NIHRDataInsights/HRCSData huggingface dataset:
Title: Using Surrogate Endpoints for Decision-Making in Adaptive Seamless Designs
Funder: Medical Research Council

Abstract: A recent innovation in confirmatory clinical trial design is the development of adaptive seamless designs (ASDs) that combine phases II and III in a single trial. In such designs, patients are initially randomised between a control and a number of experimental treatments. Part-way through the trial, based on the results of an interim analysis, more promising treatments are selected to continue with the control, with other treatments dropped from the trial. At the end of the trial selected treatments and the control are compared using all data from these groups. The use of a common control group and the early dropping of ineffective treatments in the ASD leads to considerable gain in power, or saving in number of patients required, relative to the conventional approach of separate phase II and phase III trials. The inclusion of data used for treatment selection in the final analysis leads, however, to inflation of the type I error rate if a conventional analysis is conducted and special statistical methods have been developed to avoid this. The use of ASDs is challenging when the primary endpoint is observed only after long-term follow-up, since recruitment may have closed before observation of sufficient primary endpoint data for the interim analysis. The savings associated with dropping treatments may thus be lost. Often in such a setting, an endpoint that is predictive of the primary response, possibly a validated surrogate, is observed more rapidly. It is therefore appealing to use these data, along with available primary endpoint data, at the interim analysis for treatment selection. Although this leads to additional statistical challenges, we have previously developed two methods that enable such an approach. The two methods proposed both lead to increased power from the use of the surrogate endpoint data. They have been shown to have very different properties, however, with the gain in power arising respectively primarily from individual-level and trial-level surrogacy. This suggests that a new method superior to either of these approaches could based on estimation of the relationship between the surrogate and primary endpoints from the interim analysis data. The aim of this project is a method that utilises the surrogate endpoint data as efficiently as possible. This will reduce the number of patients required, particularly those on ineffective treatments, and also accelerate the drug development process.


Research activity codes: 8.4 RESEARCH DESIGN AND METHODOLOGIES (HEALTH SERVICES)
Health categories: GENERIC HEALTH RELEVANCE
Title: Quantifying Age-related Changes in the Mechanical Properties of Tissues
Funder: Medical Research Council

Abstract: Age-related changes in the mechanical properties of dynamic tissues within the pulmonary, cardiovascular and musculoskeletal systems profoundly affect human morbidity and mortality. Despite the immense clinical and economic burdens that result from disorders such as hypertension and low back pain, to date attempts to identify and localize the key molecular mechanisms which cause age-related loss of tissue compliance and elastic recoil have been limited by inadequate methods for measuring local mechanical properties of tissue. Therefore, we will develop nanoindentation techniques to map and quantify micrometer-scale changes in tissue mechanical properties to individual tissue components. Nanoindentation is routinely used in materials science to measure the mechanical properties of small volumes of engineering materials, with micrometre spatial resolution. Using this technique, we will determine how age-related changes in the structure of soft tissue cryo-sections influence local changes in mechanical properties and hence understand the mechanisms that lead to changes in bulk tissue behaviour. To achieve this we have specified a modified commercial nanoindentation platform, to include a high quality optical microscope that utilizes molecular auto-fluorescence and differential interference contrast to identify and then quantify the micromechanical properties of discrete tissue structures. Although we have successfully used nanoindentation to characterize tissue mechanical properties in Manchester, further development of the technique will be undertaken to develop constitutive laws that describe tissue mechanical behaviour and link it to tissue microstructure. In order to achieve these goals we have assembled a multidisciplinary team of materials scientists, life scientists and clinicians to apply this technique to research projects in three organ system where age-related mechanical change profoundly affect human mortality, morbidity and well-being. These are: 1) the increase in stiffness of the vasculature that occurs during both ageing and age-related disorders such as diabetes; 2) age-related degeneration of the intervertebral disc which is associated with low back pain; and 3) commercially important changes in the mechanical properties of ageing skin. A further advantage of the technology, is that by developing its use with standard histological specimens, we can provide mechanical analysis using very small quantities of tissue samples consistent with minimally invasive biopsies. Once these techniques are established and validated we will disseminate the details via scientific publications and invite the wider research community to utilise the approach.


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: GENERIC HEALTH RELEVANCE
Title: Global chromatin interactions in post-mitotic neurons.
Funder: Medical Research Council

Abstract: The evolutionarily conserved cohesin complex has fundamental roles in chromosome biology. These include sister chromatid cohesion, post-replicative DNA repair and the control of transcription. We propose to address fundamental questions concerning the underlying mechanisms used by cohesin proteins to mediate their effects on gene expression. This project will focus on understanding the general principles governing cohesin-based chromatin organization during interphase. To do this, we will use Chromatin Interaction Analysis using Paired-End Tag sequencing. ChIA-PET is a novel technique which combines 3C and next-generation sequencing technologies to discover all long-range chromatin interactions in the nucleus. It is currently the most effective and powerful method for measuring the interaction of functional elements in a genome-wide and un-biased approach. We will use protocols for the differentiation of mouse ES cells into self-renewing but lineage restricted neural stem (NS) cells. These cells can be further differentiated into an unlimited resource of post-mitotic astrocytes and can be used to investigate the effects of cohesin depletion on chromatin organization under conditions where cohesins are not essential for cell division. Insight into how cohesin proteins work will lead to a better understanding of many aspects of chromosome biology as well as a deeper knowledge of developmental genetic diseases such as Roberts and Cornelia de Lange syndromes (caused by mutations in cohesin subunits) and cancer, where gene deregulation plays an important role.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Regulating amyloid formation: structural studies of the secretion and assembly of 'curli' fibres
Funder: Medical Research Council

Abstract: Curli represent a novel class of bacterial surface fibers that are produced by enteric bacteria such as Escherichia and Salmonella, including many pathogenic strains and species. Curli promote biofilm formation and host cell internalization as well as mediate binding to a variety of eukaryotic proteins including fibronectin and immune system components. A remarkable feature of curli is that they share biochemical and structural properties with disease-associated fibers called amyloids. Amyloids are characterized by unusually stable fibrous protein aggregates formed from a cross &#61538;-sheet structure, and are implicated in the cause of major human diseases, such as type-2 diabetes mellitus, Alzheimer?s and Parkinson?s. Unlike disease-associated amyloid formation (amyloidogenesis), which is the product of protein misfolding, curli amyloid assembly is regulated by a highly specialised biogenesis pathway. Curli biogenesis requires specific accessory proteins, that include an outer-membrane translocator, CsgG, putative chaperone proteins CsgE and CsgF and an additional protein CsgC. The biological importance of CsgG as a secretion system is underlined by its conservation across the majority of known species within the bacterial kingdom. CsgG forms a membrane pore that recruits CsgE and CsgF and regulates the export and assembly of CsgA/B subunits. CsgC plays a role in the correct assembly of CsgA. In depth studies of curli biogenesis provide a unique opportunity to discover how cells are able to control amyloid formation. In this proposal we aim to build on a robust platform of excellent preliminary data and develop sophisticated structural and functional analyses of the curli translocation complex. We will be addressing the following research questions: o How do curli accessory proteins prevent the premature polymerisation of subunits? o How is amyloid assembly propagated on the cell surface? o How is curli the translocation machinery gated for secretion? These timely studies will not only reveal new functional and mechanistic insights, but also suggest strategies for therapeutic control of human amyloidogenesis.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Structure of the Smc5-6 DNA repair and chromosome maintenance protein complex
Funder: Medical Research Council

Abstract: The SMC protein complexes, including cohesins and condensins, are required for maintenance of higher order chromosome structure and segregation. The Smc5/6 complex, the least well understood of the three SMC complexes, is required for DNA repair, rDNA stability and telomere maintenance. It consists of 8 subunits, which form three sub-complexes: the core Smc5 and Smc6 proteins with the SUMO ligase Nse2; Nse1-Nse3-Nse4, which includes the RING finger putative ubiquitin ligase Nse1; and Nse5-6. A further protein, Rad60 interacts transiently with the complex. We wish to understand the in vivo functions of the Smc5/6 super-complex in terms of its biochemistry and its structure. In particular we wish to define the functional contributions of the individual subunits, determine how they assemble in the functional complex and sub-complexes, and elucidate the structural basis for regulation and coordination of the ATPase, SUMO ligase and ubiquitin E3 ligase activities, which the complex incorporates. Towards this end we will develop expression and purification strategies for the assembled complex ex vivo from S.pombe, and the human and S.pombe complex, sub-complexes and individual proteins by recombinant expression in insect cells. We will use single-particle electron microscopy to define the overall architecture of the complex at low resolution, and combine this with high-resolution crystal structure determination of sub-complexes and individual proteins to achieve a quasi-atomic model for the full complex. In parallel, we will determine the ATPase, SUMO ligase and ubiquitin E3 ligase activities of the complex in the presence/absence of individual components (including Rad60), and with the inclusion of genetically characterised mutations in different components and domains for which the in vivo phenotype has already been defined. We will correlate these structural, biochemical and phenotypic data to define strong hypotheses for the roles of individual subunits and domains in the known functions of the Smc5/6 super-complex, and test these by epistasis and other genetic approaches in S.pombe. We will also use our structural and biochemical data in a reverse genetic approach to design targeted ?surgical? disruption of specific interfaces and interactions whose biochemical consequences can then be defined, with the aim of identifying separation-of-function mutations that affect only one of the biological processes to which Smc5/6 contributes. These studies will provide profound insight into the structure, biochemistry and in vivo function of this important protein complex.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Identification of chromosomal components that stabilize cell differentiation and restrict nuclear reprogramming
Funder: Medical Research Council

Abstract: We have developed a novel experimental procedure to analyse how certain chromosomal proteins and RNAs control gene activity in two important aspects of cell behaviour. One concerns the mechanism by which specialised cells maintain their state of differentiation. The other relates to the increasing resistance of nuclei, during development, to the experimental reversal of gene activity. We will first make a suspension of permeabilized mammalian somatic cells (?nuclei?) from which chromosomal proteins and RNAs will be progressively removed. The depletion of proteins will be achieved by increasing concentrations of KCl and Triton. We can also remove certain parts of proteins (e.g.histone tails) by proteolytic digestion. The second stage of this procedure is to transplant the depleted nuclei to living oocytes of Xenopus, which allow the extensive transcription of active genes, with multiple rounds of transcriptional initiation. Under normal conditions the removal of chromosomal proteins causes chromatin to become so dispersed that it cannot be taken into a microinjection pipette. However, we have overcome this problem by encapsulating protein-depleted nuclei so that they can be transplanted into oocytes. The result of our procedure is to be able to relate the loss or modification of particular proteins or RNAs to the continuing transcription, or induced activation, of known genes. To determine the function and likely mode of action of the chromosomal components that we identify, we propose to (1) achieve the depletion of a single type of protein or modified protein in somatic nuclei by competition with protein-specific peptides, (2) overexpress single types of proteins (or mutants) in transplanted nuclei (coupled to locus specific association studies by ChIP), (3) deplete nuclei, differing in cell identity, of proteins that account for the differences observed between their reprogramming response by oocytes, and (4) re-introduce specific RNAs into RNA-depleted nuclei. Somatic nuclei prepared by these means will be tested in oocytes for transcription of, and the association of specific factors with, individual genes. We propose also to transplant single protein-depleted nuclei to enucleated eggs to see effects on development. We can therefore understand how a particular chromosomal molecule is responsible for the continuing expression of genes in stably differentiated cells and for the resistance to the reversal of gene expression, and hence maintenance of cell differentiation, under conditions of nuclear reprogramming as related to eventual cell replacement therapy.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: MRC Program grant
Funder: Medical Research Council

Abstract: While the multiple kinases that regulate spatio-temporal events of mitotic progression are well understood, we know much less about involvement of protein phosphatases (PPs). We propose to follow two branches of research on PPs emerging from our recent studies: characterisation of Greatwall kinase?s mitotic functions, one of which is to activate Endos, an inhibitor of the B-(twins) subunit-containing form of PP2A; and regulation of centrosome and centromere/ kinetochore function by PPs identified in our RNAi screen for Drosophila PPs with mitotic functions. 1) Embryos from polo1 gwlScant/++ females have defective centrosome behaviour during syncytial divisions, leading to maternal-effect lethality; we discovered that this is suppressed by also reducing maternal Endos (endos ++/+ polo1 gwlScant females are fertile). We have isolated and wish to characterise other suppressors of polo gwlScant/++. These may be mutations that reduce Greatwall or Endos function, that increase Polo function, or interfere with downstream functions of Polo at the centrosome. We want to determine whether Greatwall can negatively regulate Polo independently of its down-regulation of PP2A or whether reduced function of both PP2A and Polo synergise to lead to defective centrosome behaviour. We will therefore characterise centrosome behaviour in living cells/embryos having reduced PP2A and in an in vitro system for microtubule nucleation from partially purified centrosomes. In so doing we will characterise the phenotypes of potential dominant mutants of Endos at its Gwl phosphorylation site and will also study Greatwall?s physical interaction with Polo and its apparent targeting to the spindle matrix. 2) Our PP RNAi screen confirmed that PP2A and PP1 are the major PPs required for mitotic progression but also revealed other PPs that regulate centrosome and centromere behaviour. Of these we want to re-examine previously proposed centrosomal functions for PP4, a member of the PP2A family. We will use proteomic approaches to identify proteins interacting with PP5, Puckered, and CG9311, each required for centrosome functions. We also want to understand PP4?s function at the centromere; we have found that it is required to localise or maintain CENP-E, with which it associates. PP1 has multiple centromeric/kinetochore functions. We will examine its interaction with Spindly, a protein proposed to load dynein onto the Ndc80 complex of the kinetochore in an Aurora B-dependent manner. We want to determine whether this Aurora B role is opposed by PP1 and whether any known PP1-inhibitory protein participates in this process.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: The 1958 Birth Cohort Biomedical Resource - facilitating access to data and samples and enhancing future utility
Funder: Medical Research Council

Abstract: This infrastructural project is targeted at strategic development of that component of the 1958 Birth Cohort (1958BC) that is known as the ?Biomedical Resource?. It will ensure that optimum utility can be extracted from the Resource during 2011-2014 and that the 1958BC will then be well placed to maintain and extend its internationally hailed contribution to research in the biomedical and social sciences. The proposal subsumes three complementary objectives: (1) secure the basic infrastructure as it now exists, thus ensuring that the successful systems that have already been implemented can be maintained into the future; (2) enhance the infrastructure from an administrative and strategic management perspective to ensure that it can face expected and unexpected future challenges and opportunities both effectively and resiliently; (3) enhance the infrastructure from a scientific perspective to ensure that both the 1958BC, and UK Bioscience, are best placed to face the scientific challenges of the future. The new science underpinning this application is focused entirely on optimising and enhancing the utility of the pre-existing Biomedical Resource ? the proposal contains no hypothesis-driven research and no funding is sought for additional data or sample collection from study participants. The responsibility for strategic development of the cohort as a whole ? including planning for future data sweeps - will remain with the Centre for Longitudinal Studies (CLS). This application reflects a considered evolution in the thinking of the funders (MRC, WT, ESRC) about strategic development of the 1958BC Biomedical Resource and of the systems and policies governing access to it. Initially, responsibility for access and strategic development lay with the Principal Investigators of the original grant. But, it later became clear that if resource utility was to be optimised it should be managed and developed by independent scientists and administrators. In 2008, responsibility for managing the 1958BC biobank therefore transferred to ALSPAC laboratories at the University of Bristol under a joint grant from MRC/WT. Then, in 2009, responsibility for oversight and strategic development of the Biomedical Resource as a whole passed to the independent access committee chaired from the University of Leicester under another small grant from MRC/WT. Following strategic discussions with MRC, WT and ESRC, the University of Leicester and University of Bristol now outline a vision for joint management of the Biomedical Resource, to include its strategic development as an infrastructure, under a grant requesting limited - but adequate - funding to ensure sustainability.


Research activity codes: 2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY);1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: GENERIC HEALTH RELEVANCE