NIHRDataInsights/HRCSData huggingface dataset:
Title: Molecular mechanisms controlling CTL killing: from genes to secretion
Funder: Wellcome Trust

Abstract: The aim of my research is to understand the molecular mechanisms that control cytotoxic T lymphocyte (CTL) polarized secretion and killing. In a recent screen of single gene deletion mice we identified novel genes that are required for CTL killing and implicate important roles for organelles including mitochondria and peroxisomes. During the course of these studies we also developed advanced (high-throughput) assays for CTL killing and a detailed map of events leading to CTL secretion. Our specific aims over the next five years will be to (i) Identify the roles of the newly discovered genes, and the organelles they implicate, in CTL killing using a combination of biochemical, genetic and high-resolution imaging approaches. (ii) Determine how transcriptional control fine-tunes CTL killing, combining gene deletion and cell biological approaches (eg micro-patterning) with single cell transcriptomics to ask how CTL modulate their responses in order to modulate their killing. (iii) Broaden the range of genetic diseases for studying CTL function and make use of emerging genomic data to identify new causal genes in immunodeficiency. With the combination of genetic and cell biological approaches that we take, we aim to bridge the current gap between genes and function in CTL.

Lay abstract: Within every teaspoon of our blood are 5 million potential killer cells. These are remarkable little cells that circulate around our bodies recognizing and destroying virally infected and cancer cells with remarkable specificity and precision. We have discovered new genes that suggest that many different components within killer cells play a part in delivering the lethal hit. We wish to work out how each part of the killer cell contributes. We will study killer cells in which the new genes are missing to see where things go wrong. We are able to film live killer cells and pin-point what is different in each case. This is particularly important right now as new cancer therapies in medicine aimed at helping killer cells are proving very effective. By understanding exactly how killer cells work, clinicians will be able to devise better therapies.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Signalling pathways that control T cell metabolism and T cell fate
Funder: Wellcome Trust

Abstract: The laboratory will map how antigen receptor, cytokine and environmental signals integrate to control the function of T lymphocytes. We will comprehensively define signaling pathways that maintain T cell metabolism, transcriptional and proteomic landscapes. Specifically, we will comprehensively delineate the molecular details of how changing the supply of oxygen, glucose and iron impact on T cell signal transduction pathways and T cell phenotype. We will explore the ability of the Prolyl hydroxylase domain protein PHD2 and the transcription factor NFIL3 to link oxygen sensing to the control of T cell function. We will define how glucose fueled signaling pathways including those mediated by AMP-activated Protein Kinase alpha1 (AMPKa1) and the O-GlcNAc transferase (OGT) control T cell fate. We will comprehensively map how the protein tyrosine phosphatases SHP-1 and SHP-2 regulate protein phosphorylation networks in T cells and how they modulate T cell proteomes and T cell function. We will also characterize signaling pathways mediated by Phosphatidylinositol 3,4,5-trisphosphate PI-3,4,5-P(3) and define how the lipid phosphatases PTEN and SHIP1 shape T cell metabolism and T cell function. These experiments will map and define the molecular processes that determine T cell fate outcomes.

Lay abstract: T lymphocytes are a subpopulation of white blood cells that control the immune system to fight viruses, bacteria and tumors. When white blood cell fail to function correctly the immune system fails usually resulting in death. The present projects will characterize molecules that act as messengers inside lymphocytes to regulate their behavior and will examine how white blood cells are controlled by the supply of oxygen and key nutrients notably glucose and iron. The control of white blood cells is critical for immune responses. Understanding how environmental signals control white blood cells is essential to identify targets relevant for the treatment of autoimmune diseases and cancer. The laboratory has an integrated research program to explore signaling pathways of communication inside lymphocytes. These studies will generate new information about mechanisms that control immune responses and identify new drug targets for therapeutic intervention in the immune system.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Ubiquitin and ubiquitin-like proteins in the immune system
Funder: Medical Research Council

Abstract: The posttranslational modification of proteins is a fundamental process in all organisms. For instance, ubiquitin and ubiquitin-like protein modifications play critical roles in virtually all aspects of eukaryotic biology, including protein degradation, cell division, and immunity. These are dynamic, tightly controlled and highly tunable processes; therefore, misregulation of the enzymes and proteins involved in these signalling pathways is associated with many diseases. Thus, understanding how these modifications regulate cell signalling pathways is fundamentally important to human health. The objective of my laboratory is to discover the mechanisms underpinning how the ubiquitin-like protein, interferon-stimulated gene 15 (ISG15), contributes to the host immune system. ISG15 is a ubiquitin-like protein that functions in the innate immune response. During viral infection, a sharp rise in ISG15 production modifies thousands of proteins to defend the host cell. Moreover, many pathogenic viruses, including coronaviruses, have evolved mechanisms to remove and redirect these modifications to subvert ISG15 signalling. Accumulating evidence strongly supports these signals serve distinct and important biological roles. However, the function of most ISG15 modifications remains unknown. Therefore, my laboratory aims to advance ISG15 research by focusing on several key priority areas. 1) To understand the molecular details of ISG15 substrate recognition and targeting 2) To identify ISG15 substrates and define their functions 3) To reveal new viral strategies to evade ISG15 signalling 4) To develop state-of-the-art technologies to study ISG15 My laboratory takes a multidisciplinary and collaborative approach to science using proteomics, structural biology, biochemistry, biophysics, chemical biology, and cell biology to answer our questions. The MRC PPU is ideal for undertaking this research due to recent investments in single-particle cryo-EM, high-end mass spectrometry, and existing expertise in ubiquitin biology, chemical biology, and immune signalling at the University. Together, I am confident that the collaborative and supportive environment here will facilitate progress in my research. The ubiquitin field has made great strides in deciphering the biological roles of ubiquitin and some ubiquitin-like proteins. I anticipate our efforts on the understudied and enigmatic ubiquitin-like protein ISG15 will similarly reveal fascinating new insights and unlock unexpected and important biological functions related to human health and disease.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;GENERIC HEALTH RELEVANCE;INFECTION
Title: Understanding how Salmonella interferes with the adaptive immune system
Funder: Wellcome Trust

Abstract: Salmonella enterica is one of the four key causative agents of foodbourne diseases and each year it affects around 1 in 10 of the global population, according the World Health Organisation (World Health Organisation, n.d.). Salmonella enterica can cause a range of illness from a mild diarrhoeal illness to a widespread systemic infection known as typhoid fever. Successful clearance of the Salmonella bacteria from our bodies during an infection relies on part of immune system called the adaptive immune system. This part of our immune system not only produces a highly specific response but also provides long-lasting immunity. Salmonella has evolved to live within the hostile environment of our cells and is able to manipulate the host cell to aid its survival. Recent work by the Holden Laboratory, Imperial College London, has shown that Salmonella produces a small protein, called SteD, that specifically interferes with a specific component of the adaptive immune system. Further work has identified two new genes required for SteD to function. In this project, I will establish how SteD hijacks these two proteins to disrupt the immune system.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;GENERIC HEALTH RELEVANCE;INFECTION
Title: Provision of multi-parameter fluorescence-activated cell sorting for functional and genomic analysis of immune cells
Funder: Wellcome Trust

Abstract: This application is for the purchase of a BD Aria-Fusion fluorescence activated cell sorter. The instrument performs high-speed multi-parameter sorting, allowing isolation of rare cell subsets and supporting single-cell genetic and functional analyses. It will enable scientists at the UCL Institute of Immunity and Transplantation (IIT) to be at the forefront of studies of the patho-physiology of the human immune system and responses to disease treatments. This state-of-the-art sorter is essential to allow us to maintain a cutting edge flow-cytometry core facility in the newly constructed Pears building, which will house the IIT from late 2020. The Pears building is a £61 million joint project between UCL and the Royal Free NHS Foundation Trust to create a world-leading centre for disease-focused immunology research. The building will accommodate some 20 research groups comprising approximately 200 scientists. The translational immunology programs of the IIT include mechanistic studies in animal models, genetic and functional analyses of the human immune system, high-dimensional analysis of clinical samples and the monitoring of patients participating in novel immunotherapy trials. The technical capability of the FACS-Aria-Fusion is therefore required to support a wide variety of cutting-edge research programs in infection and immunity.

Lay abstract: The immune system represents the body's natural defence to infections such as viruses and bacteria. However, manipulation of the immune also system is central to the treatment of many conditions. In diseases such as arthritis, diabetes and in organ transplantation there is a need to suppress the immune system, whereas modern cancer treatments stimulate immune responses to kill tumours. A detailed understanding of how the immune system functions is therefore essential to develop accurate and effective treatments across a wide range of important conditions. The immune system is made up of many types of cells, each with different functions. In order to be able to study these different cells in detail this proposal will fund a cell sorting machine to enable us to purify cells and understand their functions. This machine will be used by scientists working on many diseases and will contribute to the development of new treatments.

Research activity codes: 2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY)
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;GENERIC HEALTH RELEVANCE;INFECTION
Title: Characterising extreme innate immune response phenotypes informative for disease using a functional genomics approach
Funder: Wellcome Trust

Abstract: The overall aim is to define and characterise extreme innate immune response phenotypes in order to gain insights into the functional alleles driving such differences between individuals; biological consequences in terms of gene regulation, cellular function and disease; and opportunities for therapeutic intervention. Key goals are (1) to analyse existing transcriptomic and expression quantitative trait mapping datasets for primary monocytes activated by lipopolysaccharide (endotoxin) or interferon-gamma from a large cohort of healthy volunteers to identify extreme responders (aggregated and gene level), using genetics to resolve functional alleles then validate and establish functional consequences including through chemical probes; (2) to use genome editing to conduct high-throughput screens in human induced pluripotent stem cell derived monocytes complementing the genetic data; (3) to define key nodal genes and networks for drug target discovery and prioritisation; and (4) to characterise prioritised genes and functional alleles modulating gene transcription and epigenetic regulation relevant to disease. Anticipated outcomes are improved understanding of pathophysiology in immune-mediated disease notably sepsis; exemplars to the field of how to establish mechanism for functional alleles involving regulatory genetic variants; improved interpretation of genome-wide association studies; novel nodal points involving TLR and related pathways as drug targets; and better drug target prioritisation.

Lay abstract: This research aims to identify people who show extreme responses to lipopolysaccharide (a component of bacterial cell walls) or interferon-gamma (a chemical signalling molecule associated with infection and inflammation) when used to activate white blood cells called monocytes. The hypothesis is that genetic factors determine such differences between people. By investigating this, we hope to identify specific genes that are affected by having particular genetic variants and the functional consequences. Such information is very helpful for drug discovery. It provides information about the likely consequences of using a particular drug before large financial investments are made in developing a drug. We will analyse data from large existing cohorts of healthy volunteers who have donated blood samples. We will use a model system based on stem cells to generate the cell types of interest and then use new tools for editing the genome in a specific way (an accurate cut and paste method) so that we can test the effects of making a genetic change. We will work with experts in drug discovery to make sure that our results are taken forward and aid drug development. The work will help patients with different diseases associated with dysregulated immune function including sepsis.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;GENERIC HEALTH RELEVANCE;INFECTION
Title: Translational genomics in critical care medicine.
Funder: Wellcome Trust

Abstract: My work during the Covid outbreak has shown that genetic associations with critical illness can predict therapeutic targets, and that therapies targeting the host response improve outcome in carefully-defined subgroups of critically ill patients. I propose to extend this work to bridge the gap between genetic discovery and therapeutic application. In doing so I will build on established infrastructure and lay the foundations of a system for rapid identification and assessment of candidate drugs for respiratory critical illness. To achieve this I will: 1. ◦ Use genome-wide association studies to identify host genes associated with critical illness in viral pneumonia (Covid-19: 20,000 cases; influenza: 3000 cases). 2. ◦ Identify targets using computational approaches including integrated functional genomics and Mendelian randomisation. ◦ Complete proof-of-principle analysis to test for differential genetic effects in new patient subgroups. 3. ◦ Refine and test candidate causal variants in vitro. ◦ Establish technology for distal lung regional microdosing to validate targets in vivo in critically ill humans. At the end of this fellowship I will have established a programme of translational genomics in critical care medicine going from genomic discovery to experimental medicine in humans.

Lay abstract: Respiratory viruses that cause diseases like Covid and influenza are likely to continue to cause life-threatening illness in humans for the foreseeable future. There is a pressing need to find new treatments, and also to build efficient pipelines to find new treatments for each new disease that emerges. Studying the genomes of people who become critically ill has already led to promising new treatments in Covid - I will continue this work in Covid and influenza. My aim is to use genetics to generate and refine therapeutic hypotheses - that is, to identify drugs that might prevent death or critical illness. And then, I aim to create an effective model system to test those hypotheses in critically-ill humans: by giving doses of drug into tiny sections of their lungs, using a bronchoscope, and then to measure the effects on lung function and appearance.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;GENERIC HEALTH RELEVANCE;INFECTION
Title: Spatial and temporal regulation of immune specific myosins and their role in neuroinflammation
Funder: Wellcome Trust

Abstract: Unconventional myosins of class I can directly associate with membranes, thereby providing a dynamic link between the actin cytoskeleton and the plasma membrane or intracellular organelles. Immune cell-specific myosin 1F and myosin 1G (MYO1F and MYO1G respectively) have roles in immune cell migration and regulation of membrane tension. Studies show both motors are upregulated in microglia during neuroinflammation. To uncover the temporal regulation of these motors, a number of biophysical assays will be employed, such as in vitro motility assays, optical trap experiments and stopped-flow spectroscopy. The molecular interactions of MYO1G that determine cellular function will be explored using a combination of proteomics and cell biological assays to identify the motors’ interacting partners and elucidate its spatial regulation in vivo. The effects of two distinct phosphorylation sites on motor domain activity of MYO1G will be explored with mutations to mimic the non- and phosphorylated states. Protein crystallography studies of MYO1F and MYO1G will enable the design of small molecule inhibitors using structure-based in silico screening, with the ultimate goal to treat neuroinflammation in humans. Taken together these approaches will elucidate the cellular and physiological role of these motors and uncover the potential use of MYO1F and MYO1G as therapeutic agents.

Lay abstract: Myosin is a cytoskeletal motor that uses metabolic energy stored in ATP to do mechanical work. In the cell, myosin members of the class I family are vital for membrane dynamics and cellular trafficking. Two isoforms of myosin are found specifically in immune cells, and have roles in immune cell migration and phagocytosis. I aim to understand the molecular basis of the spatial and temporal regulation of immune cell-specific myosins. I will employ a combination of proteomics and cellular analyses to identify the interacting partners of these motors. I will also use biophysical and biochemical techniques, such as optical trap experiments and stopped-flow spectroscopy, to investigate the impact of post-translational modifications on the regulation of these motors. These studies will help to explain how dysregulation of immune-specific myosins can give rise to neuroinflammation, a common feature of neurodegenerative disease, and can be used to design potential new therapies.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Title: Development of ease-of-use flow cytometric system for multi-pathogen detection
Funder: Innovate UK

Abstract: Sepsis kills 30 000 people in the UK and costs the NHS £400 million per year. It is little known outside the medical profession but is the third most common cause of death in hospitalised patients outside of heart disease and cancer. It happens when an infection in the bloodstream tips the immune system out of balance and this system starts to attack the body rather than protect it. Many infections can potentially trigger sepsis but rapid treatment with the right antibiotic can often prevent it turning into serious sepsis. The Technology Strategy Board is supporting a group of teaching hospitals (St Thomas’s & Newcastle) in their work with BD (a US Heathcare Company with a base in Oxford) to develop a rapid test which can help doctors choose the right treatment during the critical early stages of the disease. This will save lives and reduce the huge cost of sepsis to the NHS.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION
Title: Rapid Point of Care detection of Bacterial Sepsis
Funder: Innovate UK

Abstract: This project will deliver a hand held prototype device for the diagnosis of sepsis within 3 minutes sampling. The assay detects changes before classical sepsis diagnosis and this has been shown in children and adults in settings that include the emergency room, post-surgery, oncology and intensive care settings. The project has already proven feasibility. It will now be coupled with a bespoke hand held device to deliver a test result from a 'pin-prick' of blood, allowing bed-side use from sample to result. The result will be either qualitative for diagnosis (Yes/No) or quantitative for repeated use in subsequent therapy monitoring. The product that will be developed will be the only true point-of-care device for the diagnosis and prognosis of bacterial sepsis on the market.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION
Title: A rapid near patient testing system for the detection of microbial pathogens in blood
Funder: Innovate UK

Abstract: The detection and diagnosis of healthcare associated infections in the critical care environment is extremely challenging. In the UK alone, there are over 42,000 HCAI sepsis episodes annually. Existing culture tests lack the sensitivity and speed necessary to effect time-critical, life-saving clinical decisions needed for safe and personalised patient care. Combining both existing and novel technologies, this will be the first nucleic acid based amplification platform that has been designed for the immediate clinical needs within critical care environments. Bringing novel technology solutions to the patient, will allow clinicians to adopt innovative approaches to patient management to improve survival, safety, patient experience and cost efficiency during the management of patients with suspected life-threatening infections.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION