Cancer is a serious threat to human health and is now one of major causes of death worldwide. However, the complexity of the cancer makes the development of new and specific diagnostic tools particularly challenging. A number of different strategies have been developed for biomarker discovery in cancer using microarray data. The problem that typically needs to be addressed is the scale of the data sets; we simply do not have (or are likely to obtain) sufficient data for classical machine learning approaches for biomarker discovery to be properly validated. Obtaining a biomarker that is specific to a particular cancer is also very challenging. The initial promise that was held out for gene microarray work for the development of cancer biomarkers has not yet yielded the hoped for breakthroughs. This work discusses the construction of a strategy for a systematic approach to biomarker discovery validation using lung cancer gene expression microarray data based around non-small cell cancer and in patients which either stayed disease free after surgery (a five year window) or in which the disease progressed and re-occurred. As a means of assisting the validation purposes we have therefore looked at new methodologies for using existing biological knowledge to support machine learning biomarker discovery techniques. We employ text mining strategy using previously published literature for correlating biological concepts to a given phenotype. Pathway driven approaches through the use of Web Services and workflows, enabled the large-scale dataset to be analysed systematically. The results showed that it was possible, at least using this specific data set, to clearly differentiate between progressive disease and disease free patients using a set of biomarkers implicated in neuroendocrine signaling. A validation of the biomarkers identified was attempted in three separately published data sets. This analysis showed that although there was support for some of our findings in one of these data sets, this appeared to be a function of the close similarity in experimental design followed rather than through specific of the analysis method developed.

Over the past decade, solid-state nanopores have emerged as a versatile tool for the detection and characterization of single molecules, showing great promise in the field of personalized medicine as diagnostic and genotyping platforms. While solid-state nanopores offer increased durability and functionality over a wider range of experimental conditions compared to their biological counterparts, reliable fabrication of low-noise solid-state nanopores remains a challenge. In this thesis, a methodology for treating nanopores using high electric fields in an automated fashion by applying short (0.1-2 s) pulses of 6-10 V is presented which drastically improves the yield of nanopores that can be used for molecular recognition studies. In particular, this technique allows for sub-nanometer control over nanopore size under experimental conditions, facilitates complete wetting of nanopores, reduces noise by up to three orders of magnitude and rejuvenates used pores for further experimentation. This improvement in fabrication yield (over 90%) ultimately makes nanopore-based sensing more efficient, cost-effective and accessible. Tuning size using high electric fields facilitates nanopore fabrication and improves functionality for single-molecule experiments. Here, the use of nanopores for the detection of DNA-protein complexes is examined. As proof-of-concept, neutravidin bound to double-stranded DNA is used as a model complex. The creation of the DNA-neutravidin complex using polymerase chain reaction with biotinylated primers and subsequent purification and multiplex creation is discussed. Finally, an outlook for extending this scheme for the identification of proteins in a sample based on translocation signatures is presented which could be implemented in a portable lab-on-a-chip device for the rapid detection of disease biomarkers.

Le travail présenté ici s'est penché sur les problèmes rencontrés sur ce type d'études protéomiques, et sur les solutions qui peuvent être explorées pour améliorer le débit d'évaluation des candidats biomarqueurs. Les peptides à méthionine sont généralement évités en raison de leur sensibilité à l'oxydation. Cependant, il semblait intéressant d'étudier leur modification endogène pouvant affecter les processus biologiques. Une première évaluation de l'impact de l'oxydation des apolipoproteins dans le cas de la maladie d'Alzheimer, a permis de mettre de côté ce biomarqueur potentiel, et de faire apparaître un certain nombre de problèmes liés au prélèvement et au stockage des échantillons biologiques. L'évaluation de dispositifs DBS (Dried Blood Spot) et Vivid à partir d'un panel de 32 protéines sanguines a permis de fournir une première solution envisageable pour maîtriser ces problèmes. Par la suite, un nouveau mode de quantification des peptides appelé MRM3 a été utilisé pour dépasser la complexité de la matrice biologique, et fournir une évaluation fiable des niveaux de concentration de 2 protéines plasmatiques, la C-Reactive protein et la TIMP-1, ainsi que 2 protéines urinaires, l'aquaporin-2 et la podocin. Pour améliorer la sensibilité d'analyse et réduire les coûts de solvants nécessaires aux analyses, l'évaluation d'une plate-forme de micro-chromatographie a été réalisée par comparaison à une plate-forme narrow-bore. Cette étude a permis de mettre en évidence l'impact important de l'effet matrice sur le processus analytique, nécessitant de développer de nouvelles stratégies de travail. Enfin, afin de réduire la complexité de l'échantillon, l'évaluation de cartouches d'extraction en phase solide à base de large taille de pores a été réalisé, et un protocole développé a permis d'analyser avec succès des enzymes contenus dans un échantillon de lessive commerciale. De plus, la durée nécessaire à la préparation d'échantillons biologiques a pu être fortement réduite en combinant une digestion rapide assistée par température combinée au dessalage en ligne, afin de permettre l'analyse quantitative des protéines qu'il contient seulement quelques heures après son arrivée au laboratoire / Over the past decade, interest in the use of biomarkers in clinical studies has greatly increased. Quantification of a candidate protein biomarker in complex samples (eg. plasma) requires targeted and multiplexed assays. Immunoassays are the gold standard for their quantification. However, with the need for targeted and multiplexed methods, recent developments in mass spectrometry (MS) make a viable alternative to ELISA. The present work has addressed the problems encountered in this type of proteomic studies, and solutions that can be explored to improve the workflow of candidate biomarker’s evaluation. Methionine peptides are generally avoided due to their susceptibility to oxidation. However, it seemed interesting to study how their endogenous modifications could affect biological processes. In a first time, apolipoproteins were dismissed as a potential biomarker of Alzheimer’s disease due to oxidation impact. In the same time, problems associated with biological sample collection and storage were highlighted. DBS (Dried Blood Spot) and Vivid device evaluation from a panel of 32 blood proteins has provided a first possible solution to overcome these troubles. Thereafter, a new peptide quantification method called MRM3 was used to overcome biological matrix complexity. Reliable level determinations of 2 plasma proteins (C-Reactive protein and TIMP-1) and 2 urinary proteins (aquaporin-2 and podocin) were obtained. To improve sensitivity and reduce analysis solvent costs, performances of a micro chromatography platform were compared to a narrow-bore platform. This study highlighted the significant impact of the matrix effect on the analytical process, requiring new strategie development. Finally, to reduce sample complexity, evaluation of wide pore solid-phase extraction cartridges has been achieved. A protocol was successfully developed to analyze enzymes contained in commercial laundry samples. Finally to optimize biological sample preparation time, heated-assisted digestion and online desalting step were successfully associated. Only few hours were then required for quantitative analysis

Le glioblastome est la forme la plus agressive des tumeurs du système nerveux central. Le traitement de référence consiste en l'exérèse chirurgicale, suivie d'une radiothérapie associée à une chimiothérapie concomitante et adjuvante par le témozolomide. Son bénéfice est démontré par une médiane de survie entre 12 et 14 mois. Le glioblastome est caractérisé par une population cellulaire hétérogène hautement infiltrante, angiogénique et résistante à la chimiothérapie. Dans le but d'optimiser l'effet des molécules thérapeutiques, un suivi de leur pharmacocinétique ainsi qu'une bonne caractérisation tumorale sont nécessaires. L'imagerie par désorption laser assistée par matrice en spectrométrie de masse (IMS MALDI) a été utilisée pour l'identification de marqueurs diagnostiques, pronostiques et prédictifs de réponse aux traitements. Elle a aussi permis de suivre la pharmacocinétique in situ des chimiothérapies.L'identification de protéines directement sur tissu par fragmentation en source a permis la mise en évidence de différents isotypes de tubuline, une des cibles majeures en thérapie anticancéreuse. Le couplage de cette stratégie d'identification à l'imagerie MALDI a permis d'identifier et de localiser dans des zones tumorales, des protéines impliquées dans la tumorigenèse. La distribution intra-tissulaire du bévacizumab et du témozolomide a été étudiée pour la première fois.Des marqueurs de réponse aux traitements ont ensuite été identifiés par comparaison des profils d'expression protéique de tumeurs avec et sans traitement. Ces résultats montrent l'intérêt de l'imagerie MALDI pour l'étude des chimiothérapies et permettent d'envisager son utilisation clinique future. / Glioblastoma is the most aggressive of the gliomas, a collection of tumors arising from glia or their precursors within the central nervous system. The current standard of care, comprised of surgical resection followed by radiation and the chemotherapeutic agent temozolomide, only provides patients with a 12-14 months survival period post-diagnosis. The glioblastoma is characterized by a heterogeneous population of cells that are highly infiltrative, angiogenic and resistant to chemotherapy. In order to optimize the therapy effect, a pharmacokinetic monitoring and a better understanding and characterization of tumor biology are needed. For this purpose, matrix assisted laser desorption/ionization imaging mass spectrometry imaging mass spectrometry (MALDI IMS) technology was applied to identify diagnostic, prognostic and predictive markers of therapy response; and to understand/follow the pharmacokinetic of chemotherapies. The top-down in-source decay strategy was used for protein identification directly on tissue. This strategy allowed tubulin protein isoforms distinction and identification, which is one of the main targets in cancer therapy. MALDI imaging coupled to ISD identified tumorigenesis proteins within tumor structures. Bevacizumab and temozolmide distribution was followed within brain tissue sections. For the first time a monoclonal antibody was deciphered on tissue. Finally, markers that predict therapy response were demonstrated by a comparison between protein expression profiles from tumors with and without chemotherapy treatment. These results highlight the interest of MALDI imaging for chemotherapy improvement and open the way for its use in the clinics.

Les arbovirus transmis par les moustiques Aedes représentent un problème majeur de santé publique dans les pays du Sud et certains comme la dengue et le chikungunya risquent d'émerger dans les pays du Nord. La lutte contre ces maladies repose essentiellement sur le contrôle des populations de vecteurs. Pour un meilleur contrôle de ces arbovirus, beaucoup d'efforts sont déployés pour développer de nouveaux outils. La mesure de la réponse anticorps (Ac) de l'homme contre les protéines salivaires des arthropodes a été utilisée pour évaluer son exposition aux piqûres des vecteurs et estimer le risque de transmission des pathogènes. L'objectif de notre travail a été de valider par une approche immuno-épidémiologique le concept « réponse Ac anti salive comme bio-marqueur d'exposition aux Aedes ». Nous avons également évalué la spécificité de cette réponse par rapport aux populations exposées uniquement à Ae. aegypti ou Ae. albopictus. Dans un second volet, nous avons identifié les protéines salivaires d'Ae. albopictus impliquées dans cette réponse. Et enfin, nous avons évalué la potentialité d'utiliser ce bio-marqueur comme critère d'efficacité de la lutte anti vectorielle contre Ae. albopictus. Nos résultats montrent une corrélation entre la réponse Ac anti salive et l'intensité d'exposition aux vecteurs indiquant ainsi la pertinence de son utilisation comme bio-marqueur d'exposition aux piqûres des Aedes. Nous notons une faible réaction croisée de cette réponse Ac entre la salive d'Ae. aegypti et d'Ae. albopictus. Les protéines salivaires antigéniques d'Ae. albopictus identifiées sont essentiellement impliquées dans la prise du repas sanguin. L'utilisation de ce bio-marqueur a permis de détecter la baisse de la densité vectorielle après les mesures de lutte contre Ae. albopictus, suggérant son utilité pour mesurer l'efficacité des stratégies de contrôle. L'ensemble de ces travaux contribuent à une meilleure connaissance de l'interaction de l'homme avec les Aedes. L'identification de protéines/peptides spécifiques d'espèce permettrait d'améliorer l'utilisation de ce bio-marqueur. / Aedes borne virus are considered to be public health problems in Southern countries while several such diseases like dengue and chikungunya threaten to emerge in the developed world. The control of these diseases is currently based on vector population control. Much effort is being devoted to develop new tools to control such arbovirus. Recent findings suggest that the evaluation of human antibody (Ab) response to arthropod salivary proteins is relevant to measure the level of human exposure to mosquito bites and to evaluate the risk of pathogen transmission. Using an immuno-epidemiological approach, the present study aimed to validate the concept “anti saliva Ab response, biomarker of Aedes exposure”. We evaluated the specificity of this Ab response according to populations only exposed to Ae. aegypti and Ae. albopictus, respectively. Ae. albopictus salivary proteins involved in this Ab response were also identified. We evaluated the usefulness of this biomarker for measuring the efficacy of Ae. albopictus control strategies. Our results showed a significant correlation between anti saliva Ab response and exposure level to vectors bites, thus indicating its usefulness as biomarker of Aedes exposure. We observed low Ab cross reactivity between Ae. aegypti and Ae. albopictus salivary gland extracts. The Ae. albopictus antigenic salivary proteins which were identified are mostly involved in blood feeding. The decrease of Ae. albopictus density after control measures has been detected by this biomarker, suggesting its usefulness for evaluating control strategies.This work contributes significantly to the study of human antibody response to Aedes salivary proteins which remains so far poorly documented. The identification of species specific salivary proteins/peptides should improve the use of this biomarker.

Parmi les outils existants pour l'évaluation de la qualité des milieux aquatiques, les biomarqueurs permettent de détecter précocement l'exposition et/ou les effets d'une contamination. Toutefois, en raison du manque de connaissance fondamentale de leur régulation au niveau moléculaire, peu de biomarqueurs ont été spécifiquement développés chez les invertébrés, alors que ces derniers représentent 95% de la biodiversité animale. Grâce aux récentes avancées technologiques dans le domaine du séquençage de l'information génétique et protéique, la découverte de nouvelles protéines chez ces organismes est à présent possible. Centré sur l'utilisation d'une espèce d'intérêt en écotoxicologique, l'amphipode d'eau douce Gammarus fossarum, et sur la problématique de la perturbation endocrine, ce travail doctoral a pour objectif de découvrir de nouvelles protéines impliquées dans la reproduction du gammare et de proposer des biomarqueurs spécifiques de reprotoxicité. Par une première approche protéogénomique, un important catalogue de protéines a été généré. Puis, afin d'identifier de nouvelles protéines impliquées dans la reproduction, une comparaison entre les protéomes des tissus reproducteurs mâle et femelle a été réalisée, suivi de l'étude de la dynamique du protéome au cours de différents processus physiologiques : ovogénèse, embryogénèse et spermatogénèse. Enfin, une dernière expérience sur des organismes mâles exposés à différents perturbateurs endocriniens a permis d'identifier différents candidats biomarqueurs de reprotoxicité. Cette étude ouvre la voie à des développements rapides de biomarqueurs spécifiques d'une espèce animale d'intérêt en écotoxicologie / Among the tools for assessing biologic quality of aquatic ecosystems, biomarkers are ideally suited for the early detection of contaminant exposure and/or effects. Yet, because of the lack of fundamental knowledge of their molecular regulation, few specific developments have been carried out on invertebrates even though they account for more than 95% of animal biodiversity. Thanks to recent technological advances in nucleic and proteic information sequencing, discovery of new proteins is now possible for these organisms. Focussed on the use of an ecotoxicologically relevant species, the freshwater amphipod Gammarus fossarum and the problem of endocrine disruption, this doctoral thesis aims to discover new proteins involved in gammarid reproductive function and to propose specific biomarkers of endocrine disruption. With a first proteogenomic approach, an important protein catalogue was generated. Next, to identify proteins involved in gammarid reproduction, male and female reproductive tissue proteomes were compared, followed by the study of proteome dynamics in several physiological processes: oogenesis, embryogenesis and spermatogenesis. Finally, a last experiment on male gammarids challenged with different endocrine disrupter chemicals identified several candidate biomarkers of reprotoxicity. This study paves the way for quick developments of specific biomarkers for organisms of interest in ecotoxicology

Background: Angiogenesis is the process by which new blood vessels develop from existing vasculature and is a critical step in all tumours to facilitate growth beyond a few millimetres. As this process is largely inactive in physiological circumstances in adults, it represents an attractive therapeutic target in oncology. Drugs that target the angiogenic process are classified as anti-angiogenic agents. The first anti-angiogenic drug to be approved by the FDA was bevacizumab; a recombinant humanized monoclonal antibody against VEGF. Randomised studies in colorectal cancer (and other solid malignancies) have reported prolonged progression free survival and overall survival for bevacizumab. However, standard radiological criteria, Response Evaluation Criteria In Solid Tumours (RECIST), although widely employed to assess response to therapy in clinical trials, are generally insensitive to the predominantly cytostatic effects of anti-angiogenic and other targeted therapies. Alternative methods of predicting or assessing early response to such agents are needed, particularly given the cost and toxicity implications of such treatments. However, biomarkers to aid selection of patients for anti-angiogenic therapies, including bevacizumab, remain elusive. Purpose: To investigate Dynamic Contrast Enhanced Magnetic Resonance Imaging (DCE-MRI), Diffusion Weighted Imaging (DWI) and circulating angiocytokines, measured using an ELISA multiplex, as prognostic markers in patients with metastatic colorectal cancer treated with bevacizumab and chemotherapy. Results: Seventy patients were treated. DCE-MRI and DWI parameters showed good reproducibility with coefficient of variation between 3.7 to 23% for parameters. The median progression free survival, the primary end point of the trial, was 9.3 months. The overall response rate was 44%. The clinical variables which were significant for progression free survival on univariate analysis were: performance status (p=0.005), CEA (p=0.04) and serum LDH (p=0.005). Biomarkers which were significant for progression free survival on univariate analysis were serum VEGF-A (p=0.02), serum HGF (p=0.005), sVEGFR-2 (p=0.02). In each case, low values of the biomarker were associated with improved outcome. Multivariate analysis identified Ktrans (p=0.015), performance status (p=0.008) and serum HGF (p=0.003) as the most significant predictors of progression free survival. A prolonged progression free survival was associated with a good ECOG performance status, high Ktrans and low serum HGF.Conclusions: Whilst these results are encouraging, future work is required to establish whether HGF and Ktrans are prognostic markers for metastatic colorectal cancer and their precise role in the prediction of patients likely to benefit from treatment with bevacizumab.

Currently there is no test to accurately predict stillbirth. It is proposed that better identification of placental disease in utero may aid stillbirth prediction and prevention. Pregnancies complicated by reduced fetal movement (RFM) have increased risk of stillbirth. We hypothesised that RFM is a symptom of placental dysfunction associated with adverse pregnancy outcome (APO) and that this placental abnormality can be detected antenatally and used to identify fetuses at highest-risk of APO. We tested this hypothesis by: 1) comparison of ex vivo placental structure and function between APO RFM pregnancies and their normal outcome RFM counterparts, 2) comparison of in utero estimates of placental size, vascularity, vascular and endocrine functions obtained from placental ultrasound, Doppler waveform analysis and maternal circulating placentally-derived hormone concentrations, to their ex vivo correlates and 3) examination of the predictive potential of placental biomarkers at the time of RFM.Ex vivo placentas from APO RFM pregnancies, compared to normal outcome RFM counterparts, were smaller (diameter, area, weight and volume, p<0.0001), less vascular (vessel number and density, p≤0.002), with arteries that were less responsive to sodium nitroprusside (p<0.05), and with aberrant endocrine function (reduced tissue content and/or release of human chorionic gonadotrophin (hCG), human placental lactogen (hPL) and soluble fms-like Tyrosine Kinase-1 (sFlt-1), p<0.03). Placental volume (PV) ex vivo correlated with sonographic estimated PV (p<0.004), hPL, hCG and placental growth factor (PlGF) concentrations in the maternal circulation (p<0.03). Ex vivo villous vessel number and density correlated with Doppler impedance at the umbilical artery free-loop (UAD-F, p=0.02) and intraplacental arteries (p<0.0001) respectively, whilst UAD-F impedance correlated with arterial thromboxane sensitivity (p<0.04). Examination of placental structure and function at the time of presentation with RFM identified 15 independently-predictive biomarkers. Three potential predictive models, incorporating measures of placental size (PlGF), endocrine function (sFlt-1), arterial thromboxane sensitivity and villous vascularity (UAD-F), were proposed. Using these models, sensitivity for APO was improved from 8.9% with baseline care (assessment of fetal size and gestation) to up to 37.5% at a fixed specificity of 99% (p<0.05). This series of studies shows that antenatal placental examination is possible and improves identification of pregnancies at highest risk of stillbirth in a high-risk population by up to 29%. Therefore such tests merit further development to prospectively assess their ability to predict and prevent stillbirth itself.

M.Sc. / Pollutants present in minute concentrations in aquatic environments and which possess long residence times may be accumulated by aquatic organism such as fish, resulting in adverse affects. Bioaccumulation and biomarker responses are often used to qualify and quantify pollutant exposure and effect, and for this reason form a major part of many environmental assessments. To interpret bioaccumulation and biomarker responses the physico-chemical parameters of the environment should be known. This study aimed to spatially and temporally assess the environmental partitioning of heavy metals in three South African freshwater systems, namely the Pongolapoort Dam, Olifants and Luvuvhu Rivers, and to relate these concentrations to bioaccumulation and biomarker responses in tigerfish, Hydrocynus vittatus. This is because there is relatively little known about the bioaccumulation potential and stress responses of tigerfish to pollutants and they have recently become listed as a protected species. Result from this study showed that there were few differences between seasons in terms of metal bioaccumulation in the Pongolapoort Dam with the exception of Se, Zn and Fe. Selenium and Fe concentrations were linked to concentrations found in the environment, whereas Zn was attributed to a disruption in homeostasis within the fish. Increases in MT were found during the winter months and were attributed to increased metal concentrations at this time, namely Zn and Se, whereas decreases in CEA and PC were observed at this time and were linked to depleted energy reserves, stress and a reduction in the presence of pesticides as a result of decreased runoff during the winter months. It was found in the Olifants and Luvuvhu Rivers that there were no distinct decreases in metal concentrations as the rivers flowed through the KNP, and processes such as rainfall, remobilization of sediments, distance of the study area from the source and geology played a great role in the distribution of metals. Metal concentrations in the Olifants River water, sediment and fish were, for the most part, found to be lower than previous studies, possibly due to improvement in management strategies or increased buffering of this river. Only Al and As were significantly higher in tigerfish from the Olifants River, and this was reflected in high MT concentrations. It was suggested that tigerfish from the Olifants River have developed effective mechanisms for the excretion and detoxification of heavy metals that they are exposed to as a result of extended exposure. Concentrations of AChE were also significantly inhibited in tigerfish from the Olifants River which is indicative of greater concentrations of organophosphates and carbamate pesticides than the other sites. Tigerfish from the Pongolapoort Dam had signifcantly higher levels of MT and significantly inhibited concentrations of AChE in comparison to tigerfish from the Luvuvhu River. The tigerfish from the Luvuvhu River had significantly higher concentrations of Se in muscle tissue. Tigerfish from the Luvuvhu River, also experienced stress as a result of pollution as was apparent from significantly depleted energy reserves in comparison to the other sites under study, and higher concentrations of PC and CYP1A which are typical biomarkers responding to halogenated and aromatic pesticides, such as deltamethrin and endosulfan. It was recommended that further studies be done to assess the presence of pesticides within these systems to determine the contribution of these pollutants to the state of tigerfish

Recreational abuse of the drugs cocaine, methamphetamine, and morphine continues to be prevalent in the United States of America and around the world. While numerous methods of detection exist for each drug, they are generally limited by the lifetime of the parent drug and its metabolites in the body. However, the covalent modification of endogenous proteins by these drugs of abuse may act as biomarkers of exposure and allow for extension of detection windows for these drugs beyond the lifetime of parent molecules or metabolites in the free fraction. Additionally, existence of covalently bound molecules arising from drug ingestion can offer insight into downstream toxicities associated with each of these drugs. This research investigated the metabolism of cocaine, methamphetamine, and morphine in common in vitro assay systems, specifically focusing on the generation of reactive intermediates and metabolites that have the potential to form covalent protein adducts. Results demonstrated the formation of covalent adduction products between biological cysteine thiols and reactive moieties on cocaine and morphine metabolites. Rigorous mass spectrometric analysis in conjunction with in vitro metabolic activation, pharmacogenetic reaction phenotyping, and computational modeling were utilized to characterize structures and mechanisms of formation for each resultant thiol adduction product. For cocaine, data collected demonstrated the formation of adduction products from a reactive arene epoxide intermediate, designating a novel metabolic pathway for cocaine. In the case of morphine, data expanded on known adduct-forming pathways using sensitive and selective analysis techniques, following the known reactive metabolite, morphinone, and a proposed novel metabolite, morphine quinone methide. Data collected in this study describe novel metabolic events for multiple important drugs of abuse, culminating in detection methods and mechanistic descriptors useful to both medical and forensic investigators when examining the toxicology associated with cocaine, methamphetamine, and morphine.