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.

A cancer drug's effectiveness is contingent upon on its ability to reach all parts of the tumor. The distribution of drug in the tumor depends on several transport processes and depends on the physicochemical properties of the drug. These factors can lead to highly heterogeneous distributions of drug in the tumor interstitial space, leaving parts of the tumor unreached, and make it difficult to predict cellular exposure and understand its dependence on key system parameters. Theoretical models are powerful tools that can provide insight by simulating conditions that cannot be achieved or observed experimentally. Here, a Green's function method is utilized to simulate three-dimensional time-dependent diffusion and uptake of drugs in solid tumors with realistic vascular geometry. Regimes dependent on the time scales for transport are used to determine whether spatial and temporal effects must be resolved to predict cellular exposure. Simulations are performed to show the relationship between the plasma pharmacokinetics and cellular exposure for these regimes. Steep gradients in concentration arise when time scales for diffusion and uptake are comparable, implying that models based on well mixed compartments are inaccurate. Effects of linear and nonlinear kinetics of drug uptake on cellular exposure are demonstrated. The drug doxorubicin is commonly used against solid tumors. Cellular exposure to doxorubicin is complicated in vivo by its transport and physicochemical properties. The Green's function method is used to describe the in vivo transport and kinetics of doxorubicin, using parameters derived from in vitro results. Simulations show agreement with observed in vivo distributions of doxorubicin in tumor tissue as well as in vitro kinetics, and provide a link between the two types of experimental observations. The method is applied to the class of cancer drugs called antibody-drug conjugates (ADCs) which consist of a humanized antibody conjugated to extremely toxic small molecular weight drugs. ADCs exhibit complex in vivo kinetics dependent on many design parameters. A phenomenon exhibited by ADCs is the bystander effect, i.e. non-targeted cell killing, which is difficult to analyze based on in vivo observations. Simulations results agree with the observed in vivo distribution of ADCs in tumor tissue and with experimentally observed bystander effects. In summary, the the models presented here provide a novel approach for simulating the complex transport and cellular uptake kinetics exhibited by several cancer drugs. The models give a mechanistic basis for predicting cellular exposure to drugs which can aid, explain, and direct experimental approaches for improving cancer treatment.

B-lymphocytes have traditionally been thought to contribute to immunity and autoimmune disease through terminal differentiation into plasma cells that secrete antibody. However, studies in mice and recent clinical studies have demonstrated that genetically altered B-cell function and B-cell-targeted therapies can significantly affect autoimmune diseases that were predominantly thought to be T-cell-mediated. B-cell depletion in mouse models of disease has also led to the identification of alternative B-cell effector functions that regulate normal immune responses and autoimmune disease. This review highlights multiple B-cell effector mechanisms, including the promotion of cellular immunity, the negative regulation of immune responses, and the production of pathogenic antibodies. / Dissertation

Neutralising antibodies and antigen-specific B cells are important for protection against influenza A virus. However, the antigenic evolution of influenza A viruses has made a continuing challenge to the design of vaccine and the public health. The ability to generate cross-reactive response against influenza remains unclear in human. It is important to explore the antibody and B cell repertoire at single cell level. The pandemic H1N1 and seasonal influenza vaccine induced robust antibody response in adults. However, pre- or co-vaccination with the seasonal vaccine led to a significantly reduced antibody response to pandemic H1N1 virus. Whether this interference has impact on subsequent infection rates remains undetermined. There observed substantial cross-reactive antibody response upon vaccination, as measured by HI, MN and B cell ELISpot assays. The antibody recognizing conserved proteins could be the main component of cross-reactivity against influenza A strains and subtypes. A significant expansion of influenza-specific MBC was observed after infection. Crossreactive response was also noted in the MBC response. Importantly, a robust early-phase ASC response was detected in the peripheral blood upon influenza vaccination or infection. The size of ASC response significantly correlated with serum HI, MN and anti-HA IgG titre three weeks after vaccination. The sequence analysis revealed that early-phase ASC accumulated high level of somatic mutations on Ig variable region and affinity maturation, as well as anti-influenza mAb, which suggested their origin from pre-existing MBC. Eight anti-influenza mAb were made from early-phase ASC, including one high-titre virus-neutralising HA1-specific, two other HA1-specific, one cross-reactive HA2-specific, and four cross-reactive NP-specific antibodies, indicating of the broad diversity of ASC repertoire. In conclusion, this study demonstrated the properties of antibody and B cell responses to influenza A virus at serological, cellular and sequence level. The virus-neutralising and cross-reactive mAb derived from ASC could have therapeutic potential and their analysis might direct the vaccine design in the near future.

Aseptic osteolysis is a major complication to total joint arthroplasty requiring several thousand people a year to have to undergo revisions of their joint prosthesis. The formation of the interfacial membrane has been associated with aseptic osteolysis leading to the failure of all types of total joints. Recent evidence suggests that RANKL, a potent activator of bone reabsorption, is present in the interfacial membrane. Prior research in this laboratory to determine the source of RANKL in the interfacial membrane has revealed the presence of intense areas of RANKL concentration in the membrane. These areas of RANKL concentration correspond to multiple nuclei and a distinct cellular structure in the tissue as determined through light microscopy. This structure either represents a multi-nucleated giant cell or a cluster of cells that express high concentrations of RANKL. These following studies attempted to characterize this cell and determine its lineage.The results of these studies show that the RANIU producing anomaly appears multi-nucleated in all examples with a RANKL staining pattern that makes it appear as a multi-nucleated cell. Furthermore this RANIU positive giant cell (RPGC) stains negative for markers typically seen on myeloid cells, osteoclasts, and osteoblasts. This RPGC does however stain very well for fibroblast markers and the inflammatory cytokines TNF-α, IL-1β, and IL-6. The most interesting result from these studies revealed that this cell was positive for cytomegalovirus and expressed high concentrations of TNF-a converting enzyme (TACE). These data lead to a hypothesis as to how this cell might form and how large an impact it might play in the interfacial membrane with respect to aseptic bone reabsorption.

L'hémophilie A (HA) est une maladie hémorragique héréditaire due au déficit en facteur FVIII (FVIII) de la coagulation. Le traitement préventif de l'HA est basé sur des injections répétées de FVIII. Une réponse immunitaire anti-FVIII peut se développer secondairement au traitement, mettant en jeu des anticorps (Ac) inhibiteurs (neutralisant l'activité procoagulante du FVIII) et/ou des anticorps non-neutralisants (ANN). La cartographie épitopique fine des Ac anti-FVIII permet de mieux connaître les mécanismes physiopathologiques de cette réponse immunitaire. Les travaux de cette thèse comportent deux axes principaux : un premier axe a pour objectif d'identifier des épitopes discontinus au sein des domaines C2 et A2 du FVIII, à l'aide de peptides synthétiques prédits par un algorithme informatique, utilisés ensuite dans des tests d'inhibition basés sur la technologie Luminex. Ces travaux nous ont permis d'identifier 8 peptides mimant des épitopes discontinus répartis à la surface du domaine C2 et 2 peptides correspondant à des épitopes voisins, à la surface du domaine A2. Ces études ont permis de démontrer que la combinaison de la bioinformatique et d'un outil expérimental adapté à la réponse immunitaire anti-FVIII est fructueuse. Le second axe a pour objectif d'étudier la prévalence et la spécificité épitopique des ANN à l'aide d'un test Luminex multiplexé. Cette étude a permis de mettre en évidence une prévalence d'ANN de 18,1% chez 210 hémophiles A sans inhibiteurs provenant d'une cohorte multicentrique rétrospective française. Une forte spécificité épitopique de la réponse immune pour la chaîne lourde du FVIII est observée. Les nouveaux outils que nous avons mis en place permettront d'affiner la cartographie épitopique et le suivi de son évolution chez l'hémophile A avec anticorps anti-FVIII / Haemophilia A (HA) is an inherited bleeding disorder due to factor VIII (FVIII) deficiency. The preventive treatment of HA is based on regular infusions of FVIII. Secondary to the treatment, an immune response often occurs, composed by inhibitory antibodies and by non-neutralising antibodies (NNA). Fine epitope mapping of anti-FVIII antibodies may help for a better understanding of the physiopathology of this immune response. There was two axes in this PhD thesis: the first part is dedicated to the identification of discontinuous epitopes on FVIII C2 and A2 domains, by using synthetic peptides predicted by a bioinformatic tool in inhibition tests based on Luminex technology. Results allowed us to identify 8 peptides mimicking discontinuous epitopes around the C2 domain and 2 peptides mimicking close epitopes on the A2 domain surface. These studies demonstrate that our approach combining bioinformatics with an assay adapted for the anti-FVIII immune response study is fruitful. The second part was dedicated to the evaluation of the prevalence and epitope specificity of NNA, using a multiplexed Luminex assay. A prevalence of 18.1% of NNA was thus found in 210 HA patients without inhibitors from a french multicentric retrospective cohort. An marked epitope specificity againt the heavy chain was noticed. The new tools that we developped will be helpful for refining epitope mapping and for the follow-up of the epitope specificity in HA patients with anti-FVIII Abs.

0 Abstract Cystic fibrosis is an autosomal recessive disease caused by mutation in CFTR gene coding for a chloride channel in apical membrane of epithelial cells. This disorder leads to the change in ion transport causing the increase in mucus viscosity in airways as well as changes in glycosylation of saccharide structures on the cells. Because of that these cells are the target for bacterial adhesion. Chronic bacterial infections, which lead to gradual decline of lung function and damage of lung tissue, are the major cause of death of patients suffering with cystic fibrosis. Pseudomonas aeruginosa is the main pathogen causing chronic infections in cystic fibrosis patients. This bacterium produces a biofilm protecting them from host immune system and antibiotics. Once the colonization with PA occurs, it is difficult to get rid of this pathogen. The prophylactic treatment with orally administered hen antibodies against the PA virulence structures could be a prevention of chronic PA infections. In this work we tested the antibody against the bacterial lectin PA-IIL, which is suggested to be involved in the adhesion of the pathogen on epithelial cells. First, it was verified that the prepared antibody from egg yolks of a hen immunized with the bacterial lectin PA-IIL recognizes this antigen expressed...

Au cours de sa vie, 1 femme sur 9 sera atteinte du cancer du sein, 1 sur 27 sera emportée par cette maladie et 10 à 15 % des patientes développeront des métastases dans les trois années suivant le diagnostic. Le diagnostic précis et personnalisé du cancer du sein ainsi que l'évaluation de son potentiel métastatique est donc un enjeu majeur. Une analyse plus précise des caractéristiques moléculaires d'une tumeur primaire devrait conduire à une médecine personnalisée, un traitement et un suivi plus efficace. La détection de biomarqueurs sériques serait un moyen de diagnostiquer un cancer métastatique. Dans le but de découvrir de nouveaux marqueurs, l'analyse protéomique d'échantillons de patient a un fort potentiel mais souffre de limitations techniques, incluant le manque d'anticorps stables reconnaissant des marqueurs tumoraux d'intérêt. Par l'utilisation de fragments d'anticorps aux propriétés remarquables nommé single domain antibody (sdAb), et grâce à la mise au point d'une stratégie innovante de phages display, ce travail apporte d'importantes réponses en termes de disponibilité d'anticorps, d'analyse spécifique d'échantillon et de découverte de nouvelles cibles. Nous avons élaboré une stratégie permettant la découverte de biomarqueurs et l'isolement des anticorps correspondants. Après la construction de banques de sdAb à partir de lamas immunisés par des biopsies, une nouvelles stratégie de sélection in vitro par phage display, la sélection masquée, nous a permis d'isoler des anticorps spécifiques du cancer du sein. / In a lifetime, 1 in 9 women will develop breast cancer, 1 of 27 will be swept away by the disease and from 10 to 15% of patients will develop metastases within three years of diagnosis. Accurate and personalized diagnosis of breast cancer and the detection of its metastatic potential is a major challenge. It is essential to develop new analytical methods allowing an effective monitoring of breast cancer. A closer analysis of the molecular characteristics of a primary tumor should lead to more effective personalized medicine, treatment and monitoring. The efficient detection of serum biomarkers would be a way to diagnose metastatic cancer and to modify treatment based on these results. Toward this goal, the proteomic analysis of patient samples has great potential but suffers from technical limitations, including the lack of a wide variety of antibodies and tumor marker. By the use of innovative antibody fragments with remarkable properties named single domain antibody (sdAb), and through the development of a new innovative strategy of phage display, this work provides important answers in terms of availability of antibody, specific proteomic analysis of sample and new target discovery. We have developed a strategy allowing the simultaneous discovery of new biomarkers and the isolation of corresponding antibodies. After the construction of sdAb libraries from llamas immunized with biopsies, and using a new in vitro selection strategy by phage display named masked selection, we have isolated breast cancer-specific antibodies.

To personalize treatment for cancer, correct staging of the primary tumor, nodal disease and metastatic disease is of essence. By targeting tumor specific receptors with radiolabeled antibodies, specificity and accuracy of imaging may be improved. Radio-immunodiagnostics can potentially detect small volume disease, occult metastasis and recurrent cancer in treated tissue. This thesis focuses on evaluation of radio-immunoconjugates directed towards CD44v6, which is a surface receptor overexpressed in many head and neck squamous cell carcinomas. At the outset, the monoclonal chimeric antibody cMab U36 and its cleavage products Fab’ and F(ab’)2 were labeled with 125I and assessed in vitro and in vivo (paper I). The best distribution pattern and tumor to organ ratio was achieved with F(ab’)2. Due to the immunological responses humans can develop towards chimeric antibodies, they are not optimal for clinical use, and subsequently fully human antibody fragments were developed. AbD15179, which is a monovalent fragment, was labeled with 111In and 125I and evaluated in vitro and in mice bearing CD44v6-expressing tumors. Tumor to organ ratios were improved compared to cMab U36 derived fragments, and 111In-AbD15179 displayed a more favorable distribution compared to 125I-AbD15179 (Paper II). A bivalent Fab-dHXL, AbD19384 derived from AbD15179, was then constructed and labeled with 125I and evaluated in cell- and biodistribution studies. Furthermore, an imaging study in a small animal PET was performed with 124I-AbD19384 (Paper III). Uptake in kidneys was reduced and liver uptake increased compared to AbD15179 reflecting the larger molecule. The high CD44v6 expressing tumor was clearly visualized with maximum uptake at 48 hours post injection.In paper IV human single chain fragments towards CD44v6v were selected, and the top candidates A11 and H12 were further evaluated in vitro and in vivo. Single chain fragments are small molecules exhibiting fast clearance and high affinity to the target. The study proved this by demonstrating superior tumor to blood ratios of radiolabeled A11 and H12 compared to previously studied molecules.

Master of Science / Department of Diagnostic Medicine/Pathobiology / Raymond R. R. Rowland / Open reading frame 2 (ORF2) of porcine circovirus type 2 (PCV2) codes for the 233 amino acid capsid protein (CP). Baculovirus-based vaccines that express only ORF2 are protective against clinical disease following experimental challenge or natural infection. The goal of this study was to identify regions in CP preferentially recognized by sera from experimentally infected and vaccinated pigs, and compare these responses to pigs diagnosed with porcine circovirus-associated disease (PCVAD). The approach was to react porcine sera with different CP polypeptide fragments that each contained one or more immunoreactive regions. Expression of polypeptides was performed using E.coli. Initial results showed that sera from vaccinated pigs preferentially recognized only the largest CP(43-233) polypeptide fragment and showed low levels of binding to other CP polypeptide fragments. The results of sera from pigs diagnosed with PMWS showed only minimal reactivity with CP polypeptide fragments, including the largest CP(43-233). PCV2 infected or PDNS diagnosed pigs reacted to all CP polypeptides: however, the strongest reactivity was primarily directed towards CP polypeptides containing residues in the 160-180 region. For this purpose, finer mapping studies were performed. These experiments involved reacting sera from experimentally infected PCV2 pigs and PDNS pigs with overlapping oligopeptides that covered amino acids 141-200. Overall, the results showed a subset of experimentally infected pigs and pigs with PDNS preferentially recognized the CP oligopeptide, 169-STIDYFQPNNKR-180. Alanine scanning identified Y-173, F-174, Q-175 and K-179 as important for antibody recognition. The results from this study support the notion of PCV2 modulation of immunity, including antibody responses that may represent a precursor for disease. The results from this study support the notion of PCV2 modulation of immunity. Furthermore, the methods incorporated in this study provide a means for characterizing the immune response upon vaccination, natural infection and disease.