Le secretome, un modèle adapté à l'étude des protéines sécrétées par les tumeurs.<br />Application à l'analyse du rôle joué par p53 sur la sécrétion de protéines par des cellules du cancer du poumon.

Cancer is a real public health problem and will represent in 2010 the first cause of mortality. So the knowledge of this disease and its mechanisms remains a great challenge. Malignant processes such as metastasis, invasion, or angiogenesis are tightly dependent on the composition of the extracellular medium, which is itself affected by the release of proteins by the tumor cells. The mutation of pro- and anti-oncogenic factors plays an important role in tumor progression. In this work, we want to ask the following major question: is it interesting to study by proteomics the secreted proteins by tumor to better understand tumorigenesis mechanisms and is it useful for clinical biomarker discovery? We focused on lung cancer which is the cancer with the greater mortality and incidency frequences in the world. This cancer has the greater p53 mutation rates. This protein is a major tumor suppressor known to modulate the release of proteins by the tumor cells; however, while p53-modulated intracellular proteins have been extensively studied, little is known concerning their extracellular counterparts. Here, we developed a proteomics process using iTRAQ labeling, OFFGEL isoelectric focusing and LC-MALDI-MS/MS analysis efficient to the study of this class of proteins. We used it to characterize the p53-dependent secretome of a lung tumor model in vitro. We identified 909 proteins released by these cells, among which 91 are p53-modulated. This differential secretome analysis promises more detailed of how the loss of wt-p53 contributes to tumorigenic processes through the modulation of secreted proteins. We also demonstrated that the modulation of exported proteins can be detected in vivo in total protein extracts and plasma of tumor-bearing mice. This is the first report establishing that the in vitro cell line secretome is reliable and reflects the extracellular release of proteins from tumor cells in vivo and could be used to identify putative tumor markers.Le cancer est un véritable problème de santé publique et représentera en 2010 la première cause de mortalité dans le monde. La lutte contre cette maladie est donc, plus que jamais, un enjeu capital. Les processus tumoraux associés à la carcinogénèse, tels que la métastase, l'invasion ou l'angiogenèse, dépendent étroitement de la composition du milieu extracellulaire, lui-même affecté par la sécrétion de protéines par les cellules tumorales. La mutation ou la variation d'expression de facteurs pro- ou anti-oncogénique joue un rôle important dans le développement et la progression de la tumeur. Durant ce travail de thèse, nous avons voulu apporter des éléments de réponse à la problématique suivante : l'étude par protéomique des protéines sécrétées par la tumeur apporte t'elle des informations contribuant à la compréhension des mécanismes de la tumorogenèse et peut elle permettre de mettre en valeur de nouvelles cibles d'intérêt clinique ? Nous avons ciblé notre étude sur le cancer du poumon, le plus fréquent au niveau mondial tant en terme d'incidence que de mortalité. Ce cancer présente le plus fort taux de mutation du gène p53, un anti-oncogène clé de la cellule. Cette perte de fonction module la sécrétion de nombreuses protéines dont l'investigation est primordiale, bien que paradoxalement, peu étudiée. Notre travail s'est ainsi focalisé sur l'étude de l'influence de p53 sur la modulation de la sécrétion de protéines par les tumeurs du poumon. Nous avons ainsi développé un procédé d'analyse protéomique adapté, basé notamment sur un marquage iTRAQ, une séparation par isoélectrofocalisation de type OFFGEL et une analyse LC-MALDI-MS/MS. Ce procédé a été appliqué à l'étude du rôle joué par l'expression conditionnelle de p53 sur la modulation du secretome d'une lignée cellulaire d'adénocarcinome du cancer du poumon non à petites cellules. Plusieurs protéines d'intérêt ont ainsi été caractérisées et confirmées in vivo chez la souris au niveau tumoral et plasmatique. Ces résultats apportent une meilleure compréhension du rôle primordial joué par l'altération de p53 dans la modulation de l'environnement tumoral et font des secretomes cellulaires un modèle de choix pour l'identification de marqueurs tumoraux

Le secretome, un modèle adapté à l'étude des protéines sécrétées par les tumeurs (application à l'analyse du rôle joué par p53 sur la sécrétion de protéines par des celllules du cancer du poumon)

Le cancer est un véritable problème de santé publique et représentera en 2010 la première cause de mortalité dans le monde. La lutte contre cette maladie est donc, plus que jamais, un enjeu capital. Les processus tumoraux associés à la carcinogénèse, tels que la métastase, l'invasion ou l'angiogenèse, dépendent étroitement de la composition du milieu extracellulaire, lui-même affecté par la sécrétion de protéines par les cellules tumorales. La mutation ou la variation d'expression de facteurs pro- ou anti-oncogénique joue un rôle important dans le développement et la progression de la tumeur. Durant ce travail de thèse, nous avons voulu apporter des éléments de réponse à la problématique suivante : l'étude par protéomique des protéines sécrétées par la tumeur apporte t'elle des informations contribuant à la compréhension des mécanismes de la tumorogenèse et peut elle permettre de mettre en valeur de nouvelles cibles d'intérêt clinique ? Nous avons ciblé notre étude sur le cancer du poumon, le plus fréquent au niveau mondial tant en terme d'incidence que de mortalité. Ce cancer présente le plus fort taux de mutation du gène p53, un anti-oncogène clé de la cellule. Cette perte de fonction module la sécrétion de nombreuses protéines dont l'investigation est primordiale, bien que paradoxalement, peu étudiée. Notre travail s'est ainsi focalisé sur l'étude de l'influence de p53 sur la modulation de la sécrétion de protéines par les tumeurs du poumon. Nous avons ainsi développé un procédé d'analyse protéomique adapté, basé notamment sur un marquage iTRAQ, une séparation par isoélectrofocalisation de type OFFGEL et une analyse LC-MALDI-MS/MS. Ce procédé a été appliqué à l'étude du rôle joué par l'expression conditionnelle de p53 sur la modulation du secretome d'une lignée cellulaire d'adénocarcinome du cancer du poumon non à petites cellules. Plusieurs protéines d'intérêt ont ainsi été caractérisées et confirmées in vivo chez la souris au niveau tumoral et plasmatique. Ces résultats apportent une meilleure compréhension du rôle primordial joué par l'altération de p53 dans la modulation de l'environnement tumoral et font des secretomes cellulaires un modèle de choix pour l'identification de marqueurs tumoraux.Cancer is a real public health problem and will represent in 2010 the first cause of mortality. So the knowledge of this disease and its mechanisms remains a great challenge. Malignant processes such as metastasis, invasion, or angiogenesis are tightly dependent on the composition of the extracellular medium, which is itself affected by the release of proteins by the tumor cells. The mutation of pro- and anti-oncogenic factors plays an important role in tumor progression. In this work, we want to ask the following major question: is it interesting to study by proteomics the secreted proteins by tumor to better understand tumorigenesis mechanisms and is it useful for clinical biomarker discovery? We focused on lung cancer which is the cancer with the greater mortality and incidency frequences in the world. This cancer has the greater p53 mutation rates. This protein is a major tumor suppressor known to modulate the release of proteins by the tumor cells; however, while p53-modulated intracellular proteins have been extensively studied, little is known concerning their extracellular counterparts. Here, we developed a proteomics process using iTRAQ labeling, OFFGEL isoelectric focusing and LC-MALDI-MS/MS analysis efficient to the study of this class of proteins. We used it to characterize the p53-dependent secretome of a lung tumor model in vitro. We identified 909 proteins released by these cells, among which 91 are p53-modulated. This differential secretome analysis promises more detailed of how the loss of wt-p53 contributes to tumorigenic processes through the modulation of secreted proteins. We also demonstrated that the modulation of exported proteins can be detected in vivo in total protein extracts and plasma of tumor-bearing mice. This is the first report establishing that the in vitro cell line secretome is reliable and reflects the extracellular release of proteins from tumor cells in vivo and could be used to identify putative tumor markers.GRENOBLE1-BU Sciences (384212103) / SudocSudocFranceF

[Secretome: definitions and biomedical interest]

International audienceINTRODUCTION: The secretome, or secretomics refers to the global study of proteins that are secreted by a cell, a tissue or an organism. EXEGESIS: The secretome is an important class of proteins that control many biological and physiological processes. Many secretion pathways are implicated in the release of these proteins. CONCLUSION: The secretome is a potential source suitable for the discovery of new therapeutic targets or biomarker candidates

Peptides OFFGEL electrophoresis: a suitable pre-analytical step for complex eukaryotic samples fractionation compatible with quantitative iTRAQ labeling.

International audienceABSTRACT: BACKGROUND: The proteomes of mammalian biological fluids, cells and tissues are complex and composed of proteins with a wide dynamic range. The effective way to overcome the complexity of these proteomes is to combine several fractionation steps. OFFGEL fractionation, recently developed by Agilent Technologies, provides the ability to pre-fractionate peptides into discrete liquid fractions and demonstrated high efficiency and repeatability necessary for the analysis of such complex proteomes. RESULTS: We evaluated OFFGEL fractionator technology to separate peptides from two complex proteomes, human secretome and human plasma, using a 24-wells device encompassing the pH range 3-10. In combination with reverse phase liquid chromatography, peptides from these two samples were separated and identified by MALDI TOF-TOF. The repartition profiles of the peptides in the different fractions were analyzed and explained by their content in charged amino acids using an algorithmic model based on the possible combinations of amino acids. We also demonstrated for the first time the compatibility of OFFGEL separation technology with the quantitative proteomic labeling technique iTRAQ allowing inclusion of this technique in complex samples comparative proteomic workflow. CONCLUSION: The reported data showed that OFFGEL system provides a highly valuable tool to fractionate peptides from complex eukaryotic proteomes (plasma and secretome) and is compatible with iTRAQ labeling quantitative studies. We therefore consider peptides OFFGEL fractionation as an effective addition to our strategy and an important system for quantitative proteomics studies

Detection of Yersinia pestis in Complex Matrices by Intact Cell Immunocapture and Targeted Mass Spectrometry

International audienceWe describe an immunoaffinity-liquid chromatography-tandem mass spectrometry (immuno-LC-MS/MS) protocol for the direct (i.e., without prior culture), sensitive and specific detection of Yersinia pestis in complex matrices. Immunoaffinity enables isolation and concentration of intact bacterial cells from food and environmental samples. After protein extraction and digestion, suitable proteotypic peptides corresponding to three Y. pestis-specific protein markers (murine toxine, plasminogen activator and pesticin) are monitored by targeted LC-MS/MS using the selected reaction monitoring (SRM) mode. This immuno-LC–MS/MS assay has a limit of detection of 2 × 104 CFU/mL in milk or tap water, and 4.5 × 105 CFU in 10 mg of soil

Quantification of low abundance Yersinia pestis markers in dried blood spots by immuno-capture and quantitative high-resolution targeted mass spectrometry

International audiencePlague, caused by the bacterium Yersinia pestis, is still present in several countries worldwide. Besides, Y. pestis has been designated as Tier 1 agent, the highest rank of bioterrorism agents. In this context, reliable diagnostic methods are of great importance. Here, we have developed an original workflow based upon dried blood spot for simplified sampling of clinical specimens, and specific immuno-mass spectrometry monitoring of Y. pestis biomarkers. Targeted proteins were selectively enriched from dried blood spot extracts by multiplex immunocapture using antibody-coated magnetic beads. After accelerated on-beads digestion, proteotypic peptides were monitored by multiplex LC-MS/MS through the parallel reaction monitoring mode. The DBS-IC-MS assay was designed to quantify both F1 and LcrV antigens, although 10-fold lower sensitivity was observed with LcrV. The assay was successfully validated for F1 with a lower limit of quantification at 5 ng·mL−1 in spiked blood, corresponding to only 0.1 ng on spots. In vivo quantification of F1 in blood and organ samples was demonstrated in the mouse model of pneumonic plague. The new assay could help to simplify the laboratory confirmation of positive point of care F1 dipstick

Identification and Validation of Specific Markers of Bacillus anthracis Spores by Proteomics and Genomics Approaches

International audienceBacillus anthracis is the causative bacteria of anthrax, an acute and often fatal disease in humans. The infectious agent, the spore, represents a real bioterrorism threat and its specific identification is crucial. However, because of the high genomic relatedness within the Bacillus cereus group, it is still a real challenge to identify B. anthracis spores confidently. Mass spectrometry-based tools represent a powerful approach to the efficient discovery and identification of such protein markers. Here we undertook comparative proteomics analyses of Bacillus anthracis, cereus and thuringiensis spores to identify proteoforms unique to B. anthracis. The marker discovery pipeline developed combined peptide- and protein-centric approaches using liquid chromatography coupled to tandem mass spectrometry experiments using a high resolution/high mass accuracy LTQ-Orbitrap instrument. By combining these data with those from complementary bioinformatics approaches, we were able to highlight a dozen novel proteins consistently observed across all the investigated B. anthracis spores while being absent in B. cereus/thuringiensis spores. To further demonstrate the relevance of these markers and their strict specificity to B. anthracis, the number of strains studied was extended to 55, by including closely related strains such as B. thuringiensis 9727, and above all the B. cereus biovar anthracis CI, CA strains that possess pXO1- and pXO2-like plasmids. Under these conditions, the combination of proteomics and genomics approaches confirms the pertinence of 11 markers. Genes encoding these 11 markers are located on the chromosome, which provides additional targets complementary to the commonly used plasmid-encoded markers. Last but not least, we also report the development of a targeted liquid chromatography coupled to tandem mass spectrometry method involving the selection reaction monitoring mode for the monitoring of the 4 most suitable protein markers. Within a proof-of-concept study, we demonstrate the value of this approach for the further high throughput and specific detection of B. anthracis spores within complex samples

Synovial fluid proteomic fingerprint: S100A8, S100A9 and S100A12 proteins discriminate rheumatoid arthritis from other inflammatory joint diseases.

International audienceOBJECTIVE: We investigated SF and serum proteomic fingerprints of patients suffering from RA, OA and other miscellaneous inflammatory arthritides (MIAs) in order to identify RA-specific biomarkers. METHODS: SF profiles of 65 patients and serum profiles of 31 patients were studied by surface-enhanced laser desorption and ionization-time-of-flight-mass spectrometry technology. The most discriminating RA biomarkers were identified by matrix-assisted laser desorption ionization-time of flight and their overexpression was confirmed by western blotting and ELISA. RESULTS: Three biomarkers of 10 839, 10 445 and 13 338 Da, characterized as S100A8, S100A12 and S100A9 proteins, were the most up-regulated proteins in RA SF. Their expression was about 10-fold higher in RA SF vs OA SF. S100A8 exhibited a sensitivity of 82% and a specificity of 69% in discriminating RA from other MIAs, whereas S100A12 displayed a sensitivity of 79% and a specificity of 64%. Three peptides of 3351, 3423 and 3465 Da, corresponding to the alpha-defensins-1, -2 and -3, were also shown to differentiate RA from other MIAs with weaker sensitivity and specificity. Levels of S100A12, S100A8 and S100A9 were statistically correlated with the neutrophil count in MIA SF but not in the SF of RA patients. S100A8, S100A9, S100A12 and alpha-defensin expression in serum was not different in the three populations. CONCLUSION: The most enhanced proteins in RA SF, the S100A8, S100A9 and S00A12 proteins, distinguished RA from MIA with high accuracy. Possible implication of resident cells in this increase may play a role in RA physiopathology