- 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
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.
I aim to elucidate the function of natural, chemically-modified DNA bases in the genomes of model organisms, using chemical biology and physical science approaches on genomic DNA. Modified bases are of fundamental importance to transcriptional programming and cell identity during and after development. The role of the cytosine derivative 5-formylcytosine and its influence on nucleosome formation, active enhancers, transcription and cell identity will be one area of focus to build mechanistic understanding, following on from hypotheses derived from our prior work. There will also be an investigation of 5-carboxycytosine and 5-hydroxymethyluridine and their potential links with transcription regulation. For other modified bases, such as N6-methyladenine, we will develop and use new chemical mapping/sequencing methods to elucidate their function in mammalian systems. The programme will include a systematic discovery of other natural DNA base modifications, building on and augmenting chemical methodologies I have developed to discover and profile modified bases in RNA. The function of newly identified base modifications will be investigated during the programme. The insights provided from these fundamental studies may have far-reaching consequences for normal biology and disease states. Keywords: chemical biology, nucleic acids, DNA, modified bases, epigenetics, sequencing
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.
A multi-disciplinary approach to understanding and improving hearing by cochlear implant users 28 Nov 2017
Cochlear implants (CIs) restore hearing by electrically stimulating the auditory nerve. This allows many CI users to understand speech well in quiet, but even the most successful have poor pitch perception and struggle in noisy situations. We believe there are two main reasons for these limitations.(i) Although it is possible to elicit different pitches by stimulating different electrodes, the selectivity of this place-of-excitation cue is much worse than in normal hearing (NH). (ii) It is also possible to increase pitch by increasing the pulse rate applied to each electrode, but use of this temporal cue is also much worse than in NH. We will study both of these limitations by performing analogous experiments in cats and humans, using some of the same measures in the two species. This will allow us, for the first time, to link the limitations that occur perceptually to their underlying physiological bases, and to do so even for novel stimulation methods that are not possible with existing clinical CIs. The knowledge gained wiill allow us to propose and test modifications both to implant design and audiological practice.
The pathological loss of myelin sheath from axons predisposes neurons to atrophy and subsequent death. In response to brain demyelination, a cell population called oligodendrocyte progenitor cells (OPCs) proliferate and differentiate into oligodendrocytes (OLs), which remyelinate exposed axons. In ageing remyelination often fails due to a reduction in OPC regenerative capacity. The age-related reduction in remyelination coincides with changes in the brain biochemical and mechanical properties. Preliminary data have demonstrated that exposure of aged OPCs to young-like environments improves aged OPC function in terms of proliferation and differentiation into myelinating OLs. This project aims to identify factors from the physical extracellular microenvironment, which negatively influence remyelination in the ageing CNS. In order to elucidate the underlying molecular mechanisms, the composition of the brain tissue changes with age on a biochemical and mechanical level and and its influence on the OPC proliferation and differentiation into OLs will be investigated. Moreover, the negative effects of the ageing microenvironment will be mitigated by mimicking the young brain niche using synthetic scaffolds as well as modified decellularised tissue. Understanding this interplay using a range of in vitro and in vivo methods will therefore aid the development of therapies for enhancing endogenous remyelination.
An important area in drug development is understanding low-level molecular processes and pathways that cause diseases. These cellular phenotypes are high-dimensional and are increasingly being captured using single-cell assays and high-content imaging. In understanding natural cell trait variation and engineered variants, we can elucidate the cellular consequences of disease mutations. In my project, I will exploit cellular images in a range of contexts to investigate the link between genetic variation and cell trait variability using both natural genetic variation and engineered variants. To do so, I will develop machine learning methods to extract features from high throughput microscopy data, and to accurately account for genetic, environmental, and experimental sources of variability in them. Furthermore, I will work on integrative approaches using public genomic data to bring in other omics modalities, thereby tackling key challenges in the larger aim of deciphering disease and fostering drug development. I will use existing data from the HipSci project, high throughput drug screens from AstraZeneca, and, in addition, will design and oversee the generation of datasets through high-throughput CRISPR knockouts as part of Leopold Parts’ group at the Wellcome Trust Sanger Institute and Oliver Stegle’s group at the European Bioinformatics Institute.
Integrating genomic, transcriptomic, metabolomic and behavioural data from 12 strains of C. elegans to understand gene/environment interactions under different dietary regimens 31 Jan 2017
C. elegans can grow on a range of different bacterial diets. It has already been shown that it changes its behaviour depending on the available food. Its lifespan also depends on its diet. Autophagy has been shown to mediate the increase in lifespan when the nematode is grown on certain foods. However, the mechanisms by which the environment leads to a change in beheviour and life history traits remain largely unknown. With this project, we would like to use high-throughput sequencing and metabolomics to build a quantitative and comprehensive map of the underlying molecular networks activated in a specific dietary environment. Furthermore, we would like to harness the genetic diversity of C. elegans to study the genetic basis of its phenotype as well as the interaction of its genome and environment in the determination of its behaviour and lifespan. For this purpose, we plan to extend the latest statistical techniques to integrate all layers of genomic and phenotypic data. Many of the genes involved in metabolism are conserved between humans and nematodes. Therefore, we expect that the findings will be relevant to human physiology.
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.
Regulation of the cellular trafficking of TAPBPR and its implication on MHC class I peptide presentation 31 Jan 2017
The process of antigen presentation by major histocompatibility complex (MHC) class I molecules is a crucial process in protecting the human body against intracellular infections and cancer. These molecules present the cellular proteome, in form of short peptides, at the cell surface, for the inspection by cytotoxic T lymphocytes. The MHC class I molecules acquire their peptides in the ER, a process facilitated by the peptide loading complex (PLC). As part of the PLC, tapasin was until recently believed to be the only MHC class I specific chaperone directly involved in peptide selection. However, that has changed with the Boyle laboratory's discovery that a protein called TAPBPR is a second MHC class I dedicated chaperone, intimately involved in peptide selection. It is now essential to understand the distinct roles of the two MHC class I dedicated chaperones and how they work together in determining the final peptide repertoire displayed to the immune system. My key research goals are to investigate how the cellular trafficking of TAPBPR influences its effects on class I antigen presentation and what are the cellular factors that control its trafficking.
Attachment and the transgenerational effects of loss, abuse and trauma: Exploring and testing classic ideas through historical analysis and developmental science 02 May 2017
Since it was introduced by John Bowlby, attachment research has been among the most influential paradigms for understanding the social underpinnings of infant mental health and transgenerational mental health. However, an odd artefact of the way a major research instrument was constructed in the 1980s by Mary Main has meant that to date attachment research has largely treated loss, abuse, and trauma as essentially equivalent, despite their very different clinical implications. A multidisciplinary approach will be used to investigate these concepts and examine potential differences. Work Package 1 will comprise a critical re-examination of the concepts of loss, abuse and trauma in the published and unpublished works by John Bowlby and Mary Main, exploring their reflections on how these experiences might impact parenting. In Work Package 2, hypotheses elaborated in Work Package 1 will be tested using Individual Participant Data pooled from 59 attachment studies, representing 4,542 families. Work Package 3 tests explanations for differential effects of unresolved loss, abuse and trauma on parenting and child development using longitudinal data from 400 mothers and children. The study will shed new light on transgenerational mental health processes, and insights will be disseminated to professionals and families.
Apical-basal polarity is essential for all aspects of epithelial cell function and loss of this polarity is a hallmark of cancer. We have recently found that the endodermal epithelium of the Drosophila adult midgut polarises by a different mechanism from other Drosophila epithelia and may provide a good model for endodermal epithelia in mammals. This proposal aims to understand how polarity is generated in both epithelial types. Firstly, we will examine how the canonical polarity complexes polarise the secretory epithelium of the Drosophila follicle cells. We will investigate how Cdc42 is activated to define the apical domain; we will use optogenetics and super-resolution microscopy to investigate the dynamics and composition of polarity complexes; and we will analyse how cortical polarity organises the microtubule cytoskeleton through the lateral polarity factor, Par-1. Secondly, we will perform clonal screens to identify essential epithelial polarity factors in the Drosophila midgut and characterise their functions. To test whether these factors play conserved roles in mammals, we will knock out their orthologues in mouse intestinal organoids. This research will reveal the fundamental mechanisms that polarise different epithelial types, which is an essential prerequisite for understanding epithelial function and how it is perturbed in diseases like cancer.
Obesity and associated diseases such as type 2 diabetes, cardiovascular disease and some cancers represent a significant health burden. My overall aim is to identify new therapeutic strategies for severe obesity. Using extensive genetic and clinical data on unique cohorts of individuals at both extremes of the weight distribution (severe obesity and thinness), we will comprehensively map the molecular networks that maintain energy homeostasis and their disruption in disorders of weight regulation. Building on our previous work, we will focus on dissecting cellular mechanisms that converge on leptin-melanocortin signalling using human stem-cell derived hypothalamic neurons. In human studies, we will characterise the effects of specific pathways on eating behaviour, energy expenditure and substrate utilisation. By uncovering the fundamental mechanisms that control human energy homeostasis, our goal is to identify and validate control points that can be targeted to improve outcomes in obesity associated diseases.
From Cures to Courts of Justice: The Medical Encounter and Social Order in Early Modern Spain 17 Jul 2017
Early modern encounters have mainly been studied as transactions between individual sick people and their healers. This project shifts the focus by placing encounters within the communities that structured early modern lives and the practices and expectations of social order that shaped them. The variety of encounters that took place in the Catholic kingdom of Castile provides an ideal case study to establish this fresh perspective on the politics of health care. By combining trial records, tracts on medical etiquette and literary sources, the project explores how encounters intersected with the domestic, collective and religious order of close-knit urban and rural communities. It has three main goals: 1) To reveal which assumptions about norms and stability guided the encounters. 2) To explore how in practice encounters fostered or disrupted social stability. Subsidiary goals are: to show how communities monitored, and communicated about, healing practices; to discuss how, as encounters unfolded, religious discipline intersected with other facets of social order. 3) To assess the informal and formal strategies, including legal, by which communities managed controversial encounters. Subsidiary goals are: to understand how an encounter turned into a legal dispute; to evaluate which short- and long-term consequences this process had for communities.
This project will produce a history of marriage and health in early modern England. Marriage is generally understood as an institution governed by legal and religious regulations and social norms that have taken different forms throughout history. In post-Reformation England marriage was increasingly regulated and interrogated. Performing gendered spousal roles was part of religious practice, something perpetuated by the growing culture of conduct manuals. A central obligation of marriage was to care for one another in sickness. This has underpinned histories of domestic medicine that reveal that the early modern family was active in diagnosis and cure. The two major goals of this project are (1) To assess how good health defined a successful marriage in early modern England and (2) To investigate how the social norms and expectations of marriage changed over the course of a union. As part of this inquiry, subsidiary goals will be (3) To interrogate how marital compatibility was measured, (4) How poor health of one spouse affected the other, and (5) How illness impacted on the household as a whole. Finally, this project aims (6) To uncover how cultural expectations shaped the way early modern people wrote about marriage.
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.
The nuclear envelope (NE) lies at the interface between the nucleus and the cytoskeleton. It forms a complex structure controlling cell compartmentalization and regulates many processes including nucleo-cytoplasmic transport of proteins and RNA, chromatin organization, DNA replication and DNA repair. Hence, defects in NE integrity and nuclear architecture cause drastic changes in cell homeostasis and are associated with a broad range of diseases including cancer, premature ageing syndromes, neurodegenerative diseases or muscular dystrophies, but also with physiological ageing. One of the main challenges is to understand how NE defects lead to so many types of diseases. Previous theories include changes in gene expression and mechanical weakness. My previous work has shown that subcellular processes including microtubule or chromatin organization can modulate NE function, and has identified the acetyltransferase NAT10 as a key regulatory node for control of nuclear architecture. My goal is to now investigate how NAT10 and other factors regulate the NE. I will thereby gain new understanding of how of nuclear architecture is orchestrated and how this is disrupted in age-related diseases including HGPS. This research will not only contribute to our fundamental understanding of nuclear architecture but will also potentially identify new therapeutic strategies for NE-associated syndromes.
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.
PI3Kdelta plays a critical role in development of the immune system. We have identified a cohort of patients with an immunodeficiency caused by gain of function mutations in PI3Kdelta, which we have named Activated PI3Kdelta syndrome (APDS). My fellowship proposal will determine how dysfunctional B cells contribute towards recurrent pneumonia associated with APDS. I have shown that aberrant PI3Kdelta signalling leads to significant defects in B cell development and function. I have found that hyper-activated PI3K signalling in B cells alone is responsible for increased susceptibility to Streptococcus pneumoniae in a mouse model. Surprisingly, this defect appears to be antibody independent. I have discovered a subpopulation of IL10 producing B cells that I believe represents a new type of B cell with immune-regulatory properties. I hypothesise that this B cell subset is contributing to the immunopathology secondary to pneumococcal infections in APDS, leading to bronchiectasis. My aims are: To characterise this newly discovered subset of B cells and explore the role of PI3Kdelta in their ontogeny. To determine whether IL10 is the innate cytokine that triggers antigen non-specific activation and immunopathology. To explore whether these pathogenic cells can be manipulated therapeutically using oral or inhaled PI3Kdelta inhibitors.