NIHRDataInsights/HRCSData huggingface dataset:
Title: Nucleic Acid Sensing by Innate Immune Receptors
Funder: Medical Research Council

Abstract: The innate immune response is critical for successful host defence against virus infection. Cell-intrinsic mechanisms detect virus presence and signal for the induction of innate response genes such a type I interferons (IFNs) (1). Nucleic acids are often a molecular signature of virus infection and are recognised by innate receptors such as toll-like receptors and RIG-I-like receptors. In addition to their protective role in infectious disease, some of these receptors have also been implicated in inflammatory conditions. Research in my group dissects the molecular biology of activation and regulation of the innate immune receptors that sense nucleic acids both in virus infections and in inflammatory disease. Previously, we showed that progeny viral RNA genomes are recognized by RIG-I in cells infected with negative strand RNA viruses such as influenza A virus (2). These genomes bear a triphosphate moiety on the 5’-end that is essential for RIG-I activation and IFN induction (2). Such 5’-PPP-groups are absent from cellular RNA in the cytoplasm, providing an explanation for the specific triggering of RIG-I in virus-infected cells. We also contributed to projects studying the role of MDA5 and PKR in the immune response to viral infection and the induction of interferon (3,4). Currently, we are working on three complementary aspects of the sensing of nucleic acids by innate immune receptors. Firstly, by using clinically relevant viruses such as picornaviruses and hepatitis C virus, we will characterize the types of RNA recognized by RIG-I and the related receptors MDA5 and LGP2, and the mechanisms of activation of these receptors, in infected cells. Secondly, to determine how the strength and duration of the innate immune responses is controlled we will dissect the mechanisms regulating the expression of pattern recognition receptors and downstream signalling molecules at the post-transcriptional level. Thirdly, because aberrant activation of innate nucleic acid sensing pathways can lead to inflammatory diseases through the triggering of intracellular DNA and RNA sensors and the induction of type I IFN, we are studying the molecular basis of Aicardi-Goutieres syndrome. This genetic disorder mimics virus infection and is characterized by spontaneous IFN production (5). Taken together, this work at the intersection of molecular biology and immunology will provide important insights into activation of the innate immune system by nucleic acids. Our findings will have major implications for virus infection, inflammatory and autoimmune diseases and the development of vaccine adjuvants. References: (1) Rehwinkel and Reis e Sousa 2010 Science 327: 284; (2) Rehwinkel et al 2010 Cell 140: 397; (3) Schulz et al 2010 Cell Host Microbe 7:354; (4) Pichlmair et al 2009 J Virol 83: 10761; (5) Crow and Rehwinkel 2009 Hum Mol Genet 18:R130


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION;INFLAMMATORY AND IMMUNE SYSTEM
Title: Dissecting the host immune response to bacterial and HIV carbohydrate antigens to guide vaccine design
Funder: Medical Research Council

Abstract: The elicitation of protective antibodies is a key step in successful vaccination. Bacterial conjugate vaccines elicit protective antibodies specific for the carbohydrate coat of pathogenic bacteria. This, along with the recent discovery of carbohydrate-specific antibodies that potently neutralise many circulating HIV-1 isolates, highlights carbohydrates on pathogens as important, under-researched targets for vaccine design. Very little is known about the molecular rationale of antibody recognition of carbohydrate antigens, and several basic questions remain unanswered: How do carbohydrate-specific antibodies bind with high affinity? How do they discriminate between self and non-self carbohydrates? How does the immune system elicit these types of antibodies during a viral or bacterial infection? These questions will be explored by studying carbohydrate-specific antibodies against HIV-1 and bacteria. The aims of the proposal are 1) to explore the mechanisms by which carbohydrate-specific bnAbs are elicited during HIV infection and 2) to molecularly characterise antibodies elicited against bacterial conjugate vaccines and during bacterial infection. Firstly, I will characterise the binding interactions of germ line versions of carbohydrate-specific HIV bnAbs and isolate mannose-specific antibodies from HIV-infected donors to give insight into the origin of these bnAbs in HIV infected individuals. Secondly, I will characterise the antibodies elicited through immunisation with Streptococcus pneumoniae vaccines PrevnarTM and PneumovaxTM. Antigen-specific B cell sorting will be used to isolate antibodies for subsequent characterisation at the molecular level including x-ray crystallography. The overall goal of this fellowship is to increase our fundamental understanding of the antibody recognition of carbohydrates and to build a scientific foundation for rational design of carbohydrate-based vaccines against HIV-1 and other pathogens displaying carbohydrates.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION;INFLAMMATORY AND IMMUNE SYSTEM
Title: Disulfide activated protein kinase G Ialpha as a new therapeutic target in sepsis
Funder: Medical Research Council

Abstract: Sepsis is a common and often deadly medical condition that exerts an enormous burden on healthcare systems. Previously we showed that PKGIalpha can be activated by oxidative stress independently of the classical NO-cGMP activation pathway. This alternate activation pathway involves oxidants inducing a disulfide bond between the kinases two subunits. This pathway is also relevant to sepsis, consistent with it being a time of oxidative stress that drives formation of the disulfide. This explains in part the hypotension that occurs during sepsis and partly accounts for the associated organ injury as a result of their under-perfusion. Based on the literature and pilot data presented in this application, we think that PKGIalpha oxidation can also directly damage tissue (independently of hypotension and tissue under-perfusion) by inducing apoptosis. These studies proposed here are aimed at defining the relative contributions of these two pathways to injury during sepsis. In addition, as disulfide PKGIalpha formation underlies the damage caused by both these pathways (i.e. both by hypotension as well as apoptosis), we think pharmacological interventions that blocked oxidation would be protective. Consequently, we plan on developing and testing a number of drugs for their ability to prevent PKGIalpha oxidation and limit tissue damage during sepsis.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: INFECTION;INFLAMMATORY AND IMMUNE SYSTEM
Title: Experimental Human Pneumococcal Carriage to determine optimal protection from carriage and mechanisms of mucosal immunisation against disease
Funder: Medical Research Council

Abstract: Pneumococcal disease remains a research priority world-wide with high mortality from meningitis, pneumonia and sepsis and high morbidity and expense from otitis media. Conjugate vaccination programmes have shown that both carriage and disease can be prevented leading to substantial direct and additional very large herd benefits by reduction of carriage. There could be important additional gain, however, from bringing protein vaccines to licensure in order to gain from wide strain coverage, reduced production expense and potential combination with conjugates. This Experimental Human Pneumococcal Carriage (EHPC) Programme will coordinate maximum use of a human pneumococcal challenge model to study host/pathogen interactions critical to the prevention of pneumococcal carriage and disease by vaccination. We will use a variety of pneumococcal strains to experimentally challenge human volunteers with bacteria. We will recruit both healthy subjects and those with risk factors for pneumococcal disease in order to determine both pathogen and host factors that determine susceptibility and correlates of protection. We will manage a portfolio of commercial vaccine development studies using the human challenge model in parallel with the science discovery programme. The EHPC platform itself requires a complex, expensive integrated team including clinical, microbiological and immunological teams. In order to fully exploit the scientific potential of the platform, we have established collaborations with 20 other laboratories, predominantly in the UK. Our collaborators bring outstanding international expertise, a shared vision of global vaccination against pneumococcal disease and the offer of practical help in accessing the necessary additional resources to apply cutting-edge technology to the samples this model will generate.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION;INFLAMMATORY AND IMMUNE SYSTEM
Title: An integrated metagenomic approach to understanding disease heterogeneity in severe sepsis due to community acquired pneumonia
Funder: Medical Research Council

Abstract: Sepsis represents a major public health burden worldwide with significant associated morbidity and mortality. Evidence suggests that susceptibility to sepsis and clinical outcome is modulated by genetic factors. However, current research has been limited by a complex, heterogeneous disease phenotype. Community acquired pneumonia (CAP) is the commonest cause of sepsis. Its diverse microbial aetiology remains elusive in one-third of intensive care patients and evidence suggests we underestimate the role of viral and bacterial coinfection. This fellowship aims to advance our understanding of the aetiology and host response in severe sepsis due to CAP by building on an established cohort of patients recruited through the UK Genomic Advances in Sepsis (GAinS) study. I will utilise next-generation sequencing techniques to analyse the nucleic acids of viral and bacterial species in patient plasma samples, enabling more accurate classification of disease aetiology. This metagenomic profiling will be used to inform and extend the genomic and transcriptomic analyses performed to date for the GAinS cohort, including analysis of gene expression signatures and integration with expression quantitative trait loci mapping and a genome-wide association study of sepsis survival. This integrated approach has the potential to enable clearer resolution of biological processes and define novel therapeutic targets in sepsis.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION;INFLAMMATORY AND IMMUNE SYSTEM
Title: The molecular basis of a novel mechanism of antigen presentation: phosphoantigen-dependent activation of Vgamma9/Vdelta2 T cells by BTN3A molecules.
Funder: Medical Research Council

Abstract: BTN3A proteins are members of the B7-like group of immunoglobulin receptors, which interact with and modulate the function of T cells. Recent data show that BTN3A1 influences the activation of human gammadelta (gd) T cells by direct or indirect presentation of self/non-self phosphoantigens (pAg), a mechanism relevant to the immune-surveillance of microbial infections and of transformed and stressed tissues. In response to the microbial metabolite HMB-PP and the aminobisphosphonate drug zoledronate, we have evidence that multiple BTN3A molecules are required for gd T cell activation, consistent with recruitment into a multi-protein complex. We have used a number of techniques to identify BTN3A1 interacting molecules and propose to investigate their role in regulating gd T cells. Immunoprecipitation and protein mass spectroscopy were used to identify chaperone molecules potentially required for the formation of the CD277 antibody epitope, the critical determinant of gd T cell activation. Yeast-two hybrid assays were used to identify the cytoskeletal adaptor periplakin. The amino-terminal plakin domain of periplakin, composed of six spectrin repeat alpha-helices and SH3 domain, interacts with a membrane proximal di-leucine motif in the BTN3A1 cytoplasmic tail, a mechanism with similarity to E-cadherin/p120-catenin pathways. Our data suggest a role for BTN3A in epithelial cell homeostasis, linking the cytoplasmic sensing of pAg, metabolic intermediates of the mevalonate pathway, to BTN3A protein folding and glycosylation in the endoplasmic reticulum. We propose to exploit these unpublished observations. We will conduct binding assays, crystal trials and in vitro mutagenesis to explore the interaction between the B30.2 domain of BTN3A proteins and pAg. We will investigate the role of periplakin and related molecules and probe the oligomeric coupling of different BTN3A isoforms in relation to trafficking and T cell activation.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION;INFLAMMATORY AND IMMUNE SYSTEM
Title: How does inflammation regulate CLEC-2-mediated thrombosis after infection?
Funder: Medical Research Council

Abstract: Thrombosis is a common consequence after infection and associated with poor outcome. Despite its fundamental importance in infection, it is poorly understood. In this project we want to develop our findings that have led to the identification of a novel mechanism underpinning how thrombosis is induced after infection. To identify this role for CLEC-2 we have used a murine model of invasive salmonellosis where the infection and thrombosis persists for weeks and where infection is required for the induction of thrombosis but not its maintenance. At its heart is CLEC-2-mediated activation of platelets via podoplanin ligation. This occurs through the TLR4 and IFNg-dependent recruitment of podoplanin-expressing monocytic cells to the liver. In conjunction with other peri-vascular podoplanin-expressing cells these cells appear to contact platelets through damaged regions of the vasculature resulting in their activation. The thrombi form in these damaged sites. What is significant is that targeting this mode of platelet activation is unlikely to have significant effects on other areas of haemostasis and so is attractive from a therapeutic view-point. The work raises multiple key questions. Although we cannot answer all of them in one grant we wish to focus on a number of key elements that can only be addressed in this model. These fundamental questions include: i) Can thrombosis have beneficial as well as harmful effects? ii) Do CLEC-2 and inflammation only play roles in the induction of thrombosis; iii) Does adaptive immunity promote or inhibit the longevity and extent of thrombosis; iv) How does thrombocytopenia affect thrombus development?


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION;INFLAMMATORY AND IMMUNE SYSTEM
Title: Intravenous fluid for adults with sepsis in sub-Saharan Africa: developing the design of an randomised controlled trial
Funder: Medical Research Council

Abstract: Sepsis is a life threatening organ dysfunction caused by a dysregulated host response to infection. Globally, there are 31.5m cases per year; in-hospital mortality in Malawi is 22-50%. Supportive therapy is key to good outcomes. Intravenous (iv) fluids are used to support a cardiovascular system compromised by peripheral vasodilatation, insufficient cardiac output, and leakage of fluid to the interstitium. While fluids can raise blood pressure, they do not counter the circulatory dysfunction. In high incomes settings, aggressive intravenous fluid (and intensive care [ICU]) management is associated with reduced mortality (OR 0.64). However, potentially beneficial adaptive responses to hypotension are abolished by high volumes of fluid, leading to acute respiratory distress syndrome, and worsening kidney function. This becomes apparent where ICU is not available. In LMIC, the only relevant trial in adults was stopped early due to high mortality. An uncontrolled Ugandan implementation study suggested benefit, but no dose-response effect above 1 litre in the first 6 hours (cf: 4.9l in a US study). Worryingly, the FEAST study from sub-Saharan Africa showed higher mortality in children treated with more aggressive fluid therapy. A randomised clinical trial of iv fluid treatment strategy in adults is warranted, comparing conservative therapy versus a blood-pressure-target-driven approach. This development proposal will: 1) determine current practice and inform study protocols; 2) refine inclusion criteria and demonstrate feasibility of recruitment. Using standard clinical pathways, and leveraging existing research structures, we will identify septic patients in the emergency department, intensively record their baseline and dynamic physiological responses and fluid administration over the first 6 hours, and record outcomes. A systematic review of fluid administration in research and clinical practice in LMIC will be performed.


Research activity codes: 6.3 MEDICAL DEVICES;7.3 MANAGEMENT AND DECISION MAKING
Health categories: INFECTION;INFLAMMATORY AND IMMUNE SYSTEM
Title: STEROID PROTECTION FROM TUBERCULOSIS-ASSOCIATED IMMUNE RECONSTITUTION INFLAMMATORY SYNDROME
Funder: Medical Research Council

Abstract: Patients co-infected with HIV-1 and TB are at risk of developing a highly inflammatory complication known as Immune Reconstitution Inflammatory Syndrome (TB-IRIS) upon commencing antiretroviral therapy (ART). There are no validated prognostic biomarkers for TB-IRIS and prednisone is the only treatment that has been evaluated in randomised placebo-controlled trials. A recent trial demonstrated that preventive prednisone given at the time of ART initiation reduced risk of TB-IRIS by up to 30%. Building on the availability of clinical samples from this trial, I aim to investigate how to improve early diagnosis of TB-IRIS and increase the effectiveness of treatment options. I rationalise that a biomarker signature predictive of patients with high risk of developing TB-IRIS will justify prescription of high dose prophylactic prednisone as its protective benefits outweigh the risk of adverse side-effects. I further argue that drugs targeting biological pathways specific to TB-IRIS pathogenesis may provide better protection against TB-IRIS symptoms. I will perform RNA-Seq and derive transcriptional signatures at each longitudinal timepoint. The transcriptome findings will be complemented with protein profiling in the corresponding plasma. I will dissect the transcriptomic and metabolomics metadata to identify functional pathways associated with TB-IRIS pathogenesis and those related to prednisone's mode of action in suppressing inflammation. Using in vitro experiments I will further investigate whether inhibitors to specific inflammatory signalling pathways may better suppress cytokine/chemokine production than prednisone. Finally, I will also explore if TB-IRIS may be in part due to genetic predisposition. To test this I will perform a target-specific gene polymorphism study on genes with known phenotypic changes, such as those described to associate with TB and TB-IRIS and identify whether not protection from TB-IRIS can be segregated according to genotypes.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;5.1 PHARMACEUTICALS
Health categories: INFECTION;INFLAMMATORY AND IMMUNE SYSTEM
Title: A miniaturised laser isotope ratiometer for early diagnosis of sepsis by exhaled breath analysis
Funder: Science and Technology Facilities Council

Abstract: This project aims to develop a prototype medical instrument for the rapid and accurate diagnosis of sepsis. Sepsis is a serious complication of infections, and without timely treatment can lead to multiple organ failure and death. In the UK 44,000 deaths per annum are attributed to sepsis, and 14,000 of those are thought to be preventable with improved diagnosis and reduced delays in beginning treatment. Delays in treatment of just a few hours can have a significant impact on the outcome for the patient. Current tests for sepsis require samples of blood or other fluid from the patient to be taken to a laboratory for analysis. There are two drawbacks associated with current testing: Firstly, the process of sending samples for analysis introduces delay, which in turn reduces the chances of successful treatment; secondly, patients cannot be monitored continuously and so the onset of the condition may be missed. Researchers at the Rutherford Appleton Laboratory (RAL) have developed an instrument called a laser isotope ratiometer (LIR) that should be able to identify the very early stages of sepsis by analysing the composition of exhaled breath from the patient. Changes in the ratio of naturally occurring forms carbon dioxide exhaled by patients can indicate the presence of sepsis. The LIR will be capable detecting these changes in real time by analysing subtle changes in the infrared light absorbed by the exhaled breath. Crucially the results of this analysis will be interpreted by the instrument and presented to medical staff as a simple "yes" or "no" indication of whether the patient has sepsis or not. The method is non-invasive and, for the sickest patients that are not able to breathe for themselves, the LIR could be attached to ventilators to provide continuous monitoring. During the project the instrument scientists at RAL will work with clinicians at King's College London (KCL) to determine whether the LIR can provide a reliable way of identifying patients with sepsis. This will be done through clinical trials where KCL will provide anonymised sample bags containing exhaled breath from patients with and without sepsis for blind testing by the LIR at RAL. The LIR has been successfully demonstrated in other application areas, and is being exploited commercially for the oil and gas industry. During this project the work at RAL will include preparation of an existing miniaturised version of the LIR for breath analysis, characterization of its performance, and development of the test protocol to ensure accuracy and reliability. If initial tests using sample bags are successful there will be an opportunity for the LIR to be deployed in a clinical environment at King's College Hospital for further testing. This will enable a better idea of the effectiveness of the approach, including potential cost savings.


Research activity codes: 4.5 RESOURCES AND INFRASTRUCTURE (DETECTION)
Health categories: INFECTION;INFLAMMATORY AND IMMUNE SYSTEM