NIHRDataInsights/HRCSData huggingface dataset:
Title: Natural Killer Cells as Effectors in HIV Cure Strategies
Funder: Medical Research Council

Abstract: Antiretroviral therapy (ART) successfully controls viral replication but is not a cure for HIV infection. ART requires daily medication (with significant financial costs), has side effects, and patients on ART still face higher risks of various morbidities than uninfected patients. Recent evidence from the VISCONTI cohort suggests a subset of patients treated early in infection can successfully control viraemia for a long period of time following ART cessation. Understanding this phenomenon could help generate therapeutic approaches to reduce the reservoir and guide the design of HIV cure clinical trials where ultimate efficacy will require taking patients off ART. Preliminary data from the VISCONTI cohort suggests that NK cells might play a role in PTC while the role of NK cells on reservoir size in patients on early ART has yet to be studied. Therefore, we will use samples from two large clinical cohorts of primary infected HIV patients - SPARTAC and HEATHER. The SPARTAC trial randomized patients into one of three arms: no ART (standard of care), 24 weeks of ART, and 48 weeks of ART followed by a scheduled treatment interruption. The HEATHER cohort is the largest cohort of primary infection in the UK with longitudinal samples from patients over time. Additionally, 20 patients in the HEATHER cohort will undergo a scheduled intensively monitored treatment interruption in the PITCH study. In this application, we will use samples from these 3 studies to examine the phenotype and function of NK cells to determine if NK cells can affect the size of the reservoir, the time to viral rebound in patients who stop ART, and the effect of early ART on NK function.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: BBSome trafficking: investigating a novel pathway associated with virulence in Leishmania
Funder: Medical Research Council

Abstract: My previous research showed that Leishmania parasites lacking the orthologue of the human BBSome subunit BBS1 are unable to survive in a murine host. The proposed study is based on the hypothesis that the BBSome is involved in trafficking virulence factors in these parasites. The first objective is to identify changes in the surface molecules of amastigotes in which BBSome function has been disrupted by deletion of one subunit of the complex. Surface proteins will be isolated by biotinylation and streptavidin pulldown, followed by isobaric tag quantification. Surface carbohydrates and plasma membrane lipids will be identified by mass spectrometry-based techniques. The second objective will take a global approach to find differences in protein localization patterns in amastigotes of BBSome mutant lines. Localization of Organelle Proteins by Isotope Tagging (LOPIT) combines biochemical fractionation and shotgun proteomics with isobaric tag quantification and enables the localization of large numbers of proteins to be studied simultaneously. As this technique has not been used previously on Leishmania, initial studies will be performed to generate a LOPIT profile for wild-type L. mexicana amastigotes. Following extensive cell fractionation, Western blotting will be used to find fractions that represent peak organelle densities. Fractionations will be repeated for BBSome mutant lines and the composition of equivalent fractions from different lines will be compared using isobaric tag quantification. Identified differences will be validated by endogenous epitope tagging and immunofluorescence. The third objective is to identify interacting partners of the L. mexicana BBSome using proximity-dependent biotin identification (BIOID) and NanoLuc Binary Technology (NanoBiT) complementation assays. Findings from the proposed study will provide a clearer picture of how the Leishmania BBSome functions at the molecular level and the specific effects it exerts on the cell.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: The role of immune tolerance and regulation in pneumococcal carriage and invasive disease.
Funder: Medical Research Council

Abstract: The central aim of the proposal is to elucidate the host-pathogen interactions that lead to the development of stable asymptomatic nasopharyngeal carriage with the major human pathogen Streptococcus pneumoniae. Furthermore, we aim to examine the conditions (bacterial, host and environmental) that allow these interactions to become dysregulated prior to the onset of invasive disease. We will do this through use of in vitro models with airway epithelial cells, well established in vivo infection models and clinical studies linking in with a unique human experimental pneumococcal challenge (EHPC) model. We have previously described a role for immunological tolerance in the establishment and maintance of pneumococcal carriage and in resistance to invasive pneumococcal disease. We will determine how pneumococci induce the production of transforming growth factor beta and the activity of T regulatory cells that is required for establishment of tolerance. We will examine the role of the pneumococcal toxin pneumolysin in induction of immunoregulation and determine whether additional contributions come from other pneumococcal virulence factors implicated in nasopharyngeal carriage. Additionally, we will explore how factors such as chronic infection with gastrointestinal nematodes or exposure to inhaled particulate pollutants can influence immune tolerance and predispose to invasive pneumococcal disease. These aims will be achieved through mechanistic examination of pneumocccal-exposed primary airway epithelial cell cultures, use of clinically relevant in vivo models of pneumococcal nasopharyngeal carriage, and clinical studies determining the pattern of immune regulatory marker expression in pneumococcal carriers from different at-risk groups.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Role of Mycobacterium leprae proteins and RNAs in initiating neuropathy
Funder: Medical Research Council

Abstract: Neuropathic diseases and pain due to degeneration of axons in peripheral nerves (PN) represents a significant clinical problem globally. However, much less is known about the mechanisms by which glial cells in the adult PN contribute to the initiation of axonal degeneration leading to neuropathies. In this project, we propose to gain new understanding of early events of axonal degeneration of sensory and motor neurons, the common features of neuropathic diseases, using gene products of Mycobacterium leprae (ML) which naturally infect Schwann cells and causes one of the classical examples of neuropathies, leprosy neuropathy. Proposed research will identify ML gene products, proteins and RNAs that induce innate immune factors in Schwann cells and their role in perturbing Schwann cell support to and interaction with axons of sensory and motor neurons in ex-vivo, and in vivo zebrafish models. We will also plan to study how the nerve ending damage in the epidermis without Schwann cells leads to sensory loss in the skin and the potential role of immune factors released by epidermal keratinocytes in response to ML proteins and RNAs. Based on these studies we will select the most relevant candidate ML protein and RNAs to generate transgenic mice expressing these candidate ML gene products in adult Schwann cells initiating early neuropathic conditions, which eventually permit us to test small molecule drugs with the ability to alleviate axonal degeneration, and thus develop common new therapeutics not only for leprosy neuropathy but also for other neuropathic conditions and pain.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Control of type III interferon expression and Herpes simplex virus type 1 replication by miR-200
Funder: Medical Research Council

Abstract: In our previous work we revealed by a genome-scale RNA interference (RNAi) screen that type III interferons (IFN-lambda) play a crucial role in the innate immune control of HSV-1 [1]. There is increasing evidence that IFN-lambda, which is the least well investigated IFN, is crucial in the innate immune response against a range of different RNA and DNA viruses, as well as against tumours. It is mainly important for skin and mucosal infections, infections of organs containing epithelial cells, and for viral hepatitis. In preliminary work we tested a set of about 400 cellular miRNAs by a mimic and inhibitor screen for their effect on HSV-1 replication, and identified antiviral miRNAs including several miR families with common seed target sequence such as miR-200 that strongly inhibited HSV-1. In the project proposed, we will investigate how these antiviral miRNAs inhibit HSV replication and which cellular genes are involved, with the help of the genome-scale RNAi screening results. In particular, we will investigate miR-200, which plays a role in epithelial-to-mesenchymal transition (EMT) and oncogenesis, and which is regulated by a feedback loop with the transcriptional repressors ZEB1/2. Since in preliminary results miR-200 led to an induction of IFN-lambda, we hypothesize that it inhibits HSV-1 by downregulating ZEB1/2 and thereby inducing IFN-lambda. If this is the case, miR-200 creates a link between EMT, oncogenesis and innate immunity and is one of the key regulator in these processes. Our unique approach will help to understand the mechanisms of antiviral miRNAs and could be instrumental for the development of novel anti-viral and anti-tumour therapeutics.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Determining the persister populations in sputum during tuberculosis therapy. A supplementary study to the RIFASHORT trial.
Funder: Medical Research Council

Abstract: Current standard therapy for drug-sensitive TB is associated with a relapse rate of ~5%. We urgently need tests that identify potential unsatisfactory treatment outcomes early in therapy with sufficient sensitivity and specificity to guide the implementation of clinical trials and the monitoring of individual patients. In the former case such tests could accelerate development and evaluation of new drugs and treatment regimens, in the latter the duration of therapy for individual patients could be individualised. Here we build on our studies of mycobacterial lipid bodies (LBs) and Resuscitation promoting factor dependency (Rpf-D), both of which provide established links to antibiotic tolerant persister-like phenotypes and analyses of which have, respectively, been clearly linked to relapse in human and mouse infections. Our aim is to evaluate LB and Rpf assessments in sputum samples for their capacity to predict treatment responses. By use of samples from and added to the RIFASHORT trial, we will obtain multiple readouts of the M. tuberculosis (Mtb) subpopulations in sputum that our data indicate are potentially responsible for relapse and slow responses to therapy. Critically, our recently published protocol for storage of sputum samples to enable deferred analysis of Rpf-D populations will enable assessment of this strong candidate persister readout on a scale sufficient to evaluate its potential predictive value. Recent analyses of Mtb transcription in sputum and in vitro provide a further opportunity to link clinical assessment of treatment responses to Mtb physiology and our background understanding of LBs and Rpfs. This study will address the critical need for clinical biomarkers of treatment response in TB while simultaneously adding substantial value to the RIFASHORT trial. Our study will deliver new clinical knowledge in this key area and has significant potential to both accelerate development of new treatments and enhance individual patient management.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: Assessing policy implementation and health systems impacts of Option B+ in three African countries to inform the delivery of Universal Test and Treat.
Funder: Medical Research Council

Abstract: This project addresses a critical evidence gap in assessments of health systems preparedness for Universal Test and Treat (UTT) for HIV by drawing on lessons from Option B+ policy implementation, widely viewed as its precursor. We will conduct a longitudinal mixed methods study in HIV community cohort (HCC) sites in Malawi, South Africa and Tanzania, underpinned by a conceptual framework that incorporates elements from Walt and Gilson's "policy triangle" and the WHO health systems "Building Blocks" model to explore the link between Option B+ implementation and subsequent impacts on health systems within which they are delivered. Our analysis will be informed by a political economy and "systems thinking" approach that recognises the dynamic relationship between the policy and implementation environments and the role of economic considerations in policy-making processes. We will draw on HCC data, health facility survey data, policy reviews collected in 2013, 2015 and updated with a further round in 2017, as well as data from key informant interviews with policymakers, in-depth interviews with patients and healthcare providers, and economic costing data to: 1) Identify Option B+ policy implementation gaps in each setting and consider how the actors, policy content, context and processes explain these gaps 2) Assess whether underlying costing and epidemiological assumptions in economic evaluations that demonstrate cost-effectiveness of Option B+ been met in each site 3) Describe the health systems impacts of Option B+ in each site 4) Develop strategies with policymakers to assess and promote health systems readiness for effective UTT delivery Strengths of the study include its multi-country and longitudinal perspective and the ability to triangulate findings from multiple data sources. The results will generate evidence that will help prioritise areas for health systems strengthening to achieve the intended cost-effectiveness and health outcomes of UTT.


Research activity codes: 8.1 ORGANISATION AND DELIVERY OF SERVICES;8.2 HEALTH AND WELFARE ECONOMICS;8.3 POLICY, ETHICS AND RESEARCH GOVERNANCE
Health categories: INFECTION
Title: Dose rationale for antibiotic combination therapy in infection diseases
Funder: Medical Research Council

Abstract: Parameterisation of pharmacokinetic and pharmacokinetic-pharmacodynamic (PKPD) data into nonlinear mixed-effects models is required to better understand the time course of bacterial growth and bactericidal activity of drugs. To date, little attention has been paid to how these models should be parameterised to quantify drug effects during combination therapy or explain variability associated with clinical, genetic and demographic covariate factors. In this proposal, in-vivo clinical data will be integrated with in-vitro data from innovative hollow fibre experiments using nonlinear mixed-effects modelling techniques to improve dose selection for drug combinations and to personalise the treatment of anti-infective agents in different patient groups. Moreover, the approach will be used to support the design of prospective clinical studies in tuberculosis, an area which has gained scientifically and regulatory relevance over the last decade. In previous investigations, lung tissue/lesion concentrations and antibacterial activity has been described using empirical or more mechanistic and single-state or multi-state nonlinear mixed-effects models, respectively. Here, nonlinear mixed-effects modelling approaches will be identified that enable further characterisation of bacterial growth over time in experimental conditions which mimic disease in humans. The ultimate goal is to identify new parameterisations supported with prior distributions in a Bayesian framework which facilitate the translation of nonclinical data, enabling the prediction of treatment response in patients using the software package NONMEM (aim 1). The availability of such a framework will allow the evaluation of simulation scenarios to optimise, personalise and recommend standard drug combination therapy for pulmonary tuberculosis (aim 2). In combination with optimality concepts, the proposed approach can be used to support the design of innovative and efficient prospective PKPD studies (aim 3).


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY);4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: A novel hybrid discrete-continuum cellular automaton model to study tuberculosis disease progression and treatment
Funder: Medical Research Council

Abstract: Current TB treatment requires at least six months of multiple antibiotics. More effective drugs are urgently needed to shorten treatment. The drug development pathway in TB is incompletely integrated with important unanswered questions at every stage. It remains unclear to what extent many preclinical methods capture the correct pharmacodynamic properties of a drug or reproduce the conditions under which it must act in the diseased host. Mathematical modelling can complement traditional experimental approaches to biomedical research. In contrast to modelling designed to quantify treatment response in clinical trials, my research focuses on mathematical modelling that captures disease pathology in the lung. I have developed a novel hybrid discrete-continuum cellular automaton model to study disease progression and treatment in the lung. It contains discrete individuals that mimic the spatio-temporal interactions of bacteria (both dormant and non-dormant), macrophages and T cells. The movement of cells is governed by biased random walks, whilst interactions are governed by rules defined by the latest research. Diffusion of chemokines, oxygen and antibiotics are modelled through appropriate partial differential equations. This project aims to develop a multiscale modelling and analysis framework that is able to explore and answer some of the complex questions that underlie poor treatment response and relapse. By working with identified key individuals to develop skills and acquire knowledge, my ability to enhance my model will be possible. Lesional PK will be integrated in the model, as we know that penetration into granulomas varies with antibiotic. Combination therapy will also be incorporated to allow new regimens to be simulated. The model will then be extended to 3D and a multi-lesional model will be developed using network modelling, taking strides towards a "virtual lung".


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: The role of plasma membrane calcium ATPase 4 (PMCA4) in modulating Plasmodium infection and malaria severity
Funder: Medical Research Council

Abstract: Background: Malaria is one of the biggest killers in developing countries worldwide. The rapid growth of parasite resistance to available anti-malarial drugs has become a major problem in controlling the disease. Therefore, development of new anti-malarial drugs that target novel biochemical pathways is needed. Scientific rationale: Recent genome wide analysis studies (GWAS) have identified the plasma membrane calcium ATPase 4 (PMCA4) as a powerful determinant of the susceptibility to malaria infection and the development of cerebral malaria in human patients. Consistently, our preliminary data has also shown that pharmacological inhibition of PMCA4 reduces Plasmodium infection in a mouse model of malaria as well as in human parasite P. falciparum in vitro culture. Plan of research: To further study the role of PMCA4 in mediating resistance and severity of malaria we will use mice with genetic ablation of the Pmca4 gene. We will examine if Pmca4 deletion in mice will result in the reduction of parasite burden as well as prevention of the development of experimental cerebral malaria (ECM). In addition, we will also test if treatment with novel PMCA4 inhibitors, which were identified in our laboratory, will reduce parasite infection and the occurrence of ECM in mice. Lastly, we will also study the association between human PMCA4 gene polymorphisms with malaria severity in an Indonesian population and analyse the functional implications of the polymorphisms at molecular level. Outcomes: This study will provide information on the mechanisms through which PMCA4 interferes with the dynamics of malaria infection and its severity. It may also identify PMCA4 as a novel target for malaria treatment.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Durable, practical, effective and affordable formats for insecticide-treated eave baffles that protect households and suppress malaria transmission
Funder: Medical Research Council

Abstract: Eave baffles (EBs) are a simple housing modification using widely-available netting materials, which can be treated with existing insecticide formulations. Treated EBs and window screens trap mosquitoes inside houses after they enter, and force them into lethal contact with insecticides when they attempt to exit again. Experimental prototypes of insecticide-treated EBs proved an equivalent or superior alternative to indoor residual spraying for killing malaria vectors in standardized experimental huts in southern Tanzania. EBs required >5 times less insecticide than IRS, and co-treating with a binding agent (BA) could enhance durability so that they only need to be treated every 2 to 3 years. The overall goal of this early-phase study is therefore to develop new, practical, scalable prototypes for EBs, which have been adapted to trap house-entering mosquitoes before they can attack the occupants, and can be readily installed in most rural African houses. We propose the following objectives for this early-phase study: 1. Re-assess the insecticidal efficacy of the previously evaluated experimental prototype EBs against An. funestus and An. arabiensis in experimental huts at 12, 18, 24 and 30 months post-treatment, to demonstrate long-term efficacy when co-treated with BA. 2. Develop a new EB trap design in a readily-manufactured "on a roll" format, together with broadly-scalable installation procedures, and demonstrate successful installation that reduces mosquito biting nuisance by >80% and assess user perceptions, in a random sample of rural Tanzanian houses. 3. Demonstrate equivalent insecticidal efficacy of the scalable EB trap-on-a-roll format to the previous experimental prototype, using experimental huts to measure impact on mosquito survival.


Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS
Health categories: INFECTION