Urinary proteome : caracterization and interest for the discovery of biomarker

Le cancer de la vessie représente le 4ième cancer de l'homme en Europe. Dans la majorité des cas, les primo-tumeurs sont traitées facilement par résection mais dans 60% des cas, il y a récidives sous formes plus agressives. Il est donc nécessaire de détecter au plus tôt ces récidives. A ce jour, l'examen de référence pour le diagnostic d'un cancer de la vessie est la cystoscopie. Cet examen permet d'examiner l'intérieur de la vessie à l'aide d'un système optique introduit via l'urètre. Cette méthode est spécifique et sensible mais inconfortable et invasive pour le patient. Il est donc important de trouver de nouvelles méthodes de diagnostic de tumeurs de la vessie et, de surveillance aussi sensibles et spécifiques pour réduire l'inconfort chez le patient et par la même occasion, le coût associés à la cystoscopie. La recherche de biomarqueurs protéiques dans l'urine représente une alternative majeure pour le diagnostic, le pronostic et le suivi thérapeutique de patients atteints de pathologies uro-génitales. Dans le cas présent du cancer de la vessie, la vessie joue le rôle de réservoir de cellules relarguées par la tumeur, ce qui fait de l'urine, fluide dit "proximal", le fluide idéal pour la recherche de biomarqueurs protéiques. Ces dernières années, la recherche de biomarqueurs protéiques a bénéficié de progrès spectaculaires dans le domaine de la spectrométrie de masse et de la biochimie, permettant d'accéder à une large variété de protéines sur une large gamme dynamique de concentration. De plus, l'apparition de nouvelles approches de protéomique quantitatives, telle que la stratégie "Accurate Mass and Time (AMT) tags" couplée à la quantification « label free », permet la comparaison de protéomes d'états physiologiques distincts par mesures d'abondances des protéines. Dans le cadre de ce travail de thèse, nous avons ainsi développé un protocole expérimental couvrant l'ensemble du processus de découverte de nouveaux biomarqueurs associés au cancer de la vessie dans l'urine, i.e., de la collecte et préparation des échantillons d'urine à l'évaluation de méthodes de fractionnement pour la caractérisation la plus exhaustive possible du protéome urinaire, en utilisant des méthodes de protéomiques quantitatives et des méthodes de statistiques dédiées. Ce travail nous a permis de constituer une base de données contenant 2014 protéines urinaires. Des variations d'abondances ont été mesurées pour plus de la moitié d'entre elles, au travers d'une cohorte de 98 patients constituée de patients atteints de cancers de la vessie et de patients contrôles. Une liste finale composée de 97 candidats biomarqueurs du cancer de la vessie a été établit. Cette liste contient un grand nombre de protéines exosomales potentiellement sécrétées de façon spécifique par la tumeur.Bladder cancer is the 4th type of cancer causing man death in Europe. In most cases, primary tumors can be easily removed by resection but in 60% of the cases, the tumors regrowth in more aggressive forms. Therefore, it is essential to detect early recurrence of bladder cancer. To date, the gold standard for the diagnosis of bladder cancer is cystoscopy. It allows the examination of the inside of the bladder using an optical system which is inserted in the urethra. This method is sensitive and specific but extremely uncomfortable and invasive for the patient. Therefore, it is crucial to find new diagnosis and monitoring methods for bladder tumour more comfortable for the patient, in a cost efficient way. The search for clinically useful protein biomarkers in the urine is a major alternative for the diagnosis, the prognostic and the therapeutic treatment of patients with urea-genital pathologies. In the specific case of the bladder cancer, the bladder contains the cells left by the tumour, and subsequently urine becomes the ideal fluid for biomarker investigation as a “proximal fluid”. In the last few years, the search for protein biomarkers has benefited of significant progress in the field of mass spectrometry and bio-chemistry, allowing the detection of a wide variety of proteins in a large dynamic range of concentrations. In addition, new approaches of quantitative proteomic, such as the “Accurate Mass and Time (AMT) tags” approach, coupled with the “label free” quantification, allows the comparison of proteomes from distinct physiological state by measuring protein abundances. During this thesis, we developed an experimental protocol covering the whole process of discovering new biomarkers associated to bladder cancer in urines, i.e., from the collection and preparation of urine samples, to the evaluation of the best fractioning method to define the urinary proteome using quantitative approaches and dedicated statistical methodologies. This work enables the population of a database containing 2014 urinary proteins. Abundance variations were measured for more than the half through a cohort of 98 healthy and bladder cancer patients. A final list of 97 biomarker candidates has been established. This list holds a significant number of exosomal proteins that are potentially secreted by the tumour

La relación intermateria: Una posibilidad para propiciar la formación de valores desde la clase de Lengua Española en la escuela primaria

Se realizan algunas reflexiones que permitirán incentivar en todos los docentes, la necesidad de trabajar la relación intermateria y darles un ejemplo acerca de cómo se procede para contribuir a la formación de valores desde la clase de Lengua Española. Se aborda una arista del problema: la relación intermateria en el tratamiento a la formación y fortalecimiento de valores en la escuela cubana actual a través de las asignaturas Lengua Española, Matemática e Historia, como asignaturas priorizadas, con el apoyo de otras materias: El Mundo en que Vivimos, la Informática

Proteomic signature reveals modulation of human macrophage polarization and functions under differing environmental oxygen conditions: Oxygen tension modulates macrophage polarization

International audienceMacrophages are innate immune cells which can react to a large number of environmental stimuli thanks to a high degree of plasticity. These cells are involved in a variety of tissue functions in homeostasis, and they play essential roles in pathological contexts. Macrophages’ activation state, which determines their functional orientation, is strongly influenced by the cellular environment. A large body of macrophage literature is devoted to better defining polarizations from a molecular viewpoint. It is now accepted that a multidimensional model of polarization is needed to grasp the broad phenotype repertoire controlled by environmental signals. The study presented here aimed, among other goals, to provide a molecular signature of various polarizations in human macrophages at the protein level so as to better define the different macrophage activation states. To study the proteome in human monocyte-derived macrophages as a function of their polarization state, we used a label-free quantification approach on in-gel fractionated and LysC/Trypsin digested proteins. In total, 5102 proteins were identified and quantified for all polarization states. New polarization-specific markers were identified and validated. Because oxygen tension is an important environmental parameter in tissues, we explored how environmental oxygen tension, at either atmospheric composition (18.6% O2) or “tissue normoxia” (3% O2), affected our classification of macrophage polarization. The comparative results revealed new polarization-specific makers which suggest that environmental oxygen levels should be taken into account when characterizing macrophage activation states. The proteomic screen revealed various polarization-specific proteins and oxygen sensors in human macrophages. One example is arachidonate 15-lipoxygenase (ALOX15), an IL4/IL13 polarization-specific protein, which was upregulated under low oxygen conditions and is associated with an increase in the rate of phagocytosis of apoptotic cells. These results illustrate the need to consider physicochemical parameters like oxygen level when studying macrophage polarization, so as to correctly assess their functions in tissue.&nbsp

An Rpb4/Rpb7-Like Complex in Yeast RNA Polymerase III Contains the Orthologue of Mammalian CGRP-RCP

The essential C17 subunit of yeast RNA polymerase (Pol) III interacts with Brf1, a component of TFIIIB, suggesting a role for C17 in the initiation step of transcription. The protein sequence of C17 (encoded by RPC17) is conserved from yeasts to humans. However, mammalian homologues of C17 (named CGRP-RCP) are known to be involved in a signal transduction pathway related to G protein-coupled receptors, not in transcription. In the present work, we first establish that human CGRP-RCP is the genuine orthologue of C17. CGRP-RCP was found to functionally replace C17 in Δrpc17 yeast cells; the purified mutant Pol III contained CGRP-RCP and had a decreased specific activity but initiated faithfully. Furthermore, CGRP-RCP was identified by mass spectrometry in a highly purified human Pol III preparation. These results suggest that CGRP-RCP has a dual function in mammals. Next, we demonstrate by genetic and biochemical approaches that C17 forms with C25 (encoded by RPC25) a heterodimer akin to Rpb4/Rpb7 in Pol II. C17 and C25 were found to interact genetically in suppression screens and physically in coimmunopurification and two-hybrid experiments. Sequence analysis and molecular modeling indicated that the C17/C25 heterodimer likely adopts a structure similar to that of the archaeal RpoE/RpoF counterpart of the Rpb4/Rpb7 complex. These RNA polymerase subunits appear to have evolved to meet the distinct requirements of the multiple forms of RNA polymerases

Analysis of the proteins targeted by CDSP32, a plastidic thioredoxin participating in oxidative stress responses

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Large-Scale SRM Screen of Urothelial Bladder Cancer Candidate Biomarkers in Urine

International audienceUrothelial bladder cancer is a condition associated with high recurrence and substantial morbidity and mortality. Noninvasive urinary tests that would detect bladder cancer and tumor recurrence are required to significantly improve patient care. Over the past decade, numerous bladder cancer candidate biomarkers have been identified in the context of extensive proteomics or transcriptomics studies. To translate these findings in clinically useful biomarkers, the systematic evaluation of these candidates remains the bottleneck. Such evaluation involves large-scale quantitative LC-SRM (liquid chromatography-selected reaction monitoring) measurements, targeting hundreds of signature peptides by monitoring thousands of transitions in a single analysis. The design of highly multiplexed SRM analyses is driven by several factors: throughput, robustness, selectivity and sensitivity. Because of the complexity of the samples to be analyzed, some measurements (transitions) can be interfered by coeluting isobaric species resulting in biased or inconsistent estimated peptide/protein levels. Thus the assessment of the quality of SRM data is critical to allow flagging these inconsistent data. We describe an efficient and robust method to process large SRM data sets, including the processing of the raw data, the detection of low-quality measurements, the normalization of the signals for each protein, and the estimation of protein levels. Using this methodology, a variety of proteins previously associated with bladder cancer have been assessed through the analysis of urine samples from a large cohort of cancer patients and corresponding controls in an effort to establish a priority list of most promising candidates to guide subsequent clinical validation studies

Reprogramming glioma cell cultures with retinoic acid: Additional arguments for reappraising the potential of retinoic acid in the context of personalized glioma therapy

International audienceBackground: Glioma, notably glioblastoma multiforme, is characterized by extensive inter-and intra-tumoral heterogeneity. Surprisingly, the potential for differentiation of glioma cells has not been systematically analyzed and included in patient stratification methods. In the current study, retinoic acid (RA), a neuronal differentiation agent, was assessed for the pro-differentiative and anti-proliferative effects on glioma cells. Methods: Using RA-responsive glioma culture as an experimental paradigm, we analyzed the differentiation process both by videomicroscopy and at the mRNA (RNA-seq and reverse transcription-quantitative-polymerase chain reaction) and proteomic levels. Results: Glioma cells can differentiate into neurons in response to RA by (i) extending ultra-long cytoplasmic extensions, (ii) using these extensions to move from cell to cell either by perikaryal translocation or in a "spider-flight" like process, (iii) slowing their cell cycling, (iv) acquiring several neuronal differentiation markers such as MAPT, GAP43, DCX, NRCAM, NeuroD2, NeuroG2, and NeuN, and (v) decreasing the expression of several genes associated with glioma aggressiveness. Conclusion: These results indicate the existence of a subgroup of patients harboring RA-responsive glioma cells amenable to differentiation therapy, and stratifying such patients with a functional test is easily achievable. This provides the first step to reassess the potential of RA in the context of personalized medicine

A newly identified isoform of Slp2a associates with Rab27a in cytotoxic T cells and participates to cytotoxic granule secretion

International audienceCytotoxic T lymphocytes (CTLs) and natural killer cells help control infections and tumors via a killing activity that is mediated by the release of cytotoxic granules. Granule secretion at the synapse formed between the CTL and the target cell leads to apoptosis of the latter. This process involves polarization of the CTL's secretory machinery and cytotoxic granules. The small GTPase Rab27a and the hMunc13-4 protein have been shown to be required for both granule maturation and granule docking and priming at the immunologic synapse. Using a tandem affinity purification technique, we identified a previously unknown hematopoietic form of Slp2a (Slp2a-hem) and determined that it is a specific effector of the active form of Rab27a. This interaction occurs in vivo in primary CTLs. We have shown that (1) Rab27a recruits Slp2a-hem on vesicular structures in peripheral CTLs and (2) following CTL-target cell conjugate formation, the Slp2a-hem/Rab27a complex colocalizes with perforin-containing granules at the immunologic synapse, where it binds to the plasma membrane through its C2 domains. The overexpression of a dominant-negative form of Slp2a-hem markedly impaired exocytosis of cytotoxic granules-indicating that Slp2a is required for cytotoxic granule docking at the immunologic synapse

COVID-19 vaccines associated with vasovagal malaise: A retrospective study in two mass vaccination centers and analysis of the WHO pharmacovigilance database

The association between COVID-19 vaccines and vasovagal malaise (VVM) has recently been reported in the literature. Our study aimed to describe COVID-19 vaccines associated VVM cases and to identify risk factors of COVID-19 vaccines associated VVM. To this end, we performed a descriptive study of VVM reports associated with COVID-19 vaccines from two French mass COVID-19 vaccination centers. We also extracted reports of VVM associated with all-COVID-19 vaccines in VigiBase®, the World Health Organization (WHO) pharmacovigilance database to analyze demographic data. In the two French mass vaccination center database, 408 entries reported VVM after the standard administration of tozinameran - Pfizer® (1.63/1,000 vaccinated persons). Of these cases, 213 (52.2%) occurred in women, and 193 (47.3%) occurred in the 18–29 year-old (yo) age group. In 232 cases (56.8%), patients had a history of anxiety related to needles or medical visits, 213 (52.2%) reported a fear of COVID-19 vaccination in particular, and 233 (57.1%) had a history of VVM. In VigiBase®, 336,291 notifications of COVID-19 vaccines associated with VVM were identified in the adult population during the period of analysis. The most reported age class was 18–44 years (52.4%), and women represented 71.7% of the reports. Reporting widely differed depending on the country. This study, performed in real-life conditions, highlights that VVM is associated with all-COVID-19 vaccines. Young age and history of anxiety related in young adults could be a triggering factor of vaccines-associated VVM. Further studies are needed to confirm our results