Dissertations / Theses on the topic 'Single chain variable fragments (ScFv)'

Les récepteurs aux endothélines sont des récepteurs couples aux protéines G desquels deux variants existent, type A (ETAR) et type B (ETBR). Ils sont principalement décrits pour leur rôle physiologique de régulation du flux sanguin dans tous les types de vaisseaux via les mécanismes de vasoconstriction et de dilatation, respectivement. Cependant, les récepteurs aux endothélines sont impliqués dans plusieurs désordres physiologiques dont le cancer ou l’expression de l’un ou des deux récepteurs aux endothélines est dérégulée. Nous avons développé deux stratégies complémentaires pour le ciblage des récepteurs ETB, visant à inhiber son action quand il est surexprimé : la sélection de single-chain variable fragment (scFv) à partir d’une banque large et naïve par la technologie du phage-display, et la synthèse sur mesure, assistée par une matrice de polymères à empreintes moléculaires (MIP) comme « anticorps en plastique ». La sélection de scFv a été réalisée par biopanning sur cellules transfectées entières afin de maintenir la conformation native de ETBR. Phage-scFv qui se lient uniquement à la cible et ceux qui sont internalisés suite à l’interaction scFv- récepteur ont été isolés séparément. Après confirmation de la reconnaissance des cellules CHO-ETBR par rapport aux cellules CHO-WT par les phages-scFv polyclonaux en utilisant un test ELISA et la microscopie électronique à balayage (MEB), nous avons sélectionné au total 17 clones qui ont montré une capacité de liaison augmentée par phage-ELISA monoclonal sur cellules transfectées entières, mais également sur UACC-257, une lignée cellulaire de mélanome avec une surexpression de ETBR. Des résultats préliminaires obtenus par cryométrie en flux ont montré une reconnaissance augmentée de CHO-ETBR par l’un des clones sélectionnés. La viabilité cellulaire a été affectée par certains de ces clones. Des MIP nanoparticules ont été synthétisées en utilisant un peptide synthétique comme molécule matrice qui mime un « épitope » de ETBR. Nous avons réalisé la synthèse sur une phase solide afin d’obtenir une exposition orientée de la matrice, résultant en la production de MIP avec des cavités homogènes. Les particules MIP d’une taille de l’ordre du nanomètre ont été obtenus et ont par la suite été testés pour leur capacité à reconnaitre le récepteur entier exprimé sur la surface cellulaire par imagerie cellulaire. Des nano-MIP fluorescents ont montré une reconnaissance sélective des cellules transfectées par rapport à leurs homologues non transfectées
Endothelin receptors are G-protein coupled receptors of which two variants exist, type A (ETAR) and type B (ETBR). They are mainly described for their physiological role of regulating the blood flow in all vessel types via vasoconstriction and vasodilatation mechanisms, respectively. However, endothelin receptors are involved in several physiological disorders including cancer in which the expression of one or both endothelin receptors are deregulated.We have developed two complementary strategies for targeting ETB receptors, aiming to inhibit its action when it is overexpressed: selection of single-chain variable fragments (scFv) from a large naive library by phage-display technology as « biologic antibodies », and tailor-made template-assisted synthesis of Molecularly Imprinted Polymers (MIP) as « plastic antibodies ». The selection of scFv was performed by biopanning on whole transfected cells in order to maintain the native conformation of ETBR. Phage-scFv that only bind to the target and the ones that are internalized subsequently to scFv-receptor interaction were isolatedseparately. After confirming the recognition of CHO-ETBR cells over CHO-WT cells by polyclonal phage-scFv using an ELISA assay and Scanning Electron Microscopy (S.E.M), we have selected in total 17 clones that showed increased binding ability by monoclonal phage-ELISA on whole transfected cells but also to UACC-257, a melanoma cell line with an overexpression of ETBR. Preliminary results obtained by flow cytometry showed an enhanced recognition of CHO-ETBR by one of the selected clones. Cell viability was shown to be affected by some of these clones. MIP nanoparticles were synthesized using a synthetic peptide as template molecule that mimics an « epitope » of ETBR. We performed the synthesis on a solid phase in order to obtain an oriented exposition of the template resulting in the production of MIPs with homogenous cavities. MIP particles of a size in the nanometer range were obtained and were subsequently tested for their ability to recognize the whole receptor expressed oncell surface by cell imaging. Fluorescent nano-MIPs were shown to recognize selectively transfected cells with regard to their non-transfected counterparts

Human neurocysticercosis (NC) is an important but neglected cause of epilepsy in developing countries where the parasite occurs. Expression of single-chain variable fragment (scFv) antibodies on the surface of bacteriophage is widely used to prepare antibodies with pre-defined specificities. A phage antibody library was selected against peptides displayed on phages coupled to beads and total saline extract of Taenia solium metacestodes immobilized on microtiter plate wells. After two rounds of selection 96 phage clones of each panning were selected, tested for scFv expression and specificity to each target. Specific clones were further analyzed by ELISA (Enzyme-linked immunosorbent assay), Dot-blot, sequencing and immunofluorescence. After selection, three clones were used for antigen capture to characterize its targets for future immunodiagnostic assays development. Total saline extract was fractionated on ion exchange resin diethylaminoethyl (DEAE), and fractions were tested by ELISA to detect sera IgG from: NC, other parasites and health controls (40 each). The fractions with best diagnostic parameters (sensitivity, specificity, area under curve and likelihood ratio, calculated by TG-ROC) were selected and subjected to antigen capture using each purified scFv clone. Each captured fraction was tested by ELISA to detect IgG in 30 serum samples from each group. In immunofluorescence tests, no fluorescence was observed in negative controls, and all clones showed a non-uniform staining profile, and their targets were elucidated through mass spectrometry. After ion exchange fractionation and ELISA tests, DEAE S2 fraction showed to be the best one and was used to capture new antigens. DEAE S2 showed 93.3% specificity. Among all clones, A4 and B6 captured antigens from saline extract and DEAE S2 fraction, respectively, with the best diagnostic parameters. In conclusion, antibody phage display technology is a potential approach for the study of antigen-antibody interactions, which can be used to further elucidate the biology of interaction on neurocysticercosis and to capture new antigens with potential applications in NC diagnosis and therapeutics.
A neurocistocercose humana (NC) é uma doença muito importante, porém negligenciada e é a maior causa de epilepsia em países em desenvolvimento onde a parasitose ocorre. A expressão de fragmentos de cadeia única das regiões variáveis de anticorpo (scFv) na superfície de bacteriófagos é amplamente utilizada para obter anticorpos com especificidades pré-definidas. Uma biblioteca de anticorpos foi utilizada para a seleção de clones específicos à peptídeos expostos em fagos acoplados a beads e ao extrato salino total de Taenia solium (S) imobilizado em placas de microtitulação. Após dois ciclos de seleção, 96 clones de anticorpos foram selecionados contra cada alvo, testados para expressão do scFv e especificidade pelo alvo. Aqueles clones que se mostraram específicos foram melhor analisados por ELISA (Enzyme linked immunosorbent assay), Dot blot, sequenciamento e imunofluorescência. Três clones foram selecionados para serem utilizados na captura antigênica e caracterização do antígeno verdadeiro e para captura de novos antígenos com potencial aplicação em testes diagnósticos. O extrato S foi fracionado em resina de troca iônica diethylaminoethyl (DEAE) para obter frações que foram posteriormente testadas por ELISA para detectar IgG em amostras de soro de pacientes: com NC, outras parasitoses e saudáveis, 40 amostras cada grupo. A fração com melhores parâmetros diagnósticos (sensibilidade, especificidade, área sob a curva e likelihood ratio, calculadas por TG-ROC) foi selecionada e sujeita à captura antigênica usando cada clone de scFv purificado. Cada fração capturada foi testada por ELISA para detectar IgG em 30 amostras de soro de cada grupo. Nos testes de imunofluorescência, nenhuma fluorescência foi observada com os controles negativos e todos os clones mostraram um padrão de marcação não uniforme, seus antígenos alvo foram elucidados por espectrometria de massas. Após fracionamento por troca iônica e ELISA, a fração DEAE S2 se mostrou a melhor e foi utilizada para a captura de novos antígenos. A fração DEAE S2 mostrou especificidade de 93,3%. Dentre todos os clones, o A4 e o B6 capturaram antígenos do extrato S e fração DEAE S2, respectivamente, com os melhores parâmetros diagnósticos. Em conclusão a tecnologia de exposição de anticorpos em fagos é uma técnica potencial para o estudo de interações antígeno-anticorpo utilizadas para melhor elucidar a a biologia da interação na NC e para capturar novos antígenos potencialmente aplicáveis para o diagnóstico da NC.
Doutor em Imunologia e Parasitologia Aplicadas

Human platelets glycoprotein VI (GPVI) is evidenced to be a platelet receptor of major importance in the occurrence of arterial thrombosis. Thus, it can be considered to be of great interest in diagnosis and therapeutic of atheriosclerotic diseases. Antibodies are powerful molecules which can be used in both diagnostic as well as for therapeutic purposes due to their unique characteristics. Monoclonal and recombinant antibodies have antigen restricted specificity, high affinity and can be used in various assays. Moreover, the good knowledge of their structure and molecular engineering facilities now allows the antibody modulation according to desired properties.Our group has already produced several monoclonal antibodies to human GPVI by gene gun immunization against the immunoadhesin hGPVI-Fc, which differ in fine epitopespecificity, affinity and other functional properties (Lecut et al. 2003). One, 3J24, with diagnostic potential while the other, 9O12, has a therapeutic potential because it blocks the binding of GPVI to collagen. Its Fab fragment has been extensively characterized in vitro,ex vivo and in vivo for its antithrombotic properties.Here, we designed and reshaped a single-chain antibody fragment (scFv) based on 3J24variable domains for the quantification of GPVI with diagnostic potential. We were also involved in the design, production and functional evaluation of humanized anti-GPVI recombinant antibody fragments (scFvs and Fabs) with therapeutic properties.

Master of Science
Department of Diagnostic Medicine/Pathobiology
Richard 'Dick' Hesse
Carol Wyatt
Over the last two decades molecular laboratory techniques have enabled researchers to investigate the infection, replication and pathogenesis of viral disease. In the early eighties, Dr. George Smith developed a unique system of molecular selection. He showed that the fd bacteriophage genome could be manipulated to carry a sequence of DNA coding for a protein not contained in the phage genome. Infection of the recombinant bacteriophage or phagemid into a specific strain of the bacterium, Escherichia coli, produced progeny phage with the coded protein displayed as a fusion with the phage's coat protein. Antibody phage display utilizes the same technology with the DNA encoding an antibody fragment. The DNA insert can carry the information to produce either a single chain variable fragment (scFv) producing the heavy chain variable and light chain variable (VH-VL) portion or a Fab fragment which also contains the heavy chain constant 1 with the light chain constant (CH and CL) portion of an antibody. Screening an antibody phage display library has the possibility of producing an antibody not produced in the normal course of immune selection. This decade also saw the emergence of a viral disease affecting the porcine population. The Porcine Reproductive and Respiratory Syndrome virus (PRRSV) has been one of the most costly diseases affecting the pig producer. Molecular investigations found that PRRSV is a single, positive-stranded RNA virus which codes for five structural and 12-13 nonstructural proteins producing an enveloped, icosahedral virus. An interesting characteristic of PRRSV is the ability to produce infective progeny with genomic deletions, insertions and mutations within the nonstructural protein 2 (nsp2). With this knowledge, many researchers have produced marker vaccines containing fluorescent tags with the hope of developing a DIVA (Differentiate Infected from Vaccinated Animals) vaccine. In my Master‟s studies, I studied the techniques of antibody phage display technology and how to apply these methods to producing scFvs which recognize a recombinant PRRSV nsp2 fragment protein and the native protein during infection of MARC-145 cells.

Mantle cell lymphoma (MCL) is one of several sub-types of B-cell lymphomas. The malignancy is very aggressive and average survival time is short. The hallmark of MCL is over expression of cyclin D1, however about 15% of all MCL cases do not display this over expression and are easily misdiagnosed. Recently the transcription factor Sox11 has been shown to be specifically over expressed in the nucleus of MCL-tumour cells, and polyclonal rabbit anti-Sox11 antibodies have been used to successfully identify MCL in both cyclin D1 positive and negative cases. Howev-er, human recombinant MCL-specific antibodies as have several advantages over these polyclonal rabbit antibodies; they can easily be produced in large quantities in vitro, their specificity is constant from batch to batch and they can possibly be used for therapeutic purposes. Because of this, it is desirable to produce human recombinant antibodies against proteins over expressed in MCL. In this study human recombinant IgGs have been produced towards two pro-teins over expressed in MCL, Sox11 and KIAA0882. This was done by cloning of single chain variable fragments (scFvs), previously selected from a large scFv library through phage display selection against Sox11- and KIAA0882-protein epitope signature tag (PrEST), into vectors containing human IgG constant regions followed by expression of human IgG antibodies in human embryonic kidney (HEK) 293 cells. One IgG clone for each antigen was shown to be functional and specific. Both clones were shown to have overlapping binding epitopes with their polyclonal rabbit antibody counterpart (rabbit anti-Sox11/KIAA0882) through competitive ELISA. The anti-Sox11 IgG was able to detect two bands in cell lysate in Western blot, of which one probably is Sox11 while the other band possibly could be Sox4. However, this needs to be confirmed in future experiments. The affinity of the anti-Sox11 IgG was measured in Biacore and compared to the affinity of its original scFv. This gave a rough estimation of the affinities, but the values are unreliable and the measurements need to be redone. Although more work has to be put into evaluating the potential of the produced IgGs, they compose a promising starting point to an improved understanding and improved diagnosis of MCL.

Monoclonal antibodies (mAbs) are an important tool for both therapeutic and nontherapeutic applications. Their increased demand is due to their ability to recognize and bind specifically to a wide range of antigens. In addition to full-size antibodies, one can also utilise smaller antibody fragments, single chain variable region fragments (scFvs), which like full-size mAbs, are also capable of specific antigen-binding. The constant and rapidly expanding use of antibodies and their derivatives presents a need for a fast and effective method of production. Traditionally, antibodies have been produced using hybridoma technology. They have also been successfully produced in other expression hosts such as bacteria, yeasts, insect cells and mammalian cell lines. However, these expression systems come with a few disadvantages, some of which include high maintenance costs as well as lengthy and laborious production protocols. This dissertation describes the use of phage display technology to screen for and identify scFvs that bind to three different test antigens. Phage display library technology involving the expression and presentation of antibody or antibody derivatives on the coat surfaces of phage particles. It is considered to be a preferable alternative to hybridoma technology because it eliminates the requirement for immunization of animals, making it a more rapid and animal-friendly method for the production of antibodies compared to that of hybridoma technology. A naïve mouse scFv phage display library was screened with appropriate antigens to isolate scFvs which bind to rabbit IgG, human IgG and the Shuni virus (SHUV) N protein. Isolated scFvs were sequenced, cloned and tested for binding to their cognate antigens using phage ELISA, phage dot blots and phage western blots. ScFvs displaying the highest affinities for their respective antigens were selected for cloning and expression in plants, as this expression system is scalable, cheaper, safe and facilitates posttranslational modifications to recombinant proteins such as glycosylation. Rabbit IgG and human IgG scFvs were isolated successfully from the mouse scFv phage library, however, successful binding of the scFvs to the respective antigens by western blotting and ELISAs was not demonstrated. On further investigation, it appeared that the protocols were flawed, as the secondary anti-mouse AP conjugate, iv used in the western blots and ELISAs was found to cross-react with both rabbit and human IgG. Since we were not able to pinpoint scFvs with high binding affinity, the mouse phage display library was screened for scFvs that bound to SHUV N protein instead. This was more successful in that several scFvs with high binding affinity were isolated. Three scFvs with the highest binding affinity for the SHUV N protein were selected and their nucleotide sequences determined. Due to time constraints only 2 of the identified scFvs were selected for further cloning and expression in plants. Both scFvs were cloned into the pTRA-HRPB2SEKDEL plant expression vector that contains the gene sequence for a his6x tag to assist with downstream purification as well as a horse radish peroxidase (HRP) gene. Cloning scFvs into this vector allows their fusion to HRP, resulting in the production of potential reagents for use as secondary antibodies in western blots and ELISAs. The cloned scFvs were expressed transiently in tobacco plants using Agrobacterium-mediated infiltration. Plant expression of the HRP-fused scFvs was optimized; both were optimally expressed at 5 days post infiltration (dpi) when co-expressed with a silencing suppressor (pBIN-NSs). Extraction of the scFvs from the plants was most effective when a bicine buffer with a pH of 8.4 was used. Partial purification of the scFvs was achieved by isoelectric and ammonium sulphate precipitation. Preliminary tests were done to test functionality of the partially purified scFvs, in which the ability of the scFvs to recognize and bind to the SHUV N protein in a dot blot was tested. However, both were found to be non-functional in this regard. Further investigation into the reason for the demonstration of non-functionality showed that the HRP was being spontaneously cleaved from the scFv. This study demonstrates that it is possible to isolate antigen-specific scFvs from a phage display library. However, their binding capacity needs to be analysed fully prior to incorporating them into fusion proteins which can be used as potential diagnostic reagents.

A la fin des années 80, des anticorps catalytiques ont été découverts dans le sérum de patients, en particulier de patients atteints de maladies auto-immunes. Certains anticorps catalytiques ont un effet bénéfique sur la santé, tandis que d'autres sont délétères. Afin de comprendre le lien existant entre anticorps catalytiques et pathologies auto-immunes, des travaux antérieurs ont mené à la synthèse de quatre banques de fragments d’anticorps (scFv) exposés en surface de phages, représentant différents fonds génétiques et états immunologiques. Les scFv, constitues des régions variables des chaines lourdes (H) et légères (L) des anticorps, sont codes par différents segments de gènes d'immunoglobuline : V-D- J pour la chaine lourde, V et J pour la chaine légère. Dans l'objectif de récolter des informations sur l’immunogénétique des anticorps catalytiques, la distribution des sous-groupes de gènes au sein de chaque répertoire a été étudiée, en se basant sur l’étude de plus de 300 000 séquences. L'analyse des données NGS a montré une expression différentielle des sous-groupes de gènes selon la banque d’origine, suggérant que le fond génétique et / ou l'état immunologique influencent l'expression du sous-groupe de gènes d'immunoglobuline. La présence d'anticorps potentiellement catalytiques à activité β-lactamase a ensuite été étudiée dans les quatre banques par une approche in silico de modélisation tridimensionnelle. Les résultats suggèrent que certaines banques expriment potentiellement plus d'anticorps catalytiques que d'autres. Enfin, dans le but de valider cette approche in silico, une approche in vitro a été initiée. Cinq scFv exposés à la surface des phages ont été sélectionnés lors d'un travail précèdent par un processus itératif sur la base de leur activité catalytique. Chacun possède une structure primaire et tertiaire unique. L’un d’entre eux, le scFv P90C2, a été cloné et exprimé dans des bactéries E. coli BL21 (DE3) sous forme de corps d'inclusion, puis solubilise et enfin renaturé. Bien que le scFv P90C2 soluble conserve son activité de reconnaissance, son pouvoir catalytique est complètement perdu. L’influence de différents paramètres sur la fonctionnalité du scFv a été évaluée : (i) optimisation des conditions du protocole de renaturation, (ii) choix des codons à l’origine de la séquence peptidique du scFv, et enfin (iii) influence de la protéine de fusion pIII
In the late 80s, catalytic antibodies have been discovered in the serum of patients, especially patients with auto-immune diseases. Some of the catalytic antibodies appear to have a beneficial effect on health while others are deleterious. In order to understand the link between catalytic antibodies and immune system pathologies, previous work leaded to 4 single chain Fragment variable (scFv) libraries exposed on phage surface, representing different genetic backgrounds and immunological states. The scFvs, composed with the variable regions of the heavy (H) and light (L) chains, are encoded by immunoglobulin gene subgroups V(H), D(H), J(H), V(L) and J(L). With the objective to decipher the potential origin of catalytic antibodies, a statistical representation of each subgroup within each repertoire has been done, based on more than 300 000 sequences. The NGS data analysis showed a variable expression of some gene subgroups (comprising “rare” ones) between the 4 libraries showing that the genetic background and/or the immunological state influence immunoglobulin gene subgroup expression. Then, we investigated the presence of antibodies with potent active sites in the libraries by molecular modelling. Libraries express more putative catalytic antibodies than others depending on the genetic background and the immunological state profile. Finally, in the objective to validate this in silico approach, an in vitro approach was considered. 5 scFvs exposed on phage surface have thus been selected during a previous work by iterative process on the basis of their catalytic activity: β-lactamase like activity. Each of them displays a unique primary and tertiary structure. The scFvs exposed on the phage surface must be catalytically active while expressed in soluble form too. One of the selected scFvs, P90C2, was optimized and expressed in E. coli BL21 (DE3) bacteria in the form of inclusion bodies and then solubilized and refolded. Although soluble P90C2 fully retained its binding activity, its catalytic potency was completely lost. Further experiments aimed to i) optimize refolding protocol, ii) study the impact of scFv codon-optimization, and iii) show the influence of the pIII fusion protein on the scFv catalytic activity

Les anticorps catalytiques (ou abzyme) ont fait l’objet de nombreuses recherches et ont été produits pour réaliser de nombreuses réactions. Ces protéines ont été ensuite découvertes dans le sérum d’individus sains ou atteints de pathologies, dont les pathologies autoimmunes. Les études suggèrent que ces abzymes peuvent avoir des effets bénéfiques ou délétères sur la santé des individus. L’origine des anticorps catalytiques et leur rôle restent ambigus et doivent être approfondis. Nous avons développé une nouvelle stratégie visant à étudier les abzymes, basée sur la technologie du phage display. Nous avons construit 4 banques de fragments d’anticorps, chacune présentant un répertoire immun différent (fond génétique et état d’immunitaire) : saine et naïve, saine et immunisée, autoimmune et naïve, et autoimmune et immunisée. Les stratégies d’amplification et de clonage des régions variables des immunoglobulines ont été conçues afin d’optimiser la taille et la diversité des banques. Nous avons rassemblé les 4 banques en une banque unique élargie contenant 2.7×109 séquences. L’analyse des séquences a mis en évidence des différences dans les profils d’expression des sous-groupes de gènes selon la banque. Nous avons ensuite procédé à la sélection d’abzymes à activité β-lactamase en utilisant deux cibles : un peptide cyclique, et un dérivé de sulfone pénam, inhibiteurs de l’enzyme. Nous avons sélectionné 5 abzymes. Chacun de ces immunoglobulines ont des séquences protéiques propres, incluant un potentiel site actif. Ces résultats montrent que différents motifs peuvent assurer la fonction catalytique de la β-lactamase, confirmant la flexibilité moléculaire de cette enzyme
Catalytic antibodies (or abzymes) have been the focus numerous studies for some decades and have been produced with the ability to catalyze a wide range of reactions. They have also been discovered naturally in normal physiological and pathological conditions, notably on the background of autoimmune disease. Some have beneficial effects and others are detrimental to individual’s health. Hence, the origin of abzymes and their role in the immune response are ambiguous and must be enhanced. We have developed a novel strategy for the study of abzymes based on the phage display technology. We have constructed 4 libraries representing 4 murine immune repertoires with different genetic backgrounds and immunological states : healthy and naïve, healthy and immunized, autoimmune and naïve , and autoimmune and immunized. The strategies for the amplification and cloning of the immunoglobulin (lg) variable regions have been designed to optimize the size and diversity of the libraries. We have been able to pool the four libraries to create a large repertoire of size 2.7x109. After sequence analysis, we have found a number of statistically significant differences between the libraries. We have then used two strategically chosen targets to select for antibodies endowed with β lactamase activity : a cycle peptide and a penam sulfone, both inhibitors of the enzyme. We have selected for a total of 5 lgs endowed with β lactamase activity. The selected abzymes have different amino acid sequences. 3D modeling has provides insights on potential active sites demonstrating the ability of different structures to maintain the β lactamase activity and confirming the flexibility of the active site

Les anticorps catalytiques sont étudiés pour comprendre leur rôle en conditions physiopathologiques. Ils semblent aussi représenter des outils révolutionnaires pour des études à l'interface entre la chimie, la biochimie, la biologie et immunologie. Par conséquent, la connaissance des relations de structure- fonction représente un grand intérêt. Nous avons exploré deux systèmes d'expression pour la production d'un anticorps catalytique modèle présentant une activité bêta-lactamase. Le fragment scFv recombinant a été produit dans le système d'expression procaryote. Les scFv sont souvent décrits comme des protéines difficiles à produire. Une méthode efficace a été développée pour produire de grandes quantités de scFv solubles et correctement repliés. L'anticorps catalytique entier a aussi été produit en exploitant le système d'expression eucaryote. Des cellules de mammifères ont été utilisées car elles peuvent conserver le repliement original des protéines, leur assemblage et les modifications post-traductionnelles. La structure secondaire du scFv catalytique a été analysée par dichroïsme circulaire pour s'assurer que la renaturation du scFv est en accord avec le repliement des scFv natifs. La fonctionnalité du scFv catalytique et de l'anticorps catalytique entier a été validée par deux approches : (1) le développement d'un test immuno-enzymatique (ELISA) et la résonance plasmonique de surface (RPS) et (2) le développement d'un test catalytique sensible utilisant un substrat fluorogénique. Ce travail amène à considérer de potentielles applications biotechnologiques et thérapeutiques des anticorps catalytiques.

Mycolic acids are long chain lipids from the cell walls of Mycobacterium tuberculosis. The Nkuku phage display library was previously used to obtain monoclonal antibody binders to mycolic acids. In total 11 binders were obtained of which one was selected (MAC10) for further investigation by genetic engineering as presented in this dissertation. The antibodies of the Nkuku phage display library are in the format of single chain variable fragments (scFv). ScFv’s constitute only the epitope binding domains of an antibody consisting of the VH and VL domains fused into a single chain by a flexible linker protein. The selected anti-mycolic acid scFv is referred to as mycolic acid clone 10 (MAC10). Genes encoding the scFv’s of the Nkuku phage display library were cloned into the plasmid pHEN-1, a phage display vector. This vector is not commercially available or ideally suited for expression of scFv proteins. Therefore two vectors were investigated as possible targets for subcloning. The plasmids pGE20 and pAK400 were previously used for the expression of scFv antibody proteins. Subcloning into plasmid pAK400 proved to be the more efficient of the two investigated for subcloning. This subcloning yielded the recombinant plasmid pAKJS. Following the subcloning scFv protein expression was attempted using the plasmids pMAC10 (derived from pHEN-1) and pAKJS (derived from pAK400). Expression of MAC10 using plasmid pMAC10 in both Escherichia coli TG-1 and HB2151 was constitutive. This demonstrates that plasmid pHEN-1 is a non ideal vector as expression should not occur unless induced. Expression of MAC10 did not occur when pAKJS and Escherichia coli HB2151 were used. This was due to both the vector and expression host producing inhibitor protein for the Lac Z promoter controlling expression of the scFv. The MAC10 gene was subsequently randomized using the directed evolution method, error prone PCR. Sequence analysis of the five selected mutants indicated an average mutation rate of 8.6 mutations per 1000 base pairs. From the combined total of all five mutants, transversions made up the majority of substitutions. The majority of transversion mutations occurred at A-T base pairs. Transition substation mutations that made up the minority of total mutations occurred mostly at G-C base pairs.
Dissertation (MSc)--University of Pretoria, 2012.
Biochemistry
unrestricted

Les cyanobactéries sont des micro-organismes qui préoccupent les autorités de santé publique dans le monde entier, en raison de la toxicité des cyanotoxines qu'elles produisent. Certaines cyanotoxines dont les microcystines (MC) sont des hépatotoxines inhibitrices de protéines phosphatases à sérine/thréonine. Aujourd'hui, plus de 200 variants de MCs ont été identifiés. Il s'agit d'heptapeptides monocycliques synthétisés par voie non-ribosomale dont la MC-LR (cyclo- (D-Ala-L-Leu-D-érythro-β-méthylAsp-L-Arg-ADDA-D-Glu-N-méthyl-hydro-Ala) est le variant le plus étudié en raison de sa fréquence et de sa forte toxicité. L’objectif de cette étude est le développement d'une méthode d'immunoanalyse rapide, sensible et fiable pour détecter les MCs. Le projet vise donc à développer un outil alternatif de détection de la MC-LR, qui serait mieux adapté aux analyses sur le terrain que les méthodes analytiques, biologiques ou les méthodes d'inhibition d'activité enzymatique actuellement disponibles. L'originalité de ce projet réside dans l'utilisation de deux approches différentes pour sélectionner de nouveaux anticorps spécifiques de la MC-LR. La première repose sur l'immunisation d'animaux de laboratoire, la technologie d'hybridation cellulaire et la sélection d'hybridomes sécréteurs d'anticorps monoclonaux. Si la méthodologie mise en œuvre a effectivement permis d'obtenir des immun-sérums spécifiques, la sélection des hybridomes d'intérêt reste à optimiser. La seconde stratégie mise en œuvre est basée sur la technologie du phage display pour sélectionner des fragments d'anticorps spécifiques de MC-LR à partir d'une banque de taille d’environ 109 phages, exprimant en surface des anticorps sous un format scFv (Shahsavarian et al., 2014). Plusieurs méthodes de criblage ont été développées et trois scFv ont été sélectionnés et étudiés, parallèlement à un quatrième scFv identifié dans une étude précédente (McElhiney et al., 2002), tous spécifiques à la MC-LR. Ces scFv ont été produits sous forme libre, soluble et leur spécificité à la MC-LR a été évaluée par ELISA et résonance plasmonique de surface. Les résultats obtenus montrent que les scFv sélectionnés sont tous capables de reconnaître la MC-LR. Néanmoins, ces résultats sont peu reproductibles et remettent en question le protocole de renaturation utilisé. Un travail de fond sur l’optimisation du protocole de renaturation s’avèrerait nécessaire pour les scFv ici sélectionnés, afin d’identifier les paramètres précis aboutissant à la perte ou au gain de leur fonctionnalité
Cyanobacteria are ubiquitous microorganisms that present a worldwide concern to public health authorities because of the toxicity of the cyanotoxins they produce. Some cyanotoxins are hepatotoxins such as microcystins (MCs). At least 200 variants of MCs have been identified till today. In our study, we focus on MC-LR, a monocyclic heptapeptide (cyclo-(D-Ala-L-Leu-D-erythro-β-methylAsp-L-Arg-ADDA-D-Glu-N-methyldehydro-Ala), since it is the most frequently detected and one of the most toxic. In our study, we are interested in developing a fast, sensitive and reliable method to detect MCs. The project aims to develop an alternative pollution detection method that would be better suited to field measurements than the physicochemical methods currently available. The originality of this project lies in the use of two different approaches to select a panel of antibodies suitable for the development of immunodetection tests. The first one is based on the hybridoma technology for the production of monoclonal antibodies. The second one is based on phage display technique to select antibody fragments that are specific to MC-LR from a library of approximately 109 phages, expressing on the surface scFv fragments (Shahsavarian et al., 2014). Two monoclonal antibodies were selected using the first approach, and their specificity was evaluated using ELISA technique. Along with three scFvs selected from phage display approach. An additional scFv was added to this list: 3A8, selected from a previous study (McElhiney et al., 2002) and also specific to MC-LR. The scFvs were cloned into an expression vector in order to get each clone in its scFv soluble form. Then, their specificity to MC-LR was evaluated using ELISA technique and Surface plasmon resonance. The results show a potential specificity to MC-LR. Nevertheless, these results are not very reproducible and call into question the refolding protocol used. A thorough work on this protocol optimization would be necessary, in order to find the key parameters that control the loss or gain of their functionality

This project describes the development of antibody fragments against key cell surface receptors as potential metastatic breast cancer therapeutics. As a product of an iterative screening process, an antibody fragment candidate was demonstrated to be functionally active in the inhibition of cancer cell growth and migration. This study provides a promising platform for further development of the characterised antibody fragment with the goal of generating an effective treatment for the inhibition of cancer cell survival and metastasis.

碩士
國立中正大學
分子生物研究所
103
The aim of this study is to construct a ribosome display library of single chain variable fragments (scFvs) for screening lung cancer-binding scFvs. mRNA was isolated from immunoglobulin transcripts derived by health people. Heavy and light chain genes (VH and VL) were amplified separately by RT-PCR and assembled into the VH/VL scFvs library. The scFv library was transcribed and translated in vitro using a wheat germ protein expression system. In order to isolate specific scFvs to A549 adenocarcinomic lung cancer cells, negative selection on a lung normal epithelium cell line BEAS-2B was carried out before positive selection on A549. After five rounds of screening, cell enzyme-linked immunosorbent assay (ELISA) showed that four of 192 scFv clones had high affinity to A549 cells. However, these scFvs also displayed high affinity to BEAS-2B. In the current study, a comprehensive human scFv library has been successfully constructed, however further ribosome display selection is needed to screen for A549-specific scFvs. On the other hand, because of some disadvantages of using scFvs, including decreased stability, short half-life and decreased affinity to the antigen, one approach in improving their function and affinity is to- the constant heavy chain of human immunoglobulins to scFvs. In this study, we have successfully joined a truncated human heavy chain constant fragment Fc region (the hinge region, CH2 and CH3 domains) to an scFv, and the recombinant scFv-Fc antibody was expressed in Escherichia coli and the resulting products were refolded in vitro and characterized. The Kd of the scFv-Fc was estimated to be 70 pM, which is improved up to 178-fold in binding affinity compared to the original scFv.

碩士
國立中興大學
生物化學研究所
103
Chloramphenicol (CAP) is a potent and efficient antibiotic widely used in pharmacological treatments in veterinary and human. Despite being highly effective, it shows severe toxicity as the residual CAP results in Aplastic anemia (AA) and bone marrow suppression. Due to the potential risk in public health of CAP utilization, the use in food-producing animal’s therapy has been banned. Taiwan government has established a zero tolerance policy to CAP in livestock products. Recently, the food crises have grabbed huge public attention in Taiwan. Replacing the expensive LC-MS analysis by cheap and efficient rapid immunoassay to detect the residual illegal compound can better fit to public interest. Therefore, to generate high sensitivity antibodies for immunoassay kits play a key role in improving the food safety. This study has successfully cloned CAP-scFv gene from hybridoma and constructed CAP-scFv gene onto an expression vector fused with a His-tag gene. The expression of this protein in E. coli BL21(DE3) pLysS was optimized and the expressed recombinant CAP-scFv protein was purified with Ni-IMAC. We confirmed the specificity between CAP-scFv and chloramphenicol via ELISA assay. Furthermore we also demonstrated that CAP-scFv recognizes the same molecular structure as CAP monoclonal antibody does by performing the competition assay with CAP monoclonal antibody. In the future, using the error-prone PCR approach further improve the CAP-scFv sensitivity and fusion of fluorescent to the protein flank on scFv or combination with various detection methods will be the next target to enhance the detection limit of immunoassay and create novel applications to numerous aspects.

碩士
國立成功大學
醫學檢驗生物技術學系碩博士班
98
Dengue virus (DV) is an important mosquito-borne pathogen causing dengue fever (DF), dengue hemorrhagic fever and dengue shock syndrome (DHF/DSS) in the tropical and sub-tropical region of the world. Nearly 50% of people in over 100 contries are at risk of DV infection. The surface of DV particle is covered with 90 envelope (E) protein homodimers which contacted with host cells first and were essential for viral infection through receptor-mediated endocytosis. Each monomer of E protein consists of three domains. E protein domain I (DEI) is the central domain located at the center of envelope protein. E protein domain II (DEII) is the dimerization domain contains highly conserved fusion peptide. E protein domain III (DEIII) is a type-specific and immunoglobin-like domain which is also considered a receptor binding and neutralization site. Until today, there is no effective vaccine or treatment against DV infection due to antibodies against DV may enhance DV infection through Fc receptor which is also known as antibody-dependent enhancement (ADE) effect. To avoid this ADE effect, we constructed single chain fragments of variable region (scFv) from DV and DEIII-immunized mice to search for DV specific antibody that can neutralize DV binding and infection. DV purified by polyethylene glycol (PEG) precipitation and sucrose gradient as well as recombinant DEIII expressed in E.coli Rosetta using pET43.1a(+) vector and purified by Ni2+ column were used for immunization. After four times of immunization, antibodies against DV and DEIII were found in both DV and DEIII immunized mice and DV-immunized mouse sera has higher blocking ability against DV binding as detected by flow cytometry. RNA from the spleens of DV-immunized mice was extracted and transcribed to cDNA to establish scFv library. After several rounds of bio-panning, single colonies that had higher affinity to DV were picked up. In our research, we picked up three single scFv that had high affinity to DV and confimed its blocking ability against DV binding by flow cytometry. Among these three scFv clones, anti-DV scFv 5-38 has higher blocking ability against DV binding.

碩士
國立中興大學
生物化學研究所
103
Indoleamine 2,3-dioxygenase (IDO) is an intracellular enzyme which plays an important role in tryptophan catabolism. In case of highly IDO-expressed tumor cells, the micro-environmental tryptophan was metabolized into proapoptotic kynurenines. The decline of tryprophan level and accumulation of kynurenines results in suppression of the surrounding T cell’s proliferation. Hence, this phenomenon has made the cancer cell flee from the tracking and killing of the T cells thus contributed to the gain-of-function immune-escape of the tumor cells. It is an innovative anti-cancer strategy to reboot T cell’s tumor cells recognition by inactivating IDO using a specific monoclonal antibody. Due to the fact that the antibody is too large to enter the cytosol, employing recombinant DNA technology to generate a small size single-chain variable fragment (scFv) other than large antibody might help breakthrough this bottleneck. In this project, we have successfully cloned IDO-scFv gene from hybridoma mRNA and fused the gene with a His-tag gene onto an expression vector. The optimized expression of this protein in E. coli BL21(DE3) pLysS was utilized to produce the recombinant IDO-scFv protein. Additionally, the IDO-scFv protein was purified with Ni-IMAC. Using the competition assay with IDO monoclonal antibody and its derived scFv has demonstrated that IDO-scFv could contend with its source monoclonal antibody in the same antigen site. In the future, the inhibition of IDO activity can be monitored by metabolic methods. Furthermore, to enhance scFv’s binding affinity by error-prone PCR approach or to improve scFv’s cancer-cell-targeting specificity by fusing the tumor specific protein transduction domain (PTD) flank to the scFv could promisingly inactivate IDO in the cancer cell.

碩士
國立中正大學
生物醫學研究所
101
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis, is the second leading infectious cause of mortality worldwide. ESAT-6, the early secretory antigenic target of Mycobacterium tuberculosis is a secretory protein and potent T cell antigen. It is currently used in tuberculosis diagnosis by the whole blood. The objective of this study is to establish the in vitro ribosome display method to select the high affinity of single-chain antibodies against ESAT-6. First, ESAT-6 gene, amplified from Mycobacterium tuberculosis H37RV, was cloned into the plasmid pGEX-4T1 and transformed to E. coli R2 for recombinant protein production. Second, in vitro ribosome display combinatorial single-chain variable fragment (scFv) libraries were constructed from immunoglobulin transcripts derived from TB patients. Third, the libraries were then used for five rounds of selection against the purified ESAT-6 recombinant protein. After five rounds of ribosome display, the selected scFv sequences were cloned and 192 positive colonies were obtained. The crude extract ELISA analysis screened eight scFv clones with high binding affinity to ESAT-6. Sequencing analysis indicates that the eight scFvs contain the same complementary determining regions. The Kd of the selection scFv was estimated to be 12.5 nM. A sandwich ELISA assay based on the scFv was designed for TB diagnosis from clinical blood samples. Among 45 TB patients and 45 uninfected controls, the specificity and sensitivity of the serodiagnosis were 95.6% and 55.5%, respectively. We successfully constructed a combinatorial antibody libraries derived from TB patients and established the ribosome display selection technology. The selected scFv possesses high binding affinity to ESAT6 antigen at nM level.

abstract: Alzheimer's disease (AD) is the most common form of dementia leading to cognitive dysfunction and memory loss as well as emotional and behavioral disorders. It is the 6th leading cause of death in United States, and the only one among top 10 death causes that cannot be prevented, cured or slowed. An estimated 5.4 million Americans live with AD, and this number is expected to triple by year 2050 as the baby boomers age. The cost of care for AD in the US is about $200 billion each year. Unfortunately, in addition to the lack of an effective treatment or AD, there is also a lack of an effective diagnosis, particularly an early diagnosis which would enable treatment to begin before significant neuronal damage has occurred. Increasing evidence implicates soluble oligomeric forms of beta-amyloid and tau in the onset and progression of AD. While many studies have focused on beta-amyloid, soluble oligomeric tau species may also play an important role in AD pathogenesis. Antibodies that selectively identify and target specific oligomeric tau variants would be valuable tools for both diagnostic and therapeutic applications and also to study the etiology of AD and other neurodegenerative diseases. Recombinant human tau (rhTau) in monomeric, dimeric, trimeric and fibrillar forms were synthesized and purified to perform LDH assay on human neuroblastoma cells, so that trimeric but not monomeric or dimeric rhTau was identified as extracellularly neurotoxic to neuronal cells. A novel biopanning protocol was designed based on phage display technique and atomic force microscopy (AFM), and used to isolate single chain antibody variable domain fragments (scFvs) that selectively recognize the toxic tau oligomers. These scFvs selectively bind tau variants in brain tissue of human AD patients and AD-related tau transgenic rodent models and have potential value as early diagnostic biomarkers for AD and as potential therapeutics to selectively target toxic tau aggregates.
Dissertation/Thesis
Doctoral Dissertation Chemical Engineering 2014

abstract: Specificity and affinity towards a given ligand/epitope limit target-specific delivery. Companies can spend between $500 million to $2 billion attempting to discover a new drug or therapy; a significant portion of this expense funds high-throughput screening to find the most successful target-specific compound available. A more recent addition to discovering highly specific targets is the application of phage display utilizing single chain variable fragment antibodies (scFv). The aim of this research was to employ phage display to identify pathologies related to traumatic brain injury (TBI), particularly astrogliosis. A unique biopanning method against viable astrocyte cultures activated with TGF-β achieved this aim. Four scFv clones of interest showed varying relative affinities toward astrocytes. One of those four showed the ability to identify reactive astroctyes over basal astrocytes through max signal readings, while another showed a statistical significance in max signal reading toward basal astrocytes. Future studies will include further affinity characterization assays. This work contributes to the development of targeting therapeutics and diagnostics for TBI.
Dissertation/Thesis
M.S. Bioengineering 2013

碩士
國立交通大學
應用化學系分子科學碩博士班
108
The proBrain Natriuretic Peptide is a 108-amino acids prohormone secreted by cardiomyocytes in the heart ventricles in response to volume expansion and pressure overload. The proBrain Natriuretic Peptide can be cleaved by enzyme and produce N-terminal pro hormone BNP (76-amino acid) and BNP (32-amino acid). N-terminal prohormone BNP (NT-proBNP) is a non-active prohormone containing the first 76 amino acid residues of proBNP, Brain natriuretic peptide (BNP) is a active hormone including the remaining 32 amino acids. Both proBNP, BNP and NT-proBNP are produced resulting from the change of pressure inside the heart. Therefore, to measure the concentration of these proteins can be used for evaluation of heart failure. The proBNP was employed for phage display library screening. After several generations of the screening, two single-chain fragment variable (scFv) regions with high binding affinity against proBNP were obtained. The dissociation constant (Kd) of the two selected anti-proBNP scFvs was measured to be 3.4± 0.8 μM and 476 ± 38 nM via the application of microscale thermophoresis. The measurement of proBNP was further performed by electrochemical impedance spectroscopy. The measurement limit of proBNP using the anti-proBNP scFv1 is at μM level, which is not feasible for Kd value estumation, whereas the Kd of the anti-proBNP scFv2 platform towards proBNP is 74±14 nM. The linear range of proBNP was measured from 12.3 to 333 nM. Though the selected scFvs can recognize and specifically bind to proBNP, the binding affinity needs to be improved in order for establishing an effective detection of proBNP.

博士
國立陽明大學
微生物及免疫學研究所
98
Abstract: Phage-displayed fusion antibody on virus coat protein is a well established system which can efficiently engineer the antibody from genotype to phenotype to test the antibody physical properties on targeting to the antigen in vitro. The engineered antibody can be applicable in cancer therapy for the reason that antibody can carry effectors as cargos and aim to the specific cancer region in vivo. But in the reports from America Food and Drug Administration (FDA) approved antibody therapy in clinical trail, unknown antibody targeting will cause many unrelated, unexplained symptoms during antibody treatment. In order to reduce the side effects during antibody drug therapy, knowing the mechanism of protein-protein interaction by systematic analysis from experimental results in vitro are urgently needed to shorten time-consuming drug exploitation. Phage-displayed antibody targeting can be mimicked in vitro by panning amino acids library on antibody to a specific interested target. The recognition site on both antibody and antigen can also be analyzed the physicals between amino acid side-chain interactions in protein-protein interface from x-ray co-crystal structure. Thus, it can narrow down the design region for constructing the antibody library. In this study, antibody is modified from Bevacizumab (AvastinTM), which is one of the humanized anti-VEGF (vascular endothelial growth factor) monoclonal antibodies in the IgG form, and is the first approved by the FDA as a first-line treatment for metastatic colorectal cancer in combination with chemotherapy. This antibody-antigen interaction will be used as a model system to solve the problem on the antibody instability in the form of single chain fragment variable domains (scFv) which is shortcut and linked two domains from IgG and is also benefit with penetration in vivo during therapy. The purpose of this research is focus on building the a new phage display platform to enhance the antibody library selection with inter-domain disulfide bond between antibody variable domains to stabilize the scFv, to become the single chain disulfide-stabilized antibody variable fragments (sc-dsFv). In conclusion, the carboxyl terminal of the signal sequence manipulate the mass production of the sc-dsFv expressed on phage reveals a new fusion antibody platform on phage display system for further engineering designs, which is as convenient as the scFv-phage expression system but without the defect in the instability of the scFv. After the selection from phage-displayed sc-dsFv antibody libraries, the monoclonal antibody sc-dsFv can be further mass production with stability.

Contraception through a vaccine has been a very attractive proposition and several attempts were made in the past. To achieve contraception through immunological means, several points need to be considered. First, the targeted antigen should be an important component of reproduction and interference in its actions should lead to infertility. Second, the antigen must be highly immunogenic and the antibodies elicited should be able to block the functions of the antigen. Third, the antibody titres should be effective and must sustain for longer periods. Gonadotropins fulfill all the above criteria and therefore, have been attractive targets for developing human contraceptive vaccines. The pituitary gonadotropins- Luteinizing hormone (LH) and the Follicle stimulating hormone (FSH) are the principal regulators of the reproduction process in all the mammalian species (McLachlan et al., 1995c; Moudgal et al., 1992b; Murty et al., 1979a; Selvaraj and Moudgal, 1994a; Weinbauer et al., 1991). In males, LH binds to its specific receptor-LHR, expressed on the Leydig cells and regulates the production of testosterone. This testosterone binds to the androgen receptors expressed in the Sertoli cells and along with FSH, which binds to the specific receptors present on the Sertoli cell membranes, regulate the testicular functions and the spermatogenesis (Simoni et al., 1997; Themmen and Huhtaniemi, 2000; Ulloa-Aguirre and Timossi, 1998). The well documented studies have unequivocally established that the specific immunoneutralization of either hormone by active or passive immunization, leads to disruption of the gonadal functions (Fraser et al., 1986a; Marathe et al., 1995; Moudgal et al., 1992b; Murty et al., 1979b; Shetty et al., 1996; Srinath et al., 1983b) and consequent infertility and this observation formed the basis of the human contraceptive vaccines (Moudgal et al., 1997b; Talwar et al., 2011a; Talwar et al., 2009a). Several studies using testosterone as the main male hormonal contraception method (Matsumoto et al., 1986; Matsumoto et al., 1983a) and anti-hCG vaccine as the female hormonal contraceptive vaccine reached Phase I and II clinical trials (Talwar, 1997; Talwar et al., 1994; Talwar et al., 1997) . However, these human contraceptive vaccines faced several limitations. There was a need to inhibit only particular segments of the entire reproduction process whereas others needed to remain completely unaffected. For example, in males, the FSH regulated functions, the sperm production and spermatogenesis needed to be inhibited whereas the LH/testosterone associated functions should be unaffected. Similarly in females, the functions of hCG alone, elaborated by the conceptus should be blocked without affecting either LH or FSH regulated functions, thus, maintaining the normal reproductive cycle. This however is a difficult task especially when the antigens share a large degree of homology and common subunits (Pierce and Parsons, 1981). Moreover, the issues relating to the development and sustenance of high titres of the bioneutralizing antibodies were major limitations of these human contraceptive vaccines. Therefore, despite reaching Phase I and II clinical trials, these studies did not progress further. However, the same concept of an immunocontraceptive vaccine involving the neutralization of the functions of the gonadotropins is an extremely attractive strategy for controlling the animal populations where the reproduction process could be inhibited in its entirety. The overgrowing populations of the stray animals such as dogs and cats pose problems unlike those experienced with the human overpopulation. Thus, there is an immediate need to develop the methods of controlling the populations of these animals both in the developed and the developing countries. Whereas, in countries like the US, the major emphasis is on the domestic animals, in countries like India, the populations of the stray animals need to be controlled. The current methods employed for reducing the numbers of these animals include either castration or culling of the animals. These methods are however, traumatic, unsafe and not widely accepted by the society. The animal contraceptive vaccines currently available are mostly GnRH vaccines which have high cost of production, are not safe for animal use and elicit unwanted side effects. Apart from these, the animals need multiple administrations of these vaccines to elicit high and effective antibody titres, mostly with the use of conventional but non-approved adjuvants (Boedeker et al., 2009; McCoy, 1994). As mentioned above, the gonadotropins, by virtue of their ability to control the mammalian reproduction process, are attractive targets for achieving contraception. Moreover, the ease of administration of this vaccine to neutralize the functions of the endogenous circulating hormones makes them ideal targets for developing animal immunocontraceptive vaccines. This method of neutralizing the functions of the gonadotropins is also humane and safe for the animals as opposed to the current methods which are employed to reduce their numbers. However, in case of animal contraception, particularly for strays such as dogs, where large numbers of animals need to be treated, the challenge is to develop a method to sustain the high levels of the bioneutralizing antibodies for prolonged periods preferably with a single administration of the immunogen and without the use of conventional adjuvants such as the Freund’s adjuvant. In the present study, an attempt has been made develop a strategy to achieve a sustained immune response to small quantities of the hormonal antigens, preferably with a single administration of the immunogen resulting in complete disruption of the gonadal function for prolonged periods. To achieve this goal, recent developments in the field of immunology and vaccinology have been employed. This involves targeting of the hormonal antigens to the dendritic cells. Targeting the antigens to the dendritic cells for vaccination is becoming an extremely fascinating strategy and is being used extensively to target the antigens involved in several diseases (Escudier et al., 2005; Frankel et al., 1998; Garcia et al., 2005; Nouri-Shirazi et al., 2000a; Nouri-Shirazi et al., 2000b; Steinman and Germain, 1998). Most antigens are targeted to the dendritic cells by coupling them to the antibodies specific for the receptors expressed on the dendritic cell surface. One such receptor is the DEC205, which is expressed on most of the dendritic cells (Jiang et al., 1995) and is being widely used to develop vaccines and vaccination strategies. Targeting the antigens to the dendritic cells provides advantages such as ability to induce hundred fold higher immune response to very low doses of antigen without the use of any conventional adjuvant (Bonifaz et al., 2004a). Therefore, in the present study, these features of the dendritic cells have been harnessed to target the hormonal antigens (hCG and hFSH) to the canine DEC205 receptor to induce a long-term immune response capable of disrupting the gonadal functions. Towards this goal of delivering hormonal antigens to the dendritic cells, a fragment of the canine DEC205 corresponding to the Cysteine Rich Fibronectin II domain (CR/FNII) was expressed and used to isolate several canine DEC205 specific recombinant antibodies in the form of single chain fragment variable (ScFvs) from the Tomlinson’s and the yeast human ScFv display libraries. From a pool of eight unique ScFvs screened from the Tomlinson’s libraries, three ScFvs namely B3, G10 and H4 were characterized. All these ScFvs could bind to the human DEC205 receptor but not to the mouse DEC205. Their inability to recognise the mouse DEC205 suggested that mouse could not be used as the model system for these studies and therefore, a surrogate model system was needed. As the canine CR/FNII shared a high degree of homology with the rabbit counterpart, adult rabbits have been used as the surrogate model for immunization studies after confirming the binding of the ScFvs to the rabbit dendritic cells. Since the goal of the study was to deliver the hormonal antigens to the dendritic cells, each ScFv was translationally fused to a core streptavidin fragment, thus creating bi-functional agents (ScFv-CS) capable of binding to the dendritic cells and also to any biotin-tagged antigen, thus delivering the antigen to the dendritic cells. Of the three ScFvs, the ScFv-CS-H4 which could bind to the canine CR/FNII with the KD of 25nM was used for demonstrating the ability of the ScFv-hormone complex to elicit the bioneutralizing antibody response. The ScFv-CS-H4-biotin-hCG or hFSH or both were administered to adult male rabbits along with poly IC: LC, a Toll-like receptor agonist and the antibody titres were monitored. It was possible to maintain high titres of the bioneutralizing antibodies for more than one year with a single administration of the immunogen. Testicular histology of the immunized animals showed extensive disruption of spermatogenesis with most of the germ cells being TUNEL positive undergoing apoptosis. There was complete absence of elongated spermatids and sperms in the testis indicating infertility caused by immunization with the gonadotropins. These data show that targeting the hormonal antigens to the dendritic cells leads to long-term infertility with minimal immunization. Although the ScFvs from the Tomlinson’s libraries were able to deliver the hormonal antigens to the dendritic cells and produce robust and sustained antibody response capable of disrupting the gonadal functions, the affinities of these ScFvs to DEC205 were moderate. It was felt that increasing the affinities of the ScFvs could enhance the effect with respect to the dose of the antigen that needs to be administered and the duration until which the high antibody titres could be maintained. Therefore, the yeast human ScFv display library offering higher diversity of the human ScFvs displayed, was screened for high affinity DEC205 specific binders. From a pool of several ScFvs, six unique ScFvs were characterized. The amino acid sequences of all ScFvs followed the Kabat's rules for identifying the complimentarity determining regions of the heavy and the light chains of the antibodies. All these ScFvs were unique in their amino acid sequences. The dissociation constants of all these antibodies for the canine CR/ FNII ranged from 10-9 to 10-11 M which was 20-300 fold higher than the ScFvs obtained from the Tomlinson’s libraries. The best ScFv obtained from this library was ScFv-92 with a KD value of 8 x10-11 M. All these ScFvs were able to deliver the payload antigen to both, the mouse DEC205 over-expressing cells and the bone marrow derived dendritic cells. Mice immunized with yeast display ScFvs also yielded antibody response to very small quantities of the immunogen with the highest antibody titres obtained with the ScFv-92. It was further demonstrated that all ScFvs also activated the cell-mediated immunity with significant increase in the antigen stimulated T cell proliferation. These ScFvs could also deliver the antigen to the human dendritic cells differentiated from the human monocytes in vitro, thus emphasising their utility in human vaccine development. An attempt was also made to develop nanoparticle (NP) based strategies of delivering the antigen to the dendritic cells. The PLGA-NPs, encapsulating hCG and coated with the DEC205 ScFv-92 was able to elicit high antibody response to very low doses of the antigen. This response could be sustained for 120 days and was higher than the response obtained with similar doses of hCG encapsulated NPs or hCG complexed to ScFv-92 alone. Targeting of the NPs also elicited antigen specific T cell response thus, potentiating their use in cell mediated immunity along with humoral immune responses. In conclusion, this approach of delivering the gonadotropins to the dendritic cells resulted in the production of bioneutralizing antibodies that could disrupt the gonadal functions for a prolonged period and can be effectively used in the fields for controlling the animal populations. This method fulfils all the criteria for any animal contraception. This strategy also elicits both T cell mediated and humoral immunity and can thus be used for producing vaccine against viral and parasitic infections. It can also be used for cancer immunotherapy. Another exciting feature of the strategy used in this study is the usage of ScFv-CS which allows the delivery of any biotin tagged antigen to the rodent and human dendritic cells. As discussed above, the methods for controlling the animal populations are expected to be effective, humane, safe, simple, non-surgical, single shot with long lasting effects, cheap, applicable in the fields and widely accepted by different societies. The methods presented in this study fulfill all these criteria and should be effective in controlling populations of different animal species.

博士
國立臺灣大學
植物病理與微生物學研究所
104
The genus Potyvirus is one of the important plant virus genera, and comprises 158 formal species based on ICTV Virus Taxonomy. Potyviruses can be transmitted by aphids and mechanical inoculation. Some potyviruses have broad host range and cause serious economic losses. In Taiwan, calla lily is reported to be infected by five potyviruses, Calla lily latent virus (CLLV), Dasheen mosaic virus (DsMV), Konjak mosaic virus (KoMV), Turnip mosaic virus (TuMV), and Zantedeschia mild mosaic virus (ZaMMV). To reduce the cost and time of virus indexing, the conserved 121-amino-acids core regions of the capsid protein (CP) of DsMV, KoMV, and ZaMMV were concatenated and expressed. The recombinant protein was used as an antigen to prepare and screen the potyvirus group-specific monoclonal antibody (MAb). The selected C4 MAb could detect nine potyviruses in addition to the five calla lily potyviruses. In the first part of this study, we cloned the variable regions of the heavy (VH) and light (VL) chains of the C4 MAb, and then constructed them as C4 single-chain variable fragments (scFvs). In E. coil expression system, a new PelE secretory signal peptide was used to help the secretion of C4 scFv. The data showed not only long but also short PelE signal peptide could secrete C4 scFv to medium and reduce inclusion body formation. According to western blot and I-ELISA, the soluble C4 scFv showed a binding specificity similar to that of the C4 MAb. In the second part, to identify which epitope is recognized by C4 MAb, the phage display peptide library was used to screen the C4 MAb-reactive peptides. The sequence alignment of C4 MAb-reactive peptides with potyviral CP sequences indicated that a conserved 12-amino acid (WxMMDGxxQxxY/F) sequence may be recognized by C4 MAb, and thus it was named as the C4 epitope. The results of amino acid substitution analysis indicated that tryptophan and tyrosine residues of C4 epitope are crucial for reacting with C4 MAb. Furthermore, sequence alignment of Hippeastrum mosaic virus (HiMV), which could not be detected by C4 MAb, and amino acid substitution analysis also showed the aspartic acid is also involved in binding with C4 MAb. These results of epitope mapping demonstrated the C4 epitope is a common CP epitope of potyviruses. We also tried to develop the C4 epitope as a new epitope tag. The epitope sequences of ZaMMV, KoMV, and DsMV were separately fused to the C-terminus of CP of Odontoglossum ringspot virus (ORSV), and then epitope-tagged ORSV CPs were expressed in a bacterial system and purified. The results of Western blotting and ELISA showed the C4 epitope of KoMV (Ko) had the strongest binding affinity to C4 MAb. To examine the applicability of Ko tag in planta, the transiently expressed Ko-tagged GFP and ORSV CP could be successfully detected by C4 MAb, and the Ko-tagged P19 of Tomato bushy stunt virus (TBSV) still maintained its silencing suppressor function. Furthermore, Ko-tagged EGFP could be successfully detected and subsequently immunoprecipitated by C4 MAb in a mammalian cell system. These data proved that Ko tag has the potential to become a new epitope tag in bacterial, plant, mammalian cell systems. In the third part, TuMV was used as an experimental material to develop a reverse genetic system. We obtained four full-length clone of TuMV by a two-step cloning method. In the infectivity assay, the p35S-TuMV-27 clone which had similar infectivity to p35S-TuMV-1 revealed much better infectivity than p35S-TuMV-5 and p35S-TuMV-6. The sequence comparison of TuMV-5, TuMV-6 and TuMV-27 clones indicated that they have only 1~3 nucleotide difference at the extreme 5'' end of viral genome. After 5’ replacement and 5’ G deletion analyses, these data verified that the lacking of the adenine at position 7 of 5’ UTR could reduce the infectivity. Besides, the infectious TuMV-27 clone was used to analyze which amino acid residues responsible for the lack of infectivity of pTuMV-T100 clone. Based on unique restriction enzyme sites, three fragments (AB, BH, and HX) of TuMV-T100 were used to separately replace the corresponding fragments of TuMV-27. The result of infectivity assay indicated all of these fragments contain the amino acid mutations affected infectivity. TuMV-AB and TuMV-BH could replicate in protoplasts, but could not infect N. benthamiana and C. quinoa plants. These results indicated that they may be defective in cell-to-cell movement. In contrast, TuMV-HX could induce small local lesions on C. quinoa, but its CP accumulation was lower than that of TuMV-27. The point mutation assay confirmed that CP mutation of Y219N decreased the infectivity of TuMV-27. In addition, other tyrosine mutants (TuMV-Y191A, TuMV-Y219A, and TuMV-Y224A) had similar phenotype as TuMV-Y219N. In transient expression assay, the tyrosine-mutated CP was less stable than wild-type CP. Thus, we suggested that the stability of TuMV CP may be affected by tyrosine phosphorylation.

The generation of recombinant antibodies (Abs) using phage display is a proven method to obtain a large variety of Abs that bind with high affinity to a given antigen. Traditionally, the generation of single-chain Abs depends on the use of recombinant proteins in several stages of the procedure. This can be a problem, especially in the case of cell-surface receptors, because Abs generated and selected against recombinant proteins may not bind the same protein expressed on a cell surface in its native form and because the expression of some receptors as recombinant proteins is problematic. To overcome these difficulties, we developed a strategy to generate single-chain Abs that does not require the use of recombinant protein at any stage of the procedure. In this strategy, stably transfected cells are used for the immunization of mice, measuring Ab responses to immunization, panning the phage library, high-throughput screening of arrayed phage clones, and characterization of recombinant single-chain variable regions. This strategy was used to generate a panel of single-chain Abs specific for the innate immunity receptor Toll-like receptor 2. Once generated, individual single-chain variable regions were subcloned into an expression vector allowing the production of recombinant Abs in insect cells, thus avoiding the contamination of recombinant Abs with microbial products. This cell-based system efficiently generates Abs that bind to native molecules on the cell surface, bypasses the requirement of recombinant protein production, and avoids risks of microbial component contamination.
Dissertation