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Modern medical practice and science involve complex phenotypic definitions. Understanding patterns of association across this range of phenotypes requires co-analysis of high-dimensional association studies in order to characterise shared and distinct elements. In this thesis I address several problems in this area, with a general linking aim of making more efficient use of available data. The main application of these methods is in the analysis of genome-wide association studies (GWAS) and similar studies. Firstly, I developed methodology for a Bayesian conditional false discovery rate (cFDR) for levering GWAS results using summary statistics from a related disease. I extended an existing method to enable a shared control design, increasing power and applicability, and developed an approximate bound on false-discovery rate (FDR) for the procedure. Using the new method I identified several new variant-disease associations. I then developed a second application of shared control design in the context of study replication, enabling improvement in power at the cost of changing the spectrum of sensitivity to systematic errors in study cohorts. This has application in studies on rare diseases or in between-case analyses. I then developed a method for partially characterising heterogeneity within a disease by modelling the bivariate distribution of case-control and within-case effect sizes. Using an adaptation of a likelihood-ratio test, this allows an assessment to be made of whether disease heterogeneity corresponds to differences in disease pathology. I applied this method to a range of simulated and real datasets, enabling insight into the cause of heterogeneity in autoantibody positivity in type 1 diabetes (T1D). Finally, I investigated the relation of subtypes of juvenile idiopathic arthritis (JIA) to adult diseases, using modified genetic risk scores and linear discriminants in a penalised regression framework. The contribution of this thesis is in a range of methodological developments in the analysis of high-dimensional association study comparison. Methods such as these will have wide application in the analysis of GWAS and similar areas, particularly in the development of stratified medicine.

Transverse myelitis (TM) is a rare auto-immune inflammatory disease in which the patient’s immune system attacks their spinal cord resulting in an unpredictable degree of neurologic disability, ranging from complete recovery to quadriplegia. TM patients often experience insufficient assistance towards understanding causes of the illness and have little to depend on in trying to deal with it. This study explores psychological strengths and coping strategies used by TM patients in coping with the illness. A theoretical framework of positive psychology with a strong focus on seven constructs, namely positive coping, searching for meaning, benefit finding, hope, sense of humour, resilience, as well as religion and spirituality is presented. The main data collection strategy for this study was the gathering of stories as a form of conversation. These were subjected to thematic analysis by interpretative phenomenological analysis (IPA) focused on identifiable themes and patterns of living and behaviour. The emerging patterns and identified fortigenic qualities were then considered, analysed and argued in relation to corresponding coping strategies. A model for the psychological coping and well-being of TM patients, based on emphasising the positive and constructive and considering existing models and strategies for the well-being of patients, was developed. The strategic and therapeutic model is presented in easily understandable language for the benefit of any care-giver (e.g. family member, friend or nurse) or the patient him/herself. / Thesis (PhD)--University of Pretoria, 2013. / lk2013 / Psychology / unrestricted

Along with proteins, a myriad of different molecular biomarkers, such as post-translational modifications and autoantibodies, could be used in an attempt to improve disease detection and progression. In this thesis, I build on several iterations of the proximity ligation assay to develop and apply new adaptable methods to facilitate detection of proteins, autoantibodies and post-translational modifications. In paper I, we present an adaptation of the solid-phase proximity ligation assay (SP-PLA) for the detection of post-translational modification of proteins (PTMs). The assay was adapted for the detection of two of the most commons PTMs present in proteins, glycosylation and phosphorylation, offering the encouraging prospect of using detection of PTMs in a diagnostic or prognostic capacity.  In paper II, we developed a variant of the proximity ligation assay using micro titer plate for detection and quantification of protein using optical density as readout in the fluorometer, termed PLARCA. With a detection limit considerably lower than ELISA, PLARCA detected femtomolar levels of these proteins in patient samples. In paper III, we aim to compare detection values of samples collected from earlobe capillary, venous plasma, as well as capillary plasma stored in dried plasma spots (DPS) assessed with a 92-plex inflammation panel using multiplex proximity extension assay (PEA). Despite the high variability in protein measurements between the three sample sources, we were able to conclude that earlobe capillary sampling is a suitable less invasive alternative, to venipuncture. In paper IV, we describe the application of PLARCA and proximity extension assay (PEA) for the detection of GAD65 autoantibodies (GADA). Thus, offering highly sensitive and specific autoimmunity detection.

This thesis investigates how air pollution, both natural and anthropogenic, affects changes in the proximal small intestine and ileum microbiota profile, as well as intestinal barrier integrity, histological changes, and inflammation. APO-E KO mice on a high fat diet were randomly selected to be exposed by whole body inhalation to either wood smoke (WS) or mixed vehicular exhaust (MVE), with filtered air (FA) acting as the control. Intestinal integrity and histology were assessed by observing expression of well- known structural components tight junction proteins (TJPs), matrix metallopeptidase-9 (MMP-9), and gel-forming mucin (MUC2), as well known inflammatory related factors: TNF-α, IL-1β, and toll-like receptor (TLR)-4. Bacterial profiling was done using DNA analysis of microbiota within the ileum, utilizing 16S metagenomics sequencing (Illumina miSeq) technique. Overall results of this experiment suggest that air pollution, both anthropogenic and natural, cause a breach in the intestinal barrier with an increase in inflammatory factors and a decrease in beneficial bacteria. This evidence suggests the possibility of air pollution being a potential causative agent of intestinal disease as well as a possible contributing mechanism for induction of systemic inflammation.

Autoimmuna sjukdomar är en samling komplexa, kroniska, inflammatoriska sjukdomstillstånd som kännetecknas av dysreglering av immunsystemet, vilket resulterar i inflammation och skada av vävnader, celler och organ. Dessa sjukdomar har en betydande inverkan på individens livskvalitet och bidrar ofta till ökad dödsrisk där komorbiditeter föreligger. Emellertid medför den varierande symptombilden för olika autoimmuna sjukdomar betydande utmaningar för att uppnå noggrann diagnos, prognos och utvärdering av behandling. Det finns därför ett påtagligt behov av att upptäcka nya biomarkörer.  I denna studie utfördes en omfattande analys av 944 plasmaprover med hjälp av OlinkR Explore-plattformen, vilket genererade data för 1463 unika proteiner. Baserat på uttrycksdata identifierades proteiner förknippade med de sex utvalda autoimmuna sjukdomarna multipel skleros, myosit, reumatoid artrit, systemisk skleros, Sjögrens sjukdom och systemisk lupus erythematosus samt några av deras definierade subgrupper. Dessa potentiella biomarkörer kommer eventuellt att underlätta tidig diagnos, sjukdomsdifferentiering och prognos. Flertalet av dessa proteiner har ännu aldrig kopplats till de här specifika sjukdomarna i litteraturen, särskilt inte från plasmaprover, vilket ger spännande nya perspektiv för biomarkörsutveckling. Det är dock av största vikt att genomföra robusta valideringsstudier i oberoende kohorter.  Sammanfattningsvis belyser våra resultat den potentiella brukbarheten hos dessa proteomiska plasmabiomarkörer för att förbättra tidig sjukdomsdetektering, karakterisering av subgrupper och sjukdomsdifferentiering att stimulera. Förhoppningsvis kan dessa resultat stimulera till vidare forskning inom området för biomarkörer och potentiella framsteg inom individbaserad medicin. / Autoimmune diseases are complex, chronic, inflammatory conditions characterized by dysregulation of the immune system, resulting in inflammation and damage to various tissues, cells and organs. These diseases significantly impact individuals’ quality of life and often contribute to increased mortality risk in the presence of comorbidities. However, due to the diverse array of symptoms associated with different autoimmune diseases, accurate diagnosis, prognosis, and treatment evaluation pose significant challenges. Thus, there is a pressing need for the discovery of novel biomarkers.  In this study, a comprehensive analysis of 944 plasma samples using the OlinkR Explore platform was conducted, generating data on 1463 unique proteins. Based on the expression data, associated proteins were identified for six selected autoimmune diseases, namely multiple sclerosis, myositis, rheumatoid arthritis, systemic sclerosis, Sjögren’s syndrome, and systemic lupus erythematosus, as well as some of their defined subgroups. These are prospective biomarkers and have the potential to aid in early diagnosis, therapeutic intervention, subgroup identification, disease differentiation, and disease prognosis. Notably, some of these proteins have not been previously associated with the specific diseases in the existing literature, especially not in plasma samples, thereby offering intriguing new perspectives for biomarker development. However, it is of great importance to conduct robust validation studies in independent cohorts to confirm the outcomes of this study.  In summary, our findings highlight the potential utility of these proteomic plasma biomarkers in improving the early detection, subgroup characterization, and disease differentiation of autoimmune diseases. The identification of these proteins will hopefully stimulate further investigation in the field of biomarker research and potential advancements in personalized medicine.

Inducible T-cell co-stimulator (ICOS) is a member of the CD28 family of T cell costimulatory receptors that is induced upon activation in CD4+ and CD8+ T cells. It has been established that ICOS plays a critical role in humoral immunity by supporting the generation and function of T follicular helper cells. Thus, ICOS deficiency in humans and mice leads to immunodeficiency due to impaired germinal center reaction and antibody production. ICOS can also promote expansion, survival, and cytokine expression of inflammatory T cells. However, given that ICOS is also constitutively expressed in Foxp3+ regulatory T (Treg) cells, interruption of ICOS signaling may lead to different outcomes depending on the context of immune reactions. Due to the potential opposing roles of ICOS in overall T cell immune response, the T cell subsetspecific role of ICOS needs to be clarified. In order to address the intrinsic roles of ICOS in Treg homeostasis and function, we generated mice (termed ICOS FC) in which Icos gene is specifically deficient in Foxp3+ T regulatory cells. Using flow cytometry and single-cell transcriptome analysis, we show that ICOS FC mice do not have any severe alterations in the Tcon cell activation status and subset compositions of Treg cells under a steady state condition. Consistently, no spontaneous autoimmune symptoms developed in aged ICOS FC mice. In contrast, when the mice were challenged with chemically induced skin inflammation, ICOS FC mice mounted more severe inflammatory responses. In parallel, the number of Treg cells was reduced allowing increase of inflammatory CD4+ and CD8+ T cells in the draining lymph nodes and the skin. Although very small, our single-cell transcriptome analysis identified a cluster of Treg cells coexpressing T-bet and CXCR3 (termed Th1-Treg) in the draining lymph nodes in an ICOS-dependent manner. Therefore, Treg-intrinsic ICOS deficiency had minimal impact on the overall Treg homeostasis, but weakened Treg cells’ capacity to control Th1-driven skin inflammation likely due to the impaired differentiation of Th1-Treg cells. A dual role of ICOS in T cell-driven autoimmune disease has been modeled in NOD mice. In pure NOD mice in which polyclonal T cells control the disease, ICOS germline deficiency reduced disease progression by dampening activation of pathogenic autoreactive T cells. In contrast, when the TCR repertoire was highly restricted to autoantigens in BDC2.5 TCR transgenic III NOD line, ICOS-expressing Treg cells appear to play a dominant role by halting progression of insulitis to overt diabetes. However, previous studies could not exclude the possibility of altered TCR repertoire by ICOS deficiency in germline. In this study, we tested the impact of Icos gene deletion in adult NOD mice using an inducible ubiquitous Cre system once peripheral T cell repertoire had been established. We observed reduced incidence of diabetes in pure NOD mice but accelerated disease in BDC2.5-NOD mice, very similar to germline ICOS-deficiency. These results support the prevailing view that the main function of ICOS is to regulate effector and regulatory T cells in the periphery. In sum, we demonstrated that ICOS-deficient Treg cells retain the capacity to prevent spontaneous autoimmune disease but have a compromised ability to dampen Th1-driven skin inflammation. We further confirm the notion that ICOS mainly regulates mature T cells as opposed to thymic selection process. / Le co-stimulateur inductible des lymphocytes T (ICOS) est un membre de la famille CD28 des récepteurs co-stimulateurs qui est induit suite à l'activation des lymphocytes T CD4+ et CD8+. Il a été établi que ICOS joue un rôle essentiel dans l'immunité humorale en soutenant la génération et la fonction des cellules T auxiliaires folliculaires. Le déficit en ICOS chez l'homme et la souris conduit à une immunodéficience due à une altération de la réaction du centre germinatif et de la production d'anticorps. ICOS peut également favoriser l'expansion, la survie et l'expression des cytokines des cellules T inflammatoires. Cependant, étant donné que ICOS est également exprimé de manière constitutive dans les cellules T régulatrices Foxp3+ (Treg), l'interruption de la signalisation ICOS peut conduire à des résultats différents selon le contexte des réactions immunitaires. En raison des rôles potentiellement opposés de ICOS dans la réponse immunitaire globale des lymphocytes T, le rôle spécifique de ICOS chez les sous-ensembles de lymphocytes T doit être clarifié. Afin d'étudier les rôles intrinsèques de ICOS dans l'homéostasie et la fonction des Tregs, nous avons généré des souris (appelées ICOS FC) dans lesquelles le gène Icos est spécifiquement aboli chez les cellules T régulatrices Foxp3+. À l'aide de la cytométrie en flux et de l'analyse du transcriptome unicellulaire, nous démontrons que les souris ICOS FC ne présentent aucune altération grave de l'état d'activation des cellules Tcon et des compositions de sous-ensembles de cellules Treg dans des conditions d'équilibre. De plus, aucun symptôme auto-immun spontané ne s'est développé chez les souris ICOS FC âgées. En revanche, lorsque les souris ont été confrontées à une inflammation cutanée induite chimiquement, les souris ICOS FC ont présenté des réponses inflammatoires plus sévères. En parallèle, le nombre de cellules Treg a été réduits permettant une augmentation des cellules T CD4+ et CD8+ inflammatoires dans les ganglions lymphatiques drainants et la peau. Notre analyse du transcriptome unicellulaire a identifié un petit groupe de cellules Treg coexprimant T-bet et CXCR3 (appelé Th1-Treg) dans les ganglions lymphatiques drainants d'une manière ICOS-dépendante. Par conséquent, le déficit en ICOS intrinsèque aux Tregs a eu un impact minimal sur l'homéostasie globale des Tregs, mais a affaibli la capacité des cellules Treg à contrôler l'inflammation cutanée induite par les cellules Th1, probablement en raison de la différenciation altérée des cellules Th1-Treg. V Un double rôle de ICOS dans les maladies auto-immunes induites par les cellules T a été modélisé chez les souris NOD. Dans les souris NOD pures chez lesquelles des cellules T polyclonales contrôlent l’apparition du diabète auto-immun, un déficit de ICOS réduit la progression de la maladie en atténuant l'activation des cellules T autoréactives pathogènes. En revanche, dans un contexte où le répertoire du TCR est fortement restreint aux auto-antigènes (lignée NOD transgénique BDC2.5 TCR), les cellules Treg exprimant ICOS semblent jouer un rôle dominant en arrêtant la progression vers le diabète manifeste. Cependant, des études antérieures n'ont pas pu exclure la possibilité d'un répertoire de TCR altéré par un déficit en ICOS dans la lignée germinale. Dans cette étude, nous avons testé l'impact de la délétion inductible du gène Icos chez des souris NOD adultes à l’aide d’un système Cre ubiquitaire une fois que le répertoire des cellules T périphériques a été établi. Nous avons observé une incidence réduite du diabète chez les souris NOD pures, mais une accélération de la maladie chez les souris NOD BDC2.5 très similaire au phénotype causé par une ablation de Icos de la lignée germinale. Ces résultats soutiennent l'opinion dominante selon laquelle la fonction principale de ICOS est de réguler les cellules T effectrices et régulatrices dans la périphérie. En résumé, nous avons démontré que les cellules Treg déficientes en ICOS conservent la capacité de prévenir les maladies auto-immunes spontanées, mais démontrent une capacité réduite à atténuer l'inflammation cutanée provoquée par les cellules Th1. Nous confirmons de plus l’hypothèse que ICOS régule principalement les cellules T matures au lieu du processus de sélection thymique.