Background During the first stages of development human infants are either fed human milk or human milk substitutes (infant formulas). The composition of infant formulas and human milk differ drastically, including a difference in protein constituents and bacterial load. Due to the high global frequency of infant formula use, the humanization of infant formulas to better reflect the complex nature of human milk is warranted. To better understand the role of human milk components, the fate and function of a key bacterial sensor in human milk, soluble CD14, was determined. Additionally, the microbiome of human milk was analyzed from a metagenomic standpoint in an attempt to determine which types of bacteria are present in human milk and what their potential biological function might be. Results In rodent models, ingested sCD14 persisted in the gastrointestinal tract and was transferred intact into the blood stream. Once transferred to the blood, ingested sCD14 retained its ability to recognize lipopolysaccharide and initiate an immune response in pups. This transfer of sCD14 across the epithelial barrier was also observed in human cells in vitro, where it appears to be dependent on Toll-like receptor 4. Using Illumina sequencing and the MG-RAST pipeline, the human milk metagenome of ten mothers was sequenced. DNA from human milk aligned to over 360 prokaryotic genera, and contained 30,128 open reading frames assigned to various functional categories. The DNA from human milk was also found to harbor immune-modulatory DNA motifs that may play a significant role in immune development of the infant. Conclusions Given the complex nature of human milk in comparison to its bovine or plant based substitutes, the results presented in this thesis warrant future modification of infant formulas to include non-nutritive bioactive components. Current human milk components not yet present in infant formulas include the diverse microbiome of human milk, the immune-modulatory DNAs which those microbes harbor, and bioactive human proteins such as sCD14.

The mucosal antibody repertoire of the cervical mucosa in commercial sex workers from Nairobi, Kenya, who are highly sexually exposed to human immune deficiency virus type-1 (HIV-1) but remain persistently IgG seronegative (HEPS), may represent a novel source of broadly neutralizing monoclonal antibodies (mAbs) against HIV-1. Mucosal IgA specific for HIV-1 envelope (Env) subunit gp41 has been suggested as a correlate of protection in HEPS individuals. The in depth studies at both the gene and function level required to confirm their role in HIV-1 resistance are possible only using recombinant monoclonal IgAs. Human mAbs have traditionally been selected from libraries displayed on the surface of microorganisms (phage, yeast). However, due to inherent limitations, such techniques may not be optimal for isolating such rare mAbs from a pool of cervical B cells. We have developed an antibody selection system based on surface display on mammalian cells and used this technology to isolate four novel monoclonal antibodies, against linear epitopes on gp41, from the IgA repertoire of the cervical mucosa in Kenyan HEPS. Furthermore, three of the four mAbs were shown to bind with surface expressed consensus clade B and clade C Env on mammalian cells. Characterization of the variable region cDNA of the two strongest binding mAbs reveals extensive somatic mutations with a bias of replacement mutations clustering in the complementary determining regions (CDR) indicating antigen-driven affinity maturation had occurred. Affinity matured monoclonal IgAs, such as these, may play a role in the identification of new, vulnerable epitopes on HIV-1, or act as a component in a topical microbicide.

Surfactant protein D (SP-D) is an important innate immune collectin involved in uptake and clearance of microbes and allergens in the lungs. SP-D has been shown to ameliorate allergic asthma reactions in mice; however, the mechanisms for this are not fully understood. We investigated the role of SP-D in the uptake and clearance of the model allergen ovalbumin (OVA) by macrophages. We discovered that SP-D does not bind OVA but binds fractions with contaminating proteins; ovomucin and ovomacroglobulin. We extended these findings to show that SP-D binds human alpha-2-macroglobulin (A2M) in its cleaved or intact state, in a concentration-, calcium-, and carbohydrate-dependent manner. A2M increases the innate immune potential of SP-D by increasing its ability to agglutinate the bacteria Escherichia coli and Bacillus subtilis. We found that SP-D does not increase the uptake of OVA by murine macrophage cell lines, or by alveolar macrophages in vivo in BALB/cJ mice.

The lysosomal-associated protein transmembrane 5 (LAPTM5) is a protein preferentially expressed in the immune cells. LAPTM5 was isolated in our laboratory as an interacting partner of the ubiquitin ligase, Nedd4. The intracellular domains of LAPTM5 contain three PY (L/PPxY) motifs, which bind the WW domains of Nedd4, as well as a ubiquitin-interacting motif (UIM). Here, I show that sorting of LAPTM5 from the Golgi to the lysosomes requires its association with Nedd4 and the clathrin adaptor GGA3. Although the Nedd4-LAPTM5 interaction leads to the ubiquitination of LAPTM5, this event is not necessary for LAPTM5 sorting. Rather, the Nedd4-LAPTM5 complex recruits ubiquitinated GGA3, which binds the UIM of LAPTM5. Hence, I propose a novel mechanism by which the ubiquitin ligase Nedd4, via interactions with GGA3 and cargo (LAPTM5), regulates cargo trafficking to the lysosome without requiring cargo ubiquitination. Because nothing was known about the biological function of LAPTM5, at the beginning of my Ph.D. training, I set out to determine the role of LAPTM5 in the innate immune cells. I demonstrate that LAPTM5 interacts with kinesin, a motor protein previously implicated in the anterograde movement of the late endosomal/lysosomal compartments. In dendritic cells, I show that upon maturation LAPTM5 is present within endolysosomal tubules formed by class II MHC molecules. Although I find that LAPTM5 is dispensable for the translocation of peptide-loaded MHC II molecules to the cell surface, this study extends our knowledge of the repertoire of proteins present within tubules formed by the MHC II compartments in activated dendritic cells. In macrophages, I demonstrate that LAPTM5 acts as a positive regulator of NFκB and MAPK signaling cascades, and promotes efficient proinflammatory cytokine production in response to several inducers of macrophage activation. During TNFα stimulation, LAPTM5 is required for proper initiation of NFκB signaling by acting at the receptor-proximate level. Thus, my findings indicate that LAPTM5 is an important component of inflammatory signaling cascades in macrophages and highlight a role for the endosomal/lysosomal system in regulating these cascades. Collectively, the work presented in this thesis broadens our understanding of lysosomal membrane protein sorting and function.

Surfactant protein D (SP-D) is an important innate immune collectin involved in uptake and clearance of microbes and allergens in the lungs. SP-D has been shown to ameliorate allergic asthma reactions in mice; however, the mechanisms for this are not fully understood. We investigated the role of SP-D in the uptake and clearance of the model allergen ovalbumin (OVA) by macrophages. We discovered that SP-D does not bind OVA but binds fractions with contaminating proteins; ovomucin and ovomacroglobulin. We extended these findings to show that SP-D binds human alpha-2-macroglobulin (A2M) in its cleaved or intact state, in a concentration-, calcium-, and carbohydrate-dependent manner. A2M increases the innate immune potential of SP-D by increasing its ability to agglutinate the bacteria Escherichia coli and Bacillus subtilis. We found that SP-D does not increase the uptake of OVA by murine macrophage cell lines, or by alveolar macrophages in vivo in BALB/cJ mice.

Neutrophils migrate rapidly towards a site of inflammation and mediate bacterial killing through highly regulated pathways that involve the phagocytosis of bacteria and the generation of reactive oxygen species by the NADPH oxidase complex. The Rac small GTPases have prominent roles in the regulation of neutrophil signaling pathways but the research strategies used to analyze their functions in live cells have been limited, since neutrophils are terminally differentiated and difficult to manipulate genetically. In this thesis, I describe a novel high efficiency protocol for transiently transfecting neutrophils that allowed me to investigate the roles of Rac1 and Rac2 in neutrophils in a completely new way, in real time. Using this technique, I show that a bacterial protein known to inhibit chemotaxis in vitro, selectively inhibits Rac1 activation downstream of fMLP stimulation and inhibits neutrophils polarization. Further dissecting the roles of Rac isoforms, I used various approaches to show that Rac1 and Rac2 differentially regulate free-barbed end (FBE) formation downstream of the fMLP receptor. Rac1 is responsible for ~30% of FBE whereas Rac2 is the regulator of FBE formation (~70%) through the activation of cofilin and Arp2/3. Finally, these observations led to the analysis of the mechanisms underlying the Rac1 and Rac2 functions. I show that membrane charge determines Rac1 and Rac2 differential localization during phagocytosis and chemotaxis iii based on their different aminoacid residues in the polybasic domain. This mechanism depends on lipid metabolism and the accumulation of negatively charged lipids at cellular membranes. During chemotaxis, neutrophils have a polarized accumulation of negatively charged lipids at the leading edge membrane that selectively recruit Rac1. In contrast, the lipid metabolism that occurs at the phagosome membrane decreases its negativity and selectively recruits Rac2. All together, this thesis describes the study of primary neutrophil functions from a new angle and adds some valuable information to the comprehension of effective neutrophil activation based on the analysis of Rac isoforms.

Glycosylation is one of the most abundant post-translational modifications of proteins. Glycoproteins participate in virtually all aspects of cellular functions. ST6Gal I is a glycosyltransferase highly expressed by B and T cells. Here, we interrogated the role of ST6Gal I in viral specific B and T cell immune responses, as well as examined how loss of this enzyme impacted viral pathogenesis. First, to understand how loss of ST6Gal I expression impacted viral specific humoral responses, we infected ST6Gal I-/- mice with influenza virus. We discovered that loss of ST6Gal I expression results in both reduced influenza specific antibodies levels and decreased viral-specific antibody secreting cells numbers. Following influenza infection, mice that received ST6Gal I-/- B cells showed reduced influenza-specific IgM responses compared to mice that received wild-type B cells. These experiments demonstrated that the expression of ST6Gal I by B cells is required for optimal viral-specific humoral response. We further examined how loss of ST6Gal I expression impacted the anti-influenza IgA response. We observed that immune ST6Gal I-/- mice displayed higher viral specific IgA levels and altered sialylation of IgG and IgA, which have been implicated in a human disease, IgA nephropathy. Moreover, ST6Gal I-/- mice exhibited increased immunoglobulin deposition in kidney glomeruli following influenza infection. These data suggest that ST6Gal I deficiency, together with influenza infection, may result in the initiation of a kidney disease. Finally, we examined how ST6Gal I expression regulated CD8 T cell responses. We discovered that ST6Gal I is differentially expressed during CD8 T cell activation. To understand its relevance, we infected ST6Gal I-/- mice and demonstrated that the early expansion of effector T cells was impaired in a cell intrinsic manner. Moreover, in the absence of ST6Gal I, the differentiation of CD8 T cells skewed towards memory precursor cells, whereas terminal effector cell expansion was impaired. Mechanistically, we identified delayed surface expression of IL-2Ralpha on ST6Gal I-/- CD8 T cells due to impaired IL-2/IL-2R signaling. These studies implicate that ST6Gal I expression enhances early proliferation of terminal effector CD8 T cells by promoting the rapid surface expression of IL2Ralpha during acute viral infection. 

Herpetic stromal keratitis (HSK) is an immunopathological and tissue destructive corneal lesion caused by herpes simplex virus (HSV) infection, which induces an intense inflammatory response and finally leads to blindness. Accumulating evidence using the murine model has shown that Th-1 phenotype CD4+ T cells orchestrating the inflammation mainly contribute to the immunopathological reaction in HSV-1 infected cornea. Initially various innate immune cells recruit and produce numerous inflammatory and angiogenic molecules into the corneal stroma those in turn drive the corneal immunopathology. While the basic principles of immunity to the influenza A viruses (IAV) are probably similar for all vertebrates, detailed understanding is based largely on experiments in laboratory mice. Virus clearance is normally mediated via CD8+ effector T cells but, in their absence, the class-switched antibody response can ultimately achieve the same goal. Influenza virus-specific plasma cells and CD8+ T cells persist in the long term and the recall of the CD8+ T cell response can lead to earlier virus clearance. The first part (Part I) of this dissertation focuses on the understanding of HSV-1 induced immunoinflammatory processes in the cornea and the secondary lymphoid tissues and the involvement of immuno-modulatory mechanisms following acute viral infections such as HSV and IAV. The next three parts (Part II-IV) focus on different inflammatory and counter-inflammatory mechanisms that are activated following acute viral infections. Results in Part II evaluate the role of small molecule inhibitors of VEGFR2/src kinase inhibitors in controlling the progression of the inflammatory lesions after ocular HSV infection. Results of the third section show that the host counter inflammatory mechanisms inhibit tissue damage but these may also act to constrain the effectiveness of immunity to acute infections. The fourth section describes the functional significance of HVEM expression on regulatory T cell in their expansion following HSV-1 infection. In this study, experiments were designed to understand the mechanisms involved in the regulation of immunity and resultant immunopathology using HSV-1 and IAV as the model systems and that modulation of these processes can enhance immune response and diminish immunopathology following acute infections.

Inflammatory Bowel Diseases (IBD) result from the nexus of a genetic predisposition, dysregulated immunologic insult against commensal microflora, and an environmental trigger. The intestinal epithelium is a single cell layer that separates a highly active mucosal immune system from a large antigenic load in the intestinal lumen. Innate immune recognition combined with a highly regulated adaptive immune response maintains this tolerance. The intestinal epithelium in collusion with antigen presenting cells primarily modulates this activity. In this thesis, we show that, in response to DNA isolated from bacteria, innate toll like receptor 9 (TLR9) activation in intestinal epithelial cells modulates both arms of the immune system, to regulate intestinal homeostasis, and through this mechanism, Bifidobacteria breve DNA exerts its anti-inflammatory function. / Experimental Medicine

The lungs and upper airways are mucosal surfaces that are common site for infection with an enormous variety of inhaled pathogens. Therefore, induction of immune responses in the respiratory tract is crucial for protection against respiratory diseases. One of the pathogens infecting the host via the respiratory tract is Mycobacterium Tuberculosis. The reported efficacy of the currently used Bacillus Calmette-Guérin (BCG) vaccine against tuberculosis is highly variable, ranging from 50% against pulmonary tuberculosis to 80% against disseminated tuberculosis. Recently, the current route of vaccination (intradermal) has been considered as a possible factor influencing the protective capacity of the BCG vaccine. In this regard, intradermal route most likely induces protective systemic responses while it fails to induce optimal responses in the lungs. Therefore, our working hypothesis is that vaccination should be directed towards the respiratory mucosal immunity in order to improve the degree of host protection in the lungs. In this thesis we studied the effect of the route of immunization as well as of different mucosal adjuvants on the induction of mucosal immune responses against the mycobacterial surface antigen PstS-1. We found that, the intranasal (i.n.) route of immunization was a more favorable route inducing strong local immune responses, than intraperitoneal (i.p.) route. Indeed, i.n. route immunization, unlike the i.p. route, elicited strong IgA responses in the lungs accompanied by a major influx of CD4+ T cells and a significant local production of IFN-gamma. IgA, being the predominant Ig isotype at mucosal tissues, is considered a major effector molecule involved in defense mechanisms against viral and bacterial pathogens at these sites. Therefore, we investigated the possible role of IgA in the protection of the respiratory mucosa against mycobacterial infections, using mice deficient in IgA and in the polymeric Ig receptor. We show that, deficient mice are more susceptible to mycobacterial infections than wild type mice, thereby demonstrating a role for IgA in protection against mycobacteria. Importantly, our studies revealed a reduced production of protective factors, such as INF-gamma and TNF-alpha in the lungs of deficient mice that was associated with the higher susceptibility seen in these mice compared to wild-type mice. We also conducted challenge experiments against another respiratory pathogen, Chlamydia pneumoniae, using IgA deficient mice. Likewise to mycobacteria, our data support a role for IgA in the protection of the respiratory tract against C. pneumoniae infection. Finally, we investigated the possible mechanisms explaining the reduced pro-inflammatory responses in IgA deficient mice. Our data indicated that IgA deficient mice present a defective response to stimulation with LPS or 19kDa which appears to be both, essentially due to suboptimal stimulation of macrophages and restricted to the lungs.