NIHRDataInsights/HRCSData huggingface dataset:
Title: Modelling transcriptional dynamics in human T-Cells using next generation sequencing data
Funder: Medical Research Council

Abstract: Background: Recent advances in sequencing technology (Next Generation Sequencing, or NGS) allow us to measure with great precision and exhaustively, the transcriptional activity in cells. It is essential to develop concomitant mathematical and bioinformatic techniques to deal with this abundance of data and exploit it to its full potential. In this project, we will use as an example system the DNA-damage response network in human T-cells. Understanding this system in a dynamical way is important since it comprises p53, a (mostly) pro-apoptotic transcription factor often described as the ?guardian of the genome? that is mutated in about half of human cancers. Aim: to combine genome scale data, mathematical modelling and bioinformatics to generate essential for translating the potential of the new genomics technologies into true medical advances. Objectives: (1) To develop measurement error models for next generation sequencing data (RNA-Seq and RNA-SAGE). (2) To develop accurate dynamic models of mRNA production and degradation including non-linear models and multiple transcription factor dependency. (3) To develop procedures allowing an assessment of the appropriate parametrisation of dynamic models. In broad terms, the first objective is about understanding the level of reproducibility attached to NGS. The second objective is about linking this data to models. It is the models that will provide intimate understanding and quantification of the mechanisms behind the production and degradation of messenger RNA. The third objective concentrates on the generation of effective and actionable models. Design and methodology: Four time courses of DNA damage-stressed cells will be generated and measured using NGS. This data will be analysed dynamically with ordinary differential equation models. Scientific opportunity: This project is eminently interdisciplinary, bridging together the latest advances in biotechnology with mathematical modelling. The chosen biological system is biomedically relevant and the methods developed in the course of this project will be widely applicable.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Efficient and effective use of longitudinal data
Funder: Medical Research Council

Abstract: In order to reason causally from medical studies, a minimal requirement is that the temporal ordering of events is explicitly recognised. As this principal became established there was a corresponding increase in the number of research projects recording many variables over several waves of observation. Nevertheless, some statistical analyses of this type of data still fail to recognise the critical role of time. Consequently, existing data sources contain a wealth of information and a rich temporal structure that has not been fully exploited. Introduced in my PhD thesis, the linear increments model focusses on observed changes in measured quantities, and hence offers a natural framework for acknowledging study chronology. This fellowship will develop and disseminate the linear increments approach, arguing for its routine use with longitudinal designs. An important feature of the incremental approach is that missing responses (due to dropouts, for example) pose no particular analytical problem, other than the unavoidable reduction in sample size. Several facets of the work will serve to make this statistical technology more relevant to medical practitioners. One proposed development will more neatly distinguish aspects of the model that are of principle interest from those of secondary importance, just as in a proportional hazards model the effect of treatment on survival is emphasised over the precise baseline pattern of events. Another extension will allow inference to centre on surviving patients, rather than on a manifestly hypothetical immortal cohort. Often, multiple outcomes may be clinically pertinent, and so a third aspect of the fellowship will be to enable exploration of the dynamics of related variables. An important goal of the fellowship will be to make the case that the linear increments model is the natural analogue of the popular Kaplan-Meier approach to event times. To this end, a unifying mathematical theory of dynamic observation of stochastic processes will be sought, incorporating at one extreme continuous-time survival, and discrete-time panel data at the other. Equally crucial will be the successful application of the methodology to substantive questions arising in randomised trials, observational studies and epidemiological research.


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: GENERIC HEALTH RELEVANCE
Title: Developing and applying innovative methodologies of longitudinal network data and agent-based modelling to public health
Funder: Medical Research Council

Abstract: Background: It is widely accepted that the social network within which one is embedded can affect one?s health and behavioural choices. Within a school environment peer influence and selection are two computing forces on behavioural choices and substance misuse. Research aims and objectives: To determine how social network and behavioural dynamics affect and alter interventions to prevent substance abuse in adolescents and to investigate what factors shape the evolution of young people?s school social network and consequent influence on health behaviours. Design: A longitudinal panel study over 5 waves of 8th through to 12th graders has been conducted 2001-2005 (when 11/12 to 15/16 years old) within the Belfast Youth Development Study (BYDS). BYDS documents complete network data of 5457 school children from 43 schools of single gender and coeducation, from the integrated, controlled and maintained systems and from 3 demographic areas, who have completed annual questionnaires (2013 completing all 5 waves) on lifestyle and substance abuse behaviours (alcohol, tobacco, cannabis, cocaine, ecstasy, heroin, LSD, speed) and includes the naming of up to 10 friends from within their year group. Methodology: A three-fold analysis will take place: (i) traditional Social Network Analysis (SNA) techniques to observe the peer networks in place at the individual, personal and group level at any one time; (ii) longitudinal study of the dynamics of SNA using the recently developed stochastic actor-driven models for the evolution of social networks developed by Snijders et al. (SIENA) and (iii) to capture the adaptive dynamic interdependence of actors and their behaviours, an agent-based model (ABM) will be developed to take account of diversity and feedback within the pupil population. Research questions will be addressed through the investigation and analysis of single and multiple-wave network data. ABMs will be developed in accordance to the findings of the network analysis to improve our design of future interventions to mitigate their potential harm. Scientific and medical opportunities: The purpose of the actor-driven and agent-based models is to provide greater flexibility in investigating how various characteristics of individuals and their social networks may affect the spread of substance abuse behaviours within schools, and how different policies might affect average levels of substance abuse. The analysing of such cohort data is important so as to feedback into the public health system through intervention design and policy


Research activity codes: 2.3 PSYCHOLOGICAL, SOCIAL AND ECONOMIC FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: GENERIC HEALTH RELEVANCE
Title: Fair comparisons of interventions: extending the Prior Event Rate Ratio method
Funder: Medical Research Council

Abstract: In many situations where it is not ethical or practical to perform randomized controlled trials, observational studies provide a rich source of information for assessing effectiveness of treatment interventions. Unfortunately, the modest effects of modern medical treatments can be obscured by the confounding effects of other, often unmeasured, factors. There is a growing literature on methods for addressing residual confounding but recent research highlights the limitations of existing techniques. A recently proposed and very promising solution to this problem is the Prior Event Rate Ratio (PERR) method. This method is applicable to studies where a new intervention is introduced for the first time and is based on the assumption that differences in outcomes between treated and control groups before intervention reflect the effect of all confounders, independent of the intervention effect. Simple adjustments are then possible to correct estimates of intervention effects for the aggregate effects of confounders. Previous work has shown the potential of the PERR method to remove or reduce residual confounding when analyzing effectiveness of new drug treatments using routine clinical databases. This project will broaden the scope of this method by investigating its suitability for analysis of intervention effects more generally, including hazardous exposures that would not be possible to test experimentally, in both cohort and routine clinical studies. An extensive simulation study will be performed to explore sensitivity of the method to different assumptions about issues encountered in practice including multiple unmeasured confounders, attrition bias, measurement error and differential mortality. An important contribution of our work will be the extension of the PERR approach to address the analysis of ordinal and interval outcomes, both central to research on chronic health conditions in mid and later life. The PERR method can be seen as creating a form of ?natural experiment? and has similarities to the ?controlled before-and-after? study design used in psychology and economics. One of our primary objectives will be to investigate differences in model specification and develop an integrated framework for quasi-experimental approaches in epidemiological applications. Following a detailed literature review we will make comparisons with selected alternative approaches to controlling residual confounding, such as instrumental variables, propensity scoring and Bayesian bias analysis. The proposed work will develop new tools to make more effective use of observational databases, and has the potential to make a substantial contribution to evidence-based medicine and the assessment of risks from environmental hazards not amenable to experimental investigation.


Research activity codes: 8.4 RESEARCH DESIGN AND METHODOLOGIES (HEALTH SERVICES);2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: GENERIC HEALTH RELEVANCE
Title: Generation of suppressive donor T cells to specifically control alloresponses after allogeneic stem cell transplantation
Funder: Medical Research Council

Abstract: Allogeneic haematopoietic stem cell transplantation (AHSCT) can cure patients with many diseases for which no effective alternative therapy exists. A major challenge to AHSCT is graft-versus-host disease (GvHD), mediated by alloreactive donor T cells which recognize and damage healthy patient tissues. Current methods to prevent GvHD are unsatisfactory, delaying reconstitution of beneficial donor T cells and increasing infection and disease relapse. The development of strategies to selectively reduce alloreactive T cell responses could improve the outcome of AHSCT. One such strategy is alloanergization, the inactivation of alloreactive donor T cells by allostimulation with co-stimulatory blockade. Alloanergization preserves pathogen-specific T cell responses. In early clinical studies, transplantation of alloanergized HLA-mismatched donor T cells within bone marrow resulted in rapid immune reconstitution, few infections and low rates of GvHD. We have recently shown that the strategy of alloanergization results in the generation of regulatory T cells (Treg) which specifically suppress alloreactive donor T cell responses. We therefore hypothesise that alloanergized donor cells could be used for specific prophylaxis of GvHD after AHSCT. The development of alloanergization as a strategy to generate Treg which prevent GvHD without impairing graft-versus-leukaemia (GvL) effects after AHSCT is the objective of this project. The first aim is to potentiate the generation of allospecific Treg following alloanergization. We will use in vitro assays to determine the effects of epigenetic modulation of FOXP3 expression on the frequency, suppressive function and migratory capacity of Treg generated by alloanergization of human peripheral blood mononuclear cells (PBMC). To broaden the applicability of the approach, we will also modify the strategy for use with HLA-matched unrelated donors using established approaches to augment antigen-presentation. The second aim is to determine if alloanergized cells can prevent human T cells from causing GvHD in vivo. This will be achieved using adoptive transfer of human PBMC with and without alloanergized cells into immunodeficient NOD/SCID/IL2R-/- mice in a xenogeneic model of human T cell-mediated GvHD. Finally, a critical component for successful use of alloanergized human cells to prevent GvHD after AHSCT is the preservation of GvL effects. Our third aim is to enhance donor cell-mediated GvL effects after alloanergization by employing non-haematopoietic antigen-presenting cells to spare tissue-restricted minor histocompatibility antigen-directed T cell responses, and to augment alloreactive donor NK cell responses after alloanergization. This project could lead to development of effective clinical strategies to deliver antigen-specific cellular prophylaxis of GvHD which could improve the outcome of ASCT.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.2 CELLULAR AND GENE THERAPIES
Health categories: GENERIC HEALTH RELEVANCE
Title: Role of Notch signalling during neural crest migration
Funder: Medical Research Council

Abstract: Cell migration is essential for many biological processes such as embryogenesis, wound healing, and tissue homeostasis. In cancer, cell migration plays a critical role during tumour metastasis and is responsible for 90% of deaths of these patients. Despite its importance, it remains one of the most poorly understood aspects of cancer pathogenesis. Because neural crest cells undergo extensive migration in the embryo and share numerous characteristics with metastatic cells, they represent an important model system for studying cell migration. Although neural crest and cancer cell migration have historically been considered from the perspective of single cells moving independently, metastatic cells are frequently found migrating in groups, a process known as collective cell migration. Importantly, collective cell migration endows cancer cells with a higher capacity to disseminate and increased efficiency of metastasis. The aim of this project is to investigate aspects of collective neural crest migration in zebrafish embryos, focusing on the role that the Notch pathway plays in this process. My preliminary data suggest an important role for Notch signalling in neural crest migration. The proposed experiments will expand upon these preliminary results by combining the power of genetics, offered by zebrafish transgenic lines, with live cell imaging and the generation of new tools to study single genetically altered cells in vivo. These approaches will provide a detailed molecular and cellular analysis of neural crest migration. Given the importance of cell migration in tissue homeostasis and its implication in many types of cancers, our findings in neural crest cells will shed light on the mechanism of metastasis and may unveil novel targets for cancer therapies.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: FIGCS: An in vitro model to replace ecotoxicity testing of fish to pharmaceuticals
Funder: National Centre for the Replacement, Refinement and Reduction of Animals in Research

Abstract: Registration of all human and veterinary drugs require establishment of safety to the environment, which includes toxicity testing to fish normally with lethality as end-point. Using existing OECD guidelines, a minimum of 42 fish are typically used in a single acute toxicity test and where safety to the environment cannot be established, the test is either repeated on additional species or followed by chronic studies, which again often include lethality as end-point. We have established a Fish In vitro Gill Cell System (FIGCS), which allows cells to be exposed to chemicals in test water, thus, maintaining a realistic exposure scenario. FIGCS has been demonstrated to accurately predict toxicity of metals in test water, by measurements of molecular and physiological end-points relevant to known modes of toxicity. In the proposed project we will extend the scoop of this system to an important group of environment contaminants, namely pharmaceuticals.


Research activity codes: 5.1 PHARMACEUTICALS;5.9 RESOURCES AND INFRASTRUCTURE (TREATMENT DEVELOPMENT)
Health categories: GENERIC HEALTH RELEVANCE
Title: Diet, lifestyle and biological determinants of health and disease: the EPIC-Norfolk population study
Funder: Medical Research Council

Abstract: EPIC-Norfolk is a prospective population study of 25,639 men and women aged 40-79 years resident in East Anglia recruited in 1993-97 and followed up to the present. The overall goal is to identify behavioural and biological determinants of health and chronic disease to inform interventions to improve health in later life. Particular investment has been made in better measurement of lifestyle, in particular diet and physical activity, biological phenotyping including genetics and in capturing a range of health outcomes. Extensive data already collected on the cohort includes social, psychosocial, family history, medical, anthropometric, lifestyle including detailed physical activity and dietary information with repeated 7 day diaries and food frequency questionnaires; blood lipids, glycated haemoglobin, plasma vitamin C, thyroid function and bone heel ultrasound measures. A biological bank of blood and urine samples has been established for genetic and biochemical profiling with whole genome data already available on 4000 individuals. Specific strengths of this British prospective study include the population based recruitment and size with substantial numbers of women as well as men, and older persons, and wide urban/rural and social class variations. The geographical location also enables follow up for a range of endpoints not easily available in other cohorts including diabetes, musculoskeletal, neurological and gastrointestinal conditions. We have already demonstrated the value of this approach in understanding disease aetiology, in particular, the emphasis on better exposure and endpoint measurement, in published results (over 300 publications since 2006). We are now well positioned to build on this resource to characterise the longitudinal trajectory of a population as it ages and examine determinants of healthy ageing as well as chronic disease to enable appropriate interventions in the population. The current proposal is to provide core infrastructural support to continue follow up of the cohort for health endpoints, enable a repeat survey of the cohort for objective physical and cognitive functional measures and visual health, maintain and update the data bases and biological banks, and to continue examining hypotheses on determinants of health. The cohort size, providing sufficient power to examine disease endpoints, improved accuracy of measurement of diet, physical activity and other exposures, and availability of biologic markers and improved endpoint ascertainment will enable better elucidation of the qualitative and quantitative relationship between lifestyle and biological variables and health outcomes relevant in ageing populations. We will also explore the interaction of genetic predisposition with environmental factors for health outcomes.


Research activity codes: 2.4 SURVEILLANCE AND DISTRIBUTION
Health categories: GENERIC HEALTH RELEVANCE
Title: Reducing mouse number in complex genetic experiments
Funder: National Centre for the Replacement, Refinement and Reduction of Animals in Research

Abstract: The last few years have seen a worrying increase in the number of mice used in research; in the United Kingdom Home-Office figures over 2008 showed an increase of 197,000 (9%) in the number of mice used (http://scienceandresearch.homeoffice.gov.uk/animal-research/animal-testing-faqs/). It is widely believed this is the result of new technical possibilities with genetically modified mice (overexpression models, reporters, conventional and conditional knockouts). An important factor in the increase in mouse numbers is the complex genetic experiments in which several different alleles are combined in the same animal. Because of Mendelian inheritance and limitations on possible breeding schemes due to lethal combinations, these experiments generate many animals of undesired, though still mutant, genotypes. Recent developments in the generation of fully embryonic stem cell (ES)-derived (‘F0’) animals gives the possibility of combining alleles in ES cells to be phenotyped in experimental F0 animals without additional breeding instead of generating single allele animals which need to be combined via breeding to generate experimental animals. The proposed project will generate and test new ES tools to efficiently collect all different types of alleles (gain-of-function, loss-of-function, reporters, recombinase expression) in F0-competent ES cells. It will optimize the protocols to generate F0 animals and demonstrate how modern imaging techniques can further reduce the number of animals needed to obtain statistically significant data, in the proof-of-principle experiments using time-lapse imaging of kidney organ culture. All tools (vectors, ES cells and mice where relevant) and detailed protocols will be made available to the wider scientific community. The resulting system can greatly reduce the number of genetically modified mice generated (but not used) in complex genetic experiments; in the proof of principle experiments we believe we can obtain the same output as using conventional breeding methods with a 90% reduction in mouse numbers.


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