BURA Collection:http://bura.brunel.ac.uk/handle/2438/1662026-04-17T06:54:42Z2026-04-17T06:54:42ZNovel memory phenotype Tfh cells arise without overt antigen stimulation and are important for adaptive immune responses against viral infectionBusharat, Zabreenhttp://bura.brunel.ac.uk/handle/2438/327692026-02-24T13:17:24Z2025-01-01T00:00:00ZTitle: Novel memory phenotype Tfh cells arise without overt antigen stimulation and are important for adaptive immune responses against viral infection
Authors: Busharat, Zabreen
Abstract: Pathogen-induced memory Tfh cells exert a Tfh effector response during reinfection, regulating the generation of high-affinity antibodies. Here, we define novel memory-phenotype Tfh cells which are generated from naïve T cells under homeostatic conditions. These MP Tfh cells are phenotypically and functionally similar to pathogen-induced Tfh cells. MP Tfh cells can be defined by Tfh cell specific markers, CXCR5, BCL6, and PD-1, and markers of pathogen-induced long lived Tfh cells, FR4. T-bethigh MP T cells exert an innate-like Th1 response against viral infections. The transcription factor EGR2 is a repressor of T-bet function, and we found that MP Tfh cells are distinct from T-bethigh MP T cells but express EGR2 highly. Previously, we found Egr2 is required for MP T cell homeostasis and inflammation. Here, we observed that, in Egr2/3-/- CD4+ MP T cells, MP Tfh cell development is impaired. FR4+ EGR2 + MP T cells upregulate genes related to homeostatic proliferation, Tfh cell development and metabolic pathways of pathogen-induced memory Tfh cells. MP Tfh cells can exert an adaptive function by regulating B cell-mediated IgG production in vitro whereas MP Tfr cells are involved in suppressing MP Tfh cell function, thereby preventing excessive inflammation. In vivo, MP Tfh cells support germinal centre formation and induce neutralising antibody production after infection with vaccinia virus. Thus, MP Tfh cells with similar characteristics to pathogen-induced memory Tfh cells are developed in absence of environmental antigens and to date are the only CD4+ MP T cell subset associated with an adaptive immune response against viral infection.
Description: This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London2025-01-01T00:00:00ZA comprehensive proteomics analysis of Friedreich's ataxia (FRDA)Ulukütük Gözlügöl, Zeynephttp://bura.brunel.ac.uk/handle/2438/327312026-01-27T10:47:26Z2025-01-01T00:00:00ZTitle: 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 London2025-01-01T00:00:00ZGenetic insights into the epidemiology of cataracts, prevention and alternative treatmentHashimi, Munisahttp://bura.brunel.ac.uk/handle/2438/326432026-01-15T15:14:30Z2025-01-01T00:00:00ZTitle: 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 London2025-01-01T00:00:00ZInvolvement of matricellular proteins and immune receptors in the dynamic interaction between tumour and immune cellsAL Fashtaki, Reham Adnanhttp://bura.brunel.ac.uk/handle/2438/326382026-01-15T15:15:54Z2025-01-01T00:00:00ZTitle: 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 London2025-01-01T00:00:00Z