NIHRDataInsights/HRCSData huggingface dataset:
Title: Understanding small molecule uptake by the Bacteroidetes
Funder: Wellcome Trust

Abstract: The human gut microbiome has a profound influence on virtually all aspects of human health. The composition and therefore collective function of the colonic microbiota depends on the ability of individual micro-organisms to acquire nutrients in a highly competitive environment. While very diverse at the species level, the gut microbiome is dominated by just two bacterial phyla, Gram-positive Firmicutes and Gram-negative Bacteroidetes. In the Bacteroidetes, the outer membrane (OM) is the first, and for hydrophobic molecules only, barrier for cell entry. Therefore, the intracellular fate (metabolism, bioconversion) of any small molecule is linked to its ability to traverse the OM via active transporters and diffusion channels. While extensively characterized in Proteobacteria, OM transport in the phylogenetically distant Bacteroidetes is terra incognita. In this proposal we will define the OM protein landscape of an abundant and representative member of the genus Bacteroides via quantitative proteomics under various conditions. We will also gain a thorough mechanistic understanding of (i) active import via TonB-dependent transporters and (ii) passive uptake via OM diffusion channels, using X-ray crystallography, cryo-EM and electrophysiology. The work will transform our understanding of nutrient acquisition by Bacteroidetes and will suggest ways for microbiota manipulation to benefit human health.

Lay abstract: The human gut microbiota is the bacteria-dominated collective of microorganisms that inhibits our gastro-intestinal tract. It is becoming clear that this bacterial organ affects virtually all aspects of human health in a profound way. Microbiota function is critically dependent on its composition, which in turn depends on the ability of bacteria to acquire small-molecule nutrients. Bacteria from the dominant phylum Bacteroidetes have an outer membrane (OM) surrounding the cell that forms a very efficient barrier for small-molecule passage. Thus, for nutrient uptake, Bacteroidetes require OM transport proteins that have not yet been studied. In this proposal we will determine which OM proteins are present in Bacteroidetes and how nutrients are taken up. Understanding nutrient uptake by what is arguably the most important group of gut bacteria is not only of fundamental importance, but will also inspire strategies to manipulate the composition of the gut microbiota to improve human health.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFECTION;ORAL AND GASTROINTESTINAL
Title: Mechanisms of airway defence
Funder: Medical Research Council

Abstract: The main aim of the research program is to understand how the airways respond, adapt and survive when confronted with different types of insults such as toxic particulates and drugs that target the airways. The airways play a central role in protecting our health throughout the life course. The most recent systematic analysis of the global burden of disease, which includes data from more than 200 nations, has shown that the largest increase in risk of disease results from airway exposure to pollution from ambient particulate matter (PM). It is therefore of the outmost importance that we investigate the molecular mechanisms driving induction and progression of toxicity in the airways in order to identify biomarkers of disease and rescue strategies. Toward this goal we employ airway primary cellular models from different lung compartments to understand how different molecular insults affect pathways linked to airway defence such as mucociliary clearance, oxidation pathway and immune response. Our plan is to develop an airway specific toolbox combining unbiased high-throughput assays and mechanistic studies to systematically identify key molecular events, common or different, in the adverse outcome pathways driven by potential toxicants. We employ a range of molecular tools including CRISPR-Cas9 loss of function studies, proximity mapping protein-protein interaction analysis and advanced imaging technologies such as super-resolution microscopy and volumetric EM to provide both a global and detailed view of airway cellular phenotypes. In regard to public health impact, environmental pollutants will be a primary area of focus since adverse health effects, including cardiovascular effects and respiratory symptoms and exacerbations, have been clearly linked to short and long-term exposure to PM2.5 and PM10. The health risks of pollution are especially high for patients affected by chronic obstructive pulmonary disease (COPD), asthma and children, leading to an increase in premature deaths. Moreover, we will focus on how patients are affected by rare diseases of the lungs such as motile ciliopathies, since they can be at risk population. Our knowledge and tools will be shared with the scientific community and industry partners for use in analysis of toxicity and adverse outcome pathways of novel compounds used in the clinic or introduced in the environment, such inhaled drugs and their delivery systems, new materials or environmental pollutants.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;INFECTION;RESPIRATORY
Title: Skin Microbiome in Healthy Ageing (SMiHA)
Funder: Medical Research Council

Abstract: The human body and associated microbiome represent an integrated meta-organism, where the microbiota strongly influences human physiology. The human immune system has developed alongside the microbiome to conserve commensal micro-organisms, while eradicating infectious pathogens. However, over the life course, the microbiota composition changes, modulating the immune response resulting in 'inflammageing'. While much is known about gut microbiota in ageing and longevity, the importance of the microbiota in the skin, the largest organ of the body, is only just emerging. Evidence suggests the skin microbiome is a more accurate predictor of chronological age compared to gut, therefore, human skin, with a more stable microbiome than the gut, presents an excellent system to establish how changes in the microbiome over the life course influence biological age (e.g., health status and life expectancy), and conversely how the ageing process drives the microbiome. In the UK, studies on the skin microbiome in healthy ageing are in their infancy and predominately driven by industry, thus presenting a gap in the academic knowledge base which our network 'Skin Microbiome in Healthy Ageing' will seek to address. Skin disorders occur from tiny infants to the very elderly and some 50% of the UK population suffer a microbiome-associated skin complaint each year, placing a large burden on the NHS. Furthermore, skin health and freedom from chronic skin conditions such as non-healing infected wounds is an important aspect of independence in the elderly population. Without good skin health, day to day living is compromised. Older skin is different, has different composition and structure as well as altered biofilm components, yet our understanding of how to manipulate the skin biofilm - using everyday products - is poor, and so far, only the preserve of those commercial actors who seek to make quick win claims such as 'microbiome friendly skin care' (360,000 hits in google).


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFECTION;SKIN
Title: Drug Delivery at the Immunological Synapse
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Directed secretion of soluble proteins, such as cytokines, across intercellular contacts plays a central role in establishing immune responses. A large structured interface is formed at such intercellular contacts where molecules required for adhesion and signalling accumulate to establish the immune synapse. It has been postulated that one function for such an immune synapse is to assemble a 'gasket' that to some extent isolates the synaptic cleft from the bulk extracellular environment. However, to the best of my knowledge, antibodies or other potential therapeutic agents have not been designed with a view to being able to readily penetrate and act within the context of such a gasket. Thus, I propose here to study fundamental properties of immune synapses that may impede drug/antibody delivery and apply this knowledge to the design of drugs/antibodies to act within immune synapses. I first aim to clarify the extent to which the immune synapse functions as 'gasket' and determine the underlying molecular and cellular mechanisms by which such a gasket is established. This will give important insights into the nature of the immune synapses and its importance for intercellular communication in the immune system. I then propose to assess different approaches in drug design to facilitate penetration into immune synapses, including lipid conjugation, varying drug size, and using bispecific antibodies. I propose to specifically compare the efficacy of different strategies for blocking synaptic cytokine secretion. Establishing the best approach for antibodies or other drugs to act within the context of an immune synapse can be an important consideration for the design of effective drugs for many diseases.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;5.1 PHARMACEUTICALS
Health categories: GENERIC HEALTH RELEVANCE;INFLAMMATORY AND IMMUNE SYSTEM
Title: How particle shape determines phagocytic uptake: a systems-biology analysis
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Phagocytosis allows a cell to engulf another cell (or a particle) for feeding purposes or as part of our immune response. It is a complex spatio-temporal, multi-step process, involving recognition of opsonised and unopsonised particles by cell-surface receptors, which, when ligand-bound, signal to the actin cytoskeleton and myosin motor proteins. As a consequence, remodelling of the actin cytoskeleton and contraction by motor proteins lead to zipper-like engulfment and finally enclosure of the particle by the cell membrane. Despite the signalling complexity, the engulfment process also depends on simple biophysical parameters of the cell and particle. Most importantly, engulfment depends on the shape and stiffness of the particle, important for both host-pathogen interactions and efficient drug delivery. Here, we aim to develop such a model based on biochemical reaction diffusion equations and physical conservation laws, which will be implemented and solved in 3D using a computational finite-element scheme. To address the mechanosensitivity during uptake and cup closure, the model will include the cell's porooelastic, wave-like actin cytoskeleton, its contractility by myosin motor proteins, and their regulation by Rho family GTPases. The cell membrane constitutes a moving boundary for such solutions. Model parameters will be estimated by comparison with experiments imaging uptake, using 4D fluorescence resonance confocal and scanning electron microscopy. Experiments will be used to validate the model and to test its predictions. Phagocytic cell morphology will be imaged, key myosins will be knocked down by RNAi, and the resulting phenotypes compared with simulation results. The validated model and experimental assays will then be used to determine particle shape and size for best/worse uptake. To demonstrate industrial applicability, together with collaborators we will design optimally shaped, biodegradable PLGA particles for efficient drug delivery.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;INFLAMMATORY AND IMMUNE SYSTEM
Title: Overcoming immunological barriers to regenerative medicine
Funder: Biotechnology and Biological Sciences Research Council

Abstract: The innate and adaptive immune system can present formidable obstacles to successful regenerative medicine applications. To identify and circumvent these obstacles, the co-applicants propose to form a UK Regenerative Medicine Platform (UKRMP) hub on immunomodulation. We will pool our collective clinical and laboratory-based expertise in stem cell biology, whole organ transplantation, cell therapy, endogenous tissue repair and innate and adaptive immunity to answer the following questions: 1. How do differentiated cells signal to the host innate and adaptive immune system? 2. How do transplanted cells provoke adaptive immune responses? 3. How does the inflammatory niche contribute to endogenous repair and influence the fate of transplanted cells? Each question will be tackled in one work package. In work package 1 we will use in vitro assays to compare how differentiated human cells isolated from the relevant tissue or induced from iPS cells signal to the immune system under steady state and hypoxic conditions. In work package 2 key findings from work package 1 will be validated in vivo using humanised mice. The use of iPS cell-derived dendritic cells to modulate immune tolerance and enhance Treg therapy, alone or in combination with complement inhibitory peptides, will be explored as a means of improving the survival and function of transplanted cells. In work package 3 we will examine the contribution of recently discovered subsets of macrophages, fibroblasts and dendritic cells to the inflammatory niche in the context of cell transplantation, chronic inflammation and endogenous repair. Each question will be approached in the context of the following long-term clinical deliverables: improved efficacy of photoreceptor cell therapy to treat blindness; improved repair of damaged heart and intestine; and improved survival and functionality of transplanted hepatocytes as an alternative to liver transplantation.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;5.2 CELLULAR AND GENE THERAPIES
Health categories: GENERIC HEALTH RELEVANCE;INFLAMMATORY AND IMMUNE SYSTEM
Title: The human evolutionary past: ancient DNA and computational genomics
Funder: The Francis Crick Institute

Abstract: Human biology and disease is the outcome of historical evolutionary processes, and the large-scale retrieval of ancient DNA now provides the opportunity to directly study the dynamics and signatures of these processes in the human genome through time and space. The Crick Ancient Genomics Lab will develop new molecular and computational approaches with the overarching goal to study how ecological and cultural factors have shaped human population structure and biology during momentous transitions in prehistory. Previous work of ours has studied how agriculture spread over the world from independent origins in the Near East, east Asia and west Africa to Europe, the south Pacific and southern Africa. These independent origins and subsequent migrations provide experimental replicates with which we can learn which adaptations–e.g. genes, regulatory pathways, and phenotypes–are the unifying mechanisms with which human populations have adapted to the radical change in lifestyle that agriculture and sedentism imposed. The agricultural diet is behind of many present-day health challenges such as diabetes, and the changes in food production and population density also changed selection pressures imposed by infectious disease. By learning how the earliest agriculturalists adapted to the new lifestyle and how these adaptations were conferred by admixture to forager groups as agriculturalists expanded, we can gain insights into the genomic basis of modern-day health challenges which will provide a vital evolutionary perspective to the future genomic era of precision medicine. To understand these dynamics, we are using cutting-edge ancient DNA techniques coupled with modern computational genomics to reconstruct ancient genomes from populations that lived in the past 20,000 years. This includes a focus on past populations in Africa, extending available ancient DNA and genomics tools for African ancestry populations. We will map the origins of population structure in Africa, guiding GWAS and medical genetics, and document the underpinnings of genetic diversity in the most genetically variable populations on the planet, contributing to their inclusion in precision medicine initiatives of the future. A specific hypothesis, testable only with African ancient DNA, concerns the evolution of genetic resistance to malaria in African populations, where Plasomodium vivax is common in other tropical regions but rare or absent in western and central Africa likely due to a mutation in the Duffy antigen receptor for chemokines in human populations. When and under what circumstances did this resistance evolve and what factors drove its near fixation in many African populations?


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFLAMMATORY AND IMMUNE SYSTEM
Title: Gene editing for APDS1 - a novel gene therapy approach for gain of function (GOF) mutations.
Funder: Medical Research Council

Abstract: Aim & Objectives: This project will develop and test the functional efficiency of novel gene editing therapeutic approaches for APDS1, a model for serious diseases caused by gain of function (GOF) mutations, not amenable to conventional gene therapy approaches. In vitro experiments will compare the efficacy of targeted gene disruption with gene repair on the function of various immune cells, including cell lines and primary human cells. We will then optimise conditions for gene editing in HSCs using the most efficient and least toxic gene editing approach. Finally, we will test the efficacy of gene-corrected human HSCs (ethics in place) in an established mouse model of APDS1, which will allow us to determine the degree of correction required for clinical benefit. This project will test the following hypotheses: 1. Targeted disruption of the GOF mutation in p110delta using WT CRISPR/Cas9 can restore functional PI3Kdelta signalling in corrected cells. 2. In vitro functional assays will demonstrate a correlation between of gene disruption and normal protein expression in edited primary human immune cells. 3. Correction of the GOF allelic mutation to wild type sequence can be achieved by: (a). Allelic exchange (unaffected allele acts as internal template for repair); and/or (b). Homology-directed repair (wild-type cDNA template delivered via AAV6 viral vector transduction); and/or (c). CRISPR/Cas9 nickase mutants with HDR template. 4. Gene editing confers protection against infection in vivo by reconstituting NSG mice with human cells and by investigating chimerism in an established mouse model of APDS1.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.2 CELLULAR AND GENE THERAPIES
Health categories: GENERIC HEALTH RELEVANCE;INFLAMMATORY AND IMMUNE SYSTEM
Title: The landscape of cellular interaction in quiescent and proliferative tissues
Funder: Wellcome Trust

Abstract: Interactions between each individual tissue-resident cell types govern tissue integrity. However, if and how diverse cell types of a tissue interact with one another, and their surroundings, in a dynamic microenvironment is poorly understood. To understand how changes in the network of cellular interactions govern tissue homeostasis and stem cell activity, we will perform multiplexed immunofluorescence labelling to comprehensively map out the skin during quiescent (telogen) and proliferative (anagen) states for markers of immune cells, epithelial cells, fibroblasts and extracellular matrix proteins. This will be further complemented with single cell transcriptomic analysis, with a view to elucidating cellular interactions that govern the natural flux between tissue quiescence and proliferation. Additionally, we will establish laser capture micro-dissection as a method to perform a spatial single-cell RNA-sequencing (scRNA-seq) to study the transcriptome of cells within a specified region of the tissue microenvironment. Given that current scRNA-seq is limited by the lack of spatial information, such a technique should be of wide interest to the scientific community. Our work will provide researchers a comprehensive understanding of the cellular interactions that occur in tissues that are defined by distinct stem cell activation status, which may aid identification of interactions that govern stem cell activity.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFLAMMATORY AND IMMUNE SYSTEM
Title: Functional Characterization of Jagged1 (Jag1) Expressing Skin-resident Regulatory T Cells (Tregs) in Epithelial Stem Cell Homeostasis
Funder: Wellcome Trust

Abstract: Regulatory T-cells (Tregs) are famous for their immunosuppressive functions and induce tolerance. Only recently, we come to realise they can also function as stem cells regulators, and maintain tissue homeostasis1. Recently, our lab has demonstrated that skin Tregs are functionally required for hair regeneration, by regulating hair follicle stem cells (HFSCs) activity via notch ligand Jagged1 (Jag1)3, irrespective of their well-known immunosuppressive role. Yet, the functional mechanisms of this skin Treg subset (Jag1+Tregs) remain laregely unknown. We seek to understand if Jag1+Tregs directly regulate HFSCs, via Jag1-induced notch signalling. Since notch signalling requires direct cell-cell contact, we first ask if Jag1 regulates skin Tregs physical proximity to notch receptor-expressing cells (such as HFSCs) using immunofluorescence staining. By comparing the transcriptome profiles of Tregs and HFSCs from wildtype control against those from Jag1 conditional knockout model, we determine how Jag1+Tregs self-regulate and HFSCs function. Finally, using a combination of immunofluorescence staining and murine knockout models, we will define tissue-resident cells induce and maintain Jag1 expression in skin Tregs. This project will advance our understanding of how Jag1 facilitates immune-stem cells crosstal,k and subsequently regulates murine hair regeneration. It may reveal if skin-resident Tregs can be used as therapeutic targets.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFLAMMATORY AND IMMUNE SYSTEM
Title: Investigating the crosstalk between adipocytes and macrophages during wound repair
Funder: Wellcome Trust

Abstract: Our immune system exists to help our bodies fight infection, heal wounds and remove unhealthy cells. In order to gain as much information as possible about this complex system, it is vital to investigate immunological processes in the context of a living animal. Despite evolutionary divergence from humans, the fruit fly Drosophila melanogaster contains a relevant immune cell type, making it an ideal model in which to investigate immune cell functions, such as damage signalling, cell corpse recognition and immune cell memory. It has recently emerged that fat cells also play a role in wound healing, and this project seeks to elucidate the mechanism by which fat cells contribute to the immune response. The tractable genetics of Drosophila will allow us to identify potential candidate genes by screening for which genes are “turned on” in cells that are responding to laser induced wounds. We will then increase or decrease the level of expression of these candidate genes and use real time imaging in the living Drosophila pupae to identify the effect that these genes have on immune cell and fat cell migration to wounds.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFLAMMATORY AND IMMUNE SYSTEM