<p>Age-related macular degeneration is one of the leading causes of vision loss in the world. While identification of various environmental risk factors including but not limited to smoking, ethnicity, and diet have been reported to contribute to the complex etiology of AMD, age and genetics remain the largest susceptibility factors in its pathogenesis. Initially, with the identification of the common Y402H variant in CFH, approximately 35% of the genetic determinants of AMD had been identified with the majority remaining unknown. Therefore, we set forth to A) identify additional AMD susceptibility genes that contribute to AMD through the use to next generation sequencing technologies and B) to assess associated alleles for pathogenicity in the attempt to interpret their functional contributions to AMD outcome as observed via patient serum and zebrafish analysis. In doing such, we have identified both common and rare variants that contribute to the heritability of AMD. Additionally, we report one of the first instances of a rare variant significantly increasing disease onset and a gene with increased rare mutational burden in AMD patients. All together adding to our understanding of the genetics of AMD and potentially leading to putative therapeutic targets.</p> / Dissertation

<p>Age-related hearing loss is an acute health problem affecting people worldwide, often arising due to defects in the proper functioning of sensory hair cells in the inner ear. The apical surface of sensory hair cells contains actin-based protrusions known as stereocilia, which detect sound and head movements. Since hair cells are not regenerated in mammals, it is important to maintain the functioning of stereocilia for the life of an organism to maintain hearing ability. The actin filaments within a stereocilium are extensively crosslinked by various actin crosslinking proteins, which are important for stereocilia development and maintenance. Multiple studies have shown that the stereocilia actin core is exceptionally stable whereas actin is dynamic only at the tips of stereocilia. However, whether the actin crosslinking proteins, which are nearly as abundant as actin itself, are similarly stable or can freely move in and out of the core remains unknown. Loss or mutation of crosslinkers like plastin-1, fascin-2, and XIRP2 causes progressive hearing loss along with stereocilia degeneration while loss of espin prevents stereocilia from even developing properly. Do these phenotypes stem from an unstable stereocilia core? Does crosslinking confer stability to the core? To address these questions, we generated novel transgenic reporter lines to monitor the dynamics of actin in mice carrying fascin-2R109H mutation and espin null mice and also to study the dynamics of actin crosslinkers, in vivo and ex-vivo. We established that actin crosslinkers readily exchange within the highly stable F-actin structure of the stereocilia core. In addition, we determined that stereocilia degeneration in mice carrying fascin-2R109H mutation and espin null mice could possibly occur due to a less stable actin core. These studies suggest that dynamic crosslinks stabilize the core to maintain proper stereocilia functioning. Future work warrants understanding the reason behind the importance of dynamic crosslinks within a stable stereocilia core. Actin stability not only depends on actin crosslinkers, but also on actin filament composition as evident from distinct stereocilia degeneration and progressive hearing loss patterns in hair-cell specific knockout of actin isoforms. Although beta- and gamma- actin polypeptide sequences differ by only 14 four amino acids, whether the latter determine the unique function of each cytoplasmic actin isoform was previously unknown. Here we determined that these four critical amino acids determine the unique functional importance of beta-actin isoform in sensory hair cells. Taken together, our study demonstrates that actin cytoskeletal proteins are important for the morphogenesis and</p> <p>maintenance of stereocilia.</p>

Classic Hodgkin Lymphoma (cHL) has an annual incidence of 2.4 cases per 100 000 population in the UK, and is one of the most common malignancies diagnosed in young adults aged 15 to 34. The majority of younger patients have a good long-term outcome with between 80 and 90% disease-specific survival but cHL also affects older adults in whom the prognosis is significantly poorer. The role of tumour-associated macrophages (TAM) in cHL has gained much interest, with several studies reporting an association between high numbers of CD68-positive TAM and poor prognosis. There is also a question over the prognostic significance of Epstein-Barr Virus (EBV) infection which is implicated in up to 50% of cHL cases in developed countries. Published data suggests that EBV positivity in elderly patients may be associated with a poorer outcome, whereas in younger adults may be of prognostic benefit. Differences related to age are of interest particularly as an age-related decline in immunity has been linked with the development of certain subtypes of Non-Hodgkin Lymphoma in older patients. In a retrospective study, two separate cohorts of patients with cHL were examined with the aim of identifying: • Differences in the cellular composition of the tumour microenvironment in cHL which has arisen in young and elderly adult patients; • Differences in the cellular composition of the tumour microenvironment in cHL associated with or without EBV infection; • Factors within the tumour microenvironment which may influence prognosis and may be targeted for novel treatments. One group consisted of patients aged between 15 and 34 years at diagnosis and the other, of those aged 60 or over at presentation. Tissue obtained at the time of diagnosis was examined with regard to a number of factors related to the malignant cells and the surrounding microenvironment, including the number and phenotype of macrophages, the number of plasmacytoid dendritic cells and the number of malignant Hodgkin Reed-Sternberg (HRS) cells and non-malignant ‘background’ cells undergoing apoptosis. Comparisons were made between the two age groups, also taking into account the EBV-status of tumours, cHL subtype and gender. Results confirmed the current understanding that EBV-positive cHL is more common in older patients and has a strong, but not exclusive, association with the MCHL subtype. In addition, a strong link between young males and EBV-positive disease was shown. Macrophages were found to vary between the two age groups, in number and phenotype and there were clear differences associated with the presence or absence of EBV infection. While no definite link with outcome and macrophages was identified it was apparent that the implications of macrophages in the tumour microenvironment may differ between the two age groups. The number of apoptotic cells correlated closely with the number of macrophages and in the young the number of HRS cells was associated with prognosis. Investigation of the tumour microenvironment is complex and caution is needed in interpreting studies which do not differentiate between patients according to age, as tumour characteristics may have variable implications in different age groups. In this thesis a number of clinicopathological differences were identified between the two age groups. These point to the need for further larger studies to delineate how such age-related differences may or may not be associated with immune function and how this information could be translated into treatments to improve outcomes.

INTRODUCTION: Retinal Pigment Epithelia (RPE) degeneration is a key event in the development of age-related macular degeneration (AMD). RPE dysfunction in AMD is thought to occur through the accumulation of reactive oxygen species (ROS) and oxidative damage. The transcriptional co-activators, PGC-1α and PGC-1β, are important regulators of mitochondrial biogenesis and anti-oxidant capacity. Our group has previously shown that the PGC-1α protein promotes RPE oxidative metabolism and that overexpression of the PGC-1α gene protects cells from AMD-associated pro-oxidants. On the other hand, PGC-1β gene expression has been found to be upregulated in patients with neovascular AMD, and in-vitro overexpression of PGC-1β damages cells and induces pro-oxidant conditions. OBJECTIVE: Given the divergence of PGC-1α and PGC-1β functions in RPE and their clinical relevance in AMD pathogenesis, this project will seek to investigate the impact of the upregulation of PGC-1α and PGC-1β in RPE metabolism. PGC-1α will be upregulated through treatment with compound ZLN005. A new methodology for PGC-1β expression will be developed to closely modulate in-vitro PGC-1β induction. METHODS: In-vitro experiments were performed on the ARPE-19 cell line. Cells were treated with 10µM of ZLN005 for 24 hours. Oxidative stress was induced by exposure to H2O2 and NaIO3 under serum-free conditions. Lactate dehydrogenase (LDH) levels were used to quantify cell death. Quantitative PCR (qPCR) and Western Blot were performed to measure changes in gene and protein expression respectively. Superoxide production by the mitochondria was measured to evaluate ROS levels within the cell. Intravitreal injections of 20µM ZLN005 were performed on eight-week old male C57BL/6J mice. After 24 and 72 hours of treatment, the mice were euthanized and the enucleated eyes were dissected to obtain the RPE and neural retina layers. Total RNA was extracted from these layers and qPCR was performed to measure gene expression. A tetracycline-inducible PGC-1β plasmid was designed and transfected into ARPE-19 cells. The cells were exposed to 0.01-100µg/ml doxycycline for 48-hours and qPCR was used to measure gene expression. Transfected cells were treated with ZLN005 and cell death upon exposure to oxidative stress was quantified. RESULTS: Gene expression analysis on ARPE-19 cells treated with ZLN005 showed robust upregulation of PGC-1α, PGC-1β and their associated transcription factors and enzymes. Induction of PGC-1α at the protein level was also confirmed. ZLN005 efficiently protected ARPE-19 cells from H2O2 and NaIO3 cytotoxicity and its protection was negated in PGC-1α-silenced cells. Treatment with ZLN005 also decreased mitochondrial superoxide production. ZLN005 intravitreal injections were safely administered to the animals and did not cause cataracts or other damage to the ocular tissues. While statistical significance in gene expression changes was limited due to the small sample size, anti-oxidants GPX1 and TXN2, and electron transport chain gene, ATP50, were found to be potentially induced in the neuro-retina, while FOXO3 was found to be downregulated. Evaluation of our novel tetracycline-inducible PGC-1β adenoviral vector showed that upregulation of PGC-1β was efficiently controlled by the addition of doxycycline to transfected cells. Upon exposure to H2O2, transfected cells treated with doxycycline experienced greater cell death than transfected cells not exposed to doxycycline. ZLN005 treatment was able to decrease cell death in both conditions. CONCLUSION: The present study shows that ZLN005 efficiently protects RPE cells from oxidative damage through selective induction of PGC-1α. While still preliminary, the in-vivo study indicates that ZLN005 is safe to be injected into the eye and may be able to increase the expression of mito-protective and anti-oxidant genes in the neuronal retina. In addition, our design of the tetracycline inducible PGC-1β plasmid allows for tight control over PGC-1β expression through doxycycline addition. Upregulation of PGC-1β at levels similar to those observed in clinical conditions caused increased pro-oxidant induced cell death and treatment with ZLN005 was able to protect against cell death. / 2021-06-30T00:00:00Z

Genome-wide association studies (GWAS) have delivered many novel insights about the etiology of many common heritable diseases. However, in most disorders studied by GWAS, the known single nucleotide polymorphisms (SNPs) associated with the disease do not account for a large portion of the genetic factors underlying the condition. This suggests that many of the undiscovered variants contributing to the risk of common diseases have weak effects or are relatively rare. This thesis introduces novel adaptations of techniques for improving detection power for both of these types of risk variants, and reports the results of analyses applying these methods to real datasets for common diseases. Chapter 2 describes a novel approach to improve the detection of weak-effect risk variants that is based on an adaptive sampling technique known as Distilled Sensing (DS). This procedure entails utilization of a portion of the total sample to exclude from consideration regions of the genome where there is no evidence of genetic association, and then testing for association with a greatly reduced number of variants in the remaining sample. Application of the method to simulated data sets and GWAS data from studies of age-related macular degeneration (AMD) demonstrated that, in many situations, DS can have superior power over traditional meta-analysis techniques to detect weak-effect loci. Chapter 3 describes an innovative pipeline to screen for rare variants in next generation sequencing (NGS) data. Since rare variants, by definition, are likely to be present in only a few individuals even in large samples, efficient methods to screen for rare causal variants are critical for advancing the utility of NGS technology. Application of our approach, which uses family-based data to identify candidate rare variants that could explain aggregation of disease in some pedigrees, resulted in the discovery of novel protein-coding variants linked to increased risk for Alzheimer's disease (AD) in African Americans. The techniques presented in this thesis address different aspects of the "missing heritability" problem and offer efficient approaches to discover novel risk variants, and thereby facilitate development of a more complete picture of genetic risk for common diseases.

Age-Related Macular Degeneration (AMD) is a retinal eye disease that is the leading cause of blindness in those over 50 years of age throughout the developed world. Oxidative and metabolic dysfunction of the retinal pigment epithelium (RPE) has been shown to play an important role in AMD. However, the mechanism of dysfunction in the RPE is poorly understood. The peroxisome proliferator-activated receptor-gamma coactivator 1α and β (PGC1A and PGC1B) are coactivators that interact with transcription factors to regulate mitochondria metabolism. In a previous study, it was demonstrated that one of the isoforms, PGC1A, protects RPE cells from oxidative stress through the upregulation of transcription factors that regulate important antioxidant enzymes. There is experimental and clinical evidence that demonstrates that PGC1B may play a deleterious role in the RPE cell. The objective of this study is to characterize the pathological effect of PGC1B on the RPE cell. PGC1B was overexpressed in the human retinal pigment epithelium cell line (ARPE-19) and expression of the PGC1 isoforms and their main gene targets was evaluated using quantitative polymerase chain reaction (qPCR). Cell death was evaluated under basal and pro-oxidant conditions by quantification of lactate dehydrogenase (LDH) release from the RPE cell. The effect of PGC1B gain of function on the RPE pro-angiogenic function was evaluated using the choroid explant sprouting assay and by testing the proliferative, migratory, and tube formation potential of RPE-derived conditioned media on the rhesus monkey chorioretinal cell line (RF/6A). Quantitative PCR analysis showed that overexpression of PGC1B in ARPE-19 cells leads to increased mitochondrial metabolism and decreased antioxidant enzyme expression, causing oxidative stress. After treatment with H2O2, PGC1B overexpression caused ARPE-19 cells to become more susceptible to cytotoxicity. The ex vivo choroid sprouting assay demonstrated that PGC1B overexpression in RPE is pro-angiogenic. However, cell proliferation as measured by MTT and the cell migration assay provided conflicting results on the pro-angiogenic effect of PGC1B. Previous research has demonstrated that oxidative stress in the RPE cell plays a role in AMD progression. It has been demonstrated in this study that PGC1B expression leads to increased mitochondrial metabolism and repression of antioxidant enzymes needed to prevent oxidative stress and dysfunction in the RPE cell. While experiments to test the effect of PGC1B on angiogenesis provided conflicting results, a different endothelial cell model may be better suited in demonstrating the pro-angiogenic effect of PGC1B. The hope is that the information provided from this study may be used to further our understanding of AMD and lead to the development of therapeutic targets to combat the effects of AMD.

Diseases which affect the central nervous system present a huge burden to sufferers and caregivers. In tandem with longevity, prevalences of age-related neurodegenerative diseases are increasing. However, despite the evident necessity for pharmaceutical interventions, there has been a distinct lack of drug development to combat these disorders. This is largely attributed to high financial costs of using rodent models. Thus the validation of a more cost-effective in vivo system would facilitate pharmaceutical screening. The work presented in this thesis addresses this issue by assessing the utility of zebra fish in two costly areas of translational neurobiology { lead identi cation and safety pharmacology. An aversive classical conditioning assay was developed and automated as a behavioural screening method. This robust assay allows fast assessment of cognition and cognitive decline. The effect of neurotoxin treatment on aversive learning was then assessed using this assay, demonstrating its efficacy as a screening tool for neurodegeneration research. Subsequently, a transgenic zebra fish line - expressing a mutated form of the Alzheimer's-associated human amyloid precursor protein - was assessed, demonstrating an age-related cognitive impairment. Additionally new genetic zebra fish lines were generated, which over-express genes (both endogenous and transgenic) related to Alzheimer's-like pathologies. Whilst these were not assessed within this thesis, they present promising tools for possible future investigations. Regarding safety pharmacology, regulatory bodies require all CNS-penetrant drugs be assessed for abuse potential. Zebra fish display reward responses to several common drugs of abuse (e.g. amphetamine, cocaine, morphine). Thus, the latter sections of this thesis evaluated the utility of zebra fish for assessing human abuse potential. A CPP paradigm was utilised to test a range of drugs, with the sensitivity and specificity of zebra fish compared to previous reports using rodent. Additionally, the development of a zebra fish drug discrimination assay was attempted. However the paradigms utilised failed to develop an efficacious assay.

An estimated 170.38 million elderly adults suffer from some stage of age-related macular degeneration (AMD) worldwide, a vision defect that damages the macula, the central region of the retina required for sharp vision, such as reading, driving, and recognizing faces. Genetic factors strongly modify one's risk for developing AMD, and most of these genetic changes are found in genes of the alternative complement cascade, a component of the immune system. The lack of effective AMD prevention calls for the identification of druggable molecules and pathways. In my research, I use microarrays and RNA sequencing to investigate the events occurring in early AMD, the reasons for macular susceptibility to AMD, and the events triggering aberrant blood vessel growth in late AMD. First, I found that genes associated with endothelial cells tend to be expressed at lower levels in human donors eyes affected by early AMD than in control eyes, concordant with previous studies indicating loss of choriocapillaris in early AMD. Second, I found that molecular signals across regions of the retina, retinal pigment epithelium, and choroid generally mirror the distribution of cell types in these regions. Third, I found that damage to cultured primate chorioretinal endothelial cells by the end product of complement activation, membrane attack complex, produces an environment conducive to choroidal neovascularization, a symptom of late-stage AMD. I propose a model that bridges genetic variants in the complement cascade genes with blood vessel loss in early AMD and the pathological growth of blood vessels in late AMD.

In recent years, microarray technology has revealed the widespread presence of submicroscopic deletions and duplications throughout the human genome termed copy number variants (CNVs). CNVs have a profound effect on gene expression and are an important source of normal genetic variation. In addition, a small proportion of CNVs contribute to genetically simple and complex disease. This thesis focuses on the identification of pathogenic CNVs contributing to the etiology of diseases with "missing heritability" using a well-planned study design individually tailored to each disease cohort to optimize CNV detection and interpretation. We performed a genome-wide analysis for CNVs in five disease cohorts with genetic etiology: autism, age-related macular degeneration (AMD), glaucoma, clubfoot, and Bardet-Biedl syndrome (BBS). Our results indicate that CNVs likely account for a proportion of cases for each disease cohort reported in this thesis. Approximately 20% of our cohort of individuals with autism from trio pedigrees harbors a CNV known to confer risk to develop autism and we identified other novel and rare variants that may play a role in autism pathogenesis. We also characterized a duplication of 2p25.3 identified in two male half-siblings with autism and determined that their mother was somatic mosaic for the duplication. Our work provides evidence that this novel CNV disrupting the genes PXDN and MYT1L are the autism-causing mutation in this pedigree. A comparative cases experimental design was used in the study of AMD and glaucoma. While no common "risk CNVs" were identified for either eye disorder, we did identify several rare overlapping CNVs disrupting genes known to play a role in the eye that may confer risk to disease in a small proportion of individuals. In a fourth genetically complex disease, clubfoot, we identified a duplication of 17q23.2 disrupting the genes TBX4, NACA2, and BRIP1 that segregates with the autosomal dominant clubfoot phenotype in a large pedigree with 16 affected individuals. In addition, the duplication is within the linkage interval identified for this family. We also applied microarray technology to analyze the genomes of individuals with BBS, an autosomal recessive disorder, for the presence of CNVs in known BBS genes as well as CNVs that elucidate novel candidate genes for BBS. From 34 BBS patients with an unidentified mutation, we observed one CNV, a heterozygous deletion of BBS10, unmasking a BBS10 frameshift mutation. A promising BBS candidate gene also emerged from our studies, implicated by an intragenic deletion of the gene MARK3 predicted to result in a frameshift and premature truncation of the protein. Functional studies utilizing antisense morpholino gene knockdown in the zebrafish provide additional evidence that MARK3 is a BBS gene as knockdown of zebrafish mark3 results in a Kupffer's Vesicle defect and a melanosome transport delay, two cardinal BBS phenotypes in the zebrafish. In addition to identifying CNVs involved in disease, the work outlined in this thesis provides valuable insight into the study design and interpretation of a genome-wide analysis of CNV. This includes the appropriate use of controls and publicly available control databases, methods for enriching for CNVs in a patient cohort to maximize efficiency and discovery, and the importance of analyzing all patient cohorts with heritable disease for the presence of CNVs disrupting known disease genes and CNVs that implicate novel genetic candidates. As the reliability and resolution of CNV detection continue to improve, allowing detection of > 1,000 CNVs in each individual genome, it becomes more important than ever to have a well-defined study design for both the detection and interpretation of CNVs.

Word recognition is based on the complex interplay of bottom up processing of acoustic input and corresponding top-down processing based on linguistic redundancies (i.e., contextual cues). Friedrich and Kotz (2007) investigated the timeline of integrating top-down and bottom-up processes among young adults with normal hearing using sentences presented in quiet. As a follow-up study, also with young adults with normal hearing (Experiment 1 of this dissertation), we used sentences embedded in multi-talker background noise and found similar results to Friedrich and Kotz (2007); but, with the use of principal component analysis (PCA) unveiled additional effects of phonological and semantic integration of spoken sentences presented in background noise. These past studies provide evidence of the time course of bottom-up and top-down mechanisms among young adult listeners in quiet and in noise; however, it is unknown if a similar pattern would be present among older adult listeners, which was the primary goal of the dissertation. In Experiment 2, we aimed to elucidate the time-course, and behavioral and neural correlates of word recognition primed by speech-in-noise in older adults with near normal hearing (i.e., thresholds ≤ 25 dB-HL through 3000 Hz and minimal high frequency hearing loss). Older adults often report difficulty understanding speech in the presence of background noise. Degradation in peripheral and central auditory processing along with age-related cognitive decline has been hypothesized as reasons why older adults struggle in the presence of noise.