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Funders:
The Wellcome Trust

Results

Cellular Dynamics and Regulatory Networks Controlling Endometrial Remodelling during the Window of Implantation 17 Jul 2018

The endometrium undergoes iterative cycles of menstrual shedding, regeneration, rapid growth, and differentiation in response to ovarian hormones. During the mid-luteal phase, the endometrium becomes transiently receptive to implantation, heralding the start of a process of intense tissue remodelling, characterized by secretory transformation of glandular epithelium, angiogenesis, differentiation of stromal cells into secretory decidual cells, and activation of specialized immune cells. Several reproductive disorders, including recurrent pregnancy loss, are linked to defects in tissue remodelling at implantation. However, the cellular complexity and dynamic nature of the endometrium have so far precluded precise characterization of the underlying pathological mechanisms and drivers. We will employ high-throughput single-nucleus sequencing to map the dynamic changes in gene expression and chromatin accessibility (cis-regulatory regions) in all endometrial cell types across the luteal phase in defined patient groups. The data will be back-mapped to a future successful pregnancy or miscarriage. This analysis will yield unparalleled insight into the sequence of endometrial events (i.e. changes in cell populations, cellular states, gene expression and transcriptional regulation) leading to a successful or failed pregnancy. Further, 3D organoid cultures, consisting of glands and stroma, will be used to investigate putative drivers of endometrial dysfunction and to evaluate new treatment targets.

Amount: £1,281,629
Funder: The Wellcome Trust
Recipient: University of Warwick

Modelling the feasibility of achieving 70% target vaccination coverages for rabies elimination in free-ranging dog populations in India 30 Sep 2018

Rabies kills over 20000 people every year, predominantly in India, where it is spread by the bite of infected free-ranging dogs. The WHO recommends that canine rabies can be controlled and eventually eliminated by consistently vaccinating at least 70% of the dog population in a region. However, there is little information on dog populations in India and what proportion are truly free-ranging. This influences the feasibility of conducting mass rabies vaccination campaigns and achieving the target of 70% vaccination coverage. This study will look at dog populations at selected sites in India to estimate population size and structure such as proportion of males and females, young and adult animals and the occurrence of rabies. The study will assess ownership patterns to determine what proportion of dogs are truly free-ranging. Rabies vaccination campaigns will be conducted at these study sites to determine the feasibility of achieving 70% vaccination coverage. The data on dog population and vaccination coverage will be used to mathematically model the effects of this kind of intervention, and determine the best way to implement it at these sites. The results of this study will directly inform rabies prevention and control strategies at the regional levels and in India.

Amount: £0
Funder: The Wellcome Trust
Recipient: Imperial College London

Codes within codes: How genetic variation influences disease through regional changes in methylation 30 Sep 2018

Inter-individual DNA methylation variation has been linked to a variety of traits and behaviours, such as BMI, smoking, and cancer, through epigenome-wide association studies (EWAS). However, these studies often do not incorporate gene expression and examine changes at single CpG sites. Often a regional change in methylation is required to actuate a downstream effect. I aim to produce new methods, to collapse DNA methylation data using multiple ‘omics datasets and histone marks as a guide. I will explore how collapsing DNA methylation data can be informed by gene expression, histone modifications and further regulatory information. I will use current methods to collapse DNA methylation data and develop new methods using large scale reference datasets, such as the ENCODE, Blueprint and Roadmap epigenomics projects. I will then apply these methods genome-wide and within larger datasets. I will then explore the association between regional methylation and a range of traits and explore potentially causal associations using Mendelian randomisation. These studies will give insights into the interplay between DNA methylation and other molecular traits, lay the foundations for future work collapsing DNA methylation in a biologically meaningful context, and could guide future EWAS.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Bristol

Gene Expression Heterogeneity in the Maintenance and Coordinated Differentiation of Neuromesodermal Progenitors in vivo 08 Aug 2018

Modern imaging data in biology is essentially multi-scalar in that raw image data undergoes a series of processing steps until it is at a manageable size to perform quantification and analysis. While this processing pipeline might be beneficial to one set of scientific questions, it may be inappropriate to others. Computational biologists may be interested in improving the pipeline itself, while other researchers may be interested in accessing the already processed data. Thus, a central road-block in the open sharing of large-scale imaging data is the fact that there is no one size fits all solution. This project aims to generate a web-based database that stores experimental and data descriptors together with links to the raw and processed data files. This will greatly enhance our ability to upload this data to repositories that are based placed to share the datasets in question, from the raw unprocessed data files down to feature extracted and processed data. Upon submission, the website will link to the deposited data and thereby act as an integrated platform for other researchers to access and explore the data that is available to them. Thus, researchers will be able to access our data at all levels. In built in the project is a second evaluation phase, whereby will we reach out to collaborating laboratories to assess the effectiveness of our open research platform. These will include computational biologists interested in accessing raw data files and processing pipelines, and other developmental biologists who will interact with processed datasets.

Amount: £48,563
Funder: The Wellcome Trust
Recipient: University of Cambridge

Design and evaluation of a modified vaccinia Ankara vector therapeutic vaccine for hepatitis B immunotherapy 30 Sep 2018

Hepatitis B virus (HBV) is a serious global health problem, with approximately 240 million people chronically infected. Long-term infection can lead liver failure, cancer and death. Current therapy controls but does not eradicate the infection. T cells are a type of immune cell necessary to fight HBV. During chronic hepatitis B these cells become less active. Checkpoint inhibitors are a form of immunotherapy that enables T cells to function again. In a study of woodchucks infected with a similar virus to HBV, treatment with vaccine and checkpoint inhibitor lead to better control of the virus. This project aims to use this combination of vaccine and checkpoint inhibitor, to treat patients with chronic HBV. A vaccine using a virus to carry the HBV proteins has been developed and shown to generate good immune responses in mice. We plan to develop a second vaccine to boost this response and test the vaccines together with checkpoint inhibitors in mice infected with the HBV virus. This will allow us to assess how effective this is at eradicating HBV. If the results from this study are promising, this could pave the way for clinical trials in humans with chronic HBV.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Investigating the immunomodulatory effects of extracellular vesicles derived from mesechymal stromal cells 31 May 2018

My proposed hosting group has shown that mesenchymal stromal cells (MSCs) ameliorate kidney injury in mice through paracrine effects.Their preliminary work suggests that the MSCs are entrapped in the lung following intravenous administration and mostly die within 24 hours. Host macrophages are attracted to the MSCs and are stimulated to upregulate the anti-inflammatory cytokine, IL10, which suggests they are being polarised towards an anti-inflammatory phenotype (i.e. to M2 macrophages). The main aim of my project is to explore whether extracellular vesicles (EVs) released by the MSCs are responsible for mediating their immunomodulatory effects. Specifically, I will investigate whether the EVs polarise macrophages towards an M2 phenotype. The first objective will be to use a co-culture model comprising human bone marrow-derived mesenchymal stromal cells (BM-MSCs), which have already been shown to polarise macrophages to an M2 phenotype. The BM-MSCs will be co-cultured with human macrophages using a transwell culture system, and the ability of the BM-MSCs to polarise the macrophages to M2 will be investigated using flow cytometry and quantitative reverse transcriptase PCR (qRT-PCR) to determine the levels of M1 and M2-specific markers. The effect of BM-MSC-derived EVs on macrophage polarisation will then be tested.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Liverpool

Functional characterization of a novel KMT2D-related developmental disorder 31 May 2018

The proposed research uses standard molecular biology, protein purification and biophysical structural analysis methods in a focused series of experiments that comprise a complete 6-week project. This builds on existing molecular genetics studies that have identified novel missense mutations in KMT2D (also known as MLL2) as the cause of a unique phenotype (renal tubular dysgenesis, choanal atresia and athelia). Previous studies have identified KMT2D mutations as a major cause of Kabuki syndrome, a comparatively common autosomal dominant congenital mental retardation syndrome. The missense mutations occur in a central region of the KMT2D protein (2841-3876) that does not have variants associated with Kabuki syndrome. This central region contains a series of coiled-coil domains that are likely to mediate protein-protein interactions. However, the effect of the missense mutations on KMT2D structure and interactions is completely unknown. This project will determine the structure-function relationships between KMT2D and a unique phenotype that are likely to be caused by altered protein-protein interactions, as well as describing the broader genotype-phenotype correlations in this important gene. The approach described in the proposal is the only tractable way to understand possible structure-function relationships, given the large size of the gene and encoded protein.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Leeds

Developmental gene expression profiling for novel mediators of epithelial fusion in the chick embryo 31 May 2018

Title: Developmental gene expression profiling for novel mediators of epithelial fusion in the chick embryo. Hypothesis: Tissue fusion processes in vertebrates are essential for normal embryonic development. Novel factors recently identified in our lab using transcriptome profiling during epithelial fusion within the embryonic chick eye may have roles in fusion in additional embryonic contexts. We will perform whole mount in situ hybridization for the genes NTN1, FLRT3, CYP1B1 and RGMB using chicken embryos at key fusion stages in the developing neural tube, body wall and heart. These analyses will inform us whether the protein products of these genes are required for fusion in these tissues. Uniquely in the chicken embryo, the palatal shelves do not fuse. Therefore, identification of continual gene expression in the developing non-fusing palate will also help to identify which of these factors may act to prevent fusion. Data will be collected and analysed using brightfield microscopy and optical projection tomography (OPT). Key goals: (i) Establish spatial gene expression profiles for four genes between chick embryonic stages HH16-26; (ii) determine those genes with conserved roles in fusion for multiple tissues; (iii) categorize genes into likelihood of promotion or inhibition of tissue fusion.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Edinburgh

Antibacterial Potential of RNA G-quadraplexes 31 May 2018

RNA G-quadruplexes (RG4s) are stable RNA molecules which have a unique, four-stranded structure that contain two or more layers of G-quartets. E. coli, along with other bacteria types have undergone an evolutionary depletion of RG4-forming sequences. This may likely be a result from the ability of these quadruplexes to impair translation and growth in these bacteria. The canonical structure of RG4s is as follows: (G)3-(N)1-7-(G)3-(N)1-7-(G)3-(N)1-7-(G)3-(N)1-7. This project will explore the antibacterial potential of two novel RG4s (G3A2 and G3U) against three bacterial isolates: E.coli, MSSA, and MRSA. Microtitre assays will be performed to determine the bacteriostatic or bactericidal effects of these RG4s. A control RNA that does not form a G-quadruplex will be used as a control. Minimal inhibitory concentrations (MICs) of these RG4s will be determined and they will be compared to that of currently used antibiotics (i.e. 3rd generation cephalosporins, flucoxacillin and daptamycin, respectively). The ability of heat- and salt-shock to enhance the natural competence of the RNA G-quadruplexes will also be evaluated. Key goals: This project will give rise to new information on the antibacterial potential of RNA G-quadruplexes and it will also bring forward new challenges directed towards their pharmaceutical application and future development.

The role of interferon response genes in an experimental model of Alzheimer's Disease 31 May 2018

Emerging evidence suggest that systemic infection can accelerate the onset and/or progression of cognitive decline in Alzheimer’s disease, but the underlying biological mechanism remain unknown. Exposure of AD mouse models to a real systemic infection results in exaggerated neuroinflammation and AD-like pathology and preliminary microarray analysis suggest this may be due to increased levels of type I or II interferon and/or it’s down-stream signalling pathways. Interferons are produced in response to viral and bacterial infections and well known to be associated with mood changes and depression. In this project we will test if these pro-inflammatory cytokines also play a role in progressing AD-like pathology. Brain tissue from AD mice exposed to a systemic bacterial infection has already been collected, with a control group treated with saline. The expression levels of interferons and their signalling pathways will be explored in this archived tissue and in primary neuronal cultures expressing human Tau. The in vitro cultures will allow us to test if exposure to interferon promotes spreading of tau pathology and if inhibition of the signalling pathways prevents progression of AD-like pathology. This could later be applied to in vivo AD disease models, taking into consideration behavioural changes.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Southampton

Characterisation of PI3K signalling in response to Streptococcus pneumoniae infection using zebrafish larval model 31 May 2018

Immunomodulation is a novel approach to treating infections that could be used to limit the use of antimicrobials which have become less effective due to antibiotic resistance. Regulating the innate immune response via targeting specific immune signalling may help to boost bacterial clearance without causing excessive tissue damage. One of the pathways involved in innate immune regulation is phosphatidylinositol 3-kinase (PI3K) signalling. Different classes of this kinase have been shown to be involved in phagocytosis, ROS production and antibacterial autophagy, among other processes. Therefore, PI3K is an attractive target for therapeutic immunomodulation. In this study, using zebrafish larval infection model, several different PI3K inhibitors will be tested in a chemical screen to identify the role of specific PI3K isoforms in Streptococcus pneumoniae infection. Our aim is to identify compounds that would affect survival of infected zebrafish and bacterial CFU counts in vivo. The effect of hit compounds on phagocytosis and ROS production in response to infection in vivo will be further tested using fluorescence and confocal microscopy. This project will elucidate the mechanisms that govern signalling in neutrophil and macrophage responses to infection and investigate into a prospective target for immunomodulatory treatments.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Sheffield

The role of the factor H-related proteins in kidney disease 17 Jul 2018

The complement factor H-related (FHR) proteins influence susceptibility to kidney and eye (age-related macular degeneration) disease, and to meningococcal infection. The FHR proteins are related to complement factor H (FH), the major negative regulator of complement C3 activation. Unlike FH the biological roles of the FHR proteins remain unclear. Understanding how FHR proteins damage the kidney is very important because they are associated with both rare (C3 glomerulopathy) and common (IgA nephropathy) kidney diseases that lack effective treatments. My key goals are to determine how FHR proteins mediate renal injury and if modulating FHR activity can reduce complement-mediated kidney injury. My experimental program will utilise novel mouse strains, developed during my current fellowship, to determine if absence of FHR proteins reduces kidney injury in experimental nephritis, including IgA nephropathy. I will characterise the mechanisms through which mutant FHR proteins cause C3 glomerulopathy by detailed phenotyping of the first model of FHR-associated C3 glomerulopathy. I will elucidate the mechanism through which accumulation of glomerular C3 causes kidney injury. My program will help us to understand how to manipulate these proteins therapeutically which I predict will reveal a means of modulating complement that is safe and amenable to long-term therapy.

Amount: £1,917,963
Funder: The Wellcome Trust
Recipient: Imperial College London

Molecular mechanisms of alternative splicing regulation 28 Nov 2017

Alternative pre-mRNA splicing (AS) is a widespread regulatory mechanism enabling individual genes to generate multiple protein isoforms. We have investigated the mechanisms controlling AS events that are regulated during the transition of smooth muscle cells (SMCs) between contractile and proliferative phenotypes. We have shown how the widely-expressed RNA binding proteins (RBPs) PTBP1 and MBNL1 regulate SMC splicing events. Recently, we identified RBPMS as a potential "master" regulator of SMC AS. RBPMS is sufficient to switch AS events to the SMC pattern and its activity is strongly modulated by its own AS and by phosphorylation. Critically, RBPMS is sufficient to switch AS to the SMC pattern in vitro. This offers a unique opportunity to determine the molecular anatomy of regulated splicing complexes. We will carry out detailed mechanistic analyses of RBPMS-regulated splicing using a combination of biochemical, proteomic, single-molecule, and structural approaches including Cryo-EM. We will identify critical regulatory interactions between regulatory RBPs and core splicing factors, and test their importance by genome editing and mRNA-Seq. In a complementary aim, we will investigate how peptide-ligand interactions equip PTBP1 to regulate AS and a range of other post-transcriptional processes, and whether a family of such peptide-mediated interactions extends to related RBPs.

Amount: £1,503,005
Funder: The Wellcome Trust
Recipient: University of Cambridge

Cargo transport by dynein/dynactin 10 Apr 2018

Eukaryotic cells rely on motor proteins for their internal organization and movement. I want to ask how one cytoplasmic dynein, together with its cofactor dynactin, can be responsible for almost all of the minus-end directed microtubule transport in our cells. My group will focus on endosome transport as a model system to understand which adaptor proteins are needed to link dynein to cargos. We will use in vitro reconstitution and cryo-EM to ask how different candidate adaptors interact with dynein/dynactin. We will also use structural approaches to understand how the different adaptors are themselves linked to membrane surfaces. To complement this approach we will purify endosomes and use cross-linking and mass spectrometry to search for any missing components required for dynein binding. We will take advantage of recent advances in cryo-electron tomography (cryoET) to ask how dynein/dynactin complexes and their associated connections are arranged on endosomes, both in vitro and in axons of cultured neurons. These studies will uncover the principles governing dynein/dynactin interactions with cargos and will allow us to ask how the process can be hijacked by pathogens such as herpes or rabies viruses.

Amount: £1,450,105
Funder: The Wellcome Trust
Recipient: Medical Research Council

Investigating the relationship between the cerebellum and cognition in both health and disease 30 Sep 2018

The cerebellum is traditionally ascribed only a role in motor coordination. With it containing more neurones than the rest of the central nervous system combined and with connections with almost every other area of the brain concerned with cognition, this seems exceptionally unlikely. Indeed, studies utilising magnetic resonance imaging (MRI) increasingly show strong cerebellar activity associated with cognitive processes. This is still a greatly understudied area with only a few groups researching this. We, therefore, wish to investigate the role of the cerebellum in cognition using large imaging datasets, our own high-field imaging capabilities at Cardiff and various cerebellar-specific MRI processing tools which have not yet been applied to this question. This will allow us to see how well peoples’ cognitive performance in various domains correlates with cerebellar activity and structural differences. Additionally, recent evidence suggests cerebellar structural differences in schizophrenic patients. We wish, therefore, to also investigate if schizophrenia diagnosis and genetic risk for schizophrenia similarly alters cerebellar structure and, if so, at what time during development, if certain cognitive domains are particularly affected and if cerebellar metabolite levels differ in schizophrenic patients compared to non-schizophrenic controls.

Amount: £0
Funder: The Wellcome Trust
Recipient: Cardiff University

The role of cerebellar circuitry in movement control and real-time motor learning 28 Nov 2017

The cerebellum is known to play a critical role in ongoing sensorimotor behaviour and learning of novel associations, but these processes remain poorly understood. The aim of this proposal is therefore to provide an extensive characterisation of the cellular and circuit mechanisms involved in motor control and learning in the cerebellum. We will probe cerebellar processing in head-fixed behaving animals using whisker movement as a model sensorimotor behaviour. We will measure neuronal activity using a variety of functional imaging and electrophysiological methods, combined where appropriate with opto- and pharmaco-genetic perturbation of specific circuit elements. Throughout the data-gathering process, we will work with theoreticians to generate a comprehensive network model of whisker representation in the cerebellum. Three discrete but interconnected aims will be addressed: 1) What are the organisational principles governing control of whisker movement within the cerebellar cortex? 2) What are the functional characteristics of inputs and outputs to cerebellar cortex during active whisking? 3) What are the mechanisms of real-time motor learning in the cerebellum? Together, we will provide unique quantitative information about the function of cerebellum in voluntary movement, and reveal how learning-related changes influence the neural representation of a well-controlled motor behaviour.

Amount: £1,498,083
Funder: The Wellcome Trust
Recipient: University of Bristol

Serio Seed Grant 06 Sep 2018

Amyotrophic Lateral Sclerosis (ALS) is an incurable fatal disease that affects principally Motor Neurones (MNs). Interestingly, spinal MNs have extremely long axons, which makes them particularly reliant on efficient decentralized protein translation and axonal transport. We have evidence that ALS presents characteristics of distal axonopathies, with defects in axonal transport, protein homeostasis and changes in local axonal translation reported. Moreover, most ALS-mutations often directly affect RNA processing. Against this background, understanding the links between axonal length and RNA compartmentalisation could highlight new potential therapeutic avenues. Induced pluripotent stem cells (iPSCs) have proven extremely useful in studying ALS; however, the question of how axonal length affects RNA compartmentalisation in MNs cannot be systematically addressed with current in vitro paradigms, as they do not provide efficient ways to control axonal length. I will develop a platform to study how axonal length in iPSC MNs influences local mRNA translation and RNA compartmentalisation, combiningimaging and transcriptomic analysis with bioengineered alignment substrates that allow to obtain ordered arrays of very long axons in vitro.With this platform I will conduct a pilot study on axonal compartment -specific transcriptomics in MNs and analyse the effect of ALS-mutations on local translation in long motor axons

Amount: £99,987
Funder: The Wellcome Trust
Recipient: King's College London

Development and maintenance of human thymic B cells in the autoimmune setting 31 May 2018

Type 1 Diabetes (T1D) is increasing in pre-school children, and the treatment the Government NHS system provides is financially unsustainable. The complex pathways concerning how B cells are involved in the development of T1D remain elusive. However, the Green Lab's recent novel findings revealing that the thymus is a principal target of autoimmunity in T1D and that thymic B cells are key in this event have re-evaluated our knowledge of the T1D process. In my research, I aim to aid in the achievement of translating these novel finding from mouse to man. By engrafting Human Pluripotent Stem Cells (HPSCs) into a specific strain of humanised mice (NSG-SGM3) which are devoid of key molecules required to develop a murine immune system (including a thymus), we hope to stimulate de novo formation of functional thymic tissue that resembles that seen in young diabetic children. NSG-SGM3 also have a NOD background, meaning their thymic stromal tissue contain genes which predispose T1D. Comparative studies looking at thymic tissue between NSG-GSM3 and NOD mice will be key in determining whether HPSCs promote thymus neo-genisis in humanised mice, as well as determining if our humanised mouse model recapitulates thymic B cell abnormalities of NOD mice.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of York

Investigating drugs which promote neutrophil apoptosis for the treatment of inflammatory disease 31 May 2018

Chronic Obstructive Pulmonary Disease (COPD) is a progressive and irreversible inflammatory lung condition which affects 10% of the world’s population. The pathogenesis of this disease centres around inappropriate neutrophilic persistence in the lungs due to dysregulation of apoptosis, which results in injury and ongoing cycles of inflammation. Current therapeutic strategies treat the symptoms of the disease but not the underlying cause, and long-term use leads to significant side effects. We are therefore in great need for more effective medications to treat COPD. The Prince group carried out genetic kinase screens and inhibitor assays to search for novel treatments for inflammatory diseases. They identified members of the ErbB family of receptor tyrosine kinases, which play a role in regulating neutrophil cell survival and inflammation in vivo, as targets. Various ErbB inhibitors have already been approved as medicines for the treatment of cancer and could be repurposed for COPD. This project will investigate firstly whether clinically-used ErbB inhibitors have the same apoptosis-driving effect as the research grade inhibitors with which preliminary research was carried out, and secondly whether these drugs impact the immune response to Haemophilius influenzae. This is important because COPD patients are often chronically colonised with microorganisms, including H. influenzae.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Sheffield

Identification of essential Klebsiella pneumoniae genes required for survival within urine and adherence to urinary catheters 30 Sep 2018

Urinary tract infections (UTIs) are considered to be the most common bacterial infection, affecting 150 million people annually worldwide1. UTIs are becoming increasingly difficult to treat due to the widespread emergence of bacterial antibiotic resistance mechanisms. The bacterium Klebsiella pneumoniae is the second most common causative agent of hospital-acquired UTIs and is particularly prevalent within patients fitted with a urinary catheter. To successfully cause UTIs, bacteria must be able to survive and replicate within urine. The genetic factors which regulate urine metabolism by bacterial pathogens are largely unknown. Specific genes encoded by K. pneumoniae are essential for replication in urine and adherence to urinary catheters. Due to technological advancements in genome sequencing, several techniques have been developed to assay the essentiality of every gene within a microorganism. Essential genes represent favourable targets for therapeutic treatments of bacterial infections because the absence of these genes render the bacteria non-viable. Utilising one of these techniques, termed Transposon Directed Insertion Site Sequencing (TraDIS), we aim to identify essential genes encoded by K. pneumoniae for replication within urine and adherence to catheters. The identification of conditionally essential K. pneumoniae genes offers a strategy for elucidating novel antibacterial drug targets for therapeutic treatment.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Birmingham