The neurodegenerative disorders Alzheimer??s Disease (AD) and Parkinson??s Disease (PD) are characterised by the accumulation of misfolded amyloid beta 1-42 peptide (Aβ1-42) or α-synuclein, respectively. In both cases, there is extensive evidence to support a central role for these aggregation-prone molecules in the progression of disease pathology. However, the precise mechanisms through which Aβ1-42 and α-synuclein contribute to neurodegeneration remain unclear. Organismal, cellular and in vitro models are under development to allow elucidation of these mechanisms. A cellular system for the study of intracellular Aβ1-42 misfolding and localisation was developed, based on expression of an Aβ1-42-GFP fusion protein in the model eukaryote Saccharomyces cerevisiae. This system relies on the known inverse relationship between GFP fluorescence, and the propensity to misfold of an N-terminal fusion domain. To discover cellular processes that may affect the misfolding and localisation of intracellular Aβ1-42, the Aβ1-42-GFP reporter was transformed into the S. cerevisiae genome deletion mutant collection and screened for fluorescence. 94 deletion mutants exhibited increased Aβ1-42-GFP fluorescence, indicative of altered Aβ1-42 misfolding. These mutants were involved in a number of cellular processes with suspected relationships to AD, including the tricarboxylic acid cycle, chromatin remodelling and phospholipid metabolism. Detailed examination of mutants involved in phosphatidylcholine synthesis revealed the potential for phospholipid composition to influence the intracellular aggregation and localisation of Aβ1-42. In addition, an existing S. cerevisiae model of α-synuclein pathobiology was extended to study the effects of compounds that have been hypothesized to be environmental risk factors leading to increased risk of developing PD. Exposure of cells to aluminium, dieldrin and compounds generating reactive oxygen species enhanced the toxicity of α- synuclein expression, supporting suggested roles for these agents in the onset and development of PD. Expression of α-synuclein-GFP in phosphatidylcholine synthesis mutants identified in the Aβ1-42-GFP fluorescence screen resulted in dramatic alteration of α-synuclein localisation, indicating a common involvement of phospholipid metabolism and composition in modulating the behaviours of these two aggregation-prone proteins.

Parkinson's disease is the second commonest neurodegenerative disease currently treated symptomatically. It is a multifactorial disease involving mechanisms ranging from protein aggregation to mitochondrial dysfunction, oxidative stress and dopamine dysregulation. The levels of α-synuclein have been causatively linked to the development and progression of Parkinson's disease. Therefore α-synuclein lowering strategies are valid approaches in Parkinson's disease. Neuropathologically, Lewy Bodies in the vulnerable substantia nigra of Parkinson's disease patients are less ubiquitinated and specifically less K-63 ubiquitinated than Lewy bodies in the cortex, suggesting differential activation or regulation of ubiquitin interactors. A targeted screen for such interactors revealed that the Deubiquitinating enzyme Usp8 is upregulated in the substantia nigra of Parkinson's disease brains and is inversely correlated with the degree of total and K-63 ubiquitination. Using genetic knockdown and overexpression techniques, Usp8 was found to colocalize and directly interact with α-synuclein. It was found to de-ubiquitinate α-synuclein and increase its half-life. Its knockdown increased the total and K-63 α-synuclein ubiquitination and decreased its levels by 35% at least partly by increasing its degradation via the lysosome. In vivo in the Drosophila melanogaster, Usp8 knockdown demonstrated protection against α-synuclein toxicity. It rescued in a specific manner the rough eye phenotype, the age-dependent locomotive defect and the loss of dopaminergic neurons caused by the expression of α-synuclein. Specific and effective pharmacological Usp8 inhibition also has the potential to lower α-synuclein levels. Collectively, the evidence produced in my thesis suggests that Usp8 could be a potential target for the future disease-modifying therapies in Parkinson's disease.

The experiments described in this thesis aimed to investigate the neurophysiological consequences, at the cortical level, of the neurodegenerative condition, amyotrophic lateral sclerosis (ALS). A principle tenet of this study was that ALS is, first and foremost, a disorder of the cortical motor system, the precise pathological mechanisms of which remain incompletely understood. Furthermore, the degree to which neurodegeneration can be evidenced before the onset of symptoms is thus far uncertain, and the optimal means by which to measure therapeutic response has yet to be determined. Chapter 1 introduces relevant key concepts in ALS and briefly summarises three studies completed in the early phases of pursuit for the above degree. These studies respectively considered presmyptomatic cellular ALS pathology, quantitation of disease progression and eyetracking assessment of cognitive dysfunction. Chapter 2 describes magnetoencephalography, the investigative technology utilised in the subsequent experimental chapter. In chapter 3, the effects of ALS on movement related modulation of neuronal oscillations are determined. An excessive peri-movement desynchronisation and delayed post-movement rebound was described. Functional connectivity between cortical regions at rest is appraised in chapter 4. ALS appeared to result in quite striking increases in functional connectivity, in keeping with the fMRI literature and in support of diminished intracortical inhibitory influences. The functional communication from the motor cortices is directly considered during active motor performance in chapter 5. ALS related reductions in beta-band coherence were noted in both corticospinal and inter- hemispheric communication. In conclusion, the results demonstrated considerable support for proposed excitotoxic disease mechanisms and were in alignment with reported findings in other neurodegenerative diseases. Finally, a pilot study by which the neural mechanisms for cognitive impairment in ALS are explored via antisaccade performance is described. While underpowered, the experimental design showed promise for future application.

Hyperglycemia associated with diabetes has been recognized for adverse neurodegenerative effects it has on the central nervous system (CNS). However, few cerebral histopathological studies have been completed to adequately define the neuropathology of type 2 diabetes. The aim of the study was to conduct a neuropathological survey of diabetic Zucker Diabetic Sprague Dawley (ZDSD) rat brains that included a wide variety of potential pathologies. Ten ZDSD rat brains (diabetic: n=6 non-diabetic obese: n=4) were collected for neuropathological assessments. Specific measures include assessments of gray and white matter atrophy, neurodegeneration, astrocyte activation, blood brain barrier integrity, inflammation, and amyloid protein deposit. After brain sectioning, formal thionin, immunoglobulin G (IgG), glial fibrillary acidic protein (GFAP), giemsa, congo-red, and flourojade (FJ) stains were performed for analysis. Of the several neuropathological assessments, two revealed significant differences between diabetic and non-diabetic groups. Diabetic ZDSD rats had a relative decrease in the amount of white matter in the corpus callosum underlying the cingulate cortex of the brain. Secondly, higher numbers of lymphocytes were observed in the hypothalamus of the diabetic rats compared to non-diabetic rats. Enhanced expression of GFAP was not present. No measurable differences were observed in analysis of amyloid, FJ intensity levels or immunoglobulin G (IgG) extravisation into the brain. These results suggested that ZDSD rats do not exhibit neuropathology excepting white matter atrophy and increased lymphocyte infiltration into the hypothalamus, or that the duration of 6-7 month old diabetic ZDSD rats may be insufficient to support most of our hypotheses. Future work is required to determine profiles of neuropathology in longer term of diabetic ZDSD rats.

The epigenetics of the aging brain is a growing field of study that holds great promise for the discovery of mechanisms and potential treatments for neurodegenerative diseases. In this current study, a novel, accelerated aging murine model, the I-PpoI/Cre, or ICE (Inducible Changes in the Epigenome) mouse, is studied to test its potential for demonstrating the theory of the rearrangement of chromatin (RCM) as the main cause of aging, and in particular, the mechanism through which the brain ages. Immunohistochemistry and behavioral assays are utilized to determine whether there are morphological changes, inflammatory response, and changes in learning and memory. Results showed a significant increase in microglia and astrocytes, markers of inflammation, in I-PpoI/Cre mice compared to their Cre controls. Long term memory performance was also significantly decreased in the I-PpoI/Cre mice, demonstrated through contextual fear conditioning (CFC) testing, and Morris Water Maze (MWM) testing. Results from this study are in support of the I-PpoI/Cre mouse as a model of accelerated aging of the brain, with deficits in learning and memory. Further studies are needed to further characterize this murine model of accelerated aging.

Abnormal aggregation of microtubule associated protein tau is the defining pathological hallmark of tauopathies, which include Alzheimer’s disease (AD) and related frontotemporal dementias (FTLD-tau). However, the cellular events precipitating tau pathogenesis in disease are unknown. Here, we demonstrate a novel mechanism regulating tau aggregation in tauopathies. We have previously shown that RNA binding proteins (RBPs) associated with stress granules (SGs) progressively accumulate with tau in multiple mouse models of tauopathy, as well as in human AD and FTLD-tau brain tissue. We now present a novel functional role for tau in regulating the biology of SGs in neurons. Tau facilitates the rapid formation of SGs in the soma and dendrites in response to exogenous stress, which functions to transiently reprogram protein synthesis to promote cell survival (also known as the ‘translational stress response’). However, the chronic interaction of tau with SG proteins in disease, such as with the SG nucleating protein T cell intracellular antigen 1 (TIA1), promotes tau misfolding and neurotoxicity, which can be modulated in primary neurons by pharmacological or genetic manipulations that increase (i.e. puromycin, TIA1 overexpression) or decrease (i.e. cycloheximide, TIA1 knockdown or knockout) SG formation, respectively. In order to test whether SGs also mediate the progression of tauopathy in vivo, we crossed PS19 transgenic (P301S) tau mice with Tia1-/- or C57BL/6J (background strain) mice. PS19 mice with heterozygous reduction in TIA1 (P301S TIA1+/-) developed less SGs compared to P301S TIA1+/+ mice, which was associated with marked neuronal protection, improved cognitive function, and prolonged lifespan. The behavioral neuroprotection in P301S TIA1+/- mice was associated with decreased accumulation of soluble tau oligomers, and occurred despite the increased presence of neurofibrillary tangles. Our findings suggest that TIA1 stabilizes tau in its oligomeric state, preventing its further assembly into insoluble fibrils, which are less toxic. More importantly, the studies described in this dissertation identify modulation of RBP aggregation in SGs as a promising therapeutic strategy for the treatment of AD and FTLD-tau.

The aggregation of alpha-synuclein (αS) protein from soluble monomer into solid amyloid fibrils in the brain is associated with a range of devastating neurodegenerative disorders such as Parkinson’s disease. Soluble oligomers formed during the aggregation process are highly neurotoxic and are thought to play a key role in the onset and spreading of disease. Despite their importance, these species are difficult to study by conventional experimental approaches owing to their transient nature, heterogeneity, low abundance and a remarkable sensitivity of the oligomerisation process to the chosen experimental conditions. In this thesis, well-established single-molecule techniques have been utilised to study the aggregation and oligomerisation of αS in solution.

Amyotrophic lateral sclerosis (ALS) is a major neurodegenerative disease caused by the death of motor neurons leading to paralysis. Mechanisms underlying the pathogenesis of the disease remain unknown but with the identification of causative genes from ALS patients, some processes have been linked to the disease. One of these genes is VAPB, a highly conserved protein involved in lipid transfer, vesicle metabolism and synaptic morphology. We modeled in Drosophila the disease-linked P56S mutation (DVAP-P58S) and observed with the expression of this allele neurodegeneration in the eye and loss of motor performance. These phenotypes provide an excellent opportunity to use fly’s genetics to find novel genetic interactors of DVAP and understand ALS pathomechanism. Therefore, we carried out a large scale genetic screen by crossing the ALS model with a collection of P-element overexpression lines. After the analysis of 1183 lines, we obtained 71 modifier lines that suppress DVAP-induced neurodegeneration and 14 lines that enhance this phenotype, decreasing furthermore the eye size and viability of the offspring. To confirm that the effect of modifier lines was caused by a specific gene, we validated them with independent alleles of those genes. Using different sources, we were able to confirm the effect of 63 of the 85 modifiers, providing a strong confirmation of their effect. When we studied the effect of the modifier genes co-expressed with DVAP-P58S in the nervous system, we detected that 46 lines presented the same modifying effect in adult viability and 58 in the motor performance of the adult offspring. Considering the stronger readouts, we obtained 42 genes as novel high confidence DVAP genetic interactors. To understand furthermore the way they are affecting DVAP neurodegeneration, we carried out a series of bioinformatic analyses using Drosophila and human databases. Lipid droplets, vesicle metabolism and cell proliferation appear as the most important categories found in the screen, all processes conserved when analysed with human orthologs of the modifiers. Further characterisation of the endocytosis-linked modifier Rab5 and the predicted DVAP-interactors Rab7 and Rab11, showed that the suppression effect is not only confirmed in vivo but is also conserved in human tissue from ALS patients. These data validate our genetic screen and at the same time open novel opportunities to understand ALS mechanisms and find possible therapeutic targets.

Neurodegenerative disorders are a group of age-related conditions resulting in neuronal cell death and protein accumulation. It is estimated that around 5-10% of these cases are genetically mediated. Most commonly this is by pathogenic single nuclear variants (SNVs), though combinations of rare variants (termed oligogenic variation), copy-number variation (CNVs), somatic mutations in nuclear DNA, and somatically acquired mitochondrial DNA variants have all been hypothesised to increase disease risk or cause disease. Firstly, using a combination of exome sequencing and array genotyping on 1511 post-mortem brain samples within the MRC Brain Bank, we detected 61 monogenic cases of disease, 349 brains carrying disease risk factors, and identified that variants in GRN and PRPH may increase the risk of developing dementia with lewy bodies (DLB) and Alzheimer’s disease (AD) respectively. Secondly, we detected a previously unknown systematic bias in the interpretation of oligogenic interactions with implications for our understanding of disease mechanisms and coexistent clinical diagnostic utility. Thirdly, we detected a novel copy-number gain in LAMA5 associated with Creutzfeldt-Jakob disease (CJD), and fourthly, we determine that at least 1% of the population carry high level somatic protein-coding mutations affecting at least 10% of cells within the brain. Subsequently, additional focussed deep-sequencing studies revealed that several regions of the brain are likely to contain clones of low-level somatic mutations that are pathogenic when present in the germline, and that age-related clonal mutations that arise in blood are present at high levels within the aging brain and are associated with Lewy Body pathology. Finally, using transgenic mice that over express human α-synuclein and which either accrue or transmit mtDNA mutations, we determine that the presence of mtDNA mutations exacerbate some phenotypic traits of Lewy body disorders, and may reduce the volume of critical neuroanatomical brain regions whilst paradoxically reducing α-synuclein accumulation. Taken together, these data enable the first genetically stratified brain tissue resource in the UK, describe new disease genetic risk factors (both SNVs and CNVs) for neurodegenerative disorders, and also help define the somatic genetic architecture of the human brain. In addition, we describe the in vivo interaction between mutations in the mitochondrial genome and a progressive neurodegenerative disorder in mice.

Synapses are an early pathological target in a wide range of neurodegenerative conditions including adult-onset Alzheimer’s and Parkinson’s, and diseases of childhood such as spinal muscular atrophy and neuronal ceroid lipofuscinoses (NCLs). However, our understanding of the mechanisms regulating the stability of synapses and their exceptional vulnerability to neurodegenerative stimuli remains in its infancy. To address this, we have used the NCLs to model the molecular alterations underpinning synaptic vulnerability. Our primary objective is to identify novel regulators of synaptic stability as well as highlight novel therapeutic targets which may prove effective across multiple neurodegenerative conditions where synapses are an early pathological target. The NCLs, are the most frequent autosomal-recessive disease of childhood. There are currently 14 individual genes whose mutations result in similar phenotypes including blindness, cognitive/motor deficits, seizures and premature death. This suggests that despite the difference in the initiating mutation and the degenerative processes across this collective group are likely to impact on overlapping pathways. Focusing on two murine models of NCL; one with an infantile onset - CLN1 disease (Ppt1-/-) and one with a juvenile onset - CLN3 disease (Cln3-/-) we made use of the temporo-spatial synaptic vulnerability pattern in these mice to plan proteomic and in silico analyses. This pipeline was utilised to identify perturbed protein candidates and pathways correlating with differential regional synaptic vulnerability. This ultimately allowed the generation of a list of candidate proteins, some of which were relevant to human NCL as they were altered in post mortem brain samples. Interestingly, many of the correlative candidates also appear to show conserved alterations in both NCL forms examined and other neurodegenerative diseases. Next, candidates were genetically and/or pharmacologically targeted to study their modulatory effects on neuronal stability in vivo. This was done using CLN3 Drosophila as a rapid screening assay and led to the successful characterisation of a subset of candidates as either enhancers or suppressors of the CLN3-induced phenotype in vivo. As well as identifying regulators of neuronal stability, following a similar pipeline, we identified a set of putative biomarkers of disease progression in muscle and blood in the Ppt1- /- mice, a subset of which appeared conserved in Cln3-/- mice. One of these conserved candidates presented the same directionality of change in human post mortem brain samples, indicating its relevance to the human NCL. Following this workflow from spatio-temporal profiling of murine synaptic populations, to in silico analyses and in vivo phenotypic assessment, we demonstrate that we can identify multiple protein candidates capable of modulating neuronal stability in vivo and identified putative biomarkers that tracked disease progression.