Transcriptional and translational networks linking the immune system to health and disease

The contents of this thesis are organised into seven chapters and one appendix. Chapter 1 includes two literature reviews that discuss important factors associated with the development of upper respiratory symptoms (URS) in elite athletes. The first review discusses URS, its incidence and prevalence in elite athletes as well as the effects that exercise has on the immune system at the level of immune gene expression, immune cell phenotype and immunometabolism. The second review was published in Sports Medicine and is presented here in its published form. This review discusses the relationship between exercise, the gut microbiota, the common mucosal immune system and the risk, prevalence and incidence of URS. Chapter 2 reports the incidence of URS in a cross-sectional study of elite Australian athletes, during a 30-day period, three months prior to a summer Olympic Games. Based on epidemiological data, the cohort was split into the two groups that are studied throughout this thesis; a group that did not present with URS (asymptomatic group) and a group that reported URS for a minimum of two days in the previous month (URS group). The chapter assessed the relationship between lifestyle factors and URS and used several questionnaires relating to the areas of psychology, illness, injury, training load, sleep, energy availability and travel. The assessment of lifestyle factors is a quick and non-invasive method of inquiry that can be used to highlight factors that were or were not linked with the incidence of URS in elite athletes. Chapter 3 presents an in-depth comparison of peripheral blood mononuclear cell (PBMC) phenotypes between the URS and asymptomatic groups. Immune cell phenotyping was performed to characterise PBMC sub-populations. Circulatory PBMCs are a relatively accessible and representative tissue for analysing the phenotypic and functional aspects of immune competency. Differences in immune phenotype can represent differences in immune function, which involves the reactions and processes of many cell types that represent the innate and adaptive response (1). Differences in immune function may reflect an athletes potential for developing URS (2). Immune cell phenotype was measured using mass cytometry, using the CyTOF2 mass cytometer (Fluidigm, CA, USA) and data was evaluated using a traditional gating strategy in FlowJo_V10 software (Oregon, USA) as well as using an advanced machine learning approach using the Cytobank platform (Santa Clara, USA). Chapter 4 compared the results of immune gene expression analysis using peripheral blood between the URS and the asymptomatic groups. An essential link between the genome and immune cell phenotype is gene expression. The study of gene expression can reveal key differences associated with illness (3). To undertake this analysis, novel digital gene expression technology from NanoString Technologies (NanoString Technologies, WA, USA) was used. Chapter 5 compared the metabolic profile and mitochondrial parameters of PBMCs between the URS group and the asymptomatic groups using the Cell Mito Stress Test Kit (Agilent Technologies, Santa Clara, USA). For optimal immune function, it is crucial that the metabolic requirements of immune cells are met. Exercise training is a significant physiological stress for elite athletes. Meeting the energy and nutrient requirements to maintain healthy immune function, in addition to the requirements posed by the energy demand of exercise, can be difficult to achieve for elite athletes (4). Nutritional deficiencies increase the risk of poor immune function and immune cell metabolism (5). Early evidence examining metabolic demands within immune cells has demonstrated metabolic shifts in response to various stimuli and fluctuations in substrate availability (5). Chapter 6 contains a small pilot study that compared the gut microbial profiles of a subset of the original cohort, between six female soccer players reporting URS and six asymptomatic female soccer players. The link between the gut microbiota and health is of growing interest. The gut microbiota is involved in digestion, nutrient production, metabolism, priming of the immune system in infancy and immune defence (6, 7). Although diet is the main contributor to gut microbial composition, a recent study comparing 40 elite rugby players to healthy, non-athletes, demonstrated that exercise was positively correlated with the composition of the gut microbiota (8). However, it is difficult to discern the extent to which diet and exercise shape the gut microbiota independently and to what extent these factors overlap and contribute to health (8). This pilot study used 16S rRNA sequencing using the Illumina MiSeqTM II system from Macrogen Inc. (Seoul, South Korea). To the best knowledge of this candidate, this study is the first comparison of the gut microbial profile in association with the incidence of URS. Chapter 7 discusses the general conclusions of each study presented in this thesis and how this body of research contributes to understanding the association between exercise, the immune system and upper respiratory symptoms in elite athletes.