NIHRDataInsights/HRCSData huggingface dataset:
Title: Understanding the role of the chromatin insulator CTCF in human papillomavirus gene expression and disease progression
Funder: Medical Research Council

Abstract: Infection with high-risk human papillomavirus (HR-HPV) is the cause of cancers within the anogenital and oropharyngeal tracts. The fundamental link between HR-HPV infection and neoplastic progression is well established, but the molecular changes are poorly defined. The HPV life cycle is dependent on the differentiation of the infected cell. Infection is established in the undifferentiated basal layer of the epithelium where early gene expression is initiated. Terminal differentiation of the cell results in late promoter activation and expression of late transcripts. This switch in gene expression is essential for life cycle completion, but how it is controlled has not been elucidated. We have recently demonstrated that the host cell transcriptional insulator protein CTCF binds to the HPV genome and regulates early gene expression. Our preliminary data provide strong evidence that CTCF function is essential for the transcriptional regulation of HPV gene expression by influencing transcriptional boundary formation and through the control of RNA polymerase II programming and gene splicing. Loss of CTCF binding not only enhances early gene expression but also prevents late gene expression, suggesting that CTCF function is important in the early to late switch in transcription control. We will study the function of CTCF in the differentiation-dependent control of virus gene expression using physiologically relevant models of the HPV life cycle at different body sites (anogenital and oropharyngeal) using innovative and quantitative methods. These experiments will be underpinned by the study of CTCF-HPV association in cervical cancer specimens to determine whether loss of CTCF binding contributes to cancer development. Consolidation of our findings will provide important insight into the function of CTCF in the HPV life cycle and HPV-driven disease progression and will impact on our understanding of CTCF function in gene expression control in healthy and disease states.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Accumulation and nephrotoxicity of dextrin-colistin conjugates.
Funder: Medical Research Council

Abstract: This research will test a novel bio-triggered antibiotic delivery system, based on polymer therapeutics, that has previously shown antibacterial activity across a range of Gram-negative bacteria, reduced in vivo toxicity and prolonged plasma half-life. It is hypothesised that dextrin-colistin conjugates will be tolerated at much higher doses than the free drug, which would reduce the acquisition of antibiotic resistance and improve the efficacy of treatment. This study will assess the mechanisms and extent of dextrin-colistin conjugates' nephrotoxicity, including renal cell toxicity and apoptosis, renal cell uptake and accumulation, and renal tissue distribution. Experiments will, first, use in vitro assays to assess cytotoxicity (MTT, LDH release, apoptosis) and cellular uptake, accumulation and localisation (fluorescence microscopy and flow cytometry) of 3 dextrin-colistin conjugates, compared to colistin sulfate and CMS, in a panel of human and rat kidney cell lines, compared to primary fibroblasts. In vivo biodistribution and nephrotoxicity will be evaluated in healthy rats, then in a respiratory tract infection model of Klebsiella pneumoniae. Healthy animals will receive 2 doses (8 h apart) of dextrin-colistin conjugate, colistin sulfate or CMS and samples of blood and organs will be assessed for creatinine/ colistin content and cellular degeneration using histology. These studies will determine the maximum tolerated dose for the treatments, which will be used in subsequent in vivo efficacy studies. Observations and sampling will be performed as described previously, however, in addition, organs will be recovered and the antibacterial effects will be quantified as colony forming units (CFU)/g of lung tissue. The results of this study are expected to demonstrate the improved toxicity profile and biodistribution of dextrin-colistin conjugates, to precede full-scale commercial development.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Definition and induction of broadly protective responses against HIV-1
Funder: Medical Research Council

Abstract: Development of an effective vaccine against HIV/AIDS remains one of the top global health priorities even in the context of broader prevention landscape. It is generally accepted that development of HIV vaccine is a gradual iterative process that will take many years. It is very positive that significant inroads have been made into identifying what constitutes both protective T cells and broadly neutralizing Abs (bnAb) for this most difficult of vaccines. The biggest challenges for vaccines are HIV variability and escape. Compelling evidence for an important role of CD8 T cells in controlling HIV has accumulated over the last 30 years. My group is taking a multipronged approach to HIV T-cell vaccine development combining our experimental data with novel vaccine strategies. The hypothesis we pursue is that focusing T cells on the functionally conserved regions of HIV proteins will enable early control or elimination of the transmitted/reactivated viruses. To achieve this, the vaccines must match as much as possible all HIV variants and the T cells must be robust enough to stay strong when facing natural infection, altering the natural immunodominance. This PG Renewal will support a team of scientists led by Tomas Hanke, who are at the heart of a highly rational and promising T-cell vaccine approach. We demonstrated the concept of the conserved region strategy in European and African HIV seronegative adults and also in infected patients on ART. We are now adding a new element to the vaccine, the mosaic concept and are moving towards testing this much improved 2nd generation vaccine for HIV cure and small efficacy trials. The aim for the latter will be to complement induction of Abs when bnAb vaccines remain suboptimal. In the next 5 years, we will develop next generation of vaccine vectors and immunogens; evaluate the induction and role of non-canonical CD8 T cells for human vaccine use; asses the role of conserved T-cell responses in HIV cure and prevention.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: Can norethisterone enantate (NET-EN) reduce the risk of recurrent bacterial vaginosis in women at high risk for HIV infection?
Funder: Medical Research Council

Abstract: Bacterial vaginosis (BV) is highly prevalent among women in Africa and is associated with HIV acquisition. BV has been described as a dysbiosis, or a microbial imbalance, and is treated with metronidazole; however, once treated, it often recurs rapidly. Developing robust treatment strategies to prevent recurrent BV is important for HIV prevention in key populations at high risk for HIV infection. There is evidence that hormonal contraceptives, including depot medroxyprogesterone acetate (DMPA), decrease BV recurrence; however, there is also evidence that DMPA increases the risk of HIV infection. Encouraging women to start or switch to an alternative progestin injectable such as norethisterone enantate (NET-EN) may mitigate HIV risk whilst decreasing the risk of recurrent BV. To date, there are no published studies that have investigated the effect of NET-EN on vaginal microbiota. The proposed study will investigate the effect of NET-EN and DMPA on recurrent BV, vaginal microbiota and inflammatory markers among women at high risk for HIV in the Good Health for Women Project in Kampala, Uganda. Consenting and eligible women will be treated for BV, and randomised to either NET-EN plus condoms or condoms only. Women currently using DMPA will be enrolled as an observational comparison group. All participants will be interviewed and examined; samples for vaginal microbiota, sexually transmitted infections, and inflammatory markers will be obtained. Women will be followed up after 1 week, and 1, 3, 5 and 7 months. The primary outcomes will be differences in vaginal microbiota community state types, time to recurrent BV, and inflammatory markers. Qualitative research will be carried out to assess the acceptability of, and adherence to, NET-EN. Safe and effective hormonal contraception may augment current or future (e.g. probiotic) treatment for women with recurrent BV, and results from our study may inform future clinical trials investigating BV and HIV prevention.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: UNDERSTANDING THE ROLE OF EPSTEIN BARR VIRUS IN T CELL AND NATURAL KILLER CELL LYMPHOPROLIFERATIONS AND MALIGNANCIES
Funder: Medical Research Council

Abstract: Epstein Barr virus (EBV) is a common herpesvirus that infects the majority of the human population and establishes a silent latent infection in B cells for the lifetime of the infected host. However, under poorly understood circumstances, EBV may ectopically infect T cells and NK cells. This infection always results in overt disease ranging from clonal proliferations of infected cells with hypercytokinemia to aggressive malignancies, all of which are inherently resistant to the current treatment regimens. There is an urgent need to better understand the pathobiology of EBV-associated T/NK diseases in order to develop effective novel therapeutic strategies. The aim of this research is to understand how Epstein Barr virus (EBV) drives the pathogenesis of these T/NK cell lymphoproliferative diseases. We will concentrate on four main aspects of EBV infection of T/NK cells. First, we will examine the viral and microenvironmental factors that enable the establishment of infection. We established a model of T cell differentiation and exploited the transient expression of CD21 in the T/NK cell precursors to infect these cells with EBV. We will also explore EBV entry into mature T/NK cells via an immunological synapse formed between HLA-matched, EBV-specific T-cells and plasma cells undergoing productive viral replication. Next, using these new infection models and recombinant virus technology, we will determine how EBV drives the replication and clonal outgrowth of T/NK cells and the chronic inflammatory environment characteristic of these diseases. We will then determine how EBV drives the transformation of infected T/NK cells and contributes to immune-inhibition. The viral oncogene LMP1 appears to play a major role in both transformation and immune inhibition and we will examine how. Finally, using a new flow cytometry-based assay to screen cells directly from patient blood, we will examine the EBV-positive cells for expression of potential new therapeutic targets.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Investigating the function of group 3 innate lymphoid cells in the renal tract
Funder: Medical Research Council

Abstract: Planned experiments: 1a. Confocal imaging of sections prepared from kidneys and bladder (tissues obtained from ROR-yt-GFP mice and human organ donors that have consented for research) to determine anatomical location and markers expressed (MHCII, CD80/86, IL22, IL17). Flow cytometric analysis of human kidneys, analyzing cortex and medulla samples separately, using flow panels already optimized (CD45, lineage (CD3/19/14/94), CD127, c-KIT, CRTH2 and NKp44, (Figure 3 of Case for Support)). Transcriptomic analysis of flow-sorted human kidney ILC3s will also be undertaken. 1b. Two-photon (2P) intravital imaging of RORyt-GFP/ID2-CFP double reporter mouse. ILC3 migratory speed and area patrolled will be measured using Imaris software. The ID2 reporter required will be generated during this project. 1c. Histological studies of kidney and bladder tissue (using CD3, CD4, CD11c, F4/80, CD11b and CD64 co-staining to identify ILC3s, Th17 cells, DCs and macrophages) to investigate ILC3 co-localisation with other tissue-resident cells. Dynamic interactions will be assessed using intravital, 2P imaging of a triple reporter mouse (RORyt-GFP/ID2-CFP/CD11c-EYFP). 2a. FACS analysis of kidney and bladder ILC3 following intravesical challenge with uropathogenic E coli (UPEC). Surface MHCII and CD80/86 and intracellular IL17 and GM-CSF of ILC3s will be investigated. Similar phenotyping of human kidney and bladder ILC3s will be performed following UPEC challenge in vitro. 2b. RORyt-deficient mice will be used in the UTI model and infection severity assessed (bacterial counts in kidney, bladder, blood and spleen as well as neutrophil and monocyte infiltration into the kidneys and bladder). Providing the ROR-yt deficient mice show a phenotype, we will use bone marrow chimeras to produce ILC3-specific knockouts and use them in the UTI model. 2c. 2P intravital imaging of bladder ILC3s, Th17 cells and DCs during UTI using triple reporter mice. Imaris used to analyse data.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFECTION
Title: Enhancing mucosal immunity to Streptococcus pneumoniae by nasal administration of live strains attenuated in virulence
Funder: Medical Research Council

Abstract: Despite routine vaccination of adults at risk of S. pneumoniae lung infections, these are still probably the commonest serious infectious disease in the UK. S. pneumoniae causes 40+% of the 189,000 annual admissions due to pneumonia and 25% of the 117,000 admissions due to COPD. New strategies for preventing this huge burden of disease are required. One possible strategy would be to boost mucosal immunity against S. pneumoniae by nasal administration of genetically altered S. pneumoniae strains unable to cause severe infection. We will test this strategy using an experimental human pneumococcal carriage model that has been established in Liverpool by Prof Gordon. Healthy volunteers will be given attenuated S. pneumoniae by nasal administration then challenged with wild type S. pneumoniae bacteria. The primary endpoint is reduction of colonisation rate after rechallenge with wild-type S. pneumoniae strain to 15% for EHPC subjects given the attenuated strains compared to 50% in the negative control group, as assessed by recovery of bacteria from nasal washes. In addition nasal washes and blood samples will be taken for a variety of bacteriological and immunological endpoints including: (i) density and duration of colonisation with attenuated strains; (ii) pre- and post-colonisation local and systemic antibody and cellular responses to S. pneumoniae antigens, looking for equivalence of results between EHPC subjects given attenuated and wild type S. pneumoniae; (iii) functional immune responses using sera for in vitro assays of opsonophagocytosis and for passive vaccination experiments in mice; (iv) bacteriological safety by sequencing and in vitro testing of bacteria recovered from EHPC subjects to ensure genome and phenotypic stability. The data obtained will demonstrate whether immunisation by nasopharyngeal administration of attenuated mutants is a feasible strategy for improving mucosal immunity and therefore for preventing S. pneumoniae lung infections in adults.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: Pathfinder:Experimental Human Challenge with Genetically Modified Commensals to Investigate Respiratory Tract Mucosal Immunity and Colonisation
Funder: Medical Research Council

Abstract: This is a pathfinder study to establish the utility of experimental human challenge with a genetically modified commensal bacterium as a future method to investigate pathogenesis, immunity and to discover and test new vaccines. The commensal bacterium Neisseria lactamica (Nlac) does not have a polysaccharide capsule , so any adaptive immune response to this bacterium after colonisation of the nasopharynx must be directed at non-capsular antigens, providing a good platform for assessing non-anti-polysaccharide immunity against colonising bacteria in the upper respiratory tract. A wild-type strain of Nlac Y92-1009 (Nlac), will be chromosomally modified to express the strongly immunogenic meningococcal antigen PorA (GM-Nlac). GM-Nlac will be fully characterised, in particular with respect to enhanced antimicrobial or serum resistance, and altered genome stability cf Nlac. An application will then be made to DEFRA and the National Research Ethics Service to perform a controlled infection study in which non-smoking male participants aged 18-45 will be infected intranasally at a dose of 10,000 colony forming units (selected because we previously have infected >350 volunteers with Nlac at this dose) and then permitted to re-enter the community after challenge and followed up for 4 weeks. In a comprehensive serological and cellular immunological study we will define the nature and kinetics of the PorA-specific immune response to colonising GM-Nlac and measure recombination in carried isolates over the ensuing period of carriage. PorA is phase variable so we will determine the effect of phase variation in a second challenge experiment by comparing the serological and cellular responses to GM-Nlac expressing PorA under a phase variable promoter with one that is constitutively highly expressed. We will also compare the immune response to Nlac antigens between GM-Nlac and Nlac infected participants, to understand the effect of immunodominant antigens on immunity.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: Pathfinder: Determining the efficacy of plasmapheresis as a treatment for patients with chronic Pseudomonas infections and inhibitory antibodies
Funder: Medical Research Council

Abstract: Chronic P. aeruginosa lung infections are found in patients suffering from cystic fibrosis or bronchiectasis and once P. aeruginosa colonisation is established, it is almost impossible to remove by current methods Recently we investigated patients with bronchiectasis and chronic P. aeruginosa infections. Serum was taken from each patient and tested for its ability to kill the patients colonising Pseudomonas strain. This identified a subset of patients whose sera was unable to kill their colonising strain due to a blocking factor in their serum. This inhibitory factor was identified as high titres of IgG2 antibody specific to P. aeruginosa O-antigen. The results suggested that the IgG2 bound the O-antigen (a target distal from the cell surface) where it either held complement away from the bacterial membrane, or physically blocked access of protective antibodies. Crucially, patients with impaired serum killing had worse lung function than patients with normal serum killing. Two critically ill patients with this IgG2 were treated with plasmapheresis in an attempt to remove the inhibitory antibody. Both patients had immediate benefit from the treatment. Although significant, many vital questions remain unanswered; 1) Is plasmapheresis a viable treatment option for patients with inhibitory antibodies? 2) How does having inhibitory antibodies impact on clinical status? 3) What is the prevalence of the inhibitory antibodies in patients with Pseudomonas lung infections? 4) Is plasmapheresis driving strain replacement? 5) Are other antibody subtypes involved in immune-killing inhibition? These answers will have far-reaching implications for monitering and treatment of lung infections. This project aims to answer these questions by combining our unique access to clinical samples with the techniques already established in our previous work coupled with next-gen genome sequencing.


Research activity codes: 6.4 SURGERY
Health categories: INFECTION
Title: Leaving no one behind: Identifying approaches to improving HIV treatment outcomes among older Ugandans
Funder: Medical Research Council

Abstract: This project will develop an effective intervention to address older Ugandans' ART access and adherence and their feelings of stigma and social isolation, to be evaluated in a future trial. Few studies have assessed barriers and facilitators to ART access and adherence among people living with HIV (PLWH) aged >50 years. The project, which will take place in rural Uganda, will be the first to develop a tailored social intervention that addresses older Africans' barriers to ART access and adherence. The aims are to: (1) Identify barriers and facilitators to older adults' ART access and adherence. (2a) Develop an intervention that will improve older adults' access and adherence to treatment; (2b) Establish a theory of change (ToC); (3) Refine the intervention and prepare for a future trial. Our previous research suggests that for older Ugandans, social isolation and trouble accessing health services are key obstacles to ART access and adherence. The interventions that we will focus on thus include individual, community and health system support. Together these will make up a multi-pronged approach to reduce barriers. Methodology will include: 1) Key informant interviews to assess existing resources and perceptions among community leaders and health care providers about current older PLWH ART access and adherence, and health and social needs. 2) Individual interviews among older participants in ongoing cohorts to explore themes of ART access and adherence, including social support networks and engagement with the health system. For those on ART, we will collect self-reported data on ART access and adherence. 3) Adaption of existing interventions based on older PLWH's perspectives on their barriers to access and adherence. We will formulate a ToC, including the mediators and moderators of change, and developing instruments to measure these. 4) Refining the proposed intervention through small group interviews to elicit feedback and prepare a trial protocol


Research activity codes: 3.1 PRIMARY PREVENTION INTERVENTIONS TO MODIFY BEHAVIOURS OR PROMOTE WELL-BEING;7.1 INDIVIDUAL CARE NEEDS
Health categories: INFECTION