Interferon gamma (IFN-γ) regulation of macrophages plays an essential role in innate immunity and pathogenicity of viral infections by directing large and small genome-wide changes in the transcriptional program of macrophages. Smaller changes at the transcriptional level are difficult to detect but can have profound biological effects, motivating the hypothesis of this thesis that responses of macrophages to immune activation by IFN-γ include small quantitative changes that are masked by noise but represent meaningful transcriptional systems in pathways against infection. To test this hypothesis, statistical meta-analysis of microarray studies is investigated as a tool to obtain the necessary increase in analysis sensitivity. Three meta-analysis models (Effect size model, Rank Product model, Fisher’s sum of logs) and three further modified versions were applied to a heterogeneous set of four microarray studies on the effect of IFN-γ on murine macrophages. Performance assessments include recovery of known biology and are followed by development of novel biological hypotheses through secondary analysis of meta-analysis outcomes in context of independent biological data sources. A separate network analysis of a microarray time course study investigate s if gene sets with coordinated time-dependent relationships overlap can also identify subtle IFN-γ related transcriptional changes in macrophages that match those identified through meta-analysis. It was found that all meta-analysis models can identify biologically meaningful transcription at enhanced sensitivity levels, with slightly improved performance advantages for a non-parametric model (Rank Product meta-analysis). Meta-analysis yielded consistently regulated genes, hidden in individual microarray studies, related to sterol biosynthesis (Stard3, Pgrmc1, Galnt6, Rab11a, Golga4, Lrp10), implicated in cross-talk between type II and type I interferon or IL-10 signalling (Tbk1, Ikbke, Clic4, Ptpre, Batf), and circadian rhythm (Csnk1e). Further network analysis confirms that meta-analysis findings are highly concentrated in a distinct immune response cluster of co-expressed genes, and also identifies global expression modularisation in IFN-γ treated macrophages, pointing to Trafd1 as a central anti-correlated node topologically linked to interactions with down-regulated sterol biosynthesis pathway members. Outcomes from this thesis suggest that small transcriptional changes in IFN-γ activated macrophages can be detected by enhancing sensitivity through combination of multiple microarray studies. Together with use of bioinformatical resources, independent data sets and network analysis, further validation assigns a potential role for low or variable transcription genes in linking type II interferon signalling to type I and TLR signalling, as well as the sterol metabolic network.

Tumour-associated macrophages (TAM) are a major component of the inflammatory infiltrate that typifies most malignancies. Among them, Burkitt’s lymphoma (BL), a high-grade non Hodgkin lymphoma (NHL) of B-cell origin, represents a characteristic example. Studies from our group have shown that TAM in BL exert pivotal roles that are mainly supportive of tumourigenesis such as maintaining an immunosuppressive microenvironment. In order to unravel the molecular mechanisms underlying TAM functions in BL, solid tumours from a mouse xenograft model of BL have been used to obtain TAM and assess their activation status in vivo. Laser-capture microdissection has been successfully used to procure intact macrophage sections from the tumour site, allowing the production of a pure, in situ gene expression signature of TAM in BL. Tingible-body Mφ from lymph node germinal-centres and resident tissue Mφ from resting lymph nodes of non-tumour bearing mice were chosen for direct comparison with TAM. Whole-genome microarray technology has revealed a distinct TAM gene expression profile, with 454 genes being significantly up-regulated (fc ≥ 2, p<0.05) and 1293 genes being significantly down-regulated (fc ≤ -2, p<0.05) between TAM and either of the two normal Mφ populations. Further bioinformatics analysis of gene functions has highlighted matrix remodeling, phagocytosis, and immune response among the processes most highly enriched in TAM. Importantly, mRNA and tissue expression of selected differentially expressed genes relevant to these processes was validated by real-time qPCR and immunofluorescence labeling respectively. Following the generation of the TAM profile in situ, in vitro experimental approaches were undertaken in order to investigate how specific elements of the BL microenvironment drive the observed TAM signatures. Specifically, the direct role of apoptotic tumour cells, a key component of the BL microenvironment, versus that of viable tumour cells in driving TAM matrix remodelling gene expression was assessed in short-term mouse and human Mφ-NHL cell co-cultures. From the aforementioned cluster, emphasis was given to MMP12 and MMP2 transcripts: mRNA and protein expression of these MMPs was found to be up-regulated in Mφ following viable tumour cell co-cultures and this effect was further enhanced following apoptotic tumour cell co-cultures, implying that apoptotic NHL cells could directly shape TAM matrix remodeling phenotype in BL in vivo. Whereas the mRNA of both MMPs was solely Mφ-derived in this system, MMP12 and MMP2 protein was surprisingly found also to be increased in NHL cells in the apparent absence of increased mRNA. Detailed examination of MMP12 production by NHL cells revealed that it is most likely an apoptosis-dependent process, since apoptotic NHL cells generated through different apoptosis stimuli, as well as apoptotic cell-derived microparticles, showed markedly increased MMP12 protein levels. In conclusion, the data presented in this thesis, provide the first insight into the in vivo activation status of TAM in high-grade NHL, through generation of the TAM gene signature in situ. Upon further in vitro studies, apoptotic NHL cells were shown to directly modulate the matrix remodelling component of the TAM signature as well as to actively produce matrix remodelling mediators themselves, suggesting distinct roles for tumour cell apoptosis within the NHL microenvironment that can profoundly influence the disease outcome.

The body’s humoral immune response plays a larger role in the body’s defenses beyond screening for invading pathogens. Modulation of this response is also vital for tissue regeneration, drug delivery, and vaccine development. The immune system operates within a complicated feedback loop and as such, altering the strength of the immune response can be approached from an engineering perspective. While a strong initial input can direct the response to either a pro- or anti-inflammatory bias, extreme responses can be deleterious, as in the case of allergic reactions or sepsis. Therefore, the objective of this thesis was to develop a novel biomaterials platform that can be used to alter the immune response in a tunable manner. Antibodies are not only the workhorses of the adaptive immune response but are also powerful immunomodulators through their Fc (constant fragment) regions. By coating microparticles with Fc ligands in variable surface densities, we were able to utilize the sensitivity of multivalent signaling to tune the response of the immune response. Microparticle size was also varied to decouple the effects of physical versus biochemical signaling. The goal of this thesis was to analyze the effects of Fc coated particles on two major components of the humoral immune responses: macrophages and the complement system. We first looked at the mechanical response of macrophages through phagocytosis and found that both Fc density and microparticle size had significant impacts on macrophage phagocytosis. These results also provide a particle delivery “toolbox” for future applications. We then analyzed the downstream effects of Fc particles on macrophage phenotype and on phenotype plasticity. This showed that the addition of Fc particles lead to increased production of TNFα and IL-12 and inverted the response of LPS treated macrophages. Finally, we applied our particles to activate the complement system, an often overlooked cascade of serum protein activation that results in bacterial cell lysis. Cleaved components of the complement system are also powerful chemokines and can act as a vaccine adjuvant. Fc density on particles played a large role in complement system activation, both through the classical and alternative pathway, as it lead to a binary response for smaller particles and a tunable response for larger particles. We then applied these results to create a novel form of antibiotic by using Fc particles to direct complement-mediated bacterial cytotoxicity. The use of immune activation by Fc particles was also applied to better understand and improve the tuberculosis vaccine. Our findings are significant to the biomaterials and immunology fields as we showed that Fc microparticles can generally be used to alter the immune response in a tunable manner for a broad range of applications, as well answering fundamental immunology questions.

published_or_final_version / abstract / Paediatrics and Adolescent Medicine / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Pathology / Master / Master of Philosophy

published_or_final_version / abstract / Surgery / Master / Master of Philosophy

published_or_final_version / Medicine / Master / Master of Philosophy

published_or_final_version / Surgery / Master / Master of Medical Sciences

published_or_final_version / Microbiology / Doctoral / Doctor of Philosophy

Acid Sphingomyelinase (ASMase) activity has been proposed to mediate LPS signaling in various cell types. This study shows that in macrophages, ASMase is a negative regulator of LPS-induced TNFα secretion. ASMasedeficient (asm-/-) mice and isolated peritoneal macrophages produce several fold more TNFα than their wild-type (asm+/+) counterparts when stimulated with LPS. The mechanism for these differences however is not transcriptional but post-translational. The TNFα converting enzyme (TACE) catalyzes the maturation of the 26kD precursor (proTNFα) to the active 17kD form (sTNFα). In mouse peritoneal macrophages, the activity of TACE rather than the rate of TNFα mRNA synthesis was the rate-limiting factor regulating TNFα production. Substantial portion of the translated proTNFα was not processed to sTNFα; instead it was rapidly internalized and degraded in the lysosomes. TACE activity was 2 to 3 fold higher in asm-/- macrophages as compared to asm+/+ macrophages and was suppressed when cells were treated with exogenous ceramide and SMase. In asm-/- but not in asm+/+macrophages, indirect immunofluorescence experiments revealed distinct TNFα-positive structures in close vicinity of the plasma membrane. Asm-/- cells also had higher number of EEA1-positive early endosomes. Co-localization experiments that involved inhibitors of TACE and/or lysosomal proteolysis suggest that in asm-/-cells a significant portion of proTNFα is sequestered within the early endosomes, and instead of undergoing lysosomal proteolysis it is recycled to the plasma membrane and processed to sTNFα.