Mouse Quantitative Proteomics Knowledgebase: reference protein concentration ranges in 20 mouse tissues using 5000 quantitative proteomics assays.

MotivationLaboratory mouse is the most used animal model in biological research, largely due to its high conserved synteny with human. Researchers use mice to answer various questions ranging from determining a pathological effect of knocked out/in gene to understanding drug metabolism. Our group developed >5000 quantitative targeted proteomics assays for 20 mouse tissues and determined the concentration ranges of a total of >1600 proteins using heavy labeled internal standards. We describe here MouseQuaPro; a knowledgebase that hosts this collection of carefully curated experimental data. ResultsThe web-based application includes protein concentrations from >700 mouse tissue samples from three common research strains, corresponding to >200k experimentally determined concentrations. The knowledgebase integrates the assay and protein concentration information with their human orthologs, functional and molecular annotations, biological pathways, related human diseases and known gene expressions. At its core are the protein concentration ranges, which provide insights into (dis)similarities between tissues, strains and sexes. MouseQuaPro implements advanced search as well as filtering functionalities with a simple interface and interactive visualization. This information-rich resource provides an initial map of protein absolute concentration in mouse tissues and allows guided design of proteomics phenotyping experiments. The knowledgebase is available on mousequapro.proteincentre.com. AVAILABILITY AND IMPLEMENTATION: The knowledgebase is available free of charge on http://mousequapro.proteincentre.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Student and faculty member perspectives on public health education at the Marrakech Medical School / Perceptions de la santé publique par les étudiants et les enseignants de la faculté de médecine de Marrakech

BACKGROUND: The COVID-19 pandemic has highlighted the pivotal role of public health. The aim of this study was to explore the perception of public health among medical students and faculty members (teachers). METHODS: A cross-sectional study was conducted at the medical school of Marrakech (FMPM) in May 2020. Data collection regarding the place of public health (during the training and in the practice) was done by electronic questionnaire. The analysis was descriptive and bivariate. RESULTS: 259 responses were received (78.4% were students). The female / male sex ratio = 1.27. Almost 98.5% believed that public health knowledge and experiences were relevant for clinical practice. The main activities that reflect public health were prevention and health promotion (81%), epidemiological surveillance and epidemic management (89.6%) (98.2% among teachers versus 87.2% among students, p = 0.009). During the pandemic, 85.7% of teachers and 77% of students developed an interest in public health (p = 0.196). Only 6.6% were interested in a career in public health. Compared to teachers, students had a positive perception during the pandemic (p = 0.001). CONCLUSION: The results highlight the lack of knowledge about the fields of application despite heightened sensitivity at the onset of the pandemic. Lessons can be learned in terms of improving public health training, raising awareness of the choice of this specialty and actions in favor of better visibility.

Introduction: La pandémie COVID-19 a remis en lumière le rôle pivot de la santé publique. L'objectif de cette étude était d'explorer la perception de la santé publique auprès des étudiants et des enseignants en médecine. Méthodologie: Nous avons mené une étude transversale à la faculté de médecine de Marrakech (FMPM) en Mai 2020. La collecte des données sur la place de la santé publique (dans la formation et sur le terrain) a été par questionnaire électronique. L'analyse était descriptive et bivariée. Résultats: Nous avons reçu 259 réponses (78,4 % étaient des étudiants). Le sexe ratio Femme/homme=1,27. Près de 98,5 % pensaient que les connaissances et les expériences en santé publique sont pertinentes pour la pratique clinique. Les principales activités qui reflètent la santé publique étaient la prévention et la promotion de la santé (81 %), la surveillance épidémiologique et la gestion des épidémies (89,6 %) (98,2 % chez les enseignants contre 87,2 % chez les étudiants, p=0,009). Au cours de la pandémie, 85,7 % des enseignants et 77 % des étudiants ont développé un intérêt pour la santé publique (p=0,196). Seulement 6,6 % étaient intéressés par une carrière en santé publique. Comparés aux enseignants, les étudiants avaient une perception différente positive au cours de la pandémie (p=0,001). Conclusion: Les résultats mettent en exergue la méconnaissance des champs d'application de la santé publique malgré un intérêt à l'avènement de la pandémie. Des enseignements sont à tirer en termes d'amélioration de la formation de la santé publique, la sensibilisation au choix de cette spécialité et d'actions en faveur d'une meilleure visibilité.

Process and Workflow for Preparation of Disparate Mouse Tissues for Proteomic Analysis.

We investigated the effect of homogenization strategy and protein precipitation on downstream protein quantitation using multiple reaction monitoring mass spectrometry (MRM-MS). Our objective was to develop a workflow capable of processing disparate tissue types with high throughput, minimal variability, and maximum purity. Similar abundances of endogenous proteins were measured in nine different mouse tissues regardless of the homogenization method used; however, protein precipitation had strong positive effects on several targets. The best throughput was achieved by lyophilizing tissues to dryness, followed by homogenization via bead-beating without sample buffer. Finally, the effect of tissue perfusion prior to dissection and collection was explored in 20 mouse tissues. MRM-MS showed decreased abundances of blood-related proteins in perfused tissues; however, complete removal was not achieved. Concentrations of nonblood proteins were largely unchanged, although significantly higher variances were observed for proteins from the perfused lung, indicating that perfusion may not be suitable for this organ. We present a simple yet effective tissue processing workflow consisting of harvest of fresh nonperfused tissue, novel lyophilization and homogenization by bead-beating, and protein precipitation. This workflow can be applied to a range of mouse tissues with the advantages of simplicity, minimal manual manipulation of samples, use of commonly available equipment, and high sample quality.

Microemboli After Successful Thrombectomy Do Not Affect Outcome but Predict New Embolic Events.

Background and Purpose- We aimed to determine if microemboli after endovascular thrombectomy correlate with unfavorable outcomes despite successful recanalization. Methods- This is a prospective multicenter study of consecutive patients with ischemic stroke and occlusion of anterior circulation vessels (terminal internal carotid or main trunk of the middle cerebral artery/first-order branch of the main trunk of the middle cerebral artery segments of middle cerebral artery) after successful thrombectomy (modified Treatment In Cerebral Ischemia grades 2b-3). Microembolic signals (MES) were assessed by 30 minutes of transcranial Doppler monitoring within 72 hours of the last-seen-well time. Major outcomes included modified Rankin Scale at 90 days and infarct volume on head computed tomography at 24 hours. We also assessed early outcomes based on National Institutes of Health Stroke Scale variation and recurrence of stroke, transient ischemic attack, or systemic embolism within 90 days. Results- Among 111 patients, MES were detected in 43 (39%), with a median rate of 4 counts/h (interquartile range 2-12). The occurrence of MES was not associated with a significant difference in modified Rankin Scale (ordinal shift analysis, adjusted odds ratio, 1.06 [95% CI, 0.48-2.34] P=0.85) nor in functional independence (modified Rankin Scale, 0-2: adjusted odds ratio, 0.52 [95% CI, 0.19-1.39] P=0.19). Patients with and without MES had similar infarct volumes (adjusted beta, 11.2 [95% CI, -46.6 to +22.9] P=0.51) on 24-hour computed tomography. MES did predict new embolic events (adjusted Cox hazard ratio, 6.78 [95% CI, 1.63-27.8] P=0.01). Conclusions- MES detected by transcranial Doppler following endovascular treatment of anterior circulation occlusions do not predict clinical or radiological outcome. However, such emboli are an independent marker of recurrent embolic events within 90 days.

Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue.

The mouse is the most commonly used laboratory animal, with more than 14 million mice being used for research each year in North America alone. The number and diversity of mouse models is increasing rapidly through genetic engineering strategies, but detailed characterization of these models is still challenging because most phenotypic information is derived from time-consuming histological and biochemical analyses. To expand the biochemists' toolkit, we generated a set of targeted proteomic assays for mouse plasma and heart tissue, utilizing bottom-up LC/MRM-MS with isotope-labeled peptides as internal standards. Protein quantitation was performed using reverse standard curves, with LC-MS platform and curve performance evaluated by quality control standards. The assays comprising the final panel (101 peptides for 81 proteins in plasma; 227 peptides for 159 proteins in heart tissue) have been rigorously developed under a fit-for-purpose approach and utilize stable-isotope labeled peptides for every analyte to provide high-quality, precise relative quantitation. In addition, the peptides have been tested to be interference-free and the assay is highly multiplexed, with reproducibly determined protein concentrations spanning >4 orders of magnitude. The developed assays have been used in a small pilot study to demonstrate their application to molecular phenotyping or biomarker discovery/verification studies.

Multiplexed MRM-Based Protein Quantitation Using Two Different Stable Isotope-Labeled Peptide Isotopologues for Calibration.

When quantifying endogenous plasma proteins for fundamental and biomedical research - as well as for clinical applications - precise, reproducible, and robust assays are required. Targeted detection of peptides in a bottom-up strategy is the most common and precise mass spectrometry-based quantitation approach when combined with the use of stable isotope-labeled peptides. However, when measuring protein in plasma, the unknown endogenous levels prevent the implementation of the best calibration strategies, since no blank matrix is available. Consequently, several alternative calibration strategies are employed by different laboratories. In this study, these methods were compared to a new approach using two different stable isotope-labeled standard (SIS) peptide isotopologues for each endogenous peptide to be quantified, enabling an external calibration curve as well as the quality control samples to be prepared in pooled human plasma without interference from endogenous peptides. This strategy improves the analytical performance of the assay and enables the accuracy of the assay to be monitored, which can also facilitate method development and validation.

Toward an Upgraded Honey Bee (Apis mellifera L.) Genome Annotation Using Proteogenomics.

The honey bee is a key pollinator in agricultural operations as well as a model organism for studying the genetics and evolution of social behavior. The Apis mellifera genome has been sequenced and annotated twice over, enabling proteomics and functional genomics methods for probing relevant aspects of their biology. One troubling trend that emerged from proteomic analyses is that honey bee peptide samples consistently result in lower peptide identification rates compared with other organisms. This suggests that the genome annotation can be improved, or atypical biological processes are interfering with the mass spectrometry workflow. First, we tested whether high levels of polymorphisms could explain some of the missed identifications by searching spectra against the reference proteome (OGSv3.2) versus a customized proteome of a single honey bee, but our results indicate that this contribution was minor. Likewise, error-tolerant peptide searches lead us to eliminate unexpected post-translational modifications as a major factor in missed identifications. We then used a proteogenomic approach with ~1500 raw files to search for missing genes and new exons, to revive discarded annotations and to identify over 2000 new coding regions. These results will contribute to a more comprehensive genome annotation and facilitate continued research on this important insect.

Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues.

Mouse is the mammalian model of choice to study human health and disease due to its size, ease of breeding and the natural occurrence of conditions mimicking human pathology. Here we design and validate multiple reaction monitoring mass spectrometry (MRM-MS) assays for quantitation of 2118 unique proteins in 20 murine tissues and organs. We provide open access to technical aspects of these assays to enable their implementation in other laboratories, and demonstrate their suitability for proteomic profiling in mice by measuring normal protein abundances in tissues from three mouse strains: C57BL/6NCrl, NOD/SCID, and BALB/cAnNCrl. Sex- and strain-specific differences in protein abundances are identified and described, and the measured values are freely accessible via our MouseQuaPro database: http://mousequapro.proteincentre.com . Together, this large library of quantitative MRM-MS assays established in mice and the measured baseline protein abundances represent an important resource for research involving mouse models.

Structural Basis for Multivalent MUC16 Recognition and Robust Anti-Pancreatic Cancer Activity of Humanized Antibody AR9.6.

Mucin-16 (MUC16) is a target for antibody-mediated immunotherapy in pancreatic ductal adenocarcinoma (PDAC) among other malignancies. The MUC16-specific monoclonal antibody AR9.6 has shown promise for PDAC immunotherapy and imaging. Here, we report the structural and biological characterization of the humanized AR9.6 antibody (huAR9.6). The structure of huAR9.6 was determined in complex with a MUC16 SEA (Sea urchin sperm, Enterokinase, Agrin) domain. Binding of huAR9.6 to recombinant, shed, and cell-surface MUC16 was characterized, and anti-PDAC activity was evaluated in vitro and in vivo. HuAR9.6 bound a discontinuous, SEA domain epitope with an overall affinity of 88 nmol/L. Binding affinity depended on the specific SEA domain(s) present, and glycosylation modestly enhanced affinity driven by favorable entropy and enthalpy and via distinct transition state thermodynamic pathways. Treatment with huAR9.6 reduced the in vitro growth, migration, invasion, and clonogenicity of MUC16-positive PDAC cells and patient-derived organoids (PDO). HuAR9.6 blocked MUC16-mediated ErbB and AKT activation in PDAC cells, PDOs, and patient-derived xenografts and induced antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity. More importantly, huAR9.6 treatment caused substantial PDAC regression in subcutaneous and orthotopic tumor models. The mechanism of action of huAR9.6 may depend on dense avid binding to homologous SEA domains on MUC16. The results of this study validate the translational therapeutic potential of huAR9.6 against MUC16-positive PDACs.

Well-being assessment in medical students since the COVID-19 pandemic: a mixed method study.

Introduction: Since the COVID-19, changes have occurred for the Moroccan medical students, which represent a vulnerable population. Coping with this situation could be difficult. Our objective was to estimate and understand the psychosocial barriers to the medical students' well-being at the Faculty of Medicine and Pharmacy of Marrakesh (FMPM) by evaluating their coping strategies, difficulties and needs. Methods: We conducted a mixed method study among pre-graduate medical students. For the quantitative part, we did a cross-sectional study using an online four-part self-administered questionnaire. We compared Likert scales of perceived well-being before and one year after the lockdown. The scales ranged from 0 (very low state of well-being) to 10 (complete state of well-being). Coping strategies were assessed by the Brief-COPE questionnaire. The qualitative perspective was a case-study with semi-structured interviews using an interview guide based on the literature review. Finally, a one-phase triangulation analysis, underlined by a convergence model, was done. Results: We had 355 participants for the quantitative part (participation rate of 16.6%). The mean age was 19.2±1.6. The female/male sex ratio was 1.8. The first cycle students represented 76%. The well-being mean state was better before than after the pandemic (7.8 vs 5.4; p<0.001). The main coping strategy was the acceptance of the situation (5.8±1.7). According to the students, their principal need for promoting their well-being at the faculty was having courses about technologies for studies (89.3%). For the qualitative part, we interviewed 16 students. Thirteen had a decline of their well-being after the lockdown. Isolation and adaptation to e-learning were the principal difficulties. However, mainly, they adopted engaging in coping strategies. Conclusion: The medical students' well-being decreased since the COVID-19 pandemic. Students adopting coping strategies were in the best well-being state. Psychosocial and solution-based measures should be put in place at the FMPM to foster the students' well-being.

Protein biomarkers in serum as a conservation tool to assess reproduction: a case study on brown bears (Ursus arctos).

Monitoring the reproductive characteristics of a species can complement existing conservation strategies by understanding the mechanisms underlying demography. However, methodology to determine important aspects of female reproductive biology is often absent in monitoring programs for large mammals. Protein biomarkers may be a useful tool to detect physiological changes that are indicative of reproductive state. This study aimed to identify protein biomarkers of reproductive status in serum collected from free-ranging female brown bears (Ursus arctos) in Alberta, Canada, from 2001 to 2018. We hypothesized that the expression of proteins related to reproduction in addition to energetics and stress can be used to answer specific management-focused questions: (i) identify when a female is pregnant, (ii) detect if a female is lactating, (iii) determine age of sexual maturity (i.e. primiparity) and (iv) assess female fertility (i.e. reproduction rate). Furthermore, we investigated if silver spoon effects (favourable early life conditions provide fitness benefits through adulthood) could be determined using protein expression. A target panel of 19 proteins with established relationships to physiological function was measured by peptide-based analysis using liquid chromatography and multiple reaction monitoring mass spectrometry and their differential expression was evaluated using a Wilcoxon signed-rank test. We found biomarkers of pregnancy (apolipoprotein B-100 and afamin), lactation (apolipoprotein B-100 and alpha-2-macroglobulin) and sexual maturity (corticosteroid-binding globulin), but there were no statistically significant relationships with protein expression and fertility. The expression of proteins related to reproduction (afamin) and energetics (vitamin-D binding protein) was associated with the nutritional quality of the individual's present habitat rather than their early life habitat. This study highlights potential biomarkers of reproductive status and provides additional methods for monitoring physiological function in wildlife to inform conservation.

Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma.

We proteotyped blood plasma from 30 mouse knockout strains and corresponding wild-type mice from the International Mouse Phenotyping Consortium. We used targeted proteomics with internal standards to quantify 375 proteins in 218 samples. Our results provide insights into the manifested effects of each gene knockout at the plasma proteome level. We first investigated possible contamination by erythrocytes during sample preparation and labeled, in one case, up to 11 differential proteins as erythrocyte originated. Second, we showed that differences in baseline protein abundance between female and male mice were evident in all mice, emphasizing the necessity to include both sexes in basic research, target discovery, and preclinical effect and safety studies. Next, we identified the protein signature of each gene knockout and performed functional analyses for all knockout strains. Further, to demonstrate how proteome analysis identifies the effect of gene deficiency beyond traditional phenotyping tests, we provide in-depth analysis of two strains, C8a-/- and Npc2+/-. The proteins encoded by these genes are well-characterized providing good validation of our method in homozygous and heterozygous knockout mice. Ig alpha chain C region, a poorly characterized protein, was among the differentiating proteins in C8a-/-. In Npc2+/- mice, where histopathology and traditional tests failed to differentiate heterozygous from wild-type mice, our data showed significant difference in various lysosomal storage disease-related proteins. Our results demonstrate how to combine absolute quantitative proteomics with mouse gene knockout strategies to systematically study the effect of protein absence. The approach used here for blood plasma is applicable to all tissue protein extracts.

Plasma Protein Signatures of a Murine Venous Thrombosis Model and Slc44a2 Knockout Mice Using Quantitative-Targeted Proteomics.

The plasma compartment of the blood holds important information on the risk to develop cardiovascular diseases such as venous thrombosis (VT). Mass spectrometry-based targeted proteomics with internal standards quantifies proteins in multiplex allowing generation of signatures associated with a disease or a condition. Here, to demonstrate the method, we investigate the plasma protein signatures in mice following the onset of VT, which was induced by RNA interference targeting the natural anticoagulants antithrombin and protein C. We then study mice lacking Slc44a2, which was recently characterized as a VT-susceptibility gene in human genome-wide association studies. We use a recently developed panel of 375 multiplexed mouse protein assays measured by mass spectrometry. A strong plasma protein siganture was observed when VT was induced. Discriminators included acute phase response proteins, and proteins related to erythrocyte function. In mice lacking Slc44a2, protein signature was primarily overruled by the difference between sexes and not by the absent gene. Upon separate analyses for males and females, we were able to establish a signature for Slc44a2 deficiency, in which glycosylation-dependent cell adhesion molecule-1 and thrombospondin-1 were shared by both sexes. The minimal impact of Slc44a2 deficiency on the measured plasma proteins suggests that the main effect of Slc44a2 on VT does not lay ultimately in the plasma compartment. This suggests further investigation into the role of this VT-susceptibility gene should perhaps also question the possible involvement in cellular mechanisms.

Development and validation of protein biomarkers of health in grizzly bears.

Large carnivores play critical roles in the maintenance and function of natural ecosystems; however, the populations of many of these species are in decline across the globe. Therefore, there is an urgent need to develop novel techniques that can be used as sensitive conservation tools to detect new threats to the health of individual animals well in advance of population-level effects. Our study aimed to determine the expression of proteins related to energetics, reproduction and stress in the skin of grizzly bears (Ursus arctos) using a liquid chromatography and multiple reaction monitoring mass spectrometry assay. We hypothesized that a suite of target proteins could be measured using this technique and that the expression of these proteins would be associated with biological (sex, age, sample location on body) and environmental (geographic area, season, sample year) variables. Small skin biopsies were collected from free-ranging grizzly bears in Alberta, Canada, from 2013 to 2019 (n = 136 samples from 111 individuals). Over 700 proteins were detected in the skin of grizzly bears, 19 of which were chosen as targets because of their established roles in physiological function. Generalized linear mixed model analysis was used for each target protein. Results indicate that sample year influenced the majority of proteins, suggesting that physiological changes may be driven in part by responses to changes in the environment. Season influenced the expression of proteins related to energetics, reproduction and stress, all of which were lower during fall compared to early spring. The expression of proteins related to energetics and stress varied by geographic area, while the majority of proteins that were affected by biological attributes (age class, sex and age class by sex interaction) were related to reproduction and stress. This study provides a novel method by which scientists and managers can further assess and monitor physiological function in wildlife.