NIHRDataInsights/HRCSData huggingface dataset:
Title: Genomic Health & Safety: Does Elg1 maintain genome stability by resetting chromatin factors used in DNA replication and repair?
Funder: Medical Research Council

Abstract: Maintenance of genome stability is critical to avert diseases and cancer. Loss of the genome maintenance factor Elg1 leads to genome instability and results in tumorigenesis, but we do not know why. The ultimate aim of this work is to understand how Elg1 maintains genome stability. Recently I discovered that the Elg1 Replication Factor C-like complex functions to unload the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp during DNA replication. PCNA is a central protein in DNA replication and repair, and is often used as marker of cell proliferation and malignancy. PCNA acts as a sliding scaffold for many replication and repair proteins. In the absence of Elg1, PCNA and its interacting partners accumulate on chromatin. I hypothesise that the abnormal accumulation of PCNA and its interacting partners on chromatin leads to the genome instability observed in cells lacking Elg1. To test this hypothesis, I will manipulate PCNA in budding yeast and test whether abnormal accumulation of PCNA on chromatin is responsible for genome instability in cells lacking Elg1. I will next test whether the accumulation of specific PCNA-interacting partners on chromatin contributes to genome instability, and also investigate the function of PCNA comprehensively both in DNA replication and repair. The powerful genetics approaches possible in yeast allow the sophisticated dissection of chromosome stability pathways. Lastly I will extend my investigation to human cells, to test whether similar mechanisms operate. Addressing how Elg1 maintains human chromosome stability is an important step since loss of Elg1 is directly implicated in mammalian tumors. This research will substantially advance our understanding of how cells ensure genome stability by illuminating the role of the genome maintenance factor Elg1 in PCNA regulation. Since this project studies the mechanism of action of gene that is associated with cancer, this work holds long-term potential for cancer therapy.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Gene by environment interactions in the regulation of gene expression across primary tissues and their application to obesity and related traits
Funder: Medical Research Council

Abstract: This study will identify gene by environment interactions (GEI) influencing gene expression. GEI effects have been difficult to identify at the disease and trait level owing to the large sample sizes needed to detect an interaction in a genome-wide search and the required careful measurement of environment for all subjects. Studying GEI effects on an expression level has many advantages. The effect size of genetic regulation of gene expression is quite large, reducing the need for huge and costly sample sizes. As each gene has a known physical position in the genome the statistical burden of multiple testing can be greatly reduced by limiting the search space to the local region around each gene. Environmental measures that operate on the organismal or cellular level can be assayed, including quantitative biomedical phenotypes. This study will utilize gene expression data measured with next-generation sequencing technology (RNAseq) in four primary tissues (adipose, skin, whole blood, muscle) and one cell line (transformed lymphocytes) from ~800 individuals. RNAseq data allows interrogation of effects on both total gene expression and alternative splicing. A wide array of environmental exposures will be investigated, including organism level exposures such as diet, smoking and medication, and biomedical measures such as cholesterol and insulin that influence the cellular environment. Particular attention will be paid to obesity-related exposures and their effects on adipose expression. Obesity has a dramatic impact on the physiology of adipose tissue. In this study measures of adiposity will be utilized to identify GEI regulatory effects, where adiposity is the exposure and expression the outcome variable. This will identify downstream molecular consequences of obesity, the genetic variants that mediate them, and potentially why different individuals develop different obesity associated co-morbidities.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.3 PSYCHOLOGICAL, SOCIAL AND ECONOMIC FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Establishing a national, population based cohort of children born after assisted conception in the UK.
Funder: Medical Research Council

Abstract: The primary objective of this proposed study is to produce an enhanced version of the HFEA database, improving the quality and scope of the information held on children born after ART in the UK between 1991 and October 2009 (n>106,000). This will enable researchers to use non-intrusive, population based record linkage to monitor a variety of health aspects in this cohort of children as they grow into adults. Maternal and paternal details (names, previous names and birth dates) from the HFEA database will be linked to UK birth records to identify children born to these individuals. Using child date of birth, as recorded by the HFEA, it will be possible to identify their IVF conceived offspring. Spontaneously conceived (SC) siblings will also be identified via this method. Children whose parental details match to HFEA records, but whose birth episode is not recorded by the HFEA will be considered SC siblings and will form a comparison cohort to allow within and between sibling analyses for various outcomes. Full and half sibling status will be recorded for each member of the control cohort, in addition to a unique identifier; allowing sibling pairs to be anonymously identified in future work. This initial linkage to birth records will provide names for cohort members (currently unrecorded in 90% of HFEA records), and also for the cohort of SC siblings. Further linkage to the Health & Social Care-Information Centre (HSC-IC) medical register for England and Wales and the NHS-Central Register for Scotland will then be undertaken in order to assign an NHS number and post-code to each cohort member. Once all linkage is completed (securely and without researchers having access to identifiable details), these enhanced details will be transferred securely to the HFEA for storage. This study also proposes to further enhance this database with initial linkages to Hospital Episode Statistics (HES) and monitor this generation as they grow up and further into adult life.


Research activity codes: 4.4 POPULATION SCREENING
Health categories: GENERIC HEALTH RELEVANCE
Title: 5-HT3 receptor subtypes: functional and structural characterisation
Funder: Medical Research Council

Abstract: The aim of this study is to characterize heteromultimeric 5-HT3 receptors. We will use functional experiments to characterise heteromeric 5-HT3 receptors containing 2, 3, 4 or 5 different subunits using receptors expressed in Xenopus oocytes and HEK cells. We will define the composition of binding sites at heteromeric receptors and identify the molecular interactions of agonists, partial agonists and antagonists at these binding sites using mutagenesis combined with functional data. We will then incorporate this information into a homology model. To verify this model we will solve the high resolution structures of an agonist, partial agonist and antagonist bound to a 5-HT3 receptor mimic based on AChBP (5-HTBP) which we will modify to contain the novel binding sites. We have already shown that 5-HTBP can bind to 5-HT and 5-HT3 selective ligands, and we have X-ray crystal structures with 5-HT and granisetron bound; thus we anticipate it will be relatively straightforward to obtain structural data for our heteromeric binding pockets.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;1.3 CHEMICAL AND PHYSICAL SCIENCES
Health categories: GENERIC HEALTH RELEVANCE
Title: A flexible class of Bayesian spatio-temporal models for cluster detection, trend estimation and forecasting of disease risk
Funder: Medical Research Council

Abstract: This project will develop novel statistical methodology for modelling spatially and temporally aggregated disease data, which will be implemented in a Bayesian paradigm using Markov chain Monte carlo simulation. The project will extend published research by developing a flexible general class of models, which incorporate spatio-temporal autocorrelation and flexible temporal trends. Binomial, Gaussian and Poisson likelihood models will be developed, with the linear predictor depending on covariates, spatial random effects and a flexible temporal trend component. The novel aspect of this methodology is the latter, which allows the disease rates in each area to be modelled by a mixture of temporal trends. These include smooth functions, regular parametric polynomials or sinusoidal curves, piecewise linear trends and autoregressive models, and as the parameters controlling these trends can vary spatially, they are not constrained to exhibit the same underlying shape unlike existing research. The likely spatio-temporal autocorrelation in these trends will be modelled with smooth spatially and temporally varying parameters, utilising univariate and multivariate conditional autoregressive models. Within this Bayesian modelling framework short term prediction of the rates is a relatively straightforward procedure together with appropriate prediction intervals. Software will be produced to allow others to implement this model class, which will encompass some previously published models as special cases. This will permit greater flexibility in model fitting, model testing and selection. No general purpose software currently exists to allow others to implement a range of disease mapping models without substantial programming effort, and its development in this project will be a major novel aspect. The models will then be applied to undertake substantive analyses of data concerning GP consultations, vaccine uptake, and coronary heart disease hospitalisation and mortality.


Research activity codes: 8.4 RESEARCH DESIGN AND METHODOLOGIES (HEALTH SERVICES)
Health categories: GENERIC HEALTH RELEVANCE
Title: The organisational structure of class A GPCRs: Implications for pharmacology, function and therapeutic regulation
Funder: Medical Research Council

Abstract: Basic information on the ability of G protein-coupled receptors (GPCRs) to form dimers or higher-order complexes has been available for some time. However, there is currently widespread variation in conclusions on the extent, stability, size, shape and functional consequences of such interactions. Integration of mathematics with improvements in optical microscopy have recently begun to offer means to address many of these issues. In preparation for this application we have employed multi-photon FRET with spectral resolution to interrogate single pixel images from plasma membranes of cells. Analysis of such images indicate that the M3 muscarinic acetylcholine receptor exists as a mixture of dimers and tetramers that are organised as rhombi. We will now address if this is true for other class A GPCRs and if the proportions of the species differ at different expression levels and in different cellular compartments. Within the proposed programe of work we will also integrate each of faster scan speeds, total internal reflectance and two quasi-simultaneous excitation wavelengths to determine the total concentrations of donors and acceptors and to employ single molecule tracking studies. As an alternate approach we have been developing the use of Spatial Intensity Distribution Analysis (SpIDA) to address similar questions. Given information on the interfaces that may generate quaternary structure that are becoming available from both atomic level structures of GPCRs and models generated from these, we will employ mutagenesis to disrupt quaternary complexes and then employ detailed biochemical and pharmacological studies, including the generation and use of intramolecular FRET sensor forms of GPCRs to assess the effects on allosteric communication within receptor complexes and how this influences the potency and efficacy of receptor ligands, including currently employed therapeutic medicines, as well as if this may influence or define the signalling pathways activated.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Discovering novel regulators of stem cell behaviour in a highly regenerative context
Funder: Medical Research Council

Abstract: Planarians are capable of profound regenerative feats, such that even small tissue fragments containing none of the major organs systems can regenerate to form complete animals. This regenerative potential is fuelled by a population of highly proliferative pluripotent adult stem cells that proliferate to produce post-mitotic progeny that replace missing distal structures in a regenerative blastema and contribute to reforming and rescaling organs with thin existing tissues. This requires exquisite control of stem cell proliferation levels, the balance between symmetric and asymmetrical cell division, differentiation into the correct cell types at the correct location and migration. These basic cellular behaviours are of key importance for human disease processes, particularly cancer. Given the understudied phylogenetic position of planarians it is timely to utilise them as a simple model system to make novel discoveries by screening for novel physiological functions for conserved genes. We have designed an assay that makes use of the classical observation that when proliferating stem cells are removed by planarians by X-ray irradiation of part of the animal the remaining stem cells are readily able to rescue the irradiated tissue. This approach allows us to observe stem cell behaviour as they migrate into and populate a "blank canvas" of differentiated tissues. By observing and quantifying the behaviour of stem cells and progeny as they repopulate the irradiated region we can make predictions about the interactions between proliferating cells and their recent progeny post-mitotic progeny and differentiated cells in regulating the tissue micro-environment to facilitate stem cell reconstitution. We will combine transcriptomic and proteomic expression analysis of the blank canvas as stem cells migrate and begin to reconstitute the irradiated region with an RNAi based screen of gene function to identify novel genes involved in controlling key stem cell behaviours.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: The Structural Basis of Molecular Mechanisms in Cell Guidance and Adhesion.
Funder: Medical Research Council

Abstract: The semaphorins were first characterized as guidance cues exerting repulsive effects on axon growth cones during neural development. The number of tissues and biological processes for which we now know that the semaphorins and their type 1 single membrane spanning receptors, the plexins, play key roles has hugely expanded. Examples in the nervous system include neuronal migration, axon and dendrite guidance, branching, and synaptogenesis. Semaphorin function or dysfunction is also implicated in neurogenetic disorders, nerve regeneration, bone maintenance, immune cell differentiation and function, heart development, and cancer. Our knowledge of the molecular level mechanisms which deliver these myriad biological processes is still sparse. In this research programme we will apply an integrated structural and cellular biology approach to investigate the molecular mechanisms responsible for the biological activities of the class 1, 2, 5 and 6 semaphorins and their cognate plexin receptors. We will address three cross-cutting project areas: 1. Extracellular interactions governing signalling complex assembly 2. Linkage of the extracellular and cytoplasmic segments for signal transduction 3. Sub-cellular localisation and the interface with the cytoskeleton We will generate atomic level detail using protein crystallography, and complement it with studies by electron microscopy (negative stain, and cryo). We will evaluate the functional hypotheses we generate in these molecular studies by using cellular imaging methods including electron cryo tomography as well as advanced fluorescence microscopy techniques such as localization microscopy (dSTORM) and FRET-FLIM. Our studies will also link through directly to in vivo and in vitro studies of cellular morphology and neuronal connectivity in collaborators' laboratories. Ultimately our results will inform and guide investigations into the semaphorin-plexin system as a point for therapeutic intervention (see Impact Summary).


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: MICA: Design, synthesis, and pharmacological profiling of agonists of the human orexin receptors
Funder: Medical Research Council

Abstract: Several crystal structures of ligand-bound GPCRs have been solved but the structural basis of receptor agonism remains poorly understood, especially for peptide-activated GPCRs, for which drug-like agonists would be therapeutically desirable. We have chosen the two orexin receptors (OXRs), for which our industrial partner Heptares has generated for the first time crystal structures of ligand complexes, in order to develop strategies for the structure-based design of small-molecule agonists of peptide-activated GPCRs. OXR agonists are relevant in narcolepsy, Parkinson's disease, cancer, and other indications. We will use a combination of homology modelling and torsional space interrogation techniques to generate agonist-form OXR models. These will form the basis for virtual screening of large compound databases. Predicted hits from this strategy, as well as alternative peptidomimetic and structure-based antagonist-to-agonist conversion design strands, will be assessed for OXR agonist activity in a primary screen using highly-coupled functional and reporter gene assays. Confirmed actives will be subjected to an extensive secondary assay battery comprising functional assays capable of distinguishing between different coupling pathways and potential biased signalling. Confirmed hit series will form starting points for structural elaboration and optimisation in terms of affinity, potency, selectivity, mode of agonist action, and bioavailability through medicinal chemistry. Structural hypotheses for compound design and optimisation will be greatly assisted by probing an existing set of receptor variants, in which all the residues in the ligand-binding domain have been mutated systematically, with the compounds we design and make. Once new small-molecule agonists with sufficient potency have been identified, these will be examined for CNS bioavailability and in vivo pharmacological activity as OXR agonists in a rat telemetry model.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: GENERIC HEALTH RELEVANCE
Title: NIRG: FARSPhase: a Flexible, widely Applicable, Robust, and Scalable phasing algorithm for human genetics
Funder: Medical Research Council

Abstract: Phasing is the modelling of the underlying haploid structure of diploid genotypes. It is important because inheritance actually takes place at the haploid level, even though only diploid genotypes are observed. The many phasing methods for human data can be broadly classified into: (i) heuristic methods (e.g. Long-range phasing (LRP)); and (ii) probabilistic methods (e.g. Hidden Markov Models (HMM)). Phasing is computationally intensive and the size and features of data sets make them more or less suited to particular methods. Future data sets could be: (i) huge populations of nominally unrelated individuals (e.g. 500,000 individuals, UK Biobank); (ii) smaller subsets of such populations; (iii) Isolated populations with high degrees of relatedness within them (e.g. Orkney, Iceland); (iv) Data sets with/without pedigree information; (v) data sets with several of these features (e.g. Generation Scotland); and (vi) Data sets with different types of genomic information (e.g. single nucleotide polymorphisms, low/high-coverage sequence, short/longer sequence reads). Heuristic methods, such as LRP, are suited to isolated populations with/without pedigree information or, due to their computational efficiency, to large populations of nominally unrelated individuals. Small nominally unrelated populations may not comprise enough individuals LRP to work, but they are suited to HMM because they are small enough to be computationally tractable and individuals within them share short haplotypes that HMM can model. Some data sets may be best addressed with a combination of algorithms. A combined algorithm could exploit the complementarity that exists between heuristic and probabilistic algorithms and thus be more powerful than the component algorithms. The objective of this proposal is to develop and test a Flexible, widely Applicable, Robust, and Scalable phasing algorithm that combines the best features of LRP, other heuristics methods, and HMM methods into a single framework.


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: A systems based approach to integrating genetic and longitudinal omics data to support diagnosis and prediction of common chronic disease
Funder: Medical Research Council

Abstract: This proposal will investigate the longitudinal relationships of cellular and genomic phenotypes, including global gene expression and metabolites, in 700 twins over 7 years, measured at three time-periods. To increase compliance some of the blood sampling will be performed by post as well as by routine visits. We have been using postal blood methods for the last ten years and found it works well for the assays without loss of quality and local GPs are happy to cooperate. So far 98% of samples arrive within 48 hours of blood draw. We will use RNA seq in fasting whole blood for the transcriptomics to be performed in Geneva and non-targeted Mass Spec Metabolon platform for the metabolomics performed by Metabolon Inc in the USA. We have extensively used both methods previously. The study subjects derive from the extensive TwinsUK cohort (www.twinsUK.ac.uk/phenotypes) on whom there is already extensive clinical information and cross-sectional genetic and genomic data. We will use and develop systems analysis approaches to integrate these complex data sets and make causal inferences. In particular, we will develop novel robust analytical approaches, which will combine methods for investigating multidimensional association between sets of high dimensional data with dimension reduction approaches and characterisation of internal co-variation structure in each data set. Initial cross-sectional integrative analysis will be extended to the longitudinal set-up to investigate changes in omics profiles, and predictive modelling of clinically relevant traits incorporating several types of omics phenotypes will be performed.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: GENERIC HEALTH RELEVANCE