No description available.

En recherche clinique ou environnementale, les biomarqueurs protéiques présentent un intérêt croissant. Bien que les immuno-dosages restent les méthodes de référence pour leur quantification, les récentes avancées en spectrométrie de masse (MS) font de cette technique une alternative crédible à l’ELISA. Ce travail apporte quelques éléments méthodologiques pour repousser certaines limitations de la MS. D’abord, deux dosages ont été proposés. Celui réalisé chez G. fossarum représente le premier exemple de dosage de la Vitellogénine chez un invertébré par LC-MS/MS. L’un des défis de la méthode présentée est de doser spécifiquement une protéine dans un organisme dont le génome est majoritairement inconnu. Le second dosage concerne les peptides contenant une méthionine. Nous avons développé un protocole d’oxydation des méthionines afin de s’affranchir du biais lié à leur oxydation partielle. Cette méthode a ensuite été appliquée à une protéine impliquée dans la maladie d’Alzheimer (l’Apolipoprotéine E4) dans une cohorte de 673 plasmas. Ce dosage est à ce jour l’une des plus grandes études réalisées par LC-MS/MS et montre toute la robustesse de cette approche. Enfin, l’influence de la phase mobile sur la sensibilité des dosages de peptides a été étudiée : d’abord en phase inverse, où le méthanol est une bonne alternative à l’acétonitrile ; ensuite en HILIC, où les difficultés liées à l’étude d’ions multichargés en milieu majoritairement organique ont été abordées. Les problèmes liés à la capacité de charge des colonnes ont également été soulevés. La chromatographie HILIC reste prometteuse pour la quantification de peptides puisqu’un facteur dix en sensibilité peut être apporté. / Both in clinical and environmental research, protein biomarkers are of growing interest. Although immunoassays are the gold standard for their quantification, recent advances in mass spectrometry (MS) make this technique a viable alternative to ELISA. This work provides some methodological elements to eliminate some limitations of the MS approach. First, two assays have been proposed. The first one achieved for G. fossarum represents the first example of quantification of vitellogenin in an invertebrate by LC-MS/MS. One of the challenges of the presented method is to specifically assay a protein in an organism whose genome is largely unknown. The second assay relates to methionine-containing peptides. A protocol was developped for total oxidation of methionines in order to overcome the bias due to their partial oxidation. This method was then applied to a protein involved in Alzheimer's disease (Apolipoprotein E4) in a cohort of 673 plasma samples. This assay is to date one of the largest study carried out by LC-MS/MS and shows all the robustness of this approach. Lastly, the influence of the mobile phase on the sensitivity of peptides assays was studied: first in reversed phase, where methanol is a good alternative to acetonitrile; then in HILIC, where the difficulties associated with the study of multicharged ions in a mainly organic content were discussed. Problems related to the carrying capacity of the columns were also raised.

The contamination of the environment, accidental or intentional, in particular with chemical toxins such as industrial chemicals and chemical warfare agents has increased public fear. There is a critical requirement for the continuous detection of toxins present at very low levels in the environment. Indeed, some ultra-sensitive analytical techniques already exist, for example chromatography and mass spectroscopy, which are approved by the US Environmental Protection Agency for the detection of toxins. However, these techniques are limited to the detection of known toxins. Cellular expression of genomic and proteomic biomarkers in response to toxins allows monitoring of known as well as unknown toxins using Polymerase Chain Reaction and Enzyme Linked Immunosensor Assays. However, these molecular assays allow only the endpoint (extracellular) detection and use labels such as fluorometric, colorimetric and radioactive, which increase chances of uncertainty in detection. Additionally, they are time, labor and cost intensive. These technical limitations are unfavorable towards the development of a biosensor technology for continuous detection of toxins. Federal agencies including the Departments of Homeland Security, Agriculture, Defense and others have urged the development of a detect-to-protect class of advanced biosensors, which enable environmental surveillance of toxins in resource-limited settings. In this study a Surface-Enhanced Raman Spectroscopy (SERS) immunosensor, aka a SERS-linked immunosensor assay (SLISA), has been developed. Colloidal silver nanoparticles (Ag NPs) were used to design a flexible SERS immunosensor. The SLISA proof-of-concept biosensor was validated by the measurement of a dose dependent expression of RAD54 and HSP70 proteins in response to H2O2 and UV. A prototype microchip, best suited for SERS acquisition, was fabricated using an on-chip SLISA to detect RAD54 expression in response to H2O2. A dose-response relationship between H2O2 and RAD54 is established and correlated with EPA databases, which are established for human health risk assessment in the events of chemical exposure. SLISA outperformed ELISA by allowing RISE (rapid, inexpensive, simple and effective) detection of proteins within 2 hours and 3 steps. It did not require any label and provided qualitative information on antigen-antibody binding. SLISA can easily be translated to a portable assay using a handheld Raman spectrometer and it can be used in resource-limited settings. Additionally, this is the first report to deliver Ag NPs using TATHA2, a fusogenic peptide with cell permeability and endosomal rupture release properties, for rapid and high levels of Ag NPs uptake into yeast without significant toxicity, prerequisites for the development of the first intracellular SERS immunosensor.

Along with proteins, a myriad of different molecular biomarkers, such as post-translational modifications and autoantibodies, could be used in an attempt to improve disease detection and progression. In this thesis, I build on several iterations of the proximity ligation assay to develop and apply new adaptable methods to facilitate detection of proteins, autoantibodies and post-translational modifications. In paper I, we present an adaptation of the solid-phase proximity ligation assay (SP-PLA) for the detection of post-translational modification of proteins (PTMs). The assay was adapted for the detection of two of the most commons PTMs present in proteins, glycosylation and phosphorylation, offering the encouraging prospect of using detection of PTMs in a diagnostic or prognostic capacity.  In paper II, we developed a variant of the proximity ligation assay using micro titer plate for detection and quantification of protein using optical density as readout in the fluorometer, termed PLARCA. With a detection limit considerably lower than ELISA, PLARCA detected femtomolar levels of these proteins in patient samples. In paper III, we aim to compare detection values of samples collected from earlobe capillary, venous plasma, as well as capillary plasma stored in dried plasma spots (DPS) assessed with a 92-plex inflammation panel using multiplex proximity extension assay (PEA). Despite the high variability in protein measurements between the three sample sources, we were able to conclude that earlobe capillary sampling is a suitable less invasive alternative, to venipuncture. In paper IV, we describe the application of PLARCA and proximity extension assay (PEA) for the detection of GAD65 autoantibodies (GADA). Thus, offering highly sensitive and specific autoimmunity detection.