CHARACTERIZATION OF CARBOHYDRATE BASED VACCINES Variables influencing the immunogenicity and physicochemical properties of glycoconjugate vaccinesMany aspects can influence the immunogenicity of conjugate vaccines and the main variables investigated so far are the size of the saccharide moiety, the saccharide:protein ratio in the purified conjugate, the conjugation strategy, the nature of the spacer and the protein carrier. The size of the saccharide moiety and saccharide/protein ratio were investigated in different works such as Seppälä and Mäkelä in one of the first studies on the effect of size and chemistry on the immunogenicity of dextrans-protein conjugates found that dextrans of low molecular weight conjugated to chicken serum albumin, induced strong anti-dextran responses in mice, while increasing the dextrans' size resulted in reduced immunogenicity.47 Peeters et al. showed that a synthetic tetramer of Hib capsular polysaccharide repeating unit, conjugated to a protein carrier, induced in adult mice and non-human primates antibody levels comparable to a commercial Hib conjugate and higher than those induced by a trimer, indicating that for Hib a minimum of eight sugars is needed for a proper immunological response.48 Laferriere et al. found little influence of the carbohydrate chain length on the immunogenicity of pneumococcal conjugate vaccines in mice.49 Pozsgay et al. studied the immunogenicity in mice of synthetic Shigella dysenteriae type 1 LPS oligosaccharides conjugated to human serum albumin (HSA). The authors found that octa-, dodeca-, and hexadecasaccharide fragments induced high levels of lipopolysaccharide binding IgG antibodies in mice after three injections and were superior to a tetrasaccharide conjugate. The influence of the carbohydrate/protein ratio was different for the three conjugates. The octasaccharide-HSA conjugate with the highest density evoked a good immune response, while in the case of dodeca- and hexadecasaccharide conjugates, the median density was optimal.50 These studies suggest that oligosaccharide chain length and hapten loading might be interconnected in determining the immunogenicity of glycoconjugate vaccines. The spacer is a short linear molecule that is generally linked to the polysaccharide chain or to the protein or to both moieties, depending on the chemistry, used to facilitate the coupling between the protein and sugar. There are evidences in the literature which suggest that rigid, constrained spacers like cyclohexyl maleimide, elicit a significant amount of undesirable antibodies, with the risk of driving the immune response away from the targeted epitope on the hapten.51 52 The use of a flexible alkyl type maleimido spacer has been reported as a way to overcome the previous observed immunogenicity of cyclic maleimide linkers.53 A number of protein carriers have been used so far in preclinical and clinical evaluation of conjugate vaccines. 54 55 56 57 58 59 60Proteins such as diphtheria and tetanus toxoids, which derive from the respective toxins after chemical detoxification with formaldehyde, were initially selected as carrier because of the safety track record accumulated with tetanus and diphtheria vaccination. CRM197, a non-toxic mutant of diphtheria toxin61 which instead does not need chemical detoxification, has been extensively used as carrier for licensed Hib, pneumococcal, meningococcal conjugate vaccines and for other vaccines being developed. An outer membrane protein complex of serogroup B meningococcus has been used by Merck as carrier for their Hib conjugate vaccine.62 GSK in their multivalent pneumococcal conjugate vaccine introduced the use of the Hib-related protein D as carrier for most of the polysaccharides included into the vaccine.63 64 The team of John Robbins made extensive use of the recombinant non toxic form of Pseudomonas aeruginosa exo-toxin as carrier for Staphylococcus aureus type 5 and 8 as well as for Salmonella

UDP-galactopyranose mutase (EC 5.4.99.9; UGM), the product of the glf gene, is an enzyme that catalyzes the conversion of uridine diphosphate galactopyranose (UDP-Galp) to UDP-galactofuranose (UDP-Galf). UGM activity is found in bacteria, parasites and fungi, however is absent in higher eukaryotes. This enzyme is essential for the viability of many pathogenic organisms, such as Mycobacterium tuberculosis and Escherichia coli, due to the broad distribution of Galf in crucial structures such as the cell wall or capsular polysaccharide. Not surprisingly, galactofuranose biosynthesis has become an attractive antimicrobial target due to the absence of these sugars in higher eukaryotes. The UGM homologue, UDP-Nacetylgalactopyranose mutase (UNGM), was identified in Campylobacter jejuni 11168, encoded for by the cj1439c gene. UNGM is known to function as a bifunctional mutase, which catalyzes the reversible ring contraction between the pyranose-furanose forms of UDPgalactose (UDP-Gal) and UDP-N-acetylgalactosamine (UDP-GalNAc). UNGM is essential for the virulence of C. jejuni, due to the incorporation of UDP-N-acetylgalactofuranose into the capsular polysaccharide. We report the first structure of UNGM determined by X-ray crystallography, to a resolution of 1.9 Å. Analysis of the dimeric, holoenzyme structure of UNGM has identified that the cofactor flavin adenine dinucleotide is bound within each monomer of the enzyme. Comparative analysis with UGM homologues has confirmed the conserved active site residues involved in the binding of various substrates. Docking studies suggest that UNGM binds its natural substrates in a productive binding mode for catalysis with the flavin cofactor, which is consistent with the proposed mechanism for UNGM. The mobile loops are essential for substrate binding, and we have identified that the conserved arginine residue, Arg169, and the neighboring Arg168, function to stabilize the diphosphate region of UDP, although not concurrently. The non-conserved arginine residue, Arg168, appeared to favor the stabilization of N-acetylated sugars, which is in agreement with the enzyme’s higher binding affinity for UDP-GalNAc over UDP-Gal by a factor of 0.9. We have also identified that the active site Arg59 exists in two conformations in the structure of UNGM, with one conformation directed toward the active site. Arg59 is 2.5 to 3.0 Å from the acetamido moiety of GalNAc, which is favorable for stabilization and is believed to confer specificity for this substrate.

Breast implant capsular contracture (CC) formation is a significant clinical complication post augmentation/reconstruction, which often necessitates re-operation. CC, which occurs in over half of patients post augmentation, is the formation of a fibrous internal capsule which constricts around the prosthesis leading to firmness, deformity and pain. The pathoetiology of CC is poorly understood with minimal understanding of the triggers, signalling pathways or dysregulated genes implicated in its formation. Therefore, the first aim of the present thesis was to investigate biomarkers implicated in CC formation, through whole genome microarray, quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC) on capsule samples ranging from normal capsules (Baker Grade 1) to severely contracted capsules (Baker Grade 4). After targeted enrichment analysis, microarray identified 6 genes which were significantly dysregulated in contracted capsules. After further genomic and proteomic validation, two potential diagnostic, prognostic or therapeutic biomarkers for CC, interleukin 8 (IL8) and tissue inhibitor of metalloproteinase 4 (TIMP 4), were identified as being significantly dysregulated in CC. However, the role of each of the multiple cell types which populate a contracted capsule has yet to be determined. Therefore, the role of capsular fibroblasts was investigated using immunocytochemistry, qRT-PCR, cytokine arrays and a fibroblast populated 3D collagen matrix. IL8 and TIMP were investigated, in addition to other pro-fibrotic and pro-inflammation related candidates, to identify the role of breast capsule fibroblasts in CC formation. Normal breast fibroblast populated collagen matrices were significantly more contracted after supplementation with contracted-capsule fibroblast conditioned media, in comparison to normal growth media. It was discovered that breast-derived fibroblasts were potentially instigating and/or perpetuating CC through the transformation of normal breast fibroblasts into contracted capsule fibroblast like cells, via a paracrine signalling mechanism. The results of this work on capsular fibroblasts, and the previous work on capsular tissue, increased our understanding of the cell types and signalling molecules which are dysregulated leading to CC formation. Therefore, a novel silicone implant surface potentially capable of averting CC formation could be fabricated. Acellular dermal matrix (ADM) has been used as an adjunct in breast implant augmentation/reconstruction resulting in reduced rates of CC formation. Therefore, the micro and nanoscale topography of ADM was reproduced in a silicone surface, through a novel fabrication technique utilising comprehensive characterisation of ADM with atomic force microscopy (AFM), maskless grayscale photolithography, modified deep reactive ion etching (DRIE) and replica moulding. The features of ADM were successfully re-created in silicone to within 5 nm (Sa) and 655 nm (Sz), at a length scale of 90x90 µm2. Biological evaluation revealed that ADM PDMS surfaces promoted cell adhesion, proliferation and survival when compared to commercially available implant surfaces while cell adhesion regulating genes were upregulated and pro-inflammatory/pro-fibrotic related genes were downregulated. A reduced inflammatory cytokine response was also observed. This study demonstrates that biomimetic prosthetic implant surfaces might significantly attenuate the acute in vitro foreign body reaction to silicone. In conclusion, the results of the present thesis have enhanced our knowledge and understanding of the pathological cellular and molecular mechanisms leading to CC, in addition to the design and development of a novel, biomimetic implant surface that is potentially capable of averting the identified pathological processes in vivo.

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Haemophilus parasuis is a Gram-negative bacterium responsible for Glasser's Disease in pigs, though little is known regarding its antigenic or virulence factors. Our goals were to characterize the H. parasuis capsular polysaccharide (CP), determine its role in serotype-specificity and virulence, determine if CP is immunogenic, and develop diagnostic and protective products to prevent rampant H. parasuis infection within swine herds. Material from H. parasuis was purified using carbohydrate isolation techniques and compared to CPs from other Pasteurellaceae. Rabbits were immunized with CPs to generate antisera for microscopy, immunoassays, and bactericidal assays. CP antisera were conjugated to latex particles to create an agglutination assay for detection and typing of H. parasuis. CP was conjugated to Cholera Toxin B, and used to immunize mice and piglets before challenge with H. parasuis to determine its protective efficacy against Glasser's Disease. Broth-grown cells expressed CP, which reacted with antisera in microscopy and immunoassays. Broth-grown H. parasuis cells were serum-resistant unless homologous anti-CP serum was present. In contrast, agar-grown cells did not react with antisera in immunoassays, and cells were susceptible to killing by normal swine serum. CP was not expressed on the surface of agar-grown cells unless supplemented with bicarbonate. The addition of bicarbonate also contributed to the variability in CP quantity and upregulation of genes in the CP locus. Sensitized latex particles agglutinated strongest with homologous H. parasuis CPs, cells, and agar-grown cell lysates, but also reacted weakly with higher concentrations of heterologous CPs. The latex beads did not agglutinate with non-H. parasuis swine bacterial pathogens. Mice immunized with the CP-CTB conjugate produced a significantly higher IgG2/Th2 response than unimmunized mice or mice immunized with only CP, and immunized mice had fewer bacteria in their tissues that unimmunized mice. The CP conjugate produced a robust IgG antibody response to CP when used to immunized piglets, but because the control animals also survived H. parasuis challenge, the protective efficacy remains inconclusive. Therefore, the H. parasuis CP is the antigen that confers serotype identity, and can be implemented in methods and help direct future research in disease prevention and serotype tracking in H. parasuis infections. / Ph. D.

As the survival rate increases, the importance of quality of life post-cancer is increasing. This, in conjunction with genetic screening, has increase the number of breast reconstructions 36%. The most common complication causing revision of reconstructive surgery is the formation of a dense scar capsule around the silicone implant called capsular contracture. Nearly all patients will experience this complication, though with different degrees of response, ranging from moderate scarring to major disfigurement and pain at the implant site. Presently, there is no way to predict the degree of contraction capsule formation that individual patients will suffer prospectively, nor is there clinical approach to preventing this complication. Patient information and tissue was collected in a uniform manner to address these lingering problems. Clinical data was used to construct a predictive model which can accurately predict capsular contracture severity in breast reconstruction patients. Histological analysis demonstrated differences in structure and cell composition between different capsule severities. Of particular note, a new region was described which could serve as the communication interface between innate immune cells and fibroblasts. RNA-seq analysis identified 1029 significantly dysregulated genes in severe capsules. Pathway enrichment was then performed which highlights IL4/13 signaling, extracellular matrix organization, antigen presentation, and interferon signaling as importantly dysregulated pathways. These RNA results were also compared to various clinical and histological measurements to evaluate novel correlations. PVT-1, a long non-coding RNA associated with cancer, was strongly correlated to capsules formed after cancer removal. This suggests cancerous transformations of cell types that remain after the tumor is removed. Furthermore, transgelin and caspase 7 correlated to myofibroblasts density, suggesting an abnormal fibroblasts that are resistant to cell death and may have enhanced contractile abilities. Capsule formation is a complex process however, with well controlled clinical models quantitative differences can be found. These results serve as stepping stone for the field to move beyond retrospective clinical trials and pursue treatments and preventative measures. / Ph. D.

<p>Streptococcus agalactiae, also designated group B streptococcus (GBS), is a Gram-positive coccus, and it is an important pathogen that causes invasive disease in neonates, pregnant adults, and non-pregnant adults with predisposing conditions. The group II intron GBSi1 is one of the major mobile genetic elements identified in S. agalactiae. The aim of this thesis was to characterize the GBSi1 distribution pattern, the population structure, and the influence of serotype- and clone-specific properties on the invasive capacity among clinical invasive and non-invasive isolates of S. agalactiae.</p><p>Two additional copies of GBSi1 were identified at sites different from the primarily identified scpB-lmb locus. The distribution of GBSi1 was uneven among different serotypes. Three intron copies were only found in isolates of serotype III, and these targeted all the three identified gene loci. In contrast, a single copy of GBSi1 was found in isolates of serotype II and V and only located at the scpB-lmb locus. Furthermore, at the 5′ flanking region of the scpB-lmb gene locus, a novel 2.1 kb DNA fragment with plasmid features was identified only in intron carrying isolates. This may suggest that GBSi1 once was brought into the S. agalactiae genome by an integrated plasmid.</p><p>Multilocus sequence typing was used to characterize totally 314 invasive and non-invasive S. agalactiae isolates collected in Northern and Western Sweden from the years 1988 to 2004. Five major genetic lineages (clonal complexes) were identified among both invasive and non-invasive isolates, including serotype Ia, Ib, and II to V, indicating a clonal population structure of S. agalactiae isolates. A number of genetically highly related isolates were found to express different capsular types, suggesting that capsule switching occurs rather frequently between isolates. Furthermore, non-invasive isolates belonging to the same clonal complexes displayed more heterogeneity in capsule expression as well as in the distribution patterns of mobile genetic elements than invasive isolates. This indicates that less variability is allowed in a highly selective environment such as the blood. All major clonal complexes and serotypes caused invasive disease, although their ability to do so varied greatly. CC17 was significantly associated with neonatal invasive disease; whereas CC19 was equally common among isolates from adult and neonatal disease, despite that both CC17 and CC19 expressed capsular type III. This striking difference seen between CC17 and CC19 suggests that clonal complex associated properties, in addition to capsular type, play important roles in the virulence of S. agalactiae. CC1, a new emerging clone since early 1990s, has caused substantial amount of disease among adults. In addition, mutually exclusive distribution of mobile elements GBSi1 and IS1548 was seen, and they were shown to constitute genetic markers for serotype III CC17 and CC19 isolates, respectively.</p>

Streptococcus agalactiae, also designated group B streptococcus (GBS), is a Gram-positive coccus, and it is an important pathogen that causes invasive disease in neonates, pregnant adults, and non-pregnant adults with predisposing conditions. The group II intron GBSi1 is one of the major mobile genetic elements identified in S. agalactiae. The aim of this thesis was to characterize the GBSi1 distribution pattern, the population structure, and the influence of serotype- and clone-specific properties on the invasive capacity among clinical invasive and non-invasive isolates of S. agalactiae. Two additional copies of GBSi1 were identified at sites different from the primarily identified scpB-lmb locus. The distribution of GBSi1 was uneven among different serotypes. Three intron copies were only found in isolates of serotype III, and these targeted all the three identified gene loci. In contrast, a single copy of GBSi1 was found in isolates of serotype II and V and only located at the scpB-lmb locus. Furthermore, at the 5′ flanking region of the scpB-lmb gene locus, a novel 2.1 kb DNA fragment with plasmid features was identified only in intron carrying isolates. This may suggest that GBSi1 once was brought into the S. agalactiae genome by an integrated plasmid. Multilocus sequence typing was used to characterize totally 314 invasive and non-invasive S. agalactiae isolates collected in Northern and Western Sweden from the years 1988 to 2004. Five major genetic lineages (clonal complexes) were identified among both invasive and non-invasive isolates, including serotype Ia, Ib, and II to V, indicating a clonal population structure of S. agalactiae isolates. A number of genetically highly related isolates were found to express different capsular types, suggesting that capsule switching occurs rather frequently between isolates. Furthermore, non-invasive isolates belonging to the same clonal complexes displayed more heterogeneity in capsule expression as well as in the distribution patterns of mobile genetic elements than invasive isolates. This indicates that less variability is allowed in a highly selective environment such as the blood. All major clonal complexes and serotypes caused invasive disease, although their ability to do so varied greatly. CC17 was significantly associated with neonatal invasive disease; whereas CC19 was equally common among isolates from adult and neonatal disease, despite that both CC17 and CC19 expressed capsular type III. This striking difference seen between CC17 and CC19 suggests that clonal complex associated properties, in addition to capsular type, play important roles in the virulence of S. agalactiae. CC1, a new emerging clone since early 1990s, has caused substantial amount of disease among adults. In addition, mutually exclusive distribution of mobile elements GBSi1 and IS1548 was seen, and they were shown to constitute genetic markers for serotype III CC17 and CC19 isolates, respectively.