Doctor of Philosophy / Department of Biology / Stephen Chapes / Antibodies are an essential part of the immune system. Each B cell, a type of white blood cell, produces a unique antibody. This antibody molecule is comprised of two identical light chains and two identical heavy chains. Each chain has a variable region, which is responsible for antigen binding, and a constant region, which is responsible for effector function in the host. The variable region in the heavy chain is composed of three gene segments, the variable (V), diversity (D), and joining (J) gene segments. The light chain is composed of only V- and J-gene segments. Each immunoglobulin locus contains multiple versions of each gene segment, ranging from over 130 possible V gene segments in the heavy chain to four possible J-gene segments in both the heavy and kappa light chain. The recombination of gene segments occurs in the germline DNA and results in the formation of the unique antibody. The diversity and binding abilities of the antibodies are important for a proper and robust immunological response. Of importance to binding and specificity is the complementary determining region three (CDR3) which plays a major role in determining specificity and antibody-antigen binding. Due to its uniqueness, is used as a measure of diversity in the repertoire. In this work, I used Illumina MiSeq 2x300nt high-throughput sequencing to assess the mouse splenic transcriptome. The work I present here shows the splenic immunoglobulin gene repertoire from unchallenged, unvaccinated conventionally housed mice, mice flown aboard the International Space Station (ISS), and mice challenged with tetanus toxoid (TT) and/or adjuvant (CpG) and subjected to skeletal unloading by antiorthostatic suspension (AOS). AOS is used to induce some of the physiological changes that parallel those that occur during space flight. The characterization of the repertoire includes analysis of V-, D-, and J-gene segment usage, constant region usage, V- and J-gene segment pairing, and CDR3 length and usage. The work included validation of the methodology needed for tissue preparation and storage aboard the ISS, showing that the data obtained was similar to those used in standard ground-based methodologies (Chapter 2). I further validated our nonamplified sequencing methodology with comparisons to methods that use amplification as part of the process (Chapter 3). My work characterized the antibody repertoire of the conventionally housed C57BL/6J mouse (Chapter 4), an important mouse strain in the field of immunology, and demonstrated the homogeneity of gene segment usage in unchallenged animals. We also demonstrated that short duration (~21 days) space flight does not significantly alter the antibody repertoire (Chapter 5). The work culminates in an AOS study to assess changes to the B-cell immunoglobulin repertoire after vaccination with TT and/or CpG. The results show that changes to V-, D-, and J-gene segment usage occur after antigen challenge with AOS causing decreased class switching and frequency of plasma cells. Tetanus toxoid challenge decreased multiple gene segment usage and CpG administration increased isotype switching to the IgA constant region (Chapter 6).

B lymphopoiesis in aged mice is characterized by reduced B cell precursors and an altered antibody repertoire. Aged mice maintain an ordinarily minor pool of early c-kit+ pre-B cells, indicative of poor preBCR expression, even as preBCR competent early pre-B cells are significantly reduced. Therefore, in aged mice, preBCR-mediated B2 B lymphopoiesis is significantly diminished; likely as a consequence of poor surrogate light chain expression. Notably, the remnant B1 B cell lineage present in adult bone marrow is retained in aged mice as evidenced by normal numbers (~0.3%) of Lin-CD19+B220low/- B1 B cell precursors. Of interest, B1 progenitors express substantially less lambda 5 surrogate light chain protein than do B2 pro-B cells and the surrogate light chain levels are further reduced in aged mice. B cells derived from putatively preBCR-deficient precursors, either B2 c-kit+ B cell precursors or B1 B cell progenitors, from either young or aged mice, generate new B cells in vitro that are biased to larger size, higher levels of CD43/S7, and decreased kappa light chain expression. Notably, immature B cells in aged bone marrow exhibit a similar phenotype in vivo, consistent with the changes seen in B cell precursor subpopulations. In aged mice, the B2 pathway is partially blocked with limited preBCR expression and signaling; however, continued B cell development via preBCR-deficient pathways, including B1 pathways, is observed. Increased generation of new B cells by these alternative pathways may contribute to altered phenotype, repertoire, and function in senescence.

Specific and sensitive recognition of foreign agents is a critical attribute of the overall effective immune system required for maintaining host protection against challenge from pathogenic cells. In the humoral arm of the immune system, this recognition attribute is carried out by the cell surface bound immunoglobulin-like receptors (BCR) and its soluble forms i.e. antibodies. Over several million years of evolution, the immune system has adopted several strategies for diversifying the antibody sequence and thus its ability to recognize an astronomical variety of molecules through the combinatorial assembly of a small number of DNA segments or genes. Among these immunoglobulin gene diversification strategies, antibody somatic VDJ recombination and junctional diversity are the fundamental mechanisms in generating a broad range of antibody specificities. Understanding how the genetic diversity of antibodies is affected in health and disease is critical for a wide range of medical applications, from vaccine evaluation to diagnostics and therapeutics discovery. Because of the very large number of distinct antibodies encoded by the more than 100 billion B cells in humans, it is essential to use high throughput next generation sequencing technologies in order to obtain an adequate sampling of the sequences and relative abundance of different antibodies expressed by B cells in clinical samples. The process requires rigorous methods for first, experimentally determining the sequences of antibodies in a sample and for second, informatics tools designed for distilling this information for practical purposes. This dissertation describes a variety of experimental approaches and informatics tools developed for the determination and mining of the antibody repertoire. The information from this work has led to major conclusions regarding the nature of the antibody repertoire in healthy individuals, in volunteers following vaccination, and in HIV-1 patients. / text

Master of Science / Department of Biology / Stephen K. Chapes / Immunoglobulins are receptors expressed on the outside of a B cell that can specifically bind pathogens and toxic substances within a host. These receptors are heterodimers of two chains: heavy and light, which are encoded at separate loci. Enzymatic splicing of gene segments at heavy and light chain loci within the genomic DNA in every B cell results in a highly diversified and specific repertoire of immunoglobulins in a single host. Spaceflight is known to affect reduce splenic B cell populations and B cell progenitors within the bone marrow, potentially restricting the diversity of the immunoglobulin repertoire (Ig-Rep). The objective of this thesis project was to characterize the impact of spaceflight on the kappa light-chain Ig-Rep of the C57BL/6 mouse. High-throughput sequencing (HTS) technologies have enabled the rapid characterization of Ig-Reps, however, standard Ig-Rep workflows often rely the amplification of immunoglobulin sequences to ensure the capture immunoglobulin sequences from rare B cell clones. Additionally, the Ig-Rep is often assessed in sorted B cell populations. Opportunities for spaceflight experiments are limited and costly, and the exclusive amplification of immunoglobulin sequences prior to HTS results in a dataset that cannot be mined for additional information. Furthermore, due to the difficulties of tissue collection in spaceflight, HTS of sorted B cell populations is not feasible. We optimized a protocol in which the Ig-Rep was assessed from unamplified whole tissue immunoglobulin transcripts. The Ig-Rep was characterized by gene segment usage, gene segment combinations and the region in which gene segments are joined. HTS datasets of ground control animals and animals flown aboard the International Space Station were compared to explore the impact of spaceflight on the unimmunized murine Ig-Rep.

Doctor of Philosophy / Department of Diagnostic Medicine and Pathobiology / Raymond R. R. Rowland / Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the most costly virus to the swine industry, worldwide. This study explored the application of deep sequencing techniques to understand better the virus-host interaction. On the virus side, PRRSV exists as a quasispecies. The first application of deep sequencing was to investigate amino acid substitutions in hypervariable regions during acute infection and after virus rebound. The appearance and disappearance of mutations, especially the generation of a new N-glycosylation site in GP5, indicated they are likely the result of immune selection. The second application of deep sequencing was to investigate the quasispecies makeup in pigs with severe combined immunodeficiency (SCID) that lack B and T cells. The results showed the same pattern of amino acid substitutions in SCID and normal littermates and no different mutations were identified between SCID and normal littermates. This suggests the mutations that appear during the early stages of infection are the product of the virus becoming adapted to replication in pigs. The third application of deep sequencing was to investigate the locations of recombination events between GFP-expressing PRRSV infectious clones. The results identified different cross-over occurred within three conserved regions between EGFP and GFPm genes. And finally, the fourth goal was applied to develop a set of sequencing tools for analyzing the host antibody repertoire. A simple method was developed to amplify swine VDJ repertoires. Shared and abundant VDJ sequences that are likely expressed by PRRSV-activated B cells were determined in pigs that had different neutralization activities. These sequences are potentially correlated with different antibody responses.

Streptococcus pneumoniae is a significant cause of mortality and morbidity in both children and older adults, with infection resulting in invasive disease, pneumonia and otitis media. The inclusion of pneumococcal conjugate vaccines in routine infant immunisation programmes has had a major impact on disease rates. Vaccine-induced protection against pneumococcal infection is thought to be mediated by the generation of persistent serotype-specific functional antibodies and antigen-specific memory B cells, the latter capable of generating a rapid secondary antibody response on re-exposure to antigen. Although many studies have investigated the immunogenicity of pneumococcal vaccines in different age groups by measuring serotype-specific antibodies, there is more limited information about the B cells underlying such an immune response. Important areas to investigate include the identity of the B cell subsets involved in antibody production and the potential link between memory B cells (B_MEM) and persistent antibody production by long-lived plasma cells. In this thesis I have investigated in detail the immune response to pneumococcal vaccines given to children and adults by a variety of different methods. By examining the variability of a B_MEM ELISpot method, it was shown that this assay is robust and reproducible and can be performed on fresh or frozen samples and in different laboratories. Using this technique, in a study of pre-school children, it was demonstrated for the first time that the level of pre-existing serotype 3-specific antibody is negatively correlated with, and may directly impair the B_MEM response to a booster dose of 13-valent pneumococcal conjugate vaccine (PCV-13) containing serotype 3 glycoconjugate. In the same study, it was shown that antibody persistence against most vaccine serotypes can be expected until the age of 3.5 years. A novel antigen-labelling technique was used in a detailed kinetics study of antigen-specific B cell subsets in response to either PCV-13 or 23-valent pneumococcal polysaccharide vaccine in adults. The results of this study revealed distinct B cell subset response patterns that were observed in all study participants indicating that IgM B_MEM seem to play a major role in the immune response to pneumococcal vaccines. In addition, in the same study, genome wide analysis of gene expression was performed and it was shown that vaccination with either a pneumococcal conjugate or polysaccharide vaccine results in a marked difference in numbers of differentially expressed genes 8 days following vaccination. A further tool likely to be of use in investigating B cell responses is the analysis of the antibody repertoire using next-generation sequencing techniques. In order to test the ability of these methods to detect vaccine responses, a large dataset of high-throughput B cell receptor sequences was analysed and revealed convergence of antigen-specific complementary-determining region (CDR)₃ amino acid (AA) sequences following vaccination and identified antigen-specific sequences. It was further demonstrated that for sequences directed against the H. influenzae type b (Hib) polysaccharide, diversity of immunoglobulin gene rearrangements is much greater than previously recognised. Frequencies of Hib-specific CDR₃ AA sequences were linked with anti-Hib avidity indices highlighting the potential of this method as an alternative (functional) measure of vaccine immunogenicity. These data suggest that studying the B cells and antibody repertoire post-vaccination can give novel insights into the biology that underlies the immune responses.

Le système immunitaire adaptatif joue un rôle de premier plan dans la défense contre les infections. La réponse humorale, impliquant la production d'anticorps, est un élément important de la réponse immunitaire adaptative. Au cours d'une infection, des cellules B spécifiques du système immunitaire prolifèrent et libèrent de grandes quantités d'anticorps qui se lient sélectivement à la protéine cible (antigène) trouvée sur le pathogène invasif, induisant la destruction du pathogène.Cependant, le système immunitaire ne répond pas toujours suffisamment efficacement pour détruire les agents pathogènes, et les mécanismes de tolérance empêchent la génération d'anticorps contre les protéines humaines - comme les marqueurs de surface cellulaire sur les cellules cancéreuses ou les cytokines impliquées dans des maladies inflammatoires et auto-immunes - qui pourraient être des cibles thérapeutiques importantes. Par conséquent, il existe un grand intérêt pour la recherche et le développement d'anticorps spécifiques qui peuvent être utilisés pour le traitement des patients par immunothérapie. En raison de leur grande affinité et de leur liaison sélective aux antigènes, les anticorps monoclonaux (mAbs) sont apparus comme des agents thérapeutiques puissants. Les anticorps monoclonaux dérivés de cellules B individuelles ont une séquence unique et présentent une affinité de liaison pour un antigène spécifique. Cependant, jusqu'à maintenant, la découverte des mAbs a été limitée par l'absence de méthodes à haut débit pour le criblage direct et à grande échelle de cellules B primaires non immortalisées pour découvrir les rares cellules B qui produisent des anticorps spécifiques d'intérêt clinique. Ceci est maintenant possible avec l'émergence et l'amélioration des méthodes de compartimentation in vitro pour l'encapsulation et le criblage de cellules uniques dans des gouttelettes picolitriques. Dans mon projet de doctorat, je décris le développement d'immunodosages et de dispositifs microfluidiques pour le criblage phénotypique direct de cellules individuelles à partir de populations de cellules B enrichies. Ce développement a permis une analyse détaillée de la réponse immunitaire humorale, avec une résolution à l’échelle de la cellule unique. C’est aussi un élément essentiel d'un pipeline de détection d'anticorps couplant le criblage phénotypique de cellules individuelles au séquençage d'anticorps sur cellules uniques. Il est maintenant possible, pour la première fois, de cribler des millions de cellules B individuelles en fonction de l'activité de liaison des anticorps sécrétés et de récupérer les séquences d'anticorps / The adaptive immune system plays a leading role in defense against infection. The humoral response, involving the production of antibodies, is an important component of the adaptive immune response. During an infection, specific B cells of the immune system proliferate and release large amounts of antibodies which bind selectively to the target protein (antigen) found on the invading pathogen, inducing destruction of the pathogen. However, the immune system does not always respond efficiently enough to destroy pathogens, and tolerance mechanisms prevent the generation of antibodies against human protein - such as cell surface markers on cancer cells or cytokines involved in inflammatory and autoimmune disease - that could be important therapeutic targets. Hence, there is great interest in research and development of specific antibodies that can be used for immunotherapy of patients. Due to their high affinity and selective binding to antigens, monoclonal antibodies (mAbs) have emerged as powerful therapeutic agents. Monoclonal antibodies derived from single B cells have a unique sequence and display binding affinity for a specific antigen. However, until now, the discovery of mAbs has been limited by the lack of high-throughput methods for the direct and large-scale screening of non-immortalized primary B cells to uncover rare B cells which produce the specific antibodies of clinical interest. This is now becoming possible with the emergence and improvement of in vitro compartmentalization methods for single-cell encapsulation and screening in picoliter droplets. In my PhD project, I describe the development of binding immunoassays and microfluidic devices for the direct phenotypic screening of single-cells from enriched B cell populations. This development has enabled detailed analysis of the humoral immune response, with single-cell resolution and is an essential component of an antibody-discovery pipeline coupling single-cell phenotypic screening to single-cell antibody sequencing. It is now possible, for the first time, to screen millions of single B cells based on the binding activity of the secreted antibodies and to recover the antibody sequences