve that. Using a simple blood test, the team had developed a set of biomarkers that identifies adults with HCM and identifies the severity of their disease. Dr Juan Kaski and his team are using a similar approach in this study to: - validate the new adult biomarkers in children with HCM and in pre-symptomatic gene carriers - identify new markers specific to children with HCM and gene carriers without evidence of disease - match the findings from the biomarker tests with clinical features of disease severity and progression. This study takes advantage of the only paediatric HCM bioresource in the UK at GOSH and UCL and state of the art laboratory techniques at the UCL Institute of Child Health. If successful, this project may result in faster and cheaper diagnostic tests and the development of new tools to monitor disease progression and treatments, with the potential to improve clinical outcomes and potentially significant cost benefits to the NHS.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: BLOOD;CARDIOVASCULAR
Title: The CLOTS 3 trial: a randomised controlled trial to determine whether intermittent pneumatic compression reduces the risk of post stroke deep vein thrombosis.
Funder: Chief Scientist Office (Scotland)

Abstract: Deep vein thrombosis (DVT) is common in immobile patients with a recent stroke. Anticoagulants increase the risk of bleeding which offsets their benefits with respect to DVT prevention. CLOTS Trial 1 has shown that graduated compression stockings (GCS) do not reduce the risk of post stroke DVT. Intermittent pneumatic compression (IPC) reduces the risk of DVT after surgery by about 60%. It is relatively safe compared with anticoagulants and offers a potentially useful method to reduce the risk of DVT and pulmonary embolism in stroke patients. A systematic review of all randomised trials of IPC after stroke suggests it is practical acceptable to patients and may be effective. The CLOTS 3 trial is testing IPC in immobile stroke patients.Primary Research QuestionsDoes early and routine application of IPC in addition to routine care reduce the risk of above knee DVT in the weeks following an acute stroke?Is IPC a practical and acceptable treatment for DVT prevention on stroke units?Inclusion CriteriaAny patient who is admitted to hospital within three days of a clinical stroke and who is unable to mobilise independently. Sample size & AnalysesThe trial aims to enrol at least 2000 patients. All analyses will be based on an intention to treat. Primary outcome Presence of definite or probable symptomatic or asymptomatic DVT in the popliteal or femoral veins detected on a screening compression duplex ultrasound scan or any symptomatic DVT in the popliteal or femoral veins confirmed on compression duplex ultrasound or contrast venography or MRI direct thrombus imaging within 30 days of randomisation.


Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS;6.3 MEDICAL DEVICES
Health categories: BLOOD;CARDIOVASCULAR
Title: Megakaryocyte ploidy and platelet function: defining the molecular relationship
Funder: Medical Research Council

Abstract: I aim to test the hypothesis that "Platelets generated by MKs of high ploidy are more effective in the formation of thrombus at sites of vascular wall injury than platelets generated by MKs of low ploidy". I will apply this to the clinical setting of AMI as the upregulation of the MK-platelet system may be one disease process that leads to the development of AMI. First, I will establish the differences in levels of transcripts and splicoforms between MKs of high and low ploidy status using the power of RNA-seq and replicate a subset of these by quantitative transcript profiling at the single cell level. In order to do this, I will generate mature MKs using forward programming of iPSCs and drive polyploidisation using the recently discovered compound diMF, H-1152P [Wen Q, Cell, 2012]. Next, I will use two different validated mouse models to investigate whether human platelets derived from high ploidy MKs are more functionally active ex vivo and more prothombotic in vivo than those derived from low ploidy MKs. Finally, I will compare the levels and splicoforms of the 'diagnostic transcript set' in bone marrow MKs from AMI patients enrolled to the BAMI clinical trial (Bone marrow stem cells in AMI) and controls: healthy allogeneic bone marrow donors (provided by Prof Ouwehand) and stable coronary disease patients undergoing coronary bypass surgery (provided by Prof Mathur). DNA, plasma, serum and clinical information of all patients and controls will be deposited in the NIHR BioResource, a shared resource between the Biomedical Research Centres and Units in the South East of England. I aim to identify transcript differences associated with MK ploidy, which are putative novel markers of platelet function. If my hypothesis is supported by the outcome of this grant these markers may be used to stratify treatment of AMI patients. Furthermore, research of compounds that reduce polyploidisation will be of interest as novel therapeutic and preventative strategies in AMI.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: BLOOD;CARDIOVASCULAR
Title: Understanding the role of cyclo-oxygenase isoforms in cardiovascular health and disease.
Funder: Wellcome Trust

Abstract: Arthritis is a complex disease and sufferers have cycles of flares and remissions and sufferers will often try a number of agents before finding one that gives them the best relief. COX 2-selective inhibitors, such as Celebrex and Vioxx, were welcomed by many who could not take traditional anti-inflammatory drugs, such as ibuprofen or diclofenac, often because of gastrointestinal or other intolerances, sometimes because of poor effectiveness. There is no clear reason for some of these variations in individual responses but having an array of drugs to choose from, including multiple COX-2 selective agents, allows the optimization of therapy. In 2004 Vioxx was withdrawn because of fears that it caused heart attack and stroke. It now seems that traditional anti-inflammatory drugs also cause cardiovascular side effects. Our data suggests that it will be possible to find new ways in which selective inhibitors of COX-2 could be tested so that better drugs can be produced which should have fe wer gastric and cardiovascular side effects. Our proposed program of research will study exactly how COX-2 functions in the cardiovascular system and provide detailed evidence of how new drugs can be tested.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;5.1 PHARMACEUTICALS
Health categories: BLOOD;CARDIOVASCULAR