Rheumatoid arthritis (RA) is a chronic, heterogeneous, autoimmune disease that causes inflammation of synovial joints leading to pain, stiffness and swelling. If left untreated, RA results in irreversible joint destruction and long term disability. Initial treatment with glucocorticoids and other immunosuppressive agents suppresses inflammation. However, many of these drugs are not well-tolerated due to extensive side effects or are simply ineffective. The discovery of tumour necrosis factor-α (TNF) as a key mediator of inflammation in RA led to the development of monoclonal anti-TNF antibody therapy. Since then, other biologic drugs targeting immune pathways have been developed for RA, including interleukin-6 (IL-6) blockade, B cell depletion, and T cell co-stimulation blockade. Not all patients will respond to their first biologic drug and currently there is no way to predict which patient will respond to each different class of drug. Generally, 3 – 6 months are required to determine clinical efficacy, during which time joint inflammation proceeds. Therefore, discovering biomarkers to predict treatment response is a research priority. Biologic drugs target immune pathways. As single cell technology advances and has increasing capacity to identify subtle changes in many cell subsets, I hypothesise that studying the blood immune cell landscape will define cellular biomarker profiles relevant to each individual patient’s disease.

Lanthanide-encoded polystyrene-co-methacrylic acid (P(S-MAA)) microspheres with narrow size distributions were synthesized by two-stage dispersion polymerization. I examined how the amounts of methacrylic acid (MAA) and lanthanide (Ln) salts affect the composition of the particles formed in the reaction. Also, I performed a systematic study of Ln ion release into different aqueous solutions. In normal buffers, these particles were stable against ion leakage, even upon prolonged storage and stirring. When strong chelating agent ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DTPA) were present in buffer, the loss of Ln ions increased to 15 % after 8 weeks. A preliminary kinetic study of Ln ion incorporation was performed to help understand the particle formation mechanism.

Lanthanide-encoded polystyrene-co-methacrylic acid (P(S-MAA)) microspheres with narrow size distributions were synthesized by two-stage dispersion polymerization. I examined how the amounts of methacrylic acid (MAA) and lanthanide (Ln) salts affect the composition of the particles formed in the reaction. Also, I performed a systematic study of Ln ion release into different aqueous solutions. In normal buffers, these particles were stable against ion leakage, even upon prolonged storage and stirring. When strong chelating agent ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DTPA) were present in buffer, the loss of Ln ions increased to 15 % after 8 weeks. A preliminary kinetic study of Ln ion incorporation was performed to help understand the particle formation mechanism.

La vaccination est souvent mal perçue par la population générale. Pour rassurer cette dernière, il serait intéressant de créer une plateforme vaccinale pouvant prédire, in vitro, les risques associés à la prise d’un vaccin. L’objectif de cette thèse est de mettre au point les prémices de cette plateforme. Le principe est simple: obtenir la signature inflammatoire d’un vaccin candidat pour évaluer son innocuité. Pour cela, cette signature sera comparée à celles obtenues par des vaccins actuellement sur le marché ou induites par des pathogènes.Durant cette thèse, nous avons sélectionné une liste de biomarqueurs pouvant être utilisés pour déterminer la signature inflammatoire d’un vaccin. Pour mettre au point cette liste, nous avons utilisé différents modèles inflammatoires (VIH et ligands TLR) et la cytométrie de masse. Par la suite, nous avons mis au point des tests in vitro pour obtenir les signatures inflammatoires induites par le Vaccinia Virus ou le Modified Vaccinia virus Ankara, tous deux utilisés pour éradiquer la variole. Nous avons identifié des signatures inflammatoires spécifiques pour chacun de ces virus, à la fois chez des individus sains et chez des patients infectés par le VIH.La poursuite de ces études, par l’obtention d’un grand nombre de signatures provenant de vaccins sur le marché ou induites par des pathogènes, pourrait permettre de finaliser la mise en place de cette plateforme. En effet, l’obtention de ces dernières permettrait d’obtenir des signatures de référence qui pourraient prédire la dangerosité d’un vaccin. / Vaccination is often not well regarded by the general population. To reassure this latest, it will be interesting to set up an in vitro platform predicting the vaccine safety. The aim of this thesis is to develop the beginnings of this platform. The principle is simple, to get inflammatory signature of a candidate vaccine to evaluate it safety. For that, this signature will be compared with those obtained by vaccine currently on the market or by pathogens.During this thesis, we selected a list of biomarkers that can be used to determinate the inflammatory signature of a vaccine. To obtain this list, we used different inflammatory models (HIV and TLR ligands) and the mass cytometry. Then, we had developed in vitro test to obtain inflammatory signatures induced by Vaccinia Virus or Modified Vaccinia virus Ankara, each used to eradicate the smallpox. We identified specific inflammatory signatures for each virus, both in healthy individuals and HIV-infected humans.The continuation of these studies, by obtaining a large number of signatures coming from vaccines on the market or induced by pathogens, could make it possible to finalize the setting up of this platform. Indeed, the obtaining of the latter would make it possible to obtain reference signatures which could predict the dangerousness of a vaccine.

Les anticorps sont des corrélats de protection pour différents vaccins qui sont sur le marché. Une meilleure connaissance des modes d’action des vaccins au cours de la primo-vaccination et des rappels sont nécessaires pour améliorer ceux déjà disponibles et ceux en cours de développement.En développant un pipeline d’analyse des données de cytométrie en masse, nous avons étudié l’hétérogénéité des cellules B de macaques et établi un atlas des cellules B dans diffèrent organes.Nous avons démontré que les cellules B du sang sont enrichies au cours du temps après la primo vaccination et/ou le rappel. Quand nous comparons la réponse humorale de 2 stratégies de vaccination, nous découvrons qu’à différence du rappel précoce (2 semaines après la primo-vaccination), le rappel classique (2 mois après la primo-vaccination) permet le développement des IgA, de la maturation d’affinité, des nAbs, d’ADCC et des cellules B spécifique du vaccin. Ces résultats montrent le rôle principal du décalage entre la primo vaccination et rappel. / The exact immunological event involved in the induction of long-term humoral memory induced by vaccines remain unknown. Antibody and B lymphocyte responses are dynamics and change progressively over time after a first antigen encounter. A second immunization perturbates this continuous evolution and modifies these cells and proteins tremendously. My goal was to characterize in depth vaccine-induced B cell response in the context of prime-boost immunizations because the optimal vaccine schedule is not precise enough and we lack a clear knowledge of the mechanisms behind this assumption. I utilize a model of non-human primates (NHP) immunized with Modified Vaccinia Ankara (MVA). I was interested in different events concerning the humoral immune response induced by MVA and used complementary tools to generate high throughput data, such as mass cytometry, and serology. It was developed tools to study macaque B cells longitudinally, including vaccine-specific B cells, using high-dimensional cytometry data (by developing a mass cytometry Ab panel and analytical tools). I mapped the phenotypic diversity of B cells across relevant tissues (blood, lymph nodes, spleen, and bone marrow), analyzed the Ab and B cell subsets dynamics over time and after one or two immunizations, and compared the Ab response after a short vs. a longer delay between prime and boost. Thus, these data point to a direct role for longer delay between prime and boost that allow better maturation of the humoral immune response, providing insights into how vaccine specific memory B cells may be enhanced to drive affinity maturation in new vaccine approaches.

This thesis describes the synthesis and characterization of metal-encoded polystyrene microspheres with a narrow size distribution designed for mass cytometry-based immuno- and oligonucleotide-assays. These particles were prepared by multiple stage dispersion polymerization techniques using polyvinylpyrrolidone (PVP) as a steric stabilizer. As a cytometeric technique, mass cytometry necessitated metal-encoded microspheres to perform the same roles of fluorescent microspheres used in conventional flow cytometry. The first role of the microsphere was to be able to act as a platform (classifier microspheres) for bioassays. Secondly, the microspheres should be suitable for mass cytometry machine calibration as standards. To perform these roles, metal-encoded microspheres were required to have certain size, functionality and metal content criteria. Lanthanide elements were chosen as the metals for encoding the microspheres for their low natural abundance in biological systems and for their similar chemistry. My goal was to employ two-stage dispersion polymerization, of styrene in ethanol, to introduce the lanthanide salts along with excess acrylic acid in the second stage, one hour after the initiation. Acrylic acid deemed to serve as a ligand for the lanthanide ions, through its carbonyl group, so the lanthanide ions get incorporated into the microsphere while acrylic acid is copolymerizing with styrene. Using two-stage dispersion polymerization, I could synthesize lanthanide encoded microspheres with narrow size distribution and high lanthanide content. However the lanthanide content distributions were unexpectedly much broader than the size distribution obtained. In addition, I could not attach biomolecules to the surface of such particles. In an attempt to improve the characteristics of these microspheres, I employed modified versions of multiple stage dispersion polymerization and seeded emulsion polymerization to grow functional polymer shell on the surface of the particles prepared by dispersion polymerization. Moreover, I coated the lanthanide encoded microspheres with silica shell which enabled me to grow another layer of functional-silica. Consequently, I could use these particles as classifier microspheres for mass cytometry-based immunoassays as well as fluorescence-based oligonucleotide-assays.

This thesis describes the synthesis and characterization of metal-encoded polystyrene microspheres with a narrow size distribution designed for mass cytometry-based immuno- and oligonucleotide-assays. These particles were prepared by multiple stage dispersion polymerization techniques using polyvinylpyrrolidone (PVP) as a steric stabilizer. As a cytometeric technique, mass cytometry necessitated metal-encoded microspheres to perform the same roles of fluorescent microspheres used in conventional flow cytometry. The first role of the microsphere was to be able to act as a platform (classifier microspheres) for bioassays. Secondly, the microspheres should be suitable for mass cytometry machine calibration as standards. To perform these roles, metal-encoded microspheres were required to have certain size, functionality and metal content criteria. Lanthanide elements were chosen as the metals for encoding the microspheres for their low natural abundance in biological systems and for their similar chemistry. My goal was to employ two-stage dispersion polymerization, of styrene in ethanol, to introduce the lanthanide salts along with excess acrylic acid in the second stage, one hour after the initiation. Acrylic acid deemed to serve as a ligand for the lanthanide ions, through its carbonyl group, so the lanthanide ions get incorporated into the microsphere while acrylic acid is copolymerizing with styrene. Using two-stage dispersion polymerization, I could synthesize lanthanide encoded microspheres with narrow size distribution and high lanthanide content. However the lanthanide content distributions were unexpectedly much broader than the size distribution obtained. In addition, I could not attach biomolecules to the surface of such particles. In an attempt to improve the characteristics of these microspheres, I employed modified versions of multiple stage dispersion polymerization and seeded emulsion polymerization to grow functional polymer shell on the surface of the particles prepared by dispersion polymerization. Moreover, I coated the lanthanide encoded microspheres with silica shell which enabled me to grow another layer of functional-silica. Consequently, I could use these particles as classifier microspheres for mass cytometry-based immunoassays as well as fluorescence-based oligonucleotide-assays.

Studying lymphocyte development using mass cytometry Abstract Development of mature lymphocytes, a white blood cell subtype, is crucial for the correct function of the human immune system. Currently, developmental pathways of lymphocytes can be studied using high-throughput single-cell measurements. In particular, mass cytometry enables the study of immunologically relevant pheno- typic and functional markers on a vast scale. In this work I present my individual contribution to tviblindi, a powerful software tool for analysis of cytometric data aimed at uncovering developmental trajectories. tviblindi is a package written in R, Python and C++. It provides a means to integrate prior knowledge with data analyses grounded in graph theory and algebraic topology. tviblindi is accessible to biological researchers without background in computer science or mathematics. It is an addition to the expanding field of trajectory inference in single-cell data. Furthermore, I review current knowledge of T-cell development and conduct a tviblindi analysis thereof using human thymus and peripheral blood datasets and evaluate the results. 1

Studying lymphocyte development using mass cytometry Abstract Development of mature lymphocytes, a white blood cell subtype, is crucial for the correct function of the human immune system. Currently, developmental pathways of lymphocytes can be studied using high-throughput single-cell measurements. In particular, mass cytometry enables the study of immunologically relevant pheno- typic and functional markers on a vast scale. In this work I present my individual contribution to tviblindi, a powerful software tool for analysis of cytometric data aimed at uncovering developmental trajectories. tviblindi is a package written in R, Python and C++. It provides a means to integrate prior knowledge with data analyses grounded in graph theory and algebraic topology. tviblindi is accessible to biological researchers without background in computer science or mathematics. It is an addition to the expanding field of trajectory inference in single-cell data. Furthermore, I review current knowledge of T-cell development and conduct a tviblindi analysis thereof using human thymus and peripheral blood datasets and evaluate the results. 1

Mass spectrometry (MS) as an analytical approach could provide comprehensive identification and quantitation of the biomolecules (proteins, peptides, nucleic acids, lipids) in a cell, tissue, or organism, from biomarker discovery to prediction of response to therapy or intervention. Inductively coupled plasma mass spectrometry (ICP-MS), can determine the elemental composition of materials and has been used for below ppt levels (ppq) and better in some cases (transuranics and non-metals) to detect metals and other elements in water, soil, and air or blood and urine samples. Mass cytometry is an implementation of ICP-MS to single-cell analysis; it is based on metal isotope-tagged antibodies to quantify these bioconjugates. Imaging mass cytometry (IMC), a commercially available immunohistochemistry laser ablation-inductively coupled plasma-time-of-flight-mass spectrometry (LA-ICP-TOF-MS) system, was designed for molecular biomarkers imaging in the tissue sections (e.g., brain) through metal-tagged antibodies (typically, lanthanides). This thesis highlights the contributions of ICP-TOF-MS-based approaches towards advanced developments of mass cytometry (CyTOF) and discusses its biomedical applications for investigating neurodegenerative diseases while comparing it to other imaging modalities such as PET, MRI, Allen brain, etc. In conclusion, CyTOF, as a high-dimensional imaging tool, provides information on many clinical applications, such as hematopoiesis, transplantation, cancer, and autoimmunity.