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.

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 cationic host defence peptide LL-37 is an immunomodulatory agent that plays an important role in epithelial innate immunity. Previously, concentrations of LL-37 thought to represent levels present during inflammation have been shown to elicit the production of cytokines and chemokines by epithelial cells. To investigate the potential of lower concentrations of LL-37 to alter epithelial cell responses, normal primary keratinocytes and bronchial epithelial cells were treated with pro-inflammatory stimuli in the presence or absence of 1 – 3 μg/ml LL-37. Low, physiologically relevant concentrations of LL-37 synergistically increased IL-8 production by both proliferating and differentiated keratinocytes in response to IL-1β and the TLR5 agonist flagellin, and synergistically increased IL-8 production by bronchial epithelial cells in response to IL-1β, flagellin, and the TLR2/1 agonist PAM3CSK4. Treatment of bronchial epithelial cells with LL-37 and the TLR3 agonist poly(I:C) resulted in synergistic increases in IL-8 release and cytotoxicity. The synergistic increase in IL-8 production observed when keratinocytes were co-stimulated with flagellin and LL-37 was suppressed by pretreatment with inhibitors of Src-family kinase signalling and NF-κB translocation. These data suggest that low concentrations of LL-37 may alter epithelial responses to microbes in vivo. Microarray analysis of keratinocyte transcriptional responses after LL-37 treatment suggest that LL-37 may alter the expression of growth factors and a number of genes important to innate immune responses. LL-37 may thus play a more important role than previously suspected in the regulation of epithelial inflammation; an improved understanding of the mechanisms by which LL-37 alters chemokine responses could lead to the development of novel anti-infective and anti-inflammatory therapeutics.

The aim of this thesis was to obtain some insights into mechanisms by which the immune system affects melanoma cells after anchoring agonists of phagocytic receptors (laminarin and f-MLF) to their surface. To verify the hypothesis that innate immune system plays a critical role, in vivo experiments were performed on SCID mice. To elucidate the importance of CR3, CD11b-deficient mice were used. In in vitro experiments production of inflammatory cytokines in tumor tissue was examined as well as the release of myeloperoxidase from neutrophil granules after incubation with malignant cells.

This study is focused on characterization of fibrinogen-related proteins (FREPs) from the tick Ixodes ricinus using molecular methods - PCR, cloning, qRT-PCR, RNA interference via dsRNA synthesis and injection, and also pathogen (Borrelia sp.) transmission on animal model.

Animals face frequent threats from predators and must generate appropriate behavioural responses to ensure their survival. To achieve this, they process sensory cues to correctly identify the presence and imminence of a predatory threat, and transform this information into defensive actions. However, despite much research in identifying the circuits that may be responsible for such transformations, little is known about how this occurs mechanistically. We focus on how escape behaviour in the mouse is generated from visual predatory threats, and use a combination of behavioural, neurophysiological and anatomical methods to identify the relevant neurons and understand how they perform this computation. In this work, we developed an innate decision making paradigm in which a mouse detects and assesses sensory stimuli of varying threat evidence during exploration, choosing whether to escape to a shelter, or not. The performance data in this task were best formalised with a drift-diffusion model of decision making, providing a framework to understand innate behavioural tasks in terms of evidence accumulation and boundaries. Next, we performed calcium imaging in freely-moving mice to probe for neural correlates of decision elements and flight behaviour in brain areas that we show to be necessary for the flight responses: we found that VGluT2 neurons in the deeper medial superior colliculus (dmSC) increase their activity during a repeated threatening stimulus, while VGluT2 neurons of the dorsolateral periaqueductal gray (dPAG) are silent until just before the initiation of escape, and are maximally active during escape. These results suggest that the dmSC accumulates evidence of threat which dPAG neurons threshold. This interpretation is supported by optogenetic activation of mSC-VGluT2 neurons in vivo, which recapitulates the statistics of escape probability evoked with a visual stimulus, while activation of VGluT2 neurons in the dPAG evokes an all-or-nothing escape response. Finally, using channelrhodopsin-2-assisted circuit mapping and monosynaptic viral tracing, we reveal that over half of dPAG-VGluT2 neurons receive monosynaptic connections from mSC-VGluT2 neurons with a low probability of release, allowing this synapse to act as a high-pass filter and providing a mechanism for the computation of an escape decision. These findings advance our understanding of how defensive behaviours are generated at circuit and single-cell level, and of how neurons process information in a circuit critical for implementing basic behaviours.

- 4 - Abstract Introduction: Periodic fever syndromes are clinical entities classified as autoinflammatory diseases. The most of the periodic fever syndromes have genetic predisposition (monogenic periodic fever syndromes). PFAPA (Periodic Fever, Aphtous stomatitis, Pharyngitis a Adenitis) syndrome is an idiopathic disease with unknown aetiology. Results: In our study, we described the largest clinical series of patients with PFAPA syndrome from a single center. The laboratory results have confirmed uncomplicated course of PFAPA syndrome. In our measurements we observed significantly higher levels of serum cytokines (IL-1β and IFN-γ) during episodes of fever in PFAPA patients compared to the control group. Our measurements showed increased numbers of plasma cells in the peripheral blood of PFAPA patients. We have found increased levels of naïve CD4 and CD8 T cells and approximately 2-fold higher proportion of CD8 T cells in tonsils of PFAPA patients. Significant differences were also present at levels of IFN-γ, IL-1β, IL-6 and TNF-α in stimulated supernatants compared to supernatants from unstimulated peripheral blood from patients with PFAPA syndrome. Measurements of bacterial profile showed individual microbial profile in patients. Conclusion: Removal of the tonsillar tissue with the potential...

Amphibian metamorphosis is facilitated solely by thyroid hormones (THs), L-thyroxine (T4) and 3,5,3’-triiodothyronine (T3). TH modulates the remodeling of many different organs and systems in the body of developing tadpoles, including the immune system. Previous research found evidence of T4 action on direct-response genes in outer ring deiodinase-poor premetamorphic tadpole tail fin and liver without the required conversion to T3 described by current TH dogma. The mechanisms of environmental endocrine disrupting chemicals (EDCs) may be better understood by expanding our understanding of the transcriptomic effects of both forms of THs and how they relate to estrogen signaling. Furthermore, analysis of TH-modulation of the immune system may enable a greater understanding of the devastating effects of amphibian pathogens such as Ranavirus. Premetamorphic Rana (Lithobates) catesbeiana tadpoles were exposed to physiological concentrations of T4, T3, or 17-beta-estradiol (E2) through water bath immersion. qPCR analysis was performed to assess the response of canonical TH-responsive genes thra, thrb, and thibz to these hormones in the liver and tail fin tissues of bullfrog tadpoles. E2 treatment did not elicit a response in these gene transcripts in either tissue. T3 treatment in the tail fin elicited an overall stronger response than T4, while T4 treatment in the liver recapitulated results consistent with non-genomic mechanisms of T4 signaling for thrb and thibz transcripts. Illumina Hiseq2500 was used to sequence RNA isolated from hormone-treated premetamorphic tadpole liver and tail fin tissues to assess differential transcriptomic responses and identify TH-responsive immune system-associated transcripts. The impact of TH-treatment on the general immune system in the liver and tail fin transcriptomes was also analyzed using RNA-seq data. We found that E2 modulates at least some shared TH pathways in the liver, but none in the tail fin and that the tail fin transcriptome is more affected by T3, while the liver transcriptome is more affected by T4. Additionally, evidence of immune system modulation by both THs was found in both the liver and tail fin transcriptomes. Antimicrobial peptides (AMPs) are an important component of the amphibian immune response. Details regarding the regulation, synthesis, and expression of AMPs remain obscure, although evidence of TH-modulation of specific AMPs has been identified, as well as evidence of increased expression of AMPs throughout metamorphosis. Frog skin is a prolific source of AMPs that may prove useful in the quest for alternative antimicrobial agents in the face of antibiotic resistance. Identification of new AMPs is hindered by the practical limitations of classical protein-based discovery approaches. By using known AMP characteristics and common ¬AMP properties, we developed a high throughput bioinformatics approach predicated on the use of R. catesbeiana genome resources. We mined these resources and identified novel and known AMPs that exhibited verified antimicrobial activity against various bacterial organisms. This thesis sought to elucidate the differential and modulatory effects of both forms of TH on a transcriptomic level and in the context of immunity, and to examine the utility of the bullfrog transcriptome and genomics resources in identifying and characterizing novel bullfrog-derived AMPs and elucidating aspects of AMP expression. / Graduate / 2018-12-08