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Structure and mechanism of the Ino80 chromatin remodelling complex 28 Nov 2017

Compaction of the genome into chromatin helps to protect the genetic material but also causes problems in regard to access for essential processes such as transcription, replication and repair. Chromatin remodelling complexes alter the state of chromatin through a number of processes that includes chemical modifications of nucleosomes and sliding their position on DNA. Nucleosome sliding is catalysed by a number of protein complexes, one of which is the multi-subunit INO80 complex. INO80 contains an ATP-dependent translocase motor, that is common to all nucleosome sliders, but also a variety of other subunits, most of which have unknown roles. Furthermore, not only does it require two INO80 complexes interacting with a single nucleosome to promote sliding, but the complex also has an ability to "sense" the presence of other nucleosomes to space them evenly on DNA indicating interactions with multiple nucleosomes. The mechanism for this process is poorly understood, particularly at a molecular and structural level. INO80 is highly regulated in several distinct ways, including chemical modifications, small molecule effectors and subunit interactions but none of these are well understood. Finally, how the various subunits, many of which are ATPases in their own right, contribute to INO80 activities is also unclear.

Amount: £1,701,911
Funder: The Wellcome Trust
Recipient: Imperial College London

Suppression of adaptive immunity by Salmonella 28 Nov 2017

Dendritic cells (DCs) have a crucial role in the development of adaptive immunity to bacteria. DCs transport the intracellular pathogen Salmonella from intestinal Peyer’s Patches to mesenteric lymph nodes where they present bacterial antigens to CD4+ T cells using MHCII molecules. DCs also secrete cytokines that stimulate recruitment and activation of T and NK cells. Salmonella is a globally important intracellular pathogen that survives in DCs and interferes with the processes of DC migration, cytokine production/sensing and T cell activation. The overall goal of this application is to understand mechanisms by which Salmonella interferes with these processes. Recently we identified an effector of the SPI-2 type III secretion system (SteD) that reduces the number of mature MHCII molecules on the surface of DCs. A significant component of the planned work is to understand its mechanism of action in detail. We will use candidate-based and unbiased screens, along with molecular cell biological approaches to characterize mechanisms involved in suppressing DC migration, production of IL-12 and IFN-gamma-stimulated host cell signaling. Collectively, this research will advance the field by providing novel insights into different mechanisms by which a bacterial pathogen subverts the development of adaptive immunity.

Amount: £2,170,670
Funder: The Wellcome Trust
Recipient: Imperial College London

Supramolecular peptide nanotechnology for antimicrobial therapies 04 Dec 2017

Antimicrobials remain the main means to treat and control bacterial infections, but their efficacy is now compromised due to overuse in humans, animals, agriculture, with bacteria developing resistance that renders certain antibiotics ineffective. Infections due multi-drug resistant (MDR) bacteria have emerged as one of the most significant global threats to human and animal health in the 21st century. Thus, the development of new antibiotics, or better ways to deliver existing antibiotics more effectively, is an urgent priority. Polymyxins are "old" antibiotics that have re-emerged as the last resort for treating infections caused by MDR Gram-negative bacteria. There are two polymyxins in clinical use, polymyxin B and polymyxin E (colistin), but their low stability, unpredictable pharmacokinetics and nephrotoxicity still raise significant concerns. We hypothesize that nano-engineered carriers will be able to restore and/or enhance the efficacy of polymyxins against MDR Gram-negative bacteria by improving their pharmacokinetic profiles, compared to standard mono and dual antimicrobial formulations, whilst minimizing the risks of adverse systemic effects. We will develop and optimize novel self-assembled nanocarriers for the controlled delivery of polymyxins and assess their potential to treat more effectively bacterial-related infections. This data will make the basis for future grant applications under the AMR initiatives.

Amount: £99,986
Funder: The Wellcome Trust
Recipient: Queen Mary University of London

Modelling synaptic and intrinsic plasticity in the somatosensory cortex 04 Dec 2017

Somatosensory plasticity is as key ingredient of sensorimotor learning; a better understanding of the plasticity mechanisms involved would yield insights for neuroprosthetics, motor rehabilitation, and chronic pain. In the somatosensory cortex, changes in the hand representation have been described under stimulation paradigms lasting only a few hours. Conversely, other evidence shows that cortical representations are stable over long periods of time. These disparate results raise the question of whether different plasticity mechanisms, operating on different timescales, might be involved. Recent advances in neuroimaging techniques have allowed us to observe and track plasticity in the human brain, leading to novel insights into the timescale and extent of sensorimotor learning. However, inferring specific plasticity mechanisms from these data has been challenging, as observed cortical changes are often compatible with multiple mechanisms. Here, we focus on two forms of plasticity: synaptic plasticity, which determines which specific inputs will excite a cortical neuron, and intrinsic plasticity, which determines the neuron’s overall responsiveness. We propose a computational framework that will track the effects of these two mechanisms on sensory cortical representations and make predictions that can be empirically tested using existing fMRI paradigms.

Amount: £99,605
Funder: The Wellcome Trust
Recipient: University of Sheffield

Equator From The Air 28 Nov 2017

Not available

Dynamical modelling of somatic genomes 28 Nov 2017

Cancers are complex and chaotic systems. It is becoming apparent that no two cells in a cancer are genetically identical or follow the same evolutionary trajectory. Chromosomal instability (CIN) is one way that cells generate this complexity and is a hallmark of all cancer and ageing. In cancer, it increases the level of variation available to cells and gives rise to intra-tumour genetic hetereogeneity, which makes the disease more agressive, drug tolerant, and harder to treat. We are still far from a complete understanding of how cells undergoing CIN evolve over time, in particular, we do not know how populations of cancer cells evolve and how selection acts to change these properties. Understanding this normal evolutionary behaviour will be key to separating the functional and non-functional aspects of intra-tumour heterogeneity. We will tackle this problem by understanding cancer as an emergent complex system, and use simple dynamic stochastic models to capture the essential biological features of the processes underlying CIN, including chromosome gain and loss, structural change, and genome doubling. We will use the vast amount of NGS data already available to fit these models using Bayesian inference and infer the evolutionary aspects of CIN in healthy and cancerous tissues.

Amount: £1,273,968
Funder: The Wellcome Trust
Recipient: University College London

Harnessing the potential of embryo-derived pancreas organoids to model early tumorigenesis 04 Dec 2017

Epithelial tissues maintain homeostasis through competitive cell-cell monitoring systems that detect and eliminate defective or mutant cells1-3. Retention of damaged or mutant cells would impair tissue function and initiate tumourigenesis. We have identified an evolutionarily conserved mechanism of cell competition that drives the segregation and elimination of Ras-transformed cells from simple epithelia4-6. KRas mutations (KRasG12D) are the principal oncogenic drivers of human pancreatic ductal adenocarcinoma (PDAC)7, making it an ideal model to test the significance of KRas driven cell competition. Our current data show that KRasG12D cells are lost from healthy pancreas tissues, suggesting that the normal niche may prevent early tumourigenesis. Current experimental pancreas models limit our ability to probe the biology of cell competition at the cellular level. The goal of this proposal is to grow fully differentiated pancreas organoids in culture, mosaic for KRasG12D expression. Organoids recapitulate the cellular complexity, plasticity and spatial organisation of tissues8,9. We will combine this accessible cell-based platform with advanced imaging techniques, to determine how the normal cell niche prevents expansion of KRasG12D cells, and how additional p53 mutations drive disease. Future work will investigate Eph-ephrin signalling and changes in cell polarity in early tumorigenesis.

Amount: £91,480
Funder: The Wellcome Trust
Recipient: Cardiff University

Molecular mechanisms of alternative splicing regulation 28 Nov 2017

Alternative pre-mRNA splicing (AS) is a widespread regulatory mechanism enabling individual genes to generate multiple protein isoforms. We have investigated the mechanisms controlling AS events that are regulated during the transition of smooth muscle cells (SMCs) between contractile and proliferative phenotypes. We have shown how the widely-expressed RNA binding proteins (RBPs) PTBP1 and MBNL1 regulate SMC splicing events. Recently, we identified RBPMS as a potential "master" regulator of SMC AS. RBPMS is sufficient to switch AS events to the SMC pattern and its activity is strongly modulated by its own AS and by phosphorylation. Critically, RBPMS is sufficient to switch AS to the SMC pattern in vitro. This offers a unique opportunity to determine the molecular anatomy of regulated splicing complexes. We will carry out detailed mechanistic analyses of RBPMS-regulated splicing using a combination of biochemical, proteomic, single-molecule, and structural approaches including Cryo-EM. We will identify critical regulatory interactions between regulatory RBPs and core splicing factors, and test their importance by genome editing and mRNA-Seq. In a complementary aim, we will investigate how peptide-ligand interactions equip PTBP1 to regulate AS and a range of other post-transcriptional processes, and whether a family of such peptide-mediated interactions extends to related RBPs.

Amount: £1,503,005
Funder: The Wellcome Trust
Recipient: University of Cambridge

Somatic adaptation and sex differences in human endocrine development and disease 28 Nov 2017

Our work focusses on new genetic mechanisms affecting human adrenal and reproductive function. We have recently described a multisystem growth restriction disorder caused by gain-of-function of SAMD9, where somatic adaptation can modify phenotype and mask detection of the genotype. In parallel, we developed a transcriptomic atlas of human adrenal and gonad development, mapping out sex-specific effects of organogenesis. We now plan to develop these insights to address several related fundamental questions: 1) How extensive is SAMD9 variability in endocrine and growth phenotypes and does dynamic somatic adaptation play a wider role in human disease mechanisms; 2) What are the dynamic roles of sex chromosomes and sex hormones in development (focussing on brain, adrenal gland and genital tubercle), and how does genetic variability of the X-chromosome contribute to phenotype in Turner syndrome (45,X); 3) Can we apply these concepts to discover new genetic mechanisms underlying adrenal and reproductive disorders. This work would provide novel disease models and approaches to analysis, could link the dynamics of development and sex-differences to common conditions (e.g. neurodevelopment, stress, early-onset hypertension), and would continue to elucidate the causes of human adrenal and reproductive disorders, with important implications for personalised management and development of new therapies.

Amount: £1,561,134
Funder: The Wellcome Trust
Recipient: University College London

The role of cerebellar circuitry in movement control and real-time motor learning 28 Nov 2017

The cerebellum is known to play a critical role in ongoing sensorimotor behaviour and learning of novel associations, but these processes remain poorly understood. The aim of this proposal is therefore to provide an extensive characterisation of the cellular and circuit mechanisms involved in motor control and learning in the cerebellum. We will probe cerebellar processing in head-fixed behaving animals using whisker movement as a model sensorimotor behaviour. We will measure neuronal activity using a variety of functional imaging and electrophysiological methods, combined where appropriate with opto- and pharmaco-genetic perturbation of specific circuit elements. Throughout the data-gathering process, we will work with theoreticians to generate a comprehensive network model of whisker representation in the cerebellum. Three discrete but interconnected aims will be addressed: 1) What are the organisational principles governing control of whisker movement within the cerebellar cortex? 2) What are the functional characteristics of inputs and outputs to cerebellar cortex during active whisking? 3) What are the mechanisms of real-time motor learning in the cerebellum? Together, we will provide unique quantitative information about the function of cerebellum in voluntary movement, and reveal how learning-related changes influence the neural representation of a well-controlled motor behaviour.

Amount: £1,498,083
Funder: The Wellcome Trust
Recipient: University of Bristol

The role of leukotriene A4 hydrolase in dictating inflammation and remodelling in chronic lung diseases 28 Nov 2017

Whilst inflammation and ensuing repair are critical to the body’s response to infection/injury, aberrant inflammatory and reparative processes and subsequent pathological remodelling are cardinal features of chronic lung diseases (CLDs). I believe the enzyme leukotriene A4 hydrolase (LTA4H) critically regulates inflammation/repair processes through dual activities that generate lipid mediator leukotriene B4 (LTB4) but degrade matrikine Pro-Gly-Pro (PGP). PGP is a neutrophil chemoattractant whilst LTB4 drives the recruitment/activation of numerous immune cells. Additionally, I now demonstrate that PGP regulates epithelial and fibroblast functions critical to repair/remodelling. I hypothesise that intrinsic and extrinsic perturbation of the LTA4H axis drives distinct pathological inflammatory and remodelling phenotypes in CLDs. The key goals of this proposal are: Dissect how the dual functions of LTA4H regulate pathological inflammatory and remodelling features of CLDs, and infer if novel LTA4H modulators show therapeutic potential. Understand how LTA4H is perturbed by genetic influences and environmental insults resulting persistent inflammation and pathological remodelling. Evaluate the LTA4H axis in CLD patients to ascertain why it is aberrant and how it correlates with pathological and clinical endpoints. These studies examine biological pathways that define the balance between health and disease, and will facilitate the endotyping of patients for therapeutic intervention.

Amount: £1,798,687
Funder: The Wellcome Trust
Recipient: Imperial College London

Principles of human development and germ cell program 28 Nov 2017

Specification of human primordial germ cells (hPGCs) occurs around gastrulation, a critical juncture when the specification of the primary somatic lineages also occurs. In combination with human preimplantation embryos, in vitro models and hPGCs from aborted fetuses, our objective is to elucidate the origin and properties of the early human germline. For the mechanism of the hPGC fate, we will use experimental models that simulate early human development. We aim to investigate how cells gain competence for germ cell fate, and then respond to combinatorial effects of the critical transcription factors, which induce hPGC specification. Altogether, this study will reveal the organisation of the very early human embryo, and mechanisms of hPGC and somatic outcomes, which is essential for advances in regenerative medicine. Following hPGC specification, epigenetic resetting of the early human germline leads to extensive erasure of DNA methylation and epimutations in response to the critical regulators of chromatin organisation and nuclear architecture towards the epigenetic ground state. Some conserved resistant loci ('escapees') evade reprogramming. We will explore if some escapees have been exapted to function as regulatory elements. If so, this may have a crucial influence on human development, including brain development and neuronal diseases.

Amount: £2,750,000
Funder: The Wellcome Trust
Recipient: University of Cambridge

Unravelling the physics of the pressure drop in blood flow constrictions 28 Nov 2017

A blood flow obstruction introduces an additional burden to the heart, currently characterised by the pressure drop through the obstruction. The pressure drop is only available through catheterised sensors, with associated costs and risks, or through Doppler echocardiography with limited accuracy and robustness. This programme investigates the causes of the additional cardiac burden in those conditions that experience an obstruction of the blood flow. The idea is to examine the physics of the blood flow and unravel the three components of the pressure drop (i.e. unsteady, advective and viscous). The enabling technology, to be further developed within the programme, combines advanced medical imaging and computational technologies. The goals are (1) to identify the pressure biomarkers that best predicts adverse events, and thus guide the optimal choice of therapy options; (2) to enable an easy, robust and non-invasive access to the key pressure biomarkers in clinical practice.

Amount: £1,097,073
Funder: The Wellcome Trust
Recipient: King's College London

Metabolic magnetic resonance imaging across the human heart 18 Oct 2017

During my fellowship, I proved the feasibility of measuring cardiac energetics in volunteers and patients using ultra-high field (7T) MRI scanners. The sensitivity and the separation of signals from different metabolites both improved significantly compared to standard research scanners. I recently secured £340k funding to fit a new phosphorus coil on the Oxford 7T scanner, which I am now testing in volunteers. Theory predicts that this coil will have several complementary technical advantages. These will enable mapping of cardiac energy metabolism across the whole heart, with sufficient spatial resolution to distinguish signals from healthy from diseased tissue. It will also enable quantification of cardiac energy metabolism with high precision to study single subjects rather than groups. I request funding to validate these new whole-heart methods, proving their value in three carefully-targeted groups of patients, via an extension of my fellowship. My goals are (A) to study patients in which the metabolic pattern is known by other means; (B) others where the metabolic pattern will reveal previously-inaccessible aspects of disease mechanism; and (C) to prove I can resolve metabolic changes in single patients. Success in each of these studies will give me the pilot data needed for competitive Senior Fellowship applications.

Amount: £584,259
Funder: The Wellcome Trust
Recipient: University of Cambridge

Regulated mRNA stability and translation in neural stem cell development 28 Nov 2017

Understanding how the billions of varied cells in the human brain develop from a small number of neural stem cells (NSCs) is a central question in biology and medicine. This highly complex process has largely been explained by transcriptional regulation dictating the levels of protein expression in stem cells and their progeny. Using novel single molecule approaches to quantitate transcription and protein levels, we have discovered functionally important conserved examples where the levels of transcription and protein expression do not correlate. These include pros/prox1, the regulator of NSC proliferation and differentiation and myc, the proto-oncogene regulator of stem cell size. We will characterise the mechanism of post-transcriptional regulation of pros, myc and 21 additional functionally important examples we have discovered, all of which have extremely long 3’UTRs that are bound and regulated by the same conserved RNA binding proteins, Syp and Imp. We will also measure, genome-wide, mRNA stability and characterise the trans-acting factors and cis-acting signals regulating stability and translation. The proposed programme will characterise a hitherto under-studied layer of regulation acting in addition to transcription in complex tissues, providing major new mechanistic insights into how the brain develops in health and disease.

Amount: £1,972,007
Funder: The Wellcome Trust
Recipient: University of Oxford

Towards a quantitative comprehension of the Spindle Assembly Checkpoint 28 Nov 2017

My aim is to complete a quantitative analysis of the dynamic signalling pathways that control mitosis. By combining mass spectrometry with cutting-edge microsopy I intend to measure the number of active molecules of the key mitotic regulators and determine how and where they interact to generate a highly responsive signal transduction network that ensures genomic stability by controlling sister chromatid separation and mitotic exit. I have four main aims: 1) Measure the numbers of the mitotic regulators controlling chromosome separation and analyse how they are modulated by post-translational modifications (PTMs). 2) Determine the dynamics of the spindle assembly checkpoint (SAC) in living cells by measuring the generation of the SAC effector complex and the flux of its components through the pathway. 3) Determine how changes to a kinetochore affect its ability to catalyse the generation of the MCC. 4) Determine how a defined change in the number of molecules of specific regulators alters the dynamics and strength of the SAC, and in consequence their effect on genomic stability. Together, these studies will be used to inform and discriminate between models of mitotic control to determine how the SAC combines the properties of potency and responsiveness.

Amount: £2,249,139
Funder: The Wellcome Trust
Recipient: Institute of Cancer Research

Dissecting Androgen excess and metabolic dysfunction – an Integrated SYstems approach to PolyCystic Ovary Syndrome (DAISY-PCOS) 28 Nov 2017

Polycystic ovary syndrome (PCOS) affects 5-10% of all women; androgen excess is one of its major diagnostic features. While often perceived as a reproductive disorder, PCOS is now emerging as a lifelong, complex metabolic disorder, with increased risk of type 2 diabetes, hypertension, cardiovascular disease, and, as recently documented, non-alcoholic fatty liver disease (NAFLD). However, there has been no recent breakthrough regarding risk stratification or therapeutic intervention in PCOS. Our work has provided evidence for a key role of androgens in the development of PCOS-related metabolic complications. We will combine cutting edge in vivo physiology techniques, state-of-the-art metabolomics and machine learning-based computational approaches to address our overarching hypothesis that androgens are major drivers of metabolic risk in PCOS. We will use an integrated set of in vitro, ex vivo and in vivo experimental medicine studies to test this hypothesis and answer our specific questions: Does the control of androgen excess improve metabolic function? What is the role of different androgen pathways in conveying metabolic risk? Can we integrate phenome and metabolome data by machine learning to predict metabolic risk in PCOS? Our overall aim is the identification of novel personalized approaches and therapeutic targets for patients with PCOS.

Amount: £2,389,852
Funder: The Wellcome Trust
Recipient: University of Birmingham

Assessment of placental function in complicated pregnancy using advanced MRI 04 Dec 2017

Placental insufficiency underlies the major obstetric syndromes of fetal growth restriction (FGR) and pre-eclampsia and accounts for one third of stillbirths in high-income countries. There is an unmet clinical need for a method to properly characterise placental perfusion and determine if and when a placenta is likely to fail. The objective of this work is to develop an imaging method to assess placental function in complicated pregnancy. This work will help us to better understand placenta function in FGR. This project will compare placenta properties from appropriately developing and early-onset growth-restricted pregnancies to understand the differences in the appearance of the placenta in FGR. The key goals of this work are to assess a novel Magnetic Resonance (MR) Imaging method to measure fetal and maternal placental perfusion. This technique describes an MR signal that models the blood flow properties as they change between the maternal and fetal sides of the placenta. to link this to relevant clinical information including clinical ultrasound markers and fetal MRI. to use these results to establish a comprehensive imaging project for the placenta by providing an in vivo measurement of placenta function to complement information from ultrasound imaging and ex utero microCT.

Amount: £99,804
Funder: The Wellcome Trust
Recipient: University College London

Uncovering the Molecular Mechanisms of Asymmetric Cell Divisions in Mammalian Adult Epithelia 04 Dec 2017

Loss of asymmetric cell divisions (ACDs) regulation in the normal self-renewing stem cells is entwined with the growth and progression of poorly differentiated cancers. Yet, the molecular mechanisms controlling the execution of symmetric versus asymmetric divisions in adult epithelia are still unfolding. We recently demonstrated that KIF5/kinesin-1 is essential for mammary epithelial cell divisions and cytoarchitecture by governing the trafficking of the spindle orientation and apical polarity components, respectively. Whether KIF5/kinesin-1 couples spindle orientation and polarity machineries during mitosis to promote ACDs; and whether other mechanisms are involved remain open questions. Here, we will address these questions in mammary 3D organoids. We will use CRISPR/Cas9 gene editing to generate cells expressing AID-tagged endogenous KIF5/kinesin-1 to allow inducible and rapid degradation of the microtubule motor specifically during mitosis, for a precise evaluation of the role it plays in ACDs. We generated cells expressing GFP-tagged LGN –a key player in the spindle orientation machinery–to purify and analyse the LGN-containing complex by LC-MS/MS mass spectrometry and identify novel factors that participate to ACDs. These studies will elucidate the molecular mechanisms of ACDs in the mammary epithelia and provide rational for subsequent detailed investigations in vivo of their precise roles in development and homeostasis.

Amount: £100,000
Funder: The Wellcome Trust
Recipient: University of Southampton

Investigating the influence of vitamin D status on cognitive and motor development in young African children. 21 Nov 2017

Poor child development is a major public health concern in Africa where children are exposed to risk factors such as poverty and malnutrition. Studies show that vitamin D deficiency affects African children despite sunshine throughout the year. Evidence from in vitro and animal work shows that vitamin D plays an important functional role in neurodevelopment. There is limited literature on the effects of vitamin D deficiency on child development especially in African populations and these have shown mixed results. I intend to carry out an observational study among 1583 children to establish if there is an association between vitamin D status and cognitive and motor development. Additionally, in a pilot study I will use genetic variation in vitamin D to investigate causality between low vitamin D levels and impaired development among 2583 children. This approach reflects life-long exposure and avoids the potential problems of confounding and reverse causation associated with observational studies. A significant advantage is that, through collaboration, vitamin D measurements, developmental scores and genome wide association study (GWAS) data are already available for the majority of these children. This study will inform the design of interventions to prevent vitamin D deficiency/ insufficiency and improve child development in Africa.

Amount: £119,292
Funder: The Wellcome Trust
Recipient: Kemri-Wellcome Trust Research Programme