Immune-mediated inflammatory diseases (IMID) represent a group of ostensibly unrelated, chronic and highly disabling diseases that preferentially affect different organ systems. IMID are assumed to manifest as a result of the accumulation of genetic, environmental and immunological factors. A fundamental commonality between IMID is the idiopathic nature of disease, and moreover, substantial similarities are apparent in disease etiopathogenesis. The complex assemblage of microbes and their genes that exists within and on the human body, collectively known as the microbiome has emerged as a critical factor in human health and, altered microbial populations within the gastrointestinal tract lumen and mucosa have been linked to several IMID. Accordingly, we conducted several studies investigating the association of the gut microbiome with IMID. Our main study investigated differences in the microbial profile and functional potential of multiple IMID utilizing 16S rDNA amplicon sequencing and analysis of stool. We also investigated the mucosal-associated microbiome in IBD to characterize the microbial populations and their functions residing in distinct gastrointestinal compartments from inflamed and noninflamed mucosa. We also explored a potential environmental factor; specifically assessing whether microbes present in drinking water in low or high incidence areas of IBD might contribute to disease etiology. The findings of these studies are manifold. First, we show important differences of the stool microbial profile in IMID. In doing so, we were able to identify distinct states of gut dysbiosis and have revealed numerous microbes that are consistently or uniquely disproportionate between IMID. Second, we have shown the microbial profile associated with inflamed and noninflamed mucosa and have reported that a localized dysbiosis is not observed in the presence of inflammation. Third, we have revealed that distinct gastrointestinal compartments are comprised of similar microbial communities. Lastly, we have reported the drinking water microbiome to differ between low and high incidence areas of IBD, thus suggesting a potential role in IBD etiology. Understanding the role of the gut microbiome in human disease will enable the development and application of more appropriate therapeutic strategies that specifically target microbes within the gut. / May 2017

La polyarthrite rhumatoïde (PR) est une maladie auto-immune qui mène à une inflammation chronique et à une destruction progressive des articulations. Les effecteurs principaux de cette pathologie sont les synoviocytes de type fibroblastique (FLS). Ces derniers utilisent les invadosomes, des structures riches en actine et en métalloprotéases, afin de dégrader la matrice extracellulaire (ECM). Ce phénotype pro-destructif résulte d’une activation des FLS par différents facteurs de croissance, dont le PDGF et le TGF-β. Les récepteurs à activité tyrosine kinase, dont le PDGFR, sont impliqués dans la pathogenèse de plusieurs maladies, incluant le cancer et la PR. Une activation de ces récepteurs peut mener, entre autres, à la survie, à la différenciation et à la prolifération des cellules. L’étude présentée dans ce mémoire montre que parmi les RTK les plus communs, le PDGFR est spécifiquement phosphorylé chez les cellules synoviales de patients atteints de PR, contrairement aux cellules de patients non arthritiques ou atteints d’arthrose. De plus, l’activation du PDGFR résulte en une augmentation de la formation d’invadosomes par les FLS. Nous avons aussi démontré que la formation d’invadosomes par le PDGFR nécessite l’activation de la voie de signalisation PI3K/Akt faisant intervenir les isoformes α et δ de la PI3K. De plus, l'inhibition de l’activation du PDGFR ou la neutralisation du PDGF endogène inhibe la formation des invadosomes et la dégradation de l'ECM par les synoviocytes, ce qui suggère la présence d'une boucle d'activation autocrine impliquant le PDGF. Parmi les isoformes du PDGF, nous avons démontré que le PDGF-B est exprimé de façon significativement plus élevée dans les synoviocytes provenant de patients atteints de PR. Nos données indiquent également une association entre le PDGF et le TGF-β dans la formation des invadosomes. Cette dernière implique la production autocrine de ligands du PDGFR induite par le TGFβ via la signalisation TβR1/Smad et PI3K/Akt. L’inhibition des isoformes de PI3K de classe I indique que le PI3Kα est impliquée de façon sélective dans l'expression de PDGF-B. Ces résultats démontrent que le PDGFR est un RTK nécessaire au phénotype destructeur des cellules synoviales d’arthrite. Ils fournissent aussi des preuves d'une association entre le TGF-β et le PDGFR dans la formation d’invadosomes chez les synoviocytes de patients atteints de la PR. / Abstract : Rheumatoid arthritis (RA) is an autoimmune disease that leads to chronic inflammation and progressive joint destruction. The main effectors of this pathology are fibroblast-like synoviocytes (FLS). They use invadosomes, actin-rich structures that concentrate metalloproteinases to degrade the extracellular matrix (ECM). This pro-destructive phenotype is due to the activation of FLS by various growth factors, including PDGF and TGF-β. Receptor tyrosine kinases, including PDGFR, are involved in the pathogenesis of several diseases, including cancer and RA. Activation of these receptors may lead to cell survival, differentiation and proliferation. The study presented in this thesis shows that among the most common RTKs, PDGFR is specifically phosphorylated in synovial cells of RA patients, unlike cells of non-arthritic or osteoarthritic patients. In addition, activation of PDGFR results in an increase in invadosome formation by FLS. We also shown that formation of invadosome by PDGFR requires the activation of the signaling pathway PI3K/Akt, that specifically involves the α and δ isoforms of PI3K. In addition, inhibition of PDGFR activation or neutralization of endogenous PDGF inhibits the formation of invadosomes and the degradation of the ECM by synoviocytes, suggesting the presence of an autocrine activation loop involving PDGF. Among the PDGF isoforms, we demonstrate that PDGF-B expression is significantly higher in synoviocyte cell lines from RA patients. Our data also indicates an association between PDGF and TGF-β for invadosome formation that involves autocrine production of PDGF-B induced by TGF-β through the Smad/T β R1 and PI3K/Akt pathways. Inhibition of class I PI3K isoforms indicates that PI3K α is selectively involved in the expression of PDGF-B. These results demonstrate that PDGFR is an RTK necessary for the pro-destructive phenotype of RAFLS. They also provide evidence of an association between TGF-β and PDGFR in invadosome formation by synovial cells from RA patients.

N-linked glycosylation is the most common post-translational modification (PTM) of proteins that exist in nature. N-glycosylation and change in cells serve as a criterion to monitor the activity of developmental stages and diseases severity. Currently, there is an increasing application of mass spectrometry on glycoprotein for malicious, chronic or acute diseases, such as cancers, rheumatoid arthritis (RA) or influenza. In this dissertation, several mass spectrometric assays have been utilized to, quantitatively and qualitatively, characterize protein N-glycosylation at the glycan, glycopeptide and peptide levels. The goals are to identify serum-based RA biomarker (Chapter 2), or to determine possible glycan structures from monoclonal antibody (Chapter 3), or comprehensively to study one influenza glycoprotein, hemagglutinin (Chapter 4). In Chapter 2, LC-MS/MS with CID as MS 2 is the primary technique that is applied to collect raw data for RA biomarker screening; western blot is the verification method for newfound biomarkers. This mass spectrometry based comparative analysis of N-glycoprotein in RA and healthy patients’ sera reveal 41 potential biomarkers for RA that can be applied in clinical research. Chapter 3 describes another LC-MS/MS based method developed for the structural analysis of N-glycan released from the monoclonal antibody, immunoglobin G. Higher-energy collision dissociation (HCD) was the surprior technique utilized to identify glycopeptide fragments. The results show that 19 and 23 N-glycan structures were determined from standard and modified mAb samples respectively by using SimGlycan software, while 38 and 35 glycan structures were recognized by manually mapping respectively. 13 N-glycoforms, out of 26 overlapped glycan structures, were identified with significant alterations by comparing standard sample (sample A) and modified mAb (sample B) utilizing our method. In Chapter 4, we comprehensively studied hemagglutinin by using LC-MS/MS and MALDI from both proteomic perspective and glycomics prospective. After confirmed and verified protein sequence and glycosylation sites, galactose-specific quantitation was performed with exoglycosidase digestion combined HPLC with fluorescence detection. The MALDI-MS/MS based method was utilized to confirm glycan structures. The results in this dissertation provide insights into the significance of protein glycosylation alterations as RA biomarkers, and these quantitative methods can be reapplied to any other disease biomarkers screening for clinical researchers.

The Human Leukocyte Antigen (HLA)-B27 is a Major Histocompability Complex (MHC) class I antigen that is strongly associated with development of a group of closely related arthritic diseases, collectively known as the spondyloarthropathies (SpA). However, the mechanism by which HLA-B27 confers this susceptibility is unclear. Studies have shown that HLA-B27 heavy chains can form classical heterotrimers associated with peptide and β2-microglobulin (B27HT), and also non-classical heavy chain homodimers (B27₂). B27₂ assemble intracellularly during maturation and are also expressed at the cell surface following endosomal recycling of B27HT. A pathogenic role for B27₂ has been proposed in two of the current theories of pathogenesis: the B27 homodimer theory and the B27 misfolding and UPR theory. Yet, determinations of the extent, distribution, and triggers of B27₂ expression, as well as the functional consequences of its receptor interactions in AS pathogenesis, have been hampered by the lack of a specific detection reagent. Therefore, to investigate the role of B27₂ in AS, we generated a novel antibody to B27₂ – HD6 – using phage display technology, which binds to in vitro refolded B27₂ but not B27HT complexes by ELISA. This thesis provides evidence that HD6-reactive molecules, which include B27₂, are expressed at the cell surface in both cell lines and in the context of a disease setting. Recognition is B27-specific and strongly correlated with the magnitude of B27 expression, which could account for the lack of staining in some cell subsets. Moreover, staining was comparable in cell lines expressing the disease-associated B*27:05 and the less disease-associated subtype B*27:09. In addition, I have shown cells expressing physiologic levels of B27, including EBV-transformed BCLs and AS patient PBMCs, are capable of expressing the HD6 epitope upon low pH treatment. Interestingly, these ‘acid-inducible HD6’ molecules were absent from cells lacking a functional PLC. Finally, I have shown that HD6-reactive molecules can derive from pre-existing folding B27 molecules at the cell surface, which may be inhibited by the addition of exogenous B27-binding peptides. These findings are consistent with a mechanism of pathogenesis involving the surface expression and recognition of B27₂ and/or other aberrantly folded forms of B27, as proposed in the homodimer theory. HD6 will be a powerful tool to address the potential pathogenic role of B27₂ in SpA and may additionally have therapeutic potential.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Dans la prise en charge de la polyarthrite rhumatoïde (PR), l’identification de biomarqueurs associés à un diagnostic, un pronostic mais surtout à une bonne réponse thérapeutique est un des enjeux de la prochaine décennie, d’autant que de nombreux outils sont maintenant disponibles grâce à l’étude du génome, du transcriptome et du protéome. Au cours de mon travail de thèse, je me suis intéressée à l’identification de différentes classes de biomarqueurs prédictifs de la réponse au traitement par biothérapies.Tout d’abord par une approche protéomique, j’ai identifié une combinaison de biomarqueurs protéiques sériques, MCP-1 et EGF, permettant à l’initiation du traitement par étanercept (anti-TNFα), puis par rituximab (anti-CD20), de prédire la réponse clinique à 3 mois. En parallèle, toujours chez des patients PR traités par rituximab, j’ai recherché un biomarqueur cellulaire par cytométrie de flux. J’ai ainsi pu montrer que la densité de CCR5 à la surface des lymphocytes T CD4+ circulants est faible chez les patients PR . Celle-ci est corrélée positivement à l’activité de la maladie et négativement au taux intracellulaire d’ARNm de CCR5. Trois mois après l’initiation du traitement, la densité de CCR5 à la surface des lymphocytes T CD4+ circulants augmente proportionnellement à la diminution de l’activité de la maladie. J’ai également étudié l’intérêt de biomarqueurs génétiques. Tout d’abord, en analysant le profil d’expression de 723 micro(mi)ARNs dans le sang de patients PR, j’ai montré que l’expression de 37 miARNs était dérégulée par rapport à des donneurs sains. Par ailleurs, j’ai montré que le niveau d’expression de miR-125b dans le sang des patients PR à l’initiation du traitement par rituximab permet de prédire la réponse à 3 mois. J’ai enfin exploré les polymorphismes de gènes de cytokines et de récepteurs aux cytokines afin de prédire la réponse au traitement par rituximab à 6 mois chez 63 patients atteints de PR active. Douze polymorphismes de nucléotides uniques (SNPs) ont été génotypés et ont permis d’identifier 2 SNPs du facteur de croissance transformant beta 1 (TGFb1) codon 25 et codon 10 prédictifs d’une bonne réponse au rituximab.Je me suis aussi intéressée à la thérapie génique qui est un outil thérapeutique pour délivrer des agents anti-TNF dans la PR. En effet le transfert de gène permet à l’organisme de synthétiser in situ la protéine médicament et d’éviter des administrations répétées comme c’est le cas avec les biothérapies. Le défi de demain réside plus dans le développement de vecteurs fiables et efficients. Dans un premier travail réalisé dans l’équipe de recherche du Pr Hirsch à Pittsburgh (E.U), j’ai évalué in vitro l’intérêt d’un virus adéno-associé recombinant de sérotype 2 (rAAV2) contenant un ARN double brin pour le transfert de gène dans les synoviocytes humains. Dans un contexte inflammatoire, celui-ci s’est révélé efficace lorsqu’associé à un inhibiteur du protéasome, le zLLL. Lors d’un deuxième stage effectué au sein du laboratoire du Pr Jorgensen (Montpellier), j’ai évalué le potentiel thérapeutique d’un rAAV de sérotype 5 (rAAV5) exprimant un petit ARN interférant ciblant le TNF-α dans un modèle expérimental d’arthrite. L’inhibition du TNF-α a été validée in vitro sur des macrophages murins, puis in vivo dans le modèle murin d’arthrite au collagène, après injection dans les articulations arthritiques. Depuis la fin des années 90, l’avènement des biothérapies a permis de bouleverser l’évolution de la PR. Les biomarqueurs, en particulier ceux permettant le suivi des traitements, sont des outils de choix à développer pour notre pratique clinique courante afin de choisir d’emblée le traitement le plus efficace et le mieux toléré pour chaque patient. D’autres thérapies innovantes, telles que la thérapie génique, s’appuient sur les succès des biothérapies pour permettre d’autres avancées en choisissant d’emblée les cibles les plus pertinentes. / Rheumatoid arthritis (RA) is a chronic inflammatory disease. The effective use of biologics, which block key molecules involved in the pathogenesis of RA, has dramatically improved the treatment of this chronic disease over recent years. However, for at least one-third of patients with RA biologic treatments will produce an inadequate response. Therefore, the use of predictive biomarkers of response to identify individuals who are likely to respond to specific treatments will provide benefit. An individualised approach will allow patients to receive effective treatment without unnecessary exposure to potentially toxic side effects.During my thesis, I identified predictive biomarkers in RA patients treated with biologics by using proteomics, genetics and cellular biomarkers.Genen therapy could be used to optimise drug administration by avoiding repetitive administration. I validated the interest of a recombinant adeno-associated virus in RA synovial fibroblasts.

Autor: Bc. Veronika Sýkorová Title: Comparative analysis of the effect on disease-modifying drugs and biological therapy in functional ability in patients with rheumatoid arthritis. Objective: The aim of the thesis is to compare the effect of disease-modifying drugs and biological therapy on quality of life using the disability index, which is achieved by evaluating the HAQ, grip strength the small muscles of the hand, which is tested a hand dynamometer and standing stability, which is detected by measuring on stabilometric platform. Methods: This is a pilot study using subjective and objective examination. Stabilometric and dynamometric examination and the Czech version of the Stanford Health Assessment Questionnaire validated by Rheumatology Institute in Prague 2010 were used to the analysis. Evaluation of the collected data was done using two-way analysis of variance with repetition. Results: Biological therapy and disease-modifying antirheumatic drugs have significant impact on quality of life, the strength of the small muscles of the hand and standing stability in patients with rheumatoid arthritis. Disease-modifying antirheumatic drugs have reached significant results than the biological therapy in quality of life, forces the small muscles of the right hand and standing stability. Biological...

Two novel B cell populations were characterized in peripheral blood of patients with common variable immunodeficiency and healthy controls were observed using flow cytometry in the study supported by the grant IGA MZ ČR NKT11414-3. These B cell populations were defined as CD19+ CD27- CD21+ CD38low CD24+ IgM+ FO I and CD19+ CD27- CD21+ CD38low CD24++ IgM++ cells. Since none of found populations has ever been described, the aim of this thesis was to characterize these populations with focus on analysis of variable regions of the heavy chains of immunoglobulins and genes coding proteins participating in the process of VHDHJH formation (Rag 1, Rag 2, and TdT) produced by cells of these populations. Flow cytometry, single cell sorting, single-cell RT-PCR, IgVH, Rag 1, Rag 2, and TdT specific PCR amplification and cycle sequencing were employed to perform the molecular analysis in individual B lymphocytes. Both populations in two patients with common variable immunodeficiency, two healthy controls, and in two patients with autoimmune diseases - rheumatoid arthritis and systemic lupus erythematosus (as the disease control) - were examined. Finally, the statistical analysis was used to evaluate the differences in expression of variable regions of the heavy chains of immunoglobulins and in Rag1 and 2, and...

Rheumatoid arthritis (RA) is a chronic autoimmune disease that is associated with formation of autoantibodies, activation of inflammatory cascade and up-regulation of several cytokines. These processes lead to persistent synovial inflammation, joint damage and systemic manifestations. The aim of this diploma thesis is to characterize the role of a novel cytokine interleukin-20 (IL-20) in the pathogenesis of RA and to investigate its involvement in different stages of the disease as a potential surrogate biomarker. In this work, several methods including Enzyme-Linked Immunosorbent Assay (ELISA), Immunohistochemistry and Real-Time quantitative Polymerase Chain Reaction (RT-qPCR) have been employed. We demonstrated increased expression of IL-20 in the synovial tissue of RA compared with control osteoarthritis (OA) patients. Along with the up-regulation at sites of inflammation, concentrations of IL-20 were higher in the synovial fluid compared with circulating levels of IL-20. Furthermore, serum and synovial fluid IL-20 levels significantly correlated with RA disease activity. Synthesis of IL-20 was significantly increased in peripheral blood mononuclear cells (PBMCs) and synovial fibroblasts upon stimulation with some TLR ligands and pro-inflammatory cytokines. Although not regulating PBMCs functions in...

Charles University in Prague Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Jana Jeřábková Supervisor: Doc. PharmDr. Petr Pávek, Ph.D. Title of diploma thesis: Interaction of selected anthocyanidins with farnesoid X receptor Human farnesoid X receptor (FXR) is a member of nuclear receptor superfamily that act as ligand-activated transcription factors. FXR binds to specific regulatory DNA regions and induces expression of many target genes. These regulated genes are involved in bile acid metabolism and transport, maintaining blood lipids, liporoteins and glucose homeostasis and also contribute to maintain intestinal bacterial balance, hepatoprotection and liver regeneration. The interest of recent studies is to test the range of FXR ligands for treatment and prevention of many diseases such as cholestais, cholesterol gallstone disease, steato-hepatitis, dyslipidemia, atherosclerosis, type 2 diabetes mellitus, metabolic syndrome, liver cancer and other forms of cancer such as breast cancer. In this experimental diploma thesis we are focused on testing of potencial ligands of human farnesoid X receptor from the group of natural plant pigments anthocyanidins (cyanidin, delphinidin, malvidin, pelargonidin, peonidin and petunidin) using the human hepatoma cell line...