- Total grants
- Total funders
- Total recipients
- Earliest award date
- 09 Jun 1998
- Latest award date
- 29 May 2020
- Total GBP grants
- Total GBP awarded
- Largest GBP award
- Smallest GBP award
- Total Non-GBP grants
An Extended Pilot for the Human Cell Atlas: Adult tissues, human development and inflammation-mediated pathologies 30 Sep 2018
The Human Cell Atlas (HCA) is an international, collaborative effort that "...aims to define all human cell types in terms of their distinctive patterns of gene expression, physiological states, developmental trajectories, and location". Here, we will contribute directly to the first phase of the HCA by forming an ‘extended pilot’ to implement UK infrastructure for large-scale, high quality human cell atlas experiments. We will generate a high-level atlas, with spatial resolution, for multiple adult human tissues along with matched data from human fetal material. We will then illustrate the power of a deep and focused investigation of a single tissue (skin) to produce highly-detailed data describing its cellular composition and spatial organisation. Finally, for selected tissues that have been profiled in adults and fetal material, we will analyse samples from immune-mediated disorders as a comparison with our reference data to gain deeper understanding of the pathological mechanisms. This will demonstrate the utility of the HCA as a ‘healthy reference’ for comparison with disease. Throughout, we will generate profound biological insight from primary human cells and lay a foundation of technology development and optimisation with a set of hardened and scalable methods for single-cell RNA-sequencing, spatially-resolved gene expression, and tissue imaging.
Plasmodium falciparum causes disease by infecting erythrocytes and by transferring parasite-derived effectors to non-infected erythrocytes (non-IEs), altering their physical properties. The parasites also impact other cells of the circulatory system inducing inflammation. These parasite-host interactions are key to the pathogenesis of severe malaria but little is known about how parasite-derived effectors are transferred to non-infected cells. Secreted extracellular vesicles play an important role in intercellular interactions in other systems, and could be an overlooked master regulator in malaria, but little is known about P. falciparum extracellular vesicles (PfEVs). However, I have established a protocol for isolating PfEVs from clinical isolates. Proteome analysis of one revealed that PfEVs contain erythrocyte-adhesive and exported parasite proteins implicated in rigidifying erythrocytes. I hypothesize that: 1) PfEVs transfer effectors from parasites to host cells including non-IEs and 2) antibodies can neutralise PfEVs and protect against disease. To test this, I will use clinical isolates from children with severe and uncomplicated malaria to 1) describe the protein and RNA content of PfEVs, 2) investigate the impact of PfEVs on non-IEs and immune cells and 3) evaluate the protective role of anti-PfEV antibodies against severe disease.
On January 1, 2018, California enacted Senate Bill 27 (SB27), first-of-its-kind and potentially precedent-setting legislation, which will require a veterinarian’s prescription for use of antimicrobial drugs and ban non-therapeutic antimicrobial uses for routine disease prevention and growth promotion in livestock. To assess the effectiveness of this important legislation at reducing antimicrobial resistant bacterial infections in humans, we propose the following specific aims: Aim 1. Quantify the effect of SB27 on E. coli, Campylobacter and Salmonella resistance rates from retail meat. Aim 2. Estimate the proportion of human Campylobacter, Salmonella, and extraintestinal pathogenic E. coli infections caused by strains of food-animal origin in California. Aim 3. Characterize the effect of SB27 on the antimicrobial susceptibility of Campylobacter, Salmonella, and extraintestinal E. coli infections caused by strains of food-animal origin in California. Implementation of SB27 provides a unique natural experiment to assess the effectiveness of restrictive agricultural antimicrobial-use policies at reducing antimicrobial-resistant human infections. The proposed research will have a positive impact by prospectively measuring the effect of this policy on the antimicrobial susceptibility of E. coli (an important colonizing opportunistic pathogen) and Campylobacter and Salmonella (two frank foodborne pathogens) and thereby maximizing the information gained from this singular opportunity
The role of leukotriene A4 hydrolase in dictating inflammation and remodelling in chronic lung diseases 28 Nov 2017
Whilst inflammation and ensuing repair are critical to the body’s response to infection/injury, aberrant inflammatory and reparative processes and subsequent pathological remodelling are cardinal features of chronic lung diseases (CLDs). I believe the enzyme leukotriene A4 hydrolase (LTA4H) critically regulates inflammation/repair processes through dual activities that generate lipid mediator leukotriene B4 (LTB4) but degrade matrikine Pro-Gly-Pro (PGP). PGP is a neutrophil chemoattractant whilst LTB4 drives the recruitment/activation of numerous immune cells. Additionally, I now demonstrate that PGP regulates epithelial and fibroblast functions critical to repair/remodelling. I hypothesise that intrinsic and extrinsic perturbation of the LTA4H axis drives distinct pathological inflammatory and remodelling phenotypes in CLDs. The key goals of this proposal are: Dissect how the dual functions of LTA4H regulate pathological inflammatory and remodelling features of CLDs, and infer if novel LTA4H modulators show therapeutic potential. Understand how LTA4H is perturbed by genetic influences and environmental insults resulting persistent inflammation and pathological remodelling. Evaluate the LTA4H axis in CLD patients to ascertain why it is aberrant and how it correlates with pathological and clinical endpoints. These studies examine biological pathways that define the balance between health and disease, and will facilitate the endotyping of patients for therapeutic intervention.
Epigenetic memory needs to be globally reprogrammed in the early mammalian embryo for cells to attain broad developmental potency including naïve pluripotency. Exit from pluripotency in turn requires rapid establishment of epigenetic memory in the form of epigenetic priming. This involves both ‘activating priming’ whereby lineage specific genes are protected from repressive marking to safeguard their future transcriptional activation during tissue and organ development, and ‘repressive priming’ by which genes of a different lineage are suppressed. These large-scale dynamics raise fundamental questions about the impact of epigenetic memory on pluripotency and differentiation, which we address in this research programme. First, we will attempt to disable global demethylation in vitro and in vivo by manipulating the epigenetic coordinator UHRF1 at the transcriptional and posttranscriptional levels. Second, using genetic and epigenetic manipulation we will determine the mechanisms and downstream consequences on lineage and tissue development of ‘activating priming’ factors we have recently identified. Third, we will investigate the role and targets of ‘repressive priming’ and epigenetic heterogeneity in cell fate decisions and lineage development. New insights gained into memory erasure and epigenetic determinants of cell fate will illuminate and guide strategies for using ES, iPS, and multipotent stem cells in regenerative medicine.
Following the 2015 oral cholera vaccine (OCV) mass campaign of 160,000 people in Nsanje District, Malawi, the International Vaccine Institute (IVI) was funded to setup diarrheal disease surveillance in Nsanje and adjacent Chikwawa districts. Surveillance is ongoing at 22 and 18 health care facilitiesin Nsanje and Chikwawa, respectively. Research activities include to 1) analyse the vaccine effectiveness (VE) in Nsanje, through a 1:4 case-control study and 2) conduct a cost-of-illness study to help estimate OCV cost-effectiveness. The IVI is working in parallel in neighboring Mozambique. Diarrheal disease surveillance is ongoing in the Cuamba study area and an OCV has been conducted in 08/2018. The Mozambique study area borders the Malawian Nsanje/Chikwawa districts. We propose to continue the research in Malawi through extending the surveillance work and the case-control study, to ensure the assessment of long-term VE and cost-effectiveness. Further, the extent of herd protection through OCV needs to be assessed; the Chikwawa setting, after the 2018 OCV campaign constitutes the perfect scenario. The GFTCC is currently preparing a research agenda for "End cholera by 2030" roadmap and the Malawi/Mozambique scenario with surveillance ongoing in both countries, provides an unique opportunity to answer research questions identified through the GFTCC.
An empirical ethics study of the introduction of AI techniques to the assessment of cognitive decline 26 Jul 2018
The proposed research will examine how ethical concerns arise in the development of AI tools for screening and diagnosis and how and by whom they are addressed, focusing on the example of dementia. Further, it will examine the range of personal data on which such applications draw, and consider whether and how this affects what constitutes health data. The study proposes that applications of AI to dementia screening and diagnosis represent a particularly important case for investigation, given considerations about the nature of informed consent, and sensitivities associated with diagnosis, its communication and implications for individuals and families. The study will involve qualitative and ethnographic research with experts and members of the public to Identify applications of AI to dementia research, and outline central social and ethical concerns; Examine how ethical considerations are being negotiated in the development of AI tools ; Explore expert, public and patient perceptions of what constitutes reasonable use of different forms of personal data; Conduct a workshop to expand discussion and support future project development The project will result in outputs for clinical, policy and social science audiences, and form the basis for applications for funding to develop this work further.
STRONGER-SAFE: Understanding transmission and optimising interventions for an enhanced S.A.F.E. strategy for trachoma elimination 05 Apr 2017
Trachoma is the leading infectious cause of blindness worldwide. It is intrinsically linked to poverty in both cause and effect. Preventing blindness from trachoma has broad and profound impact on health and well-being. It is caused by repeated infection with Chlamydia trachomatis (Ct). The WHO-endorsed SAFE-Strategy aims to control infection through annual, single-dose, community-wide azithromycin treatment coupled with Water/Sanitation/Hygiene (WASH) and fly-control measures to suppress transmission. However, particularly in hyperendemic regions, the current approach is not having the anticipated impact. There are two critical issues. Firstly, current azithromycin schedules appear insufficient. Secondly, transmission routes are poorly defined and the very limited evidence-base makes it hard to focus WASH interventions and guide programmatic decisions. We propose the following: 1) Conduct intensive observation of human behaviour and hygiene practice, and fly behaviour, combined with Ct infection mapping, to identify major routes of transmission. 2) Develop and test contextually appropriate, practical, targeted WASH and fly-control approaches to interrupt Ct transmission. 3) Our modelling work indicates double-dose azithromycin two weeks apart is much more effective in controlling Ct. In a cluster-randomised trials we will test whether intensified double-dose treatment coupled with targeted transmission-interrupting strategies can control trachoma more effectively.
Health and economic benefits of water-sensitive revitalisation in informal urban settlements 06 Oct 2016
Urbanisation is a major demographic trend globally. Informal settlements account for much urban growth, exacerbating the inextricably linked challenges of sanitation, water provision, and public health. The conventional ‘big pipes’ solution to these challenges has changed little in 150 years, comes at major financial, environmental, and social costs, and frequently overlooks informal settlements. We have pioneered an alternative, water-sensitive approach that integrates sustainable design with the management of the water-cycle, benefiting human health and urban ecosystems. This decentralised, climate-change sensitive approach provides financial flexibility for multistage developments and adaptability to future technologies. It promises a solution to the water services challenges of informal settlements, yet has only been demonstrated in developed world settings. We will examine whether the water-sensitive approach can be applied to revitalise developing-world informal settlements to improve environmental and public health outcomes. Our evidence-based assessment of its efficacy across 24 settlements, poorly served by water infrastructure in Makassar and Suva, will deliver the first public health and environmental data on the benefits and risks of water-sensitive approaches. Our scientific, economic and implementation findings will provide the basis for profound changes to infrastructure policies, investments, loan strategies, and their sustainability across the Asia-Pacific and the developing world.
Mammalian embryogenesis entails close partnership between embryonic and extra-embryonic tissues to regulate changes in embryo architecture and developmental potency. We aim for an integrated view of how these events progress hand in hand during key stages of mouse and human embryogenesis. The first architectural changes of the embryo are polarisation and compaction that trigger the separation of embryonic and extra-embryonic lineages. Yet their own trigger remains unknown. We will dissect potential triggering pathways and through genetic manipulations determine their importance for cell fate. Embryo remodelling at implantation is intimately associated with pluripotent-state transitions. We will harness our novel techniques for embryo culture throughout implantation to uncover mechanisms behind these events in relation to signalling partnerships between embryonic and extra-embryonic tissues. By arranging partnership between embryonic and extra-embryonic stem cells in 3D-culture we have recapitulated embryo-like morphogenesis and spatio-temporal gene-expression. We will characterise tissue interactions in such stem cell-derived embryos to understand principles of self-organisation. Our work established an unprecedented opportunity to study human early post-implantation embryogenesis in-vitro. We will build the first morphological and transcriptional atlas of human development beyond implantation. This will bring understanding of normal development and shed light upon why many pregnancies fail at early stages.
Intestinal infections affect billions of people worldwide, resulting in nearly 1.4 million deaths each year. The commensal microbiota can prevent pathogenic infection, as demonstrated by increased susceptibility to infection upon antibiotic use; however, the precise mechanisms of microbiota-mediated protection are not well-characterized. I have recently discovered that colonization of mice with commensal Enterococcus faecium leads to improved intestinal barrier function and decreased Salmonella and Clostridium difficile pathogenesis. I went on to uncover a mechanism by which a unique enzyme, SagA, from these bacteria activates intestinal epithelial cells (IECs) to increase anti-microbial peptide (AMP) expression and mucin distribution. These studies revealed several host and microbiota factors involved in pathogen tolerance. My proposed independent research will identify the mechanisms by which commensal bacteria modulate IECs and intestinal immunity. Utilizing advance microscopy, proteomics and sequencing approaches, I will characterize the effects of E. faecium, SagA and other microbiota metabolites on IEC gene expression and function and subsequent pathogen resistance. Using proteomics-based bioorthogonal reporters and intersectional genetics, I will then dissect how microbial modulation of IECs affects the differentiation and function of intraepithelial lymphocytes. Elucidating the IEC programs triggered by commensal bacteria will enable better strategies to prevent and treat intestinal infections.
Exploring the genomes of rare childhood tumours: genetic and epigenetic driver mechanisms. 19 Nov 2015
As the first wave of cancer genome sequencing efforts conclude, studying rare tumours has emerged as a fruitful endeavour. Rare cancers have provided remarkable insights into tumour biology, with potential to be translated into patient care. Scarcity of fresh frozen tumour material, however, has precluded the study of many types of rare tumours. As massively parallel sequencing of fixed formalin paraffin embedded (FFPE) tissue is now technically feasible, sequencing rare tumours stored in p athology archives has become a tractable endeavour. I therefore propose to study rare solid childhood tumours. I intend to describe the landscape of cancer genes in 20 different tumour types (n = 200 tumours). In addition, I will define the methylome of each tumour to study whether it is a clinically useful diagnostic adjunct. A further question I propose will investigate the role of epigenetic mechanism to tumour development. In many cancers, including the bone sarcomas I studied previously, a cancer-causing (driver) variant remained elusive in some patients. A pertinent question is whether epigenetic mechanisms explain these tumours, which I will address in 25 tumours through integrative analyses of DNA, RNA, and DNA methylation sequences.
Deep evolutionary history of bacterial pathogens 05 Jul 2016
How old are bacterial pathogens, and what evolutionary steps have they undergone? Comparative genomics can accurately resolve recent demography and genealogy of bacterial pathogens. Some historical pathogenic lineages have also been reconstructed by taking advantage of ancient genomes (aDNA), including the causes of plague, cholera, tuberculosis and leprosy. Although ground-breaking, these lineages were relatively easy to analyse using conventional tools due to limited genetic diversity and little recombination, and prior studies on existing genomic diversity. Generating a historical framework for most bacterial pathogens that currently threaten human health, and our food supply, is much more challenging because historical records do not provide unambiguous bacterial identification. Furthermore, the long-term population structure and genealogies of most bacteria are not well defined due to high levels of genetic diversity and frequent recombination, including Salmonella enterica. We will reconstruct the long-term evolutionary history of bacterial pathogens using both metagenomic data from ancient samples and population genetic data from present-day bacteria. We will use the latest developments in aDNA sequencing, develop new bioinformatic approaches for metagenomic analyses, and create a big-data overview of modern genetic diversity. This strategy will be implemented for S. enterica, and then applied to other pathogens.
The evolution of influenza virus: studies of within host and between host evolution to improve pandemic risk assessment and vaccine updates. 08 Dec 2015
The evolution of Influenza A viruses poses substantial public health challenges through pandemics and the continual evolution of seasonal strains. Transmissibility is a key phenotype of influenza A virus evolution and, despite a number of methodological shortcomings, is measured most frequently by ferret transmission experiments. We will develop novel laboratory, mathematical, and bioinformatic methods to accurately quantify the transmissibility of influenza viruses. We will compare non-human H7N9 viruses, that currently circulate in poultry and occasionally zoonose to humans, to the successfully emergent 1968 H3N2 pandemic virus. We will infer the avian precursor to the 1968 pandemic virus and measure its transmissibility and that of likely key intermediates by synthesizing hemagglutinin (HA) variants. We will develop novel laboratory and bioinformatic approaches to measure within-host evolution and thus quantify within- and between-host evolutionary trajectories. We will use the same techniques to compare the seasonal evolution of H3N2 HA during the period 2007 to 2009 with its pandemic emergence. Our results will: increase fundamental understanding of the key phenotypes of the HA gene, improve our ability to risk assess non-human strains, and provide a probabilistic framework with which to predict antigenic drift.
Characterization of novel E3 ubiquitin ligases that are enriched in LGR5-positive intestinal stem cells and niche. 03 Oct 2015
In the intestine, LGR5-positive (LGR5+) crypt base columnar cells comprise a well-defined adult stem cell population. FACS isolation of LGR5-positive intestinal stem cells have facilitated the expression profiling of LGR5+ stem cells, which established stem cell-specific genes of the adult intestine. Amongst are two homologous E3 ubiquitin ligases, RNF43 and ZNRF3, the inactivation of which resulted in unrestricted expansion of intestinal stem cells and formation of adenomas due to hyper-activat ion of Wnt signalling. This has started uncovering the importance of E3 ligases in regulating intestinal stem cells. Besides RNF43 and ZNRF3, additional uncharacterized E3 ubiquitin ligases are enriched in intestinal stem cells. By using cell-surface marker CD24 to sort and profile Paneth cells, novel additional E3 ubiquitin ligases were also detected in these niche cells. These novel E3 ubiquitin ligases are the focus of this research plan, since it is anticipated that they play an important ro le in stem cells, niche cells and their interaction. The plan includes: 1) Functional screening of candidate E3s using primary 3D intestinal organoid culture; 2) Identifying target proteins of candidate E3s using surface proteome analysis and IP-MS; and 3) Validating the role of candidate E3s using mouse genetics in vivo.
Generation and validation of isogenic TP53 knock-out AML cell lines for use in genome-wide drop-out screens 01 Apr 2016
Acute myeloid leukaemia (AML) is an aggressive cancer with a poor prognosis, for which mainstream treatments have not changed significantly for decades. To identify new therapeutic targets in AML, Dr Vassiliou's group recently performed CRISPR-Cas9 dropout screens and identified 492 AML-specific cell-essential genes, including several established anti-leukaemic drug targets and many novel therapeutic candidates. Going forward they will apply this technology to AML subtypes defined by particular somatic mutations. One subtype of AML is defined by TP53 gene mutations and is associated with an abysmal prognosis, with For this, I will design and test different gRNAs for their effectiveness in knocking-out TP53. Cas9-expressing MOLM13 and MV4-11 cell lines will be transfected (separately) with lentiviruses carrying TP53-targeting or control gRNAs. Pooled cells will then be single-cell-sorted and clones assessed for TP53 knock-out efficiency using qRT-qPCR and western blotting. The best clones will then be used for downstream genome-wide screens.
Mechanistic role of CUX1 in haematopoiesis and leukaemogenesis and identification of therapeutic vulnerabilities in CUX1-deficient malignancies. 13 Nov 2014
Complete or partial monoallelic losses of chromosome 7 [-7/del(7q)] are recurrent lesions observed in myelodysplasia (MDS) and acute myeloid leukaemia (AML), suggesting that chromosome 7q harbours tumour suppressors that promote disease development. Although these gene targets have been elusive, we recently identified inactivating mutations in the chromosome 7q transcription factor gene, CUX1, in MDS and AML cases, thereby implicating CUX1 as a key target gene lost in -7/del(7q) MDS and AML. In support, CUX1 mutations were found to confer adverse survival similar to the poor prognosis of -7/del(7q) MDS and AML cases. This proposal firstly aims to elucidate the function of CUX1 in haematopoiesis and leukaemogenesis in vivo by using a novel conditional Cux1 knockout mouse model we have generated. Secondly, by using genome-editing and transposon-mediated expression systems to generate epitope-tagged cell lines, this proposal aims to identify CUX1 target genes and interacting proteins that are critical mediators of CUX1 function. Finally, CUX1-deficient cells will be subjected to large-scale drug-sensitivity and genome-wide genetic synthetic lethality screens to identify drugs and genetic pathways that specifically target CUX1-deficient tumours. These complementary approaches will enhance our understanding of the role of CUX1 in cancer and identify potential new treatments for these poor-prognosis disorders.