NIHRDataInsights/HRCSData huggingface dataset:
Title: Epigenetic Barriers to Cell Fate Reprogramming
Funder: Medical Research Council

Abstract: This project investigates the epigenetic basis for memory of the differentiated state of a cell and how it acts as a barrier to efficient nuclear reprogramming. The aim is to improve the efficiency of nuclear reprogramming and hence new cell type generation by interfering with the epigenetic mechanisms stabilizing the differentiated state of a cell. We propose to investigate the epigenetic basis of cellular memory using nuclear transfer (NT) to amphibian eggs. First, we will address the extent of cellular memory in NT embryos using donor nuclei from different cell types and differentiation status. We will identify by RNAseq the genes showing donor cell type specific memory of gene expression and then ask if this memory increases with the differentiation status of the donor cell. Since cellular memory genes resist the reprograming process and remain expressed in the wrong cell type of NT-embryos, we propose that memory genes are associated with certain epigenetic modifications that cannot be efficiently removed by the egg and hence act as a barrier to efficient reprogramming. To identify these modifications, we will next investigate the genomic distribution of candidate epigenetic marks in the donor cells at different stages of embryonic development via ChIPseq and determine how they localise with regard to memory genes. Lastly, after identifying the epigenetic features correlating with memory genes, we will ask which of those features impose a barrier to successful reprogramming. This will be done by transplanting nuclei with modified chromatin to enucleated eggs. We will look for the improved generation of new cell-types and tissues in the resulting embryos by analyzing their gene expression patterns. Furthermore, we will score the developmental outcome of NT embryos. We expect to identify chromosomal components that can be removed for efficient reprogramming and cell-type generation, and hence improve the prospect of successful cell replacement therapies.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: DECIPHERING THE BIOLOGICAL CHARACTERISTICS OF HUMAN HAEMOGENIC ENDOTHELIUM
Funder: Medical Research Council

Abstract: Haematopoietic stem cells (HSCs) provide a continuous supply of blood cells throughout life and have been used for decades in the clinic to treat haematopoietic malignancies and diseases. However shortage of compatible bone marrow donors remains a major limitation for the wider application of this treatment. Alternative sources of HSCs usable in the clinic could be derived from the in vitro differentiation of pluripotent stem cells. However, this therapeutical aim can only be achieved with a full understanding of the differentiation processes and the thorough characterization of clinically useful cell populations. To date, this remains one of the principal limitations and most difficult challenge of the regenerative medicine field. All blood cells, including HSCs, are derived from mesoderm precursors which differentiate into a transient and specialized population of endothelial cells termed haemogenic endothelium (HE). Through an endothelial to haematopoietic transition, HE cells give rise to blood progenitors. This transition has been documented in most species studied to date and was shown to occur during both extra-embryonic and intra-embryonic haematopoiesis. As such, the HE plays a central role in the establishment of the haematopoietic system. However, despite its fundamental importance, we know very little about this cell population. Due to the limited access to in vivo-derived tissues, the in vitro differentiation of human pluripotent stem cells offers a powerful model system for the in-depth study of the HE. Here, we propose to investigate at the molecular and cellular level the plasticity, heterogeneity and potential of human HE cells generated upon the differentiation of pluripotent stem cells. Findings from this project will advance our understanding of early human haematopoiesis and inform the design and optimization of protocols for the generation of haematopoietic cell populations usable in the clinic for regenerative medicine purposes.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: How does the expression of one gene affect that of its neighbour?
Funder: Medical Research Council

Abstract: Classically it has been presumed that genes are autonomous in their expression. However, there is increasing evidence that in both health and disease, gene expression is not autonomous. In all eukaryotic genomes highly co-expressed genes and housekeeping genes cluster. In cell fate specification, blocks of up or down regulated genes are observed and in cancers we see unusual blocks of genes downregulated. Importantly, the first gene therapy trials had to be stopped as the expression of the introduced gene affected the expression of an oncogenic neighbour. What is less clear is what the underlying mechanisms are for such non-autonomous expression. Here we take advantage of an emerging model system for the analysis of gene-gene interactions, the DIRAS3/GNG12-AS1 expression in humans. We have discovered that DIRAS3 transcription is modulated through transcriptional interference (TI) from an lncRNA, GNG12-AS1. We have found that we can inhibit GNG12-AS1 either at its transcription level or post-transcriptionally by selective siRNA targeting. We intend to use this system to test two models for TI, one that considers polymerase collision/pausing, and another that transcription of one locus alters promoter accessibility at the other. The techniques that we will use will be allele-specific capture chromatin conformation (C-HiC) and Nuclear run assays (GROseq), R-loop and RNAPII ChIP in combination with gene editing to examine the effects of transcription through specific genomic features on TI. The results of these studies will lead a better understanding of non-autonomous gene expression, which is key to understanding the potential pitfalls of gene therapy, the effects of genome rearrangements (in cancers or in evolutionary time) as well as guide epigenetic therapies aimed at reversibly modulating gene expression.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Human Pluripotency
Funder: Medical Research Council

Abstract: The goals of the proposed research are: (i) to fully characterise human naïve pluripotency; (ii) to define parameters for robust self-renewal and resetting pluripotency; (iii) to delineate the pathway to multi-lineage specification and commitment. Acquiring the knowledge to harness the naïve form of human pluripotency and thence to reproduce the molecular and cellular ontogeny of pluripotency progression in the embryo should enable more consistent and efficient differentiation behaviour. The concept that differentiation biases observed among conventional human pluripotent stem cells may be muted by transition through naïve pluripotency will then be examined. The specific research objectives and tasks are: I. Regulatory network of the human naïve state i. Examination of core pluripotency regulators ii. Differential transcriptome analysis iii. Functional genetic screens iv. Validation and characterisation of lead candidates v. Modelling human naïve gene regulatory circuitry II. Culture optimisation and transgene free resetting i. Improvement to naïve PSC culture ii. Global characterisation of consistent identity iii. Homogeneity of self-renewal iv. Transgene-free resetting III. Commitment and differentiation i. Pathway to multilineage competence ii. Consistent multilineage differentiation iii. Restoration of balanced differentiation The study is focussed on human pluripotent stem cells with associated human embryo studies. Key methods to be deployed include: genetic engineering of reporters and inducible transgenes; CRISPR/Cas9 based genetic screens; high throughput transcriptome profiling, methylome profiling, ATAC-seq and ChIP seq with associated bioinformatics; human embryo culture and cell line derivation. Exploitation of the results will be led by the academic research sector but new know-how and intellectual property is also anticipated to foster collaborations and licencing arrangements with service industry and Pharma.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: GENERIC HEALTH RELEVANCE
Title: Circadian rhythms and the control of NRF2-based antioxidant signalling as a therapeutic target in dermal tissue repair and pathological wound healing
Funder: Medical Research Council

Abstract: This proposal will determine whether and how genetic targeting of circadian clocks in fibroblasts modulates healing responses during cutaneous wound repair, and test novel time-scheduled pharmacological interventions for efficacy in treating pathological wound repair. Using unique fluorescent collagen 1 reporter as well as fibroblast-specific clock-deficient mice, we will monitor temporal changes in fibroblast activation during wound repair. Wounds from mice injured at different circadian phases will be analysed for a range of histological parameters (e.g. collagen deposition) and matrix gene expression. Purified fibroblasts from wounds will be used for ex vivo culture. Parallel analyses will include clock gene expression, proliferation/migration assays as well as analysis of candidate signalling pathways by targeted PCR arrays. To identify circadian elements that drive transcriptional regulation of matrix genes such as collagen 1, we will perform advanced in vitro molecular studies to determine collagen 1 promoter activity following over-expression or knockdown of clock transcription factors and NRF2. We will confirm in vitro findings both in mouse tissues and in human Scleroderma fibroblasts. To test whether circadian gating mechanism in fibroblasts couples redox signalling to NRF2 antioxidant program during wound repair, we will use state-of-the-art techniques for measuring reactive oxygen species (ROS), NRF2 activity and oxidative damage markers in wound tissues. To determine sub-cellular sites of ROS production, in situ imaging with specific ROS probes will be used in explanted wound fibroblasts. Finally, we will test whether chronotherapy is more effective in improving wound repair in both animal and human translational models. Following in vitro optimisation studies, we will test whether time-scheduled NRF2 activator improves delayed healing in a preclinical model of type II diabetes and in human fibroblasts from Scleroderma patients.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Creating responsive health systems: improving the use of feedback from service users in quality assurance and human resource management in Bangladesh
Funder: Medical Research Council

Abstract: The AIM of this project is to assist the policymakers in designing a comprehensive health systems intervention to make the Bangladesh's health system more responsive. Specific project OBJECTIVES are to work closely with national and local decision-makers to: 1. Develop an in-depth understanding of the nature and contents of, and key reasons for, feedback received from health service users at Upazila level; 2. Analyse the processes of collecting and responding to service users' feedback at Upazila level, as well as the key contextual facilitators and constraints influencing these processes; 3. Assess the approach to, and processes of, service quality assurance and human resource management, focusing specifically on the use of feedback from service users at Upazila level; 4. Using results of objectives 1-3, develop a comprehensive health systems intervention to improve the use of feedback from service users in quality assurance and human resource management processes at Upazila level. This project focuses on Bangladesh, a low income Asian country where the Ministry of Health and Family Welfare (MOHFW) is implementing a program allowing service users to send feedback via SMS texts. This 18-months project will analyse the national user feedback data and focus in-depth on two Upazila Health Complexes (UHC) in one district. Throughout the project, we will work closely with decision-makers, to facilitate the shared understanding, adoption of results into policy and practice and achieving its highest impact. The project results will be communicated widely through development of policy briefs, presentations at management meetings, development of newsletters and press-releases, to ensure their uptake in policy and practice in Bangladesh and wider.


Research activity codes: 8.1 ORGANISATION AND DELIVERY OF SERVICES;8.3 POLICY, ETHICS AND RESEARCH GOVERNANCE
Health categories: GENERIC HEALTH RELEVANCE
Title: Social, behavioural and economic drivers of inappropriate antibiotic use by informal private healthcare providers in rural India.
Funder: Medical Research Council

Abstract: This is an exploratory study of the social, economic and behavioural drivers of antibiotic use in informal providers in rural areas of the state of West Bengal in India. In pluralistic health systems of low and middle income countries (LMICs), including in India, the bulk of healthcare at first contact is delivered by providers who may not have a formal medical qualification but practice a range of biomedical treatments, including treatment with antibiotics. They are known by different names such as drug sellers, village doctors or rural medical practitioners and are found all over Asia and Africa. Evidence suggests that their antibiotic use is high and irrational, and interventions that have focused on training and recognition of IPs have not succeeded in lowering their antibiotic use. Antibiotic use is one of the most critical components of IPs' quality of care that needs to be addressed urgently. Excessive dispensing/prescription of antibiotics by healthcare providers including IPs in LMICs is one of the reasons for overuse of antibiotics in humans leading to increasing antibiotic resistance which is a major global health threat today. We will conduct structured interviews with a sample of 100 IPs each in two districts (total 200), selected through stratified random sampling, followed by in-depth interviews and observations at 30 IP clinics, focus group discussions with community members and key informant interviews with government, pharmaceutical and formal medical sector representatives. In small group workshops with IPs, communities, and with the other stakeholders, we will present ideas for different interventions and seek feedback from participants on what they think would be the most effective and feasible. This will help us develop a plan for implementing and evaluating a comprehensive intervention in future.


Research activity codes: 8.1 ORGANISATION AND DELIVERY OF SERVICES
Health categories: GENERIC HEALTH RELEVANCE
Title: Midlife Pace of Aging in the Dunedin Study
Funder: Medical Research Council

Abstract: Declining fertility rates, aging of the baby-boomers, and increasing life expectancy are leading to population aging. As the population ages, this increases the public-health burden of age-related conditions, such as cardiovascular disease, type 2 diabetes, and dementia. Treating un-prevented diseases in late life has proven costly and ineffective. It is now known that potentially preventable risk exposures and physiological causes of age-related disease emerge in childhood. It is also now known that the pathogenesis of age-related diseases involves gradually accumulating decline in organ systems, beginning in the first half of the life course. Consequently, new interventions aiming to prevent age-related diseases will have to be applied to individuals while they are yet young, before they reach midlife. Translation of basic-science geroscience discoveries into preventive interventions for young humans is lacking because virtually nothing is known about the process of biological aging during the first half of the life course. This prompts our proposal to study the pace of biological aging from the twenties forward. We will use the Dunedin Multidisciplinary Health & Development Study, a longitudinal study of a birth cohort now entering its fifth decade. We propose to administer a full-day data-collection protocol to the 1004 living members of the birth cohort. To assess each cohort member's pace of biological aging we will: (a) measure biomarkers across multiple organ systems, and (b) statistically model correlated change in these biomarkers assessed at ages 26, 32, 38, and 45 years. We will describe individual variation in the pace of aging, plus its developmental origins, genomic signatures, functional consequences, associated cognitive changes, and economic costs. We will identify attributes that set apart individuals whose bodies are months or years younger than their chronological age.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Reducing inequalities in child health: understanding pathways, interventions and policies
Funder: Medical Research Council

Abstract: AIM: To elucidate causal pathways and consequences of health inequalities in children, and to quantify the impact of interventions and policies to interrupt the generation of inequalities in health across the life course. RESEARCH QUESTION 1: To what extent do key exposures, for example health behaviours and family income, mediate the association between childhood disadvantage and important child health outcomes such as mental health or asthma? RESEARCH QUESTION 2: Does childhood illness have different impacts on educational attainment and early adult transitions into employment depending on the socio-economic conditions in which the children grow up? RESEARCH QUESTION 3: To what extent do interventions that target mediating pathways, such as poverty or risk factor reduction, reduce health and socioeconomic inequalities in childhood? METHODS: 1) Causal mediation analysis in longitudinal data 2) Simulation of trials of interventions 3) Evaluation of natural policy experiments 4) Data linkage. I will use some of the world's largest contemporary datasets on children including the Millennium Cohort Study (MCS); the Welsh Electronic Cohort for Children (WECC); and the Danish National Birth Cohort (DNBC). I will focus on outcomes that influence later adult health, are socially patterned, and amenable to intervention (e.g. measures of child development, mental health, asthma). I will use the estimates from causal mediation analyses, combined with estimates from controlled trials, to model the effect of public health, welfare and education interventions interventions on child health and social inequalities. I will apply recently developed methods for evaluating natural policy experiments. SCIENTIFIC AND MEDICAL OPPORTUNITIES: Results will inform policy makers and the wider public. Health outcomes for children in the UK are poor leading to huge human and economic costs. I will develop a better understanding of how to reduce inequalities in child health.


Research activity codes: 2.3 PSYCHOLOGICAL, SOCIAL AND ECONOMIC FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Cell biological mechanisms underlying stem cell competition
Funder: Medical Research Council

Abstract: The ability of a stem cell to contribute to long term tissue homeostasis depends on its ability to remain in the niche and compete with its neighbours for limited space. This competition is normally a stochastic process but can be biased in favour of a stem cell carrying an oncogenic mutation, such that the mutant clone displaces all wild type cells. The driving force underlying this is an increased cell cycle rate. Conversely, stem cells that leave the niche and differentiate also undergo a selective process, whereby the cell with the highest activity of the growth-promoting TOR pathway differentiates while its neighbours with lower TOR remain in the niche. Thus, there are two opposing inputs that govern the decision a stem cell makes to either self-renew or differentiate. I use the genetically tractable Drosophila testis as a model to investigate the cell biological mechanisms that confer competitive abilities to a stem cell relative to its neighbours. In aim 1, I will use live imaging to observe stem cell competition in vivo and describe the relationship between the cell cycle rate and competition. I will carry out a genetic screen for candidate cell cycle regulators in clonal competition assays. Finally, by performing RNA-seq on FACS purified stem cells, I will identify the transcriptional targets of three signalling pathways that affect competitiveness through increased proliferation. In aim 2, I will use live imaging to determine whether competition during differentiation coordinates the development of two separate lineages (soma and germline) to maintain tissue homeostasis. Moreover, I will determine how qualitative changes in protein translation are necessary to promote differentiation of a stem cell lineage. My work will provide a better understanding of the cell biology underpinning the ability of stem cells to compete with each other, and point to future applications in which manipulating the competitiveness of stem cells can enhance stem cell therapy.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Human germline in vitro models for development and the epigenetic program
Funder: Medical Research Council

Abstract: We have carried out detailed computational analysis of the transcriptome and epigenome of in vitro (~Wk2.5), and in vivo Wk5. 5-Wk9 PGCs. This has provided an initial experimental framework, and testable predictions for extrinsic and intrinsic factors needed for further development of PGCs. PGC specific reporter cell lines will provide development-monitoring assays for advanced PGCs by high-throughput live cell imaging. Long-term culture with hourly quantitative information of the fluorescence activation allows for simultaneous testing of 576 conditions. We will screen for cytokines and small compounds to stimulate development of PGCs, using the candidates identified by bioinformatic modeling, complemented by unbiased screening with commercial compound libraries, including small molecules to lower the epigenetic barriers for development. For intrinsic factors, we will focus on transcriptional factors that are specifically activated sequentially in vivo PGCs. We will conduct co-culture of nascent PGCs with human/porcine gonadal or Sertoli cells to provide a favorable niche, combined with extrinsic and/or intrinsic approaches to increase the probability of finding the best conditions for PGC development. Our immediate aim is combine all the information to generate equivalent of ~Wk10 PGCs in culture, which covers a period of significant epigenetic program leading to comprehensive erasure of DNA methylation. These PGCs will be compared bioinformatically with in vivo gonadal counterparts, gametes and seminoma. We aim to understand the overall mechanisms that regulate PGC development, together with the mechanisms of germ cell programming, as well as causes of disorders, by using patient specific iPSCs and gene modifications. We will also perform global gene inhibition and activation screening with CRISPR/Cas9. When appropriate, we will collaborate on some aspects, for example on the mitochondrial bottleneck and purification in early PGCs.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE