The redoxomics of PTEN: walking a fine line between damage and signaling:mass spectrometry-based approaches to study the effect of oxidation on PTEN function, structure, and protein-protein interactions

The research described in this PhD thesis focuses on proteomics approaches to study the effect of oxidation on the modification status and protein-protein interactions of PTEN, a redox-sensitive phosphatase involved in a number of cellular processes including metabolism, apoptosis, cell proliferation, and survival. While direct evidence of a redox regulation of PTEN and its downstream signaling has been reported, the effect of cellular oxidative stress or direct PTEN oxidation on PTEN structure and interactome is still poorly defined. In a first study, GST-tagged PTEN was directly oxidized over a range of hypochlorous acid (HOCl) concentration, assayed for phosphatase activity, and oxidative post-translational modifications (oxPTMs) were quantified using LC-MS/MS-based label-free methods. In a second study, GSTtagged PTEN was prepared in a reduced and reversibly H2O2-oxidized form, immobilized on a resin support and incubated with HCT116 cell lysate to capture PTEN interacting proteins, which were analyzed by LC-MS/MS and comparatively quantified using label-free methods. In parallel experiments, HCT116 cells transfected with a GFP-tagged PTEN were treated with H2O2 and PTENinteracting proteins immunoprecipitated using standard methods. Several high abundance HOCl-induced oxPTMs were mapped, including those taking place at amino acids known to be important for PTEN phosphatase activity and protein-protein interactions, such as Met35, Tyr155, Tyr240 and Tyr315. A PTEN redox interactome was also characterized, which identified a number of PTEN-interacting proteins that vary with the reversible inactivation of PTEN caused by H2O2 oxidation. These included new PTEN interactors as well as the redox proteins peroxiredoxin-1 (Prdx1) and thioredoxin (Trx), which are known to be involved in the recycling of PTEN active site following H2O2-induced reversible inactivation. The results suggest that the oxidative modification of PTEN causes functional alterations in PTEN structure and interactome, with fundamental implications for the PTEN signaling role in many cellular processes, such as those involved in the pathophysiology of disease and ageing.

Elemental analysis of glass and ink by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and laser induced breakdown spectroscopy (LIBS)

The necessity of elemental analysis techniques to solve forensic problems continues to expand as the samples collected from crime scenes grow in complexity. Laser ablation ICP-MS (LA-ICP-MS) has been shown to provide a high degree of discrimination between samples that originate from different sources. In the first part of this research, two laser ablation ICP-MS systems were compared, one using a nanosecond laser and another a femtosecond laser source for the forensic analysis of glass. The results showed that femtosecond LA-ICP-MS did not provide significant improvements in terms of accuracy, precision and discrimination, however femtosecond LA-ICP-MS did provide lower detection limits. In addition, it was determined that even for femtosecond LA-ICP-MS an internal standard should be utilized to obtain accurate analytical results for glass analyses. In the second part, a method using laser induced breakdown spectroscopy (LIBS) for the forensic analysis of glass was shown to provide excellent discrimination for a glass set consisting of 41 automotive fragments. The discrimination power was compared to two of the leading elemental analysis techniques, μXRF and LA-ICP-MS, and the results were similar; all methods generated >99% discrimination and the pairs found indistinguishable were similar. An extensive data analysis approach for LIBS glass analyses was developed to minimize Type I and II errors en route to a recommendation of 10 ratios to be used for glass comparisons. Finally, a LA-ICP-MS method for the qualitative analysis and discrimination of gel ink sources was developed and tested for a set of ink samples. In the first discrimination study, qualitative analysis was used to obtain 95.6% discrimination for a blind study consisting of 45 black gel ink samples provided by the United States Secret Service. A 0.4% false exclusion (Type I) error rate and a 3.9% false inclusion (Type II) error rate was obtained for this discrimination study. In the second discrimination study, 99% discrimination power was achieved for a black gel ink pen set consisting of 24 self collected samples. The two pairs found to be indistinguishable came from the same source of origin (the same manufacturer and type of pen purchased in different locations). It was also found that gel ink from the same pen, regardless of the age, was indistinguishable as were gel ink pens (four pens) originating from the same pack.

Improved dynamic headspace sampling and detection using capillary microextraction of volatiles coupled to gas chromatography mass spectrometry

Sampling and preconcentration techniques play a critical role in headspace analysis in analytical chemistry. My dissertation presents a novel sampling design, capillary microextraction of volatiles (CMV), that improves the preconcentration of volatiles and semivolatiles in a headspace with high throughput, near quantitative analysis, high recovery and unambiguous identification of compounds when coupled to mass spectrometry. The CMV devices use sol-gel polydimethylsiloxane (PDMS) coated microglass fibers as the sampling/preconcentration sorbent when these fibers are stacked into open-ended capillary tubes. The design allows for dynamic headspace sampling by connecting the device to a hand-held vacuum pump. The inexpensive device can be fitted into a thermal desorption probe for thermal desorption of the extracted volatile compounds into a gas chromatography-mass spectrometer (GC-MS). The performance of the CMV devices was compared with two other existing preconcentration techniques, solid phase microextraction (SPME) and planar solid phase microextraction (PSPME). Compared to SPME fibers, the CMV devices have an improved surface area and phase volume of 5000 times and 80 times, respectively. One (1) minute dynamic CMV air sampling resulted in similar performance as a 30 min static extraction using a SPME fiber. The PSPME devices have been fashioned to easily interface with ion mobility spectrometers (IMS) for explosives or drugs detection. The CMV devices are shown to offer dynamic sampling and can now be coupled to COTS GC-MS instruments. Several compound classes representing explosives have been analyzed with minimum breakthrough even after a 60 min. sampling time. The extracted volatile compounds were retained in the CMV devices when preserved in aluminum foils after sampling. Finally, the CMV sampling device were used for several different headspace profiling applications which involved sampling a shipping facility, six illicit drugs, seven military explosives and eighteen different bacteria strains. Successful detection of the target analytes at ng levels of the target signature volatile compounds in these applications suggests that the CMV devices can provide high throughput qualitative and quantitative analysis with high recovery and unambiguous identification of analytes.

Development of advanced capillary electrophoresis techniques with UV and mass spectrometry detection for forensic, pharmaceutical and environmental applications

Capillary electrophoresis (CE) is a modern analytical technique, which is electrokinetic separation generated by high voltage and taken place inside the small capillaries. In this dissertation, several advanced capillary electrophoresis methods are presented using different approaches of CE and UV and mass spectrometry are utilized as the detection methods. ^ Capillary electrochromatography (CEC), as one of the CE modes, is a recent developed technique which is a hybrid of capillary electrophoresis and high performance liquid chromatography (HPLC). Capillary electrochromatography exhibits advantages of both techniques. In Chapter 2, monolithic capillary column are fabricated using in situ photoinitiation polymerization method. The column was then applied for the separation of six antidepressant compounds. ^ Meanwhile, a simple chiral separation method is developed and presented in Chapter 3. Beta cycodextrin was utilized to achieve the goal of chiral separation. Not only twelve cathinone analytes were separated, but also isomers of several analytes were enantiomerically separated. To better understand the molecular information on the analytes, the TOF-MS system was coupled with the CE. A sheath liquid and a partial filling technique (PFT) were employed to reduce the contamination of MS ionization source. Accurate molecular information was obtained. ^ It is necessary to propose, develop, and optimize new techniques that are suitable for trace-level analysis of samples in forensic, pharmaceutical, and environmental applications. Capillary electrophoresis (CE) was selected for this task, as it requires lower amounts of samples, it simplifies sample preparation, and it has the flexibility to perform separations of neutral and charged molecules as well as enantiomers. ^ Overall, the study demonstrates the versatility of capillary electrophoresis methods in forensic, pharmaceutical, and environmental applications.^

Applications of capillary electrophoresis and mass spectrometry for the analysis of thiosalts

Thiosalt species are unstable, partially oxidized sulfur oxyanions formed in sulfur-rich environments but also during the flotation and milling of sulfidic minerals especially those containing pyrite (FeS₂) and pyrrhotite (Fe₍₁₋ₓ₎S, x = 0 to 0.2). Detecting and quantifying the major thiosalt species such as sulfate (SO₄²⁻), thiosulfate (S₂O₃²⁻), trithionate (S₃O₆²⁻), tetrathionate (S₄O₆²⁻) and higher polythionates (SₓO₆²⁻, where 3 ≤ x ≤ 10) in the milling process and in the treated tailings is important to understand how thiosalts are generated and provides insight into potential treatment. As these species are unstable, a fast and reliable analytical technique is required for their analysis. Three capillary zone electrophoresis (CZE) methods using indirect UV-vis detection were developed for the simultaneous separation and determination of five thiosalt anions: SO₄²⁻, S₂O₃²⁻, S₃O₆²⁻, S₄O₆²⁻ and S₅O₆²⁻. Both univariate and multivariate experimental design approaches were used to optimize the most critical factors (background electrolyte (BGE) and instrumental conditions) to achieve fast separation and quantitative analysis of the thiosalt species. The mathematically predicted responses for the multivariate experiments were in good agreement with the experimental results. Limits of detection (LODs) (S/N = 3) for the methods were between 0.09 and 0.34 μg/mL without a sample stacking technique and nearly four-fold increase in LODs with the application of field-amplified sample stacking. As direct analysis of thiosalts by mass spectrometry (MS) is limited by their low m/z values and detection in negative mode electrospray ionization (ESI), which is typically less sensitive than positive ESI, imidazolium-based (IP-L-Imid and IP-T-Imid) and phosphonium-based (IP-T-Phos) tricationic ion-pairing reagents were used to form stable high mass ions non-covalent +1 ion-pairs with these species for ESI-MS analysis and the association constants (Kassoc) determined for these ion-pairs. Kassoc values were between 6.85 × 10² M⁻¹ and 3.56 × 10⁵ M⁻¹ with the linear IP-L-Imid; 1.89 ×10³ M⁻¹ and 1.05 × 10⁵ M⁻¹ with the trigonal IP-T-Imid ion-pairs; and 7.51×10² M⁻¹ and 4.91× 10⁴ M⁻¹ with the trigonal IP-T-Phos ion-pairs. The highest formation constants were obtained for S₃O₆²⁻ and the imidazolium-based linear ion-pairing reagent (IP-L-Imid), whereas the lowest were for IP-L-Imid: SO₄²⁻ ion-pair.

Analysis of bio-derived platform chemicals in ionic liquid media by desorption/ionization mass spectrometry

In this work, desorption/ionization mass spectrometry was employed for the analysis of sugars and small platform chemicals that are common intermediates in biomass transformation reactions. Specifically, matrix-assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI) mass spectrometric techniques were employed as alternatives to traditional chromatographic methods. Ionic liquid matrices (ILMs) were designed based on traditional solid MALDI matrices (2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (CHCA)) and 1,3-dialkylimidazolium ionic liquids ([BMIM]Cl, [EMIM]Cl, and [EMIM]OAc) that have been employed as reaction media for biomass transformation reactions such as the conversion of carbohydrates to valuable platform chemicals. Although two new ILMs were synthesized ([EMIM][DHB] and [EMIM][CHCA] from [EMIM]OAc), chloride-containing ILs did not react with matrices and resulted in mixtures of IL and matrix in solution. Compared to the parent solid matrices, much less matrix interference was observed in the low mass region of the mass spectrum (< 500 Da) using each of the IL-matrices. Furthermore, the formation of a true ILM (i.e. a new ion pair) does not appear to be necessary for analyte ionization. MALDI sample preparation techniques were optimized based on the compatibility with analyte, IL and matrix. ILMs and IL-matrix mixtures of DHB allowed for qualitative analysis of glucose, fructose, sucrose and N-acetyl-D-glucosamine. Analogous CHCA-containing ILMs did not result in appreciable analyte signals under similar conditions. Small platform compounds such as 5-hydroxymethylfurfural (HMF) and levulinic acid were not detected by direct analysis using MALDI-MS. Furthermore, sugar analyte signals were only detected at relatively high matrix:IL:analyte ratios (1:1:1) due to significant matrix and analyte suppression by the IL ions. Therefore, chemical modification of analytes with glycidyltrimethylammonium chloride (GTMA) was employed to extend this method to quantitative applications. Derivatization was accomplished in aqueous IL solutions with fair reaction efficiencies (36.9 – 48.4 % glucose conversion). Calibration curves of derivatized glucose-GTMA yielded good linearity in all solvent systems tested, with decreased % RSDs of analyte ion signals in IL solutions as compared to purely aqueous systems (1.2 – 7.2 % and 4.2 – 8.7 %, respectively). Derivatization resulted in a substantial increase in sensitivity for MALDI-MS analyses: glucose was reliably detected at IL:analyte ratios of 100:1 (as compared to 1:1 prior to derivatization). Screening of all test analytes resulted in appreciable analyte signals in MALDI-MS spectra, including both HMF and levulinic acid. Using appropriate internal standards, calibration curves were constructed and this method was employed for monitoring a model dehydration reaction of fructose to HMF in [BMIM]Cl. Calibration curves showed wide dynamic ranges (LOD – 100 ng fructose/μg [BMIM]Cl, LOD – 75 ng HMF/μg [BMIM]Cl) with correlation coefficients of 0.9973 (fructose) and 0.9931 (HMF). LODs were estimated from the calibration data to be 7.2 ng fructose/μg [BMIM]Cl and 7.5 ng HMF/μg [BMIM]Cl, however relatively high S/N ratios at these concentrations indicate that these values are likely overestimated. Application of this method allowed for the rapid acquisition of quantitative data without the need for prior separation of analyte and IL. Finally, small molecule platform chemicals HMF and levulinic acid were qualitatively analyzed by DESI-MS. Both HMF and levulinic acid were easily ionized and the corresponding molecular ions were easily detected in the presence of 10 – 100 times IL, without the need for chemical modification prior to analysis. DESI-MS analysis of ILs in positive and negative ion modes resulted in few ions in the low mass region, showing great potential for the analysis of small molecules in IL media.

Development of Advanced Capillary Electrophoresis Techniques with UV and Mass Spectrometry Detection for Forensic, Pharmaceutical and Environmental Applications

Capillary electrophoresis (CE) is a modern analytical technique, which is electrokinetic separation generated by high voltage and taken place inside the small capillaries. In this dissertation, several advanced capillary electrophoresis methods are presented using different approaches of CE and UV and mass spectrometry are utilized as the detection methods. Capillary electrochromatography (CEC), as one of the CE modes, is a recent developed technique which is a hybrid of capillary electrophoresis and high performance liquid chromatography (HPLC). Capillary electrochromatography exhibits advantages of both techniques. In Chapter 2, monolithic capillary column are fabricated using in situ photoinitiation polymerization method. The column was then applied for the separation of six antidepressant compounds. Meanwhile, a simple chiral separation method is developed and presented in Chapter 3. Beta cycodextrin was utilized to achieve the goal of chiral separation. Not only twelve cathinone analytes were separated, but also isomers of several analytes were enantiomerically separated. To better understand the molecular information on the analytes, the TOF-MS system was coupled with the CE. A sheath liquid and a partial filling technique (PFT) were employed to reduce the contamination of MS ionization source. Accurate molecular information was obtained. It is necessary to propose, develop, and optimize new techniques that are suitable for trace-level analysis of samples in forensic, pharmaceutical, and environmental applications. Capillary electrophoresis (CE) was selected for this task, as it requires lower amounts of samples, it simplifies sample preparation, and it has the flexibility to perform separations of neutral and charged molecules as well as enantiomers. Overall, the study demonstrates the versatility of capillary electrophoresis methods in forensic, pharmaceutical, and environmental applications.

Elemental Analysis of Glass and Ink by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) and Laser Induced Breakdown Spectroscopy (LIBS)

The necessity of elemental analysis techniques to solve forensic problems continues to expand as the samples collected from crime scenes grow in complexity. Laser ablation ICP-MS (LA-ICP-MS) has been shown to provide a high degree of discrimination between samples that originate from different sources. In the first part of this research, two laser ablation ICP-MS systems were compared, one using a nanosecond laser and another a femtosecond laser source for the forensic analysis of glass. The results showed that femtosecond LA-ICP-MS did not provide significant improvements in terms of accuracy, precision and discrimination, however femtosecond LA-ICP-MS did provide lower detection limits. In addition, it was determined that even for femtosecond LA-ICP-MS an internal standard should be utilized to obtain accurate analytical results for glass analyses. In the second part, a method using laser induced breakdown spectroscopy (LIBS) for the forensic analysis of glass was shown to provide excellent discrimination for a glass set consisting of 41 automotive fragments. The discrimination power was compared to two of the leading elemental analysis techniques, µXRF and LA-ICP-MS, and the results were similar; all methods generated >99% discrimination and the pairs found indistinguishable were similar. An extensive data analysis approach for LIBS glass analyses was developed to minimize Type I and II errors en route to a recommendation of 10 ratios to be used for glass comparisons. Finally, a LA-ICP-MS method for the qualitative analysis and discrimination of gel ink sources was developed and tested for a set of ink samples. In the first discrimination study, qualitative analysis was used to obtain 95.6% discrimination for a blind study consisting of 45 black gel ink samples provided by the United States Secret Service. A 0.4% false exclusion (Type I) error rate and a 3.9% false inclusion (Type II) error rate was obtained for this discrimination study. In the second discrimination study, 99% discrimination power was achieved for a black gel ink pen set consisting of 24 self collected samples. The two pairs found to be indistinguishable came from the same source of origin (the same manufacturer and type of pen purchased in different locations). It was also found that gel ink from the same pen, regardless of the age, was indistinguishable as were gel ink pens (four pens) originating from the same pack.

High-resolution pore-water and solid-phase analyses of sediment cores GeoB6520-3 (Hydrate Hole) and GeoB6521-2 (Worm Hole) of the northern Congo Fan

The geochemical cycling of barium was investigated in sediments of pockmarks of the northern Congo Fan, characterized by surface and subsurface gas hydrates, chemosynthetic fauna, and authigenic carbonates. Two gravity cores retrieved from the so-called Hydrate Hole and Worm Hole pockmarks were examined using high-resolution pore-water and solid-phase analyses. The results indicate that, although gas hydrates in the study area are stable with respect to pressure and temperature, they are and have been subject to dissolution due to methane-undersaturated pore waters. The process significantly driving dissolution is the anaerobic oxidation of methane (AOM) above the shallowest hydrate-bearing sediment layer. It is suggested that episodic seep events temporarily increase the upward flux of methane, and induce hydrate formation close to the sediment surface. AOM establishes at a sediment depth where the upward flux of methane from the uppermost hydrate layer counterbalances the downward flux of seawater sulfate. After seepage ceases, AOM continues to consume methane at the sulfate/methane transition (SMT) above the hydrates, thereby driving the progressive dissolution of the hydrates "from above". As a result the SMT migrates downward, leaving behind enrichments of authigenic barite and carbonates that typically precipitate at this biogeochemical reaction front. Calculation of the time needed to produce the observed solid-phase barium enrichments above the present-day depths of the SMT served to track the net downward migration of the SMT and to estimate the total time of hydrate dissolution in the recovered sediments. Methane fluxes were higher, and the SMT was located closer to the sediment surface in the past at both sites. Active seepage and hydrate formation are inferred to have occurred only a few thousands of years ago at the Hydrate Hole site. By contrast, AOM-driven hydrate dissolution as a consequence of an overall net decrease in upward methane flux seems to have persisted for a considerably longer time at the Worm Hole site, amounting to a few tens of thousands of years.

Determination of multi-mycotoxin occurrence in maize based porridges from selected regions of Tanzania by liquid chromatography tandem mass spectrometry (LC-MS/MS), a longitudinal study

Residents of certain areas of Tanzania are exposed to mycotoxins through the consumption of contaminated maize based foods. In this study, 101 maize based porridge samples were collected from villages of Nyabula, Kikelelwa and Kigwa located in different agro-ecological zones of Tanzania. The samples were collected at three time points (time point 1, during maize harvest; time point 2, 6 months after harvest; time point 3, 12 months after harvest) over a 1-year period. Ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) was used to detect and quantify 9 mycotoxins: aflatoxin B1 (AFB1), aflatoxin B2 (AFB2), aflatoxin G1 (AFG1), aflatoxin G2 (AFG2), fumonisin B1 (FB1), fumonisin B2 (FB2), deoxynivalenol (DON), ochratoxin A (OTA) and zearaleneone (ZEN) in the samples following a QuEChERS extraction method. Eighty two percent of samples were co-contaminated with more than one group of mycotoxins. Fumonisins (FB1 + FB2) had the highest percentage occurrence in all 101 samples (100%) whereas OTA had the lowest (5%). For all three villages the mean concentration of FB1 was lowest in samples taken from time point 2. Conversely, In Kigwa village there was a distinct trend that AFB1 mean concentration was highest in samples taken from time point 2. DON concentration did not differ greatly between time points but the percentage occurrence varied between villages, most notably in Kigwa where 0% of samples tested positive. ZEN occurrence and mean concentration was highest in Kikelelwa. The results suggest that mycotoxin contamination in maize can vary based on season and agro-ecological zones. The high occurrence of multiple mycotoxins found in maize porridge, a common weaning food in Tanzania, presents a potential increase in the risk of exposure and significant health implications in children.

Development of Imaging Mass Spectrometry Analysis of Lipids in Biological and Clinically Relevant Applications

La spectrométrie de masse mesure la masse des ions selon leur rapport masse sur charge. Cette technique est employée dans plusieurs domaines et peut analyser des mélanges complexes. L’imagerie par spectrométrie de masse (Imaging Mass Spectrometry en anglais, IMS), une branche de la spectrométrie de masse, permet l’analyse des ions sur une surface, tout en conservant l’organisation spatiale des ions détectés. Jusqu’à présent, les échantillons les plus étudiés en IMS sont des sections tissulaires végétales ou animales. Parmi les molécules couramment analysées par l’IMS, les lipides ont suscité beaucoup d'intérêt. Les lipides sont impliqués dans les maladies et le fonctionnement normal des cellules; ils forment la membrane cellulaire et ont plusieurs rôles, comme celui de réguler des événements cellulaires. Considérant l’implication des lipides dans la biologie et la capacité du MALDI IMS à les analyser, nous avons développé des stratégies analytiques pour la manipulation des échantillons et l’analyse de larges ensembles de données lipidiques. La dégradation des lipides est très importante dans l’industrie alimentaire. De la même façon, les lipides des sections tissulaires risquent de se dégrader. Leurs produits de dégradation peuvent donc introduire des artefacts dans l’analyse IMS ainsi que la perte d’espèces lipidiques pouvant nuire à la précision des mesures d’abondance. Puisque les lipides oxydés sont aussi des médiateurs importants dans le développement de plusieurs maladies, leur réelle préservation devient donc critique. Dans les études multi-institutionnelles où les échantillons sont souvent transportés d’un emplacement à l’autre, des protocoles adaptés et validés, et des mesures de dégradation sont nécessaires. Nos principaux résultats sont les suivants : un accroissement en fonction du temps des phospholipides oxydés et des lysophospholipides dans des conditions ambiantes, une diminution de la présence des lipides ayant des acides gras insaturés et un effet inhibitoire sur ses phénomènes de la conservation des sections au froid sous N2. A température et atmosphère ambiantes, les phospholipides sont oxydés sur une échelle de temps typique d’une préparation IMS normale (~30 minutes). Les phospholipides sont aussi décomposés en lysophospholipides sur une échelle de temps de plusieurs jours. La validation d’une méthode de manipulation d’échantillon est d’autant plus importante lorsqu’il s’agit d’analyser un plus grand nombre d’échantillons. L’athérosclérose est une maladie cardiovasculaire induite par l’accumulation de matériel cellulaire sur la paroi artérielle. Puisque l’athérosclérose est un phénomène en trois dimension (3D), l'IMS 3D en série devient donc utile, d'une part, car elle a la capacité à localiser les molécules sur la longueur totale d’une plaque athéromateuse et, d'autre part, car elle peut identifier des mécanismes moléculaires du développement ou de la rupture des plaques. l'IMS 3D en série fait face à certains défis spécifiques, dont beaucoup se rapportent simplement à la reconstruction en 3D et à l’interprétation de la reconstruction moléculaire en temps réel. En tenant compte de ces objectifs et en utilisant l’IMS des lipides pour l’étude des plaques d’athérosclérose d’une carotide humaine et d’un modèle murin d’athérosclérose, nous avons élaboré des méthodes «open-source» pour la reconstruction des données de l’IMS en 3D. Notre méthodologie fournit un moyen d’obtenir des visualisations de haute qualité et démontre une stratégie pour l’interprétation rapide des données de l’IMS 3D par la segmentation multivariée. L’analyse d’aortes d’un modèle murin a été le point de départ pour le développement des méthodes car ce sont des échantillons mieux contrôlés. En corrélant les données acquises en mode d’ionisation positive et négative, l’IMS en 3D a permis de démontrer une accumulation des phospholipides dans les sinus aortiques. De plus, l’IMS par AgLDI a mis en évidence une localisation différentielle des acides gras libres, du cholestérol, des esters du cholestérol et des triglycérides. La segmentation multivariée des signaux lipidiques suite à l’analyse par IMS d’une carotide humaine démontre une histologie moléculaire corrélée avec le degré de sténose de l’artère. Ces recherches aident à mieux comprendre la complexité biologique de l’athérosclérose et peuvent possiblement prédire le développement de certains cas cliniques. La métastase au foie du cancer colorectal (Colorectal cancer liver metastasis en anglais, CRCLM) est la maladie métastatique du cancer colorectal primaire, un des cancers le plus fréquent au monde. L’évaluation et le pronostic des tumeurs CRCLM sont effectués avec l’histopathologie avec une marge d’erreur. Nous avons utilisé l’IMS des lipides pour identifier les compartiments histologiques du CRCLM et extraire leurs signatures lipidiques. En exploitant ces signatures moléculaires, nous avons pu déterminer un score histopathologique quantitatif et objectif et qui corrèle avec le pronostic. De plus, par la dissection des signatures lipidiques, nous avons identifié des espèces lipidiques individuelles qui sont discriminants des différentes histologies du CRCLM et qui peuvent potentiellement être utilisées comme des biomarqueurs pour la détermination de la réponse à la thérapie. Plus spécifiquement, nous avons trouvé une série de plasmalogènes et sphingolipides qui permettent de distinguer deux différents types de nécrose (infarct-like necrosis et usual necrosis en anglais, ILN et UN, respectivement). L’ILN est associé avec la réponse aux traitements chimiothérapiques, alors que l’UN est associé au fonctionnement normal de la tumeur.

Identification of protein targets of nevirapine reactive metabolites using click chemistry and mass spectrometry-based differential proteomics

Abstract : Adverse drug reactions (ADRs) are undesirable effects caused after administration of a single dose or prolonged administration of drug or result from the combination of two or more drugs. Idiosyncratic drug reaction (IDR) is an adverse reaction that does not occur in most patients treated with a drug and does not involve the therapeutic effect of the drug. IDRs are unpredictable and often life-threatening. Idiosyncratic reaction is dependent on drug chemical characteristics or individual immunological response. IDRs are a major problem for drug development because they are usually not detected during clinical trials. In this study we focused on IDRs of Nevirapine (NVP), which is a non-nucleoside reverse transcriptase inhibitor used for the treatment of Human Immunodeficiency Virus (HIV) infections. The use of NVP is limited by a relatively high incidence of skin rash. NVP also causes a rash in female Brown Norway (BN) rats, which we use as animal model for this study. Our hypothesis is that idiosyncratic skin reactions associated with NVP treatment are due to post-translational modifications of proteins (e.g., glutathionylation) detectable by MS. The main objective of this study was to identify the proteins that are targeted by a reactive metabolite of Nevirapine in the skin. The specific objectives derived from the general objective were as follow: 1) To implement the click chemistry approach to detect proteins modified by a reactive NVP-Alkyne (NVP-ALK) metabolite. The purpose of using NVP-ALK was to couple it with Biotin using cycloaddition Click Chemistry reaction. 2) To detect protein modification using Western blotting and Mass Spectrometry techniques, which is important to understand the mechanism of NVP induced toxicity. 3) To identify the proteins using MASCOT search engine for protein identification, by comparing obtained spectrum from Mass Spectrometry with theoretical spectrum to find a matching peptide sequence. 4) To test if the drug or drug metabolites can cause harmful effects, as the induction of oxidative stress in cells (via protein glutathionylation). Oxidative stress causes cell damage that mediates signals, which likely induces the immune response. The results showed that Nevirapine is metabolized to a reactive metabolite, which causes protein modification. The extracted protein from the treated BN rats matched 10% of keratin, which implies that keratin was the protein targeted by the NVP-ALK.

Speciation analysis of Arsenic in fish and rice samples using liquid chromatography-inductively coupled plasma mass spectrometry

Chemical speciation in foodstuffs is of uttermost importance since it is nowadays recognized that both toxicity and bioavailability of an element depend on the chemical form in which the element is present. Regarding arsenic, inorganic species are classified as carcinogenic while organic arsenic, such as arsenobetaine (AsB) or arsenocholine (AsC), is considered less toxic or even non-toxic. Coupling a High Performance Liquid Chromatographer (HPLC) with an Inductively Coupled Plasma Mass Spectrometer (ICP-MS) combines the power of separation of the first with the selectivity and sensitivity of the second. The present work aims at developing a method, using HPLC-ICP-MS technique, to identify and quantify the chemical species of arsenic present in two food matrices, rice and fish. Two extraction methods, ultrasound and microwave, and different settings were studied. The best method was chosen based on recovery percentages. To ensure that no interconversion of species was occurring, individual spikes of each species of arsenic were made in both matrices and recovery rates were calculated. To guaranty accurate results reference material BCR-627 TUNA FISH, containing certified values for AsB and DMA, was analyzed. Chromatographic separation was achieved using an anion exchange column, HAMILTON-PRP X-100, which allowed to separate the four arsenic species for which standards were available (AsB, dimethylarsenic (DMA), arsenite (AsIII), arsenate (AsV). The mobile phase was chosen based on scientific literature and adjusted to laboratory conditions. Different gradients were studied. As a result we verified that the arsenic species present in both matrices were not the same. While in fish 90% of the arsenic present was in the form of arsenobetaine, in rice 80% of arsenic was present as DMA and 20% as inorganic arsenic.

Exploring complex chemical systems: insights from mass spectrometry, electrochemistry and continuous cell culture

The work presented herein covers a broad range of research topics and so, in the interest of clarity, has been presented in a portfolio format. Accordingly, each chapter consists of its own introductory material prior to presentation of the key results garnered, this is then proceeded by a short discussion on their significance. In the first chapter, a methodology to facilitate the resolution and qualitative assessment of very large inorganic polyoxometalates was designed and implemented employing ion-mobility mass spectrometry. Furthermore, the potential of this technique for ‘mapping’ the conformational space occupied by this class of materials was demonstrated. These claims are then substantiated by the development of a tuneable, polyoxometalate-based calibration protocol that provided the necessary platform for quantitative assessments of similarly large, but unknown, polyoxometalate species. In addition, whilst addressing a major limitation of travelling wave ion mobility, this result also highlighted the potential of this technique for solution-phase cluster discovery. The second chapter reports on the application of a biophotovoltaic electrochemical cell for characterising the electrogenic activity inherent to a number of mutant Synechocystis strains. The intention was to determine the key components in the photosynthetic electron transport chain responsible for extracellular electron transfer. This would help to address the significant lack of mechanistic understanding in this field. Finally, in the third chapter, the design and fabrication of a low-cost, highly modular, continuous cell culture system is presented. To demonstrate the advantages and suitability of this platform for experimental evolution investigations, an exploration into the photophysiological response to gradual iron limitation, in both the ancestral wild type and a randomly generated mutant library population, was undertaken. Furthermore, coupling random mutagenesis to continuous culture in this way is shown to constitute a novel source of genetic variation that is open to further investigation.

Development of Imaging Mass Spectrometry Analysis of Lipids in Biological and Clinically Relevant Applications

La spectrométrie de masse mesure la masse des ions selon leur rapport masse sur charge. Cette technique est employée dans plusieurs domaines et peut analyser des mélanges complexes. L’imagerie par spectrométrie de masse (Imaging Mass Spectrometry en anglais, IMS), une branche de la spectrométrie de masse, permet l’analyse des ions sur une surface, tout en conservant l’organisation spatiale des ions détectés. Jusqu’à présent, les échantillons les plus étudiés en IMS sont des sections tissulaires végétales ou animales. Parmi les molécules couramment analysées par l’IMS, les lipides ont suscité beaucoup d'intérêt. Les lipides sont impliqués dans les maladies et le fonctionnement normal des cellules; ils forment la membrane cellulaire et ont plusieurs rôles, comme celui de réguler des événements cellulaires. Considérant l’implication des lipides dans la biologie et la capacité du MALDI IMS à les analyser, nous avons développé des stratégies analytiques pour la manipulation des échantillons et l’analyse de larges ensembles de données lipidiques. La dégradation des lipides est très importante dans l’industrie alimentaire. De la même façon, les lipides des sections tissulaires risquent de se dégrader. Leurs produits de dégradation peuvent donc introduire des artefacts dans l’analyse IMS ainsi que la perte d’espèces lipidiques pouvant nuire à la précision des mesures d’abondance. Puisque les lipides oxydés sont aussi des médiateurs importants dans le développement de plusieurs maladies, leur réelle préservation devient donc critique. Dans les études multi-institutionnelles où les échantillons sont souvent transportés d’un emplacement à l’autre, des protocoles adaptés et validés, et des mesures de dégradation sont nécessaires. Nos principaux résultats sont les suivants : un accroissement en fonction du temps des phospholipides oxydés et des lysophospholipides dans des conditions ambiantes, une diminution de la présence des lipides ayant des acides gras insaturés et un effet inhibitoire sur ses phénomènes de la conservation des sections au froid sous N2. A température et atmosphère ambiantes, les phospholipides sont oxydés sur une échelle de temps typique d’une préparation IMS normale (~30 minutes). Les phospholipides sont aussi décomposés en lysophospholipides sur une échelle de temps de plusieurs jours. La validation d’une méthode de manipulation d’échantillon est d’autant plus importante lorsqu’il s’agit d’analyser un plus grand nombre d’échantillons. L’athérosclérose est une maladie cardiovasculaire induite par l’accumulation de matériel cellulaire sur la paroi artérielle. Puisque l’athérosclérose est un phénomène en trois dimension (3D), l'IMS 3D en série devient donc utile, d'une part, car elle a la capacité à localiser les molécules sur la longueur totale d’une plaque athéromateuse et, d'autre part, car elle peut identifier des mécanismes moléculaires du développement ou de la rupture des plaques. l'IMS 3D en série fait face à certains défis spécifiques, dont beaucoup se rapportent simplement à la reconstruction en 3D et à l’interprétation de la reconstruction moléculaire en temps réel. En tenant compte de ces objectifs et en utilisant l’IMS des lipides pour l’étude des plaques d’athérosclérose d’une carotide humaine et d’un modèle murin d’athérosclérose, nous avons élaboré des méthodes «open-source» pour la reconstruction des données de l’IMS en 3D. Notre méthodologie fournit un moyen d’obtenir des visualisations de haute qualité et démontre une stratégie pour l’interprétation rapide des données de l’IMS 3D par la segmentation multivariée. L’analyse d’aortes d’un modèle murin a été le point de départ pour le développement des méthodes car ce sont des échantillons mieux contrôlés. En corrélant les données acquises en mode d’ionisation positive et négative, l’IMS en 3D a permis de démontrer une accumulation des phospholipides dans les sinus aortiques. De plus, l’IMS par AgLDI a mis en évidence une localisation différentielle des acides gras libres, du cholestérol, des esters du cholestérol et des triglycérides. La segmentation multivariée des signaux lipidiques suite à l’analyse par IMS d’une carotide humaine démontre une histologie moléculaire corrélée avec le degré de sténose de l’artère. Ces recherches aident à mieux comprendre la complexité biologique de l’athérosclérose et peuvent possiblement prédire le développement de certains cas cliniques. La métastase au foie du cancer colorectal (Colorectal cancer liver metastasis en anglais, CRCLM) est la maladie métastatique du cancer colorectal primaire, un des cancers le plus fréquent au monde. L’évaluation et le pronostic des tumeurs CRCLM sont effectués avec l’histopathologie avec une marge d’erreur. Nous avons utilisé l’IMS des lipides pour identifier les compartiments histologiques du CRCLM et extraire leurs signatures lipidiques. En exploitant ces signatures moléculaires, nous avons pu déterminer un score histopathologique quantitatif et objectif et qui corrèle avec le pronostic. De plus, par la dissection des signatures lipidiques, nous avons identifié des espèces lipidiques individuelles qui sont discriminants des différentes histologies du CRCLM et qui peuvent potentiellement être utilisées comme des biomarqueurs pour la détermination de la réponse à la thérapie. Plus spécifiquement, nous avons trouvé une série de plasmalogènes et sphingolipides qui permettent de distinguer deux différents types de nécrose (infarct-like necrosis et usual necrosis en anglais, ILN et UN, respectivement). L’ILN est associé avec la réponse aux traitements chimiothérapiques, alors que l’UN est associé au fonctionnement normal de la tumeur.