NIHRDataInsights/HRCSData huggingface dataset:
Title: MICA:The Potential of Multipoint Adult Progenitor Cells as a Novel Therapeutic Strategy in Alcoholic Hepatitis
Funder: Medical Research Council

Abstract: This project aims to determine whether alcoholic hepatitis (AH) may be amenable to treatment by multipotent adult progenitor cell (MAPC) infusions, and to investigate the underlying mechanisms. I hypothesise that MAPC can reduce liver injury in AH by reducing hepatic sinusoidal endothelial cell (HSEC) activation and ingress of inflammatory effector cells, whilst enhancing neutrophil phagocytic activity. Our department has established a murine model of AH using NRF2-/- mice, fed a Lieber-DeCarli (LdC) diet and alcohol. Objectives: (1) I seek to validate our AH murine model by characterising the evolving immunological and regenerative response during injury and recovery. During injury and repair, I will assess liver injury, analyse leukocyte composition using flow cytometry and use DNA labelling techniques to quantify hepatocyte proliferation. Human blood samples will be used for clinical correlation. (2) I will determine the effect of MAPC on the inflammatory and regenerative response in this mouse model. Infusions will vary in dose (0.125x10^6 to 1x10^6) and will be given either during or after injury (day 13 or 17), to determine optimal dosing and timing of delivery. (3) I will determine the effect of MAPC on HSEC activation, through study of patterns of adhesion molecule expression. PCR and immunostaining will quantify levels of ICAM, VCAM and VAP1 in human HSEC. Confocal microscopy will be used in mice. (4) To determine the molecular mechanisms of MAPC action, I will identify potential molecules secreted by MAPC that may mediate their effects on HSEC activation or affect oxidative stress. This will be tested by modulating candidate factors using neutralising antibodies/ siRNA. I will also test effects of MAPC on neutrophil phagocytosis and T-cell proliferation in co-culture studies in vitro. Defining efficacy and mechanism of action of MAPC in this pre-clinical model of AH will develop a better understanding of potential new treatments.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: ORAL AND GASTROINTESTINAL
Title: Transcriptional profiling of circulating leukocyte populations in primary biliary cholangitis
Funder: Medical Research Council

Abstract: Primary biliary cholangitis (PBC) is an autoimmune liver disease characterised by destructive cholangitis affecting the small, intrahepatic bile ducts, leading in many patients to end-stage liver disease with attendant need for liver transplantation. The only licenced therapies are ursodeoxycholic acid (UDCA) and obeticholic acid (OCA). It is well-established that the liver biochemistry on treatment with UDCA (so-called 'UDCA response') strongly predicts long-term outcome. Current guidelines therefore recommend that UDCA response after 12 months of treatment be used to risk-stratify patients and determine eligibility for second-line treatment, e.g. with OCA. The problem with this step-up approach is that patients in greatest need of second-line treatment end up waiting longest to receive it. Methods are needed to identify high-risk patients at baseline for early introduction of second-line agents. Our group previously developed the UDCA Response Score (URS) to predict UDCA response - but this is a complicated equation, which might inhibit its use in practice. In the proposed CRTF, I aim to discover and validate genetic and transcriptional biomarkers for UDCA response. I will undertake genotype-phenotype analysis of 5,700 well-characterised, genotyped cases in the UK-PBC Research Cohort to identify variants associated with UDCA response, from which I will derive a genetic risk score (GRS) with validation in external cohorts. I will undertake transcriptional profiling using RNA-sequencing of peripheral blood leukocyte subsets isolated from newly-diagnosed PBC patients prior to their starting treatment with UDCA, aiming to identify the minimum panel of differentially expressed genes (DEGs) that best classifies subsequent UDCA response, which may in future be developed as transcriptional biomarkers. I will determine whether the GRS or DEGs outperform or improve the URS, and where appropriate, work with industry to develop these biomarkers for clinical application.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: ORAL AND GASTROINTESTINAL
Title: Strain resolved metagenomics for medical microbiology
Funder: Medical Research Council

Abstract: The aim of this proposal is to develop methods to extract strain genomes directly from metagenome data. This has the potential to revolutionise the in situ study of microbial communities by allowing us to determine the medically relevant microbial units, their abundances and their genomes. This will be a substantial leap forward from 16S rRNA gene taxonomic profiling or read based metagenomics that treats the community as a 'bag of genes'. Both ignore the genome context of predicted genes, crucial information for inferring pathogenicity or the functional role of commensal organisms in the human microbiota. Assembly of metagenome data is challenging because species can be present in multiple strains. This leads to repeat regions between strains, and complex assembly graphs that give fragmentary assemblies. It is possible to bin these fragments together as a post assembly step using information on abundance across samples but it would be more powerful to integrate this information directly into the assembly process. We will develop Bayesian algorithms based on graphical models to find the optimal paths and their number through the graph. Each path will then define a strain haplotype at high resolution. Long repeats may still cause issues and to address this we will devise the graph algorithms such that long read technologies can also be used. This will allow simultaneous resolution of strain haplotypes on shared regions and their long-range accessory genome structure. We will apply these methods to a longitudinal study of changes in the microbiota of patients with pediatric Crohn's disease (CD) during treatment with exclusive enteral nutrition (EEN). We will resolve changes in abundance of microbes at the strain level for children that do or do not enter remission. We will use CD as a test bed for these methods, but this paradigm will be universally applicable to microbial communities from diverse environments ranging from the human gut through to soil.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: ORAL AND GASTROINTESTINAL
Title: Understanding the pathogenesis of Epstein-Barr virus-associated complications arising in patients treated with immune checkpoint regulators
Funder: Medical Research Council

Abstract: Background: Immune checkpoint regulators (iCR) have revolutionised the management of some cancer types, but are associated with immune related adverse events including immune related colitis (irColitis). Whilst we know the bacterial microbiome mediates response and complication in iCR therapy, little is known about the effects of the viriome. EBV is a ubiquitous viral pathogen present in 95% of the population; we have recently made the first link between this virus and complications of iCR. In a series of 13 patients suffering immune related colitis following ipilimumab, all four colonic perforations were associated with the recently recognised EBV positive mucocutaneous ulcer (EBVMCU). The presence of EBVMCU in this context is unexpected, but treatment related immunosuppression and specific CTLA-4 mediated effects are implicated. Purpose of the study: 1. Characterise the clinicopathological features of EBVMCU in irColitis. 2. Examine the effects of iCR on EBV specific immunity. Plan of investigation: The study will comprise two components: 1. A multicentre study to characterise the clinicopathological features of EBVMCU in irColitis. We will retrospectively examine the surplus diagnostic FFPE material of all resection specimens (n~40) and a subset of biopsy specimens (n=50). We will perform the following experiments: i. Effects of CTLA-4 polymorphisms on EBVMCU development in irColitis ii. Immune cell composition determined by VECTRA multiplex immunofluorescence iii. T/B-cell clonality to determine if there are clonal expansion within EBVMCU We will also seek to identify any colectomy specimens prospectively, with a view to examine lesional EBV specific immunity. 2. Prospectively examine the effects of iCR therapy on EBV immune surveillance in 50 patients. We will prospectively examine changes in systemic EBV viral load and EBV specifiv T-cell immunity following iCR therapy prospectively in a cohort of 50 patients.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: ORAL AND GASTROINTESTINAL
Title: Role of DNA methylation in regulating intestinal epithelial cell function in health and paediatric Inflammatory Bowel Diseases
Funder: Medical Research Council

Abstract: Objective 1: Mucosal biopsies will be obtained from Terminal Ileum and Sigmoid Colon. Samples will be processed immediately for epithelial cell purification using magnetic bead sorting and generation of intestinal organoids according to established protocols. DNA and RNA will be extracted simultaneously. NLRC5 promoter DNA methylation analyses will be performed using bisulfite pyrosequencing and expression of NLRC5 as well as MHC-I related genes tested using RT-PCR and western blotting. Exposure of organoids to IFN-gamma will determine the impact of DNA methylation on the inducibility of MHC-I signaling. Locus specific, targeted de-methylation will be performed using a CRISPR/Cas9 based method and correlation between DNA methylation and clinical phenotype investigated using various computational approaches. Objective 2: We will generate NLRC5 knock-out and over-expressing human gut organoids using CRISPR/Cas9 genome editing and piggyBac transposon-based vector system respectively. Organoids from healthy individuals obtained from 2 gut segments will be modified and co-cultured with IFN-gamma. Following, we will perform genome wide expression (RNAseq) and proteomic Tandem Mass Tag profiling on organoids. Generated data will be analysed using novel computational methods such as diffusion-based approaches, which will allow identification of NLRC5 and/or IFN-gamma dependant signalling pathways operative in the human intestinal epithelium. Objective 3: In order to assess the functional impact of NLRC5 expression and MHC-I signaling on the intestinal epithelium in health and CD we will test intestinal epithelial barrier by measuring Transepithelial Electrical Resistance and efflux of FITC-dextran across organoids grown as monolayers. Additionally, we will test innate host response to viral infections and co-culture blood derived CD8+ T-cells with gut organoids and study their interaction using two-photon microscopy.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: ORAL AND GASTROINTESTINAL
Title: LAP-like non-canonical autophagy in pancreatic acinar cells and its role in the pathophysiology of acute pancreatitis
Funder: Medical Research Council

Abstract: The project involves collaboration between laboratories from the University of Liverpool (UoL) and University of East Anglia (UEA) and is focused on characterising cellular mechanisms of acute pancreatitis. Acute pancreatitis is a frequent inflammatory disease of pancreas for which there is currently no specific treatment. Elucidation of cellular mechanisms of this disease is paramount for the development of therapy. Abnormal pancreatic activation of trypsinogen and consequent damage of pancreatic acinar cells are important initiating factors of this disease. Exposure of the acinar cells to the inducers of acute pancreatitis results in formation of endocytic vacuoles. These organelles are formed as a consequence of abnormal compound exocytosis. The project is based on important findings made by participating laboratories: UoL group found that endocytic vacuoles are the sites of trypsinogen activation in pancreatic acinar cells, whilst UEA group recently characterised the mechanism of LC3-associated phagocytosis (LAP) and produced genetically-modified LAP-deficient mice. Collaboration between the groups has revealed that endocytic vacuoles undergo non-canonical autophagy similar in its properties to LAP. This suggests a novel mechanism of injurious trypsinogen activation in pancreatic acinar cells. Following this unexpected discovery we are planning to characterise the role of LAP-like non-canonical autophagy in experimental models of acute pancreatitis. Three such models, reflecting different aetiologies of human disease, are available in UoL. Another focus of the study will be on elucidating the molecular mechanism of LAP-like non-canonical autophagy and determining its role in death/damage of the acinar cells. In addition to experimental models of acute pancreatitis the project will involve confocal microscopy, correlative light-electron microscopy and standard cell and molecular biology techniques. We have relevant experience with all of these methods.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: ORAL AND GASTROINTESTINAL
Title: Regulatory T cell therapy for IBD
Funder: Medical Research Council

Abstract: Ulcerative colitis (UC) and Crohn's disease (CD) , together IBD, are chronic, incurable diseases of the GI tract resulting in significant morbidity and potentially life threatening complications. IBD affects more than 300,000 people in the UK and incurs costs to the NHS in the region of £1bn per year. Current therapies have limitations in terms of occasionally life-threatening side effects and also limited effectiveness; steroid-free remission rates for individual therapies tend to be 30-40% at best. Regulatory T cells (Tregs) have been identified as a potential therapy for patients with a range of disorders including CD. However, the ability to use them therapeutically has been limited by difficulties including performing ex vivo expansion, maintaining a non-inflammatory phenotype, delivery to the target organ and optimising treatment. In this program, I aim to research the mechanism of action of Treg therapy in patients with CD, the ability of Tregs to target the gut, the optimisation of Tregs as a treatment, the importance of a genetic variant, rs61839660, on Treg function and the potential to apply Treg therapy to another disease, UC, potentially paving the way for expansion to other disease areas. We are starting a Phase 1b/2a trial using ex vivo expanded CD4+CD25hiCD127loCD45RA+Tregs, optimised for gut homing using RAR568 and rapamycin, as a treatment for treatment-refractory Crohn's disease. Using samples from this, we will explore the phenotype of Tregs, after re-infusion, in both the peripheral blood and in the gut using techniques including ELISA, flow cytometry and TCR sequencing. In addition, we shall track the deuterated Tregs to investigate distribution and kinetics. Treg therapy optimisation will be investigated focussing on the effects of IL-2 co-therapy, initially in blood from UC patients, to inform the design of a clinical trial. In collaboration with the UK IBD Bioresource, gene editing may allow further optimisation of Treg therapy.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: ORAL AND GASTROINTESTINAL
Title: PBC Predict: Prediction models and predictive biomarkers for primary biliary cholangitis
Funder: Medical Research Council

Abstract: Primary biliary cholangitis (PBC) is an autoimmune liver disease that eventually leads to cirrhosis. Current guidelines recommend a step-up approach to treatment, whereby first-line therapy must fail before second-line agents are considered. Patients with more aggressive disease therefore wait longer to receive effective therapy. Many patients have inadequate response to all available medications, leaving them at risk of progressive liver disease. PBC is therefore a major cause of liver-related morbidity and mortality. There is a critical need in PBC for novel agents, and for simple, robust approaches (especially biomarkers) for early risk and treatment stratification, so that medications may be allocated at diagnosis based on the patient's predicted need for treatment and his or her likelihood of response. This is the essence of precision medicine. UK-PBC is an ambitious collaboration between Academia, Industry and the NHS to develop precision medicine for PBC. In the proposed project, building on previous success, we will expand the existing, unique UK-PBC Research Cohort to more than 10,000 participants; collect maximal clinical data about participants from diverse NHS sources; and use these data to develop accurate clinical prediction models of treatment response and disease progression, suitable for risk and treatment stratification in clinical practice. We will undertake genotype-phenotype analysis to delineate the genetic basis of this phenotypic variation, and develop genetic risk scores and predictive models incorporating clinical and genetic variables. Finally, we will undertake epigenetic and transcriptional profiling of PBMC subsets from an inception cohort of treatment naïve patients to discover epigenetic and transcriptional biomarkers for risk and treatment stratification. Via integrated analysis of genetic, epigenetic and transcriptional datasets, we will pinpoint causal variants, genes and pathways to guide re-purposing of drugs.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: ORAL AND GASTROINTESTINAL
Title: Quantifying the transmission routes of gastroenteritis in Pakistan and developing targeted interventions
Funder: Medical Research Council

Abstract: Gastroenteritis contributes to stunting and cognitive impairment in children, particularly following bacterial and parasitic infection. Transmission mechanisms, including food, e.g. vegetables and poultry, drinking water, and person-to-person contact, are intensified by social determinants, such as poverty and inequality. The health burden is particularly high in LMICs, such as Pakistan. Critically, it is in these countries that we know least about the importance of different transmission routes. Water Sanitation and Hygiene interventions have been disappointing. We believe that this can be improved by basing interventions on evidenced transmission pathways, and knowledge of the societal structures and behaviours that facilitate infection and are amenable to intervention. We will combine social science, molecular biology and microbial ecology, bioinformatics, epidemiology, and environmental engineering, to quantify transmission routes for non-viral gastro-enteric pathogens at multiple locations in Pakistan and determine the social context influencing transmission. Work packages include structured sampling for infection in patients and healthy people to quantify and characterise bacterial and parasitic pathogens selected for their impact on acute gastroenteritis and evidence linking them to enteric dysbiosis, growth and cognitive development (Shigella, E. coli, Campylobacter, Salmonella including Typhi, Cryptosporidium and Giardia). Domestic, environmental and food chain sampling will support tracking of sources and transmission. Complementary work will (i) seek to understand societal and cultural features relevant to gastrointestinal infection and control and (ii) evaluate approaches to agriculture and wastewater treatment to decrease pathogen burden in the environment and on food. Findings from this work will inform identification and prioritisation of interventions and will be followed by an evaluation of the most promising feasible intervention.


Research activity codes: 3.1 PRIMARY PREVENTION INTERVENTIONS TO MODIFY BEHAVIOURS OR PROMOTE WELL-BEING;3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: ORAL AND GASTROINTESTINAL
Title: Determining how CD4+ T cells regulate adult liver stem cells during regeneration
Funder: Medical Research Council

Abstract: The liver regenerates mainly through hepatocyte proliferation during acute liver injury but this process is fundamentally impaired during chronic liver injury. Ductular Reaction (DR), the compensatory remodelling of bile ducts occurs during chronic liver injury and is essential for liver regeneration. My research has revealed that cholangiocytes can act as liver stem cells during DR when hepatocyte regeneration is inhibited, and proximate lymphocytic infiltration was observed. CD4 T-cells infiltrate the liver during DR and my preliminary data show that CD4 T-cells can regulate DR, but the type of CD4 T-cells which regulate this process and the mechanisms are unknown. I hypothesize that CD4 T-cell subsets act concurrently to regulate the regenerative capacity of cholangiocytes alongside modulating the immune response. Through this fellowship, I will use multiple transgenic mouse models to determine 1) the dynamics of CD4 T-cell infiltration during liver regeneration and its effects on DR and epithelial plasticity; 2) the molecular interactions and mechanisms at play that control the differentiation capacity of potential resident liver stem cells. These advances will result in the identification of novel factors that control DR, cellular differentiation and facilitate the development of new treatment for chronic liver injury.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: ORAL AND GASTROINTESTINAL
Title: IBD-RESPONSE: Defining microbial predictors of responsiveness to biological therapies in Crohn's disease and ulcerative colitis
Funder: Medical Research Council

Abstract: IBD-RESPONSE will identify and validate a predictive model for response or failure to biological therapies in Crohn's disease and ulcerative colitis (UC), the major forms of inflammatory bowel disease (IBD) using microbiome (including microbial species and function data), and integrated clinical and human genome data. Recent immune oncology studies have identified that certain gut bacteria are associated with response or failure to immune modifying treatment, and that in mouse models, manipulation of these microbes can influence treatment outcomes. Limited data from small and heterogenous populations in IBD also suggest an association between treatment outcomes and gut microbes. We will assimilate the largest global cohort in this field to generate longitudinal gut microbiome metagenomic sequence data of stool from 1,125 patients commencing first-line biologicals, and in the event of treatment failure will follow subjects through second, and if required, third-line agents. For replication, we will generate gut microbial sequence data from patients experiencing a disease flare within an independent cohort (PREdiCCt) that studies environmental and dietary triggers of IBD relapse. Our bioinformatic pipelines will identify microbial species and genes/pathways that predict treatment response, identify how timing of stool collection impacts on this prediction, study functional pathways of these microbes, compare stool metagenomes to 16S rRNA gene amplicon sequencing data from intestinal tissue to compare luminal and mucosal microbial communities, as well as utilise human genomic data for our subjects (made available by a parallel sequencing programme) to explore host human genome-gut microbiome functional interactions. Our study will establish the largest biorepository of longitudinal stool and matched tissue in the world with detailed linked phenotypic data, in this important clinical group of subjects that will be open to other researchers to use in the future.


Research activity codes: 4.4 POPULATION SCREENING;6.9 RESOURCES AND INFRASTRUCTURE (TREATMENT EVALUATION)
Health categories: ORAL AND GASTROINTESTINAL