No description available.

In Nature, antibodies are capable of recognizing a huge variety of different molecular structures on the surface of antigens. The primary factor that defines the structural diversity of the antibody antigen combining site is the length variation of the complementarity determining region (CDR) loops. Following antigen stimulation, further diversification through the process called somatic hypermutation (SHM) leads to antibodies with improved affinity and specificity. Sequence diversification by SHM is mainly achieved by introduction of point substitutions and a small percentage of insertions/deletions (indels). Although the percentage of indels in affinity matured antibodies is low, probably due to the low rate incorporation of in-frame indels throughout the course of the SHM diversification process, it is likely that the antibody fold can accommodate higher diversity of affinity-enhancing indels. By in vitro evolution, other researchers have sampled either only restricted diversity of indels or extended diversity of insertions only in specific positions chosen based on structural information and natural length variation. The aim of this thesis was to study the impact of random and high diversity indels on antibody affinity by in vitro evolution. New approaches for construction of libraries with in-frame amino acid indels were applied to enable sampling of indels of different lengths across the entire antibody variable domains. I followed two different approaches for construction of indel libraries. Firstly, a recently developed random approach allowed the construction of libraries with random insertions and deletions. Secondly, a semi-random approach was developed to build libraries with different lengths of insertions that could be widely applied in future in vitro antibody affinity maturation campaigns. Libraries constructed by either of these approaches yielded variants with insertions with improved affinity. Overall, this thesis demonstrates that insertions besides offering alternative routes to affinity maturation can also be combined with point substitutions to take advantage of additive effects on function.

Affinity maturation increases the affinity of B-cell derived antibodies to their cognate antigens. In this study, we characterized the kinetic, structural, dynamic and thermodynamic evolution of antibodies during affinity maturation. Through single B-cell cell sorting, paired heavy and light chain sequencing, phylogenetic analysis, antibody expression, and physicochemical characterization, we were able to longitudinally analyze the stages of affinity maturation of anti-PA (B.anthracis protective antigen) antibodies. Following repeated immunizations, we observed up to an 10,000-fold increase in antibody affinity, mainly through a decrease in the off-rates. For detailed maturation analysis, we chose three antibodies lying along a single clonal branch--the clone’s unmutated common ancestor (UCA), a medium affinity antibody (MAAb) appearing after second immunization, and a high-affinity antibody (HAAb) appearing after third immunization. Most of the mutations that occur between the UCA and HAAb resulted in key changes to structural conformation. In particular, mutations change residues in the CDR-H3 region inducing the folding of the CDR-loops into a conformation that is more complementary to PA. This advantageous new antibody conformation is preserved in the unbound state, indicating that though the UCA and MAAb appear to use an induced fit and/or conformational selection mechanism, the HAAb is more rigidly lock-and-key. Thermodynamic results support this interpretation. In the first maturation step from UCA to MAAb, enthalpic improvement indicates optimization of noncovalent interactions. The second step from MAAb to HAAb predominantly involves entropic improvement by which the advantageous conformation made accessible in the first step is made more dominant via the narrowing of effectively accessible conformations, which allows better contact with PA. This is also reflected by a less significant improvement in the enthalpic component of PA-binding. Studies examining the evolving protein-dynamic characteristics further support this interpretation. In summary, we observed that a single energetic component is not responsible for increased affinity in the maturation pathways we studied. From UCA to MAAb, affinity increases through optimization of noncovalent interactions. From MAAb to HAAb, affinity increase is achieved through changes that stabilize the favorable conformation in the unbound state. A better understanding of affinity maturation can have implications for antibody engineering and vaccine development.

No description available.

Tumor targeting and molecular imaging of protein markers specific for or overexpressed in tumors can add useful information in deciding upon treatment and assessing the response to treatment for a cancer patient. The epidermal growth factor receptor (EGFR) is one such tumor-associated receptor, which expression is abnormal or upregulated in various cancers and associated with a poor patient prognosis. It is therefore considered a good target for imaging and therapy. Monoclonal antibodies and recently also antibody fragments have been investigated for in vivo medical applications, like therapy and imaging. In molecular imaging a small sized targeting agent is favorable to give high contrast and therefore, antibody fragments and lately also small affinity proteins based on a scaffold structure constitute promising alternatives to monoclonal antibodies. Affbody molecules are such affinity proteins that are developed by combinatorial protein engineering of the 58 amino acid residue Z-domain scaffold, derived from protein A. In this thesis, novel Affibody molecules specific for the EGFR have been selected from a combinatorial library using phage display technology. Affibody molecules with moderate high affinity demonstrated specific binding to native EGFR on the EGFR-expressing epithelial carcinoma A431 cell line. Further cellular assays showed that the EGFR-binding Affibody molecules could be labeled with radiohalogens or radiometals with preserved specific binding to EGFR-expressing cells. In vitro, the Affibody molecule demonstrated a high uptake and good retention to EGFR-expressing cells and was found to internalize. Furthermore, successful imaging of tumors in tumor-bearing mice was demonstrated. Low nanomolar or subnanomolar affinities are considered to be desired for successful molecular imaging and a directed evolution to increase the affinity was thus performed. This resulted in an approximately 30-fold improvement in affinity, yielding EGFR-binding Affibody molecules with KD´s in the 5-10 nM range, and successful targeting of A431 tumors in tumor-bearing mice. To find a suitable format and labeling, monomeric and dimeric forms of one affinity matured binder were labeled with 125I and 111In. The radiometal-labeled monomeric construct, 111In-labeled-ZEGFR:1907, was found to provide the best tumor-to-organ ratio due to good tumor localization and tumor retention. The tumor-to-blood ratio, which is often used as a measure of contrast, was 31±8 at 24 h post injection and the tumor was clearly visualized by gamma-camera imaging. Altogether, the EGFR-binding Affibody molecule is considered a promising candidate for further development of tumor imaging tracers for EGFR-expressing tumors and metastases. This could simplify the stratification of patients for treatment and the assessment of the response of treatment in patients. / QC 20100723

No description available.

B cells play crucial roles in the development of the two human autoimmune diseases, type 1 diabetes (T1D) and systemic lupus erythematosus (SLE). In the past decade, numerous studies showed positive responses of B cell depletion therapies in these two diseases. However, the beneficial effects are temporary and accompanied with adverse events. In this dissertation, we aimed to identify novel targets for a better modulation of disease development using mouse models. These diseases have circulating autoantibodies that are mostly mutated with an IgG isotype, indicating B cells that are producing them have been through the process of affinity maturation. Activation-induced cytidine deaminase (AID) is a core enzyme that regulates somatic hypermutation (SHM) and class switch recombination (CSR), the two key mechanisms in affinity maturation. We showed that genetic ablation of AID significantly inhibited the development of TID in NOD mice. Homologous recombination (HR) pathway is important for the repair of AID-induced DNA double strand breaks during CSR. 4,4'-Diisothiocyano-2,2'-stilbenedisulfonic acid, also known as DIDS, is a small molecule that inhibits HR pathway and subsequently leads to apoptosis of class switching cells. DIDS treatment remarkably retarded the progression of TID, even when started at a relatively late stage, indicating the potential of this treatment for disease reversal. In both approaches, we observed a notable expansion of CD73+ B cells, which exerted an immunosuppressive role and could be responsible for T1D resistance. Next we examined the effect of targeting affinity maturation through these two approaches in lupus-prone mice. The genetic abrogation of AID in BXSB mice significantly ameliorated lupus nephritis and prolonged their lifespan. AID-deficient mice also exhibited improvement on disease hallmarks with increased marginal zone B cells and more normal splenic architecture. DIDS treatment notably reduced class switching when B cells were stimulated in vitro. However, the administration of DIDS did not strikingly alter the course of SLE in either BXSB mice or MRL/lpr mice. These findings demonstrated that affinity maturation could be a potential target for T1D and SLE, while further explorations into targeting other components in the repair pathway are warranted for SLE. Lastly, we assessed the effect of maternal AID modulation on the SLE development in the offspring using BXSB mouse model. Interestingly, the absence of maternal AID resulted in offspring that developed significantly more severe lupus nephritis compared to control. The offspring born to AID-deficient dams also exhibited elevated levels of pathogenic autoantibodies and exacerbated disease features. Therefore, the modulation of maternal AID could influence the SLE development in the offspring, and future investigations are needed to determine the underlying mechanisms responsible for the disease acceleration. / Doctor of Philosophy / The failure of the immune system to differentiate self from non-self leads to the development of autoimmune diseases. Type 1 diabetes (T1D) and systemic lupus erythematosus (SLE) are complex autoimmune diseases affecting millions of people in the world. Despite intensive research regarding these two diseases, no known cure is available indicating an imperative need for the development of novel therapies. With the importance of B cells in the pathogenesis of these two diseases, intensive research focused on whole B cell depletion therapies. However, these therapies exhibited high risks of infections as a result of depleting all the B cells. In this dissertation, we sought to selectively target specific B lymphocyte subsets that are crucial contributing factors in the development of T1D and SLE. While the effect of therapeutic treatment varied among different mouse models, the genetic manipulation of specific B cells successfully retarded the progression of both T1D and SLE and extended the lifespan of the mice. Further studies shed light on the possible mechanisms that are responsible for the disease inhibition. These data proved that targeting specific B cell compartment could be a potential disease management in T1D and SLE patients. In addition, using the established mouse model, we demonstrated the modulation of maternal factors significantly impact the SLE development in the offspring. Future experiments to identify the underlying mechanisms could provide more targets for the therapeutic development.

Antibodies have become indispensable tools in diagnostics, research and as therapeutics. There are several strategies to generate monoclonal antibodies (mAbs) in order to avoid the drawbacks of polyclonal antibodies (pAbs) for therapeutic use. Moreover, the growing interest in precision medicine requires a well-characterized target and antibody to predict the responsiveness of a treatment. This thesis describes the use of epitope information and display technologies to generate and characterize antibodies. In Paper I, we evaluated if the epitope information of a well-characterized pAb could be used to generate mAbs with retained binding characteristics. In Paper II, the epitope on the complement protein C5 towards Eculizumab was mapped with surface display, the results of which explained the non-responsiveness of Eculizumab treatment among a patient group due to a mutated C5 gene. With this in mind, we showed efficacy in treatment of the mutated C5 variants using a drug binding to another site on C5, suggesting that our approach can be used to guide treatment in precision medicine. In Paper III, a Gram-positive bacterial display platform was evaluated to complement existing platforms for selection of human scFv libraries. When combined with phage display, a thorough library screening and isolation of nano-molar binders was possible. In Paper IV, a solid phase method for directed mutagenesis was developed to generate functional affinity maturation libraries by simultaneous targeting of all six CDRs. The method was also used to create numerous individual mutants to map the paratope of the parent scFv. The paratope information was used to create directed libraries and deep sequencing of the affinity maturation libraries confirmed the viability of the combination approach. Taken together, precise epitope/paratope information together with display technologies have the potential to generate attractive therapeutic antibodies and direct treatment in precision medicine. / <p>QC 20170418</p>

Die Modifizierung von Proteinsequenzen unter anderem durch den Austausch von Aminosäuren ist ein zentraler Aspekt in evolutionären Prozessen. Solche Prozesse ereignen sich nicht nur innerhalb großer Zeiträume und resultieren in der Vielfalt des Lebens, das uns umgibt, sondern sind auch täglich beobachtbar. Diese mikroevolutionären Prozesse bilden eine Grundlage zur Immunabwehr höherer Wirbeltiere und werden durch das humorale Immunsystem organisiert. Im Zuge einer Immunantwort werden Antikörper wiederholt der Diversifizierung durch somatische Hypermutation unterworfen. Ziele dieser Arbeit waren, neue Kenntnisse über die Mikroevolution von Antikörpern während der Immunantwort zu gewinnen und die Beziehung zwischen Aminosäureaustauschen und Affinitätsänderungen zu verstehen. Zu diesem Zweck wurde zunächst gezeigt, dass die SPOT Synthese eine präzise Methode ist, um Signalintensitäten drei verschiedenen Bindungsaffinitätsklassen zuzuordnen. Antikörper-Peptid Bindungsdaten, die aus SPOT Synthese Experimenten generiert wurden, bildeten die Grundlage zur Konstruktion der Substitutionsmatrix AFFI - der ersten Substitutionsmatrix, die ausschließlich auf Bindungsaffinitätsdaten beruht. Diese bildete die Grundlage für die Gewinnung eines reduzierten Aminosäuresatzes. Durch einen theoretischen Ansatz konnte gezeigt werden, dass der reduzierte Aminosäuresatz eine optimale Basis für die Epitopsuche darstellt. Für den Prozess der somatischen Hypermutation und Selektion wurde ein neuer Ansatz präsentiert, um für die Affinitätsreifung relevante Mutationen zu identifizieren. Die Analyse zeigte, dass das Spektrum der selektierten Mutationen viel umfangreicher ist als bisher angenommen wurde. Die Tatsache, dass auch einige stille Mutationen stark bevorzugt werden, deutet darauf hin, dass entweder die intrinsische Mutabilität stark unterschätzt wurde oder, dass Selektion nicht nur auf Affinitätsreifung von Antikörpern basiert sondern auch auf ihrer Expressionsrate. / A central task of the evolutionary process is the alteration of amino acid sequences, such as the substitution of one amino acid by another. Not only do these amino acid changes occur gradually over large time scales and result in the variety of life surrounding us, but they also happen daily within an organism. Such alterations take place rapidly for the purposes of defense, which in higher vertebrates, is managed by the humoral immune system. For an effective immune response, antibodies are subjected to a micro-evolutionary process that includes multiple rounds of diversification by somatic hypermutation resulting in increased binding affinity to a particular pathogen. The goal of this work was to provide insights into the microevolution of antibodies during the immune response, including the relationship between amino acid substitutions and binding affinity changes. A preliminary step in this work was to determine the accuracy of the SPOT synthesis technique, which could be shown to be an accurate method for assigning measured signal intensities to three different binding affinity classes. A substitution matrix based on data produced with these binding experiments was constructed and named AFFI. AFFI is the first substitution matrix that is based solely on binding affinity. A theoretical approach has additionally revealed that an AFFI-derived reduced set of amino acids constitutes an optimal basis for epitope searching. For the process of somatic hypermutation and selection, a novel approach to identify mutations relevant to affinity maturation was presented. The analysis revealed that the spectrum of mutations favored by the selection process is much broader than previously thought. The fact that particular silent mutations are strongly favored indicates either that intrinsic mutability has been grossly underestimated, or that selection acts not only on antibody affinity but also on their expression rates.

Ein zentrales Merkmal der humoralen Antwort ist die im Laufe der Zeit ansteigende Affinität der Antikörper gegenüber dem Antigen, ein Phänomen, das man generell als Affinitätsreifung bezeichnet. Die Affinitätsreifung von Antikörpern ist an die transiente Ausbildung von Keimzentren gebunden, die man nach Immunisierung mit einem T-Zell-abhängigen Antigen in sekundär lymphatischen Geweben wie der Milz beobachtet. Innerhalb der Keimzentren durchlaufen B-Zellen einen mikro-evolutionären Prozess, in dessen Verlauf es zu einer Diversifizierung der von den B-Zellen kodierten B-Zell-Rezeptoren durch somatische Hypermutation und anschließender Selektion derjenigen B-Zellen mit den besten Bindungseigenschaften gegenüber dem Antigen kommt. In den letzten Jahren waren große Fortschritte hinsichtlich der Aufklärung der molekularen Mechanismen die zur Diversifizierung der B-Zell-Rezeptoren beitragen zu verzeichnen, wohingegen die Dynamik, der Mechanismus und die treibenden Kräfte der Selektion bisher weitgehend unverstanden sind. In Kürze zusammengefasst trägt die vorliegende Arbeit durch folgende Erkenntnisse zum Verständnis der Evolution von B-Zellen in Keimzentren bei: (1) nicht-synchronisiertes Wachstumsverhalten von Keimzentren, (2) mehrstufige Selektionsstrategie (Verknüpfung von lokaler und globaler Selektion durch Rezirkulation von ausgewanderten Keimzentrums-B-Zellen), (3) zentrale Rolle von Makrophagen für die Homöostase von Keimzentren und die Verhinderung von Autoimmunität, (4) bisher angenommene molekulare Signaturen sind unzulänglich, um positiv und negativ selektierte B-Zellen zu unterscheiden und (5) das Überleben bzw. positive Selektion von Keimzentrums-B-Zellen ist von der Abwesenheit überschüssiger, nachteiliger Mutationen in den CDRs abhängig. / Central to the humoral immune response is the commonly observed improvement of antibody affinity over time, a phenomenon referred to as affinity maturation. Affinity maturation takes place in so-called germinal centers (GC) that are transiently formed in secondary lymphoid tissues (e.g. spleen) following immunization with T cell-dependent antigens. Within GC, B lymphocytes are subjected to a micro-evolutionary process that includes multiple rounds of diversification of their B cell receptors (BCRs) by somatic hypermutation (SHM) and subsequent selection of those B cells showing improved binding characteristics towards the antigen. However, despite recent advances in defining the mechanisms contributing to diversification of B lymphocytes within GC, the dynamics, mechanisms and forces of their selection are poorly understood. The current thesis provides new insights into the evolution of B cells within GC by proposing: (1) non-synchronized GC formation and growth, (2) a multilevel selection strategy (intercalation of local and global selection by recirculation of GC emigrant B cells), (3)a central role for macrophages in retaining germinal center B cell homeostasis and preventing autoimmunity, (4) the failure of commonly supposed molecular signatures to demarcate positively and negatively selected B cells and (5) the survival fate of GC B cells is particularly driven by absence of excess mutations within CDRs that have an adverse effect with respect to antigen binding.