NCube/papyrus huggingface dataset:
Structural dynamics of the selectivity filter in HCN1 ion channel

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels belong to the voltage-gated cation channel superfamily and are responsible for the generation of funny current (If) in cardiac and neuronal cells. Despite the overall structural similarity to voltage-gated potassium (Kv) and cyclic nucleotide-gated (CNG) ion channels, they show distinctive selectivity pattern for K+ and Na+ ions. Specifically, their increased permeability to Na+ ions is critical to its role in depolarizing cellular membranes. They are also one of the only known proteins to select between Na+ and Li+ ions, making HCNs semi-selective channels. Here we investigate the unique selectivity properties of HCN channels using molecular dynamics simulations. Our simulations suggest that the HCN1 pore is very flexible and dilatated compared to Kv channels and that there is only one stable ion binding site within the selectivity filter which discriminates them from both Kv and CNG channels. We also observe that ion co-ordination and hydration differ within the selectivity filter of HCN1 compared to Kv and CNG channels. Additionally, the co-ordination of K+ ions by the carbonyl groups of the selectivity filter is more stable compared to Na+ and Li+ ions, which may explain the channel's distinct selectivity properties.

Keyphrases: HCN Channel, Ion channel, Selectivity filter, Structural dynamics, MD simulation, Lithium ion selectivity, Canal HCN, Simulation MD
Identification des mécanismes de résistance de V. cholerae aux peptides antimicrobiens

According to the World Health Organization, cholera remains a significant health problem, causing 100,000 death per 4 millions infections per year. V. cholerae, the etiologic agent of cholera and a Gram-negative bacterium, is generally transmitted via contaminated food or water. During infection, the microbiota and intestinal epithelium acts as a barrier by producing antimicrobial peptides (AMP). Resistance to AMP has emerged as a virulence factor in pathogens and specifically in V. cholerae. As AMP are considered as novel molecular therapeutic agents, it is truly important to better understand strategies of resistance of V. cholerae. The aim of this study is to identify unknown mechanisms involved in V. cholerae resistance to AMP. For this purpose, after protein sequencing by mass spectrometry (MS-MS) and bioinformatics, we identified the OmpV porin, member of the outer membrane protein family and the Lap protease as new protein candidates for strategies of resistance. We characterized the V. cholerae A1552 strain deleted for ompV (DompV). We confirmed OmpV implication in AMP resistance by minimum inhibitory concentration and did not observed any differences in growth or permeability in the presence of AMP between the wild-type (wt) and the (DompV) strains. The work presented here suggest an implication of outer membrane vesicules in V. cholerae resistance mechanisms to some AMP as LL-37.

Keyphrases: V. cholerae, antimicrobials peptides, bacteria resistance, Outer membranes vesicules
Un modèle macrophagique humain pour étudier la dynamique d’activation de l’inflammasome

Inflammasomes are multiproteic complexes that are involved in innate immunity and are activated by multiple signals of dangers. Hereditary mutations in inflammasome components lead to its excessive activation that is responsible for human auto-inflammatory disease. While these mutations are supposed to alter the dynamic of inflammasome activation, there is no current human model allowing the dynamic study of this complex. I generated a human cellular model expressing an endogenous FLAG3x ASC protein, an adaptator protein common to several inflammasomes, in the human monocytic/macrophagic THP-1 cell line. This model was created through CRISPR-Cas9 genome engineering using a recombination template allowing the in frame integration of the sequence encoding the FLAG3X peptide at the PYCARD locus encoding ASC. I generated and validated the expression and the functionality of 6 FLAG3x-ASC THP-1 cell lines. Furthermore, these cell lines are devoided of CRISPR-Cas9 off-target effect. In this model, I further reproduced a genetic variant of the inflammasome component NLRC4 observed in a patient presenting with autoinflammatory manifestation. The functional validation of the FLAG3x-ASC THP-1 harboring the NLRC4 variant is on-going. This project will allow to study the dynamic of the activation of the inflammasome in healthy and pathological conditions. Those results will help refine our comprehension of inflammasome complexation and regulation in response to danger signals.

Keyphrases: Inflammasome, NLRC4, ASC, CRISPR-Cas9, Monocytes/Macrophages
Détection innée des cellules infectées au VIH-1 par les cellules dendritiques plasmacytoïdes : étude du rôle régulateur de la protéine Vpu de souches pandémiques et non pandémiques

Human immunodeficiency virus (HIV), which is responsible for acquired immune deficiency syndrome (AIDS) has infected over 70 million people, approximately half of which have died from the illness. While there are treatments today that can prevent progression towards AIDS, there is currently no vaccine and no treatment that would completely cure people living with HIV. Plasmacytoid dendritic cells (pDC) limit the establishment of the infection by producing large amounts of type-I IFN (IFN-I) after sensing HIV. IFN-I not only establishes an antiviral environment, but also initiates the innate immune response. This pDC response is regulated, in part, by the pDC-specific receptor immunoglobulin-like transcript 7 (ILT7), which inhibits IFN-I production, upon engagement of its ligand, bone marrow stromal antigen 2 (BST2). BST2 is also an HIV host restriction factor that tethers budding virions at the surface of the infected cell, to limit spread. The HIV-1 accessory protein Vpu counteracts BST2’s restriction through downregulation at the cell surface and displacement away from viral assembly sites. This displacement, which enables ILT7 activation, has a double role: relieving the restriction by BST2 on viral release and repressing IFN-I by pDCs. We screened Vpu variants from pandemic and non-pandemic HIV-1 strains, and found that this function is mostly present in the pandemic group M, although not in variants from clade C which are responsible for half of the global infections. This phenotype in the clade C variants tested was associated with an inability to efficiently displace BST2 in infected T cells. Functional analyses in sensing assays, however, reveal that Vpu variants unable to enhance BST2-mediated ILT7 activation may have evolved compensatory mechanisms to dampen IFN-I production by p

Keyphrases: BST2, Vpu, HIV/AIDS, Innate immunity, Plasmacytoid dendritic cells, Restriction factors, Accessory proteins
The effect of calcium homeostasis on HSV-1 propagation

During a lytic infection, Herpes Simplex Virus type 1 (HSV-1) must go through multiple steps of fusion to replicate and propagate properly. For this purpose, the virus has evolved consequently by taking advantage of the cellular machinery using host factors and proteins. In the literature, processes underlying HSV-1’s entry have been extensively elucidated. However, it remains unclear how newly synthesized viral particles egress from the host cell, and what cellular factors are implicated in this process. Results published by our laboratory suggest that the cellular protein, Extended Synaptotagmin 1 (E-Syt1), has a negative and global impact on the viral propagation when down regulated by RNA interference. Consequently, this study aims to confirm and deepen our understanding of E-Syt1’s role on HSV-1, particularly during viral egress. Since activation of E-Syt1 is linked to the increase in cytoplasmic calcium concentration, we also investigated calcium involvement during later stages of viral propagation. Interestingly, overexpression of E-Syt1 had no measurable effect on HSV-1 propagation whereas calcium has a dual effect on viral propagation. While early calcium sequestering (4 and 6 hours post-infection) using chelators represses viral egress, no significant effect was detected when chelators were added at later time points (12 and 16 hours post-infection). Our results give interesting insights on how HSV-1 relies on intracellular calcium homeostasis to properly mediate viral egress. These results may lead to the discovery of new mechanisms or cellular proteins that are regulated by calcium and hijacked by HSV-1 during lytic replication.

Keyphrases: HSV-1, viral egress, calcium, time points, E-Syt1
Caractérisation des mécanismes responsables des effets variables du récepteur des lipoprotéines de faible densité sur l’intégrité des cellules endothéliales lymphatiques

The lymphatic system plays a key role in the removal of cholesterol from the artery wall and lymphatic dysfunction is known to occur prior to the onset of atherosclerosis. This dysfunction is associated with reduced expression of the low-density-lipoprotein receptor (LDLR) and is first independent of circulating cholesterol levels. It has been shown that mice lacking proprotein subtilisin/kexin type 9 (PCSK9), a proprotein that degrades LDLR, have improved lymphatic function while mice lacking LDLR had a lymphatic dysfunction. We now aim to better understand the mechanisms by which the presence of PCSK9 in lymph or the modulation of LDLR on lymphatic endothelial cells (LECs) affects lymphatic function. Incubation of LECs with PCSK9 and specific targeting of LDLR expression with silencing RNAs were used to further evaluate how PCSK9 or modulation of LDLR affect the metabolism and integrity of LECs. Our results demonstrate that PCSK9 does not induce the secretion of inflammatory cytokines and does not affect the expression of lymphatic markers. LDLR silencing RNA leads to a decrease of membrane-bound lymphatic endothelial cell markers. A decrease in LDLR expression also led to a decrease in the content of some intracellular lipids and particularly phospholipids, sphingolipids and triglycerides. These results suggest that loss of LDLR expression, but not circulating PCSK9, could lead to alterations in the lymphatic endothelium caused by loss of membrane integrity which could in turn affect lymph transport.

Keyphrases: LDL receptor, Lymphatics, Endothelial cells, Atherosclerosis
Évaluation de nouvelles méthodes de prédiction et de dépistage précoce de l’albuminurie chez les patients avec diabète de type 2

Type 2 diabetes (T2D) is a serious chronic disease and its prevalence keeps increasing all over the world. The most severe and common diabetes complication is nephropathy of which the first symptom is albuminuria. Our first objective is to evaluate if early screening of albuminuria allows for a better patient care of this condition in general practitioner practice. Our second objective is to validate the efficacy of our polygenetic risk score (PRS) on the risk prediction of albuminuria on Canadian cohort composed of hypertensive TD2 patients from groupe de médecine familiale (GMF) and family health team (FHT) in Quebec and in Ontario (CLINPRADIA I). The PRS identified the 30% of T2D patients at high risk of developing albuminuria. Indeed, the albuminuria prevalence of the 30% of subjects at high genetic risk based on the PRS was 2.6 times higher than the remaining patients of CLINPRADIA I. In the same cohort, we established that the introduction of the point of care testing (POCT) improves the practice and the adherence of physicians to the guidelines for the treatment of albuminuria. The values of albuminuria and the number of patients with albuminuria decreased significantly after the introduction of the POCT. We can conclude from our results that the use of our PRS enables the early identification of the patients at high risk of albuminuria while the POCT enables the early detection of patients with albuminuria who benefited from an early intervention.

Keyphrases: Hypertension, POCT, Type 2 diabetes, Microvascular complications, Diabetic nephropathy, Albuminuria, Prediction, Screening, Polygenic risk score
Le cœur métabolique : la métabolomique afin de mieux caractériser l’infarctus du myocarde

Background:  In acute coronary syndromes, ticagrelor improved survival compared to clopidogrel. Pleiotropic effects of this drug are not entirely elucidated. Untargeted metabolomics coupled with computational analyses has the potential to help understanding pathophysiological changes of cellular metabolism associated with different disease states and therapies. Objectives:  The purpose of this study is to unveil a discriminant metabolomics signature comparing ST-elevation myocardial infarction (STEMI) patients treated with clopidogrel and ticagrelor. Methods:  The study population consists of 175 participants with STEMI from the PLATO Trial who underwent percutaneous coronary intervention (PCI), randomized to receive clopidogrel (n=88) or ticagrelor (n=87), matched for age, sex, dyslipidemia and diabetes status. Untargeted mass spectrometry (MS)-based metabolomics profiling in plasma was performed at baseline (BL; acute disease state) and repeated at hospital discharge after an average of 4 days of hospitalization (DC; post-treatment state), for each individual. Data analysis was done through differential quantification analysis, analysis of variance, co-modulation network construction and machine learning techniques. Results:  Eight (8) metabolites were differentially modulated by treatment between groups at DC, six (6) of which belong to the polyunsaturated fatty acids omega-3 (n3) and omega-6 (n6) biosynthesis pathways. Participants treated with ticagrelor harbor a significantly higher plasmatic level of α and γ linolenate (n3 and n6), dihomo-linolenate (n6), stearidonate (n3), docosahexaenoate (DHA; n3), eicosapentaenoate (EPA; n3) and arachidonate (AA; n6).  Conclusion:  In patients with STEMI undergoing PCI, untargeted metabolomics reveals that metabolites involved in omega-3 and omega-6 biosynthesis are significantly higher at discharge in the ticagrelor treatment group when compared to clopidogrel, suggesting that the remodeling of the metabolic network after myocardial infarction may interact with the response to antiplatelet drugs.

Keyphrases: clopidogrel, ticagrelor, myocardial infarction, metabolomics, bioinformatics, antiplatelet, omega fatty acids
Premières expériences cliniques en formation médicale : entre éthique clinique et pédagogie médicale

The intrinsic ethical nature of medical practice makes clinical ethics an essential part of the medical school curriculum. The Faculty of medicine of the University of Montréal has recently introduced discussion and writing workshops on complex situations experienced by students during their first clinical rotations. This project is a qualitative thematic analysis of the students’ writings. We have listed the main ethical issues retrieved, have reported them quantitatively and have analyzed what was experienced by students while going through these complex situations by focusing on narrative passages of their stories. Students face ethical dilemmas related to communication, consent and autonomy of patients, justice or deontology. A significant proportion of the issues are specific to their student status, namely issues related to learning and authority. We have also documented that their personal experiences with complex situations are conveyed by discussion about feelings and emotions, by adopting a critical stance on events, by naming the role they have played in the case, by putting forth solutions, and by reflecting on the impact that these situations have had on them. Our results show that the students’ status in hospitals remains very hierarchical, which entails several complex situations and influences their experience and how they react to them. Our findings suggest that the themes identified and the way in which the students discuss them partly reflect their medical education, which among others stands for the universal concern for patients’ best interest observed through their works. Finally, the introspection generated by such narratives is of great interest for students’ ethical, professional and personal growth. It is important that students’ specific ethical dilemmas and the distress they can engender remain an ongoing concern, and we need to make even more room for ethical discussions and writings during and after medical training.

Keyphrases: Clinical ethics, Medical education, Hidden curriculum, Moral distress, Narrative ethics, Medical curriculum, Clerckship
Facteurs de risque pour les maladies inflammatoires de l’intestin : caractérisation de l’impact de variants rares d’IFIH1 sur la réponse épithéliale antivirale

Inflammatory Bowel Disease (IBD), including Cronh’s disease and ulcerative colitis, are chronic inflammatory diseases of the gastro-intestinal tract. IBD is associated with a disturbance of the immune response to the microorganisms of the intestinal lumen. Sequencing studies conducted by the laboratory of Dr. John Rioux, in collaboration with his colleagues of the International IBD Genetics Consortium, identified four rare and independent variants in IFIH1, associated to IBD. The protein of IFIH1 (MDA5) interacts with certain RNA viruses to trigger the innate mechanism of antiviral defense. Our hypothesis was that these IFIH1 variants decreased the intestinal epithelial antiviral response, following an infection. We first worked with lymphoblastoid cell lines (LCLs) obtained from IBD patients who are homozygotes or compound heterozygotes for the different variants, as well as from control individuals (IFIH1 wt). These LCLs were reprogrammed into human induced Pluripotent Stem Cells (hiPSCs), before being differentiated into intestinal epithelial cultures. Our results first confirmed the impact the variants on the genetic and protein structure for these models. Then, the antiviral response was triggered by the stimulation of LCLs and intestinal epithelial cells, with agents (molecular and viral) known to stimulate MDA5. We have demonstrated that these IFIH1 variants did indeed induce a lower antiviral response, characterized by lower IFNs expression, compared to control cell lines. Finally, modulation of IFNs could be an interesting avenue for the treatment of IBD patients with the causal variants.

Keyphrases: Inflammatory bowel diseases, Antiviral response, Innate immunity, Genetic, Intestinal organoids
Faisabilité de l'écho-Doppler de la veine hépatique dans un département d’urgence

Shock is a common condition and a major cause of death in emergency units. Clinical evaluation, vital signs and laboratory tests can lack specificity to identify the cause of shock and do not allow an optimal evaluation of the hemodynamic status of unstable patients. A poor evaluation of the hemodynamic state could lead to inappropriate treatment and the consequence may be fatal. Overestimation of the need for vascular filling can lead to complications such as pulmonary edema; while underestimation may give rise to persistent hypovolemia with hypoperfusion or unrecognized shock resulting in multi-organ failure. The current methods used to assess hemodynamic status are central venous pressure, Swan-Ganz catheters, and trans-esophageal echocardiography. Although already difficult to perform in the emergency department, all of these methods are invasive and retain a high potential for morbidity. However, there are valid alternative methods for obtaining a non-invasive estimate of the average pressure of the right atrium, including subxiphoid ultrasound with measurements of the inferior vena cava (IVC) collapsibility and ultrasound Doppler measurements of the hepatic veins (HV). However, the measurement of the collapsibility of the IVC is subject to several confounding factors and has failed to become a standard of care for evaluating patients’ volemic status. Measuring the flow of the hepatic vein, on the other hand, seems to be a more interesting option for better assessing the filling pressure of the right atrium. Indeed, the Doppler ultrasound of hepatic veins remains a potentially promising instrument that may well reflect the pressures of the right atrium and thus of the central venous pressure. It is important to emphasize that for the unstable patient, every minute is precious and that saving time contributes to eliminate factors likely to compromise the vital prognosis.    The main objective of our study is to measure the time it takes to acquire images. We compared the duration of image acquisition between IVC ultrasound and HV Doppler in healthy volunteers. The average image acquisition time for the IVC and HV was 89.1 and 117.8 seconds respectively. The difference in mean time was 28.6 seconds (95% CI -73.2 · + 15.8, t = 1.33, 24 dL, p = 0.196). The difference for image acquisition time was less than 30 seconds. In practice, we believe that this difference can be considered clinically acceptable for rapid decision-making.  Regarding the failure rate between the two techniques, we did not find any significant difference: 1 failure for IVC and 5 failures for HV with a difference of 13% (0.133), p = 0.09; while the success rate is the same, 25 for each. The evaluation of the hepatic vein by ultrasonography was feasible, simple and fast in the majority of volunteers selected in our study. Key words: Doppler ultrasonography, inferior vena cava, hepatic veins, shock, hemodynamic status

Keyphrases: Doppler ultrasonography, hepatic vein, inferior vena cava, shock, hemodynamic status
Processus de validation d’une base de données haute résolution dans une unité de soins intensifs pédiatriques

Objective: Our objective was to evaluate the data quality of our high-resolution electronic database (HRDB) implemented in the pediatric intensive care unit (PICU) of HSJ.  Design: A descriptive report and analysis of a prospective validation of a HRDB. Setting: A 32 beds pediatric medical, surgical and cardiac PICU in a tertiary care free-standing maternal-child health center in Canada. Population: All patients admitted to the PICU with at least one vital sign recorded using a cardiorespiratory monitor connected to the central monitoring station. Measurements and Main Results: Between June 2017 and August 2018, data from 295 patient days were recorded from medical devices and 4,645 data points were video recorded and compared to the corresponding data collected in the HSJ-PICU HRDB. Statistical analysis showed excellent overall correlation, agreement and reliability. Bland-Altman analysis showed excellent accuracy and precision between recorded and collected data within clinically significant pre-defined limits of agreement. Conclusions: This prospective validation study performed on a representative sample showed excellent overall data quality.

Keyphrases: Pediatrics, Critical care, Database, Electronic health record