- Total grants
- Total funders
- Total recipients
- Earliest award date
- 24 Jan 2017
- Latest award date
- 30 Dec 2017
- Total GBP grants
- Total GBP awarded
- Largest GBP award
- Smallest GBP award
- Total Non-GBP grants
Myelinating and non-myelinating Schwann cells are reprogrammed after nerve injury into repair Schwann cells, specialized for maintaining survival of injured neurons and supporting axonal regeneration. This process is regulated by Schwann cell-intrinsic signals, such as the transcription factor c-Jun, however few other candidates have been identified. It is, currently, unknown how Schwann cell reprogramming is initiated, but unidentified extrinsic signals from injured axons are likely candidates. I aim to delineate the spatial and temporal regulation of Schwann cell-intrinsic downstream signals in real-time and define their role in repair Schwann cell function and axonal regeneration. Secondly, I aim to test the hypothesis that axon-derived signals initiate Schwann cell reprogramming during nerve injury. I will use cell culture, in vivo mouse models and a live and dynamic zebrafish larval model of nerve injury. This study will be the first to investigate how axon-intrinsic mechanisms of nervous system injury interplay with glial cell molecular responses to nerve damage, in real-time. Using cutting edge techniques in two species, this project will significantly advance our understanding of Schwann cell-axonal biology and tissue repair. Excitingly, this research may identify new potential therapeutic targets to improve poorly regenerating human nerves and treat patients with neuropathies.
The role of Eros in Innate and Adaptive Immunity 30 Sep 2017
I will investigate the role of a novel protein, Eros, in immunity. I discovered the fundamental importance of this protein by demonstrating that Eros-deficient mice die from Salmonella infection because their phagocytes cannot make reactive oxygen species. This is because Eros is essential for expression of vital components of the phagocyte NADPH oxidase. My work represents the only paper on this protein. I have found that Eros-deficiency has effects that go far beyond the generation of reactive oxygen species. In particular: Eros regulates the expression of other key macrophage proteins including P2X7, a key activator of the NLRP3 inflammasome Eros regulates the expression of numerous cytokines from CD4+ T cells. Eros -/- T cells make 10-fold more IL-4 than control cells In mouse and human systems, I will investigate the molecular mechanisms by which Eros: controls the abundance of a subset of proteins working on the hypothesis that it is a novel component of the protein quality control pathway using structural, biochemical and cell biological techniques. controls T cell cytokine secretion. I will spend time working with John O'Shea, a world leader in this field.
21st Century Families: Parent-child relationships and children's psychological wellbeing 25 Jul 2017
New pathways to parenthood have recently emerged that did not exist, nor had even been imagined, at the turn of the 21st century. Individuals who were previously unknown to each other have begun to meet over the internet with the purpose of having children together; transgender men and women have begun to have children through medically assisted reproduction; single heterosexual men have begun to use surrogacy to become single fathers by choice; and women have begun to use identifiable egg donors to have children. These emerging family structures raise new ethical, social and psychological concerns, particularly regarding the potentially negative consequences for children. The proposed research will provide empirical evidence from a multidisciplinary perspective on the social and psychological consequences for children of growing up in family arrangements involving non-cohabiting co-parents, transgender parents, elective single fathers and identifiable egg donors. In this emotive area of family life on which people often hold strong opinions, our aim is to challenge prejudice and assumption with evidence on the actual consequences – good, bad or neutral – for children. The ultimate goal of the proposed research is to increase understanding of diversity in family life and improve the lives of 21st century children.
Biomechanics of Ciliated Tissues 11 Jul 2017
Many of the paradigmatic events in embryonic development involve geometric or even topological rearrangements of tissues in response to mechanical forces generated within them. While these processes are familiar and much studied from genetic and biochemical perspectives, there is a striking contrast between the great depth of such biological detail and the glaring lack of quantitative mechanical understanding of the forces and responses involved. We propose to close the theory-experiment loop in specific, carefully chosen examples of these problems, to gain a quantitative understanding of the underlying biomechanics. We seek to solve three outstanding problems: (i) the link between cell shape changes and cell sheet morphology as found in gastrulation, neurulation, and related problems in embryogenesis; (ii) the mechanism of generation of cilia orientational polarity in tissues; (iii) the origin of metachronal wave formation in carpets of cilia. The research will combine state-of-the-art light-sheet microscopy, micromanipulation, high-speed imaging and microfluidics with emerging theoretical tools for understanding complex geometrical transformations of tissues and the stochastic nonlinear dynamics of eukaryotic flagella.
During my fellowship, I proved the feasibility of measuring cardiac energetics in volunteers and patients using ultra-high field (7T) MRI scanners. The sensitivity and the separation of signals from different metabolites both improved significantly compared to standard research scanners. I recently secured £340k funding to fit a new phosphorus coil on the Oxford 7T scanner, which I am now testing in volunteers. Theory predicts that this coil will have several complementary technical advantages. These will enable mapping of cardiac energy metabolism across the whole heart, with sufficient spatial resolution to distinguish signals from healthy from diseased tissue. It will also enable quantification of cardiac energy metabolism with high precision to study single subjects rather than groups. I request funding to validate these new whole-heart methods, proving their value in three carefully-targeted groups of patients, via an extension of my fellowship. My goals are (A) to study patients in which the metabolic pattern is known by other means; (B) others where the metabolic pattern will reveal previously-inaccessible aspects of disease mechanism; and (C) to prove I can resolve metabolic changes in single patients. Success in each of these studies will give me the pilot data needed for competitive Senior Fellowship applications.
Using an innovative optogenetic approach within the zebrafish neural tube, I will directly explore how the polarity of individual cells drives the tissue organisation of a whole organ. In combination with 4D live imaging and functional abrogation, I will use light to specifically and reversibly manipulate apicobasal polarity, cleavage furrow formation and PI3K pathway signalling on a subcellular level. I will assess how apicobasal polarity and division are interrelated during morphogenesis of vertebrate epithelial tubes and how this relationship contributes to tissue integrity. Early zebrafish neuroepithelial divisions are highly predictable and coincident with de novo apicobasal polarisation. This provides a tractable model to assess a potential feedback loop between apical protein localisation and cleavage furrow positioning during epithelial establishment. The PI3K pathway is likely key to integrating apicobasal polarity with division. Within established epithelia, PI3K pathway defects are prevalent in cancers. I will manipulate PI3K pathway signalling within individual cells or groups of cells within an otherwise normal zebrafish neural tube. This in vivo method for manipulating cancer-linked signalling will allow me to test whether apicobasal polarity dysregulation is a cause or consequence of tissue disruption, providing clues to the cellular mechanisms of disease initiation.
Fractionating the human frontoparietal cortex: combining meta-analytic and real-time optimization approaches 08 Nov 2017
Disruptions in the same set of frontal and parietal brain regions are seen across a striking range of psychiatric and neurological conditions. This network of regions has been referred to as multiple-demand (MD) system and can be divided into at least two closely coupled subnetworks. However, despite extensive research efforts, the specific functional mechanism each subnetwork supports remains poorly understood using available neuroimaging technology. To overcome these limitations, I have recently developed a novel technique based on real-time neuroimaging and machine learning: Neuroadaptive Bayesian Optimization (NaBO). The key goal of this fellowship is to develop a complementary approach that leverages the strength of large-scale, automated meta-analyses and NaBO to obtain a fine-grained functional mapping between MD subnetworks and the cognitive processes they support. This approach will exploit the wealth of data generated by neuroimaging to date (meta-analysis) for defining a prior model of how cognitive functions relate to MD subnetworks and then refine this model in unprecedented detail (NaBO). The resulting model will be validated using behavioural assessment. Advancing our understanding of these subnetworks in normal brain function is an important first step for developing targeted clinical interventions and informing the design of sensitive diagnostic test batteries.
DNA in our cells is frequently subject to a wide array of molecularly-distinct forms of damage. To cope with this, life has evolved multiple DNA repair and associated processes, collectively termed the DNA-damage response (DDR). While considerable progress has been made in identifying DDR proteins and their regulators, much remains to be learned about how they operate and are controlled. Building on our successful proof-of-concept studies, we will carry out genome-wide and focused genetic screens via state-of-the-art CRISPR-Cas9 approaches and haploid-cell based chemical mutagenesis. Together with ensuing validation and mechanistic studies, the proposed research has the following interconnected goals: To identify novel genetic and functional relationships between DDR genes/proteins, and between these and other cellular components, thereby providing fundamental insights into how mammalian cells respond to DNA damage and defining how such responses are controlled and coordinated. To establish how defects and deregulation of certain DDR processes affect cellular sensitivity and resistance to established and emerging cancer therapies, and to explore the potential clinical relevance of these affects. To expand our knowledge of how DDR processes are affected by protein post-translational modifications, particularly ubiquitylation and phosphorylation.
Investigating How Epithelial-Endothelial Interactions Regulate Epithelial Cell Fate And Morphogenesis in Human Lung Development 31 Jan 2017
The mammalian lung has a complex tree-like epithelial structure tightly intertwined with vascular vessels. Endothelial cells, which line vascular vessels, have been reported to play an instructive role in maintaining tissue-specific stem cells and regulating regeneration. However, how endothelial-epithelial crosstalk functions in lung development, especially in alveolar cell fate specification and lung morphogenesis remain unknown. I propose three specific aims to address these questions. Aim 1: I will investigate specific functions and molecular mechanisms of lung epithelial-endothelial crosstalk. These co-culture experiments will take advantage of a human embryonic lung organoid culture system set up in the Rawlins lab and commercially available, or freshly derived, human endothelial cells. Aim 2: I will test the hypothesis that endothelial cells have heterogeneous behavior during normal lung development. Using lineage tracing in mouse I plan to label endothelial cells to better understand structure of pulmonary vascular vessels and then use monoclonal labeling to investigate clonal heterogeneity. Aim 3: I will test the hypothesis that developing lung endothelial cells are transcriptionally heterogeneous. I will use the single cell RNA-Seq technique to generate transcriptome libraries for human endothelial cells in different regions of lung, investigating their heterogeneity and identifying any specific markers for them.
The rapid turnover of the mammalian intestinal epithelium is fuelled by division of stem cells residing at the bottom of the crypts of Lieberkühn. Our understanding of how stem cells populate the intestine in humans lags behind that of the murine system. In the latter, stem cells populate the crypts by a process of neutral drift. Moreover the number of functional stem cells per crypt and their replacement rate has been quantified in the mouse intestinal epithelium. However, it is not known how extrinsic factors, such as regular drug use, influence these dynamics. In humans, randomised clinical trials have linked low-dose aspirin to a reduction in colorectal cancer incidence and mortality. However, the mechanism is unclear. Since tumours originate from stem cells, I plan to conduct an in vivo study to investigate the impact of aspirin on murine intestinal stem cell dynamics. In the human system, functional stem cell numbers and replacement rates are still not well characterised. Somatic mutations can be used as clonal marks to investigate these parameters in patient samples. I thus aim to find and validate novel human somatic clonal marks and collect data for mathematical modelling of human intestinal stem cell dynamics.
Understanding the Pathogenesis of Inflammatory Bowel Disease via Whole-genome Sequencing 31 Jan 2017
We will use a new whole-genome deep-coverage IBD dataset (15x+ coverage, 20 000 cases, 50 000 controls) to conduct genetic association studies. Several analyses are currently planned. The first study will use the data from >1000 IBD patients, who are part of a deep clinical phenotyping experiment, on their response to treatment with anti-TNF medication. We are hoping to determine specific genetic variants associated with successful treatment, non-response, loss of response, and unfavourable drug reactions. Once more samples are sequenced, we will attempt to discover novel low-frequency, rare, and very rare genetic variants associated with IBD. A recent low-coverage sequencing study has identified a rare missense variant in ADCY7 that doubles the risk of ulcerative colitis. In addition, a burden of very rare, damaging missense variants in genes associated with Crohn's disease was detected. The increased coverage and the size of the dataset may confirm the significance of such variants. Discovery of novel rare variants brings important insights into IBD biology, and improves the overall understanding of the genetic landscape of complex diseases.
Functional proteomic analysis of novel antiviral restriction factors in primary leukocytes 31 Jan 2017
This project aims to identify and characterise novel antiviral restriction factors (ARFs) that play key roles in preventing infection of primary leukocytes. ARFs may function by preventing viral entry or exit at the cell surface, or replication at various intracellular stages. I will focus on the subset of plasma membrane (PM) ARFs, which will be identified by two properties: interferon (IFN) induction and virally-induced downregulation. For this I will employ tandem mass tag-based MS3 mass spectrometry, enabling quantitation of PM proteins in primary leukocytes. Key Goals: 1. Use IFNs and infection with two important human pathogens, human cytomegalovirus and HIV as a functional screen to identify novel cell surface ARFs 2. Investigate how these ARFs inhibit viral infection, and how are they targeted for destruction by viruses. The use of IFN as part of the functional screen will additionally enable exploration of the difference in effects between IFNalpha, beta and lambda at the PM, a subject which is currently surprisingly poorly understood. This will provide important insights into human immunity in its own right. Understanding how viruses interacts with and targets ARFs for destruction will have important implications for therapy.
Human cytomegalovirus (HCMV) is a betaherpesvirus which causes lifelong subclinical infection in healthy adults, but significant mortality and morbidity in neonates and immunocompromised individuals. Like all herpesviruses, it establishes latent infection; HCMV undergoes latency in early myeloid lineage cells. Reactivation occurs when these cells differentiate into macrophages and dendritic cells, and reactivation events in immunocompromised individuals often fail to be controlled by the host immune system causing life-threatening disease. The HCMV genome encodes a G protein coupled receptor, US28, which is expressed during both lytic and latent infection, and is essential for establishing latency. I wish to understand how US28 functions in early myeloid lineage cells to establish latency. I will be using existing proteomic analyses as a basis for investigating a number of host proteins as potential mediators and effectors of latency; a number of host proteins are modulated by US28, some of which may be implicated in immune evasion by the virus. I also aim to understand the role of G proteins in establishing latency, given the varying functions of US28 in lytic and latent infection. I hope to establish a picture of the mechanisms by which US28 manipulates the host cell to facilitate latent infection.
Integral membrane protein cargo are constantly moved in coated tubular/vesicluar carriers between the cell's organelles and its limiting membrane in order to maintain membrane identity and function. That these transport processes are of fundamental importance is reflected by the fact that ~30% of mammalian proteins are either components of the vesicle/tubule transport machinery or are its cargo. Coated vesicular/tubular carrier formation including cargo selection requires the interplay of a network of peripheral membrane proteins and membrane components including phospholipids, small GTPases, docking proteins and the cargo itself. The coat must also prepare and facilitate the carrier for fusion with its target. AP2, AP3, COPI and retromer/VARP based coats along with their accessory/regulatory factors are vital for producing a fully functional endosomal system. We will use a combination of X-ray crystallography, NMR and the fast developing techniques of single particle cryoEM and cryo electron tomography allied with biochemical/biophysical studies to formulate theories concerning the architecture, assembly routes and control/regulation of the formation of these four key tubular/vesicular transport carriers. Specific function abolishing mutations designed on the basis of these studies will allow us to test and further explore our theories in cells using a wide range of in vivo techniques.
Visualizing Citizen Voice in a Moment of 'Big Data'
Dynamic neural remapping across the sleep-wake cycle: A mechanistic link between sensory re-organisation and GABA 05 Sep 2017
Across a single day, we undergo behavioral, physiological and neurochemical changes, from vigilant wakefulness to unconscious sleep. Despite the loss of consciousness, sensory processing continues in sleep. Attempts to assess the degree to which sensory processing differs between wakefulness and sleep have yielded contradicting results with studies showing greater, smaller or comparable responses to the same stimuli when comparing the two states. Hence, it remains unclear precisely how sensory processing is modulated throughout the sleep-wake cycle. Most studies have focused on responses to specific stimuli, neglecting the relationship between different stimuli. We suggest a new comprehensive approach to elucidate how vigilance state dynamically shapes sensory processing, by combining electroencephalography (EEG), functional magnetic resonance imaging (fMRI) and magnetic resonance spectroscopy (MRS) together with state-of-the-art computational tools, measuring neural distances between stimuli to quantify sensory remapping across the sleep-wake cycle. We hypothesize that gamma-Aminobutyric Acid (GABA), an inhibitory neurotransmitter implicated in sleep regulation and correlated with sensory sensitivity, has a central role in sensory remapping. Thus, in this research proposal, the key goals are:(i) to elucidate the temporal and spatial dynamics of sensory remapping throughout the sleep-wake cycle, and (ii) to investigate whether sensory remapping across the sleep-wake cycle is GABA-dependent.
KRAB-ZFPs and the establishment of lineage- and species-specific gene regulatory networks 31 May 2017
KRAB-ZFPs constitute a large yet neglected family of proteins with around 350 members in human and mouse. Collectively, they target transposable elements and until recently were thought to be mostly involved in their transcriptional repression in embryonic stem cells. During my post-doctoral work, I unveiled the binding sites of most (222) human KRAB-ZFPs, but the role played by the majority of them could not be fully explained by current theorems. Instead, we found that many target ancient transposable elements which often contain regulatory platforms; we also obtained correlative evidence that these could affect the expression of nearby genes. We hypothesize that evolutionary conserved KRAB-ZFPs can use their heterochromatin-inducing capabilities to modify accessibility of these transposable element-derived regulatory elements. We propose to functionally demonstrate this potential by using large scale enhancer screens in multiple cell types. Furthermore, we want to follow-up on these findings by genetic manipulations aimed at characterizing the biological processes affected by a few KRAB-ZFPs, including the generation of mouse models. Finally, we want to better understand the evolution dynamics of KRAB-ZFP binding sites and verify if they can lead to lineage- and species-specific rewiring of gene regulatory networks.
Dopaminergic neurons respond to reinforcing stimuli and mediate teaching signals to the memory centers of the brain. Synaptic modulation by dopamine, in turn, affects how the dopaminergic neurons themselves are activated by stimuli, promoting further learning based on prior experience. The genetically and anatomically accessible circuit of the Drosophila mushroom body (MB), a key center for associative learning, provides a tractable system to discover evolutionarily conserved mechanisms underlying function of dopaminergic system. Sparse activity in the 2,000 Kenyon cells of the MB represents the identity of sensory stimuli. Along the parallel axonal fibers of Kenyon cells, we have shown that dopaminergic neurons and MB output neurons form 16 matched compartmental units. These anatomically defined units are also units of associative learning. Our latest results using genetic drivers to precisely control dopamine release in specific compartments by optogenetic stimulation suggest that a single dopaminergic neuron can depress or potentiate synapses, depending on the activity of postsynaptic Kenyon cells. We propose to identify the molecular mechanisms of this bi-directional plasticity. We will also identify the anatomical pathways for feedback of memory-based information onto dopaminergic neurons and probe the functions of this feedback in second-order conditioning.