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The Nuffield Department of Medicine (NDM) at the University of Oxford has a global reach and significant breadth in terms of capabilities and capacity.
Unveiling sub-populations in critical care settings: a real-world data approach in COVID-19.
BackgroundDisease presentation and progression can vary greatly in heterogeneous diseases, such as COVID-19, with variability in patient outcomes, even within the hospital setting. This variability underscores the need for tailored treatment approaches based on distinct clinical subgroups.ObjectivesThis study aimed to identify COVID-19 patient subgroups with unique clinical characteristics using real-world data (RWD) from electronic health records (EHRs) to inform individualized treatment plans.Materials and methodsA Factor Analysis of Mixed Data (FAMD)-based agglomerative hierarchical clustering approach was employed to analyze the real-world data, enabling the identification of distinct patient subgroups. Statistical tests evaluated cluster differences, and machine learning models classified the identified subgroups.ResultsThree clusters of COVID-19 in patients with unique clinical characteristics were identified. The analysis revealed significant differences in hospital stay durations and survival rates among the clusters, with more severe clinical features correlating with worse prognoses and machine learning classifiers achieving high accuracy in subgroup identification.ConclusionBy leveraging RWD and advanced clustering techniques, the study provides insights into the heterogeneity of COVID-19 presentations. The findings support the development of classification models that can inform more individualized and effective treatment plans, improving patient outcomes in the future.
The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health
Abstract Background Salmonella enterica subspecies enterica serovar Typhi (abbreviated as ‘Typhi’) is the bacterial agent of typhoid fever. Effective antimicrobial therapy reduces complications and mortality; however, antimicrobial resistance (AMR) is a major problem in many endemic countries. Prevention through vaccination is possible through recently-licensed typhoid conjugate vaccines (TCVs). National immunisation programs are currently being considered or deployed in several countries where AMR prevalence is known to be high, and the Gavi vaccine alliance has provided financial support for their introduction. Pathogen whole genome sequence data are a rich source of information on Typhi variants (genotypes or lineages), AMR prevalence, and mechanisms. However, this information is currently not readily accessible to non-genomics experts, including those driving vaccine implementation or empirical therapy guidance. Results We developed TyphiNET (https://www.typhi.net), an interactive online dashboard for exploring Typhi genotype and AMR distributions derived from publicly available pathogen genome sequences. TyphiNET allows users to explore country-level summaries such as the frequency of pathogen lineages, temporal trends in resistance to clinically relevant antimicrobials, and the specific variants and mechanisms underlying emergent AMR trends. User-driven plots and session reports can be downloaded for ease of sharing. Importantly, TyphiNET is populated by high-quality genome data curated by the Global Typhoid Pathogen Genomics Consortium, analysed using the Pathogenwatch platform, and identified as coming from non-targeted sampling frames that are suitable for estimating AMR prevalence amongst Typhi infections (no personal data is included in the platform). As of February 2024, data from a total of n = 11,836 genomes from 101 countries are available in TyphiNET. We outline case studies illustrating how the dashboard can be used to explore these data and gain insights of relevance to both researchers and public health policy-makers. Conclusions The TyphiNET dashboard provides an interactive platform for accessing genome-derived data on pathogen variant frequencies to inform typhoid control and intervention strategies. The platform is extensible in terms of both data and features, and provides a model for making complex bacterial genome-derived data accessible to a wide audience.
Characterising the Behaviour of a Structured PDE Model of the Cell Cycle in Contrast to a Corresponding ODE System.
Experimental results have shown that anti-cancer therapies, such as radiotherapy and chemotherapy, can modulate the cell cycle and generate cell cycle phase-dependent responses. As a result, obtaining a detailed understanding of the cell cycle is one possible path towards improving the efficacy of many of these therapies. Here, we consider a basic structured partial differential equation (PDE) model for cell progression through the cell cycle, and derive expressions for key quantities, such as the population growth rate and cell phase proportions. These quantities are shown to be periodic and, as such, we compare the PDE model to a corresponding ordinary differential equation (ODE) model in which the parameters are linked by ensuring that the long-term ODE behaviour agrees with the average PDE behaviour. By design, we find that the ODE model does an excellent job of representing the mean dynamics of the PDE model within just a few cell cycles. However, by probing the parameter space we find cases in which this mean behaviour is not a good measure of the PDE population growth. Our analytical comparison of two caricature models (one PDE and one ODE system) provides insight into cases in which the simple ODE model is an appropriate approximation to the PDE model.
Continuous Indexing of Fibrosis (CIF): improving the assessment and classification of MPN patients.
The grading of fibrosis in myeloproliferative neoplasms (MPN) is an important component of disease classification, prognostication and monitoring. However, current fibrosis grading systems are only semi-quantitative and fail to fully capture sample heterogeneity. To improve the quantitation of reticulin fibrosis, we developed a machine learning approach using bone marrow trephine (BMT) samples (n = 107) from patients diagnosed with MPN or a reactive marrow. The resulting Continuous Indexing of Fibrosis (CIF) enhances the detection and monitoring of fibrosis within BMTs, and aids MPN subtyping. When combined with megakaryocyte feature analysis, CIF discriminates between the frequently challenging differential diagnosis of essential thrombocythemia (ET) and pre-fibrotic myelofibrosis with high predictive accuracy [area under the curve = 0.94]. CIF also shows promise in the identification of MPN patients at risk of disease progression; analysis of samples from 35 patients diagnosed with ET and enrolled in the Primary Thrombocythemia-1 trial identified features predictive of post-ET myelofibrosis (area under the curve = 0.77). In addition to these clinical applications, automated analysis of fibrosis has clear potential to further refine disease classification boundaries and inform future studies of the micro-environmental factors driving disease initiation and progression in MPN and other stem cell disorders.
Crystallographic fragment screening reveals ligand hotspots in TRIM21 PRY-SPRY domain.
Tripartite motif-containing protein 21 (TRIM21), and particularly its PRY-SPRY protein interaction domain, plays a critical role in the immune response by recognizing intracellular antibodies targeting them for degradation. In this study, we performed a crystallographic fragment screening (CFS) campaign to identify potential small molecule binders targeting the PRY-SPRY domain of TRIM21. Our screen identified a total of 109 fragments binding to TRIM21 that were distributed across five distinct binding sites. These fragments have been designed to facilitate straightforward follow-up chemistry, making them ideal starting points for further chemical optimization. A subsequent fragment merging approach demonstrated improved activity. To enable functional validation of compounds with full length human TRIM21, we established a NanoBRET assay suitable for measuring target engagement to the main Fc binding site in life cells. The high-resolution structural data and observed binding modes across the different sites highlight the versatility of the PRY-SPRY domain as a target for small-molecule intervention. The presented data provide a solid foundation for structure-guided ligand design, enabling the rational design of more potent and selective compounds, with the goal to develop bivalent molecules such as Proteolysis Targeting Chimeras (PROTACs).
Dual ENPP1/ATM depletion blunts DNA damage repair boosting radioimmune efficacy to abrogate triple-negative breast cancer.
The ATP-hydrolytic ectoenzyme ENPP1 has been implicated in the metastasis and recurrence in triple-negative breast cancer (TNBC), primarily by contributing to tumor cell survival and treatment resistance. However, the precise mechanisms remain unclear. In a model of local recurrence (LR), circulating tumor cells (CTC) engrafting in the post-resection tumor bed developed a radioresistant phenotype linked to an ENPP1+-gene signature which was also identified in TNBC patients, suggesting ENPP1´s role in genome integrity. Blockade of ENPP1 using a permeable ENPP1 inhibitor (AVA-NP-695) reduced radioresistance, mechanistically attributed to decreased homologous recombination (HR) resulting in persistent DNA damage, as evidenced by enhanced tail moment and sustained γH2AX formation. This impaired DNA damage repair (DDR) sensitized tumor cells to ionizing radiation (IR). Notably, several DDR inhibitors (i) (including PARPi and ATMi) showed the highest synergy score in a targeted pharmacological screening. In vivo, dual ENPP1/ATM inhibition heightened radiosensitivity, compromised tumor cell survival and enhanced STING-TBK1 signaling by preventing ENPP1-mediated cGAMP hydrolysis. This resulted in robust innate and long-lasting adaptive antitumor immune memory responses, leading to significant tumor regression. Remarkably, combined treatment post-IR reduced spontaneous metastasis and local recurrence, and induced abscopal effects that impacted distant tumor spread in orthotopic tumor models. Thus, these findings position ENPP1 as a critical link between genome integrity and immunosuppression, offering promising translational opportunities for treating local or distant dissemination in TNBC.
Acceptability and feasibility of glucose-6-phosphate dehydrogenase (G6PD) testing using SD Biosensor by village malaria workers in Cambodia: a qualitative study.
INTRODUCTION: Plasmodium vivax is the predominant cause of malaria in the Greater Mekong Subregion. To ensure safe treatment with primaquine, point-of-care glucose-6-phosphate dehydrogenase (G6PD) testing was rolled out in Cambodia at the health facility level, although most malaria patients are diagnosed in the community. The current study aims to explore the acceptability and feasibility of implementing community-level G6PD testing in Cambodia. METHODS: Semistructured interviews and focus group discussions (FGD) were conducted. Across eight study sites in three provinces, 142 respondents, including policymakers, programme officers, healthcare providers and patients, participated in 67 interviews and 19 FGDs in 2022 and 2023. Data were analysed thematically using an adapted framework derived from Bowen et al's feasibility framework and Sekhon et al's acceptability framework. RESULTS: All stakeholders attributed value to the intervention. Acknowledging an intervention's different values can help discern policy implications for an intervention's successful implementation. Building and maintaining confidence in the device, end users, infrastructure and health systems were found to be key elements of acceptability. In general, health centre workers and village malaria workers (VMWs) had confidence that VMWs could conduct the test and administer treatment given appropriate initial training, monthly refresher training and the test's repeated use. More is required to build policymakers' confidence, while some implementation challenges, including the test's regulatory approval, stability above 30°C and cost, need to be overcome. CONCLUSION: Implementation of G6PD testing at the community level in Cambodia is an acceptable and potentially feasible option but requires addressing implementation challenges and building and maintaining confidence among stakeholders.
Factors affecting integration of an early warning system for antimalarial drug resistance within a routine surveillance system in a pre-elimination setting in Sub-Saharan Africa.
To address the current threat of antimalarial resistance, countries need innovative solutions for timely and informed decision-making. Integrating molecular surveillance for drug-resistant malaria into routine malaria surveillance in pre-elimination contexts offers a potential early warning mechanism for further investigation and response. However, there is limited evidence on what influences the performance of such a system in resource-limited settings. From March 2018 to February 2020, a sequential mixed-methods study was conducted in primary healthcare facilities in a South African pre-elimination setting to explore factors influencing the flow, quality and linkage of malaria case notification and molecular resistance marker data. Using a process-oriented framework, we undertook monthly and quarterly data linkage and consistency analyses at different levels of the health system, as well as a survey, focus group discussions and interviews to identify potential barriers to, and enhancers of, the roll-out and uptake of this integrated information system. Over two years, 4,787 confirmed malaria cases were notified from 42 primary healthcare facilities in the Nkomazi sub-district, Mpumalanga, South Africa. Of the notified cases, 78.5% (n = 3,758) were investigated, and 55.1% (n = 2,636) were successfully linked to their Plasmodium falciparum molecular resistance marker profiles. Five tangible processes-malaria case detection and notification, sample collection, case investigation, analysis and reporting-were identified within the process-oriented logic model. Workload, training, ease of use, supervision, leadership, and resources were recognized as cross-cutting influencers affecting the program's performance. Approaching malaria elimination, linking molecular markers of antimalarial resistance to routine malaria surveillance is feasible. However, cross-cutting barriers inherent in the healthcare system can influence its success in a resource-limited setting.
Epidemiology and excess mortality of antimicrobial resistance in bacteraemias among cancer patients: a cohort study using routinely collected health data from regional hospital trusts in Oxford and Oslo, 2008-2018.
OBJECTIVES: We investigated the epidemiology and impact on mortality of antimicrobial resistance (AMR) in cancer patients with bacteraemia at Oxford University Hospitals (OxUH), UK, and Oslo University Hospital (OsUH), Norway, during 2008-2018. DESIGN: Historical cohort study. SETTING: Regional hospital trusts with multiple sites in OxUH and OsUH. METHODS: Patients with cancer and blood cultures positive for one of six pathogen groups during a hospital stay within 3 years following their first cancer diagnosis were followed for 30 days after their first bacteraemia episode. We determined the number of cases and the proportion of infections with an AMR phenotype. Excess mortality and the population-attributable fraction (PAF) due to AMR were estimated by contrasting observed mortality at the end of follow-up with an estimated counterfactual scenario where AMR was absent from all bacteraemias, using inverse probability weighting. MAIN OUTCOME MEASURE: 30-day all-cause mortality following the first bacteraemia episode. MAIN EXPOSURE MEASURE: A resistant phenotype of the causative pathogen. RESULTS: The study included 1929 patients at OxUH and 1640 patients at OsUH. The highest resistance proportions were found for vancomycin resistance in enterococci (85/314, 27.1%) and carbapenem-resistance in Pseudomonas aeruginosa (63/260, 24.2%) at OxUH, and third-generation cephalosporin resistance in Escherichia coli (62/743, 8.3%) and Klebsiella pneumoniae (14/223, 6.3%) at OsUH. Observed mortality for all infections was 26.4% at OxUH, with an estimated counterfactual mortality without AMR of 24.7%, yielding an excess mortality of 1.7% (95% CI: 0.8 to 2.5%). The PAF was 6.3% (95% CI: 2.9 to 9.6%), meaning an estimated 32 of 509 deaths could be attributed to AMR. Limited events at OsUH precluded a similar estimate. CONCLUSIONS: Despite estimating modest excess mortality, the mortality attributable to resistance in these two high-income, low-prevalence settings highlights the potential for escalation if global resistance trends continue to worsen.
Evidence of focusing the MHC class I immunopeptidome by tapasin.
Major Histocompatibility Complex class I (MHC-I) molecules bind and present peptides to cytotoxic T cells, protecting against pathogens and cancer. MHC-I is highly polymorphic and each allotype is promiscuous, and capable of binding a unique and diverse repertoire of peptide ligands. The peptide editing chaperone tapasin optimizes this allotype specific repertoire of peptides, resulting in the selection of high affinity peptides. MHC-I allotypes differ in the extent they engage tapasin. This suggests that tapasin-dependent MHC-I allotypes should present a less diverse repertoire that is enriched in higher-affinity peptides, and which are present in higher abundance, than tapasin independent MHC-I allotypes, which should present a broader repertoire containing peptides with a lower average affinity. Experimental verification of this hypothesis has been confounded by the different peptide binding specificities of MHC-I allotypes. Here, we independently investigated the peptide focusing function of tapasin by introducing a point mutation into a tapasin independent MHC-I allotype that dramatically increased its tapasin dependence without substantially altering its peptide binding specificity. This allowed us to demonstrate ligand focusing by tapasin at both the repertoire level in cellulo, and by using an in vitro system in which tapasin was artificially tethered to MHC-I, at the individual peptide level. We found that tapasin had a greater influence on tapasin dependent MHC-I molecules, and that tapasin modulated peptide selection according to peptide-MHC-I complex stability, disfavoring short-lived peptide-MHC-I complexes. Thus, tapasin dependent MHC-I molecules experience greater tapasin filtering, resulting in less diverse MHC-I immunopeptidomes that are enriched in high affinity peptide-MHC-I complexes.
Strict advantage of complex quantum theory in a communication task
Standard formulations of quantum theory are based on complex numbers: Quantum states can be in superpositions, with weights given by complex probability amplitudes. Motivated by quantum theory promising a range of practical advantages over classical for a multitude of tasks, we investigate how the presence of complex amplitudes in quantum theory can yield operational advantages over counterpart real formulations. We identify a straightforward communication task for which complex quantum theory exhibits a provably lower communication cost than not just any classical approach, but also any approach based on real quantum theory. We certify the necessity of complex quantum theory for optimal approaches to the task through geometric properties of quantum state ensembles that witness the presence of basis-independent complexity. This substantiates a strict operational advantage of complex quantum theory. We discuss the relevance of this finding for quantum advantages in stochastic simulation.
Deep palaeoproteomic profiling of archaeological human brains.
Palaeoproteomics leverages the persistence, diversity, and biological import of ancient proteins to explore the past, and answer fundamental questions about phylogeny, environment, diet, and disease. These insights are largely gleaned from hard tissues like bone and teeth, as well-established protocols exist for extracting ancient proteins from mineralised tissues. No such method, however, exists for the soft tissues, which are underexplored in palaeoproteomics given permission for destructive analysis routinely depends on a proven methodology. Considering less than one-tenth of all human proteins are expressed in bone, compared to three-quarters in the internal organs, the amount of biological information presently inaccessible is substantial. We address this omission with an optimised LC-FAIMS-MS/MS workflow yielding the largest, most diverse palaeoproteome yet described. Using archaeological human brains, we test ten protocols with varied chemistries and find that urea lysis effectively disrupts preserved membrane regions to expose low-abundant, intracellular analytes. Further, we show that ion mobility spectrometry improves unique protein identification by as much as 40%, and represents a means of "cleaning" dirty archaeological samples. Our methodology will be useful for improving protein recovery from a range of ancient tissues and depositional environments.
A Novel Toolkit of SARS-CoV-2 Sub-Genomic Replicons for Efficient Antiviral Screening.
SARS-CoV-2 is classified as a containment level 3 (CL3) pathogen, limiting research access and antiviral testing. To address this, we developed a non-infectious viral surrogate system using reverse genetics to generate sub-genomic replicons. These replicons contained the nsp1 mutations K164A and H165A and had the spike, membrane, ORF6, and ORF7a coding sequences replaced with various reporter and selectable marker genes. Replicons based on the ancestral Wuhan Hu-1 strain and the Delta variant of concern were replication-competent in multiple cell lines, as assessed by Renilla luciferase activity, fluorescence, immunofluorescence staining, and single-molecule fluorescent in situ hybridization. Antiviral assays using transient replicon expression showed that remdesivir effectively inhibited both replicon and viral replication. Ritonavir and cobicistat inhibited Delta variant replicons similarly to wild-type virus but did not inhibit Wuhan Hu-1 replicon replication. To further investigate the impact of nsp1 mutations, we generated a recombinant SARS-CoV-2 virus carrying the K164A and H165A mutations. The virus exhibited attenuated replication across a range of mammalian cell lines, was restricted by the type I interferon response, and showed reduced cytopathic effects. These findings highlight the utility of sub-genomic replicons as reliable CL2-compatible surrogates for studying SARS-CoV-2 replication and drug activity mechanisms.
Features influencing the health and economic impact of preventing COVID-19 in immunocompromised individuals.
Many immunocompromised individuals mount inadequate immune responses following COVID-19 vaccination, thus relying on other social distancing behaviours, particularly shielding, for protection, impacting their quality of life. However, little is known about historical/current levels and effectiveness of shielding or factors influencing individuals' decision to continue shielding. Long-acting antibody pre-exposure prophylaxis (LAAB-PrEP) provides direct protection against COVID-19 in immunocompromised individuals who have been and may continue to shield. However, the proportion and incidence of circulating variants for which LAAB-PrEP would be effective is unpredictable. Given this uncertain behavioural and immuno-epidemiological context, we developed a modelling framework to explore features that most impact health outcomes and cost effectiveness of long-term administration of LAAB-PrEP against COVID-19 infection in immunocompromised individuals in the English context. The model predicted that the incremental cost-effectiveness ratio (ICER) of LAAB-PrEP against COVID-19 in immunocompromised individuals will be largely driven by features of utility of shielding, current/future shielding behaviour, cost of shielding, risk of COVID-19 hospitalisation among immunocompromised individuals and the time horizon used for the cost-effectiveness analysis. The model estimated that for realistic ranges of influential factors, it is possible for LAAB-PrEP to be cost effective under the conditions that most immunocompromised individuals would shield indefinitely if it were not available but would switch to LAAB-PrEP if it were. Thus, if individuals stop shielding when taking LAAB-PrEP, then LAAB-PrEP is cost effective.
Docking for Smoothened antagonist chemotypes not susceptible to a vismodegib-resistance mutation.
The G protein-coupled receptor Smoothened (SMO) plays a pivotal role in embryonic development transducing the Hedgehog morphogen signal into the cell. Aberrant activation of the pathway is associated with various cancer types. Antagonizing SMO has been recognized as a therapeutic strategy exemplified by drugs such as vismodegib and sonidegib, but despite initial remission, cancer recurrence is frequent due to resistance mutations. Utilizing a structure-based design approach, we have identified three unprecedented chemotypes to antagonize SMO with potencies in the low micromolar range. In total, 67 compounds identified through molecular docking were assayed in four rounds with hit rates of 27% and 63% during hit identification, i.e. the first two rounds. Importantly, the potency of ligands with two of the chemotypes identified in this work is not strongly affected by the vismodegib resistance mutation D473G. The mutation affects potency and maximal inhibitory effect of these ligands only in a way similar to SANT-1, a SMO ligand unencumbered by the mutation. Our study thus shows a successful application of structure-based design for the discovery of novel SMO antagonist chemotypes.
The effect of D-cycloserine on brain connectivity over a course of pulmonary rehabilitation - A randomised control trial with neuroimaging endpoints.
Combining traditional therapies such as pulmonary rehabilitation with brain-targeted drugs may offer new therapeutic opportunities for the treatment of chronic breathlessness. Recently, we asked whether D-cycloserine, a partial NMDA-receptor agonist which may enhance behavioural therapies, modifies the relationship between breathlessness related brain activity and breathlessness anxiety over pulmonary rehabilitation. However, whether any changes are supported by alterations to underlying brain structure remains unknown. Here we examine the effect of D-cycloserine over a course of pulmonary rehabilitation on the connectivity between key brain regions associated with the processing of breathlessness anxiety. 72 participants with mild-to-moderate COPD took part in a longitudinal study in parallel to their pulmonary rehabilitation course. Diffusion tensor brain imaging and clinical measures of respiratory function were collected at three time points (before, during and after pulmonary rehabilitation). Participants were assigned to 250mg of D-cycloserine or placebo, which they were administered with on four occasions in a randomised, double-blind procedure. Following the first four sessions of pulmonary rehabilitation (visit 2), during which D-cycloserine was administered, improvements in breathlessness anxiety were linked with increased insula-hippocampal structural connectivity in the D-cycloserine group when compared to the placebo group. No differences were found between the two groups following the completion of the full pulmonary rehabilitation course 4-6 weeks later (visit 3). The action of D-cycloserine on brain connectivity appears to be restricted to within a short time-window of its administration. This temporary boost of the brain connectivity of two key regions associated with the evaluation of how unpleasant an experience is may support the re-evaluation of breathlessness cues, illustrated improvements in breathlessness anxiety. Trial registration ClinicalTrials.gov (NCT01985750).