Le remodelage ventriculaire gauche (VG) en post-infarctus du myocarde (IDM) est associé à une augmentation du risque d’insuffisance cardiaque et de décès, mais il demeure difficile à prédire en pratique clinique.L’objectif principal de ma thèse était la recherche de biomarqueurs circulants du remodelage VG par l’approche protéine candidate et par protéomique différentielle dans la population REVE-2.Par l’approche protéine candidate, nous avons confirmé que le peptide natriurétique detype B (BNP) était un puissant facteur prédictif du remodelage VG en post-IDM. La métalloprotéase matricielle-8 (MMP-8), la MMP-9, l’hepatocyte growth factor (HGF), la Créactive protéine (CRP), la troponine I ont également fait la preuve de leur association.Par l’approche protéomique différentielle, en électrophorèse 2D différentielle en fluorescence (2D-DIGE), la clusterine a été identifiée comme biomarqueur potentiel,positivement associée au remodelage VG, nécessitant toutefois des travaux de confirmation.Par SELDI TOF MS, nous avons sélectionné 26 pics définis par leur rapport m/z, commebiomarqueurs potentiels du remodelage VG, dont 12 ont pu être identifiés et devrontdésormais être validés : le pic de m/z 2777 a été identifié comme le peptide N-terminal issu del’albumine après clivage par la pepsine. Les autres pics correspondraient à des fragments protéolytiques de protéines que sont le fibrinogène, le complément C3, C4 et C1q.La découverte de nouveaux biomarqueurs du remodelage VG devrait permettre d’améliorer la stratification du risque en post-IDM afin d’identifier les patients devant bénéficier d’un suivi plus rapproché et peut-être d’une prise en charge thérapeutique plus agressive / Left ventricular (LV) remodelling after myocardial infarction (MI) indicates a high risk of heart failure and death but remains difficult to predict in clinical practice. Biomarkers may help to refine risk stratification. The main purpose was to find circulating biomarkers of LV remodelling after MI, using two strategies : candidate protein approach and differential proteomic approach, working on a population with a clearly defined phenotype, the REVE-2 study, a prospective multicenter study including 246 patients with a first anterior Q-wave MI. Blood samples were obtained at hospital discharge, at 1 month, 3 months and 1 year. An echocardiography was performed at the same time except for the 1st month to assess LVR.By candidate protein approach, we confirmed that B-type natriuretic peptide (BNP) was a powerful predictor of LV remodelling after MI. Additional biomarkers, such as matrix metalloproteinase-8 (MMP-8), MMP-9, hepatocyte growth factor (HGF), C-reactive protein (CRP) and cardiac troponin I were found to be associated with LV remodelling, highlighting several pathways implicated in pathophysiology of LV remodelling. We have also shown that biomarkers in association (BNP and cardiac troponin I, BNP and MMP-8, BNP and MMP-9) could improve risk stratification in post-MI by selecting groups of patients at higher risk.As the ideal biomarker was still not identified, we applied a differential proteomic approach, with no a priori hypothesis, in order to characterize proteomic signature of LV remodelling. The use of a protein enrichment kit, consisting of a library of combinatorial hexapeptide ligands, compressed the protein concentration range of plasma and serum, through the simultaneous onestep dilution of high-abundance and concentration of lowabundance proteins. Protein enrichment kit prior to two-dimensional (2D) electrophoresis or SELDI TOF MS (surface-enhanced laser desorption–ionization time of flight) analysis enabled the detection of proteins that were not detected in native blood sample and the accessibility to proteolytic fragments obtained from major proteins. Clusterin (apolipoprotein J) was identified as a potential biomarker of LV remodelling by 2D-DIfferential Gel Electrophoresis (2D-DIGE). Clusterin was quantified by Western blot and ELISA and was found to be positively associated with LV remodelling. However, this association was not found with all LV remodelling parameters nor at each time during the year following MI, requiring further analysis. Differential proteomic approach by SELDI TOF MS selected 26 m/z peaks, as potential biomarkers of LV remodelling. Of them, 12 were identified by mass spectrometry. The 2777 m/z peak was identified directly from the ProteinChip array as being the N-terminal peptide (24–48 aa) generated from albumin by pepsin cleavage. Other peaks were identified after purification using chromatographic columns or liquid-phase isoelectric focusing : most of them were found to be proteolytic fragments of proteins like fibrinogen, C3, C4 and C1q complement. Identifications have now to be validated with specific techniques, usually by immmunoprecipitation and Western blot analysis.Finding new biomarkers of LV remodelling could help refine risk stratification and identify patients in whom more aggressive therapy and/or more frequent follow-up could be needed.

No description available.

<p>Type 2 diabetes mellitus (T2DM) is a heterogeneous disease affecting millions of people worldwide. Both genetic and environmental factors contribute to the pathogenesis. The disease is characterized by alterations in many genes and their products. Historically, genomic alterations have mainly been studied at the transcriptional level in diabetes research. However, transcriptional changes do not always lead to altered translation, which makes it important to measure changes at the protein level. Proteomic techniques offer the possibility of measuring multiple protein alterations simultaneously.</p><p>In this thesis, the proteomic technique surface enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF MS) has been applied and evaluated in the context of T2DM research. Protocols for pancreatic islet and serum/plasma protein profiling and identification have been developed. In addition, the technique was used to analyze the influence of genetic background versus diabetic environment by determining serum protein profiles of individuals with normal glucose tolerance (NGT) and T2DM with or without family history of diabetes. In total thirteen serum proteins displayed different levels in serum from persons with NGT versus patients with T2DM. Among these proteins, apolipoprotein CIII, albumin and one yet unidentified protein could be classified as being changed because of different genetic backgrounds. On the other hand, ten proteins for instance transthyretin, differed as a result of the diabetic environment.</p><p>When plasma protein patterns of NGT and T2DM individuals characterized by differences in early insulin responses (EIR) were compared, nine proteins were found to be varying between the two groups. Of these proteins five were identified, namely two forms of transthyretin, hemoglobin α-chain, hemoglobin β-chain and apolipoprotein H. However no individual protein alone could explain the differences in EIR. In conclusion, SELDI-TOF MS has been successfully used in the context of T2DM research to identify proteins associated with family history of diabetes and β-bell function. </p>

Background and aims : Crohns disease (CD) and ulcerative colitis (UC) known as inflammatory bowel diseases (IBD) are chronic immuno-inflammatory pathologies of the gastrointestinal tract. These diseases are multifactorial, polygenic and of unknown etiology. Clinical presentation is non specific and diagnosis is based on clinical, endoscopic, radiological and histological criteria. Novel biomarkers are needed to improve early diagnosis and classification of these pathologies as well as to monitor or predict the effects of therapy. Methods We performed a study with 120 serum samples collected from patients classified in 4 groups: 30 CD, 30 UC, 30 inflammatory controls (IC) and 30 healthy controls (HC), according to accredited criteria. We compared protein sera profiles obtained with a Surface Enhanced Laser Desorption Ionization-Time of Flight-Mass Spectrometer (SELDI-TOF-MS). Data analysis with an original multivariate statistical method based on multiple decision trees algorithms allowed us to select new potential biomarkers. Eight of them were purified and identified by mass spectrometry and antibody based methods. Moreover, a similar analysis was applied on sera taken from patients before and after treatment with Infliximab. We obtained multivariates models based on biomarkers able to predict the response and monitor changes in protein profiles before and after therapy. One biomarker was identified by an antibody based method and is able to predict clinical response to anti-TNF therapy. Results : Multivariate analysis generated models that could classify samples with good sensitivity and specificity (minimum 80%) discriminating IBD versus HC and IC or CD versus UC. The discrimination of these multivariate models and those of some identified combined biomarkers were compared to ASCA and ANCA tests and showed better or equivalent power of discrimination. Eight biomarkers were purified and identified: Platelet aggregation Factor 4 (PF4), the Myeloid Related Protein 8 (MRP8), the Fibrinopeptide A (FIBA), the Haptoglobin α2 subunit (Hpα2). They were detected in sera by classical methods, when available. Unique decision tree was built with these biomarkers and correlations with characteristics of patients and between biomarkers were calculated. Finally, we also adressed with a similar strategy predictor of response to Infliximab therapy. Conclusions : SELDI-TOF-MS technology combined with the use of the multiple decision trees method, as robust statistical tool, led to the selection of protein biomarker patterns and of specific biomarkers which could be helpful for diagnosis of inflammatory bowel diseases and prediction of therapy effects as well as understanding of these diseases pathophysiology. Buts : La maladie de Crohn (CD) et la rectocolite ulcéro-hémorrhagique (UC), désignées conjointement sous le nom « Inflammatory Bowel Disease » (IBD), sont deux maladies inflammatoires chroniques de lintestin. Ces pathologies nont pas une étiologie formellement identifiée et semblent être multifactorielles et polygéniques. Leurs présentations cliniques sont aspécifiques et leur diagnostic est actuellement basé sur les données cliniques, endoscopiques, radiologiques et histologiques. Ainsi, de nouveaux marqueurs spécifiques et sensibles de ces pathologies sont nécessaires afin daméliorer le diagnostic précoce et la classification de ces pathologies, ainsi que pour suivre, voire prédire la réponse aux traitements. Méthodes : Une étude protéomique a été réalisée sur 120 échantillons sériques provenant de patients classés en 4 groupes (30 CD, 30 UC, 30 IC et 30 HC), suivant les critères accrédités. Nous avons comparé les profils protéiques obtenus par « Surface Enhanced Laser Desorption Ionization-Time of Flight-Mass Spectrometer » (SELDI-TOF-MS). Lanalyse des données avec une méthode statistique multivariée originale, basée sur la construction darbres de décisions multiples, nous a permis de sélectionner certains biomarqueurs potentiels. Huit dentre eux ont été identifiés par spectrométrie de masse et des techniques de reconnaissance spécifique par anticorps. De plus, une analyse similaire a été effectuée sur des échantillons provenant de patients avant et après traitement par Infliximab. Nous avons obtenu à partir des profils protéiques, des modèles de classification statistiques multivariés et finalement certains biomarqueurs potentiels de prédiction de la réponse au traitement. De plus, un biomarqueur a été identifié par reconnaissance via un anticorps spécifique. Résultats : Lanalyse multivariée a généré des modèles de classification présentant de bonnes sensibilités et spécificités (minimum 80%) pour la discrimination des patients IBD versus contrôles ou encore, CD versus UC. Les résultats ont été comparés avec ceux des tests ASCA et ANCA et montrent une efficacité équivalente ou supérieure. Huit biomarqueurs ont été purifiés et identifiés : le facteur dagrégation plaquettaire 4 (PF4), la protéine MRP8 ou «Myeloid Related Protein 8», le fibrinopeptide A (FIBA), la sous-unité α2 de lhaptoglobine (Hpα2). Ces protéines et peptides ont été détectés, lorsque possible, dans le sérum par les méthodes classiques. Un arbre de décision multiple a été construit sur base de ces biomarqueurs. Les corrélations entre ceux-ci et avec les caractéristiques des patients ont été également évaluées. Conclusions : La technique SELDI-TOF-MS combinée à lutilisation des arbres de décisions multiples en temps que méthode danalyse statistique robuste, a mené à lobtention de signatures protéiques caractéristiques et à la sélection de biomarqueurs spécifiques qui peuvent se révéler utiles au diagnostic des pathologies IBD, au suivi, comme à la prédiction des effets des thérapies et à la compréhension de la physiopathologie de ces maladies

Type 2 diabetes mellitus (T2DM) is a heterogeneous disease affecting millions of people worldwide. Both genetic and environmental factors contribute to the pathogenesis. The disease is characterized by alterations in many genes and their products. Historically, genomic alterations have mainly been studied at the transcriptional level in diabetes research. However, transcriptional changes do not always lead to altered translation, which makes it important to measure changes at the protein level. Proteomic techniques offer the possibility of measuring multiple protein alterations simultaneously. In this thesis, the proteomic technique surface enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF MS) has been applied and evaluated in the context of T2DM research. Protocols for pancreatic islet and serum/plasma protein profiling and identification have been developed. In addition, the technique was used to analyze the influence of genetic background versus diabetic environment by determining serum protein profiles of individuals with normal glucose tolerance (NGT) and T2DM with or without family history of diabetes. In total thirteen serum proteins displayed different levels in serum from persons with NGT versus patients with T2DM. Among these proteins, apolipoprotein CIII, albumin and one yet unidentified protein could be classified as being changed because of different genetic backgrounds. On the other hand, ten proteins for instance transthyretin, differed as a result of the diabetic environment. When plasma protein patterns of NGT and T2DM individuals characterized by differences in early insulin responses (EIR) were compared, nine proteins were found to be varying between the two groups. Of these proteins five were identified, namely two forms of transthyretin, hemoglobin α-chain, hemoglobin β-chain and apolipoprotein H. However no individual protein alone could explain the differences in EIR. In conclusion, SELDI-TOF MS has been successfully used in the context of T2DM research to identify proteins associated with family history of diabetes and β-bell function.

<p>Eosinophil granulocytes are tissue dwelling leukocytes that are implicated in host defence, particularly against helminthic parasites; they also participate in most inflammatory disorders. Although eosinophils have important roles in host defence mechanisms, their actions can also be harmful to the host as in the allergic inflammation where lung epithelium is destructed due to the release of toxic granule proteins. </p><p>The focus of the present thesis work has been to characterize the molecular and functional heterogeneity of the granule protein Eosinophil Cationic Protein (ECP). We investigated a coding ECP gene polymorphism (arg97thr) in an African population endemically exposed to the <i>Schistosoma mansoni</i> parasite and found a correlation between ECP genotype and disease manifestations; ECP^97arg was more effective in terms of host defence against the parasite, but was also correlated to development of liver fibrosis in infected subjects. </p><p>We purified ECP^97arg and ECP^97thr from healthy blood donors and showed that they differ in their cytotoxic activities; ECP^97arg was cytotoxic whereas ECP^97thr was non-cytotoxic. They did not differ in terms of RNase activity or in their ability to stimulate fibroblast-mediated collagen gel contraction. </p><p>We developed a new SELDI-TOF MS assay to enable the study of the structure of ECP in more detail and showed that ECP is produced in several glycosylated forms, and that the degree of glycosylation determines the cytotoxic activity. Enzymatic deglycosylation significantly enhanced the cytotoxic activity of highly glycosylated ECP-variants.</p><p>To summarize, in this thesis we demonstrated that the cytotoxic activity of ECP is dependent on both a gene polymorphism and post-translational modifications, and that the cytotoxic activity is distinct from other functions of ECP. We speculate that ECP is synthesised in heavily glycosylated variants as a means to protect the host from its harmful effects and that ECP is activated by deglycosylation when required at the site of inflammation.</p>

Eosinophil granulocytes are tissue dwelling leukocytes that are implicated in host defence, particularly against helminthic parasites; they also participate in most inflammatory disorders. Although eosinophils have important roles in host defence mechanisms, their actions can also be harmful to the host as in the allergic inflammation where lung epithelium is destructed due to the release of toxic granule proteins. The focus of the present thesis work has been to characterize the molecular and functional heterogeneity of the granule protein Eosinophil Cationic Protein (ECP). We investigated a coding ECP gene polymorphism (arg97thr) in an African population endemically exposed to the Schistosoma mansoni parasite and found a correlation between ECP genotype and disease manifestations; ECP97arg was more effective in terms of host defence against the parasite, but was also correlated to development of liver fibrosis in infected subjects. We purified ECP97arg and ECP97thr from healthy blood donors and showed that they differ in their cytotoxic activities; ECP97arg was cytotoxic whereas ECP97thr was non-cytotoxic. They did not differ in terms of RNase activity or in their ability to stimulate fibroblast-mediated collagen gel contraction. We developed a new SELDI-TOF MS assay to enable the study of the structure of ECP in more detail and showed that ECP is produced in several glycosylated forms, and that the degree of glycosylation determines the cytotoxic activity. Enzymatic deglycosylation significantly enhanced the cytotoxic activity of highly glycosylated ECP-variants. To summarize, in this thesis we demonstrated that the cytotoxic activity of ECP is dependent on both a gene polymorphism and post-translational modifications, and that the cytotoxic activity is distinct from other functions of ECP. We speculate that ECP is synthesised in heavily glycosylated variants as a means to protect the host from its harmful effects and that ECP is activated by deglycosylation when required at the site of inflammation.

Wavelet methods possess versatile properties for statistical applications. We would like to explore the advantages of using wavelets in the analyses in two different research areas. First of all, we develop an integrated tool for online detection of network anomalies. We consider statistical change point detection algorithms, for both local changes in the variance and for jumps detection, and propose modified versions of these algorithms based on moving window techniques. We investigate performances on simulated data and on network traffic data with several superimposed attacks. All detection methods are based on wavelet packets transformations. We also propose a Bayesian model for the analysis of high-throughput data where the outcome of interest has a natural ordering. The method provides a unified approach for identifying relevant markers and predicting class memberships. This is accomplished by building a stochastic search variable selection method into an ordinal model. We apply the methodology to the analysis of proteomic studies in prostate cancer. We explore wavelet-based techniques to remove noise from the protein mass spectra. The goal is to identify protein markers associated with prostate-specific antigen (PSA) level, an ordinal diagnostic measure currently used to stratify patients into different risk groups.

<p>Pancreatic β-cells sense the concentration of glucose in the systemic circulation through metabolism of the sugar molecule. Failure to correlate the blood sugar concentration to an appropriate metabolic signal disrupts the function of the β-cell as a controller of glucose homeostasis and may contribute to the development of type 2 diabetes mellitus. Release of insulin is pulsatile and this thesis presents data that support that metabolism drives such pulsatile release. It is also found that increase in insulin release in response to elevation of the glucose concentration is only seen when the rise in glucose induces a prompt and sustained increase in mitochondrial metabolism. Such activation of mitochondrial metabolism depended on the metabolic state of the β-cell prior to the glucose challenge. In this context, prolonged periods of elevated levels of fatty acids are harmful to the pancreatic β-cell. To study the protein expression changes induced by fatty acids a protocol for islet protein profiling and identification of differently expressed proteins were developed. By using this protocol it was discovered that oleate decreased the cellular level of the chaperone peptidyl-prolyl isomerase B. The protocol was also used to study protein expression in islets obtained from mice fed a high-fat and/or a high-sucrose diet. Excess of glucocorticoids in the systemic circulation also cause a diabetic phenotype. Tissue response to glucocorticoids is regulated by the intracellular concentration of the active form of glucocorticoids, which is formed from the inactive form by the enzyme 11β-hydroxysteroid dehydrogenase type 1. It was found that pancreatic islets produce 11β-HSD1 protein in relation to substrate availability and that the amount of islet 11β-HSD1 protein was negatively correlated with insulin secretion.</p>

Pancreatic β-cells sense the concentration of glucose in the systemic circulation through metabolism of the sugar molecule. Failure to correlate the blood sugar concentration to an appropriate metabolic signal disrupts the function of the β-cell as a controller of glucose homeostasis and may contribute to the development of type 2 diabetes mellitus. Release of insulin is pulsatile and this thesis presents data that support that metabolism drives such pulsatile release. It is also found that increase in insulin release in response to elevation of the glucose concentration is only seen when the rise in glucose induces a prompt and sustained increase in mitochondrial metabolism. Such activation of mitochondrial metabolism depended on the metabolic state of the β-cell prior to the glucose challenge. In this context, prolonged periods of elevated levels of fatty acids are harmful to the pancreatic β-cell. To study the protein expression changes induced by fatty acids a protocol for islet protein profiling and identification of differently expressed proteins were developed. By using this protocol it was discovered that oleate decreased the cellular level of the chaperone peptidyl-prolyl isomerase B. The protocol was also used to study protein expression in islets obtained from mice fed a high-fat and/or a high-sucrose diet. Excess of glucocorticoids in the systemic circulation also cause a diabetic phenotype. Tissue response to glucocorticoids is regulated by the intracellular concentration of the active form of glucocorticoids, which is formed from the inactive form by the enzyme 11β-hydroxysteroid dehydrogenase type 1. It was found that pancreatic islets produce 11β-HSD1 protein in relation to substrate availability and that the amount of islet 11β-HSD1 protein was negatively correlated with insulin secretion.