NIHRDataInsights/HRCSData huggingface dataset:
Title: The regulation of endo-lysosomal trafficking, growth and exosome biogenesis bydevelopmental signalling cascades.
Funder: Wellcome Trust

Abstract: Late endosomes and lysosomes, intracellular compartments often considered to be sites for macromolecular degradation, have recently been implicated in other fundamental cell biological processes. For example, they regulate growthand biogenesis of secreted vesicles called exosomes, which have postulated roles in development. How these processes and membrane trafficking in endo-lysosomes are linked to developmental signals that control them is poorlyunderstood. Building on my preliminary results using a genetic model with giant endo-lysosomes, the Drosophila secondary cell, I will further characterise the regulation of endo-lysosomal functions by developmental (growth factor) signalling cascades and DNA binding proteins in the steroid receptor family. I will also explore whether there are different populations of exosomes in secondary cells that are differentially regulated by growth factor signals, and whether this regulation is dependent on a feedback mechanism involving loading growth factor signalling components into secreted exosomes. The kinase complex mTORC1 is thought to mediate endo-lysosomal


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Investigation into the role of ADP-ribosyltransferases in DNA repair.
Funder: Wellcome Trust

Abstract: The focus of this proposed project is to better undestand the role of ADP-ribosyltranferases (ARTs) in DNA repair. PARP1 and PARP2 are known to function in the repair of single strand breaks (SSBs), whereas the recently characterised PARP3 facilitates double strand break (DSB) repair via non-homologous end joining (NHEJ). The specific aims of this project are to determine if any redundancy exists between PARP1 and PARP3 in facilitating DNA repair following DNA single strandbreaks, to determine to the substrates of PARP3 in response to DNA damage, andto determine the contribution of the catalytic domain of DNA damage responsiveARTs to their specific repair outcome. Key goals of the work include generating PARP1 and PARP3 deficient cell lines,both alone and in combination; determining the phenotypes of these disrupted cell lines; optimising mass spectrometry protocols for the reliable detection of in vivo poly ADP-ribosylation; identifying the substrates of PARP3 in response to DNA damage in defined genetic backgrounds; cloning chimeric ARTs


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Investigating the role of KDM2A in CpG island function and transcription regulation.
Funder: Wellcome Trust

Abstract: KDM2A is recruited to CpG islands (CGIs) throughout the genome. CGIs are regions of non-methylated DNA, and are associated with the majority of mammalian gene promoters. Here it has been proposed that KDM2A catalyses the removal of dimethyl histone H3 lysine 36, an abundant modification that can inhibit transcription initiation. Localised removal of this inhibitory mark byKDM2A may contribute to the generation of a promoter-associated transcriptionally permissive chromatin landscape. I aim to directly examine the role that KDM2A plays in regulating CpG island associated chromatin architecture and gene expression. To achieve this, initially a simple transgene reporter system will be used to determine the effect that KDM2A recruitment has on gene expression and to determine which regions of the protein to contribute this activity. Transcription regulation by KDM2A will next be investigated genome-wide, using KDM2A knockout mouse embryonic stem cells. Transcription and chromatin architecture in the wild-type and KDM2A knockout cells will then be examined in detail. This will


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: The SNX17-CCC complex: an alternative retromer?
Funder: Wellcome Trust

Abstract: Endosomes are important protein sorting platforms. Retromer, a conserved ancient complex, is the molecular machinery by which proteins can sort to the TGN and the plasma membrane. However, SNX17 sorting is not dependent upon retromer and the mechanism by which SNX17 cargo, such as B1 integrin, recyclesback to the plasma membrane is unknown. Preliminary data from our lab and fromcollaborators Ezra Burstein and Dan Billadeau suggests that SNX17 associates with the CCC complex and that this is needed for correct recycling of B1 integrin. We propose that the CCC complex forms an alternative retromer which facilitates SNX17 cargo sorting. This PhD will investigate the biochemical basis of the SNX17-CCC complex interaction as well as establishing the global functional relevance both in vitro and in vivo. Components of the CCC complex have been associated with diseases such as XLID, Alzheimer's and dementia, which emphasises the need to investigate this mechanism with the hope that novel therapeutics can be generated.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Molecular and functional characterisation of endosome to TGN recycling mediated by retromer
Funder: Wellcome Trust

Abstract: The endolysosomal system is a sorting platform for internalised transmembrane proteins (cargo) and lipids from both the biosynthetic and the endocytic pathway. Cargo recycling to the plasma membrane (PM) or retrogade retrieval tothe trans-Golgi network (TGN) relies on retromer, an evolutionary conserved protein complex. Two decades of work on retromer biology have led to the identification of very few retromer cargo but the recent use of proteomic revealed that over 100 retromer cargo take the endosome-to-PM route. However endosome-to-TGN cargo pool hasn't been investigated in a similar way because the lack of a technique able to accurately appreciate variations in TGN resident proteins. Here I aim to develop a global retromer transport assay to investigate endosome-to-TGN retromer trafficking through a combination of SILAC based quantitative proteomics with the recently developed APEX technology. I will use the latter to resolve the TGN and trans-Golgi proteome and build a comprehensive retromer cargo list comparing these proteomes in control and retromer components- suppressed cells. Finally, retromer can sort cargo from endosome to TGN via different routes and I will use super resolution LM and EMtechniques to investigate how cargo sub-pools correlates with different sorting domains.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Role of clathrin light chains and other binding partners in generating functional diversity of clathrin heavy chains.
Funder: Wellcome Trust

Abstract: This project aims to study clathrin heavy chain (CHC) binding interactions andhow these interactions diversify clathrin function. CHCs trimerise into a triskelion and can assemble into cage-like lattices on cellular membranes to sequester specific cargo for vesicular transport. There are two isoforms of clathrin heavy chains. Whereas CHC17 binds clathrin light chains (CLC), equivalent binding partners for CHC22 remain to be identified. CLCs modulate CHC17 cage assembly and mediate binding to Hip proteins, which recruit actin to the plasma membrane. Upregulation of both CLCs and Hip proteins are associated with forms of metastatic cancer. In this project, we will focus on three aspects of clathrin interactions: (1) We will investigate how CLC isoforms alter CHC17 clathrin trimer stability, tensile strength and disassembly - physical properties that can govern clathrin function and cargo selectivity (2) We will develop a high-throughput screen for an inhibitor of CLC-Hip interaction. This will provide the platform for drug development and research in metastatic cancer (3) A list of candidates for CHC22 interactions,derived from known binding partners, will be tested and binding regions will be mapped. This will give insight in CHC22 cellular function and allow for inhibitor screening for these interactions.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: New interdisciplinary methods to characterise side-chain and metastable protein conformations and probe the conformational sampling of intrinsically disordered proteins.
Funder: Wellcome Trust

Abstract: Traditionally, structural biology focuses on the backbone conformation of rigid proteins. Protein side-chains often populate multiple conformations and are harder to probe since flexibility limits the use of crystallographic methods. Additionally, current molecular dynamic force-fields are not yet ideal for side-chain sampling and appropriate NMR methods are limited. However, side chains frequently play critical roles in biochemical processes such as ligand binding, catalysis and protein folding. Similar technical challenges are encountered in the study of low population excited states and flexible or intrinsically disordered proteins, which have also been shown to be key in numerous cellular processes and pathologies. Thus, there is a clear need for new, interdisciplinary methods to characterise side-chains, excited states and disordered proteins. The objective of the proposed research projectis to develop experimental and theoretical methods to probe the structure and dynamics of (1) side-chains and (2) metastable protein conformations. Novel NMR pulse sequences will be developed and new experimental parameters identified that can be used to (3) both validate and steer molecular dynamics simulations. These methods will not only further our understanding of the function and behaviour of side-chains but also facilitate the investigation ofmany other flexible systems inaccessible to current methods.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: Sulfonium Salts as Precursors for 18F-labelling of Small Molecule PET Tracers.
Funder: Wellcome Trust

Abstract: Positron emission tomography (PET) has become an invaluable tool for diagnostic imaging and medical research as it allows quantification of biochemical processes in vivo with unsurpassed sensitivity and specificity. Due to its near ideal physicochemical properties fluorine-18 is the radioisotope of choice for imaging applications with PET, yet the lack of efficient and practical methods for the incorporation of 18F limits the availability of clinically relevant radiotracers. In particular, late stage labelling of compounds bearing functional groups that are prerequisite to biological activity remains challenging. The Arstad group have recently developed a new radiochemical strategy for aromatic labelling of drug-like small molecules based on the unique reactivity of sulfonium salts with fluoride-18. In this project, we aim to investigate the structural requirements for labelling with 18F and to broaden the scope of the existing method by establishing complimentary synthetic routes. To demonstrate clinicalapplicability, the strategy will be used to simplify radiosyntheses of existing radiotracers, to improve the imaging properties of established tracers, and to develop novel diagnostic imaging agents. The work has the potential to open up new prospects for imaging applications with PET. Ultimately, the development of new diagnostic agents can lead to improved human health.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: GENERIC HEALTH RELEVANCE
Title: Extensions to Sequential Monte Carlo methods applied to the sequentially Markovian coalescent model for demographic inference from whole-genome sequence data
Funder: Wellcome Trust

Abstract: Joe Zhu and Gerton Lunter have recently developed a method (SMC^2) for demographic inference using whole-genome sequence data by applying the particle filtering technique (a Sequential Monte Carlo method) to the sequentially Markovian coalescent model.This project will will expand upon three aspects of SMC^2. The first task is to optimize eter parameter estimation within SMC^2. The second aim is to relax simplifying assumptions made in otherprograms of its kind. The kind. The third task is the natural extension of the algorithm to unphased anderror prone data, for use in low-coverage sequence data such as ancient DNA.


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: Inducible CRISPR:Cas transcription regulators for de novo assembly of gene regulatory networks
Funder: Wellcome Trust

Abstract: The CRISPR:Cas9 system has proven to be a simple and versatile tool to engineer biology. Initially used for genome editing, CRISPR:Cas9 was rapidly repurposed to carryout programmed transcriptional regulation. The next frontier in expanding its potential will be set off by the design of inducible systems responsive to exogenous cues and/or endogenous metabolites. Leveraging the sensor/actuator capabilities of allosteric self-cleaving ribozymes (aRz), which can be modulated by various ligands, I propose to re-engineer theRNA component of the system to create inducible CRISPR transcriptional regulators (iCRISPR-TR). This conceptual framework is expected to play a pivotal role in synthetic biology, empowering scientists to create complex devices able to rewire cell behavior upon sensinga disease state. Throughout the project, aRz sequences will be tested and their activity optimized via in vivo evolution in human cell lines (Aim 1). Promising candidates will then be implemented to power our iCRISPR-TR strategies (Aim 2). A systematic characterization of all devices at the transcript/protein level will provide novel insight into CIRSPR:Cas dynamics, which will feedback into our designs. Finally, to demonstrate the potential of this innovative platforms, microRNA sensing iCRISPR-TR will be used to reprogram latent phase EBV infected B-cells(Aim 3).


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Complex genetic phenotypes and their association with age-related disease in large cohorts.
Funder: Wellcome Trust

Abstract: Telomere attrition and mitochondrial DNA dysfunction induce cellular senescence and apoptosis via p53-mediated pathways. Leucocyte telomere length (LTL) and mitochondrial DNA (mtDNA) copy number are therefore related to age-related diseases associated with inflammation, oxidative stress and disordered cell turnover. Whilst most high-throughput assays measure average LTL, critical shortening at specific telomeres may trigger a cells entry into replicative senescence. The proposed research aims to improve standardisationfor pre-existing assays characterising intra-/inter-subject variability in average and individual LTL, and mtDNA copy number, in multiple age-groups, andrelate these genetic phenotypes to growth, and pathologies involving accelerated ageing. Objectives: 1.To assess average LTL in subjects from the Avon Longitudinal Study of Parents and Children, and the British Women's Heartand Health Study. a.To employ a reference telomere construct for standardisation of quantitative PCR. 2.To develop a high-throughput assay measuring individual LTL, combining qPCR, individual LTL assays and locally-developed ratiometric techniques. 3.To perform genome-wide/gene-centric scans of LTL. 4.To replicate LTL-phenotype associations (cardiovascular disease, COPD/asthma) and to study associations between LTL/mtDNA copy number and intermediate phenotypes/risk factors. a.To refine associations in extreme phenotypes. 5.To investigate LTL in relation to growth and puberty. 6.To determine novel LTL/mtDNA copy number associations using phenome scans.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: The role of PRDE-1 in piRNA biogenesis.
Funder: Wellcome Trust

Abstract: Small non-coding RNAs (sRNAs) have gene-regulatory roles in many organisms including animals. In eukaryotes sRNAs act with Argonaute proteins to regulate target RNAs via Watson- Crick base-pairing (Stefani and Slack, 2008). Amongst sRNAs, piRNAs are crucial during development (Mani and Juliano, 2013). piRNAs are often germline enriched and associate with the PIWI clade of Argonaute proteins to repress the activity of transposons. In many species, loss of the piRNA pathway results in defective germline development, meiotic arrest and sterility. Little is known about piRNA biogenesis. The newly identified nuclear factor PRDE-1 is essential for piRNA biogenesis in the nematode


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: The development of olfactory ensheathing cells.
Funder: Wellcome Trust

Abstract: Olfactory ensheathing cells (OECs), the glia of the olfactory nerve, promote axon sprouting and remyelinate axons when grafted into spinal cord lesions. Our lab's discovery that OECs are derived from neural crest cells, not the olfactory epithelium as previously thought, potentially means that homogeneous populations of patient-specific OECs for spinal cord repair could be expanded in culture from the neural crest stem cells that persist in skin and hair follicles. First, however, we need to understand OEC differentiation and how OECs differ from Schwann cells (the neural crest-derived glia of all other peripheral nerves), which are lesseffective in spinal cord repair. Our lab and others also showed recently that defective OEC


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Investigating the Molecular Mechanisms that Contribute to Loser Cell Status inDrosophila melanogaster.
Funder: Wellcome Trust

Abstract: Cell competition is a form of cell-cell interaction that selects the best cells within tissues, acting as a cellular quality control and likely contributing to preserve tissue health. It occurs when cells of differing fitness levels come into contact, causing weaker loser cells - which are perfectly viable on their own to be eliminated by fitter winner cells through the induction of cell death. Despite the growing interest in this phenomenon, little is known about the molecular mechanisms responsible for sensing fitness or for loser cell elimination during cell competition. My PhD project aims to address these questions focusing on two main aims:1) Identify novel genes that play a role in cell competition. The Piddini lab has identified 217


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Targeted mRNA Trafficking in Pathfinding Axons of the Developing Visual System.
Funder: Wellcome Trust

Abstract: Building properly wired neural circuits involves guidance of axons towards synaptic targets in the brain. In the growth cone of pathfinding axons, targeted mRNA transport and localised translation is important for autonomously regulating navigational responses tocertain extracellular guidance cues. Still however, axonal mRNA trafficking remains poorly understood. We know very little about which mRNAs are differentially trafficked on guidance cue stimulation or mechanisms underpinning axonal mRNA transport. Using the well-characteriseddeveloping visual system as an experimental platform, this research proposal aims to explore the functional and mechanistic basis of targeted mRNA trafficking during axon guidance. We


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Biomechanics of collective chemotaxis
Funder: Wellcome Trust

Abstract: Collective chemotaxis (CCT), whereby groups of cells collectively migrate in response to chemotactic signals, is a fundamental mode of migration in development and metastatic cancers. The biomechanics of this process has been largely overlooked, with most work focusing on spontaneous migration of epithelial sheets despite evidence that strong cell-cell adhesions are not required for collective migration. Additionally, chemotactic signals are important for directional migration in vivo. We propose to use neural crest (NC) cells, a highly invasive mesenchymal cell population that extensively migrate throughout the embryo, to address the biomechanics of CCT. We will perform high-resolution time-lapse imaging of Xenopus NC to assess physical properties of CCT such as velocity and viscosity. Traction force microscopy, FRET tension sensors and atomic force microscopy shall be used to measure the physical forces required for CCT. Finally, the molecular mechanisms necessary for the biomechanics of this process shall be identified, in particular through chemical and mechanical manipulation of the actomyosin cytoskeleton tounderstand how it contributes to providing forces for CCT. Collectively, theseresults will provide a novel insight into the biomechanics of CCT which could have important implications for morphogenetic processes, regeneration and diseases like invasive tumours.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: How do cells interpret the multiple signals they receive into the complex behaviours of gastrulation?
Funder: Wellcome Trust

Abstract: During early development the embryo generates a complex architecture from multipotent cells. One of the first events is the establishment of bilateral symmetry: during gastrulation, cells rearrange themselves as they acquire different fates, all controlled by signals from different subpopulations of cells. Although we know many of the players, we know surprisingly little aboutwhich particular signal regulates which cell behaviour, or how cells integratesignals to generate regional complexity. Using the chick embryo as a model, wewill first create an atlas of cell behaviours and signalling activity in normal embryos and during experimentally-induced twinning. Subsequently, we will investigate the individual contribution of each of the pathways, and combinations thereof, to these complex cellular decisions, using gain- and loss-of-function experiments in normal embryos and fragments. Finally, we aim to integrate this knowledge by creating an agent model with predictive power, relating signalling to cellular behaviours during normal development and twinning. Together this project will disentangle the roles of different signals in establishing polarity, assigning cell fates and selecting from a vast array of possible cell behaviours during amniote gastrulation, which are also relevant to human twinning.


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