Includes bibliographical references (leaves 108-126). / Infection by the parasitic nematode Nippostrongylus brasiliensis involves migration through the lungs, causing significant damage and generating chronic lung pathology. The resolution of N. brasiliensis infection and also the induction of pulmonary pathology, including goblet cell hyperplasia and acute airway inflammation, depend on IL-4Rá signalling. A key feature of IL-4Rá signalling is the induction of a strong TH2 response which induces the development of alternatively activated macrophages (AAMs). AAMs are associated with tissue remodelling and the control of exacerbated inflammation. In order to investigate potential roles for IL-4Rá in N. brasiliensis' induced lung pathology, we infected mice deficient for IL-4Rá on macrophages and neutrophils (LysMCreIL-4Rá-/lox), IL-4Rá -/- and control mice (IL-4Rá-/lox) with N. brasiliensis and examined lung pathology at days 5, 42 and 180 post infection (p.i.).All three mice strains showed similar emphysemic-like pathology (alveolar dilatation) and airway hyperresponsiveness (AHR) which was well developed by day 42 p.i. and remained chronic. However, LysMCreIL-4Rá-/lox mice consistently demonstrated earlier and increased pulmonary inflammation when compared to IL-4Rá-/lox control mice and IL-4Rá-/- mice. Immunological studies at day 5 p.i. revealed that there were increased CD4+ and CD8+ T-cell numbers and increased CD4+ IL-4 and IL-13 production in the lungs of LysMCreIL-4Rá-/lox mice when compared to control and IL- 4Rá-/- mice. LysMCreIL-4Rá-/lox mice also showed decreased pulmonary arginase activity, indicative of a reduction of AAMs. RNA transcript analysis of isolated alveolar macrophages showed a strong association with promoting inflammation in LysMCreIL-4Rá-/lox mice. Together these data demonstrate that IL-4Rá-responsive macrophages control pulmonary inflammation and play an important protective role in the lung following N. brasiliensis infection.

Includes abstract. Includes bibliographical references (p. 109-125).

Sudden unexpected death in the young (SUDY) is the tragic fatality of seemingly healthy individuals aged between one and 40 years. Little is known about the demographics and risk factors of these cases at Salt River Mortuary (SRM), Cape Town. Therefore, this project aimed to retrospectively investigate the burden and profile of SUDY cases admitted to SRM, between 1 January 2016 and 31 December 2018. Of the total 11 588 cases admitted over this period, 833 (7.2 %) were SUDY cases, wherein males comprised the majority (64.3 %). Individuals were a median age of 31 ± 10.3 years at death, and the main location of death was ‘residential' (43.5 %). There were also significantly more males than females in the age category of 31 - 40 years who were found outdoors compared to all other locations (p < 0.001). Risk factors included physical activity, substance abuse, and co-morbidities with concomitant use of chronic medication. More than a third of individuals experienced breathlessness prior to death (45.0 %). Of cases with a confirmed natural cause of death, the main organ systems involved were pulmonary, cardiovascular, central nervous system and gastrointestinal, which parallels international trends. Akin to local studies, in analogous amounts, TB and pneumonia were the leading causes of death. Additionally, 21.1 % of cases were identified as candidates for genetic testing which may resolve undetermined cases or elucidate underlying predisposing factors to sudden death. Fortunately, 81.8 % had biological samples available for these retrospective analyses. Cases often had missing documentation which advocates for training to ensure compliance to standardised procedures. This study shows that males aged 31 ± 10.3 years with pulmonary and cardiac-related co-morbidities are the most vulnerable for SUDY whilst sleeping. Awareness interventions targeted at this population are thus needed in an attempt to reduce these tragic fatalities.

Background: Pregnancy at advanced maternal age (AMA) is associated with an increased risk of aneuploidy. In the Western Cape's public health sector maternal age alone is widely used to screen women for high risk of pregnancies affected by aneuploidy. The weekly pregnancy counselling clinic (PCC) at Groote Schuur Hospital (GSH) offers genetic counselling (GC) for women who are of AMA to inform them about their age-related aneuploidy risk, offer invasive diagnostic testing (IDT) and discuss the option of voluntary termination of an affected pregnancy. A recent audit at GSH showed that the uptake of IDT was low and other literature reports that South Africans tend to have a conservative view regarding termination of pregnancy (TOP). This study sought to understand what women expect from the GC service at PCC as well as what their experiences are of the service. Methods: This qualitative phenomenological study used a pragmatic approach and participants were recruited through purposive sampling. Semi-structured, in-person interviews were conducted after women had completed their GC sessions at PCC. Thematic analysis was used to analyse the data. Results: The results of this study suggest that participants (n=7) received very little information about their GC appointments at referring clinics, and that they generally did not have prior knowledge about age-related aneuploidy risks. Finding out about the age-related risk of aneuploidy was an emotional experience for the participants, but other factors, including normal ultrasound results, provided relief. The participants' choices regarding IDT and attitudes towards TOP reflected that of available literature as the uptake was low and most participants reported that they would not consider a TOP. The women reported that they would use the knowledge they gained during GC to educate other women in their communities about the pregnancy risks associated with increased maternal age. Generally, the participants believed that GC was useful and appreciated the opportunity. Conclusion: The participants in this study had limited health literacy and knowledge regarding AMA risks and GC. As a result, participants had no expectations of GC. However, the participants felt that GC was useful in helping them prepare for the possibility of a child with DS, and generally viewed the service in a positive light. Additionally, this study's results suggests that there is a need to educate women in local communities regarding AMA pregnancy risks.

We investigated immune responses beyond conventional T cells in the context of BCG vaccination and tuberculosis disease.

Studies have shown that the protection against L. mexicana infection is potentiated by a type 1 response, driven by IL-12 production by dendritic cells. In contrast, IL-4 and IL-13 cytokines are associated with susceptibility to L. mexicana causing cutaneous leishmaniasis. This has been demonstrated in studies involving BALB/c mice deficient in IL-4, IL-13, and IL-4Rα infected with L. mexicana. To determine the specific cell in IL-4Rα-/- BALB/c mice that contribute to the control of L. mexicana infections, studies on cell-specific IL-4Rα deficient mice need to be investigated. IL4Rα-CD4+T deficient mice revealed sex-dependent protection from L. mexicana infection, suggesting the critical role of non-lymphocyte cells in conferring protection against L. mexicana amastigote infection. Macrophage/neutrophil-specific IL-4Rα deficient mice are protected from L. major infection in the footpad. Surprisingly, this mouse strain infected in the base of the tail failed to control L. mexicana amastigote infection. Nonetheless, IL-4Rα-DC deficient mice were hyper-susceptible to L. major infection. This conundrum suggests that different Leishmania species, site of infection, and developmental stages of parasite dictate the outcome of the disease. Here, mice with a deficiency of IL-4Rα signaling on DCs and macrophage/ neutrophil cells were subcutaneously infected with L. mexicana promastigotes in the footpad, and skin lesion progression was measured, and the clinical phenotype was evaluated by investigating both humoral and cellular immune responses. Mouse strains had similar footpad lesion progression, parasite loads, humoral responses, expansion of CD4+ and CD8+ T cells, their activation, memory phenotypes, and infiltration of DCs, macrophages, and neutrophils into the lymph nodes compared to their littermate IL-4Rα-/lox controls. Interestingly, IL‐12p70 and IL‐10 produced by BMDCs and BMDMs were similar. Nevertheless, nitrite/urea production was not affected. Together, this study suggests that, unlike L. major, IL-4Rα signaling on DCs and macrophage/ neutrophil cells does not contribute to the susceptibility or resistance to BALB/c mice to infection with L. mexicana.

In 2020, the World Health Organization (WHO) reported 1.5 million tuberculosis (TB)- associated deaths and an incidence of 10 million new cases. The causative, Mycobacterium tuberculosis (Mtb), evades host immune responses by skewing macrophage polarization towards a less microbicidal alternative state to avoid classical effector killing functions. However, the molecular details underlying these evasion mechanisms remain incomplete and current therapy is challenged with drug resistance. Host-directed therapy (HDT) has recently gained attention, with long non-coding RNAs (lncRNAs) as potential targets due to their emerging roles in pathogenic immune responses. We previously performed cap analysis gene expression (CAGE) transcriptomics on IFN-γ stimulated (classically activated) and IL-4/IL-13 stimulated (alternatively activated) mouse macrophages, identifying 151 differentially expressed lncRNAs following Mtb infection. We validated the top 11 differentially expressed lncRNAs and two were chosen for this study, lncRNA-125, whose expression was regulated at different levels unstimulated and in response to IFN-γ and IL-4/IL-13, and lncRNA-612 whose expression was only induced by IFN-γ stimulation. Interestingly, the expression of lncRNA125 and lncRNA-612 was downregulated following Mtb infection. Therefore, this study aimed at functionally validating these lncRNAs in unstimulated, IFN-γ and IL-4/IL-13 stimulated and/or Mtb-infected mouse and human macrophages by a loss-of-function approach using chemically engineered antisense oligonucleotides (gapmeRs). Knockdown of lncRNA-125 by gapmeRs reduced Mtb growth and anti-inflammatory cytokine production mediated by increased apoptosis, nitrite and pro-inflammatory cytokine production in IL-4/IL-13 prestimulated mouse macrophages. Whereas knockdown of lncRNA-125 in IFN-γ pre-stimulated mouse macrophages favoured Mtb growth and anti-inflammatory cytokine production, with reduction of apoptosis, nitrite and pro-inflammatory cytokine production. Therefore, indicating that lncRNA-125 regulates macrophage polarization during Mtb infection. Knockdown of lncRNA-125 in human macrophages resulted in reduced Mtb growth and increased proinflammatory cytokine production in unstimulated, IFN-γ and IL-4/IL-13 pre-stimulated BMDMs infected with Mtb. Comparatively, gapmeR knockdown of lncRNA-612 reduced Mtb growth and increased pro-inflammatory cytokine production in IFN-γ pre-stimulated mouse and human macrophages. In mouse macrophages, these responses were mediated by increased apoptosis and nitrite production, with reduced anti-inflammatory cytokine production. Overall, these findings highlight lncRNAs as novel host factors to be further investigated as targets for TB diagnostics and adjunctive HDTs.

Immunity to nematode infections requires a host T helper 2 (Th2) response promoted by epithelial cell driven IL-33 induction of cytokine secretion of Interleukin (IL)-4, 5 and 13 by a range of immune cells including innate lymphoid cells type 2 (ILC2s) and CD4+ T cells. This induces effector responses such as goblet cell mucus secretion and mast cell activation driving disease resolution. Finding candidate molecules and discrete cell populations that enhance these responses would provide new targets for treating infection via specific host immune-modulation and would contribute to the development of effective vaccines against nematode infections. In this study we addressed how novel components of host adaptive and innate immunity can contribute to pulmonary control of Nippostrongylus brasiliensis infections. Murine reinfection studies with the parasitic nematode N. brasiliensis have shown development of a Th2 CD4+ T cell responses in the lung to be essential for immunity to secondary N. brasiliensis infection. To test if T cell recruitment from secondary lymphoid tissue contributed to this immunity, we used the drug Fingolimod (FTY720) to block T cell egress from lymph nodes (LN) to peripheral tissue. T cell egress from the LN was required for resolution of a primary infection but not for secondary infection. The presence of tissue-resident IL-4Rα responsive CD4+ T cells in the lung was sufficient for protective immunity to N. brasiliensis reinfection. These results demonstrated that effective CD4+ T cell Th2 immunity can be generated at peripheral sites by pre-existing T cell populations, independently of T cell recruitment from secondary lymphoid organs (SLO). Additionally, we identify that the pulmonary epithelial cell-secreted collectin, surfactant protein D (SP-D), is an important component of host immunity to N. brasiliensis infection. We demonstrate here that SP-D production is induced following N. brasiliensis infection in a Th2 dependent manner, it bound preferentially to lung stage L4 parasites and enhanced macrophage and ILC2 protective responses essential for controlling infection. vi Taken together the data presented in this thesis provides two new important insights into pulmonary host immunity to parasitic helminth infections.

Immunity to nematode infections requires a host T helper 2 (Th2) response promoted by epithelial cell driven IL-33 induction of cytokine secretion of Interleukin (IL)-4, 5 and 13 by a range of immune cells including innate lymphoid cells type 2 (ILC2s) and CD4+ T cells. This induces effector responses such as goblet cell mucus secretion and mast cell activation driving disease resolution. Finding candidate molecules and discrete cell populations that enhance these responses would provide new targets for treating infection via specific host immune-modulation and would contribute to the development of effective vaccines against nematode infections. In this study we addressed how novel components of host adaptive and innate immunity can contribute to pulmonary control of Nippostrongylus brasiliensis infections. Murine reinfection studies with the parasitic nematode N. brasiliensis have shown development of a Th2 CD4+ T cell responses in the lung to be essential for immunity to secondary N. brasiliensis infection. To test if T cell recruitment from secondary lymphoid tissue contributed to this immunity, we used the drug Fingolimod (FTY720) to block T cell egress from lymph nodes (LN) to peripheral tissue. T cell egress from the LN was required for resolution of a primary infection but not for secondary infection. The presence of tissue-resident IL-4Rα responsive CD4+ T cells in the lung was sufficient for protective immunity to N. brasiliensis reinfection. These results demonstrated that effective CD4+ T cell Th2 immunity can be generated at peripheral sites by pre-existing T cell populations, independently of T cell recruitment from secondary lymphoid organs (SLO). Additionally, we identify that the pulmonary epithelial cell-secreted collectin, surfactant protein D (SP-D), is an important component of host immunity to N. brasiliensis infection. We demonstrate here that SP-D production is induced following N. brasiliensis infection in a Th2 dependent manner, it bound preferentially to lung stage L4 parasites and enhanced macrophage and ILC2 protective responses essential for controlling infection. vi Taken together the data presented in this thesis provides two new important insights into pulmonary host immunity to parasitic helminth infections.

Neonatal alloimmune thrombocytopenia (NAIT) is caused by maternal alloantibodies against fetal platelet antigens inherited from the father and which are absent from maternal platelets. In Caucasians, antibodies against the Leu33 (HPA-1a) polymorphism of integrin β3 (part of the platelet αIIbβ3 complex) account for >70% of cases. Antenatal screening for these antibodies does not currently take place in the UK, partly because of the absence of sensitive, predictive tests. We hypothesized that the poor sensitivity and predictive abilities of current assays are due to the use of β3 in an inappropriate conformation, resulting in sub-optimal binding of HPA-1a antibodies. We hypothesized firstly that in vitro induced changes to αIIbβ3 might alter accessibility of the HPA-1a epitopes to alloantibodies, thus reducing assay sensitivity. Secondly, we hypothesized that HPA-1a antibodies are stimulated by, and preferentially recognise, β3 in association with αv, a molecule present on placental syncytiotrophoblasts, and that reactivity against platelet αIIbβ3 reflects only cross-reactivity with αvβ3. Our first hypothesis was proven by demonstrating that use of the cation chelating compound EDTA, used by many diagnostic laboratories as a component of assay reagents or present in blood samples as anticoagulant, resulted in significantly reduced assay sensitivity. These findings were confirmed in an international workshop. Support for our second hypothesis was provided by demonstrating enhanced reactivity of a small panel of examples of anti-HPA-1a against αvβ3 compared to αIIbβ3 and by molecular modelling data. We also showed that HPA-1a antibodies can inhibit platelet function by using a novel application of the ROTEM® delta thromboelastograph and an immunofluorescence assay in which we demonstrated blocking of platelet function using a monoclonal antibody, PAC-1, that binds only to activated αIIbβ3. These studies provide possible explanations for the poor sensitivity and predictive abilities of current assays and suggest further areas for research.