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Results

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.

Amount: £3,878,823
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

Plasmodium falciparum extracellular vesicles in malaria pathogenesis and immunity 21 Nov 2017

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.

Amount: £10,695
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

MAXIMIZING THE KNOWLEDGE GAINED FROM CALIFORNIA SENATE BILL 27 30 Sep 2018

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

Amount: £155,000
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

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.

Amount: £17,000
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

Reprogramming the epigenome: erasing memory and creating diversity 10 Apr 2018

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.

Amount: £241,260
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

Cholera vaccine effectiveness in Nsanje and Chikwawa, Malawi 30 Sep 2018

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.

Amount: £3,918
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

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.

Amount: £88,369
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

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.

Amount: £100,000
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

Programme Costs 2017/18 30 Sep 2017

No data entered.

Amount: £821,760
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

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.

Amount: £364,741
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

Embryo architecture, potency and tissue interactions during mouse and human development 11 Jul 2017

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.

Amount: £64,017
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

Intestinal epithelial cells: at the interface of the microbiota and mucosal immunity 22 Feb 2017

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.

Amount: £13,200
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

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.

Amount: £2,000
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

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.

Amount: £704,856
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

Socialising the Genome 31 Mar 2015

Not available

Amount: £40,000
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

New genetic, imaging and microfluidics technologies for single cell genomics 11 Jun 2015

Two major limitations of single cell genomics is (i) the loss of information about the original location within the sample of the sequenced cell and (ii) low throughput at high cost with only hundreds of cells analysed per day. Miniaturising single cell analysis to pico-litre volumes will critically facilitate higher throughput (10^4 - 10^6cells) at lower costs and sidesteps restrictions in handling. Combined with genetic technologies to record lineage history and spatially localise cells this w ill allow questions to be address at single cell resolution that are essential to understand cell diversification following tissue-contextual interactions and the impact it has on gene transcription. 1) We will develop microfluidics based devices to increase sequencing throughput by increasing the number of cells processed at a low cost, and at the same time enabling the complex handling and manipulation of small cell numbers with minimal loss. 2) We will develop genetic technology to: i) record within the genome the lineage history of each cell, for readout at any stage of interest and ii) to provide a unique fluorescent signature to cells to enable us to provide spatial and temporal context to their transcriptional profiles.

Amount: £194,641
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

Anopheles-Plasmodium interactions: mosquito immune response and parasite immune evasion strategies. 07 Jul 2015

Malaria parasites entering the mosquito midgut are eliminated by robust mosquito immune reactions, and only few remain to continue the transmission cycle. My principal research questions are: how mosquito immune reactions are activated on parasites and how some parasites evade these reactions. By answering these questions, I aim to gain fundamental understanding of the Anopheles-Plasmodium interactions leading to disease transmission. This knowledge could aid future translational research for th e development of malaria transmission-blocking interventions, contributing to the global effort for malaria elimination.

Amount: £20,930
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

Towards understanding and treatment of MeCP2-related disorders 07 Jul 2015

Mutations in the MECP2 gene are responsible for two autism spectrum disorders (ASDs): Rett Syndrome[1] (loss of function) and MECP2 Duplication Syndrome[2] (over-expression). Involvement in monogenic ASDs has prompted intensive study of MeCP2 protein, but its functional role remains uncertain. As either too little or too much MeCP2 protein leads to profound intellectual disability, understanding how this protein contributes to brain function is a priority. A prominent view is that MeCP2 is a multifunctional hub protein implicated in diverse pathways. A simpler alternative, suggested by the restricted distribution of Rett syndrome (RTT)-causing mutations, is that MeCP2 is primarily a transcriptional repressor that binds methylated DNA[3] and recruits a co-repressor complex[4]. This research programme is designed to distinguish these hypotheses through a series of experiments that challenge each. It will use the resulting basic knowledge to develop small molecules that may be used therapeutically. The following component questions will be addressed: 1. What are the determinants of MeCP2 binding to chromatin in vivo? Although the protein has been shown to bind methylated DNA, additional determinants have been proposed. 2. Is the ability to bind both DNA and NCoR/SMRT sufficient for MeCP2 function? Our previous work suggests that these two discrete interaction domains are of over-riding functional importance for MeCP2 function. We will create mutations in mice that test this hypothesis. 3. How and why is gene expression affected by varying levels of MeCP2? The reported effects of MeCP2-deficiency on brain gene expression are inconsistent, rangingfrom no clear effects, to mostly activation or mostly repression[5]. We will use homogeneouspopulations of cultured human neurons to resolve this question. 4. Can we identify therapeutic options for treatment of Rett syndrome and MECP2 Duplication Syndrome? Our earlier work established proof-of-principle that Rett syndrome is a reversible condition and therefore in principle curable[6]. So far, however, there are no effective treatments for any MeCP2-related condition. Based on our molecular insights into thebiochemical consequences of specific Rett mutations, we will collaboratively seek small molecules that stabilise or disrupt the structure/interactions of wildtype and mutant MeCP2.

Amount: £44,212
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

The host response to Staphylococcus aureus infection. 01 Apr 2015

How is the host response to Staphylococcus aureus orchestrated? How does S. aureus trigger release of nerve growth factor (NGF) from host cells? How does NGF trigger host effector immunity to S. aureus?

Amount: £121,000
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute

A strategic vision to drive the control of enteric fever through vaccination 28 Oct 2014

The overall aim of this strategic award is to provide the science to underpin the implementation of new vaccines for the control of enteric fever, uniquely, in different epidemiological settings in Africa and Asia. The vision described here will: Provide missing data on disease burden, antibiotic resistance and transmission needed to support and implement conjugate vaccines for enteric fever, using epidemiological data collection and application of knowledge from (para)typhoid human challenge models. Establish the host factors that determine susceptibility to enteric fever to inform vaccine implementation strategies. Provide a comprehensive approach to diagnostics to allow a more accurate assessment of disease burden, vaccine impact and to inform epidemiological models. Investigate the mechanisms of natural and vaccine-induced protection in human challenge models (UK), test in human-to-mouse studies, and validate in field settings (Nepal, Bangladesh and Malawi) and to develop correlates of protection for use in driving vaccine implementation. Model disease dynamics and the balance between direct and indirect vaccine impact in different settings using the biological and epidemiological data emerging from the programme Strengthen research capacity in enteric fever endemic regions of the world and provide the data for vaccine implementation advocacy

Amount: £431,440
Funder: The Wellcome Trust
Recipient: Wellcome Trust Sanger Institute