NIHRDataInsights/HRCSData huggingface dataset:
Title: The Role of Cyclin-Dependent Kinase-9 Inhibition in Promoting the Resolution of Chronic Inflammation
Funder: Medical Research Council

Abstract: By demonstrating that CDK inhibitor drugs (CDKi) promote the resolution of lung inflammation through a process which involves 'driving' neutrophil apoptosis, we achieved a key aim of many years of MRC-funded research - showing that resolution mechanisms could be harnessed for potential therapeutic benefit. While CDKi (e.g., R-roscovitine) are beginning to be trialled in humans for various cancers, it is recognised that their specificity and toxicity profiles are not yet ideal. We have now generated persuasive in vitro and in vivo preliminary data that CDK9 is the key target of the CDKi in a process that involves down-regulation of Mcl-1. The importance of CDK9 in vivo is supported by pilot data using transgenic zebrafish treated with morpholino antisense oligimers to specifically knockdown CDK9. We have also discovered that CDKi inhibit release of pro-inflammatory mediators from stimulated macrophages (without inhibiting efferocytosis) in what is likely to represent an additional pro-resolution benefit. We have recently shown identical pro-resolution effects of CDKi in eosinophilic inflammation, in bleomycin-induced fibrosis and, excitingly, in a mouse model of atherogenesis. In the proposed programme we will interrogate the hypothesis that CDK9 is pivotal in maintaining chronic inflammation and their inhibition induces the resolution of chronic inflammatory/scarring diseases of the lungs and other organs. Specifically we will: 1. Test our hypothesis in zebrafish, employing a novel model of chronic atheromatous inflammation and using specific molecular knockdown approaches in genetically modified fish. 2. Confirm the pivotal status of CDK9 in models of chronic inflammation in mice, prioritising the use of a myeloid-specific inducible CDK9 knockout mouse. 3. Establish proof-of-concept assays of pro-resolution effects of CDK9 inhibition in human inflammatory macrophages to provide a platform for drug discovery.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Maximising Therapeutic Utility for Rheumatoid Arthritis using genetic and genomic tissue responses to stratify medicines.
Funder: Medical Research Council

Abstract: Research objectives: Two parallel workstrands (WS) will investigate synovial tissue and blood correlates (WS.1) and large scale blood based screening (WS.2) to identify biomarkers of response to four drugs which from the main steps in treatment escalation in rheumatoid arthritis (RA): methotrexate (MTX), anti-tumour necrosis factor (anti-TNF) and rituximab (RTX) and tocilizumab (TOC). Methodology and experimental design: WS.1: We shall search for tissue-driven biomarkers and blood correlates in the largest synovial tissue biobank of this type (2 time points 0 & 6 months biopsy) in the world & clinical datasets (over 200 patients immediately available). In addition, in a prospective randomised clinical trial (adaptive design) we will test the hypothesis that discrete cellular and molecular signatures in the synovial tissue ("pathotypes") will enrich for response to existing biologic therapies. WS.2: we will take advantage of the large observational cohorts of patient samples either already collected or which could be collected for minimal cost to undertake a comprehensive analysis to identify that will reliably identify responders/non-responders to each of the drugs. These collections include biological samples from over 3,000 anti-TNF-, 1,500 MTX- and 1,200 RTX-treated subjects. Proposed techniques and approaches: The two WSs are fully integrated through "multi-omic" approaches that constitute cross-cutting themes (CTs) incorporating genetic, genomic, transcriptomic, and proteomic studies. Both WSs converge in a large analytical and modelling package driven by experts in Bioinformatics and Statistics to identify individual or, more likely, a combination of factors that predict treatment response to each of the four drugs. A preliminary health economic assessment of identified biomarkers will also be undertaken. Exploitation of results: In collaboration with our Industry partners we have drawn up plans to commercialize potential diagnostics for patient benefit


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
Title: ThRIL;A 'first-in-human' study, evaluating the safety, tolerability with an investigation into the efficacy of Tregs in liver transplant recipients
Funder: Medical Research Council

Abstract: Liver transplantation(LT) is a successful treatment for end-stage liver disease. Despite this long-term survival remains suboptimal because of the morbidity and mortality associated with long-term use of immunosuppression(IS). However IS weaning early post LT has been largely unsuccessful, supporting the need for active tolerance induction strategies. CD4+CD25+FOXP3+cells(Tregs) play an important role in immunoregulation. We have shown that in vitro expanded murine and human Tregs promotes transplantation tolerance in animal models. The safety of these cells has been already demonstrated in phase I trials of bone marrow transplantation. ThRIL will be the first combined phase I/II clinical trial of Treg therapy in solid organ transplantation. The protocol we have devised involves the isolation and expansion of Tregs, harvested at time of transplantation from blood of LT recipients. We have expertise in expansion of large numbers of functionally suppressive and stable Tregs from healthy controls at GMP standard. We have obtained similar results using blood from LT recipients. ThRIL is an open label, randomised, controlled, parallel group, single ascending dose study, investigating the safety and tolerability of Treg immunotherapy with a cohort expansion to investigate for a signal of efficacy. Patients will be treated with ATG at time of transplantation, and started on Tacrolimus. Rapamycin will be started at 2 months, with an infusion of Tregs at 3 months post transplantation. Two dose levels of Tregs will be assessed, a low (1.0x10^6cells/kg) and high (4.5x10^6cells/kg) dose (3 active:1 control). The chosen doses are comparable to what has been safely used in published clinical trials (3x10^6cells/kg). The cohort of patients receiving the dose which is safe and well tolerated will be expanded to investigate an efficacy signal, providing the evidence required to take the development of Treg immunotherapy towards a larger Phase II/III study.


Research activity codes: 6.2 CELLULAR AND GENE THERAPIES;6.4 SURGERY
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Understanding basic mechanisms of CD4 immunity and its regulation in relation to autoimmunity and cancer pathogenesis
Funder: Medical Research Council

Abstract: Research Objectives (1) To determine whether OX40 and CD30 drive the pathology ofother models of CD4 mediated autoimmunity; (2) To investigate the support of Tregs (effector and memory) by lymphoid tissue inducer cells (LTi); (3) To understand mechanisms of tumour resistance in FoxP3KO mice deficient in OX40 and CD30; Methodology and Experimental design: (1) The impact of OX40 and CD30 deficiency will be tested in established models of CD4 driven autoimmunity; (2) The survival requirements for Tregs will be tested in vivo in genetically modified animal models; (3) The impact of OX40 and CD30 deficiency on blockade of Treg function will be dissected in murine models of anti-tumour immunity to optimize specifically anti-tumour immunity without concomitant autoimmunity.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Understanding the molecular pathways that underlie dectin-1 mediated cytokine responses
Funder: Medical Research Council

Abstract: The proposed research will examine the intracellular signaling mechanisms that control the production of cytokines downstream of the C-type lectin dectin-1 and investigate the cross talk between dectin-1 and Toll like receptor signaling. To do this a range of techniques will be used to examine these processes in primary macrophages and dendritic cells isolated from either mice or humans. The use of primary murine macrophages allows us to exploit relevant gene targeted mice to study protein function. This technique is essential to study the function of specific proteins in primary macrophages. While siRNA can be used for some of the experiments, it is frequently inefficient in macrophages and does not provided the same degree of experimental confidence in its results as gene targeting. Primary human macrophages will also be studied in order to ensure that our results translate into human systems. In addition to this small molecule kinase inhibitors, screened for selectivity by the International Center for Kinase Profiling in Dundee, will also be used to study these systems. In order to study the APC phenotype a range of experimental techniques will be used. These will include multiplex ELISAs, qPCR and expression profiling techniques in addition to standard cell culture and biochemical techniques. The project will make extensive use of SILAC based phospho-proteomics to characterize intracellular signaling events in macrophages stimulated by dectin-1 in comparison to TLR2. This will allow us to create a map of the relevant signaling networks and provide the basis for further work to identify the critical events in allowing dectin-1 to strongly activate IL-10 induction while repressing IL-12.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Defining the role of STAT1 acetylation in adaptive immunity.
Funder: Medical Research Council

Abstract: Preliminary data demonstrates that antigen, the initiator of proliferation in adaptive immunity, dramatically alters the anti-viral and anti-proliferative transcriptional effects of IFN. Further experiments suggest that this occurs by the acetylation of STAT1. This proposal tests this hypothesis and defines antigen-induced STAT1 acetylation's role in adaptive immune responses. A conditional BAC transgenic murine model, in which lymphocytes only express acetylation-resistant STAT1, with normal STAT1 elsewhere, will be developed to interrogate acetylated-STAT1's function. The model will define the significance of STAT1 acetylation in protective immune responses by challenging the mice with antigen, delivered by vaccination and virus, and assaying their adaptive immune responses. By challenge of the mice with pristane to induce murine lupus, I will investigate the role of lymphocyte acetylation in auto-immunity. To investigate how acetylation alters STAT1 responses, I will use the cutting-edge technical innovation of orthogonal unnatural amino-acid incorporation to generate site-specifically acetylated STAT1. Using a combination of surface plasmon resonance, confocal microscopy, immunoprecipitation and western blotting, acetylated STAT1 will be assessed for binding to nuclear importins, cellular localisation and phosphorylation. Translational experiments will then test the hypothesis that antigen, by acetylating STAT1 and blocking anti-viral IFN signalling, leaves CD4+ T cells susceptible to the T cell tropic virus, HIV. Human CD4+ T lymphocytes expressing acetylated STAT1 and acetylation-resistant STAT1 will be assayed for HIV resistance using pseudotyped virus. With the murine model, modified human cell lines and staff training gained from this, I will then be poised to further apply these findings to the specific murine and cell biological models of the extensive range of human illness affected by adaptive immunity and STAT1.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Regulation of Intestinal Dendritic Cell Development and Function
Funder: Medical Research Council

Abstract: Dendritic cells (DC) in the intestinal lamina propria (LP) are crucial for determining whether tolerance or active immunity is generated against the different antigens which bombard the gut. LP DC have several unique properties, including expression of CD103 and generation of retinoic acid from dietary vitamin A. It was assumed that these CD103+ DC were specialised for inducing tolerance against food proteins and commensal bacteria, whereas a distinct group of CD103- DC induced effector T cells when protective immunity is required, or when tolerance breaks down in coeliac disease or Crohn's disease. However the nature of CD103- DC in the intestine has been the subject of dispute and misconceptions, as they share markers with macrophages, which have distinct immune functions. As it is also now clear that CD103+ DC are more heterogeneous than previously suspected, the functions of LP DC in tolerance and immunity need to be explored more precisely. Recently we have developed novel strategies which allow bona fide DC to be identified accurately, finding novel populations of CD103- DC, as well as CD11b+ and CD11b- subsets of CD103+ DC. Here we will use a combination of phenotypic, genetic and functional approaches to compare how the individual subsets of DC behave in steady state intestine and in models of intestinal inflammation or after mimicking protective immunity. By studying the molecular and cellular basis of DC development in vivo and at the single cell level, we will determine how the subsets are related to each other and will examine if the unusual nature of intestinal DC reflects tissue specific precursors, or if it is "conditioned" by the intestinal microenvironment. We will then explore the local factors involved. By characterising the mechanisms controlling intestinal DC development and function under different conditions, we hope to identify targets which could be exploited for treatment of inflammatory bowel disease or for improving vaccine efficacy.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: MICA: CRAC channels, Ca2+ signalling and allergy
Funder: Medical Research Council

Abstract: Mast cells contribute to the development both of allergies, which have reached epidemic proportions in the U.K., and nasal polyposis, a chronic inflammatory response of the upper airways and which affects just over 2% of the population. Mast cells activation requires a rise in cytoplasmic Ca2+, and this is brought about by activation of store-operated CRAC channels. We have recently identified a role for CRAC channels in nasal polyposis and have discovered new physiological mechanisms that control channel activity. Furthermore, our work has revealed a novel potential strategy for treating polyposis based on our findings of how CRAC channels are regulated and which involves simultaneously targeting of K+ channels and leukotriene receptors. We now plan to test systematically this approach, using a new system we have developed for studying mast cells in a quasi-native environment. We also plan novel studies on the regulation of CRAC channels in mast cells, including control provided by the mitochondrial protein mitofusin 2 and the role of calmodulin tethered to the channel. This is particularly important because it provides a mechanism whereby activation of Orai1 selectively stimulates expression of chemokines and cytokines and is therefore a very attractive target to manipulate synthesis of inflammatory mediator production.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: MICA: Phenotyping immune responses in asthma and respiratory infections - a systems approach to understanding changes from childhood to adulthood
Funder: Medical Research Council

Abstract: Asthma, allergies and respiratory tract infections (RTIs) are the most common acute and chronic diseases and their prevalence and severity vary greatly from childhood to adulthood, with large swings occurring through puberty. This study will combine world-leading expertise in infection and immunity, a population based birth cohort study and computational analysis to identify novel mechanisms related to increased susceptibility to asthma, allergies and RTIs. We will harness the power of systems biology to the rich clinical, immunological, genetic and environmental data sets, in hundreds of subjects, either already available in the Manchester Allergy and Asthma Study birth cohort, or in new datasets collected as part of this proposal to generate: - complete clinical follow up and sampling of the cohort from birth to adulthood at 18yrs - next generation sequencing of targeted relevant immune genes - complex functional characterisation of immune responses to viral and bacterial infections, gene methylation studies and component resolved allergy diagnostics in blood collected in childhood (8yrs), early (11yrs) and late (14yrs) puberty and adulthood (18yrs) Using a flexible probabilistic framework, we will extrapolate knowledge from generated/existing data and formulate new hypotheses that will lead to functional experiments testing these hypotheses in in vitro and in vivo models. Statistical inference and experimental data on the roles of specific molecules or pathways will iterate in the hypothesis generation/validation process. We will elucidate the development of functional antiviral and anti-bacterial immune responses and of epigenetic marks from childhood to adulthood and their relation to susceptibility to asthma, allergies and RTIs, and to underlying genetic polymorphisms. These approaches together will lead to identification of new targets for development of novel diagnostic and therapeutic approaches for treatment/prevention of asthma, allergies and RTIs


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: The circadian clock as a therapeutic target for inflammatory arthritis
Funder: Medical Research Council

Abstract: This project will investigate how the clock impacts on pathogenic pathways underlying inflammatory arthritis, and test novel clock-modulatory ligands for efficacy in treating this disorder. To track temporal changes in the inflammatory environment within sites of disease, joints from arthritic mice (collagen induced arthritis) will be harvested at different circadian phases and analysed for local cytokine production (ELISA, Bioplex array, QPCR) and cellular infiltrates (flow cytometry). Temporal tracking of gene transcription in FACS purified cultures of cells from inflamed joints will identify effector cells orchestrating rhythmic production of inflammatory signals. To interrogate the role of individual cellular timers on disease rhythmicity and progression, arthritis will be induced in mice with targeted clock deletions in inflammatory cells (T cells or macrophages). Disease rhythmicity (temporal tracking of inflammatory markers, twice daily assessments of paw swelling) and severity (daily scoring, terminal histological assessment of joints) will be monitored. The contribution of circadian fluctuations in circulating glucocorticoids (GCs) to the entrainment of peripheral inflammatory oscillators will be addressed via application of corticosterone pellets to arthritic animals. The effects of clamping GC levels at the night-time high on rhythmic cytokine production will be tracked pre- and post- clamp. To validate targeting the clockwork as a treatment for inflammatory arthritis, clock-acting compounds will be tested ex vivo using murine inflammatory cells (macrophages, T-cells and synoviocytes). In subsequent intervention studies, novel compounds will be administered to mice after arthritis induction. Disease severity, inflammatory markers and histological joint damage will be assessed. Finally, in translational studies I will test the efficacy of these compounds in inflammatory cells isolated from arthritic patients and healthy controls.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: MEF2 targets and their functions in Drosophila immunity
Funder: Medical Research Council

Abstract: This proposal follows from our recent work, in which we have explored the function of the transcription factor MEF2 in immune-regulated gene expression in the Drosophila fat body. We have shown that MEF2 regulates two distinct suites of genes. In flies not experiencing an acute immune challenge, MEF2 is phosphorylated at a conserved site to promote the expression of enzymes of triglyceride and glycogen synthesis. Upon infection, MEF2 is dephosphorylated and interacts with the TATA binding protein (TBP) to bind a distinct sequence at the TATA box of many antimicrobial peptides; it is required for the expression of these genes as well. Both functions are critical: flies with MEF2 knocked down in the fat body have essentially no fat or glycogen and are severely immunocompromised against a wide variety of pathogens. The loss of phospho-MEF2 causes the loss of metabolic transcripts seen after infection with Gram-negative bacteria. Here, we propose to use ChIP-chip to identify MEF2 binding sites in fat body from infected and uninfected flies, and RNAseq to determine which transcriptional changes depend on MEF2 activity. These datasets will allow us to identify binding sites for the MEF2-TBP complex as well as direct and indirect MEF2 targets. We will then explore the biological roles of transcription factors that interact with MEF2 using in vivo functional screens. Finally, we will integrate all of these data to derive a transcriptional circuit describing the functions of MEF2 and its interactors in Drosophila immune regulation and metabolism. The project will thus identify new transcriptional circuitry downstream of, and in parallel to, this novel and exciting immune-metabolic transcriptional switch, and characterize at least some of these elements at a functional level.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM