Medicine (RMH) - Theses
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ItemUnderstanding mechanisms enabling long-lasting immunity to malaria( 2023-07)An efficacious vaccine that generates long-lasting immunity is critically needed to reduce the global burden of malaria and protect young children in high transmission areas, who are most at risk of severe disease and death. However, despite four decades of development, the most advanced malaria vaccine induces only moderate and short-lived protection and other candidate vaccines are yet to demonstrate more sustained efficacy. Advancement in malaria vaccine design is impeded by an absence of established correlates of immunity, limiting targets for directed vaccine improvements. Host-specific factors, such as age, previous malaria infection and nutritional status, may modulate immune function and impair vaccine responsiveness, highlighting the need for an extensive characterisation of immune function in children in malaria endemic regions. In this thesis, we explored correlates and determinants of sustained immunity to malaria and examined how vaccine modification may improve long-lasting protection. We first considered immune and host factors associated with antibody-mediated protection and antibody maintenance in clinical samples. We investigated the value of antibody avidity, previously reported as a marker of robust and high-quality immune induction, as a possible correlate of long-lasting malaria immunity following vaccination in children and adults. Our findings suggest that avidity is an unreliable marker of antibody maintenance and antibody functional properties. In malaria, monocytes may be key effector cells of antibody-mediated functions which have shown protective associations in vaccine trials. We found that monocytes in children with malaria infection expressed high levels of cell surface receptors relevant to functions in malaria immunity. Given the importance of potent antibody responses to generate protective and sustained immunity, we also explored the role of undernutrition in IgG responses to routine vaccinations in children living in regions of endemic malaria transmission and found that underweight and wasting were associated with reduced vaccine-induced antibody levels. Finally, we used mouse models to investigate vaccine strategies and dietary modifications that may alter the magnitude and longevity of antibodies induced by malaria vaccines. We demonstrated differences in antibody maintenance generated by different vaccine approaches, including varying adjuvants and antigens, and that deficiencies in critical micronutrients, such as zinc, may impair the antibody response to vaccination, an effect modulated by adjuvant selection. The work in this thesis supports the role of monocytes in immunity, shows that nutritional factors impact vaccine antibody levels, and demonstrates that vaccine formulation – including adjuvant and antigen selection – and host factors, such as zinc deficiency, interact to modulate the induction and maintenance of antibody responses to vaccination. In summary, we illustrate the challenges and complexity of inducing sustained immunity with malaria vaccines, providing foundations for future work characterising the interplay of host factors, the immune system and vaccine features to support vaccine-induced immunity to malaria.
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ItemBiomarkers of Treatment Response in Multiple Sclerosis( 2023-04)Timely initiation of efficacious disease modifying therapy is the cornerstone of therapeutic management in multiple sclerosis (MS) as it preserves brain functional reserve by attenuating the underlying inflammatory processes. Achieving this goal however, is complicated by the individuality of disease trajectories and heterogenous response to therapies. In this context, it is imperative to identify patients that are at a higher risk for experiencing aggressive MS in the form of recurrent relapses or rapid worsening of disability and consider a more proactive treatment strategy. Various clinical outcome prediction tools have been proposed to date for this purpose with a few clinicodemographic predictors that they share in common such as number of prior relapses, imaging markers of disease activity, older age and male sex. However, these tools have been limited in their ability to provide a comprehensive adjustment for all the possible markers and predictors of disease activity due to the risk of model overparameterisation by including too many variables. A recently developed model of treatment outcome prediction in MS utilised homogeneity analysis to summarise a wide array of background clinicodemographic variables into three principal components to predict probability of clinical outcomes for individual patients over a four-year prediction horizon. This model provides a framework that can be further optimised by experimental inclusion of newly emerging biomarkers in the field to firstly determine their additive predictive value when considered alongside a comprehensive clinical model and secondly to enhance overall model performance. In this thesis, firstly external validity of the developed base model was evaluated using a non-overlapping underrepresented cohort from the Middle East. Once its generalisability was established, models were developed and adjusted to assess the additive predictive value of three emerging biomarkers in the field of MS. Neurofilament light chain was investigated as an acute marker of neuronal injury while volumetric magnetic resonance (vMRI) imaging parameters were investigated markers of chronic neurodegeneration. Lastly, vitamin D was assessed a proposed modulator of treatment response especially in those treated with interferon beta. We found that while higher NfL was associated with worse clinical outcomes in models without the clinicodemographic predictors, it failed to contribute unique prognostic information toward predicting medium-term outcomes in comparison with the solely clinical models. Findings for vMRI showed that lower brain volumes both globally and regionally were associated with higher disease activity in models without the clinicodemographic information. Similarly, however, these associations did not translate into superior predictive performance when compared with the base models. Lastly, we found no evidence of the association between vitamin D and medium-term clinical outcomes in any of the performed analyses. These findings suggest that continued utilisation of background and routinely collected clinicodemographic information is crucial for clinical decision making and that the utility of new biomarkers need to be assessed alongside real-world routine clinical practice before their widespread adoption. Such studies will also help elucidate the pragmatic clinical use of such biomarkers by clarifying their clinical trajectories in real world settings.
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ItemMalnutrition and nutrition interventions in older adults( 2023-05)Malnutrition is highly prevalent in older adults and is characterised by unintentional weight and muscle mass loss among others. Malnutrition increases the risk of sarcopenia, a condition defined as low muscle mass and muscle strength below a clinically relevant threshold. Both conditions are associated with poor functional performance in older adults. Nutrition interventions are shown to be effective in the treatment of malnutrition, specifically when combined with an exercise intervention. The effect of nutrition interventions may be enhanced by methods such as using indirect calorimetry to determine energy targets and strategies such as specific patterns of protein intake. This thesis focuses on malnutrition and its intervention on body composition and functional outcomes in older adults. In a cohort of geriatric rehabilitation inpatients, malnutrition at admission was associated with poor functional recovery. During the geriatric rehabilitation admission, body weight and muscle mass improved in patients with malnutrition, sarcopenia or underweight. At least a quarter of patients with malnutrition, sarcopenia or underweight did not receive dietetic interventions as part of routine clinical care and the patients who received dietetic interventions did not have greater improvements in body weight or body composition. In a quasi-experimental study in a sub-sample of this population, using indirect calorimetry to determine energy targets in nutrition interventions did not lead to greater improvements in clinical outcomes. Inadequate dietary intake remained a major challenge for the success of nutrition interventions in geriatric rehabilitation patients. A systematic review and a meta-analysis showed that protein supplementation alone is effective in improving muscle mass in community-dwelling older adults, but the gain in muscle mass was not associated with the dose, frequency or timing of supplementation. This thesis highlights the importance of diagnosing malnutrition and the need for improved personalised nutritional care in geriatric patients. Ensuring adequate dietary intake remains critical in clinical care and in future studies investigating the effect of strategies optimising nutrition interventions in older adults.
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ItemAssessment of mineral metabolism in Chronic Kidney Disease – Mineral and Bone Disorder (CKD-MBD)( 2023-05)Patients with chronic kidney disease (CKD) experience significantly poorer outcomes compared to the general population, including greater all-cause and cardiovascular-related mortality. Increased morbidity and mortality is partly attributable to the propensity for patients with CKD to be older and have an elevated burden of co-morbidities and cardiovascular risk factors. However, it is also clear that additional pathological processes specific to CKD play a role. Decline in kidney function is paralleled by progressive abnormalities in mineral and bone metabolism. This multi-system process is collectively referred to as Chronic Kidney Disease – Mineral and Bone Disorder (CKD-MBD), and is almost universally present in advanced stages of CKD. CKD-MBD is thought to be a significant driver of adverse outcomes in CKD. This thesis presents a series of related works that explore the application of markers of mineral metabolism in CKD-MBD, including their association with clinical outcomes. Novel markers are utilised to examine mineral metabolism in health and also disease states, including in response to potentially therapeutic interventions. Altered phosphate homeostasis is considered to be central to the conventional understanding of CKD-MBD. Chapter 2 re-examines the use of serum phosphate as a marker of adverse risk in a large contemporary cohort of incident dialysis patients. Both high and low levels of serum phosphate were found to be independently association with increased mortality, regardless of dialysis modality (haemodialysis and peritoneal dialysis), suggesting that serum phosphate remains a robust marker of patient risk. Over the past decade calciprotein particles (CPP) have emerged as a novel marker of mineral metabolism and have been suggested to explain some of the association between phosphate and pathological events in CKD. CPP are endogenous mineral-protein colloids that are thought to be a critical protection against ectopic mineralisation in normal mineral physiology, but may become injurious in CKD due to altered levels and composition. Notably though our understanding of CPP metabolism in health and in CKD is limited. Chapter 3 and 4 focus on the role that CPP may play in normal mineral handing. Chapter 3 provides evidence that CPP may be formed as part of the normal response to nutritional mineral loading, but that post-prandial metabolism of CPP precursors, calciprotein monomers (CPM), appears to be perturbed in CKD. Chapter 4 found that serum levels of CPP are dynamically linked to bone turnover, consistent with the hypothesis that bone may also be an important determinant of serum levels of CPP. Chapter 5 and 6 utilise samples from two recently completed interventional trials to examine potential therapeutic strategies to modify serum levels of CPP in individuals with CKD. Despite theoretical benefits, lanthanum carbonate, a non-calcium based intestinal phosphate binder, did not lower levels of CPP in individuals with non-dialysis requiring CKD (Chapter 5). In a cohort of patients with kidney failure being treated with haemodialysis, changing from a standard high flux dialyser to a novel mid cut-off dialyser did not appear to be associated with any change in CPP (Chapter 6). Finally, in Chapter 7 the potential role of CPM in the progression of CKD was studied. In an observational cohort, higher levels of CPM were associated with increased risk of progression of CKD. This association was independent of a range of traditional risk factors and raises the possibility that altered CPM metabolism in CKD may contribute to the progression of CKD itself. In summary, this thesis explores the use of conventional and novel markers of mineral metabolism. It is expected that an enhanced capacity to assess the evolution of disordered homeostasis in CKD will provide new avenues to better risk assess patients with the ultimate goal of developing new therapeutic strategies in this population.
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ItemIdentifying Antibody Responses Associated with Protection from Severe Malaria in Children( 2023-04)Malaria is a major global public health burden that affects individuals in 87 countries and causes 600,000 deaths annually. The majority of cases of severe malaria and malaria related deaths occur in children under the age of five, who lack protective immunity that is acquired by adulthood in endemic regions. Antibodies are a key component of protective immunity, however, the target antigens of antibodies and the functions of antibodies that confer protection are unclear. Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) expressed on the surface of parasite infected erythrocytes is a highly variant, multi-domain protein that mediates adhesion to a range of vascular endothelial cell receptors including Intercellular Adhesion Molecule-1 (ICAM-1) and Endothelial Protein C Receptor (EPCR). PfEMP1 is an important virulence factor and is a strong candidate target of protective antibodies against severe malaria. Therefore, the overall objective of this thesis was to understand the antibody response to PfEMP1 antigens that may confer protection from severe malaria in children. This thesis aimed to: 1) characterize the antibody response to PfEMP1 antigens that are associated with protection from cerebral malaria (the most severe form of malaria) in a cohort of Malawian children; 2) characterize the antibody response to PfEMP1 antigens that are associated with protection from severe malaria in a cohort of Papua New Guinean children; 3) assess the association of disease severity with antibody dependent neutrophil and monocyte phagocytosis of infected erythrocytes expressing important PfEMP1 variants. For aims 1 and 2 we applied systems serology, which involves measuring multiple features of antibodies targeting multiple recombinant antigens and using machine learning with statistical methods to identify the best correlates of protection. For aim 3, we selected parasite-infected erythrocytes expressing two PfEMP1 variants (that bind to ICAM-1) and measured antibody dependent neutrophil phagocytosis (ADNP) and antibody dependent cell phagocytosis (ADCP) of opsonized infected erythrocytes by flow cytometry. The important findings of this thesis were: 1) in both Malawian children and Papua New Guinean children, a combination of a small subset of PfEMP1 specific antibody responses could be used to differentiate between children with severe and uncomplicated malaria with high accuracy; 2) in both cohorts, DBL-beta3 domains that bind to ICAM-1 receptor were targets of antibodies associated with protection from severe malaria. We also affirmed that 3) in addition to measuring the quantity of antigen specific antibodies, the biophysical properties and Fc interactions (or ‘Fc features’) of PfEMP1 specific antibodies are useful correlates of protection from severe malaria. A range of antibody Fc features were associated with protection, suggesting there are multiple pathways to protection from severe malaria. The antibody responses associated with protection included Fc-gamma-RIIIb binding to antibodies targeting DBL-beta3 domains that bind to ICAM-1, suggesting that antibodies to ICAM-1 binding PfEMP1 may induce killing mechanisms by neutrophils. In the final chapter, we found that 4) ADNP of ICAM-1+EPCR binding infected erythrocytes was associated with protection from cerebral malaria in Malawian children but was not associated with protection from severe malaria in Papua New Guinean children. Additionally, 5) ADCP of ICAM-1 binding infected erythrocytes was not associated with protection from severe malaria in either cohort of children. In considering the different methodological approaches used in this thesis, we concluded that systems serology is an effective approach to identify correlates of protective immunity to PfEMP1 but currently cannot replace more complex cell-based assays like ANDP and ADCP. Overall, this thesis highlights the important role of functional antibodies to PfEMP1 in protection from severe malaria in children from diverse geographic regions and supports the development of a DBL-beta domain based therapeutic.
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ItemNovel Mechanisms, Determinants and Therapies in Atrial Fibrillation( 2023-01)Atrial fibrillation (AF) is the most common sustained cardiac rhythm disorder and is associated with increased morbidity and mortality. Since the first description of AF initiation by triggers from pulmonary veins sleeves, pulmonary vein isolation has become the standard ablation strategy in patients with AF. However, freedom from the arrhythmia particularly in persistent AF remains suboptimal and it is now clear that in these patients AF is maintained by an atrial substrate beyond the pulmonary veins. This thesis aims to evaluate novel mechanisms that influence the atrial substrate in AF (chapters 2,3, and 4), the role of genetic predisposition on the atrial substrate and arrhythmia outcomes post ablation (chapter 5), and the impact of catheter ablation on cognitive function, markers of psychological distress, and arrhythmia outcomes (chapters 6, 7, and 8). Chapter 1 outlines our current understanding of the atrial substrate in atrial fibrillation and its association with traditional risk factors for AF. We delineate the role of genetics in AF, focusing on the AF-polygenic risk score and its role in AF management. Lastly, we review the impact of catheter ablation on cognitive function, markers of psychological distress, and catheter ablation timing on arrhythmia outcomes. Chapter 2 describes the electroanatomic characteristics and ablation outcomes in a case series of symptomatic patients with a clinical syndrome of atrial tachycardia/atrial fibrillation and extensive right atrial free wall substrate. An extensive low voltage zone in the trabeculated RA free wall constituted an unusual substrate for AF. These patients also demonstrated unstable atrial tachycardias originating from the same zone. Radiofrequency ablation to render the low voltage zone electrically inert was an effective strategy to manage AF and atrial tachycardia and improve symptoms. Chapter 3 characterises the wavefront activation patterns of extent of left and right atrial septal electrical dissociation in a cohort of 8 patients with longstanding persistent AF. Two advisor HD grid catheters were positioned on either side of the interatrial septum and unipolar recordings of AF and sinus rhythm were analysed offline. We observed complete wavefront dissociation between the left and right interatrial septum with no evidence of transseptal conduction, indicating that the two sides function as electrically discrete structures. No stable septal drivers were observed. Chapter 4 characterises the wavefront activation pattern at the pulmonary vein (PV) sleeve in 13 patients with longstanding AF using high density phase mapping. Pulmonary vein sleeve unipolar recordings were collected during AF using the 64-electrode Baskett Catheter. A robust inverse mapping technique was used to reconstruct the recorded unipolar atrial EGMs on the PV surface and the resulting phase maps were used to identify incoming and outgoing wavefronts (WF) at the PV junction (reentry), and focal and rotor activity originating within the PV sleeves. Electrical activity generated by PV sleeves during PeAF was due mainly to macroscopic reentry initiated by incoming waves, frequently with a ratio>1. That is, the PVs act less as AF drivers than as “echo chambers” which sustain and amplify fibrillatory activity. Chapter 5 examines the association between AF-polygenic risk score (AF-PRS), the left atrial substrate and ablation outcomes. Amongst 95 patients who their AF-PRS calculated and detailed electroanatomic mapping of the left atrium, we observed that patients with high AF-PRS had more advanced left atrial electrical remodelling and lower arrhythmia free survival post ablation when compared to low AF-PRS. Chapter 6 focuses on the impact of catheter ablation on cognitive function in a cohort of 100 patients randomised to catheter ablation versus medical therapy. All patients underwent 6 neurocognitive tests at baseline, 3, 6, and 12 months. A reliable change index was calculated to detect changes compared to baseline. We observed that in patients randomised to catheter ablation there was higher prevalence of new onset cognitive dysfunction at 3 months post catheter ablation when compared to medical therapy. However, this was transient and fully reversible at 12 months with no observed cases of cognitive dysfunction. In addition, 14% of patients in the ablation arm demonstrated improvements in their cognitive function at 12 months compared to medical therapy (0%). Chapter 7 examines the impact of catheter ablation on markers of psychological distress in a cohort of 100 patients randomised to catheter ablation versus medical therapy. All patients underwent comprehensive psychological testing using the Hospital Anxiety and Depression Score (HADS) and Beck Depression Inventory Score (BDI-II). In addition, Quality of life measures were assessed using the AF symptoms severity score (AFSSS) and the Short Form-36 questionnaire (SF-36). Patients randomised to the ablation arm reported improvement in their makers of psychological stress (HADS and BDI-II) in addition to improvement in qualify life measures. This improvement was associated with sinus rhythm and cessation of antiarrhythmic medications during follow up. Chapter 8 evaluates the impact of AF catheter ablation timing on arrhythmic recurrence outcomes. A total of 89 patients were randomised to either undergo ablation within 1 month of recruitment (early ablation arm) or 12 months after recruitment (delayed ablation arm). All patients were followed up for 12 months and their arrhythmia recurrence, AF burden and antiarrhythmic drug use was recorded. Both groups had comparable atrial arrhythmia free survival, median AF burden and antiarrhythmic drug use at 12 months.
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ItemNovel Immunologic Assessment of Aplastic Anaemia and Post-Transplant Poor Graft Function for the Purposes of Therapeutic Intervention( 2023-03)Engraftment post allogeneic stem cell transplantation (alloSCT) is defined by two intersecting domains; 1) restoration of normal haematopoiesis, 2) confirmation that this haematopoiesis is derived from a donor source. Poor Graft Function (PGF) is defined by the presence of multilineage cytopenias in the setting of complete donor chimerism and is a significant complication of alloSCT as it causes morbidity and mortality due to effects of bone marrow failure (BMF). Aplastic anaemia (AA) is an acquired, BMF syndrome resulting in the autoimmune destruction of haematopoietic tissue and subsequent pancytopenia. PGF is a controversial syndrome due to the numerous ways it has been defined in prior literature. In this thesis I investigate the underlying immunologic mechanisms as well as novel treatments for both PGF and AA. I will define the risk factors and outcomes for PGF in a large retrospective analysis of institutional databases. To assess the underlying immunology of PGF and AA I will apply multiple analytic techniques to patient samples. Finally, I describe a clinical trial framework that forms the basis for a currently operating Phase II study evaluating the efficacy and safety of atorvastatin and n-acetyl cysteine (NAC) in the treatment of PGF and relapsed refractory AA. The framework for this study can also be utilised to test novel therapies discovered as part of this thesis.
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ItemIntegrating genomics into diagnostic and management strategies for patients with Bone Marrow Failure Syndromes( 2023-03)The bone marrow failure syndromes (BMFS) are a heterogeneous group of diseases with differing underlying pathogenic processes and treatment approaches. Diagnosis remains challenging as these conditions can mimic each other, both in clinical presentation, on morphological examination of the bone marrow and their shared potential to transform to haematological malignancy. The BMFS are associated with poor outcomes and there remain many gains to be made in improving both diagnostic and treatment strategies. Both comprehensive clinical data interrogation and genomic analysis by next generation sequencing (NGS) were employed in an effort to examine the clinical, genomic and molecular determinants of outcome in patients with BMFS. The focus of this thesis was to integrate genomics into diagnostic and management strategies to improve outcomes for patients with BMFS. Initially, the utility of comprehensive genomic sequencing to attain accurate diagnosis in patients presenting with bone marrow failure (BMF) was analysed. This work was a prospective demonstration evaluation study. The observed utility of germline and somatic genetic testing in patients presenting with hypocellular BMF and hereditary predisposition to haematological malignancy (HPHM) led to availability of clinical accredited BMF testing, the uptake and outcomes of which were then analysed in the real world setting. The comprehensive dataset of the Australian Aplastic Anaemia and other Bone Marrow Failure Syndromes Registry (the AAR) was interrogated to examine the treatments applied in and outcomes of patients with immune aplastic anaemia (iAA). The AAR was modernised to facilitate enrolment of patients with both traditional inherited BMF (IBMF) and also novel germline conditions, including those recently discovered and described as conferring a HPHM. Consideration of whether a HPHM exists is now considered to represent a crucial component of new leukaemia diagnostic work up. The AAR provides an opportunity to document the Australian experience and natural history of patients with BMFS/HPHM and permit further research including facilitating offering clinical trials and novel therapies to patients with these individually rare conditions. Recognising the poor outcomes of patients with BMFS and HPHM, interview and survey of key stakeholders (patients, patient advocates and clinicians caring for patients with BMFS/HPHM) was performed to formally identify issues faced and barriers experienced by this diverse patient group and their families and care providers. A comprehensive model of care (MoC) for patients with BMFS/HPHM was developed which incorporates the results of stakeholder assessment and also the observations determined during earlier studies detailed above. The MoC is undergoing evaluation with a hybrid implementation-effectiveness study to determine both patient and clinician acceptability and satisfaction with this approach. Overall, the work presented in this thesis demonstrates strategies to improve diagnosis, management and outcomes of Australian patients with BMFS/HPHM and their families.
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ItemInvestigation of the synergy between Alzheimer’s Disease and epilepsy through data-driven molecular networks( 2023-03)Overview: In the recent years, a bi-directional association between Alzheimer’s Disease (AD) and epilepsy has been observed, with AD-like cognitive impairments often presenting in epilepsy patients, and high rates of epileptic seizures seen in a sub-set of AD patients. These seizure-prone AD patients reportedly show accelerated cognitive decline and more aggressive disease progression compared to those without seizures. The mechanism and primary mode of action of this association remains unknown, although a synergistic interaction has been proposed. The general aim of this doctoral research was to investigate the electrical and molecular properties of the above-mentioned pathophenotypes and elucidate the mechanisms underlying the potential synergy between AD-like amyloid pathology and epileptiform activity, and their role in accelerated cognitive decline. Introduction and literature review: The introductory sections of Chapter 1 provide an overview of the current literature on epilepsy and Alzheimer’s Disease, focusing on pathophysiological mechanisms commonly implicated in both syndromes. The subsequent sections discuss several benchmark studies that first reported on the increased co-occurrence of seizures among AD patients, followed by a critical review of the most prominent as well as recently emerged hypotheses that aim to provide mechanistic insight into the nature of the proposed bi-directional association between AD and acquired epilepsy. The concluding sections provide a gentle introduction into the emerging field of network medicine, systems- based analysis, interrogation methods of high-throughput biological data and the general framework of computational models and methodology that was implemented throughout this work. Experimental chapters: The first and second experimental chapters aim to characterize the molecular signature of a brain affected by amyloid pathology and seizures. Utilizing proteomic and metabolomic data from two collaborative studies as well as publicly available transcriptomic data, Chapter 2 describes the molecular signature of human AD and that of most widely used mouse models of AD, while Chapter 3 captures the molecular profile of well- established rat models of genetic (GAERS) and acquired (post SE) epilepsies. Informed by the insight gained from Chapters 2 and 3, the third experimental chapter (Chapter 4) aimed to capture the shared molecular signature associated with AD and temporal lobe epilepsy (TLE) – the most common type of epilepsy comorbid with AD. A hypothesis-free, systems-level approach was used to characterize the pathophysiological state of each disease on a molecular level by constructing data-driven gene coexpression networks representing the respective pathologies. The topology and architecture as well as the preservation of functional gene modules between the two networks were compared through network preservation analysis, identifying two clusters of synaptic reorganization and signalling-associated genes as highly preserved between AD and TLE. The fourth and final experimental chapter (Chapter 5) aims to investigate the mechanism and potential mediators of the bi-directional relationship between amyloid pathology and epilepsy by examining the effect of recurrent seizures on hallmark features of AD pathology such as amyloid plaque deposition and cognitive performance. RNA sequencing and bioinformatic analysis of mouse hippocampal tissue was conducted in order to investigate the molecular mechanisms of synergy between recurrent seizures and already- present AD pathology as well as identify key mediators of accelerated disease progression, which could serve as promising targets for intervention. Discussion and conclusions: Informed by computational analysis from chapters 2, 3 and 4, and reinforced by experimental evidence from chapter 5, the final chapter of this thesis (Chapter 6) provides a synthesis of the newly gained insights into the strong synergistic nature of the relationship between amyloid pathology and recurrent seizures. A subsequent extensive review of the most current molecular neuroscience research facilitated interpretation of our results, leading to the proposal of a “dual-pathology” disease model for epilepsy and AD. In this paradigm, the synergistic self-propagating interaction between epileptiform activity and amyloid pathology defines a distinct subpopulation of “dual-pathology” patients, characterized by faster disease progression and more severe cognitive decline. Furthermore, I describe specific cellular pathways mediating the synergy between amyloid pathology and recurrent seizure activity and introduce a mechanistic framework underlying the chain of events through which this synergy leads to accelerated cognitive deterioration. Each step in this framework or chain of events is reinforced by a benchmark proof-of-concept study published in leading peer- reviewed journals and which, with the exception of the most recent 2022-2023 studies, have been independently replicated by other research groups. The concluding sections of this chapter emphasize the utility of integrating phenotypic and electroencephalographic data from in vivo studies with high-throughput “omics” data into network-based computational models for a holistic examination of pathophysiological mechanisms underlying complex diseases and identification of novel therapeutic targets.
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ItemThe Role of Intestinal Ultrasound in prognosticating Clinical Outcomes in IBD as a Treat-to-Target tool (RIOTT)( 2022-10)Inflammatory Bowel Disease is a chronic relapsing inflammatory gastrointestinal disease, with many patients reporting extra-intestinal manifestations. The disease course is heterogenous, and symptoms do not accurately reflect the degree of active inflammation. Persistent inflammation leads to progressive structural bowel damage with the development of strictures, fistulising complications in Crohn’s disease and dysplasia and refractory colitis with increased risk of colectomy in ulcerative colitis. Repeated objective reassessment of disease activity is required, however repeated ileo-colonoscopy to assess for endoscopic mucosal healing is resource intensive and poorly accepted by patients.[1] Intestinal Ultrasound is optimally placed as a safe, non-invasive, and well tolerated modality to aid in the care and treatment decisions of IBD. Limiting its uptake has been a lack of evidence demonstrating its role as a prognostic marker in IBD, its ability to reflect other objective markers of disease activity and its utility as a treat to target tool. To address these limitations, this thesis examined several important questions. Firstly, the role of IUS in predicting clinical outcomes in both UC and CD, secondly whether transmural healing as determined by IUS is associated with higher biologic drug levels and thirdly whether IUS can be used as a non-invasive tool to assess for inflammation that reliably reflects disease activity and are responsive to effective treatment. A systematic narrative literature review was performed to address the clinical utility of IUS as a prognostic marker in Crohn’s disease. It was found firstly that sonographic markers of inflammation are responsive to treatment, and bowel wall thickness and hyperaemia on Doppler imaging are most accurate at predicting outcomes in CD. Secondly, a failure to achieve improvement in sonographic inflammation is predictive of persistent endoscopic mucosal inflammation. Thirdly, sonographic transmural remission confers prognostic benefits and may be superior to that of mucosal healing alone. Further analysing the prognostic value of IUS, the significance of sonographic healing in the context of clinical remission was examined in two retrospective studies, in CD and UC. Sonographic inflammation was defined as abnormal BWT >3mm and/or hyperaemia and/or abnormal bowel wall stratification and/or mesenteric inflammatory fat. In CD, poorer clinical outcomes were demonstrated in those with evidence of sonographic inflammation, including an increased risk of medication escalation, corticosteroid use, hospitalisation, and surgery. In a smaller cohort of UC patients with clinical remission, patients with sonographic healing did not have significantly improved clinical outcome compared to those with sonographic inflammation. Higher numerical rates of medication escalation, corticosteroid use, and hospitalisation were observed in those UC patients with sonographic inflammation compared to those with sonographic remission, but this failed to reach statistical significance. Evidence supporting an exposure response relationship is established for maintenance use of infliximab in IBD, with high levels associated with mucosal healing. It was therefore hypothesised that a relationship between serum infliximab levels and sonographic inflammation would also exist. This was confirmed, with those patients with undetectable infliximab trough level having higher median BWT compared to those with a detectable level. Median infliximab trough levels were higher in those CD patients with sonographic healing compared to those with sonographic inflammation (4.8mg/mL versus 3.1mg/mL, p=0.049). The presence of hyperaemia on Doppler was independently associated with lower trough levels in both CD and UC patients. Other sonographic makers of inflammation such as loss of stratification, and mesenteric fat hypertrophy where not significantly associated with serum trough levels in either UC or CD. This thesis then proposes a prospective study protocol examining the role of IUS to predict clinical relapse in those with remission. Secondly, a randomized trial protocol that lays out a methodology to explore the benefits of serial IUS compared to standard clinical examination without IUS in active IBD is described. This final study aims to assess the utility and feasibility of IUS within a treat-to-target strategy. Due to pandemic impacts on healthcare the prospective research was unable to be completed but are ongoing. In conclusion, these studies support the use of IUS as an objective biomarker in IBD. They demonstrate the role of IUS in predicting long-term outcomes in CD and demonstrate that higher infliximab levels are associated with greater rates of sonographic remission. Ongoing prospective research is underway to confirm the prospective utility in CD and explore it’s use further in UC. However, our small studies to date suggest that incorporating IUS into treat-to-target algorithms in CD may be beneficial, whilst we await further research outcomes in UC.