Development of metabolic labeling strategies to study changes in protein expression

Résumé : Les progrès techniques de la spectrométrie de masse (MS) ont contribué au récent développement de la protéomique. Cette technique peut actuellement détecter, identifier et quantifier des milliers de protéines. Toutefois, elle n'est pas encore assez puissante pour fournir une analyse complète des modifications du protéome corrélées à des phénomènes biologiques. Notre objectif était le développement d'une nouvelle stratégie pour la détection spécifique et la quantification des variations du protéome, basée sur la mesure de la synthèse des protéines plutôt que sur celle de la quantité de protéines totale. Pour cela, nous volions associer le marquage pulsé des protéines par des isotopes stables avec une méthode d'acquisition MS basée sur le balayage des ions précurseurs (precursor ion scan, ou PIS), afin de détecter spécifiquement les protéines ayant intégré les isotopes et d'estimer leur abondance par rapport aux protéines non marquées. Une telle approche peut identifier les protéines avec les plus hauts taux de synthèse dans une période de temps donnée, y compris les protéines dont l'expression augmente spécifiquement suite à un événement précis. Nous avons tout d'abord testé différents acides aminés marqués en combinaison avec des méthodes PIS spécifiques. Ces essais ont permis la détection spécifique des protéines marquées. Cependant, en raison des limitations instrumentales du spectromètre de masse utilisé pour les méthodes PIS, la sensibilité de cette approche s'est révélée être inférieure à une analyse non ciblée réalisée sur un instrument plus récent (Chapitre 2.1). Toutefois, pour l'analyse différentielle de deux milieux de culture conditionnés par des cellules cancéreuses humaines, nous avons utilisé le marquage métabolique pour distinguer les protéines d'origine cellulaire des protéines non marquées du sérum présentes dans les milieux de culture (Chapitre 2.2). Parallèlement, nous avons développé une nouvelle méthode de quantification nommée IBIS, qui utilise des paires d'isotopes stables d'acides aminés capables de produire des ions spécifiques qui peuvent être utilisés pour la quantification relative. La méthode IBIS a été appliquée à l'analyse de deux lignées cellulaires cancéreuses complètement marquées, mais de manière différenciée, par des paires d'acides aminés (Chapitre 2.3). Ensuite, conformément à l'objectif initial de cette thèse, nous avons utilisé une variante pulsée de l'IBIS pour détecter des modifications du protéome dans des cellules HeLa infectée par le virus humain Herpes Simplex-1 (Chapitre 2.4). Ce virus réprime la synthèse des protéines des cellules hôtes afin d'exploiter leur mécanisme de traduction pour la production massive de virions. Comme prévu, de hauts taux de synthèse ont été mesurés pour les protéines virales détectées, attestant de leur haut niveau d'expression. Nous avons de plus identifié un certain nombre de protéines humaines dont le rapport de synthèse et de dégradation (S/D) a été modifié par l'infection virale, ce qui peut donner des indications sur les stratégies utilisées par les virus pour détourner la machinerie cellulaire. En conclusion, nous avons montré dans ce travail que le marquage métabolique peut être employé de façon non conventionnelle pour étudier des dimensions peu explorées en protéomique. Summary : In recent years major technical advancements greatly supported the development of mass spectrometry (MS)-based proteomics. Currently, this technique can efficiently detect, identify and quantify thousands of proteins. However, it is not yet sufficiently powerful to provide a comprehensive analysis of the proteome changes correlated with biological phenomena. The aim of our project was the development of ~a new strategy for the specific detection and quantification of proteomé variations based on measurements of protein synthesis rather than total protein amounts. The rationale for this approach was that changes in protein synthesis more closely reflect dynamic cellular responses than changes in total protein concentrations. Our starting idea was to couple "pulsed" stable-isotope labeling of proteins with a specific MS acquisition method based on precursor ion scan (PIS), to specifically detect proteins that incorporated the label and to simultaneously estimate their abundance, relative to the unlabeled protein isoform. Such approach could highlight proteins with the highest synthesis rate in a given time frame, including proteins specifically up-regulated by a given biological stimulus. As a first step, we tested different isotope-labeled amino acids in combination with dedicated PIS methods and showed that this leads to specific detection of labeled proteins. Sensitivity, however, turned out to be lower than an untargeted analysis run on a more recent instrument, due to MS hardware limitations (Chapter 2.1). We next used metabolic labeling to distinguish the proteins of cellular origin from a high background of unlabeled (serum) proteins, for the differential analysis of two serum-containing culture media conditioned by labeled human cancer cells (Chapter 2.2). As a parallel project we developed a new quantification method (named ISIS), which uses pairs of stable-isotope labeled amino acids able to produce specific reporter ions, which can be used for relative quantification. The ISIS method was applied to the analysis of two fully, yet differentially labeled cancer cell lines, as described in Chapter 2.3. Next, in line with the original purpose of this thesis, we used a "pulsed" variant of ISIS to detect proteome changes in HeLa cells after the infection with human Herpes Simplex Virus-1 (Chapter 2.4). This virus is known to repress the synthesis of host cell proteins to exploit the translation machinery for the massive production of virions. As expected, high synthesis rates were measured for the detected viral proteins, confirming their up-regulation. Moreover, we identified a number of human proteins whose synthesis/degradation ratio (S/D) was affected by the viral infection and which could provide clues on the strategies used by the virus to hijack the cellular machinery. Overall, in this work, we showed that metabolic labeling can be employed in alternative ways to investigate poorly explored dimensions in proteomics.

Multi-phase post-mortem CT angiography: development of a standardized protocol.

The objective of this work was to develop an easily applicable technique and a standardized protocol for high-quality post-mortem angiography. This protocol should (1) increase the radiological interpretation by decreasing artifacts due to the perfusion and by reaching a complete filling of the vascular system and (2) ease and standardize the execution of the examination. To this aim, 45 human corpses were investigated by post-mortem computed tomography (CT) angiography using different perfusion protocols, a modified heart-lung machine and a new contrast agent mixture, specifically developed for post-mortem investigations. The quality of the CT angiographies was evaluated radiologically by observing the filling of the vascular system and assessing the interpretability of the resulting images and by comparing radiological diagnoses to conventional autopsy conclusions. Post-mortem angiography yielded satisfactory results provided that the volumes of the injected contrast agent mixture were high enough to completely fill the vascular system. In order to avoid artifacts due to the post-mortem perfusion, a minimum of three angiographic phases and one native scan had to be performed. These findings were taken into account to develop a protocol for quality post-mortem CT angiography that minimizes the risk of radiological misinterpretation. The proposed protocol is easy applicable in a standardized way and yields high-quality radiologically interpretable visualization of the vascular system in post-mortem investigations.

Harmonization guidelines for HLA-peptide multimer assays derived from results of a large scale international proficiency panel of the Cancer Vaccine Consortium.

PURPOSE: The Cancer Vaccine Consortium of the Cancer Research Institute (CVC-CRI) conducted a multicenter HLA-peptide multimer proficiency panel (MPP) with a group of 27 laboratories to assess the performance of the assay. EXPERIMENTAL DESIGN: Participants used commercially available HLA-peptide multimers and a well characterized common source of peripheral blood mononuclear cells (PBMC). The frequency of CD8+ T cells specific for two HLA-A2-restricted model antigens was measured by flow cytometry. The panel design allowed for participants to use their preferred staining reagents and locally established protocols for both cell labeling, data acquisition and analysis. RESULTS: We observed significant differences in both the performance characteristics of the assay and the reported frequencies of specific T cells across laboratories. These results emphasize the need to identify the critical variables important for the observed variability to allow for harmonization of the technique across institutions. CONCLUSIONS: Three key recommendations emerged that would likely reduce assay variability and thus move toward harmonizing of this assay. (1) Use of more than two colors for the staining (2) collect at least 100,000 CD8 T cells, and (3) use of a background control sample to appropriately set the analytical gates. We also provide more insight into the limitations of the assay and identified additional protocol steps that potentially impact the quality of data generated and therefore should serve as primary targets for systematic analysis in future panels. Finally, we propose initial guidelines for harmonizing assay performance which include the introduction of standard operating protocols to allow for adequate training of technical staff and auditing of test analysis procedures.

Studies on survival, biological activities and behavior of Biomphalaria glabrata, the host snail of Schistosomiasis, submitted to increased hydrostatic pressure: a technique

To study changes in survival, in biological activities and behavior of planorbids submitted to increased hydrostatic pressure, we developed a technique using two transparent chambers and a hydraulic piston. The apparatus permitted renewal of the liquid medium without substantial variations in pressure, thus eliminating excretion products and maintaining the desired O2 level and thereby permitting us to evaluate the effects of pressure independently of the occurrence of anoxia. Pressure was maintained without any contact of the liquid medium with compressed air, a situation which reproduced with relative fidelity what occurs in nature and assured the presence of the same amounts of gases in the two observation chambers (Control and Experimental). Biomphalaria glabrata was found to be able to survive at least 48 hours when submitted to 49.02 x 10**4 Pa (equivalent to a water depth of 48.8 m), continuing to day egg masses and showing few behavioral changes when compared with the control group.

Estudio de diferentes estrategias de operación en la reacción entre dihidroxiacetona fosfato y Z-S-alaninal catalizada por Rhamnulosa-1-fosfato aldolasa

Proyecto de investigación realizado a partir de una estancia el grupo de Biotecnología e Ingeniería de Bioprocesos del Imperial College London entre abril y julio del 2007. La catálisis enzimática es una tecnología en continua expansión en el campo de la síntesis y producción de compuestos enantioméricamente puros con actividad biológica. Concretamente las aldolasas son enzimas de gran interés industrial como biocatalizadores en síntesis asimétrica de compuestos quirales ya que catalizan la formación de enlaces C-C mediante reacciones de adición aldólica con una alta regio y estereoespecíficidad. Uno de los compuestos es el precursor de iminociclitoles, que son moléculas de gran potencial terapéutico en el tratamiento de un amplio rango de enfermedades debido a su actividad como inhibidores de glicosidasas y glicosiltransferasas. Sin embargo, para conseguir esta reacción existen problemas de solubilidad de los reactivos y productos en medios homogéneos. Una posible solución es el empleo de medios bifásicos en biorreactores de membrana. Se ha estudiado el potencial de un Biorreactor de Membrana para Biotransformaciones desarrollado en dicha reacción y, a la vez, diferentes estrategias de operación que lleven al máximo rendimiento de producto y/o faciliten su purificación tras la reacción.

Scan statistics analysis of forest fire clusters

Spatio-temporal clusters in 1997?2003 fire sequences of Tuscany region (central Italy) have been identified and analysed by using the scan statistic, a method which was devised to evidence clusters in epidemiology. Results showed that the method is reliable to find clusters of events and to evaluate their significance via Monte Carlo replication. The evaluation of the presence of spatial and temporal patterns in fire occurrence and their significance could have a great impact in forthcoming studies on fire occurrences prediction.

Modified 'dumbbell' technique: a simple and intuitive method to position balloon-expandable stent valves.

Intraoperative cardiac imaging plays a key role during transcatheter aortic valve replacement. In recent years, new techniques and new tools for improved image quality and virtual navigation have been proposed, in order to simplify and standardize stent valve positioning and implantation. But routine performance of the new techniques may require major economic investments or specific knowledge and skills and, for this reason, they may not be accessible to the majority of cardiac centres involved in transcatheter valve replacement projects. Additionally, they still require injections of contrast medium to obtain computed images. Therefore, we have developed and describe here a very simple and intuitive method of positioning balloon-expandable stent valves, which represents the evolution of the 'dumbbell' technique for echocardiography-guided transcatheter valve replacement without angiography. This method, based on the partial inflation of the balloon catheter during positioning, traps the crimped valve in the aortic valve orifice and, consequently, very near to the ideal landing zone. It does not require specific echocardiographic knowledge; it does not require angiographies that increase the risk of postoperative kidney failure in elderly patients, and it can be also performed in centres not equipped with a hybrid operating room.

Technique for the detection of Toxoplasma gondii antigens in mouse urine

A simple and rapid staphylococcal coagglutination test for the detection of Toxoplasma gondii antigens in mice urine is described. A suspension of protein-A containing Staphylococcus aureus coated with rabbit hyperimmune serum was used as reagent. The sensitivity of the antigen assay was found to be at least 118 ng of the antigen protein per ml. No coagglutination was observed when the reagent was challenged against antigenic solutions of other parasites. The suitability of the method for detecting antigens of T. gondii in urine samples was studied by experimental toxoplasma infection in mice. Before the staphylococcal test, the urine samples were double serially diluted in 0.1 M PBS. From the second day on all samples from infected mice were positive at 1/16 dilution. At this dilution, all samples from non infected mice were negative or did not produce coagglutination. This method might be used in the rapid etiological diagnosis also in human cases of acute toxoplasmosis.

Mecanismes de reacció de sistemes catalítics amb èmfasi en carbens de Fischer i quantificació de l'aromaticitat en petites molècules inorgàniques cícliques i planes.

El tema principal del treball és sobre l'estudi teòric de l'estructura i reactivitat en carbens de Fischer de la forma (CO)5Cr=C(X)R (X= OH, NH2, OMe, NMe2 i R= CHCH2 i Ph). Particularment, el nostre interès va sorgir del tipus de reaccions de cicloadicció que donen lloc a la síntesi de productes naturals i fàrmacs de gran valor afegit. Hem estudiat els mecanismes de reacció dels casos més comuns de cicloanul•lació: la reacció de benzanul•lació de Dötz i ciclopentanulacions que es troben en competència amb el primer cas, derivats de l'inserció de acetilè i fenilacetilè. En l'últim pas de les reaccions que comporten la formació d'un sistema de més d'un anell, hi tenim una migració del complex metàl•lic de crom d'un extrem a un altre anomenat com rearranjament haptotròpic. Aleshores, hem investigat sobre els mecanismes de migració haptotròpica de Cr(CO)3 sobre hidrocarburs aromàtics policíclics analitzant l'efecte de la mida i la curvatura del sistema així com la complexació d'un segon fragment metàl•lic a la manera de coordinació als anells. D'una altre banda, vam estudiar l'aromaticitat en 54 cúmuls cíclics de molecules inorgàniques mitjançant metodologia desenvolupada al nostre grup de recerca i altres. Vam proposar la tècnica del scan-NICS com nova mesura quantitativa d'aromaticitat i reportar l'escassa correlació entre els distints índexs d'aromaticitat a la literatura. Finalment, com resultat de col•laboracions en estades de recerca, he desenvolupat propostes de mecanismes de reacció en sistemes catalítics de isonitrils i fosfinetà-amides i en dímers de gassos nobles.

Die Inguinal-Hernienplastik nach Lichtenstein: Eine einfache und komplikationsarme Technik, besonders geeignet für die Tageschirurgie [The Lichtenstein inguinal hernia-plasty: a simple and complication-free technique, especially suited for ambulatory surgery].

A consecutive series of 353 patients who underwent Lichtenstein mesh repair for inguinal hernia from the 1st of July 1994 to the 30th of July 1995 were studied. We analysed our indication, technique, complications, follow-up and outcome. Special consideration was given to the advantages and acceptance of day-case surgery. Our results suggest that the Lichtenstein repair should be considered as a new standard procedure, especially outside of hernia centres.