NIHRDataInsights/HRCSData huggingface dataset:
Title: A BIOMARKER AND PATHWAY DISCOVERY PROGRAMME IN INFLAMMATORY DISEASE
Funder: Medical Research Council

Abstract: Autoimmune and inflammatory diseases are chronic, relapsing remitting conditions affecting up to 10% of the population, a figure that is rising rapidly in both the developed and developing worlds. These diseases are often difficult to definitively diagnose and follow very variable courses, with some patients following an aggressive course while others follow a more benign course. Early diagnosis and the ability to predict likely course will be key to the introduction of treatments tailored to the individual patient and therefore likely to be more efficacious. Using transcriptional analysis of purified leukocyte subsets we have begun to uncover gene signatures with such diagnostic and predictive utility in several immune-mediated diseases. We will complete the analysis of samples generated over the last ten years and in addition to extend these analyses into new diseases and additional cell types. For these new studies we will use high-throughput, multi-chromatic, fluorescence activated cell sorting to isolate rarer populations of cells at high purity and with sufficient yield to allow downstream analyses. We will also move away from microarray-based measurements of cellular transcriptomes to the use of next generation sequencing-based RNA-Seq, which will be cost-effective and provide a more comprehensive view of both the mRNA and MiRNA transcriptomes. In addition to these cell population level transcriptomic analyses we will also perform cutting edge single cell transcriptomics to examine the heterogeneity of specific populations. Finally, we will reanalyse existing and novel genome-wide association datasets stratified by clinical outcome to identify novel genetic variants associated, not with disease prevalence, but with disease prognosis. It is anticipated that the integrated analysis of these genomic and genetic data with detailed clinical data using existing and novel software tools will lead to the identification of useful novel biomarkers


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;5.1 PHARMACEUTICALS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Leukocyte guidance and gradient interpretation in vivo
Funder: Medical Research Council

Abstract: Neutrophil migration to sites to infection or injury is a major driving force of inflammation. However, little is known about how neutrophils sense inflammatory guidance cues in vivo. We will address this knowledge gap by exploiting the zebrafish model, which uniquely combines amenability to in vivo imaging and genetic manipulation. In previous work, we identified a zebrafish homologue of a well-known human chemokine, CXCL8. Using a combination of in vivo imaging, quantitative and molecular approaches, we discovered that this chemokine forms tissue-bound gradients by binding extracellular proteoglycans and that neutrophis pursue these gradients in a complex manner by adjusting 'gears'. My objective is to further elucidate neutrophil guidance mechanisms by using and extending the tools I established. First, we will explore how neutrophils interpret chemokine gradients in vivo. For this we will probe intracellular gradient sensing events using appropriate fluorescent probes and high-resolution imaging. This will provide unprecedented insight into the information processing underlying complex neutrophil migration behaviours. Secondly, we will investigate how tissue proteoglycans regulate chemokine signaling and concentration at sites of inflammation. For this we will functionally assess chemokine mutants, as well as identify and genetically perturb candidate proteoglycans. This will illuminate the molecular and environmental requirements for functional gradient formation. Finally, we will explore the bigger picture of neutrophil inflammatory responses and ask how different cues, beyond chemokines, contribute to neutrophil guidance. This will provide insight into the function of poorly understood guidance cues and help obtain a more integrated understanding of neutrophil inflammatory responses. Thus, our studies will provide a better understanding of the molecular mechanisms underlying neutrophil guidance, which may open new avenues for treating inflammatory diseases.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Investigating Yap as a Novel Therapeutic Target for Rheumatoid Arthritis
Funder: Medical Research Council

Abstract: Rheumatoid arthritis (RA) causes devastating joint damage. Despite significant therapeutic advances, two major problems remain unresolved: 1) up to 30% of patients fail to respond to treatment; 2) progression of joint damage can occur even when clinical remission is achieved, suggesting that joint destruction and inflammation are at least partly uncoupled. Hallmark of RA is synovitis, with pathological outgrowth of synovium (pannus) sustained by proliferation of mesenchymal stem cells/fibroblast-like synoviocytes (MSC/FLS). The pannus is a tumour-like structure resulting from uncontrolled tissue growth. A key molecular pathway that controls tissue growth is the Hippo pathway, restricting the activity of Yes-associated protein (Yap). Our preliminary findings indicate that (i) Yap expression is high in MSC/FLS in inflammatory arthritis and (ii) high levels of Yap activity cause MSC/FLS proliferation. We hypothesise that Yap is a key player in the stromal cell expansion during synovitis leading to pannus formation. To investigate whether Yap activation in synovial stromal cells causes pannus formation and induces an RA-like invasive MSC/FLS phenotype, we will generate transgenic mice in which expression of constitutively active Yap is Dox-inducible in stromal cells in the joint. Conversely, to determine whether Yap inhibition in the synovium ameliorates arthritis, we will use Yap-flox mice to knockout Yap in the antigen-induced arthritis. Finally, we will explore pharmacological targeting of Yap in arthritis by administering a recently identified Yap inhibitor. We will use our established double-nucleoside-labelling scheme to investigate proliferation of MSC/FLS in synovium, and will assess synovial pannus formation and erosions. We will also assess invasiveness of the MSC/FLS ex vivo following Yap activation or inhibition. In conclusion, this study will elucidate the role of Yap in pannus formation and provide proof-of-concept of Yap as a therapeutic target for RA.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: MICA: Targeting C5aR in chronic inflammation, renal fibrosis and late graft dysfunction
Funder: Medical Research Council

Abstract: The proposed research will explore the therapeutic potential for targeting C5aR in chronic inflammation, renal fibrosis and late graft dysfunction. We will employ a novel, orally bioavailable small inhibitor of C5aR (CCX168), a compound that is currently studying in Phase II clinic trial in subjects with ANCA-associated renal vasculitis, and the transgenic mice (huC5aRtg) in which mouse C5aR has been replaced by human C5aR under fully native transcriptional control. Using this novel system, we will determine whether targeting C5aR attenuates renal chronic inflammation and fibrosis in a native kidney IR injury model and syngeneic kidney transplant model; and whether targeting C5aR improves long term graft function in an allogeneic kidney transplant model. We will test different protocols of CCX168 administration aiming to target C5aR at both the acute and the tissue repair phases (day -1 to 20), the acute phase only (day -1 to 3) and at the tissue repair phase only (day 3 to 20). The outcome will have clinical implications for prevention and intervention as well as improve our understanding of how C5aR signalling contributes to renal fibrosis. Performing kidney transplantation between donor and recipient mice specifically carrying the target receptor will enable us to dissect the impact of C5aR signalling on donor and recipient cells and its influence on renal fibrosis and late graft function. In addition to in vivo studies, we intend to explore cellular and molecular mechanisms involved in C5aR mediated renal fibrosis by using several cell culture systems (i.e. renal fibroblasts, renal tubular epithelial cells and myeloid derived cells).


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Identifying a crucial pathway by which regulatory T-cells control immunity via integrin alphavbeta8 and TGF-beta.
Funder: Medical Research Council

Abstract: T-cell-mediated immunity is essential in protection from pathogens, but aberrant responses can lead to inflammatory diseases such as inflammatory bowel disease and multiple sclerosis. Key cells in preventing harmful T-cell responses are CD4+ Foxp3+ regulatory T-cells (Tr). Mutations that prevent Tr development cause severe T-cell mediated inflammation in mice and humans, and transfer of Tr into mice protects from ongoing inflammation. Indeed, current human clinical trials are attempting to use Tr as a therapy in human inflammatory disorders. Thus, it is crucial that the mechanisms by which Tr control T-cell responses are determined, to aid development of future Tr-based therapies for inflammatory disease. Our exciting preliminary data reveal a novel pathway by which Tr suppress inflammation. We find that Tr activate latent forms of the cytokine TGF-beta, via expression of the integrin alphav beta8 (avb8). Importantly, expression of integrin avb8 is essential for Tr to suppress inflammatory T-cells in a mouse model of colitis. Thus, our data suggest that TGF-beta activation by Tr, via a specific integrin, is fundamentally important in Tr-mediated control of inflammatory T-cell responses. However, many important questions remain. Are specific Foxp3+ Tr subsets specialised to activate TGF-beta via integrin avb8, and what are the mechanisms by which avb8 supports Tr-mediated T-cell suppression? Is the pathway important in other inflammatory diseases, or is it specific for T-cell regulation in the gut? Is the pathway dysregulated in human inflammatory disease? Using conditional KO mice, in vitro immune cell assays and human tissue samples, we will address these important questions, uncovering a central mechanism by which Tr regulate inflammatory T-cell responses via TGF-beta activation. Such work is crucial in identifying potential therapeutic targets for promotion of Tr function, with the aim of dampening T-cell responses in inflammatory disease.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Characterisation of the Mechanism of B Cell Receptor Triggering
Funder: Medical Research Council

Abstract: B cell activation is initiated in response to antigen binding to the B cell receptor (BCR). While much is known about the downstream signalling following B cell activation, what remains unresolved is how antigen binding to the extracellular domain triggers this signalling cascade. In this project we aim to gain a clearer understanding of the exact mechanism of BCR triggering. We have three key aims: (1) To establish the oligomerisation state of the BCR in the resting, non-antigen bound state using Two Colour Co-incidence Detection (TCCD). (2) To establish whether there is any evidence to support the Kinetic Segregation (KS) model in BCR triggering. We plan to use hen egg-white lysozyme (HEL) as our antigen and present it to HEL-reactive B cells in a planar lipid bilayer system. We will present antigen of varying lengths in order to test the idea that the size of the gap between membranes affects B cell triggering, through the physical exclusion of inhibitory phosphatases which we will label using fluorescent probes. (3) Finally, we will use the above methods to establish whether there are any differences in BCR triggering across different B cell subsets from anti-HEL specific transgenic mice. A thorough understanding of these early events in B cell activation is necessary for a comprehensive understanding of the B cell immune response and what constitutes immunogenic and tolerogenic antigens. This work has significant potential clinical implications. Abnormal B cell activation can result in autoimmune diseases, hypersensitivity and lymphoid cancer. The ability to manipulate the triggering mechanism therefore has potential therapeutic implications for future drug design. Furthermore, full utilisation of the B cell response could be harnessed to optimise immunity induced by vaccination.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: T-bet as a master regulator of mucosal immunity and inflammatory bowel disease.
Funder: Medical Research Council

Abstract: Inflammatory bowel disease (IBD) is a chronic immune mediated disease of unknown cause. Inappropriate activation of mucosal immunity directed against commensal gut bacteria is likely to be instrumental. Innate immune cells, such as dendritic cells (DCs) and innate lymphoid cells (ILCs) are crucial players mediating host-microbe interactions in the gut. We are using a combination of techniques in order to address these important questions in a multidisciplinary manner. 1. The role of T-bet in vivo: we will define the functional role of the transcription factor T-bet in DCs and ILCs in homeostatic, inflammatory interactions and infections with intestinal bacteria by interrogating constitutive and lineage-conditional knock out mouse lines (e.g. NKp46-Cre x T-betfl/fl, CD11c x T-betfl/fl) Experimental models of acute and chronic intestinal inflammation will be employed to define the functional role of T-bet in different intestinal innate immune cells in these knockout lines. We will also define the transcriptional mechanisms controlled by T-bet and GATA3 by ChIP-seq and RNA-seq technology in ILCs and DCs. 2. The role of T-bet in the ontogeny and plasticity of ILC: we will utilise a newly generated T-bet-Cre x Rosa26YFPfloxstop to fate-map ILCs in vivo. This line will be interrogated under homeostatic condition and after infectious and inflammatory stimuli. 3. The role of the host microbiota in disease: using next generation sequencing and transplant of microbiota, we will determine the bacterial species responsible for colitis and how the immune system modulate the composition of the microbiome.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: The use of next generation sequencing to measure the effects of antibiotics on resistance in the host microbiota
Funder: Medical Research Council

Abstract: Aims: I will develop a semi-quantatitive assay of antibiotic resistance genes (resistome) using b Next Generation Sequencing (NGS) and bioinformatic analysis of faecal samples. 1) Samples from 20 patients will be used to develop the assays to compare against conventional culture-based resistance assessment. 2) A Cross-Sectional Study of 100 patients will investigate: The extent to which environmental exposure to resistant bacteria affects the resistance profile, the baseline distribution of the resistome, and whether the duration and route of antibiotic use affects resistance in the faecal flora. 100 participants will allow the standard deviation of the 'resistome' to be estimated within 14% with 95% confidence (2-sided alpha=0.05) Methods 1) Appropriate ethical approval and patient consent will be obtained. 2)Conventional microbiology performed using culture on selective medium and qualitative assessment of resistance. 3) Genomic analysis : DNA extraction using mechanical disruption and Qiagen faecal DNA kit, Illumina Miseq and Hiseq sequencing platforms. Bio-informatics analysis using the Oxford MMMC pipeline, including BLAST searches and de-novo assembly against reference genes. 4) Epidemiological analysis using conventional statistical analysis. Opportunities arising from this study: 1) Translational: this study will provide direct evidence on antibiotic selection pressure to support choice of antibiotic in guidelines and evidence to persuade clinicians to reduce antibiotic use. 2) Scientific: the assay would potentially form a primary superiority endpoint for an intervention trial comparing antibiotic strategies. Clinical outcomes and antibiotic consumption are expected to form secondary non-inferiority and superiority endpoints respectively. It will also expand the existing knowledge on mechanisms of resistance selection in the host microbiome.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: MICA: Suppressing inflammation to enhance antigen-specific immunity in older humans using p38MAPK inhibitors and vitaminD3
Funder: Medical Research Council

Abstract: We will use two human experimental models to clarify mechanisms behind decreased immune responses during ageing. This involves injecting clinically approved antigens (varicella zoster skin test antigens, tuberculin PPD) into the upper forearm in young (<25 yrs) and elderly individuals (>70 years), followed by skin biopsy or suction blister induction to isolate cells from the site of the response. We will also inject saline or apply the irritant cantharadin to the skin to study the propensity for non-specific inflammation during ageing. Preliminary data suggest that non-specific inflammation is increased in older individuals. We will perform global gene expression analyses of these biopsies taken from old subjects who have been pre-treated with either a p38 inhibitor or vitamin D3 to determine whether the inhibition of baseline inflammation can enhance the response to antigen challenge. The global gene expression profiles will be interrogated by signalling pathway modelling and by analysis with a cell specific gene expression atlas developed by the Co-PIs at the Roslin Institute. This will identify the resident leukocytes are responsible for the high baseline inflammation and these cells will be further investigated in vitro. We will also investigate the phenotype and function of antigen specific T cells that will be isolated from the site of antigen challenge in the skin before and after p38 inhibitor or vitamin D3 treatment. Zostavax and BCG provide live attenuated vaccination strategies against VZV and TB that are less effective in the elsderly. It is not known whether this may reflect altered viral replication kinetics in ageing skin resulting in reduced antigenicity. Each vaccine will be administered by intradermal injection into young and elderly individuals. Biopsies of the injection sites will be subjected to RNAseq analysis (Illumina HiSeq platform) to obtain quantitative host and pathogen transcriptomic data.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: MICA: Childhood Arthritis Response to Treatment consortium - partnership to define stratified medicine tools for childhood inflammatory arthritis
Funder: Medical Research Council

Abstract: The primary goal of this partnership is to create the Childhood Arthritis Response to Treatment consortium (CHART), which aims to improve directly the clinical care of children with Juvenile idiopathic arthritis (JIA), by bringing together the major ongoing UK studies of JIA treatment response, and includes patients/families affected by JIA, as well as clinicians and researchers from across the UK, in order to develop a robust platform that will enable a stratified approach to treatment interventions in JIA. Predictors of response to medication to inform treatment stratification are much needed in JIA. Unopposed joint inflammation in non-responsive patients is associated with increased disability, and creates personal / economic burden for many years into adult life. Currently no validated biomarkers exist that can identify children who will fail to respond, or whose disease is resistant to either methotrexate or biologic agents. CHART will bring together existing large JIA cohort studies, key stakeholders (scientists, clinicians, patients and families), and their collaborative infrastructure and networks, to work together. The specific objectives of the CHART consortium, during this partnership are to: 1. Evaluate the clinical data and sample protocols in the currently available JIA cohort studies 2. Collate and align the data available within a common platform 3. Define and agree standardised 'core' clinical dataset, response outcome measures, sample protocols and IT for going forward 4. Expand and extend the existing cohorts by inclusion of cases from existing and new centres, using the agreed common standardised core data set and protocols The creation of the Consortium, generation of the large combined JIA dataset in a single platform, and agreement of harmonised data and sample collection protocols, will ensure that the Consortium is ideally placed to obtain future funding to achieve our longterm goals of stratified medicine for JIA.


Research activity codes: 7.4 RESOURCES AND INFRASTRUCTURE (DISEASE MANAGEMENT)
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: A systems-genetics approach to dissect inflammation in fibrosis
Funder: Medical Research Council

Abstract: The overall aim of this project is the identification of the genetic determinants of inflammation in wound healing and more generally in fibrosis. We will undertake a systems-genetics approach where genetic determinants of complete transcriptome in primary bone marrow derived macrophages of an outbred mice population will be integrated with a genome-wide association study (GWAS) for wound healing in the same population. To achieve this, we have cultured bone marrow derived macrophages from 1370 outbred mice and also collected the wound healing phenotype by using the ear punch model. Our preliminary GWAS for wound healing using the genotype/haplotype data (7 million single nucleotide polymorphisms) in these mice showed that it is a heritable and polygenic trait. We also showed that Tnfa, Ccl2 and Tgfb1, Vegfa, four major wound healing-associated genes known to be expressed in macrophages correlated positively and negatively respectively with the ear wound area in BMDMs from 92 outbred mice. We will perform mRNA sequencing by high throughput sequencing (RNA-seq) in 250 outbred mice. This will generate a comprehensive catalogue of the genetic determinants of macrophage gene expression (expression Quantitative Trait Loci; eQTLs), splicing QTLs (sQTLs) and gene co-expression networks. We will use the complete macrophage transcriptome for correlation with the wound healing phenotype and integrate the results with the GWAS for wound healing to identify master genetic regulators (mGR) of networks associated with wound healing. We will functionally validate these mGR in mice macrophages and establish whether they are present in human tissues from scleroderma patients where macrophage-mediated inflammatory fibrosis is well known. We will finally test whether the wound healing-associated networks in mice are also enriched for genetic susceptibility signals in 3 inflammatory fibrotic conditions: idiopathic pulmonary fibrosis, scleroderma and Crohn's disease.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM