NIHRDataInsights/HRCSData huggingface dataset:
Title: Structure and membrane remodelling mechanism of the DP1/Reticulon family of ER proteins.
Funder: Medical Research Council

Abstract: DP1 proteins and the related reticulon family members are membrane remodelling proteins essential for maintaining smooth ER tubules and the edges of ER sheets. As a result, mutations in these proteins lead to motor neuron diseases such as hereditary spastic paraplegia (HSP). The current paradigm for how these proteins curve membranes involves helical hairpins within the Reticulon Homology Domain (RHD) that are proposed to only partially insert into the membrane. We have developed an experimental system for testing this model and found that the RHD of Yop1p from S. cerevisiae contains four helices long enough to fully cross the membrane. However, we have discovered an amphipathic helix (APH) in Yop1p that is highly conserved amongst DP1 family members (both in the amino acid properties and its location C-terminal to the RHD) and that is essential for Yop1p function in membrane tubule formation. Thus, while the transmembrane domain is required for RHD function, its exact role requires further investigation. The experimental system developed for Yop1p enables determination of the first 3D structure of an RHD and thus testing of structure-function relationships, which are essential for understanding the mechanism by which mutations in highly conserved amino acid positions of human DP1s such as REEP1 cause HSP. The more complete understanding of the Yop1p RHD secondary structure has also enabled a more reliable sequence alignment with the reticulons, suggesting that the RHDs have a similar transmembrane architecture, and potentially also contain an amphipathic helix C-terminal to the RHD. Thus, we will test whether the human DP1s and human reticulons contain amphipathic helices that interact with membranes, and whether this region is required for the human REEPs that are involved in HSP.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: DNA Misfolding and the Maintenance of Genome Stability: an Integrated Molecular, Cellular and Genomic Investigation of DNA Double-Strand Break Repair
Funder: Medical Research Council

Abstract: We will: 1. Compare and contrast recombination between sister chromatids in replication-dependent DSBR with recombination between sister chromatids in replication-independent DSBR. 2. Determine the molecular structures implicated in chromosomal DSBR by recombination and to relate these structures to the genomic consequences of DSBR. We will use three experimental approaches to integrate our understanding of DSBR at cellular, molecular and genomic levels. We will: A. Use live cell imaging to visualise DSBR. This will include determining the cellular location of events, dynamic movements of proteins and DNA and timing of reactions. B. Isolate and determine the structures of DSBR intermediates at a single chromosomal locus. This will involve multidimensional gel electrophoresis and electron microscopy of DNA molecules. C. Use genomic technologies such as ChIP-seq and Solexa sequencing to obtain quantitative data on the consequences of DSBR at a genomic scale. We will couple these data with stochastic modelling in collaboration with Dr El Karoui and Prof. Danos to derive mechanistic information from the data. Throughout these studies, we will use mutants that inactivate or modify the activities of key recombination proteins. Our previous MRC programme funding places us in the unique position of having developed sophisticated E. coil systems for the accomplishment of these aims. These include a way of generating replication-dependent DSBs at the site of a chromosomal palindrome cleaved by SbcCD and a way of generating replication-independent DSBs based on I-SceI cleavage. The breaks generated by both system are fully repairable. We have also developed systems for the analysis of DSBR including: live cell imaging, pulsed field gel electrophoresis, 2D native-native gel electrophoresis, ChIP-seq and Solexa DNA sequencing. In the course of the new programme, we will add 2D native-denaturing gel electrophoresis and electron microscopy to our toolkit.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Regulating protein translation to protect from UV-induced damage
Funder: Medical Research Council

Abstract: Post-transcriptional regulation of gene expression ultimately determines the rate of protein translation and is therefore crucial for virtually all cellular processes. Global reduction of protein synthesis is a well-known early response to UV-stress, yet the intrinsic selective mechanisms that subsequently determine cell death or survival are largely unknown. We propose to decipher the functional roles of protein synthesis in regulating epidermal stem cell fate by determining the global and specific protein translation rates in response to UV-exposure in vivo. We will then evaluate the importance of post-transcriptional methylation pathways in mediating cell survival under UV-stress. Using a combination of system-wide approaches, mouse models and in vitro differentiation assays, we propose to (1) measure protein production in distinct UV-radiated epidermal stem cell populations; (2) profile the translational landscape of UV-radiated epidermal stem cell populations; (3) identify cytosine-5 RNA methylation as regulatory mechanism to promote cell survival in response to UV-stress. Our comprehensive approach will answer how protein synthesis contributes to the UV-stress response and might lead to the discovery of novel therapeutic strategies for skin diseases, aging and cancer.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: CSF1R in homeostasis and immunity
Funder: Medical Research Council

Abstract: Cellular differentiation requires that particular lineage-specific genes are expressed at the right level, and the right time, coordinated with all of the other genes that are required for a particular cellular function. At the individual locus level, such coordination involves the complex interaction of promoters, enhancers, silencers and boundary elements. There have been few mammalian genes in which each of these elements has been identified and its function studied in detail, so there are no general models of mammalian locus control. The current project aims to identify the control elements of a complex gene, that encoding the CSF-1 receptor. The gene is of particular interest because it controls the development of macrophages, central cells in innate immunity. It is targetted by mutations in neurodegenerative disease, and it is also a target for therapies, both agonists and antagonists. It is also tractable as a model system because we now have genome scale information identifying the boundaries of the transcriptional unit, all of the elements that are in open chromatin in macrophages and their conservation in mammalian genomes, and all of the candidate transcriptional regulators that are expressed in cells that express CSF1R, and the way that their expression correlates with CSF-1 receptor expression in cells undergoing differentiation. The only way that we can now progress our understanding of this locus is to delete the proposed control elements in the germ line. This has become feasible with the advent of CRISPRs. We will generate a range of CSF1R mutants with deletions in each of the putative control elements. In the second phase of the project, we will use those lines to examine the function of CSF1R-dependent macrophages in development, immunity, physiology and homeostasis.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Function of Nuclear Myosin Motors: A Biochemical and Single Molecule Characterization.
Funder: Medical Research Council

Abstract: A combination of single molecule (Total internal reflection fluorescence and atomic force microscopy) and transient kinetics will be used to investigate the function of nuclear myosin I and VI, and their roles in transcription. This will provide a detailed insight into the regulation and mechanism of gene expression. An overriding hypothesis is that myosins are anchored to DNA and aid RNA polymerase (RNAP) activity through interactions with monomeric actin (short polymeric) on the RNAP complex. NMI will be characterised to determine its motor properties in relation to its cytoplasmic isoform (Myosin Ic). NMI and Myosin VI interactions with DNA and monomeric actin will then be explored. Transient kinetics will be able to determine the binding conditions on millisecond time scales with microgram quantities of protein. And single molecule imaging will allow visualisation of how the motors bind and potentially move DNA. This combined approach will determine the strength of the interactions, identify binding sites, how binding occurs and effects upon the motor proteins and reveal their mechanism of action. Also, through single molecule tracking of fluorescently labelled myosin and DNA, it will then be possible to determine if the motors can generate motility when bound to DNA. Investigations will then focus on the transcription complex. Kinetic and hydrodynamic approaches will be used to measure interactions between myosin and RNAP. While single molecule methods will localise myosin on RNAP. Finally, a novel assay will be developed to measure RNAP activity. The assay will require the design of a fluorescent mRNA biosensor, which will bind rapidly and specifically to mRNA allowing the activity to be tracked in real-time. This sensitive approach will allow the effect of myosin motors to be explored in a highly controlled environment. This effect can then be related to the characterisation measurements to understand how the myosin triggers responses during transcription.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: A multi-country analysis of temperature-mortality associations from a climate change perspective
Funder: Medical Research Council

Abstract: Non-optimal outdoor temperature is a known risk factor for human health, with increased mortality risk associated with both high and low exposures. Several studies have attempted to quantify the related impact in a changing climate, considering the predicted increase in average temperature and extreme weather events. However, temperature-mortality associations show a substantial geographical and temporal heterogeneity that is still largely unexplained, and little is known about the factors determining vulnerability or resilience of populations to the effects of temperature. This information is critical to produce reliable impact projections under climate change, and to develop effective public health policies to attenuate the health burden. This project aims to address these research gaps by offering a systematic evaluation of the association and future impact of temperature on mortality across populations with markedly different characteristics. This project benefits from the availability of the largest data set ever collected for this purpose, including data from 384 locations within 13 countries between 1972 and 2012. Analyses will be based on flexible analytical methods recently developed for modelling complex temperature-health relationships. A first assessment will explore the role of climatological, demographic, socio-economic and infrastructural characteristics in modifying the mortality risk of temperature. This information will be used in second assessment to project the impact under composite scenarios accounting for potential changes in susceptibility due to secular trends and implementation of mitigation and adaptation strategies. This project will provide a comprehensive characterization of the health effects of temperature and the related climate change impact, and a platform to quantitatively evaluate the benefits of alternative public health policies and adaptation measures.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: GENERIC HEALTH RELEVANCE
Title: GENETIC AND ENVIRONMENTAL INFLUENCES ON AGEING WELL IN THE UK BIOBANK
Funder: Medical Research Council

Abstract: The onsets of age-related conditions can be simultaneously delayed in mice by calorie restriction and by targeting pathways including nutrient sensing, mTOR signalling and clearance of senescent cells. Much less is known about determinants of ageing trajectories in humans. We propose two main work packages for identifying conventional markers and for genome wide association study analysis, both focussing on the 215,000 respondents aged 60 to 69 years old in UK Biobank: WP1: Identifying factors associated with best health status in the seventh decade of life: We will define this ageing well group as those free of major diseases and who are consistently in the healthiest range of measures of muscle strength, cognition, lung function, bone mineral density and blood pressure. WP2: Identifying factors associated with parental longevity: We will apply an empirical classification of relative parental longevity, using reported ages of death of parents. The novel aspects of the proposal include: 1. A focus on the timing of onset of major disease or impairment in ageing. Disease specific studies are likely to be less sensitive to ageing effects, so our project should help account for unexplained variance. 2. Our two ageing well phenotypes will identify groups more accurately and in much larger numbers than possible thus far. 3. Ability to estimate the heritability of the chosen phenotypes using the Biobank array data, allowing improvement in the classification for SNP discovery. 4. We have arranged replication in independent cohorts. 5. We are planning fine characterisation of top genetic findings in transcriptomic and methylomic datasets linked to very detailed phenotypic data, plus transcriptomic studies in human tissue panels. 5. We have exceptionally strong agreed consultant collaboration from international leaders in this field.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Cardiff Fetal Tissue Bank: Quality assured tissue for biomedical research and clinical trial in neurodegenerative disease
Funder: Medical Research Council

Abstract: The CFTB and SWIFT tissue banks provide a combined infrastructure facility to supply quality assured research grade and clincial grade human fetal tissues to support basic, translational and clinical trial applications. Both Banks recruit donors consented for medical and surgical terminations of pregnancy between 6-14 week of fetal development. Tissues are allocated to one of two streams, for processing either under standard cat II human tissue safety protocols in the laboratory for research use (SWIFT), or under GMP in a dedicated clinical grade clean room with appropriate environmental control, monitoring, standardised operating procedures, training, documentation and quality assurance protocols licenced for human use (e.g. cell transplantation) in man (CFTB). The two banks are fully accredited under HTA research and human use licences, respectively. Whereas the facility was established to support our own programme in cell transplantation in Huntington's and Parkinson's diseases, this is a unique facility providing a rare and valuable resource, and we seek to maximise utility by operating as a fresh fetal tissue bank to supply diverse research programmes in developmental and stem cell biology, immunology and cell transplantation throughout the UK and Europe. We are currently supplying quality assured tissues to approx. 20 other centres, but there are reasonable expectations that the rapid growth in experimental regenerative medicines and cell therapies will raise a significant range of new applications which we will be positioned to supply, breaking an intrinsic bottleneck in the difficulties of sourcing new supplies of this sensitive tissue source. The SWIFT/CFTB supply is of fresh fetal tissue, in which the cells are living and exhibit high viability for in vitro growth and expension, and are already being used as a source of cells for generation of clinical-grade iPS cells derived from developing fetal brain. As such, we do not compete with the HDBR.


Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: GENERIC HEALTH RELEVANCE
Title: Development of a multilevel and mixture-model framework for modelling epigenetic changes over time (resubmission)
Funder: Medical Research Council

Abstract: Epigenetic modifications (e.g. DNA methylation) are increasingly used to investigate how the environment and lifestyle impact upon disease risk. Recent technological advances have facilitated the large scale generation of longitudinal epigenetic data, and there is a need to develop statistical tools for use in this field. There are three main motivations for analyses of epigenetic changes over time: to identify areas of methylation which are more/less stable over time; to examine how exposures (e.g. environmental exposures, or behaviours such as smoking) are associated with the epigenetic changes; and to investigate the potential health consequences of epigenetic changes. Analyses are complicated by the high-dimensionality of the epigenetic space and correlation within CpG regions. We will develop multilevel and mixture methods for more robust analysis of dynamic epigenetic data. We will use MLMs to identify sites and regions which vary over time. We will compare three ways of pre-analysis dimension reduction, including extending DPPCA for application to epigenetic data. We will develop multivariate MLMs for modelling epigenetic change at several sites with respect to exposure/outcome. Current GGMM and Bayesian Mixture Models will be extended and used to derive latent classes of change across several CpG sites, and to identify the small number of CpG sites with evidence of effects which change over time. We will then develop methods to assess whether genetic variation changes over time, for example are specific to particular developmental stages. Power and performance of all methods under a range of study designs will be compared, using simulations. Data from ALSPAC and other longitudinal studies available to the co-applicants, will be used to benchmark our methods and conclusions. These data will be from 450k and bisulphite sequencing datasets, but the methods will be applicable to any application with a large number of correlated measurements.


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: HOD: Handling missing data and time-varying confounding in causal inference for observational event history data
Funder: Medical Research Council

Abstract: Observational studies play an important role in the evaluation of treatment effects on long-term outcomes, when randomised controlled trials are not feasible because of size, time, budget and ethical constraints. Because of the absence of randomisation in observational studies, it is crucial to adequately control potential confounding from various factors (time-invariant and time-varying) in order to obtain causal effects of treatments. There has been rich literature on how to control potential confounding in observational studies such as using standard techniques-propensity score (PS) methods. However, there are various important methodological issues that have not been addressed adequately in the existing literature, including 1) partially missing confounder data in PS estimation; 2) sensitivity analysis for unmeasured confounding; 3) time-varying confounding; 4) multi-state treatment and outcome processes. In the present application we aim to propose a programme of methodological research to address the above issues for the analysis and interpretation of data from observational studies, with a particular focus on event history data. We will develop and validate diagnostic tools in measuring the balance between treatment groups in terms of both observed values of confounders and their missing data patterns. We will provide a detailed evaluation of different missing data methods and PS methods, using balance diagnostic tools developed. We will develop general Monte Carlo sensitivity analysis methods for unmeasured confounding and non-ignorable missing data in measured confounders for common models for event history data analysis. We will develop robust time-varying PS methods for obtaining causal treatment effects when there are missing data in important time-varying confounders and explore a multistate framework to handle time-varying confounding in more general treatment and outcome processes for observational event history data.


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: PheneBank: automatic extraction and validation of a database of human phenotype-disease associations in the scientific literature
Funder: Medical Research Council

Abstract: PheneBank will exploit state of the art text mining (TM) together with existing ontological resources to collect fragmented biological results about the phenotypic profiles of human diseases and integrate this into a machine understandable semantic database and tool set for use by the clinical and scientific communities in their workflows. TM will be used to automatically extract phenotype, disease and gene terms from the full text scientific literature and harmonise these to ontological resources. Importantly, we will exploit grammatical parsing (the BLLIP parser) for recovering discontinuous terms and then a de-compositional approach in which the elements of the complex phenotype terms are individually linked to ontologies (e.g. Gene Ontology: processes, UBERON for structures). Harmonisation will explore learn-to-rank techniques to optimize concept selection from an array of tools such as cTAKES/MetaMap. Following this, typed relations between terms will be filtered using a range of machine learning classifiers on grammatical parse trees. Domain adaptation techniques will be tested for both term and relation extraction. Validation will follow standard protocols for text mining, including construction of a gold standard annotated corpus of 5000 sentences sampled from cited literature with a focus on rare human diseases. Phenotypic profiles will be built from strongly associated and related terms (e.g. phenotype-disease) by exploring a range of measures (e.g. Jaccard index, Information Content). Validation will use existing expert curated profiles in the OMIM and OrphaNet databases. Additionally we will explore the cross-species harmonisation of the human phenotype terms to closely associated mouse phenotypes. This will take place through conceptual mappings of PheneBank terms to the HPO and MP. The semantic database will include phenotypes and associated links for querying, navigation and download in a variety of formats (OWN/RDF/JSON).


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE