NIHRDataInsights/HRCSData huggingface dataset:
Title: Molecular mechanisms connecting signal transduction and RNA processing: Structural studies of the STAR family of protein
Funder: Medical Research Council

Abstract: Cellular processes are tightly regulated at different levels by various signaling pathways depending on extracellular stimulations. I aim at better understanding the interplay between signaling pathways and post-transcriptional gene regulation. Post-transcriptional gene regulation consists of major events in cells, such as alternative splicing, RNA export, or translation regulation, that are still not fully understood. The project I intend to develop seeks at unraveling at the molecular level the functional properties of the STAR (Signal Transduction and Activation of RNA) family of protein. These proteins provide a direct connection between cell signaling and post-transcriptional modifications. The STAR family is involved in many cellular processes such as signal transduction, post-transcriptional gene regulation, tumorigenesis and viral metabolism. All these proteins are involved in the regulation of alternative splicing and RNA export. Importantly, Sam68, the best characterized member of this family, has important roles in post-transcriptional gene regulation that are connected with tumor progression and retroviral life cycle. STAR proteins contain a STAR domain responsible for RNA binding, several proline and tyrosine rich sequences that promote phosphorylation by diverse kinases, arginine-glycine rich sequences that are methylated by methyltransferase enzymes, and nuclear localization signals allowing the protein to shuttle between the nucleus and the cytoplasm. There are no structures of a full STAR domain free or in complex with RNA. I therefore plan to solve the NMR structures of STAR domains of different STAR proteins free and in complex with their RNA targets in order to define a general mechanism for RNA recognition by STAR family members. In addition, Sam68 regulate the export of HIV-1 RNAs by binding the viral RNA and the Rev protein. I plan to study biochemically and structurally the trimolecular complex formed between Sam68, Rev and the HIV-1 RNA. Phosphorylation and arginine methylation of STAR proteins affect their RNA binding capability and therefore their functions in post-transcriptional gene regulation. An aspect of the project will be to study structurally theses domains in complex with signaling molecules to understand how post-translational modifications are achieved in STAR proteins and how these modifications affect the RNA binding capacities. Summarizing, I will apply my knowledge of molecular biology, biochemistry, NMR, protein/RNA structural biology, and docking to unravel the structural properties of the STAR family. Since STAR proteins play an important role in tumor progression and HIV RNA export, these structural studies will help initiating application for optimized viral and cancer therapies.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Membrane curvature as an organizing principle for eukaryotic cell biology
Funder: Medical Research Council

Abstract: Cell shape is adapted to function. Organelle shape is likewise optimised for the processes that take place on and within these microenvironments. Our research focuses on the dynamic regulation of cell and organelle shape and the ways in which transport containers bud from membranes and fuse with other membranes. An understanding of these processes is necessary to fully appreciate synapse function, the mechanisms of cell surface receptor expression, signalling within the cell and the uptake of nutrients. Furthermore, these pathways may be hijacked by viruses and toxins to gain entry into cells and may be dysregulated in pathological conditions such as cancer. We have found that the dynamic regulation of membrane curvature can occur through the interplay between the regulated insertion of membrane bending proteins (e.g. ENTH domains/amphipathic helices) and the sensing of membrane curvature by BAR domain-containing proteins. To further understand this process we solved the structures of a number of BAR domains, and have defined the molecular pathways on which they function. We have also defined the molecular mechanisms by which ENTH domains and amphipathic helices bend membranes. In particular we have indentified how the amphipathic helices of alpha-synuclein are involved in vesicule production from mitochondria under stress conditions. We found how alpha-synuclein, which is mutated in Parkinson’s, is recruited to mitorchondria for homeostasis – showing how this pathway may be disrupted in Parkinson’s disease. The use of such tools by the cell is not limited to the uptake of nutrients and signalling from the surrounding environment (endocytosis) but is also essential for most trafficking pathways within cells. We have tried to move in 2 directions with our new understanding. In the first instance we apply our knowledge to understand the complexity of neuronal connections and the ability of neurons to fire in a fast and reliable manner. In the second instance we have moved to a deeper understanding of transport container formation with controlled in vitro reconstitution of membrane budding stages (for example, some of the stages of clathrin-mediated endocytosis). We believe that we will eventually be able to manipulate and investigate at will, the control points and detailed mechanisms of endocytosis. The current view of clathrin-mediated endocytosis is simplistic, since there are probably many different pathways involving clathrin and many distinct adaptor proteins, so that cells can tightly control which ligands are taken up at any point in time and space thereby regulating surface receptor expression. The complete reconstitution of clathrin-mediated endocytosis will also allow us to test different models and to examine the role of each individual protein.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Structure of medically-important membrane proteins
Funder: Medical Research Council

Abstract: Integral membrane proteins are fundamental to the survival of all cells. Transporters allow essential nutrients to be taken up by the cell and other transporters excrete toxic metabolites. Receptors in the plasma membrane bind signalling molecules and transduce signals into the cytoplasm, thus giving multicellular organisms exquisite control over cellular functions. Although great progress has been made in understanding some of these transport and signalling processes, more membrane protein structures are required in different conformational states to allow a molecular understanding of transport and signalling. This is particularly the case for mammalian membrane proteins, which are usually unstable in detergents and often difficult to purify in a functional state. We have developed methodologies for stabilising GPCRs in any conformation and have determined multiple structures of the beta 1 adrenoceptor (b1AR) and the adenosine A2A receptor (A2AR) in different conformations and with ligands of varying efficacy. We therefore have a detailed mechanistic insight into how these receptors are activated by agonists and couple to G proteins. This shows that these two receptors are activated by agonists in different ways and with different energy landscapes, despite the overall conservation of structure. Our future work will address why GPCRs couple differentially to varying G proteins and arrestins. This will entail determining structures of GPCRs coupled to different G proteins and arrestins by electron cryo-microscopy and X-ray crystallography. We will also study the kinetics of association of these complexes, and how different ligands, lipids and salts affect this process. This will lead to a detailed understanding of how signalling occurs in cells where there are multiple different G proteins and receptors present. Thi will allow the development of novel therapeutics that target specific G proteins or the arrestin pathway, which will reduce side effects of treatments.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: In vivo mechanisms of neurotoxicity
Funder: Medical Research Council

Abstract: Neurodegenerative diseases, such as Alzheimers, Parkinsons, Huntingtons disease and amyotrophic lateral sclerosis, have enormous clinical and economic impact world wide. Irrespective of the final pattern of clinical symptoms, they all are caused by an irreversible loss of neurons, which cannot be cured. But before neuronal death, there are neuronal dysfunction and synaptic impairment, which potentially can be treated.||My background is in prion diseases, modelling these in transgenic mice to look at mechanisms of neurotoxicity and developing new therapeutic approaches. In particular, I focused on the changes of early prion neurotoxicity and recovery from it. This new programme uses mouse models to understand the early molecular events in prion and other neurodegenerative diseases, looking in parallel at potential therapeutic targets for prevention of neuronal dysfunction and death.||Our main aims are to:|1. Characterise pre-degenerative neuronal changes.|2. Understand what triggers ultimate commitment to death in a malfunctioning neuron.|3. Define the molecular targets and the temporal window for functional recovery.||Initially, these questions will be addressed using our established mouse model of prion disease where early pathology is associated with a pivotal point in neuronal survival/death, and there is potential for recovery. We will use molecular biological, biochemical and neurophysiological techniques, as well as neuronal imaging in culture and in vivo to characterise the underlying cellular and synaptic changes, including alterations in signalling pathways and ion channels.||The broader aims of the programme are:|4. to generate new mouse models to look at individual pathways implicated in early dysfunction and their effect on neuronal function and death.|5. to address therapeutic strategies for the treatment of neurodegeneration.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Core - Neural circuitry of action: function and dysfunction
Funder: Medical Research Council

Abstract: Movement is our only way to interact with the environment, to explore it and modify it. We study the organization and function of neural circuits controlling movement in mice, with particular focus on goal oriented movements. We seek to understand three fundamental aspects of motor control: 1) How animals produce an accurate body-bound map of the surrounding space that can be used to direct targeted movements 2) Which neuronal populations are directly involved in orchestrating goal-oriented movements towards salient positions of this map 3) How, during development, these neuronal populations are assembled into functional networks with the degree of specificity needed to coordinate movements. In order to answer these questions we focus on the motor network controlling head movements. The head movement system has the advantage of being relatively simple, if compared to the limb system, with only one individual joint and a limited set of muscles. Moreover, in rodents, target directed head movements are possibly the most commonly used strategy to interact with the world. The reduced dimensionality of these systems offers an unprecedented opportunity to reconstruct the complete connectome of a motor network. This will facilitate our understanding of the genetics of its assembly and logic of its function. In line with our focus on neural circuits, we also work on the development of novel methods to trace and manipulate neural circuits in vivo in ways that are not currently possible. The main aim of this part of the work is the development of non-cytotoxic trans-synaptic tracers that would allow long-term circuit manipulation, recording and visualization. Using these methods, we aim at understanding the contribution of network dynamics to motor function as well as understanding the molecular underpinning of neural-networks communication in health and disease.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Organelle Cross Talk and Membrane Dynamics
Funder: Medical Research Council

Abstract: Cells and tissues communicate with one another through the release of hormones and neurotransmitters that are recognized by signaling receptors on target cells. As such, cell-cell communication is tightly coupled to membrane trafficking pathways that control the secretion of signaling factors and the targeting of cell-surface receptors. Our group is investigating the structural requirements and physiological roles for membrane lipid dynamics in cell signaling and membrane trafficking pathways. This work is revealing novel roles for ‘intracellular synapses’ between the between the endoplasmic reticulum (ER) and plasma membrane (PM). We are elucidating how the assembly and disassembly of ER-PM contacts are regulated and how distinct ER-PM contacts modulate phosphoinositide (PI) kinase regulatory networks. PI kinase signalling networks control several key cellular processes including cell growth and survival, cell polarity, and membrane trafficking pathways. Consequently, defects in PI kinase regulatory networks have been implicated in numerous human diseases including cancer, diabetes, and neurodegenerative disorders. It is vital that we understand how cells maintain and use these essential signalling molecules. We are currently undertaking multidisciplinary approaches–including cell biological assays, high-resolution microscopy, proteomics, lipidomics, and biochemical approaches–to make new discoveries into the regulation of PI kinase signaling networks by ER-PM cross talk. We expect that these investigations will reveal new insights into the complex regulatory processes that ensure the temporal and spatial specificity of membrane trafficking systems, including regulated exocytosis and endocytosis necessary for pulsatile insulin secretion and neurotransmission. Moreover, we have found that ER-PM cross talk is essential for normal ER morphology and function. Loss of ER-PM contacts causes dramatic changes in ER organization and architecture, resulting in activation of ER stress response pathways. Recent findings have placed ER stress as a key component of neurodegenerative diseases including Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and amyotrophic lateral sclerosis (ALS). We are currently elucidating the vital roles for PM-ER contacts in ER membrane homeostasis, as well as the essential cellular pathways induced in response to membrane stress.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Chemical tools for studying conventional and non-conventional modes of ubiquitylation
Funder: Medical Research Council

Abstract: E3 ligases (E3s) mediate the transfer of ubiquitin to specific substrates and play important roles in both health and disease. The cellular regulation and function of the vast majority of the >600 E3s remain poorly understood. The activity of E3s can be regulated by posttranslational mechanisms, including phosphorylation, and aberrant E3 activity is emerging as a hallmark of certain diseases. Development of new tools that allow the unbiased assessment of the activity state of E3s in normal and diseased cells and tissues would provide field-changing insight into the cellular roles of E3s, and may uncover novel therapeutic targets. We have developed new chemical biological tools which for the first time allow the activity of endogenous HECT and RBR E3s to be determined directly. We have validated these tools against the E3 termed Parkin that is mutated in Parkinson’s disease. Our work demonstrated that these tools can be used to garner valuable insights into the regulatory aspects of a disease-relevant E3 and that they have value as a biomarker platform for assessing disease susceptibility. We have also discovered a novel class of E3 that that was only possible through the application of our tools. E3s were previously believed to be composed of RING, HECT and RBR subtypes. We have shown that there is fourth type of E3 which we term RCR. The apparent sole member of the RCR class is a neuron-associated E3 known as MYCBP2. MYCBP2 is a positive regulator of an axon degeneration pathway and hence may be a valuable therapeutic target for addressing a range of neurological disorders. Remarkably, MYCBP2 has a unique mechanism and transfers the ubiquitin molecule onto non-lysine residues within protein substrates. Future work in our lab will involve the functional studies on MYCBP2 and non-lysine ubiquitylation in axon degeneration. We will also be applying our tools to try and understand which other poorly characterised E3s might regulate disease-relevant signalling pathways.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Developing network methodologies for disease classification
Funder: Medical Research Council

Abstract: For objective (1) I will develop an integrated framework of complex networks and convolutional neural networks for health data which will build upon geometric deep learning [3], building established connections with Prof Pierre Vandergheynst of the École Polytechnique Fédérale de Lausanne (EPFL). Complex physiological networks will be derived from the multidimensional, complex datasets in the UK Biobank, which will then be utilised in this framework to gather important insights into health and disease and develop enhanced large-scale classification strategies. For objective (2) I will build on pilot work (unpublished) which applies novel complex network methods [4,5] to detect AD from task-related EEG signals. This will be extended for the following: (i) refinement and continued development of theoretical approaches to analyse functional connectivity (ii) adaptations for application to high spatial resolution fMRI and MRI data (iii) applied to resting-state fMRI in large datasets such as the Lothian Birth Cohort and UK Biobank (iv) employment of powerful classification and regression approaches such as support vector machines Such methods are also of great relevance to an array of different pathologies, including other forms of dementia, epilepsy, Parkinson's disease and schizophrenia, to which the strategy proposed will be generalised. This project is in alignment with HDR UK priorities, developing novel data analyses and classification strategies for key national health problems, establishing national leadership, developing international collaborations, and strengthening interdisciplinary skills. References: see Summary


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Biostatistics and functional genomics in dementia
Funder: Medical Research Council

Abstract: The UK Dementia Research Institute (UK DRI) is an initiative funded by the Medical Research Council, Alzheimer's Society and Alzheimer's Research UK. Funding details for UK DRI programmes will be added in 2019. This programme will bridge the gap between statistical genetic association and tractable biological mechanisms and dissect complex pathways using novel mathematical approaches Our aims are to 1. Integrate biological data with large genetic datasets to detect disease-relevant mechanisms 2. Apply non-linear multivariate mathematical approaches (sCCA, SVM, etc) for disease stratification 3. Develop novel mathematical approaches tailored to identifying patterns in non-linear multidimensional “omics” space 4. Share algorithms, data, software tools with all members of UK DRI via DPUK platform Outcomes: Successful completion of these aims will deliver insights into fundamental biology, provide the resources and reagents (in the form of actionable causal and protective mutations, implicated pathogenic pathways, patient strata, advanced robust methodology for data analyses) that will fuel mechanistic and translational research, deliver novel therapeutic targets, inform clinical practice and provide guidance on optimal analysis approaches for large “omics” datasets.


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS;2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Neural Circuits for Goal-oriented Actions
Funder: Medical Research Council

Abstract: Movement is our only way to interact with the environment, to explore it and modify it. We study the organization and function of neural circuits controlling movement in mice, with particular focus on goal oriented movements. We seek to understand three fundamental aspects of motor control: 1) How animals produce an accurate body-bound map of the surrounding space that can be used to direct targeted movements 2) Which neuronal populations are directly involved in orchestrating goal-oriented movements towards salient positions of this map 3) How, during development, these neuronal populations are assembled into functional networks with the degree of specificity needed to coordinate movements. In order to answer these questions we focus on the motor network controlling head and eyes. The head-eyes system has the advantage of being relatively simple, if compared to the limb system, with only one individual joint and a limited set of muscles. Moreover, in rodents, target directed head movements are possibly the most commonly used strategy to interact with the world. The reduced dimensionality of these systems offers an unprecedented opportunity to reconstruct the complete connectome of a motor network. This will facilitate our understanding of the genetics of its assembly and logic of its function. On a parallel line of research we investigate neural circuits responsible for automatic movements such as those involved in locomotion. In particular, we try to understand the genetics of the assembly of neuronal circuits engaged in motor antagonism, such as those driving flexor extensor alternation during walking. We have previously identified that elements of these antagonistic circuits are genetically homogeneous but temporally segregated with respect to the time of their birth and yet they display very specific and divergent patterns of connectivity. Our present goal is to understand how the observed birth order differences impinge on the transcriptional landscape of these neurons and how this in turn reflects on their connectivity pattern. We have recently developed viral strategies, based on genetically modified trans-synaptic rabies virus, that allow us to identify and functionally manipulate neurons directly controlling the activity of defined muscles. By using such a viral based approach in combination with mouse genetics we plan to generate a detailed map of neurons controlling functionally distinct sets of muscles. Our work aims to understand how genetically identified elements of these motor circuits modulate specific aspects of the motor output, such as target localization, displacement towards target and appropriate coordination of antagonistic muscles. We investigate these questions using and developing a variety of methodologies. These include mouse genetics, viral strategies for circuit tracing and functional manipulation, in vivo electrophysiology, optogenetics and behavioral analysis.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL