http://bura.brunel.ac.uk/handle/2438/8615 2026-04-27T04:08:18Z 2026-04-27T04:08:18Z Pandya, Snehal P. http://bura.brunel.ac.uk/handle/2438/33206 2026-04-26T18:50:00Z 2025-01-01T00:00:00Z

Title: Effect of polygenic risk scores for Alzheimer's disease on brain structure, cerebrospinal fluid, and cognition Authors: Pandya, Snehal P. Abstract: Background: Apolipoprotein E (APOE) is the most studied gene in relation to, and has the strongest genetic association with, sporadic Alzheimer’s disease (AD). The APOE epsilon 4 (ɛ4) risk variant is found in approximately 14% of the general population and in approximately 37% of the AD population, globally. This indicates that the presence of ɛ4 is not required for the development of sporadic AD. In fact, sporadic AD is considered a polygenic disease with thousands of causative variants. Therefore, there is a need to investigate other genes and associated variants, and the concurrent effect of these on sporadic AD. Polygenic risk scores (PRSs) are ideal for this purpose as they consider multiple genetic variants/single nucleotide polymorphisms (SNPs) that have genome-wide significance, simultaneously. However, PRSs are difficult to calculate since numerous factors must be taken into consideration, and there is no optimal procedure. Nonetheless, PRSs can improve understanding of genotype-to-phenotype associations and risk predictions. Aim: The aim of the current research is to investigate whether PRSs for AD can predict cross-sectional regional grey matter volume (Experiment One), cross-sectional cerebrospinal fluid (CSF) biomarkers (Experiment Two Part A), cross-sectional cognitive markers (Experiment Two Part B), longitudinal CSF biomarkers (Experiment Three Part A), and/or longitudinal cognition (Experiment Three Part B) across the continuum of sporadic AD. Methodology: Participants from the Alzheimer's Disease Neuroimaging Initiative (n = 738; mean age in years: 73.94 ± 7.58) were analysed using various binomial hierarchical logistic regression models, and multiple hierarchical linear regression models, that controlled for numerous demographic and clinical variables. Participants were stratified by several variables to assess risk of AD in different groups. Three PRSs were constructed: PRSwithAPOE, PRSwithoutAPOE, and APOEonlyPRS. SNPs relating to APOE were from the entire APOE region, and three statistical thresholds were calculated for each of the three PRSs. Results: Overall, PRSwithAPOE and APOEonlyPRS were associated consistently with outcome measures. Generally, PRSwithAPOE and APOEonlyPRS were: associated negatively with bilateral hippocampus (right (R) > left (L)), bilateral amygdala (R > L), bilateral entorhinal area, and R middle occipital gyrus; associated positively with CSF amyloid-beta 42 (Aβ42) more than they were with CSF phosphorylated-tau181 (p-tau181), cross-sectionally; associated negatively with memory and visuospatial cognition, cross-sectionally; associated with CSF p-tau181 more than they were with CSF Aβ42, longitudinally; associated positively with longitudinal cognitive decline. Discussion: The results highlight that stratification by amyloid positivity improves risk prediction over stratification by clinical diagnosis. The findings also concur to previous literature indicating that CSF amyloid decreases early on in AD after which it reaches a plateau, whereas changes in tau continue throughout the disease. The current research presents a novel, systematic, and thorough approach to evaluate risk of sporadic AD, including: a multi-modal approach that assesses outcome measures that are used to diagnose individuals with AD clinically (i.e., brain structure, CSF biomarkers, and symptomology); the use of both cross-sectional and longitudinal study designs; a multi-stratification approach whereby participants are divided in several ways to assess risk in different groups – for some groups, findings have been reported for the first time (to knowledge). Conclusion: This work highlights the added value of non-ɛ4-APOE SNPs and non-APOE SNPs (i.e., both PRSwithAPOE and APOEonlyPRS) in detecting associations with AD-specific cross-sectional and longitudinal outcome measures. In parallel with existing literature, an ideal threshold has not been determined in the current research. However, it may be that certain thresholds identify associations better according to the outcome measure at hand. Additionally, the current research demonstrates the clinical relevance of PRSs for AD and that these may support diagnosis and prognosis of AD. It is recommended that future investigations assess PRSwithAPOE and APOEonlyPRS with longitudinal CSF biomarkers, in independent samples, and in ethnically diverse populations. Description: This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London

2025-01-01T00:00:00Z Ulukütük Gözlügöl, Zeynep http://bura.brunel.ac.uk/handle/2438/32731 2026-01-27T10:47:26Z 2025-01-01T00:00:00Z

Title: A comprehensive proteomics analysis of Friedreich's ataxia (FRDA) Authors: Ulukütük Gözlügöl, Zeynep Abstract: First and foremost, I would like to express my deepest gratitude to my Principal Supervisor, Dr. Sara Anjomani Virmouni, for her invaluable guidance, constructive feedback, and unwavering support throughout this journey. Her mentorship has been instrumental in shaping both my research and academic growth. I am also sincerely grateful to members of my supervisor team, Supervisor, Prof. Michael Themis. Additionally, I extend my thanks to Dr. Victor Hernandez, my Research Development Advisor, for his guidance especially during the first year of my PhD. I extend my sincere appreciation to Ministry of National Education, TURKEY, for their financial support as well as to Brunel University of London for providing access to the facilities and resources required for this research. My heartfelt appreciation goes to my collaborators, whose contributions have been vital to my research. I appreciate Associate Professor Faraz Mardakheh from the Barts Cancer Institute (Queen Mary University of London) for conducting proteomics analysis in human FRDA cells. I am also thankful to Professor Richard Wade-Martins' team at Oxford University for providing Human iPS-derived cardiomyocytes and to Professor Marek Napierala’s laboratory at the University of Texas Southwestern Medical Centre for supplying Human iPSCs. I would like to acknowledge Dr. Raha Pazoki from Brunel University London for her support in bioinformatics, particularly in creating the transcriptomics analysis heat map. I am also grateful to Dr. Saqlain Suleman, a postdoctoral researcher in our group, for his academical support and help. Additionally, I extend my thanks to Dr. Zenouska Ramchunder, another postdoctoral researcher in our group, for her academical help and endless support. I want to thank my beloved parents for their endless love, trust, and support throughout my journey. Their encouragement and sacrifices have given me the strength to overcome challenges and reach this milestone. I am forever grateful for everything they have done to help me achieve my dreams.I also want to thank my dear soulmate and husband, Haci, for his patience, love, and support. Even when we were far apart, his constant encouragement and understanding made our bond stronger. I am deeply grateful for his steady presence and for our love that has grown even through tough times. I wish to thank the team members of the Brunel technician staff for their assistance, which greatly facilitated the experimental aspects of this study. Their expertise and support have been invaluable in ensuring the smooth execution of laboratory work. I am also grateful to my colleagues in the Ataxia lab for their encouragement, collaboration, and insightful discussions. Their support has made this journey both intellectually enriching and personally rewarding. Finally, I extend my deepest appreciation to everyone who has contributed, directly or indirectly, to the successful completion of this thesis. Your support has been invaluable, and I am truly grateful. This thesis would not have been possible without the support and guidance of many individuals and organizations. Description: This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London

2025-01-01T00:00:00Z Hashimi, Munisa http://bura.brunel.ac.uk/handle/2438/32643 2026-01-15T15:14:30Z 2025-01-01T00:00:00Z

Title: Genetic insights into the epidemiology of cataracts, prevention and alternative treatment Authors: Hashimi, Munisa Abstract: Cataract, a leading cause of visual impairment and blindness, remains a significant global health challenge, particularly in the context of an aging population. As the global population continues to age, the burden of cataract on healthcare systems, especially in developing countries, is expected to increase. Cataract involves the clouding of the lens, and surgical extraction remains the sole treatment option. Understanding the genetic mechanisms underlying cataract, identifying preventive measures, and exploring alternative treatments are critical to reducing this burden. This thesis utilised UK Biobank generated genome-wide association study (GWAS), and publicly available GWAS data to investigate the shared genetic mechanisms between cataract subtypes and cataract-associated risk factors. It also assessed alcohol consumption, vitamin D levels and deficiency, and lanosterol as potential modifiable risk factors or alternative treatment options. Genetic correlations were identified between overall cataract and type 2 diabetes (T2D), asthma and diabetic cataract, senile and diabetic cataract, and asthma and overall cataract. Co-localisation analysis highlighted genes of interest, including WWP2 and CDKN2B-AS1 between overall cataract and T2D, and HLA-DQB1 between asthma and overall cataract. Mendelian randomisation analyses found no evidence of a causal relationship between vitamin D levels, vitamin D deficiency, or alcohol consumption and cataract. Similarly, lanosterol was not supported as a viable alternative treatment option. In summary, while this study identified genetic links between cataracts and associated risk factors; it did not provide supporting evidence for vitamin D, alcohol, and lanosterol as effective preventive measures or alternative treatment options. Description: This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London

2025-01-01T00:00:00Z AL Fashtaki, Reham Adnan http://bura.brunel.ac.uk/handle/2438/32638 2026-01-15T15:15:54Z 2025-01-01T00:00:00Z

Title: Involvement of matricellular proteins and immune receptors in the dynamic interaction between tumour and immune cells Authors: AL Fashtaki, Reham Adnan Abstract: Background: Osteosarcoma (OS) is the most common primary malignant bone tumour in children and young adults, characterised by high metastatic potential and poor prognosis in advanced stages. Despite recent therapeutic advances, metastatic OS remains challenging to treat. Increasing evidence highlights the tumour microenvironment (TME), particularly immune cell components such as macrophages, as key modulators of tumour progression. Ovarian cancer (OC) is a significant cause of cancer-related deaths among women worldwide. It is a highly metastatic malignancy that shares similar molecular and immunological features with OS, including late-stage diagnosis, immune evasion, and extracellular matrix (ECM) remodelling. Matricellular proteins (MCPs) are non-structural extracellular matrix proteins that regulate cell– matrix interactions and signalling rather than providing structural support. They influence cell adhesion, migration, proliferation, and differentiation, and are often upregulated in cancer, promoting tumour growth, angiogenesis, and metastasis. Comparative analysis of OS and OC may reveal shared immune–metabolic pathways that contribute to tumour aggressiveness. This project investigates how MCPs and the interactions with immune cells influence tumour behaviour, survival, and metastatic progression within the TME. Using OC and OS as model systems, it integrates bioinformatic analyses, experimental validation, and functional assays to elucidate the molecular and immune mechanisms underpinning cancer progression and metastasis. Methods: Publicly available transcriptomic datasets for OS (GSE42352, GSE12865) and ovarian cancer (GSE18520, GSE54388, GSE14407) were analysed to identify differentially expressed genes (DEGs). The UniProt tool was used for functional annotation, with an emphasis on immune receptor (IR), cell adhesion (CAD), and ECM pathways. Survival analyses were performed using the KM Plotter. Candidate genes were validated in vitro using RT-qPCR and Western blotting in OS cell lines (MG63, SaOS-2, MNNG, 143B) and THP-1 monocytes differentiated into M0, M1, and M2 macrophages via PMA and cytokine stimulation. In addition, MNNG and 143B cells were treated with the FPR3 agonist WKYMVm and antagonist WRW4 (10 μM and 50 μM) for 24 h to directly assess the functional impact of FPR3 signalling on OS cell motility. Proliferation and scratch migration assays were performed using tumour- and macrophage-conditioned media. Secretomes were subjected to ultracentrifugation to assess the roles of soluble and vesicle-bound factors. Co-culture experiments were conducted to examine the bidirectional effects of macrophage-tumour signalling. Results: Initial bioinformatics analyses revealed a significant enrichment of DEGs associated with ECM remodelling, immune signalling, and poor survival in both OS and OC datasets. In OC, D24 (Cluster of Differentiation 24), DCN (Decorin), and OGN (Osteoglycin/Mimecan) were associated with adverse prognosis. In OS, SPP1 (osteopontin) and FPR3 (formyl peptide receptor 3) were upregulated, whereas LEPR (leptin receptor) was consistently downregulated across patient tissues, and it was a common gene among OC and OS. Functional assays demonstrated that M2- conditioned media enhanced the migration and proliferation of OS cells. Ultracentrifugation experiments suggested that vesicle-bound factors mediate these effects on the target cells. The reciprocal communication between osteosarcoma cells and macrophages establishes a pro-metastatic feedback loop. In vitro experiments using RT-qPCR and Western blotting revealed the differential expression of key genes involved in tumour progression and immune regulation across various osteosarcoma cell lines. Genes such as FPR3, LEPR, and SPP1 displayed variable mRNA and protein levels, indicating distinct molecular profiles between the cell lines. These differences highlight the heterogeneity of osteosarcoma and suggest that specific gene expression patterns may be linked to variations in tumour behaviour, immune interactions, and metastatic potential. Treatment of MNNG and 143B cells with the FPR3 agonist WKYMVm significantly increased migration velocity at both 10 μM and 50 μM, while the antagonist WRW4 effectively reduced migration, particularly at 50 μM. M2 macrophages showed high expression of CD163, FPR3, LEPR, and SPP1, reflecting their tumour-promoting, anti-inflammatory phenotype.THP-1 cells treated with OS-conditioned media upregulated CD163, consistent with M2 polarisation, whereas OS cell lines treated with macrophage supernatants displayed increased SPP1 and LEPR, particularly under M2 stimulation. Conclusion: This study identified SPP1, FPR3, and LEPR as key immune-metabolic mediators in OS, highlighting their roles in tumour–macrophage crosstalk and metastasis. The combination of in silico and in vitro findings supports a model in which the TME, particularly M2 macrophages, enhances OS progression via dynamic signalling pathways. These findings provide a foundation for targeting tumour–immune interactions in future OS therapies and suggest new directions for precision medicine strategies in metastatic cancers. Notably, LEPR was also consistently downregulated in OC, indicating a shared immunometabolism mechanism that may contribute to metastatic progression across tumour types. Description: This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London

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