NIHRDataInsights/HRCSData huggingface dataset:
Title: Identifying and critiquing different approaches to developing complex interventions (INDEX study)
Funder: Medical Research Council

Abstract: The aim of this study is to produce guidance for researchers on how to develop complex interventions to improve health or health care outcomes. The objectives are to: 1. Identify and describe the different approaches taken to intervention development, the rationales for their use, and any implications for the future utility of the interventions. 2. Compare and contrast different intervention development approaches, the methods of data collection and analysis they used, considering strengths and limitations overall and for different contexts. 3. Understand the history and challenges of intervention development from the perspectives of experienced researchers and wider stakeholders e.g. research funders, public and patient representatives. 4. Measure stakeholder consensus on the key aspects of intervention development and explore the reasons for any lack of consensus. 5. Offer guidance to researchers on good practice, with examples from different approaches. The design is a sequential mixed methods study in 3 phases. In phase 1 we will undertake two systematic reviews of literature on intervention development. The first will identify expert description and critiques of different approaches and methods. The second will identify primary intervention development research to improve health or health care outcomes. In phase 2 we will identify the challenges of intervention development in a qualitative interview study, and consider with stakeholders how to bring together the learning from our data collection. In phase 3 we will undertake a consensus exercise to identify core aspects of intervention development.


Research activity codes: 8.4 RESEARCH DESIGN AND METHODOLOGIES (HEALTH SERVICES)
Health categories: GENERIC HEALTH RELEVANCE
Title: Novel clinical trial designs for establishing potential efficacy of complex interventions
Funder: Medical Research Council

Abstract: Aim: This work aims to develop, implement and disseminate methods to design and analyse early trials for assessing potential efficacy of complex interventions, addressing cases with several endpoints of varying importance, and multilevel data structures. Research plan: 1a) Assuming all parameters other than the treatment effect are known, I will develop a hypothesis testing approach to designing an early phase complex intervention trial, building on existing phase II drug trial designs and sample size determination methods. 1b) I will develop an alternative Bayesian approach, allowing uncertainty in parameters to be specified through prior probability distributions. 1c) I will extend this to a fully decision-theoretic framework, enabling acceptable trade-offs between the various endpoints of interest to be specified. 1d) I will develop and apply all methods using several illustrative examples. These applications will involve discussions with clinicians and trial statisticians, providing opportunities to establish their acceptability and feasibility. 2) I will implement the methods in R and Stata, using efficient optimisation algorithms and a user-friendly interface. 3) I will develop documentation of the software and associated tutorial materials to provide online. Impact: Proper implementation of the methods developed in this research will ensure that only complex interventions of sufficient promise proceed to evaluation in a confirmatory trial. By ensuring that only the most promising interventions reach this stage, the rate at which new interventions are made available to patients will increase. This amounts to a more efficient use of the limited resources available for evaluating new interventions, reducing the amount of research funds, research time and participant time spent on unnecessary phase III trials of ineffective interventions.


Research activity codes: 3.1 PRIMARY PREVENTION INTERVENTIONS TO MODIFY BEHAVIOURS OR PROMOTE WELL-BEING;8.4 RESEARCH DESIGN AND METHODOLOGIES (HEALTH SERVICES)
Health categories: GENERIC HEALTH RELEVANCE
Title: Development of a fully Bayesian framework for the identification and estimation of subgroup effects in Randomised Controlled Trials
Funder: Medical Research Council

Abstract: We will develop a fully Bayesian framework for subgroup analysis encompassing both a novel statistical modelling approach (objective 1) and a systematic web-based framework for the elicitation of expert opinion on subgroup effects (objective 2). The framework will be refined using a number of case studies. To facilitate translation, guidance will be developed based on the case studies describing the use of the framework (objective 3). The statistical model is central to our approach. Our key proposal is not simply to apply shrinkage, but to explicitly incorporate a mixture component to differentiate reproducible subgroup effects from chance effects. This is similar to the use of slab and spike priors for variable selection. The hierarchical Bayesian framework allows direct inclusion of information elicited from experts. It also naturally extends to allow information on subgroup effects to be "shared" across studies and endpoints and can incorporate either individual patient data or reported summary statistics. To understand the performance of our models in real live settings, we will compare the (i) sensitivity and specificity of the identification of subgroup effects and (ii) bias and interval coverage for estimation of identified subgroup effects in a series of simulation studies. We will develop web based tools that will facilitate clearer, quantifiable and readily interpretable statements of the prior plausibility of subgroup effects. These tools, and methods of elicitation, will be tested during our case studies. In particular we will test various scales for elicitation to determine which are meaningful to experts. In order to support the practical use of the tools developed under objectives 1 and 2, we will develop guidance describing and critically examining the use of the statistical model and elicitation tools in three distinct stages of technology development: (i) clinical trial planning (ii) the consideration of further studies based on subgroup analysis


Research activity codes: 8.4 RESEARCH DESIGN AND METHODOLOGIES (HEALTH SERVICES)
Health categories: GENERIC HEALTH RELEVANCE
Title: Pilot study of the utility of text mining and machine learning tools to accelerate systematic review and meta-analysis of findings of in vivo research
Funder: Medical Research Council

Abstract: Firstly we will convene an expert panel to establish "required" and "desired" performance thresholds for the performance of text mining and machine learning tools. Then, for each of the three tasks of identifying and retrieving relevant publications, extracting meta-data from identified publications, and extracting outcome data from relevant publications we will (1) where not already performed, conduct a systematic review to identify all candidate approaches; (2) implement the most promising approaches using existing systematic review datasets; and then (3) prospectively validate these approaches in ongoing systematic reviews. These tasks will be conducted by a team which brings together expertise in text mining and machine learning as applied to systematic review (Thomas, Ananiadou) and in the conduct of systematic reviews of in vivo data (Sena, Rice, Macleod), supported by external collabortators. The development datasets are (1) a systematic review of in vivo studies in neuropathic pain, (2) a systematic review of in vivo publications from leading UK institutions, and (3) a selection of in vivo publications describing different outcome measures curated on the CAMARADES database. For the validation datasets we will use a systematic review of in vivo models of depression. For each, we will ascertain the sensitivity, specificity and where relevant the accuracy of the text mining/ machine learning approach, and the reduction in human work (eg number of articles needed to screen) possible whilst maintaining performance at the "desired" threshold.


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: HSM Polygenic score methodology in the emerging field of Polygenic Epidemiology
Funder: Medical Research Council

Abstract: The latest analyses of GWAS data reveal a substantial polygenic component to most common human diseases. This poses a huge challenge to using genetics for phenotype prediction, and thus to effectuating stratified medicine. However, the development of prediction methods tailored to the polygenicity of human disease can transform results. While the stringent GWAS significance threshold has ensured the discovery of genuine genotype-phenotype associations, it can be barrier to prediction. Phenotype prediction from genetic profile is typically optimised when applying a far more liberal threshold for SNP selection. While even polygenic prediction is inaccurate at an individual-level, its aggregation across samples enables a raft of applications that perform association testing. The first polygenic score methods have now been proposed and applied to genome-wide SNP data. However, the increasing rate in their application is preceding careful examination of their relative power and accuracy. To address this, we perform the first comprehensive comparison study of their performance and build a simulation framework, accompanied by software tool and web application, to enable future benchmarking of polygenic methods across a consistent platform. The polygenic risk score approach is the focus for method development here. Unlike the alternatives, PRS both exploits large-scale GWAS summary data and permits individual-level prediction. This combination will be key to realising stratified medicine as GWAS sample sizes grow and we outline a range of strategies to exploit the PRS approach for stratified medicine. To date, only a single PRS method has been developed and utilised for a variety of applications. We introduce a suite of PRS methods, each tailored to their application. This sensitivity to the relevant scientific question is expected to yield substantial gains in power. Novel applications of PRS, such as testing direction of causality, are also proposed.


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: Exploratory trials of complex public health interventions: development of guidance for researchers and funders
Funder: Medical Research Council

Abstract: We shall use systematic reviews, a Delphi exercise and horizon scan to develop guidance on exploratory trials of complex public health interventions - those conducted before a full scale effectiveness trial to develop or refine the intervention, and to estimate key trial design parameters. We shall conduct 1) a scoping review of current practice, to identify the aims, terminology and range of methods used in exploratory trials; 2) a systematic review of current guidance and recommendations, to identify what is seen as good or bad practice, and the key gaps and areas of inconsistency. The reviews will use comprehensive database searches, supplemented by hand searches and citation tracking, double screening using pre-defined eligibility criteria, and narrative synthesis. We shall conduct a web-based Delphi exercise to identify expert consensus on key aspects of the purpose, design and conduct of exploratory trials, and the key areas of disagreement. Round 1 will produce a comprehensive list of issues, based on the reviews and experts' views; round 2 will validate this with a wider group of experts; round 3 will present a set of recommendations to gauge levels of agreement, and the basis for any disagreement. Each round will be followed by qualitative and quantitative analysis of responses to gauge levels of agreement and identify points of disagreement. After round 3 we shall draft guidance, and hold a consensus workshop to resolve outstanding disagreements and refine the document. We shall conduct a horizon scan of novel approaches to exploratory trials in medicine and surgery, to identify innovations that could be applied to complex public health interventions. We shall undertake scoping reviews, key informant interviews and two expert workshops. Outputs will include a database of exploratory trials of complex public health interventions, guidance on the design and conduct of such trials, and a research agenda for innovation in exploratory trials in public health.


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: Use of fluorescence correlation spectroscopy to study GPCR oligomerisation and allosterism in membrane micro domains of single living cells.
Funder: Medical Research Council

Abstract: The techniques of fluorescence correlation spectroscopy (FCS) and photon counting histogram analysis (PCH) will be used to monitor the number, diffusional charactersitics and brightness of ligand-bound (using fluorescent agonists and antagonist ligands) and free (tagged using GFP, Halotag or SNAP tag technologies) receptors in small defined regions of the plasma membrane (~0.2 square microns) in multiple areas of a single living cell. This will provide insight into the ligand-binding characteristics, composition and molecular size of oligomeric structures containing cell surface receptors such as G protein-coupled receptors (GPCRs). Stoichiometry of GPCR homo- and hetero-dimer complexes will be investigated using antibody cross-linking and subsequent FCS/PCH analysis. This will be confirmed in parallel experiments using raster image correlation spectroscopy (RICS), number and brightness analysis and two-colour super resolution microscopy (dSTORM; Zeiss Elyra). Kinetic studies in single cells and in multiple areas of the plasma membrane (FCS, PCH) will evaluate the kinetics of ligand-receptor binding interactions and the extent of cooperativity (negative or positive) across dimer interfaces. This work will also provide important information on ligand binding residence times and the amino acid residues involved in conveying allosteric influences across oligomeric interfaces. Bioluminescence resonance enegy transfer (BRET) between a fluorescent ligand and the novel bioluminescent protein NanoLuc fused to the N-terminus of the GPCR under study will allow alternative strategies to investigate allostery. Intramolecular fluorescence resonance energy transfer (FRET) approaches will be used to look at conformation changes induced by agonists in different GPCRs. BRET and FRET strategies will also be used to study signalling bias from particular oligomeric configurations. The techniques above will be applied to native cells from the cardiovascular system.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Novel homology-directed gene targeting to enhance biomedical modeling
Funder: Medical Research Council

Abstract: Unfertilized mouse eggs will be injected with a sperm (ICSI), CRISPR (gRNA) and Cas9 genome engineering components, plus an exogenous construct to promote targeted DNA integration by homology-directed repair (HDR). This approach harnesses sperm chromatin decondensation during fertilisation; decondensation depletes the paternal genome of almost all nucleoprotein, making it an extremely good substrate for recombination. Previous methods to engineer whole animals inject the Cas9 machinery into embryos that have long-since completed fertilisation, skipping this recombinogenic decondensation step. We have shown that sperm injection harnesses decondensation to enhance recombination in random transgenesis and homology-independent Cas9-mediated editing. We now seek to optimise DNA integration by HDR in a sperm injection protocol that we have already demonstrated in preliminary experiments. We will demonstrate targeted DNA integration following sperm injection with CRISPR, Cas9 cRNA and proven targeting constructs. These target Oct4, Rex1 or Cdx2 genes, resulting in characteristic fluorescence patterns in preimplantation embryos after culture in vitro for 3.5 days. Gene targeting in embryos with promising expression patterns will be confirmed by RT-PCR and genomic PCR, which we routinely apply to preimplantation embryos. This in vitro system allows us to optimise the protocol without having to produce offspring, cutting costs, time and animal numbers. The method promises to streamline mouse and large animal genome-engineered biomedical modeling. We will demonstrate targeting in mouse offspring by transferring embryos after micromanipulation to recipient surrogate mothers. Offspring will be characterized phenotypically, to confirm that the method does not introduce unexpected phenotypes, and genetically by PCR and Southern blotting to reveal the percentage of offspring harbouring alleles with the anticipated targeted configuration.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: GENERIC HEALTH RELEVANCE
Title: Applications of Mass Spectrometry to Membrane Protein Drug Development
Funder: Medical Research Council

Abstract: Our research objective is to develop and apply mass spectrometry (MS) to drug development for membrane proteins. Specifically we will deliver new insight into drug resistance phenomena, off-pathway side-effects of drugs that bind to membrane proteins and new assemblies for antibiotic targeting. We will first look at the mechanisms operating in multi-drug resistance (MDR) efflux pumps and outer membrane porins. Together these complexes control the influx and efflux of antibiotics into, and out of, cells. Using MS, coupled with ion mobility, the simultaneous binding of drugs and lipids can be probed and their effects on the population of different conformers determined. We will use the solute carrier family of membrane proteins, also involved in MDR, to develop our drug binding strategies. Our second theme is to study the mechanism of off-pathway drug binding to membrane protein targets. To do so we will have to overcome one of the major challenges in the field: that of maintaining the stability of membrane protein drug complexes in the absence of the lipid bilayer. A third major area is characterising membrane protein assemblies that could serve as new targets for antibiotics. Here we will study complexes involved in outer membrane protein biogenesis in E. coli, specifically the beta-barrel assembly machine complex, and the lipid II flippase and elongation machinery. Both complexes play critical roles in the synthesis and assembly of bacterial cell wall components; their subunit composition, overall architecture and functional mechanisms, however, remain unclear. We will monitor oligomeric state, interaction partners and lipid binding properties of these dynamic membrane embedded machineries. Through well-established links with pharmaceutical and biotechnology companies, as well as a close working relationship with the MS industry we will be in an excellent position to exploit our research findings.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: GENERIC HEALTH RELEVANCE
Title: How does signaling induce human primordial germ cells?
Funder: Medical Research Council

Abstract: We will use axolotl embryos and hESC to establish the link between FGF signalling and the molecular mechanisms of germ cell specification. Our goal is to understand how the Elk-1/Med23 axis represses mesoderm differentiation and activates the regulatory network for PGC development. This work will contribute to development of methods for in vitro production of human gametes. The project includes two work streams. 1.- Axolotl animal caps will be programmed to produce PGCs and used to identify direct targets of Elk-1 transcriptional repression or activation, and to identify the biochemical mechanisms through which Elk-1 represses somatic specification during PGC induction. 2- Induction of PGCLC from hESC will be used to test the role of Med23 in human PGCs. hPGCLC will be FACS sorted and gene expression will be assessed by qPCR or RNA-seq. ChIP-seq will be performed on hPGCLC using conventional methods. Key informatics techniques will include: 3- RNA seq will be carried out following standard Illumina protocols with biological triplicates for all experiments. For transcriptomes, annotation will be derived from our axolotl transcriptome collection via reciprocal blast and/or other annotation pipelines such as blast2go. Differential expression analyses will be performed using DeSeq2 or TopHat/Bowtie/Cufflinks or equivalent pipelines to identify targets of Elk-1 and Med23. The intersection of these datasets should reveal PGC specific targets of the Elk-1/Med23 axis. 4- ChIP sequencing, to identify super enhancers for PGC specification, will be analysed using DiffBind or equivalent packages to identify Med23 targets which differ in the presence and absence of BMP in hPGCLC. Proximity of sequenced regions to specific genes will be determined by standard methods. Sequenced targets will be analyzed for Elk-1, Smad-1 and Nanog binding sites. Together, this will enable identification of candidate PGC specific super enhancers for further validation.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Unravelling the role of beta-catenin in ground state pluripotency
Funder: Medical Research Council

Abstract: Mouse Embryonic Stem Cells (mESCs) are pluripotent cells, which can be indefinitely expanded in vitro, and pushed into specific differentiated states by proper stimuli. Under standard culture (serum+LIF), mESC population is heterogeneous in pluripotency gene expression and propensity to self-renewal/differentiate. Conversely, serum-free medium (2i+LIF) establishes ground state pluripotency, characterised by homogeneous pluripotency genes levels. Ground state cultures rely on Chiron, a drug that, through inhibition of the Gsk3 kinase, stabilises beta-catenin (b-catenin), the effector protein of Wnt/b-catenin pathway. Intriguingly, b-catenin is involved not only in self-renewal, but also in differentiation. The specific role of b-catenin stabilisation in 2i+LIF is still debated. We recent proved heterogeneity and oscillations of b-catenin in ground state cultures, despite homogeneity of pluripotent markers. These results motivate the research ideas of this proposal, aimed at assessing the role of b-catenin in ground state pluripotency. Current ground state cultures with Chiron do not allow: 1) Distinguishing b-catenin dependent from independent effects; 2) Decoupling b-catenin levels from dynamics, due to intrinsic feedback loops; 3) Distinguishing transcriptional and post-translational functions of b-catenin. Therefore, we will implement in mESCs deleted for endogenous b-catenin an inducible tool, enabling to generate fine-tuned perturbations of exogenous, Chiron-insensitive b-catenin. Differently from previous studies, we will generate a gradient of levels, dynamics and transcriptional activity of exogenous b-catenin, aided by mathematical modelling. We will assess the pluripotency of mESCs perturbed for b-catenin; also, we will determine how b-catenin interacts with the ground state transcriptional network, using a data-driven computational approach. Outputs of this project will indicate how to perturb mESCs decision-making by b-catenin modulation.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE