Prognostic impact of variant histology in bladder cancer: Would early and aggressive treatment shift the paradigm?

INTRODUCTION

Bladder cancer (BC) is an increasingly frequent malignancy worldwide. Several variant histologies (VH) have been described in BC with a distinct clinical behavior.

OBJECTIVES

This study aims to assess the prognostic impact of VH in BC, comparing its outcomes to pure urothelial carcinoma PUC in both non-muscle invasive (NMIBC) and muscle-invasive (MIBC) settings.

METHODS

We included patients with primary BC, comparing those with VH with those with PUC, with an age and sex-matched proportion of 1:3, considering stage at diagnosis, recurrence-free, progression-free, and overall survival (OS). A total of 616 patients were included in the study, (460 UC and 151 VH).

RESULTS

After first TURBT, MIBC was present in 99 (64.1%) of patients with VH, and 95 (20.6%) with UC (p<0.001). Concerning NMIBC, we observed higher rates of progression to MIBC amid patients with VH (p=0.009). Nodal involvement (p=0.020) and metastatic disease (p<0.001) were significantly higher within the VH group. A higher OS was observed among patients with NMIBC of PUC (p<0.001). There were no statistically significant differences of metastasis-free survival and OS between VH and UC groups within the MIBC setting.

CONCLUSION

We confirmed that VH presents a more aggressive clinical course compared to PUC. An earlier radical treatment within the NMIBC setting could increase the oncological outcomes of the VH patients.

A multinational survey of companion animal veterinary clinicians: How can antimicrobial stewardship guidelines be optimised for the target stakeholder?

Antimicrobial stewardship initiatives are widely regarded as a cornerstone for ameliorating the global health impact of antimicrobial resistance. Within companion animal health, such efforts have largely focused on development and dissemination of antimicrobial stewardship guidelines (ASGs). However, there have been few attempts to understand veterinarian attitudes towards and knowledge of ASGs or to determine how awareness regarding ASGs might best be increased. An online survey regarding ASGs was formulated for veterinarians who treat companion animals. The survey was distributed across 46 European and associated countries between 12 January and 30 June, 2022. In total, 2271 surveys were completed, with 64.9% of respondents (n = 1474) reporting awareness and usage of at least one ASG. Respondents from countries with greater awareness of ASGs tended to report more appropriate use of antimicrobials (Spearman's rank coefficient = 0.6084, P ≤ 0.001), with respondents from countries with country-specific ASGs tending to score highest across both awareness and appropriate use domains. Respondents prioritised guidance around antimicrobial choice (82.0%, n = 1863), duration of treatment (66.0%, n = 1499), and dosage (51.9%, n = 1179) for inclusion in future ASGs, with 78.0% (n = 1776) of respondents preferring ASGs to be integrated into their patient management system. Awareness of ASGs and their use in companion animal veterinary practice appears to be greater than previously reported, with respondents tending to report antimicrobial prescription decision making broadly in line with current clinical recommendations. However, further initiatives aimed at maximising accessibility to ASGs both within countries and individual veterinary practices are recommended.

Systematic analysis of drug combinations against Gram-positive bacteria

Drug combinations can expand options for antibacterial therapies but have not been systematically tested in Gram-positive species. We profiled ~8,000 combinations of 65 antibacterial drugs against the model species Bacillus subtilis and two prominent pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Thereby, we recapitulated previously known drug interactions, but also identified ten times more novel interactions in the pathogen S. aureus, including 150 synergies. We showed that two synergies were equally effective against multidrug-resistant S. aureus clinical isolates in vitro and in vivo. Interactions were largely species-specific and synergies were distinct from those of Gram-negative species, owing to cell surface and drug uptake differences. We also tested 2,728 combinations of 44 commonly prescribed non-antibiotic drugs with 62 drugs with antibacterial activity against S. aureus and identified numerous antagonisms that might compromise the efficacy of antimicrobial therapies. We identified even more synergies and showed that the anti-aggregant ticagrelor synergized with cationic antibiotics by modifying the surface charge of S. aureus. All data can be browsed in an interactive interface ( https://apps.embl.de/combact/ ).

D-amino acids signal a stress-dependent run-away response in Vibrio cholerae

To explore favourable niches while avoiding threats, many bacteria use a chemotaxis navigation system. Despite decades of studies on chemotaxis, most signals and sensory proteins are still unknown. Many bacterial species release D-amino acids to the environment; however, their function remains largely unrecognized. Here we reveal that D-arginine and D-lysine are chemotactic repellent signals for the cholera pathogen Vibrio cholerae. These D-amino acids are sensed by a single chemoreceptor MCPDRK co-transcribed with the racemase enzyme that synthesizes them under the control of the stress-response sigma factor RpoS. Structural characterization of this chemoreceptor bound to either D-arginine or D-lysine allowed us to pinpoint the residues defining its specificity. Interestingly, the specificity for these D-amino acids appears to be restricted to those MCPDRK orthologues transcriptionally linked to the racemase. Our results suggest that D-amino acids can shape the biodiversity and structure of complex microbial communities under adverse conditions.

Antimicrobial usage in farm animal practices in the UK: A mixed-methods approach

Antimicrobial resistance (AMR) is a growing One Health problem. Monitoring antimicrobial usage in farm animals is crucial for tackling AMR. A cohort study using the electronic clinical records during 2019 from 23 farm animal veterinary practices across the UK belonging to two corporate groups, with a range of 2-14 veterinarians per practice, estimated the usage of antimicrobials and highest priority critically important antimicrobials (HP-CIAs). Risk factors for using HP-CIAs were evaluated using hierarchical mixed-effects logistic regression modelling with practice ID and farm ID added as random effects. Using a qualitative approach, veterinarians from one of the participating practice groups were recruited for a qualitative study to explore the barriers and facilitators in relation to antimicrobial use. Semi-structured interviews were conducted with participants and analysed thematically. During the year 2019, 98,824 antimicrobial prescribing events overall were recorded from the treatment records of the 23 participating practices. The median count of antimicrobial events per practice was 3226 (range 263-22,159). There were 17,111/98,824 (17.3%) HP-CIAs events overall, with a median of 15.4% at practice level (range 4.8-22.1%). Penicillins were the most frequently used antimicrobials 29,539/98,824 (29.9%) followed by tetracyclines 19,015/98,824 (19.2%). HP-CIA use was strongly clustered, with more clustering seen at the farm level (intraclass correlation coefficient (ICC)= 0.56) than at the practice level (ICC= 0.32). Country, route of administration, season and practice type were significantly associated with the usage of HP-CIAs. Four main themes were identified from the analysis of the veterinarians' interviews: pressure from the industry, drug-related factors, knowledge level of veterinarians and clinical factors. Supermarket contracts and farm assurance schemes were facilitators for reducing antimicrobial use and the use of HP-CIAs. Ease of administration and the withdrawal period of the antimicrobials influenced veterinarians' choice of antimicrobials. The clinical condition and clinical signs presented on farm were reported to influence participating veterinarians' prescribing decision. Participants showed a good understanding of AMR, responsible use of antimicrobials and the term 'critically important antimicrobials'. In conclusion, integrating the quantitative and qualitative findings can inform policymaking on antimicrobials stewardship in farm practice. By estimating the relative levels of clustering of antimicrobial use at the practice and farm level, as well as identifying major risk factors for using HP-CIAs, more targeted interventions can be designed to promote responsible antimicrobial use in farm practice. Furthermore, better understanding the industry pressures on farms to reduce antimicrobials usage could reduce the barriers for responsible antimicrobial use by veterinarians.

Deep thermal profiling for detection of functional proteoform groups

The complexity of the functional proteome extends considerably beyond the coding genome, resulting in millions of proteoforms. Investigation of proteoforms and their functional roles is important to understand cellular physiology and its deregulation in diseases but challenging to perform systematically. Here we applied thermal proteome profiling with deep peptide coverage to detect functional proteoform groups in acute lymphoblastic leukemia cell lines with different cytogenetic aberrations. We detected 15,846 proteoforms, capturing differently spliced, cleaved and post-translationally modified proteins expressed from 9,290 genes. We identified differential co-aggregation of proteoform pairs and established links to disease biology. Moreover, we systematically made use of measured biophysical proteoform states to find specific biomarkers of drug sensitivity. Our approach, thus, provides a powerful and unique tool for systematic detection and functional annotation of proteoform groups.

Bacterial retrons encode phage-defending tripartite toxin-antitoxin systems

Retrons are prokaryotic genetic retroelements encoding a reverse transcriptase that produces multi-copy single-stranded DNA1 (msDNA). Despite decades of research on the biosynthesis of msDNA2, the function and physiological roles of retrons have remained unknown. Here we show that Retron-Sen2 of Salmonella enterica serovar Typhimurium encodes an accessory toxin protein, STM14_4640, which we renamed as RcaT. RcaT is neutralized by the reverse transcriptase-msDNA antitoxin complex, and becomes active upon perturbation of msDNA biosynthesis. The reverse transcriptase is required for binding to RcaT, and the msDNA is required for the antitoxin activity. The highly prevalent RcaT-containing retron family constitutes a new type of tripartite DNA-containing toxin-antitoxin system. To understand the physiological roles of such toxin-antitoxin systems, we developed toxin activation-inhibition conjugation (TAC-TIC), a high-throughput reverse genetics approach that identifies the molecular triggers and blockers of toxin-antitoxin systems. By applying TAC-TIC to Retron-Sen2, we identified multiple trigger and blocker proteins of phage origin. We demonstrate that phage-related triggers directly modify the msDNA, thereby activating RcaT and inhibiting bacterial growth. By contrast, prophage proteins circumvent retrons by directly blocking RcaT. Consistently, retron toxin-antitoxin systems act as abortive infection anti-phage defence systems, in line with recent reports3,4. Thus, RcaT retrons are tripartite DNA-regulated toxin-antitoxin systems, which use the reverse transcriptase-msDNA complex both as an antitoxin and as a sensor of phage protein activities.

Drug Target Identification in Tissues by Thermal Proteome Profiling

Drug target deconvolution can accelerate the drug discovery process by identifying a drug's targets (facilitating medicinal chemistry efforts) and off-targets (anticipating toxicity effects or adverse drug reactions). Multiple mass spectrometry-based approaches have been developed for this purpose, but thermal proteome profiling (TPP) remains to date the only one that does not require compound modification and can be used to identify intracellular targets in living cells. TPP is based on the principle that the thermal stability of a protein can be affected by its interactions. Recent developments of this approach have expanded its applications beyond drugs and cell cultures to studying protein-drug interactions and biological phenomena in tissues. These developments open up the possibility of studying drug treatment or mechanisms of disease in a holistic fashion, which can result in the design of better drugs and lead to a better understanding of fundamental biology. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Rtpca: an R package for differential thermal proximity coaggregation analysis

Summary

Rtpca is an R package implementing methods for inferring protein–protein interactions (PPIs) based on thermal proteome profiling experiments of a single condition or in a differential setting via an approach called thermal proximity coaggregation. It offers user-friendly tools to explore datasets for their PPI predictive performance and easily integrates with available R packages.

Availability and implementation

Rtpca is available from Bioconductor (https://bioconductor.org/packages/Rtpca).

Supplementary information

Supplementary data are available at Bioinformatics online.

SARS-CoV-2 infection remodels the host protein thermal stability landscape

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global threat to human health and has compromised economic stability. In addition to the development of an effective vaccine, it is imperative to understand how SARS-CoV-2 hijacks host cellular machineries on a system-wide scale so that potential host-directed therapies can be developed. In situ proteome-wide abundance and thermal stability measurements using thermal proteome profiling (TPP) can inform on global changes in protein activity. Here we adapted TPP to high biosafety conditions amenable to SARS-CoV-2 handling. We discovered pronounced temporal alterations in host protein thermostability during infection, which converged on cellular processes including cell cycle, microtubule and RNA splicing regulation. Pharmacological inhibition of host proteins displaying altered thermal stability or abundance during infection suppressed SARS-CoV-2 replication. Overall, this work serves as a framework for expanding TPP workflows to globally important human pathogens that require high biosafety containment and provides deeper resolution into the molecular changes induced by SARS-CoV-2 infection.

Hepatocyte size fractionation allows dissection of human liver zonation

Human hepatocytes show marked differences in cell size, gene expression, and function throughout the liver lobules, an arrangement termed liver zonation. However, it is not clear if these zonal size differences, and the associated phenotypic differences, are retained in isolated human hepatocytes, the "gold standard" for in vitro studies of human liver function. Here, we therefore explored size differences among isolated human hepatocytes and investigated whether separation by size can be used to study liver zonation in vitro. We used counterflow centrifugal elutriation to separate cells into different size fractions and analyzed them with label-free quantitative proteomics, which revealed an enrichment of 151 and 758 proteins (out of 5163) in small and large hepatocytes, respectively. Further analysis showed that protein abundances in different hepatocyte size fractions recapitulated the in vivo expression patterns of previously described zonal markers and biological processes. We also found that the expression of zone-specific cytochrome P450 enzymes correlated with their metabolic activity in the different fractions. In summary, our results show that differences in hepatocyte size matches zonal expression patterns, and that our size fractionation approach can be used to study zone-specific liver functions in vitro.

Isocotoin suppresses hepatitis E virus replication through inhibition of heat shock protein 90

Hepatitis E virus (HEV) causes 14 million infections and 60,000 deaths per year globally, with immunocompromised persons and pregnant women experiencing severe symptoms. Although ribavirin can be used to treat chronic hepatitis E, toxicity in pregnant patients and the emergence of resistant strains are major concerns. Therefore there is an imminent need for effective HEV antiviral agents. The aims of this study were to develop a drug screening platform and to discover novel approaches to targeting steps within the viral life cycle. We developed a screening platform for molecules inhibiting HEV replication and selected a candidate, isocotoin. Isocotoin inhibits HEV replication through interference with heat shock protein 90 (HSP90), a host factor not previously known to be involved in HEV replication. Additional work is required to understand the compound's translational potential, however this suggests that HSP90-modulating molecules, which are in clinical development as anti-cancer agents, may be promising therapies against HEV.

A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles

Detecting ligand-protein interactions in living cells is a fundamental challenge in molecular biology and drug research. Proteome-wide profiling of thermal stability as a function of ligand concentration promises to tackle this challenge. However, current data analysis strategies use preset thresholds that can lead to suboptimal sensitivity/specificity tradeoffs and limited comparability across datasets. Here, we present a method based on statistical hypothesis testing on curves, which provides control of the false discovery rate. We apply it to several datasets probing epigenetic drugs and a metabolite. This leads us to detect off-target drug engagement, including the finding that the HDAC8 inhibitor PCI-34051 and its analog BRD-3811 bind to and inhibit leucine aminopeptidase 3. An implementation is available as an R package from Bioconductor (https://bioconductor.org/packages/TPP2D). We hope that our method will facilitate prioritizing targets from thermal profiling experiments.

2D-thermal proteome profiling (2D-TPP) is a powerful assay for probing interactions of proteins with small molecules in their native context. Here the authors provide a statistical method for false discovery rate controlled analysis for 2D-TPP applications.

Author Correction: A new antibiotic selectively kills Gram-negative pathogens

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The functional landscape of the human phosphoproteome

Protein phosphorylation is a key post-translational modification regulating protein function in almost all cellular processes. Although tens of thousands of phosphorylation sites have been identified in human cells, approaches to determine the functional importance of each phosphosite are lacking. Here, we manually curated 112 datasets of phospho-enriched proteins, generated from 104 different human cell types or tissues. We re-analyzed the 6,801 proteomics experiments that passed our quality control criteria, creating a reference phosphoproteome containing 119,809 human phosphosites. To prioritize functional sites, we used machine learning to identify 59 features indicative of proteomic, structural, regulatory or evolutionary relevance and integrate them into a single functional score. Our approach identifies regulatory phosphosites across different molecular mechanisms, processes and diseases, and reveals genetic susceptibilities at a genomic scale. Several regulatory phosphosites were experimentally validated, including identifying a role in neuronal differentiation for phosphosites in SMARCC2, a member of the SWI/SNF chromatin-remodeling complex.

Thermal proteome profiling for interrogating protein interactions

Thermal proteome profiling (TPP) is based on the principle that, when subjected to heat, proteins denature and become insoluble. Proteins can change their thermal stability upon interactions with small molecules (such as drugs or metabolites), nucleic acids or other proteins, or upon post-translational modifications. TPP uses multiplexed quantitative mass spectrometry-based proteomics to monitor the melting profile of thousands of expressed proteins. Importantly, this approach can be performed in vitro, in situ, or in vivo. It has been successfully applied to identify targets and off-targets of drugs, or to study protein-metabolite and protein-protein interactions. Therefore, TPP provides a unique insight into protein state and interactions in their native context and at a proteome-wide level, allowing to study basic biological processes and their underlying mechanisms.

Outer membrane lipoprotein NlpI scaffolds peptidoglycan hydrolases within multi-enzyme complexes in Escherichia coli

The peptidoglycan (PG) sacculus provides bacteria with the mechanical strength to maintain cell shape and resist osmotic stress. Enlargement of the mesh‐like sacculus requires the combined activity of peptidoglycan synthases and hydrolases. In Escherichia coli, the activity of two PG synthases is driven by lipoproteins anchored in the outer membrane (OM). However, the regulation of PG hydrolases is less well understood, with only regulators for PG amidases having been described. Here, we identify the OM lipoprotein NlpI as a general adaptor protein for PG hydrolases. NlpI binds to different classes of hydrolases and can specifically form complexes with various PG endopeptidases. In addition, NlpI seems to contribute both to PG elongation and division biosynthetic complexes based on its localization and genetic interactions. Consistent with such a role, we reconstitute PG multi‐enzyme complexes containing NlpI, the PG synthesis regulator LpoA, its cognate bifunctional synthase, PBP1A, and different endopeptidases. Our results indicate that peptidoglycan regulators and adaptors are part of PG biosynthetic multi‐enzyme complexes, regulating and potentially coordinating the spatiotemporal action of PG synthases and hydrolases.

A new antibiotic selectively kills Gram-negative pathogens

The current need for novel antibiotics is especially acute for drug-resistant Gram-negative pathogens^1,2. These microorganisms have a highly restrictive permeability barrier, which limits penetration of most compounds^3,4. As a result, the last class of antibiotics acting against Gram-negative bacteria was developed in the 60s². We reason that useful compounds can be found in bacteria that share similar requirements for antibiotics with humans, and focus on Photorhabdus symbionts of entomopathogenic nematode microbiomes. Here we report a new antibiotic that we name darobactin, from a screen of Photorhabdus isolates. Darobactin is coded by a silent operon with little production under laboratory conditions, and is ribosomally synthesized. Darobactin has an unusual structure with two fused rings that form post-translationally. The compound is active against important Gram-negative pathogens both in vitro and in animal models of infection. Mutants resistant to darobactin map to BamA, an essential chaperone and translocator that folds outer membrane proteins. Our study suggests that bacterial symbionts of animals harbor antibiotics that are particularly suitable for development into therapeutics.

Improved predictions of time-dependent drug-drug interactions by determination of cytosolic drug concentrations

The clinical impact of drug-drug interactions based on time-dependent inhibition of cytochrome P450 (CYP) 3A4 has often been overpredicted, likely due to use of improper inhibitor concentration estimates at the enzyme. Here, we investigated if use of cytosolic unbound inhibitor concentrations could improve predictions of time-dependent drug-drug interactions. First, we assessed the inhibitory effects of ten time-dependent CYP3A inhibitors on midazolam 1′-hydroxylation in human liver microsomes. Then, using a novel method, we determined the cytosolic bioavailability of the inhibitors in human hepatocytes, and used the obtained values to calculate their concentrations at the active site of the enzyme, i.e. the cytosolic unbound concentrations. Finally, we combined the data in mechanistic static predictions, by considering different combinations of inhibitor concentrations in intestine and liver, including hepatic concentrations corrected for cytosolic bioavailability. The results were then compared to clinical data. Compared to no correction, correction for cytosolic bioavailability resulted in higher accuracy and precision, generally in line with those obtained by more demanding modelling. The best predictions were obtained when the inhibition of hepatic CYP3A was based on unbound maximal inhibitor concentrations corrected for cytosolic bioavailability. Our findings suggest that cytosolic unbound inhibitor concentrations improves predictions of time-dependent drug-drug interactions for CYP3A.

Project INSIDE: towards autonomous semi-unstructured human-robot social interaction in autism therapy

This paper describes the INSIDE system, a networked robot system designed to allow the use of mobile robots as active players in the therapy of children with autism spectrum disorders (ASD). While a significant volume of work has explored the impact of robots in ASD therapy, most such work comprises remotely operated robots and/or well-structured interaction dynamics. In contrast, the INSIDE system allows for complex, semi-unstructured interaction in ASD therapy while featuring a fully autonomous robot. In this paper we describe the hardware and software infrastructure that supports such rich form of interaction, as well as the design methodology that guided the development of the INSIDE system. We also present some results on the use of our system both in pilot and in a long-term study comprising multiple therapy sessions with children at Hospital Garcia de Orta, in Portugal, highlighting the robustness and autonomy of the system as a whole.

Thermal proteome profiling in bacteria: probing protein state in vivo

Increasing antibiotic resistance urges for new technologies for studying microbes and antimicrobial mechanism of action. We adapted thermal proteome profiling (TPP) to probe the thermostability of Escherichia coli proteins in vivoE. coli had a more thermostable proteome than human cells, with protein thermostability depending on subcellular location-forming a high-to-low gradient from the cell surface to the cytoplasm. While subunits of protein complexes residing in one compartment melted similarly, protein complexes spanning compartments often had their subunits melting in a location-wise manner. Monitoring the E. coli meltome and proteome at different growth phases captured changes in metabolism. Cells lacking TolC, a component of multiple efflux pumps, exhibited major physiological changes, including differential thermostability and levels of its interaction partners, signaling cascades, and periplasmic quality control. Finally, we combined in vitro and in vivo TPP to identify targets of known antimicrobial drugs and to map their downstream effects. In conclusion, we demonstrate that TPP can be used in bacteria to probe protein complex architecture, metabolic pathways, and intracellular drug target engagement.

Species-specific activity of antibacterial drug combinations

The spread of antimicrobial resistance has become a serious public health concern, making once-treatable diseases deadly again and undermining the achievements of modern medicine^1,2. Drug combinations can help to fight multi-drug-resistant bacterial infections, yet they are largely unexplored and rarely used in clinics. Here we profile almost 3,000 dose-resolved combinations of antibiotics, human-targeted drugs and food additives in six strains from three Gram-negative pathogens-Escherichia coli, Salmonella enterica serovar Typhimurium and Pseudomonas aeruginosa-to identify general principles for antibacterial drug combinations and understand their potential. Despite the phylogenetic relatedness of the three species, more than 70% of the drug-drug interactions that we detected are species-specific and 20% display strain specificity, revealing a large potential for narrow-spectrum therapies. Overall, antagonisms are more common than synergies and occur almost exclusively between drugs that target different cellular processes, whereas synergies are more conserved and are enriched in drugs that target the same process. We provide mechanistic insights into this dichotomy and further dissect the interactions of the food additive vanillin. Finally, we demonstrate that several synergies are effective against multi-drug-resistant clinical isolates in vitro and during infections of the larvae of the greater wax moth Galleria mellonella, with one reverting resistance to the last-resort antibiotic colistin.

Successful Treatment of Strongyloides stercoralis Hyperinfection in a Kidney Transplant Recipient: Case Report

Strongyloides stercoralis (SS) can cause hyperinfection and disseminated infection in immunosuppressed individuals, with risk of mortality. We report the case of a cadaveric kidney transplant recipient who developed gastrointestinal symptoms and eosinophilia, approximately 3 months after transplantation. Stool examination and esophagogastroduodenoscopy with biopsies were positive for SS larvae. The patient was started on oral ivermectin and immunosuppression was reduced, but still the clinical picture got worse with metabolic ileus and respiratory symptoms, with the need for administration of subcutaneous ivermectin and combined therapy with albendazol. The patient survived and graft function was preserved. The patient was unlikely to be the source of infection. We also present a review of cases of SS infection in kidney transplant recipients.

Thermal proteome profiling: unbiased assessment of protein state through heat-induced stability changes

In recent years, phenotypic-based screens have become increasingly popular in drug discovery. A major challenge of this approach is that it does not provide information about the mechanism of action of the hits. This has led to the development of multiple strategies for target deconvolution. Thermal proteome profiling (TPP) allows for an unbiased search of drug targets and can be applied in living cells without requiring compound labeling. TPP is based on the principle that proteins become more resistant to heat-induced unfolding when complexed with a ligand, e.g., the hit compound from a phenotypic screen. The melting proteome is also sensitive to other intracellular events, such as levels of metabolites, post-translational modifications and protein-protein interactions. In this review, we describe the principles of this approach, review the method and its developments, and discuss its current and future applications. While proteomics has generally focused on measuring relative protein concentrations, TPP provides a novel approach to gather complementary information on protein stability not present in expression datasets. Therefore, this strategy has great potential not only for drug discovery, but also for answering fundamental biological questions.

Intracellular drug bioavailability: a new predictor of system dependent drug disposition

Intracellular drug exposure is influenced by cell- and tissue-dependent expression of drug-transporting proteins and metabolizing enzymes. Here, we introduce the concept of intracellular bioavailability (F_ic) as the fraction of extracellular drug available to bind intracellular targets, and we assess how F_ic is affected by cellular drug disposition processes. We first investigated the impact of two essential drug transporters separately, one influx transporter (OATP1B1; SLCO1B1) and one efflux transporter (P-gp; ABCB1), in cells overexpressing these proteins. We showed that OATP1B1 increased F_ic of its substrates, while P-gp decreased F_ic. We then investigated the impact of the concerted action of multiple transporters and metabolizing enzymes in freshly-isolated human hepatocytes in culture configurations with different levels of expression and activity of these proteins. We observed that F_ic was up to 35-fold lower in the configuration with high expression of drug-eliminating transporters and enzymes. We conclude that F_ic provides a measurement of the net impact of all cellular drug disposition processes on intracellular bioavailable drug levels. Importantly, no prior knowledge of the involved drug distribution pathways is required, allowing for high-throughput determination of drug access to intracellular targets in highly defined cell systems (e.g., single-transporter transfectants) or in complex ones (including primary human cells).

Identification of Triazolothiadiazoles as Potent Inhibitors of the dCTP Pyrophosphatase 1

The dCTP pyrophosphatase 1 (dCTPase) is involved in the regulation of the cellular dNTP pool and has been linked to cancer progression. Here we report on the discovery of a series of 3,6-disubstituted triazolothiadiazoles as potent dCTPase inhibitors. Compounds 16 and 18 display good correlation between enzymatic inhibition and target engagement, together with efficacy in a cellular synergy model, deeming them as a promising starting point for hit-to-lead development.

Characterisation of antimicrobial usage in cats and dogs attending UK primary care companion animal veterinary practices

There is scant evidence describing antimicrobial (AM) usage in companion animal primary care veterinary practices in the UK. The use of AMs in dogs and cats was quantified using data extracted from 374 veterinary practices participating in VetCompass. The frequency and quantity of systemic antibiotic usage was described.Overall, 25 per cent of 963,463 dogs and 21 per cent of 594,812 cats seen at veterinary practices received at least one AM over a two-year period (2012-2014) and 42 per cent of these animals were given repeated AMs. The main agents used were aminopenicillin types and cephalosporins. Of the AM events, 60 per cent in dogs and 81 per cent in cats were AMs classified as critically important (CIAs) to human health by the World Health Organisation. CIAs of highest importance (fluoroquinolones, macrolides, third-generation cephalosporins) accounted for just over 6 per cent and 34 per cent of AMs in dogs and cats, respectively. The total quantity of AMs used within the study population was estimated to be 1473 kg for dogs and 58 kg for cats.This study has identified a high frequency of AM usage in companion animal practice and for certain agents classified as of critical importance in human medicine. The study highlights the usefulness of veterinary practice electronic health records for studying AM usage.

CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil

Target engagement is a critical factor for therapeutic efficacy. Assessment of compound binding to native target proteins in live cells is therefore highly desirable in all stages of drug discovery. We report here the first compound library screen based on biophysical measurements of intracellular target binding, exemplified by human thymidylate synthase (TS). The screen selected accurately for all the tested known drugs acting on TS. We also identified TS inhibitors with novel chemistry and marketed drugs that were not previously known to target TS, including the DNA methyltransferase inhibitor decitabine. By following the cellular uptake and enzymatic conversion of known drugs we correlated the appearance of active metabolites over time with intracellular target engagement. These data distinguished a much slower activation of 5-fluorouracil when compared with nucleoside-based drugs. The approach establishes efficient means to associate drug uptake and activation with target binding during drug discovery.

Direct Measurement of Intracellular Compound Concentration by RapidFire Mass Spectrometry Offers Insights into Cell Permeability

One of the key challenges facing early stage drug discovery is understanding the commonly observed difference between the activity of compounds in biochemical assays and cellular assays. Traditionally, indirect or estimated cell permeability measurements such as estimations from logP or artificial membrane permeability are used to explain the differences. The missing link is a direct measurement of intracellular compound concentration in whole cells. This can, in some circumstances, be estimated from the cellular activity, but this may also be problematic if cellular activity is weak or absent. Advances in sensitivity and throughput of analytical techniques have enabled us to develop a high-throughput assay for the measurement of intracellular compound concentration for routine use to support lead optimization. The assay uses a RapidFire-MS based readout of compound concentration in HeLa cells following incubation of cells with test compound. The initial assay validation was performed by ultra-high performance liquid chromatography tandem mass spectrometry, and the assay was subsequently transferred to RapidFire tandem mass spectrometry. Further miniaturization and optimization were performed to streamline the process, increase sample throughput, and reduce cycle time. This optimization has delivered a semi-automated platform with the potential of production scale compound profiling up to 100 compounds per day.

Assessment of pharmacokinetic changes of meropenem during therapy in septic critically ill patients

Background

Meropenem is a carbapenem antibiotic commonly used in critically ill patients to treat severe infections. The available pharmacokinetic (PK) data has been mostly obtained from healthy volunteers as well as from clinical studies addressing selected populations, often excluding the elderly and also patients with renal failure. Our aim was to study PK of meropenem in a broader population of septic critically ill patients.

Methods

We characterized the PK of meropenem in 15 critically ill patients during the first 36 hrs of therapy. Aditionally, whenever possible, we collected a second set of late plasma samples after 5 days of therapy to evaluate PK intra-patient variability and its correlation with clinical course.

Patients received meropenem (1 g every 8 hrs IV). Drug plasma profiles were determined by high-performance liquid chromatography. The PK of meropenem was characterized and compared with clinical parameters.

Results

Fifteen septic critically ill patients (8 male, median age 73 yrs) were included. The geometric mean of the volume of distribution at the steady state (V_ss)/weight was 0.20 (0.15-0.27) L/kg. No correlation of V_ss/weight with severity or comorbidity scores was found. However the Sequential Organ Failure Assessment score correlated with the V_ss/weight of the peripheral compartment (r² = 0.55, p = 0.021). The median meropenem clearance (Cl) was 73.3 (45–120) mL/min correlated with the creatinine (Cr) Cl (r² = 0.35, p = 0.033).

After 5 days (N = 7) although V_ss remained stable, a decrease in the proportion of the peripheral compartment (V_ss2) was found, from 61.3 (42.5-88.5)% to 51.7 (36.6-73.1)%. No drug accumulation was noted.

Conclusions

In this cohort of septic, unselected, critically ill patients, large meropenem PK heterogeneity was noted, although neither underdosing nor accumulation was found. However, Cr Cl correlated to meropenem Cl and the V_ss2 decreased with patient’s improvement.

A high-throughput cell-based method to predict the unbound drug fraction in the brain

Optimization of drug efficacy in the brain requires understanding of the local exposure to unbound drug at the site of action. This relies on measurements of the unbound drug fraction (f_u,brain), which currently requires access to brain tissue. Here, we present a novel methodology using homogenates of cultured cells for rapid estimation of f_u,brain. In our setup, drug binding to human embryonic kidney cell (HEK293) homogenate was measured in a small-scale dialysis apparatus. To increase throughput, we combined drugs into cassettes for simultaneous measurement of multiple compounds. Our method estimated f_u,brain with an average error of 1.9-fold. We propose that our simple method can be used as an inexpensive, easily available and high-throughput alternative to brain tissues excised from laboratory animals. Thereby, estimates of unbound drug exposure can now be implemented at a much earlier stage of the drug discovery process, when molecular property changes are easier to make.

Induction therapy with basiliximab and full HLA mismatch

INTRODUCTION

Induction therapy reduces rejection episodes among patients at high immunologic risk. Antithymocyte globulins appear to be superior to basiliximab in this population, despite the greater potential risk of infection and neoplasia. The aim of this study was to evaluate graft function and acute rejection episodes in 6 HLA-mismatched patients who underwent induction with basiliximab but had no other immunologic risk factors.

METHODS

We analyzed retrospectively patients who were transplanted using basiliximab for induction therapy during a 4 year period, comparing patients with full HLA mismatches with those who had 5 or fewer mismatches. None of the patients had other immunological risk factors for rejection.

RESULTS

We observed no significant differences between the groups concerning demographic features, cold ischemia times, and panel reactive antibodies. Graft function at 12 and 24 months was not different between both groups. Acute rejection episodes were also not different between groups.

DISCUSSION

In this population of full HLA mismatches and no other immunological risk factors, induction immunosuppression therapy with basiliximab was safe in terms of graft function and acute rejection episodes.

Infected donors in renal transplantation: expanding the donor pool

INTRODUCTION

The shortage of suitable organ donors is now the most important limiting factor in the field of transplantation and more expanded criteria have been accepted to overcome this problem.

OBJECTIVE

The objectives of this study were to evaluate the outcome of patients who received an organ from an infected donor and to compare them with patients who received organs from noninfected donors.

METHODS

Retrospective analysis of all patients who underwent transplantation in our unit between January 2008 and June 2011 was performed. The definition of infected donor included: (1) documented bacteremia at the time of transplantation; and (2) organ-related infection, either with or without isolation from biological products (urine, liquor, and bronchial secretions).

RESULTS

Nineteen of 77 transplant recipients (24.7%) received organs from infected donors. There were 9 cases of pneumonia, 4 cases of meningitis with bacteremia, 5 cases of urinary tract infection, 1 case of bacteremia due to Staphylococcus aureus, and 1 case of ventriculo-peritoneal shunt infection. All these recipients were prescribed antibiotic prophylaxis for 10.9 ± 3.2 days, according to the antibiotic administered to the donor. Significant differences between both groups were not observed concerning demographics features, graft thrombosis, arterial disruption, delayed graft function, rejection episodes, and renal graft and patient survivals at 12 months. The recipients of infected donor kidneys were mostly treated with basiliximab for induction therapy. There was a trend toward fewer infectious complications among patients who received organs from infected donors (21.1% vs 44.8%; P = .065) and shorter hospital stay durations (median, 11 vs 17.5 days; P = .041).

DISCUSSION

Kidney transplantation using organs from infected donors did not seem to be associated with a greater risk of complications. Antibiotic therapy initiated in the donor and continued in the recipient may explain these results, perhaps by reducing infectious complications that necessarily prolong the hospital stay.

Current British veterinary attitudes to the use of perioperative antimicrobials in small animal surgery

A questionnaire was sent to 2951 mixed and small animal veterinary practices to examine the use of perioperative antimicrobials in cats and dogs in the UK. The percentage of respondents who always used antimicrobials in two surgical procedures classified according to NRC criteria as 'clean' was 25.3 per cent for removal of a 1&emsp14;cm cutaneous mass and 32.1 per cent for routine prescrotal castration. Factors considered important in decision-making about when to use antimicrobial agents included immunosuppression, presence of a drain, degree of wound contamination, potential for spillage of visceral contents and implantation of prosthesis. The most common antimicrobial agents mentioned were potentiated amoxicillin (98.0 per cent), amoxicillin (60.5 per cent), clindamycin (21.8 per cent), enrofloxacin (21.7 per cent), cephalexin (18.6 per cent) and metronidazole (12.7 per cent). Forty-three per cent of all responding veterinarians listed a long-acting preparation for perioperative use. The routes used were subcutaneous (76.1 per cent), intravenous (25.8 per cent), intramuscular (19.8 per cent), oral (13.5 per cent) and topical (7.7 per cent). Antimicrobials were given before surgery (66.6 per cent), during surgery (30.2 per cent), immediately after surgery (12.0 per cent) and after surgery (6.3 per cent). This survey has identified the suboptimal use of perioperative antimicrobials in small animal surgery with improvements needed with respect to timing, duration, choice of antimicrobial and a more prudent selection of surgical cases requiring prophylaxis.

Antimicrobial usage in dogs and cats in first opinion veterinary practices in the UK

OBJECTIVES

To provide baseline data on patterns of antimicrobial usage in dogs and cats through the analysis of data stored in electronic practice management systems.

METHODS

Clinical data from 11 first opinion veterinary practices were extracted for the year 2007. Descriptive statistical analysis was performed to assess the usage of antimicrobials.

RESULTS

Widespread usage of systemic broad-spectrum antimicrobials was observed. Antimicrobials most frequently used in both species were potentiated amoxicillin (44·4% and 46.1% in cats and dogs, respectively) and amoxicillin (14·3% and 20·7%). Cephalexin (13·4%) and cefovecin (15·0%) were also commonly used in dogs and cats, respectively. Systemic critically important antimicrobials in human medicine were widely used in dogs (60·5%) and cats (82·7%). Topical antimicrobials used in both species included fusidic acid (48·4% and 54·8%), framycetin (20·4% and 13·4%), polymyxin B (12·6% and 9·3%) and neomycin (6·5% and 6·6%).

CLINICAL SIGNIFICANCE

Inappropriate usage of broad-spectrum antimicrobials may contribute to the development of antimicrobial resistance and loss of efficacy of antimicrobials in veterinary settings. Data recorded in practice management systems were demonstrated to be a practical source for monitoring antimicrobial usage in pets.