Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, neuropathologically characterized by neurofibrillay tangles and deposition of amyloid-β (Aβ) peptides. Several mutations in the gene for amyloid precursor protein (APP) cause familial AD and affect APP processing leading to increased levels of Aβ42. However, the Arctic Alzheimer mutation (APP E693G) reduces Aβ levels. Instead, the increased tendency of Arctic Aβ peptides to form Aβ protofibrils is thought to contribute to the pathogenesis. In this thesis, the pathogenic mechanisms of the Arctic mutation were further investigated, specifically addressing if and how the mutation affects APP processing. Evidence of a shift towards β-secretase cleavage of Arctic APP was demonstrated. Arctic APP did not appear to be an inferior substrate for α-secretase, but the availability of Arctic APP for α-secretase cleavage was reduced, with diminished levels of cell surface APP in Arctic cells. Interestingly, administration of the fatty acid docosahexaenoic acid (DHA) stimulated α-secretase cleavage and partly reversed the effects of the Arctic mutation on APP processing. In contrast to previous findings, the Arctic mutation generated enhanced total Aβ levels suggesting increased Aβ production. Importantly, this thesis illustrates and explains why measures of both Arctic and wild type Aβ levels are highly dependent upon the Aβ assay used, with enzyme-linked immunosorbent assay (ELISA) and Western blot generating different results. It was shown that these differences were due to inefficient detection of Aβ oligomers by ELISA leading to an underestimation of total Aβ levels. In conclusion, the Arctic APP mutation leads to AD by multiple mechanisms. It facilitates protofibril formation, but it also alters trafficking and processing of APP which leads to increased steady state levels of total Aβ, in particular at intracellular locations. Importantly, these studies highlight mechanisms, other than enhanced production of Aβ peptide monomers, which could be implicated in sporadic AD.

The diffusible soluble oligomeric amyloid β-peptide (Aβ) has been identified as a toxic agent in Alzheimer’s disease that can cause synaptic dysfunction and memory loss, indicating its role as potential therapeutic targets for AD treatment. Recently an oligomer-specific sandwich biotin-avidin interaction based assay identified the Aβ oligomer dissociation potency of a series of dihydroxybenzoic acid (DHBA) isomers. Because the sandwich assay is an ensemble method providing limited size information, fluorescence correlation spectroscopy (FCS) was employed to provide single molecule resolution of the disassembly mechanism. Using FCS coupled with atomic force microscopy, we investigated the size distribution of fluorescein labeled synthetic Aβ oligomers at physiological concentrations, and monitored in real time the change of size and mole fraction of oligomers in the presence of dissociating agents or conditions. The higher-order dissociation process caused by DHBA isomers produced no transient oligomeric intermediates, a desirable feature for an anti-oligomer therapeutic. Urea and guanidine hydrochloride, in contrast, produced a linear dissociation with a progressive decrease of size and mole fraction of oligomers. FCS allows the facile distinction of small molecule Aβ oligomer dissociators that do not produce stable potentially toxic oligomeric Aβ intermediates.

La maladie d'Alzheimer est une maladie neurodégénérative sénile, entrainant une perte progressive et irréversible des fonctions cognitives et comportementales. Les deux principales caractéristiques pathologiques observées chez les patients atteints d'Alzheimer sont la présence d'enchevêtrements neurofibrillaires intracellulaires (majoritairement constitués par la protéine Tau hyperphosphorylée) et l'agrégation extracellulaire de plaques séniles ou amyloïdes (majoritairement constituées du peptide Amyloïde-β (Aβ)).Si l'étiologie complexe de la maladie reste à établir, la participation du stress oxydant (en partie induit par le peptide Aβ) est largement admise. Il a ainsi été proposé que la mort neuronale puisse être due à l'accumulation de dommages oxydatifs au niveau de la molécule d'ADN, qui pourrait en outre être associée à un dysfonctionnement du système de réparation de ce dernier. Dans notre étude, nous avons cherché à préciser les effets spécifiques du peptide Aβ sur les systèmes de réparation de l'ADN d'une lignée de neuroblastome humain (APP751). Cette dernière sécrète le peptide Aβ à des concentrations très physiologiques. Nous avons observé dans ce modèle une augmentation des dommages oxydatifs à l'état basal et plus encore à l'issue d'un stress additionnel, métallique ou oxydant. De manière surprenante le système BER, associé à la réparation des lésions oxydatives, est apparu sous-exprimé en présence d'Aβ, et réduit d'avantage après l'application d'un stress. Ces observations suggèrent une incapacité de la lignée sécrétrice d'Aβ à répondre à une attaque extérieure, ce qui est vraisemblablement susceptible d'engendrer une accumulation de dommages au niveau de la molécule d'ADN. L'autre fait marquant de ce travail, est la surexpression de facteurs généralement associés au NER, en présence d'Aβ couplé à un stress oxydant. Ces facteurs présentent une multifonctionnalité au sein de la cellule et leur stimulation pourrait représenter la mise en place d'un processus apoptotique plutôt que l'initiation de la réparation de l'ADN. Ces travaux nous ont permis d'établir pour la première fois un lien entre la sécrétion du peptide Aβ et la perturbation des systèmes de réparation de l'ADN, phénomènes susceptibles d'entrainer la mort cellulaire observée en excès dans la maladie d'Alzheimer.

Amyloidogenic diseases, such as Alzheimer's disease (AD) and Type II Diabetes (T2D), are characterized by the accumulation of amyloid aggregates. Despite having very different amino-acid sequences, the underlying amyloidogenic proteins form similar supramolecular fibril structures that are highly stable and resistant to physical and chemical denaturation. AD is characterized by two toxic lesions: extracellular amyloid β-peptide (Aβ) plaques and intracellular neurofibrillary tangles composed of microtubule-associated protein tau. Similarly, a feature of T2D is the deposition of islet amyloid polypeptide (IAPP) aggregates in and around the pancreas. The mechanisms by which Aβ, tau, and IAPP aggregate, and cause cell death is unknown; thus, gaining greater insight into the stabilizing forces and initial unfolding events is crucial to our understanding of these amyloidogenic diseases. This work uses molecular dynamics (MD) simulations to study the secondary, tertiary, and quaternary structure of Aβ, tau, and IAPP. Specifically, this work used the Drude polarizable force field (FF), which explicitly represents electronic polarization allowing charge distributions to change in response to perturbations in local electric fields. This model allows us to describe the role charge plays on protein folding and stability and how perturbations to the charge state drive pathology. Studies were conducted to address the following questions: 1) What are the stabilizing forces of fibril and oligomeric structures? 2) How do charge-altering mutations modulate the conformational ensemble and thermodynamic properties of Aβ? 3) How do charge-altering post-translational modifications of Aβ and tau modulate changes in the conformational ensembles? These studies establish that shifts in local microenvironments play a role in fibril and oligomer stability. Furthermore, these studies found that changes in protein sequence and charge are sufficient to disrupt and change the secondary and tertiary structure of these amyloidogenic proteins. Overall, this dissertation describes how charge modulates protein unfolding and characterizes the mechanism of those changes. In the long term, this work will help in the development of therapeutics that can target these changes to prevent protein aggregation that leads to cell death. / Doctor of Philosophy / Protein aggregation is the hallmark of many chronic diseases, such as Alzheimer's disease (AD) and Type II Diabetes (T2D). The formation of two toxic aggregates: amyloid β-peptide (Aβ) plaques and neurofibrillary tangles composed of microtubule-associated protein tau are some of the key characteristics of AD. In addition, the formation of islet amyloid polypeptide (IAPP) aggregates in the pancreas is thought to play a role in the development of T2D. The pathways by which the proteins Aβ, tau, and IAPP aggregate are unknown; thus, gaining a greater insight into the properties that may cause these diseases is necessary to develop treatments. By studying these proteins at the atomistic level, we can understand how small changes to these proteins alter how they misfold in a way that promotes toxicity. Herein, we used a computational technique called molecular dynamics (MD) simulations to gain new insights into how protein structure changes. We explored the dynamics of these proteins and investigated the role that charge plays in protein folding and described how charge modulates protein folding and characterized the mechanism of those changes. This work serves as a characterization of protein folding and sets the ground for future structural studies and drug development.

Ces dernières années, de nombreuses études ont prouvé que la protéine précurseur de l'amyloïde (APP) joue un rôle clé dans le processus de formation de la mémoire, le développement des connexions synaptiques et la régulation de la force synaptique. L’importance d’APP naît du fait que son clivage protéolytique produit le peptide bêta-amyloïde (Aβ), considéré comme l'un des facteurs cruciaux dans le développement de la maladie d'Alzheimer. Les recherches se sont donc concentrées sur Aβ plutôt que sur le domaine intracellulaire APP (APP-ICD). Récemment, il a été démontré qu’APP-ICD affecte l'induction de la plasticité synaptique, et Aβ à haute concentration est connu pour induire une dépression synaptique. Ici, nous montrons qu’APP-ICD et Aβ fonctionnent ensemble et induisent une dépression synaptique en modifiant la transmission synaptique par effet additif. L’activation de la caspase-3 clivant APP-ICD est nécessaire pour la dépression à long terme. Nous constatons que l’activation de la caspase-3 et son site de clivage d’APP-ICD, ainsi que le clivage d’APP par la gamma-sécrétase sont nécessaires à la dépression synaptique dépendante d’Aβ. La microglie assure la clairance d’Aβ et certains effets de plasticité. Nous démontrons qu’elle médie partiellement la dépression synaptique dépendante d’Aβ. Les mécanismes par lesquels APP-ICD et Aβ médient la dépression synaptique ne sont pas connus. Ici, nous discutons de pistes possibles pour la recherche future, notamment des changements dans l'homéostasie du calcium en tant que cible thérapeutique potentielle. Comprendre comment APP-ICD et Aβ travaillent ensemble pour induire une dépression synaptique aiderait à développer de meilleurs traitements pour la maladie d'Alzheimer. / In recent years, more and more evidence has proven that the amyloid precursor protein (APP) plays a key role in the process of memory formation, the development of synaptic connections, and the regulation of synaptic strength. APP rose to prominence since its proteolytic cleavage produces the amyloid-beta (Aβ) peptide, which is believed to be one of the crucial factors in the development of Alzheimer disease. Therefore, most of the research focused on Aβ, while APP intracellular domain (APP-ICD) received much less attention. In a recent study, APP-ICD was shown to affect the induction of synaptic plasticity, and Aβ at high concentration is known to induce synaptic depression. Here we show that APP-ICD works together with Aβ to induce synaptic depression, meaning they have an additive effect that changes synaptic transmission. Caspase-3 cleaves APP-ICD, and its activation is required for long-term depression. We found that the caspase-3 cleavage site of APP-ICD and caspase-3 activation are needed for Aβ-dependent synaptic depression. We also show that cleavage of APP by gamma-secretase is needed for the effect. Microglia mediate clearance of Aβ as well as some plasticity effects. We demonstrate that microglia partially mediate Aβ-dependent synaptic depression. The mechanisms of how APP-ICD and Aβ mediate synaptic depression are not known, here, we discuss possible avenues for future research, specifically changes in calcium homeostasis as a potential therapeutic target. Hence, understanding how APP-ICD and Aβ work together to induce synaptic depression would aid in developing better treatments for Alzheimer disease.

In this thesis, new methods that address some current limitations in nanoelectrospray mass spectrometry (nESI-MS) analysis are presented. One of the major objectives is the potential gain in sensitivity that can be obtained when employing the proposed techniques. In the first part of this thesis, a new emitter, based on the generation of electrospray from a spray orifice with variable size, is presented. Electrospray is generated from an open gap between the edges of two individually mounted, pointed tips. The fabrication and evaluation of two different types of such emitters is presented; an ESI emitter fabricated from polyethylene terephtalate (Paper I), and a high-precision silicon device (Paper II). Both emitters were surface-treated in a selective way for an improved wetting of the gap and to confine the sample solution into the gap. In the second part of this thesis, different methods for improved sensitivity of nESI-MS analysis have been developed. In Paper III, a method for nESI-MS analysis from discrete sample volumes down to 1.5 nL is presented, using commercially available nESI needles. When analyzing attomole amounts of analyte in such a small volume of sample, an increased sensitivity was obtained, compared to when analyzing equal amounts in conventional nESI-MS analysis. To be able to analyze smaller sample volumes, needles with a narrower orifice and a higher flow resistance were needed. This triggered the development of a new method for fabrication of fused silica nESI needles (Paper IV). The fabrication is based on melting of a fused silica capillary by means of a rotating plasma, prior to pulling the capillary into a fine tip. Using the described technique, needles with sub-micrometer orifices could be fabricated. Such needles enabled the analysis of sample volumes down to 275 pL, and a further improvement of the sensitivity was obtained. In a final project (Paper V), nESI-MS was used to study the aggregation behavior of Aβ peptides, related to Alzheimer’s disease. An immunoprecipitation followed by nESI-MS was employed. This technique was also utilized to study the selectivity of the antibodies utilized. / QC 20101112

For many years, it has been known that Rheumatoid arthritis (RA) is a negative risk factor for the development of Alzheimer’s disease (AD). It has been commonly assumed that RA patients’ usage of non-steroidal anti-inflammatory drugs (NSAIDs) have helped prevent the onset and progression of AD pathogenesis. Furthermore, experiments in animal models of Alzheimer’s disease have looked to inhibit inflammation, and have demonstrated some efficacy against AD-like pathology in these models. Thus many NSAID clinical trials have been performed over the years, but all have proven unsuccessful in AD patients. This suggests that intrinsic factors within RA pathogenesis itself may underlie RA’s protective effect. My dissertation research goal was to investigate this inverse relationship between RA and AD, in order to more precisely pinpoint critical events in AD pathogenesis toward developing therapeutic strategies against AD. It seemed improbable that any secreted factors, produced in RA pathogenesis, could maintain high enough concentrations in the circulatory system to cross the blood brain barrier and inhibit AD pathogenesis, without affecting all other organ systems. It did seem possible that the leukocyte populations induced in RA, could traverse the circulatory system, extravasate into the brain parenchyma, and impede or reverse AD pathogenesis. We thus investigated the colony-stimulating factors, which are up-regulated in RA and which induce most of RA’s leukocytosis, on the pathology and behavior of transgenic AD mice. We found that G-CSF and more significantly, GM-CSF, reduced amyloidosis throughout the treated brain hemisphere one week following bolus intrahippocampal administration into AD mice. We then found that 20 days of subcutaneous injections of GM-CSF (the most amyloid-reducing CSF in the bolus experiment) significantly reduced brain amyloidosis and completely reversed cognitive impairment in aged cognitively-impaired AD mice, while increasing hippocampal synaptic area and microglial density. These findings, along with two decades of accrued safety data using Leukine, the recombinant human GM-CSF analogue, in elderly leukopenic patients, suggested that Leukine should be tested as a treatment to reverse cerebral amyloid pathology and cognitive impairment in AD patients. It was also implied that age-related depressed hematopoiesis may contribute to AD pathogenesis.

Studies presented in this dissertation were conducted to gain more insight into the role of phospholipid asymmetry and amyloid-β (Aβ)-induced oxidative stress in brain of subjects with amnestic mild cognitive impairment (aMCI) and Alzheimer disease (AD). AD is a largely sporadic, age-associated neurodegenerative disorder clinically characterized by the vast, progressive loss of memory and cognition commonly in populations over the age of ~65 years, with the exception of those with familial AD, which develop AD symptoms as early as ~30 years-old. Neuropathologically, both AD and FAD can be characterized by synapse and neuronal cell loss in conjunction with accumulation of neurofibrillary tangles and senile plaques. Elevated levels of oxidative stress and damage to brain proteins, lipids, and nucleic acids are observed, as well. Likewise, aMCI, arguably the earliest form of AD, displays many of these same clinical and pathological characteristics, with a few exceptions (e.g., no dementia) and to a lesser extent. Studies in this dissertation focused on the contributions of oxidative stress to the exposure of phosphatidylserine (PtdSer) to the outer-leaflet of the lipid membrane, how and when PtdSer asymmetric collapse contributes to the progression of aMCI, AD, and FAD, and the role played by methionine-35 (Met-35) of Aβ in oxidative stress and damage, as measured in a transgenic mouse model of Aβ pathology. Normally, the PtdSer is sequestered to the cytosolic, inner-leaflet of the bilayer by the adenosine triphosphate (ATP)-dependent, membrane-bound translocase, flippase, which unidirectionally transports PtdSer inward against its concentration gradient. Oxidative stress-induced modification of flippase and/or PtdSer, however, leads to prolonged extracellular exposure of PtdSer on the outer membrane leaflet, a known signal for both early apoptosis and selective recognition and mononuclear phagocytosis of dying cells. Within the inferior parietal lobule (IPL) of subjects with aMCI and AD, a significant collapse in PtdSer asymmetry was found in association with increased levels of both pro- and anti-apoptotic proteins, Bax, caspase-3, and Bcl-2. Moreover, a significant collapse in PtdSer asymmetry was also found in whole brain of human double-mutant knock-in mouse models of Aβ pathology, together with significantly reduced Mg2+ATPase activity, representing flippase activity, and increased levels of pro-apoptotic caspase-3. Significant PtdSer externalization corresponded to the age at which significant soluble Aβ(1-42) deposition occurs in this particular mouse model (9 months), and not of plaque deposition (12 months), suggesting that elevated levels of Aβ(1-42), together with increasing oxidative stress and apoptosis, may contribute to altered PtdSer membrane localization. Also in this dissertation, transgenic mice carrying Swedish and Indiana mutations on the human amyloid precursor protein (APPSw,In) and APPSw,In mice carrying a Met35Leu mutation on Aβ were derived to investigate the role of Met-35 in Aβ(1-42)-induced oxidative stress in vivo. Oxidative stress analyses revealed that Aβ-induced oxidative stress requires the presence of Met-35, as all indices of oxidative damage (i.e., protein carbonylation, nitration, and protein-bound 4-hydroxy-2-trans-nonenal [HNE]) in brain of Met35Leu mice were completely prevented. Moreover, immunohistochemical analyses indicated that the Met35Leu mutation influences plaque formation, as a clear reduction in Aβ-immunoreactive plaques in Met35Leu mice was found in conjunction with a significant increase in microglial activation. In contrast, behavioral analyses suggested that spatial learning and memory was independent of Met-35 of Aβ, as Met35Leu mice demonstrated inferior water-maze performance compared to non-transgenic mice. Differential expression and redox proteomic analyses to pinpoint proteins significantly altered by the APPSw,In and Met35Leu mutations was performed, as well. Expression proteomics showed significant increases and decreases in APPSw,In and Met35Leu mouse brain, respectively, in proteins involved in cell signaling, detoxification, structure, metabolism, molecular chaperoning, protein degradation, mitochondrial function, etc. Redox proteomics found many of these same proteins to be oxidatively modified (i.e., protein carbonylation and nitration) in both APPSw,In and Met35Leu mouse brain, providing additional insights into the critical nature of Met-35 of Aβ for in vivo oxidative stress in a mammalian species brain, and strongly suggesting similar importance of Met-35 of Aβ(1-42) in brain of subjects with aMCI and AD. Taken together, studies presented in this dissertation demonstrate the role of oxidative stress-induced alteration of PtdSer asymmetry and Met-35 in Aβ-induced oxidative stress in aMCI, AD, and FAD brain.

Aucun traitement de la maladie d’Alzheimer (MA) n’existe, justifiant le développement de stratégies thérapeutiques. La toxicité des oligomères solubles du peptide amyloïde β (Aβ) est centrale dans les pertes synaptiques et cellulaires précoces dans la maladie. Dans le cadre de cette hypothèse, nous proposons qu’empêcher ces effets puisse prévenir le déclin cognitif dans la MA. Les facteurs neurotrophiques sont de bons candidats pour prévenir la mort cellulaire mais nécessitent une application ciblée et continue. Nous avons utilisé la technologie d’encapsulation cellulaire pour produire des bioréacteurs implantables contenant des cellules C2C12 sécrétant le facteur neurotrophique ciliaire (CNTF). Notre objectif était d’établir la preuve du concept que la production à long terme de CNTF in situ dans le cerveau puisse prévenir les déficits cognitifs liés à l’Aβ.Nos études prouvent que le CNTF produit par les bioréacteurs prévient la cytotoxicité et l’apoptose induites par le peptide Aβ in vitro. La neuroprotection dépend de l’activation de la PI3-Kinase et du facteur STAT3. In vivo, l’implantation des bioréacteurs dans le cerveau prévient les troubles cognitifs induits par l’injection icv d’Aβ ou retarde leur apparition chez la souris Tg2576. Dans nos deux modèles précliniques de la MA, la protection comportementale est associée au maintien des protéines synaptiques dans l’hippocampe. Aussi, la production in situ de CNTF est une approche thérapeutique préventive efficace contre la toxicité et les déficits cognitifs liés à l’Aβ. Ces résultats suggèrent également que l’implantation de cellules encapsulées est un bon procédé pour délivrer des molécules thérapeutiques au cerveau / No cure against Alzheimer’s Disease (AD) exists yet, justifying the development of therapeutic strategies. Toxicity of soluble amyloid β peptide is a key-player in early synaptic and cellular loss in AD. According to this hypothesis, we propose that preventing Aβ peptide effects could prevent cogninitive decline in AD. Neurotrophic factors are good candidates to prevent cell death but require a targeted and continuous delivery. We used the cell encapsulation technology to produce graftable bioreactors that contain C2C12 cells secreting the Ciliary Neurotrophic factor (CNTF). Our goal was to realize the proof-of-concept that CNTF long term in situ delivery could prevent Aβ-induced cognitive decline.Our studies prove that bioreactor-produced CNTF prevents Aβ-induced cytotoxicity and apoptosis in vitro. Neuroprotection relies on PI3K and STAT3 activation. In vivo, bioreactor implantation in brain prevents cognitive impairment induced by Aβ icv injection or delays their appearance in Tg2576 mice. In both of our preclinical model of AD, behavioral protection was associated with synapse maintenance in hippocampus.Therefore, in situ long term CNTF delivery is an efficient preventive therapeutic strategy against toxicity and Aβ-linked cognitive disturbances. These results also suggest that encapsulated cells graft is a good way to deliver therapeutic molecules to the brain

Alzheimer’s Disease, also called AD, is a horrible, degenerative brain disease that more than 35 million people over the world have. Today, there is no cure for this disease, only treatments that are temporarily relieving the symptoms. The two proteins that is thought to be the main cause of AD is amyloid β (Aβ) and tau. Previously, people have tried studying Aβ in vivo using green fluorescent protein fusion together with Aβ. However, this is difficult since the aggregation of Aβ will lead to loss of fluorescence. This study aimed to crystallize the fusion protein mNG-A β1-42 and to investigate its properties as a molecular fluorescent Aβ-amyloid specific probe. Dynamic light scattering (DLS) was used to confirm that the majority of the protein was not in the form of soluble aggregates. The DLS experiments were followed by several rounds of crystallization trials. Initial screening and the subsequent narrowing down of potential conditions where mNG-Aβ1-42 could form crystals. Several staining experiments were conducted as well, including staining brain tissue from mouse with both Swedish and Arctic mutation, from human patients with sporadic AD and from human patients with AD with the Arctic mutation. The DLS experiments showed that the protein used in the crystallization experiments mostly consisted of molecular particles of the same radius. However, there was clear evidence of some larger species present that could have been a potential problem for crystallization. Crystallization experiments suggested that PEG 8000 was the most promising precipitant amongst other conditions identified for crystallization of mNG-Aβ1-42. However, the study was ultimately unsuccessful in developing crystals of sufficient high quality for diffraction studies to commence. The staining experiments demonstrated that mNG-Aβ1-42 could bind both by itself and with another amyloid probe, Congo red, and with antibodies in brain tissue from mouse with both Swedish and Arctic mutation, from human patients with sporadic AD and from human patients with AD with the Arctic mutation. In conclusion, several characteristics of mNG-Aβ1-42 were revealed in this study.