How Can Viral Dynamics Models Inform Endpoint Measures in Clinical Trials of Therapies for Acute Viral Infections?

Acute viral infections pose many practical challenges for the accurate assessment of the impact of novel therapies on viral growth and decay. Using the example of influenza A, we illustrate how the measurement of infection-related quantities that determine the dynamics of viral load within the human host, can inform investigators on the course and severity of infection and the efficacy of a novel treatment. We estimated the values of key infection-related quantities that determine the course of natural infection from viral load data, using Markov Chain Monte Carlo methods. The data were placebo group viral load measurements collected during volunteer challenge studies, conducted by Roche, as part of the oseltamivir trials. We calculated the values of the quantities for each patient and the correlations between the quantities, symptom severity and body temperature. The greatest variation among individuals occurred in the viral load peak and area under the viral load curve. Total symptom severity correlated positively with the basic reproductive number. The most sensitive endpoint for therapeutic trials with the goal to cure patients is the duration of infection. We suggest laboratory experiments to obtain more precise estimates of virological quantities that can supplement clinical endpoint measurements

Limited Tumor Tissue Drug Penetration Contributes to Primary Resistance against Angiogenesis Inhibitors

Resistance mechanisms against antiangiogenic drugs are unclear. Here, we correlated the antitumor and antivascular properties of five different antiangiogenic receptor tyrosine kinase inhibitors (RTKIs) (motesanib, pazopanib, sorafenib, sunitinib, vatalanib) with their intratumoral distribution data obtained by matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). In the first mouse model, only sunitinib exhibited broad-spectrum antivascular and antitumor activities by simultaneously suppressing vascular endothelial growth factor receptor-2 (VEGFR2) and desmin expression, and by increasing intratumoral hypoxia and inhibiting both tumor growth and vascularisation significantly. Importantly, the highest and most homogeneous intratumoral drug concentrations have been found in sunitinib-treated animals. In another animal model, where - in contrast to the first model - vatalanib was detectable at homogeneously high intratumoral concentrations, the drug significantly reduced tumor growth and angiogenesis. In conclusion, the tumor tissue penetration and thus the antiangiogenic and antitumor potential of antiangiogenic RTKIs vary among the tumor models and our study demonstrates the potential of MALDI-MSI to predict the efficacy of unlabelled small molecule antiangiogenic drugs in malignant tissue. Our approach is thus a major technical and preclinical advance demonstrating that primary resistance to angiogenesis inhibitors involves limited tumor tissue drug penetration. We also conclude that MALDI-MSI may significantly contribute to the improvement of antivascular cancer therapies

Health economic analyses of latent tuberculosis infection screening and preventive treatment among people living with HIV in lower tuberculosis incidence settings: a systematic review [version 2; peer review: 1 approved, 1 approved with reservations]

INTRODUCTION: In lower tuberculosis (TB) incidence countries (<100 cases/100,000/year), screening and preventive treatment (PT) for latent TB infection (LTBI) among people living with HIV (PLWH) is often recommended, yet guidelines advising which groups to prioritise for screening can be contradictory and implementation patchy. Evidence of LTBI screening cost-effectiveness may improve uptake and health outcomes at reasonable cost. METHODS: Our systematic review assessed cost-effectiveness estimates of LTBI screening/PT strategies among PLWH in lower TB incidence countries to identify model-driving inputs and methodological differences. Databases were searched 1980-2020. Studies including health economic evaluation of LTBI screening of PLWH in lower TB incidence countries (<100 cases/100,000/year) were included. RESULTS: Of 2,644 articles screened, nine studies were included. Cost-effectiveness estimates of LTBI screening/PT for PLWH varied widely, with universal screening/PT found highly cost-effective by some studies, while only targeting to high-risk groups (such as those from mid/high TB incidence countries) deemed cost-effective by others. Cost-effectiveness of strategies screening all PLWH from studies published in the past five years varied from US$2828 to US$144,929/quality-adjusted life-year gained (2018 prices). Study quality varied, with inconsistent reporting of methods and results limiting comparability of studies. Cost-effectiveness varied markedly by screening guideline, with British HIV Association guidelines more cost-effective than NICE guidelines in the UK. DISCUSSION: Cost-effectiveness studies of LTBI screening/PT for PLWH in lower TB incidence settings are scarce, with large variations in methods and assumptions used, target populations and screening/PT strategies evaluated. The limited evidence suggests LTBI screening/PT may be cost-effective for some PLWH groups but further research is required, particularly on strategies targeting screening/PT to PLWH at higher risk. Standardisation of model descriptions and results reporting could facilitate reliable comparisons between studies, particularly to identify those factors driving the wide disparity between cost-effectiveness estimates. REGISTRATION: PROSPERO CRD42020166338 (18/03/2020)

Plasma proteomic profiling in postural orthostatic tachycardia syndrome (POTS) reveals new disease pathways

Postural orthostatic tachycardia syndrome (POTS) is a cardiovascular autonomic disorder characterized by excessive heart rate increase on standing, leading to debilitating symptoms with limited therapeutic possibilities. Proteomics is a large-scale study of proteins that enables a systematic unbiased view on disease and health, allowing stratification of patients based on their protein background. The aim of the present study was to determine plasma protein biomarkers of POTS and to reveal proteomic pathways differentially regulated in POTS. We performed an age- and sex-matched, case–control study in 130 individuals (case–control ratio 1:1) including POTS and healthy controls. Mean age in POTS was 30 ± 9.8 years (84.6% women) versus controls 31 ± 9.8 years (80.0% women). We analyzed plasma proteins using data-independent acquisition (DIA) mass spectrometry. Pathway analysis of significantly differently expressed proteins was executed using a cutoff log2 fold change set to 1.2 and false discovery rate (p-value) of < 0.05. A total of 393 differential plasma proteins were identified. Label-free quantification of DIA-data identified 30 differentially expressed proteins in POTS compared with healthy controls. Pathway analysis identified the strongest network interactions particularly for proteins involved in thrombogenicity and enhanced platelet activity, but also inflammation, cardiac contractility and hypertrophy, and increased adrenergic activity. Our observations generated by the first use a label-free unbiased quantification reveal the proteomic footprint of POTS in terms of a hypercoagulable state, proinflammatory state, enhanced cardiac contractility and hypertrophy, skeletal muscle expression, and adrenergic activity. These findings support the hypothesis that POTS may be an autoimmune, inflammatory and hyperadrenergic disorder

Quantitative proteomics of patient fibroblasts reveal biomarkers and diagnostic signatures of mitochondrial disease

\ua9 2024, Correia et al. This is an open access article published under the terms of the Creative Commons Attribution 4.0 International License.BACKGROUND. Mitochondrial diseases belong to the group of inborn errors of metabolism (IEM), with a prevalence of 1 in 2,000–5,000 individuals. They are the most common form of IEM, but, despite advances in next-generation sequencing technologies, almost half of the patients are left genetically undiagnosed. METHODS. We investigated a cohort of 61 patients with defined mitochondrial disease to improve diagnostics, identify biomarkers, and correlate metabolic pathways to specific disease groups. Clinical presentations were structured using human phenotype ontology terms, and mass spectrometry–based proteomics was performed on primary fibroblasts. Additionally, we integrated 6 patients carrying variants of uncertain significance (VUS) to test proteomics as a diagnostic expansion. RESULTS. Proteomic profiles from patient samples could be classified according to their biochemical and genetic characteristics, with the expression of 5 proteins (GPX4, MORF4L1, MOXD1, MSRA, and TMED9) correlating with the disease cohort, thus acting as putative biomarkers. Pathway analysis showed a deregulation of inflammatory and mitochondrial stress responses. This included the upregulation of glycosphingolipid metabolism and mitochondrial protein import, as well as the downregulation of arachidonic acid metabolism. Furthermore, we could assign pathogenicity to a VUS in MRPS23 by demonstrating the loss of associated mitochondrial ribosome subunits. CONCLUSION. We established mass spectrometry–based proteomics on patient fibroblasts as a viable and versatile tool for diagnosing patients with mitochondrial disease

Predicted Impact of COVID-19 on Neglected Tropical Disease Programs and the Opportunity for Innovation

Due to the COVID-19 pandemic, many key neglected tropical disease (NTD) activities have been postponed. This hindrance comes at a time when the NTDs are progressing towards their ambitious goals for 2030. Mathematical modelling on several NTDs, namely gambiense sleeping sickness, lymphatic filariasis, onchocerciasis, schistosomiasis, soil-transmitted helminthiases (STH), trachoma, and visceral leishmaniasis, shows that the impact of this disruption will vary across the diseases. Programs face a risk of resurgence, which will be fastest in high-transmission areas. Furthermore, of the mass drug administration diseases, schistosomiasis, STH, and trachoma are likely to encounter faster resurgence. The case-finding diseases (gambiense sleeping sickness and visceral leishmaniasis) are likely to have fewer cases being detected but may face an increasing underlying rate of new infections. However, once programs are able to resume, there are ways to mitigate the impact and accelerate progress towards the 2030 goals.</p

Designing antifilarial drug trials using clinical trial simulators

Lymphatic filariasis and onchocerciasis are neglected tropical diseases (NTDs) targeted for elimination by mass (antifilarial) drug administration. These drugs are predominantly active against the microfilarial progeny of adult worms. New drugs or combinations are needed to improve patient therapy and to enhance the effectiveness of interventions in persistent hotspots of transmission. Several therapies and regimens are currently in (pre-)clinical testing. Clinical trial simulators (CTSs) project patient outcomes to inform the design of clinical trials but have not been widely applied to NTDs, where their resource-saving payoffs could be highly beneficial. We demonstrate the utility of CTSs using our individual-based onchocerciasis transmission model (EPIONCHO-IBM) that projects trial outcomes of a hypothetical macrofilaricidal drug. We identify key design decisions that influence the power of clinical trials, including participant eligibility criteria and post-treatment follow-up times for measuring infection indicators. We discuss how CTSs help to inform target product profiles

PATH-SAFE consortium recommendations for genomic surveillance of foodborne diseases, using Salmonella as an exemplar

Whole-genome sequencing (WGS) for foodborne disease (FBD) surveillance provides many benefits, including new insights in disease transmission, virulence and antimicrobial resistance (AMR), fast and precise outbreak tracing and source attribution, as well as, enabling streamlined and reproducible analysis through digital data that from a technical point of view can be easily shared. The National foodborne disease genomic data platform, developed as part of the PATH-SAFE programme, will offer a trusted environment for WGS data sharing and analysis for UK agencies involved in FBD surveillance. The platform has initially been built for Salmonella with the intention to expand it to other organisms later. Where possible, the platform has drawn on existing and validated solutions as implemented in EnteroBase, PubMLST and Pathogenwatch. The platform is hosted on CLIMB-BIG-DATA and has been built to enable interoperability between analytical tools and databases. Although a fully interoperable bioinformatics system for FBD and AMR surveillance is not practically feasible at this time, it should be a long-term goal. Recommendations on which tools to use for molecular surveillance of Salmonella have been developed in consultation with Community Input Advisory Groups (CIAGs) on 1) technical aspects of FBD surveillance, 2) AMR risk determinants, 3) data standards for FBD surveillance, 4) considerations for international molecular FBD surveillance. The purpose of this document is to act as a standard reference for methodologies for genomic surveillance of FBD to support FSA goals and achieve the benefits laid out above. The recommendations have been developed using non-typhoidal Salmonella as an example

PATH-SAFE consortium recommendations for genomic surveillance of food-borne diseases Escherichia coli and Listeria monocytogenes

Whole-genome sequencing (WGS) for food-borne disease (FBD) surveillance provides many benefits, including new insights in disease transmission, virulence and antimicrobial resistance (AMR), fast and precise outbreak tracing and source attribution, as well as streamlined and reproducible analysis through digital data that, from a technical point of view, can be easily shared. The National foodborne disease genomic data platform (the PATH-SAFE platform) will offer a trusted environment for WGS data sharing and analysis for UK agencies involved in FBD surveillance. Following the successful implementation of the platform for Salmonella, in the second phase the platform will be expanded to Escherichia coli and Listeria monocytogenes. Where possible, the platform will draw on existing and validated solutions. For de novo genome assembly, EToKI and vanilla SPAdes provide the best results for E. coli, and Pathogenwatch provides the best results for L. monocytogenes. Analysis of genomic data is greatly enhanced by assigning genomes into well-defined cluster groups, which should be available on the PATH-SAFE platform. Specifically, tools for MLST and cgMLST should be available on the PATH-SAFE platform for both E. coli and L. monocytogenes. In addition, HierCC and ClermonTyping tools should be available for E. coli. The platform should implement tools for clustering E. coli and L. monocytogenes based on MLST/cgMLST profiles. Clusters should be named according to their HierCC codes. The PATH-SAFE platform should implement a tool for predicting E. coli serotypes from sequence data. ECTyper has been selected as the only up-to-date tool for this purpose. Although serotype determination of E. coli isolates is useful for historical reasons, the platform should be designed in a way that makes it easy to switch to hierarchical clustering of isolates. The identification of genetic virulence determinants is essential in the analysis of E. coli and L. monocytogenes. VirulenceFinder and AdhesiomeR should be implemented in the PATH-SAFE platform for virulence determinant identification in E. coli. The Pasteur L. monocytogenes Scheme has been selected for virulence determinant identification in L. monocytogenes, although none of the available databases seems to include all known genes determining virulence in L. monocytogenes. As the PATH-SAFE platform is expanded to new food-borne pathogens, integrating a tool to differentiate species will be useful. Speciator has been validated and shown to be 99.9% in agreement with Kraken in correctly assigning E. coli genomes. The number of metadata fields should be small initially to facilitate upload of data and use of the PATH-SAFE platform and to be consistent with UK GDPR obligations. Minimum metadata requirements of the platform should be compatible with the metadata collected by each agency. They should also be compatible with concerns around data sharing and legal obligations. All metadata must be processed in line with UK GDPR guidelines and align with organisational policies and relevant legislation. The PATH-SAFE platform should implement a gated access model that will allow participating agencies to share additional metadata with trusted partners and at the same time minimise the risk of leaking sensitive information. The PATH-SAFE platform should have an automated QC mechanism for validating uploaded metadata. Options for both bulk upload of metadata and for upload of individual metadata fields should be offered by the platform. In addition, functionality for regular automated uploads could be provided. Experiences with implementing WGS for FBD surveillance in the UK, Switzerland and Canada show that collaboration of reference laboratories carrying out sequencing analyses and epidemiological and One Health units providing metadata is critical for prioritising isolates for outbreak investigations