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The immune response to a given cancer can profoundly influence a tumour's trajectory and response to treatment, but the ability to analyse this component of the microenvironment is still limited. To this end, a number of immune marker gene signatures have been reported which were designed to enable the profiling of the immune system from transcriptomics data from tissue and blood samples. Our initial analyses of these resources suggested that these existing signatures had a number of serious deficiencies. In this study, a co-expression based approach led to the development of a new set of immune cell marker gene signatures (ImSig). ImSig supports the quantitative and qualitative assessment of eight immune cell types in expression data generated from either blood or tissue. The utility of ImSig was validated across a wide variety of clinical datasets and compared to published signatures. Evidence is provided for the superiority of ImSig and the utility of network analysis for data deconvolution, demonstrating the ability to monitor changes in immune cell abundance and activation state. ImSig was also used to examine immune infiltration in the context of cancer classification and treatment. Patient-matched ER+ breast cancer samples before and after treatment with letrozole were analysed. Significant elevation of infiltration of macrophages and T cells on treatment was observed in responders but not in non-responders, potentially revealing a biomarker for response. ImSig was also used to study the immune infiltrate in 12 cancer types. By computing the relative abundance of immune cells in these samples, their relationship to survival was investigated. It was interesting to observe that half of the cancers showed trends towards poor prognosis with increased infiltration of immune cells. ImSig alongside the network-based framework can also be used for a more explorative analysis such as to identify biomarkers and activation or differentiation states of immune cells. Melanoma is a highly immunogenic cancer and has shown tremendous success with immune checkpoint inhibitors in a subset of patients. In chapter-6, the molecular subgrouping of melanoma was explored using a network-based approach. Despite the plethora of evidence suggesting various aspects of the immune system to contribute towards the response to immunotherapy in melanoma, there has been little to no effort to consider this heterogeneity while developing molecular subgroups. The use of ImSig was therefore explored for the stratification of melanoma patients into immuno-subgroups. The subgrouping methodology divided the tumours into four groups with different immune profiles. Interestingly, these groupings showed prognostic significance, reiterating the need to consider the heterogeneity of immune cells in future studies. On identifying the most dominant phenotypes that contribute towards prognosis of these patients and in comparison to the published subgroupings of melanoma, we argue that the subgroup of samples enriched in keratin genes are not clinically meaningful. ImSig and the associated analysis framework described in this work, support the retrospective analysis of tissue derived transcriptomics data enabling better characterisation of immune infiltrate associated with disease, and in so doing, provide a resource useful for prognosis and potentially in guiding treatment.

Haemostasis is a highly regulated system, involving a myriad of cell types (endothelium, immune cells, platelets, etc.), proteins (enzymes, receptors, etc.) and signalling molecules (sterols, nucleotides, etc.). Haematophagous organisms, such as ticks, have evolved a number of strategies to overcome host haemostatic responses to feed effectively. Salivary apyrases are a class of nucleotide-metabolising enzymes that blood-feeding parasites utilise to modulate extracellular nucleotides, like ATP and ADP, to prevent platelet activation and aggregation. This specific enzyme function has evolved in blood-feeding parasites from the ecto-ATPdase/CD39 (E-NTPDases)-, Cimex-type- and 5’-nucleotidase/CD73 enzyme families. Furthermore, most arthropod apyrases are ascribed to the 5’-nucleotidase/CD73 enzyme family. The salivary apyrase from Ornithodoros savignyi has not been characterised to a specific enzyme family and the presence of 5’-nucleotidase homologs have not been demonstrated. Therefore, in this study 5’-nucleotidase homologous transcripts were identified from O. savignyi salivary gland DNA, using a 5’-nucleotidase specific degenerate primer and RACE protocols. Two full-length putative 5’-nucleotidase isoforms were identified that shared significant sequence identity and similarity to a 5’-nucleotidase from R. (B.) microplus and putative apyrases from I. scapularis and R. appendiculatus. Utilising computational tools, iso-electric points, molecular weights and cellular localisation were determined. The isoforms were predicted to be soluble secreted proteins, which correlated with the trend observed for parasitic apyrases in the 5’-nucleotidase family. Phylogenetic analysis of the 5’-nucleotidase family revealed that the O. savignyi 5’-nucleotidase isoforms claded monophyletically with the putative apyrases from I. scapularis and R. appendiculatus, excluding the 5’-nucleotidase from R. (B.) microplus. Molecular modelling of these two proteins showed a similar protein structure to a periplasmic ecto-5’-nucleotidase from E. coli. The similar architecture revealed a high conservation of key residues involved in dimetal coordination, catalysis and substrate binding, therefore a similar catalytic mechanism was proposed. It was hypothesised that the isoforms identified may be putative apyrases. To test this hypothesis, the 5’-nucleotidase isoform I was recombinantly expressed in yeast. Cross-reactivity was demonstrated with a polyclonal anti-apyrase antibody produced from O. savignyi native apyrase. The latter implied that the native apyrase may be a member of the 5’-nucleotidase enzyme family. However, no sequence information for native apyrase was available for comparison and therefore native enzyme was purified with ion exchange chromatography. Subsequent, Edman N-terminal sequencing and MS/MS analysis with purified enzyme identified peptide sequence fragments that shared a high degree of sequence identity with both 5’-nucleotidase isoforms. It was concluded that native apyrase is a mixture of the isoforms identified from O. savignyi salivary gland DNA. These results represent the first confirmation of a tick apyrase that belongs to the 5’-nucleotidase family of enzymes. Further confirmation will be achieved by testing activity of the recombinant protein and future experiments may assess the potential of this protein as a vaccine candidate. / Dissertation (MSc)--University of Pretoria, 2009. / Biochemistry / unrestricted

Plasmodium falciparum (P. falciparum) infection modulates the response of innate immune cells. The aim of this work was to study the impact of P. falciparum infection and P. falciparum-derived molecules on the response of dendritic cells (DC) and monocytes. In paper I we investigated the effects of natural hemozoin (nHZ), a P. falciparum-derived molecule, on the phenotype and functionality of DC. We found that exposure to nHZ impaired the capacity of DC to mature. Paper II is a follow-up on paper I, where the underlying transcriptional events preceding the nHZ-induced impairment of DC maturation were investigated. More specifically, we examined the involvement of certain transcription factors, subunits of chromatin remodeling complexes and histone modifications in the regulation of DC maturation. Our findings suggest that nHZ-exposure of DC does not lead to recruitment or enrichment of molecules needed for transcriptional activation. In paper III we investigated P. falciparum effects in vivo in sympatric ethnic groups with differential susceptibility towards P. falciparum infection living in Burkina Faso. The aim of this study was to establish the transcriptional networks underlying the relatively better protection against P. falciparum infection observed in the Fulani ethnic group compared to other sympatric ethnic groups. Our findings reveal differential gene expression in monocytes of infected Fulani compared to uninfected Fulani and the difference concerned multiple classes of genes including signal transduction, immunological responses and chromatin remodelers. The results provide new aspects on molecules and regulatory mechanisms that are involved in the relatively more protective response against P. falciparum infection. Taken together, the work presented in this thesis leads to a deeper understanding of the P. falciparum-induced modulation of responses of innate immune cells and the underlying mechanisms possibly regulating those responses. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript.</p>

It is clear that the voltage-gated proton channel HVCN1 plays an essential role in a range of cell types, in particular immune cells. Previous published work has confirmed the existence of proton channels in both murine and human macrophages. However, the role of HVCN1 in macrophages has not been investigated. Given that the current literature on voltage-gated proton channels in immune cells has found HVCN1 to be involved in several cellular processes (such as the respiratory burst and signalling events) it is important to establish its functional role in macrophages, which are a crucial constituent of the immune system. The aim of my thesis was to investigate the function of voltage-gated proton channels in macrophages with the use of mice with a disrupting mutation within the Hvcn1 gene, which results in HVCN1 loss. In particular, I wanted to address how Hvcn1-/- macrophages responded to LPS activation. I hypothesised that HVCN1 regulates the respiratory burst of macrophages and that it potentially modulates mitochondrial ROS production, and in doing so, may affect several functional aspects of macrophage biology.

BACKGROUND: Immune cells promote periodontal bone loss through an unresolved inflammatory response to bacterial pathogens. The limited availability of ex vivo gingival immune cells severely impedes identification of cell types and cell-specific functions that drive human periodontitis and thus impedes the development of effective pharmacotherapeutics. Previous studies have largely relied on mRNA analysis and confocal microscopy to imprecisely estimate gingival immune cell function. The aim of the study was to develop a cell type-specific technique to quantitate function of resident gingival immune cells. METHODS: Diseased tissues from chronic periodontitis in non-diabetes or type 2 diabetes subjects or relatively healthy gingival tissues were removed during standard-of-care surgery for pocket reduction surgery or crown lengthening, respectively. Gingiva was dissociated with collagenase to generate single cell suspensions, then 9-color flow cytometry was used quantitate and/or isolate myeloid cells (CD11b+), B cells (CD20+), T cells (CD4+ or CD8+) and natural killer (NK) cells (CD56+). We stimulated the sorted cells with lineage-appropriate activators for 36 hrs and measured cytokine production by ELISPOT, an assay that identifies individual cytokine-producing cells by fixed “spots” on a solid support. RESULTS: A higher proportion of gingival CD4+ T helper cells and not CD8+cytoxic T cells from subjects with periodontal disease with or without type 2 diabetes produce pro-inflammatory cytokines compared to CD4+ T cells from crown lengthening subjects. CD4+ T cells were the dominant cell population in gingiva from all three groups, and all groups contained similar proportions of cytotoxic (CD8+) T cells, myeloid cells (CD11b+), B cells (CD20+) and natural killer cells (CD56+). CONCLUSION: The combination of flow cytometry, cell sorting and ELISPOT identified CD4+ T cells as dominant immune cells in human periodontal lesions, and identified T cell cytokines that may uniquely promote periodontitis in type 2 diabetes.

Hematopoietic systems in vertebrates have been the focus of intense study. However immunocyte development is well characterized in very few invertebrate groups. The sea urchin is an attractive model for the study of immune cell development. Larval immunocytes, pigment cells and derivatives of the blastocoelar cells, emerge from a small population of precursors specified at blastula stage. Analyses from the genome reveal a complex system of immune receptors and effectors and a near complete set of homologues of vertebrate transcriptional regulators. Characterization of the expression profile and function of sea urchin homologues of key vertebrate hematopoietic transcription factors imply a conserved role in immunocyte development. SpGatac, an orthologue of the vertebrate Gata-1/2/3 transcription factors and SpScl, an orthologue of Scl/Tal-2/Lyl-1 transcription factors are both required for immune cell specification in the embryo. An important cis-regulatory mechanism that restricts SpGatac expression to the blastocoelar cells involves repression by SpGcm in the pigment cells. Characterization of the expression of several additional transcription factors, including SpE2A, an orthologue of vertebrate E2A/HEB/ITF2, SpId, an orthologue of the Class V bHLH factors that modulate E-protein function, and SpLmo2, an orthologue of the cofactor part of the transcriptional complex that includes Scl and Gata family members, suggests the existence of a conserved regulatory complex for hematopoiesis. Two isoforms of the SpE2A gene were identified. The shorter isoform shares genomic organization and sequence conservation with the mouse paralogue of E2A, HEBAlt. Expression of SpE2A and SpE2AAlt is consistent with a function in immunocyte development in the sea urchin embryo. Findings of the counterpart to a key vertebrate regulatory system functioning in the development of immunocytes in the simple sea urchin embryo lay the foundation for comparative immunocyte developmental gene regulatory network analyses. These will in turn lead to a greater understanding of the evolution of immune systems across phyla and will provide simple invertebrate model systems for detailed comparative investigations of regulatory function with direct relevance to vertebrates.