Biology subjects

Baron, C.

Publications and source records attributed to Baron, C..

14 recordsLinked to original sources

bioRxiv2026

Serotypic heterogeneity in the response to pneumococcal vaccine

The assessment of pneumococcal vaccine response currently relies on a single IgG concentration threshold, identical for all serotypes, as recommended by the WHO and AAAAI. However, the recommended thresholds do not take the wide inter-serotype variability into account. The purpose of this study was to determine if the antibody threshold linked to a functional immune response varies according to serotype. We performed a retrospective analysis on 729 samples from adults at risk of invasive pneumococcal disease (IPD), sent between 2018 and 2024 to assess vaccine response. Specific IgG concentrations for seven vaccine serotypes were measured by ELISA and compared to opsonophagocytic assay (OPA) results, a functional test considered as the gold standard. For each serotype, we determined the most predictive IgG concentration (PIC) for a positive OPA result using ROC curves, Youdens index, and bootstrap analysis with 1,000 resamples. The resulting PIC were then compared using non-parametric tests (Kruskal-Wallis test followed by Dunns post-hoc test with Holms correction). The PIC varied considerably among serotypes, ranging from 0.84 to 4.74 {micro}g/mL. This variability was found to be statistically significant (p<0.0001). Areas Under the Curve (AUC), ranging from 0.73 to 0.87, demonstrate good diagnostic performance. Overall, the application of serotype-specific thresholds in patients significantly change the classification of vaccination status compared to a single threshold (Cochran, McNemar). These results indicate that the protective antibody threshold is not universal. A serotype-specific approach would allow a more precise and relevant assessment of the pneumococcal vaccine response. Author summaryThe introduction of the 7-valent pneumococcal conjugate vaccine (PCV-7) in the early 2000s significantly changed the epidemiology of invasive pneumococcal disease by modifying serotype distribution. However, vaccine-induced immunity varies across serotypes, and this heterogeneity remains incompletely understood. In this study, we first assessed differences in vaccine responses according to serotype. We then determined predictive serotype-specific immunoglobulin concentration for the seven routinely serotypes tested in our laboratory, defined as the minimal levels required to induce a positive opsonophagocytic activity (OPA) response. The results enable a more accurate assessment of serotype-specific vaccine immunity, supporting improved patient stratification and guiding booster vaccination in individuals with insufficient responses.

immunology↗

bioRxiv2026

Ex vivo drug testing in metastatic biopsies reveals patient-specific vulnerabilities to cancer targeting and immune activating drugs

Biomarker-guided therapies in oncology often fail to induce considerable responses in patients with advanced cancer. As a complementary approach, direct drug testing on individual patient samples is highly attractive yet is currently hampered by the lack of assays that combine (i) fast reporting, (ii) the ability to inform about immune-mediated responses, (iii) robust quantification, and (iv) scalability for parallel assessment of multiple drugs. Here, we introduce our patient-derived ex vivo drug response assay (PEDRA) that fulfills all these requirements. Using malignant pleural effusions (MPEs) from five non-small cell lung cancer (NSCLC) patients with detailed clinical treatment histories, we tested 52 guideline-recommended therapies and eight investigational antibody-drug conjugates (ADCs). In all patients, PEDRA identified treatment options that outperformed the therapies the patients had received. The results reflected clinical observations as well as expectations derived from mutational profiling and disease courses. To extend the applicability of PEDRA beyond MPEs to other metastatic lesions, we generated a protocol starting from core needle biopsies. Owing to its reproducible and quantitative nature, PEDRA may provide a valuable diagnostic tool to guide time-sensitive clinical therapy decisions. Additionally, PEDRA has great potential for preclinical testing of investigational drugs, thereby reducing the need for animal experiments.

cancer biology↗

bioRxiv2024

Insights into Heart Failure Metabolite Markersthrough Explainable Machine Learning

Understanding molecular traits through metabolomics offers an avenue to tailor cardiovascular prevention, diagnosis and treatment strategies more effectively. This study focuses on the application of machine learning (ML) and explainable artificial intelligence (XAI) algorithms to detect discriminant molecular signatures in heart failure (HF). In this study, we aim to uncover metabolites with significant predictive value by analyzing targeted metabolomics data through ML models and XAI methodologies. After robust quality control procedures, we analyzed 55 metabolites from 124 plasma samples, including 53 HF patients and 71 controls, comparing Logistic Regression (Logit) models with Support Vector Machine (SVM) and eXtreme Gradient Boosting (XGB), all achieving high accuracy in predicting group labels: 84.20% ({sigma} =5.46), 85.73% ({sigma} =6.25), and 84.80% ({sigma} =7.84), respectively. Permutation-based variable importance and Local Interpretable Model-agnostic Explanations (LIME) were used for group-level and individual-level explainability, respectively, complemented by H-Friedman statistics for variable interactions, yielding reliable, explainable insights of the ML models. Metabolites well-known for their association with heart failure, such as glucose and cholesterol, but also more recently described association such C18:1 carnitine, were reaffirmed in our analysis. The novel discovery of lignoceric acid (C24:0 fatty acid) as a critical discriminator, was confirmed in a replication cohort, underscoring its potential as a metabolite marker. Furthermore, our study highlights the utility of 2-way variable interaction analysis in unveiling a network of metabolite interactions essential for accurate disease prediction. The results demonstrate our approachs efficacy in identifying key metabolites and their interactions, illustrating the power of ML and XAI in advancing personalized healthcare solutions. See Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/616718v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@d50da1org.highwire.dtl.DTLVardef@171d4d7org.highwire.dtl.DTLVardef@4c8aaaorg.highwire.dtl.DTLVardef@123c1ed_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Inner membrane components of the plasmid pKM101 type IV secretion system TraE and TraD are DNA-binding proteins

The increase of antimicrobial resistance constitutes a significant threat to human health. One of the mechanisms responsible for the spread of resistance to antimicrobials is the transfer of plasmids between bacteria by conjugation. This process is mediated by type IV secretion systems (T4SS) and previous studies have provided in vivo evidence for interactions between DNA and components of the T4SS. Here, we purified TraD and TraE, two inner membrane proteins from the Escherichia coli pKM101 T4SS. Using electrophoretic mobility shift assays and fluorescence polarization we showed that the purified proteins both bind single-stranded and double-stranded DNA in the nanomolar affinity range. The previously identified conjugation inhibitor BAR-072 inhibits TraE DNA binding in vitro, providing evidence for its mechanism of action. Site-directed mutagenesis identified conserved amino acids that are required for conjugation that may be targets for the development of more potent conjugation inhibitors.

biochemistry↗

bioRxiv2023

Structure-based design of small molecule inhibitors of the cagT4SS ATPase Cagα of Helicobacter pylori

We here describe the structure-based design of small molecule inhibitors of the type IV secretion system of Helicobacter pylori. The secretion system is encoded by the{square}cag{square}pathogenicity island, and we chose Cag, a hexameric ATPase and member of the family of VirB11-like proteins, as target for inhibitor design. We first solved the crystal structure of Cag in a complex with the previously identified small molecule inhibitor 1G2. The molecule binds at the interface between two Cag subunits and mutagenesis of the binding site identified Cag residues F39 and R73 as critical for 1G2 binding. Based on the inhibitor binding site we synthesized 98 small molecule derivates of 1G2 to improve binding of the inhibitor. We used the production of interleukin-8 of gastric cancer cells during H. pylori infection to screen the potency of inhibitors and we identified five molecules (1G2_1313, 1G2_1338, 1G2_2886, 1G2_2889 and 1G2_2902) that have similar or higher potency than 1G2. Differential scanning fluorimetry suggested that these five molecules bind Cag, and enzyme assays demonstrated that some are more potent ATPase inhibitors than 1G2. Finally, scanning electron microscopy revealed that 1G2 and its derivatives inhibit the assembly of T4SS-determined extracellular pili suggesting a mechanism for their anti-virulence effect.

biochemistry↗

bioRxiv2023

Inhibition of the type IV secretion system from antibiotic-resistant Helicobacter pylori clinical isolates supports the potential of Cagα as an anti-virulence target

Helicobacter pylori resistance to antibiotics is a growing problem and it increasingly leads to treatment failure. While the bacterium is present worldwide, the severity of the clinical outcomes is highly dependent on the geographical origin and genetic characteristics of the strains. One of the major virulence factors identified in H. pylori is the cag pathogenicity island (cagPAI), which encodes a type IV secretion used to translocate effectors into human cells. Here, we investigated the genetic variability of the cagPAI among 13 antibiotic-resistant H. pylori strains that were isolated from patient biopsies in Quebec. Seven of the clinical strains carried the cagPAI, but only four could be readily cultivated under laboratory conditions. We observed variability of the sequences of CagA and CagL proteins that are encoded by the cagPAI. All clinical isolates induce interleukin-8 secretion and morphological changes upon co-incubation with epithelial gastric cancer cells and two of them produce extracellular T4SS pili. Finally, we demonstrate that molecule 1G2, a small molecule inhibitor of the Cag protein from the model strain H. pylori 26695, reduces interleukin-8 secretion in one of the clinical isolates. Co-incubation with 1G2 also inhibits the assembly of T4SS pili, suggesting a mechanism for its action on T4SS function.

microbiology↗

bioRxiv2023

Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results

Studies combining metabolomics and genetics, known as metabolite genome-wide association studies (mGWAS), have provided valuable insights into our understanding of the genetic control of metabolite levels. However, the biological interpretation of these associations remains challenging due to a lack of existing tools to annotate mGWAS gene-metabolite pairs beyond the use of conservative statistical significance threshold. Here, we computed the shortest reactional distance (SRD) based on the curated knowledge of the KEGG database to explore its utility in enhancing the biological interpretation of results from three independent mGWAS, including a case study on sickle cell disease patients. Results show that, in reported mGWAS pairs, there is an excess of small SRD values and that SRD values and p-values significantly correlate, even beyond the standard conservative thresholds. The added-value of SRD annotation is shown for identification of potential false negative hits, exemplified by the finding of gene-metabolite associations with SRD [≤]1 that did not reach standard genome-wide significance cut-off. The wider use of this statistic as an mGWAS annotation would prevent the exclusion of biologically relevant associations and can also identify errors or gaps in current metabolic pathway databases. Our findings highlight the SRD metric as an objective, quantitative and easy-to-compute annotation for gene-metabolite pairs that can be used to integrate statistical evidence to biological networks.

systems biology↗

bioRxiv2022

TraC of the conjugative plasmid pKM101 is secreted as a monomer in outer membrane vesicles and stimulates conjugation

Gram-negative bacteria use membrane-bound type IV secretion systems to assemble pili on the cell surface, followed by cell-cell contact with recipient cells and transfer of plasmid DNA. The process at the cell-cell contact stage of conjugative DNA transfer is not well understood. We here present a biochemical and genetic characterization of the TraC protein that is a minor component of the pili determined by the IncN plasmid pKM101 from Escherichia coli. The cellular and secreted forms of TraC are monomers, TraC preferentially localizes at the cell poles and it is also detected in extracellular membrane vesicles. Purified TraC does not impact the infection with bacteriophages, but we detect binding of TraC to recipient cells and partial complementation of a traC deletion strain by the addition of purified TraC. These results suggest that the protein contributes to conjugation at the cell-cell contact stage.

microbiology↗

bioRxiv2022

Cryo-EM structure of the Agrobacterium tumefaciens T-pilus reveals the importance of positive charges in the lumen

Agrobacterium tumefaciens is a natural genetic engineer that transfers DNA into plants and this is the most frequently applied process for the generation of genetically modified plants. DNA transfer is mediated by a type IV secretion system localized in the cell envelope and extracellular T-pili. We here report the cryo-electron microscopic structures of the T-pilus at 3.2[A] resolution and that of the related plasmid pKM101-determined N-pilus at 3[A] resolution. Both pili contain a main pilus protein (VirB2 in A. tumefaciens and TraM in pKM101) and phospholipids arranged in a 5-start helical assembly. They contain positively charged amino acids in the pilus lumen and the lipids are positively charged in the T-pilus (phosphatidylcholine) conferring overall positive charge to the lumen. Mutagenesis of the lumen-exposed Arg91 residue in VirB2 resulted in protein destabilization and loss of pilus formation. Our results reveal that different phospholipids can be incorporated into type IV secretion system pili and that the charge of the lumen is of functional importance.

biochemistry↗

bioRxiv2022

VE607 Stabilizes SARS-CoV-2 Spike In the "RBD-up" Conformation and Inhibits Viral Entry

SARS-CoV-2 infection of host cells starts by binding of the Spike glycoprotein (S) to the ACE2 receptor. The S-ACE2 interaction is a potential target for therapies against COVID-19 as demonstrated by the development of immunotherapies blocking this interaction. Here, we present the commercially available VE607, comprised of three stereoisomers, that was originally described as an inhibitor of SARS-CoV-1. We show that VE607 specifically inhibits infection of SARS-CoV-1 and SARS-CoV-2 S-expressing pseudoviral particles as well as authentic SARS-CoV-2. VE607 stabilizes the receptor binding domain (RBD) in its "up" conformation. In silico docking and mutational analysis map the VE607 binding site at the RBD-ACE2 interface. The IC50 values are in the low micromolar range for pseudoparticles derived from SARS-CoV-2 Wuhan/D614G as well as from variants of concern (Alpha, Beta, Gamma, Delta and Omicron), suggesting that VE607 has potential for the development of drugs against SARS-CoV-2 infections.

microbiology↗

bioRxiv2021

Enabling complex fibre geometries using 3D printed axon-mimetic phantoms

PurposeTo introduce a method to create 3D-printed axon-mimetic phantoms with complex fibre orientations to characterize the performance of diffusion MRI models and representations in the presence of orientation dispersion. MethodsAn extension to an open source 3D printing package was created to 3D print a set of five 3D-printed axon-mimetic (3AM) phantoms with various combinations of bending and crossing fibre orientations. A two-shell diffusion MRI scan of the five phantoms in water was performed at 9.4T. Diffusion tensor imaging (DTI), diffusion kurtosis imaging (DKI), the ball and stick model, neurite orientation density and dispersion imaging (NODDI), and Bingham-NODDI were all fit to the resulting diffusion MRI data. A fiducial in each phantom was used to register a ground truth map of that phantoms crossing angles and/or arc radius to the diffusion-weighted images. Metrics from each model and representation were compared to the ground-truth maps, and a quadratic regression model was fit to each combination of output metric and ground-truth metric. ResultsThe mean diffusivity (MD) metric defined by DTI was insensitive to crossing angle, but increased with fibre curvature. Axial diffusivity (AD) decreased sharply with increasing crossing angle. DKIs diffusivity metrics replicated the trends seen in DTI, and its mean kurtosis (MK) metric, decreased with fibre curvature, except in regions with high crossing angles. The estimated stick volume fraction in the ball and stick model decreased with increasing fibre curvature and crossing angle. NODDIs intra-neurite volume fraction was insensitive to crossing angle, and its orientation dispersion index (ODI) was strongly correlated to crossing angle. Bingham-NODDIs intra-neurite volume fraction was also insensitive to crossing angle, while its primary ODI (ODIP) was also strongly correlated to crossing angle and its secondary ODI (ODIS) was insensitive to crossing angle. For both NODDI models, the volume fractions of the extra-neurite and CSF compartments had low reliability with no clear relationship to crossing angle. ConclusionsThis study demonstrates that inexpensive 3D-printed axon-mimetic phantoms can be used to investigate the effect of fibre curvature and crossings on diffusion MRI representations and models of diffusion signal. As a proof of concept, the dependence of several representations and models on fibre dispersion/crossing were investigated. As expected, Bingham-NODDI was best able to characterize planar fibre dispersion in the phantoms.

neuroscience↗

bioRxiv2021

Acidity and sulfur oxidation intermediate concentrations controlled by O2-driven partitioning of sulfur oxidizing bacteria in a mine tailings impoundment

Acidification of freshwater in mining impacted areas is a major global environmental problem catalyzed by sulfur-oxidizing bacteria (SOB). To date, little is known about the active bacteria in mine tailings impoundments and their environmental niches. Here, biological sulfur oxidation was investigated over four years in a mine tailings impoundment, integrating sulfur geochemistry, genome-resolved metagenomics and metatranscriptomics. We demonstrated oxygen driven niche partitioning of SOB and their metabolic pathways that explain acidity generation and thiosulfate persistence. Four chemolithoautotrophic SOB, Halothiobacillus, Thiobacillus, Sulfuricurvum and Sediminibacterium comprised 37% to 73% of the analyzed communities. The impoundment waters alternated between the dominance of Halothiobacillus versus a Thiobacillus, Halothiobacillus, Sulfuricurvum and Sediminibacterium consortia. Halothiobacillus dominance was associated with lower pH values ([~]4.3), higher [H+]/[SO42-] and lower [S2O32-], collectively indicative of extensive sulfur oxidation. Halothiobacillus, which couple sulfur oxidation via the Sox pathway to aerobic respiration or NO2- reduction, were present throughout the depth profile, yet their expression of sox genes occurred only in upper highly oxygenated waters. Conversely, when consortia of Thiobacillus, Halothiobacillus, Sulfuricurvum and Sediminibacterium dominated, recycling/disproportionating reactions were more prevalent. Thiobacillus, which dominated deeper micro-oxic/anoxic waters, oxidized sulfur primarily through the rDSR pathway, coupled to NO3-/NO2- reduction, resulting in lower [H+]/[SO42-] and higher [S2O32-] relative to upper waters. These field results mirror the Sox/rDSR-geochemical patterns of experimental SOB enrichments and reveal opportunities for biological treatments of recalcitrant reduced sulfur compounds, as well as gene-based monitoring and in situ RNA detection to predict the onset of problematic geochemistry.

microbiology↗

bioRxiv2021

Test-retest reproducibility of in vivo oscillating gradient and microscopic anisotropy diffusion MRI in mice at 9.4 Tesla

Background and PurposeMicrostructure imaging with advanced diffusion MRI (dMRI) techniques have shown increased sensitivity and specificity to microstructural changes in various disease and injury models. Oscillating gradient spin echo (OGSE) dMRI, implemented by varying the oscillating gradient frequency, and microscopic anisotropy ({micro}A) dMRI, implemented via tensor valued diffusion encoding, may provide additional insight by increasing sensitivity to smaller spatial scales and disentangling fiber orientation dispersion from true microstructural changes, respectively. The aims of this study were to characterize the test-retest reproducibility of in vivo OGSE and {micro}A dMRI metrics in the mouse brain at 9.4 Tesla and provide estimates of required sample sizes for future investigations. MethodsEight adult C57Bl/6 mice were scanned twice (5 days apart). Each imaging session consisted of multifrequency OGSE and {micro}A dMRI protocols. Metrics investigated included {micro}A, isotropic and anisotropic kurtosis, and the diffusion dispersion rate ({Lambda}), which explores the power-law frequency dependence of mean diffusivity. The dMRI metric maps were analyzed with mean region-of-interest (ROI) and whole brain voxel-wise analysis. Bland-Altman plots and coefficients of variation (CV) were used to assess the reproducibility of OGSE and {micro}A metrics. Furthermore, we estimated sample sizes required to detect a variety of effect sizes. ResultsBland-Altman plots showed negligible biases between test and retest sessions. ROI-based CVs revealed high reproducibility for both {micro}A (CVs < 8 %) and {Lambda} (CVs < 15 %). Voxel-wise CV maps revealed high reproducibility for {micro}A (CVs [~] 10 %), but low reproducibility for OGSE metrics (CVs [~] 50 %). ConclusionMost of the {micro}A dMRI metrics are reproducible in both ROI-based and voxel-wise analysis, while the OGSE dMRI metrics are only reproducible in ROI-based analysis. {micro}A and {Lambda} may provide sensitivity to subtle microstructural changes (4 - 8 %) with feasible sample sizes (10 - 15).

neuroscience↗

bioRxiv2018

Fragment-based screening identifies inhibitors of the ATPase activity and of hexamer formation of Cagα from the Helicobacter pylori type IV secretion system

Type IV secretion systems are membrane-bound multiprotein complexes that mediate the translocation of macromolecules across the bacterial cell envelope. In Helicobacter pylori a type IV secretion system is encoded by the cag pathogenicity island that encodes 27 Cag proteins and most of these are essential for bacterial virulence. We here present our work on the identification and characterization of inhibitors of Cag, a hexameric ATPase and member of the family of VirB11-like proteins that is essential for translocation of the CagA cytotoxin into mammalian cells. We conducted fragment-based screening using a differential scanning fluorimetry assay and identified 16 molecules that stabilize the protein during thermal denaturation suggesting that they bind Cag. Several of these molecules affect binding of ADP and four of them inhibit the ATPase enzyme activity of Cag. Analysis of enzyme kinetics suggests that their mode of action is non-competitive, suggesting that they do not bind to the ATPase active site. Cross-linking analysis suggests that the active molecules change the conformation of the protein and gel filtration and transmission electron microscopy show that molecule 1G2 dissociates the Cag hexamer. Analysis by X-ray crystallography reveals that molecule 1G2 binds at the interface between Cag subunits. Addition of the molecule 1G2 inhibits the induction of interleukin-8 production in gastric cancer cells after co-incubation with H. pylori suggesting that it inhibits Cag in vivo. Our results reveal a novel mechanism for the inhibition of the ATPase activity of VirB11-like proteins and the identified molecules have potential for the development into antivirulence drugs.

microbiology↗