Neurological disorders are the biggest concern globally and ageing contributes in worsening the disease scenarios. In AD or AD like diseases, there is abnormal accumulation of extracellular amyloid beta produced due to abnormal processing of the transmembrane amyloid precursor protein, by β and γ-secretases. It spreads in the cortical and limbic regions of the brain leading to neuronal toxicity, impairment in memory and neurological functions. Aβ deposition in the CNS is common in aging HIV patients. Neurotoxic protein Tat, results in increased Aβ in combination with drugs of abuse cocaine. We examined the role of Withaferin A, against Aβ induced neurotoxicity. Our in-vitro dose optimization study demonstrates that lower concentrations (0.5–2 μM) of WA significantly reduce the Aβ40, without inducing cytotoxicity in the APP plasmid transfected SH-SY5Y cells (SHAPP). We demonstrate that Aβ secretion is increased in the presence of Tat (50 ng/ml) and coc (0.1 μM), WA reduces the Tat and coc induced increase in Aβ40. Additionally, we studied the role of WA against NF-kB mediated neuroinflammation, and observed that WA inhibits the expression of NFkB2 and RELA transcription factors, which play a major role in the expression of inflammatory chemokines. Further, to address the issue of minimal drug bioavailability in the CNS, we developed the WA loaded liposomal nanoformulation (WA-LNF) and characterized its size (499+/-50nm), toxicity and drug binding efficacy (28%). Our in-vitro 3D BBB transmigration of WA-LNF demonstrated ~40% transmigration efficiency. Furthermore, it was imperative for us to understand the mechanism of action of WA, therefore we studied the molecular mechanism of interaction of WA with Aβ protein by in-silico molecular dynamics simulations. We demonstrated that WA binds to the middle region of Aβ protein and the amino acid motif involved were FAEDVGS highlighting the mid-region Aβ capture by WA. 3 Hydrogen bonds were formed between WA and the amino acids, ASN17, GLY15 and SER16. This study reports WA as a potent neuroprotectant against amyloid induced neurotoxicity. Our study may have an immense therapeutic potential to target Aβ in the CNS, in the ageing patients and/or PLWH and/or ageing drug abusers.

Transgenic animal models are invaluable research tools for elucidating the pathways and mechanisms involved in the development of neurodegenerative diseases. Mechanistic clues can be revealed by applying labelling techniques such as immunohistochemistry or in situ hybridisation to brain tissue sections. Precision in both assigning anatomical location to the sections and quantifying labelled features is crucial for output validity, with a stereological approach or image-based feature extraction typically used. However, both approaches are restricted by the need to manually delineate anatomical regions. To circumvent this limitation, we present the QUINT workflow for quantification and spatial analysis of labelling in series of rodent brain section images based on available 3D reference atlases. The workflow is semi-automated, combining three open source software that can be operated without scripting knowledge, making it accessible to most researchers. As an example, a brain region-specific quantification of amyloid plaques across whole transgenic Tg2576 mouse brain series, immunohistochemically labelled for three amyloid-related antigens is demonstrated. First, the whole brain image series were registered to the Allen Mouse Brain Atlas to produce customised atlas maps adapted to match the cutting plan and proportions of the sections (QuickNII software). Second, the labelling was segmented from the original images by the Random Forest Algorithm for supervised classification (ilastik software). Finally, the segmented images and atlas maps were used to generate plaque quantifications for each region in the reference atlas (Nutil software). The method yielded comparable results to manual delineations and to the output of a stereological method. While the use case demonstrates the QUINT workflow for quantification of amyloid plaques only, the workflow is suited to all mouse or rat brain series with labelling that is visually distinct from the background, for example for the quantification of cells or labelled proteins.

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Intra- und extrazelluläre ß-Amyloid-Ablagerungen (Abeta) sind ein neuropathologisches Hauptmerkmal der Alzheimerschen Demenz (AD). Aktuelle Studien belegen, dass nicht Abeta-Plaques, sondern Abeta-Oligomere die Schädigung von Synapsen und Nervenzellen verursachen und dass ihre Konzentration gut mit der Schwere der kognitiven Dysfunktion korreliert. Allerdings sind Abeta-Peptide eine heterogene Gruppe schwer wasserlöslicher Peptide mit zahlreichen C- und N-terminalen Modifikationen. Dabei hängt die Tendenz von Abeta-Peptiden Oligomeren zu bilden, ihre proteolytische Resistenz und ihr neurotoxisches Potential maßgeblich von ihrer N-terminalen Struktur ab. Abeta-Peptide, die N-terminal einen Pyroglutamyl-Laktamring (pE-Abeta) aufweisen, machen einen Hauptbestandteil der Abeta-Last in den frühen Stadien der AD aus. Diese modifizierten Abeta-Peptide aggregieren schneller als unmodifiziertes Abeta, sind gegen Proteolyse geschützt und wirken als Aggregationskeim für andere Abeta-Spezies. Das Enzym Glutaminylzyklase (QC) katalysiert die n-terminale pE-Modifikation von Abeta in vitro und in vivo und wird in Neuronenpopulationen gefunden, für die ein starker Verlust von Synapsen und Neuronen im Zusammenhang mit der AD beschrieben wurde. Diese Arbeit stellt die schichtspezifische Verteilung von QC im temporalen Kortex und der hippocampalen Formation von Alzheimerpatienten und Kontrollen vergleichend dar und zeigt einen direkten Zusammenhang zwischen der Überexpression von QC und der Vulnerabilität betreffender Neuronenpopulationen auf. Darüber hinaus bestätigen die vorgestellten Ergebnisse die These, wonach QC und pE-Abeta das Potential haben, nach axonalem Transport eine Kaskade in efferenten Hirnregionen zu initiieren, an deren Ende der Verlust von Nervenzellen steht. Diese Erkenntnisse unterstützen das Interesse an QC als Gegenstand zukünftiger Grundlagenforschung und Wirkstoffentwicklungen für die Therapie der AD. / Intra- and extracellular s-amyloid (Abeta) deposits are a major neuropathological hallmark of Alzheimer\'s disease (AD). Recent studies demonstrate that Abeta oligomers rather than Abeta plaques cause severe damage of synapses and nerve cells and in addition the concentration of Abeta oligomers correlates well with the severity of cognitive dysfunction. However, Abeta peptides are a heterogeneous group of poorly water-soluble peptides with various C- and N-terminal modifications. Biophysical properties of these peptides such as their propensity to form oligomers, their proteolytic resistance and their neurotoxic potential particularly depends on their N-terminal structure. Abeta-peptides that contain a pyroglutamyl-a-lactam ring at their N-Terminus (pE-Abeta) constitute a major component of the Abeta load in the early stages of AD. These modified Abeta-peptides aggregate faster than unmodified Abeta, are protected against proteolysis and act as aggregation seed for other Abeta-species. The enzyme glutaminyl cyclase (QC)catalyzes the cyclization of Abeta to pE-Abeta in vitro and in vivo and is found in neuronal populations for which a strong loss of synapses and neurons in the context of AD is described. This thesis presents the layer-specific distribution of QC in the temporal cortex and the hippocampal formation of Alzheimer\'s patients and controls, showing a direct correlation between the overexpression of QC and the vulnerability of respective neuronal populations. Moreover, the presented results confirm the hypothesis that QC and pE-Abeta have the potential to initiate a cascade leading to the loss of nerve cells due to axonal transport and release in efferent brain regions. These findings support the interest in QC as a subject of fundamental research and future drug developments for the treatment of AD.

Amyloid beta (Aβ) has been postulated to be the principle initiator of the pathogenesis of Alzheimer’s disease (AD). Therefore, understanding the underlying mechanisms of Aβ induced neurotoxicity in the early stages of AD would be essential for finding potential therapeutic targets of AD. Aβ-binding alcohol dehydrogenase (ABAD) has been shown to be a mitochondrial binding site for Aβ. Expression of ABAD has been found to be increased in brains of AD sufferers. Two dimensional electrophoresis studies have revealed that endophilin 1 was upregulated in Tg mAPP/ABAD mice brains as compared to Tg mAPP, Tg ABAD and non-Tg mice brains. Increased expression of endophilin 1 has also been found in brains of AD patients as compared to non-demented control brain tissues. Endophilin1 has been reported to regulate c-Jun N-terminal kinase (JNK) activation. In this study, expression of dominant negative forms of endophilin 1 (DN-endophilin 1) in mouse cortical neurons exhibited a significant reduction of Aβ induced JNK activation. Furthermore, using cell counting methods, it was shown that the transfection of DN-endophilin 1 increased neuron survival after Aβ treatment. Aβ has also been proposed to disrupt the interaction of ABAD and Cyclophilin D (CypD), which would trigger mitochondrial permeable transition, thereby leading to neurotoxicity. For fluorescence resonance energy transfer (FRET) analysis of the interaction of ABAD and CypD, a mitochondria targeted, EYFP tagged ABAD plasmid (pMito-ABAD-EYFP) and an ECFP tagged CypD (pCypD-ECFP) plasmid were developed. Positive FRET signals in SK-N-SH cells co-expressing pMito-ABAD-EYFP and pCypD-ECFP indicated that ABAD interacts with CypD in the mitochondria of mammalian cells. RAGE (receptor for advanced glycation end products) has been reported to bind to Aβ and mediate the toxic effects of Aβ peptides on neurons and microglia. It has been shown previously that Tg mAPP/DN-RAGE mice display preserved cognitive function as compared to Tg mAPP mice. To investigate possible mechanisms involved in rescuing cognitive function by RAGE blockage, two dimensional electrophoresis was used to analyze differential protein expression between Tg mAPP and Tg mAPP/DN-RAGE mice cortex. Altered expression of four proteins, including NADH dehydrogenase flavoprotein 2 (NDUFV2), glyoxalase 1 (GLO1), proteasome subunit beta type 4 (PSMB4, or β7 subunit of proteasome) and nitrilase family, member 2 (Nit2) have been observed between Tg mAPP/DN-RAGE mice cortex and Tg mAPP mice cortex. NDUFV2 is a 24kDa subunit of complex 1 which is involved in ATP synthesis. GLO1 is a cytosolic enzyme that plays a role the glutathione-dependent detoxification of α-oxoaldehydes, such as methylglyoxal. PSMB4 is a subunit of the 26s proteosome which is in the degradation of ubiquitinylated proteins. The function of Nit2 is still unclear.

Les protéines sont au coeur de la vie. Ce sont d'incroyables nanomachines moléculaires spécialisées et améliorées par des millions d'années d'évolution pour des fonctions bien définies dans la cellule. La structure des protéines, c'est-à-dire l'arrangement tridimensionnel de leurs atomes, est intimement liée à leurs fonctions. L'absence apparente de structure pour certaines protéines est aussi de plus en plus reconnue comme étant tout aussi cruciale. Les protéines amyloïdes en sont un exemple marquant : elles adoptent un ensemble de structures variées difficilement observables expérimentalement qui sont associées à des maladies neurodégénératives. Cette thèse, dans un premier temps, porte sur l'étude structurelle des protéines amyloïdes bêta-amyloïde (Alzheimer) et huntingtine (Huntington) lors de leur processus de repliement et d'auto-assemblage. Les résultats obtenus permettent de décrire avec une résolution atomique les interactions des ensembles structurels de ces deux protéines. Concernant la protéine bêta-amyloïde (AB), nos résultats identifient des différences structurelles significatives entre trois de ses formes physiologiques durant ses premières étapes d'auto-assemblage en environnement aqueux. Nous avons ensuite comparé ces résultats avec ceux obtenus au cours des dernières années par d'autres groupes de recherche avec des protocoles expérimentaux et de simulations variés. Des tendances claires émergent de notre comparaison quant à l'influence de la forme physiologique de AB sur son ensemble structurel durant ses premières étapes d'auto-assemblage. L'identification des propriétés structurelles différentes rationalise l'origine de leurs propriétés d'agrégation distinctes. Par ailleurs, l'identification des propriétés structurelles communes offrent des cibles potentielles pour des agents thérapeutiques empêchant la formation des oligomères responsables de la neurotoxicité. Concernant la protéine huntingtine, nous avons élucidé l'ensemble structurel de sa région fonctionnelle située à son N-terminal en environnement aqueux et membranaire. En accord avec les données expérimentales disponibles, nos résultats sur son repliement en environnement aqueux révèlent les interactions dominantes ainsi que l'influence sur celles-ci des régions adjacentes à la région fonctionnelle. Nous avons aussi caractérisé la stabilité et la croissance de structures nanotubulaires qui sont des candidats potentiels aux chemins d'auto-assemblage de la région amyloïde de huntingtine. Par ailleurs, nous avons également élaboré, avec un groupe d'expérimentateurs, un modèle détaillé illustrant les principales interactions responsables du rôle d'ancre membranaire de la région N-terminal, qui sert à contrôler la localisation de huntingtine dans la cellule. Dans un deuxième temps, cette thèse porte sur le raffinement d'un modèle gros-grain (sOPEP) et sur le développement d'un nouveau modèle tout-atome (aaOPEP) qui sont tous deux basés sur le champ de force gros-grain OPEP, couramment utilisé pour l'étude du repliement des protéines et de l'agrégation des protéines amyloïdes. L'optimisation de ces modèles a été effectuée dans le but d'améliorer les prédictions de novo de la structure de peptides par la méthode PEP-FOLD. Par ailleurs, les modèles OPEP, sOPEP et aaOPEP ont été inclus dans un nouveau code de dynamique moléculaire très flexible afin de grandement simplifier leurs développements futurs. / Proteins are at the center of life. They are formidable molecular nanomachines specialized and optimized during million years of evolution for well-defined functions in the cell. The structure of proteins, meaning the tridimensional setting of their atoms, is closely related to their function. Absence of structure for a subset of proteins is also recognized to be as crucial. Amyloid proteins is a striking example : they fold into an ensemble of various structures hardly observable experimentally that are associated with neurodegenerative diseases. This thesis, firstly, is on the study of the structural ensemble of the amyloid proteins amyloid-beta (Alzheimer) and huntingtin (Huntington) during their folding and aggregation. Our results describe in details, with an atomic resolution, the characteristic interactions present in the structural ensemble of these two proteins. Concerning the amyloid-beta protein (AB), our results show the structural differences between three of its physiological forms during its first aggregation steps in an aqueous environment. We have then compared these results with those obtained during the past few years by several other research groups using various experimental and simulation protocols. Clear trends come out of this comparison regarding the influence of AB physiological form on its structural ensemble during its first aggregation steps. Their distinct aggregation pathways are rationalized by the identified differences. For their part, the identified similarities offer targets for therapeutical compounds disrupting the aggregation of the neurotoxic oligomers. Concerning the huntingtin protein, we identify the structural ensemble of its functional region at its N-terminal in an aqueous environment and in a phospholipid membrane. In agreement with the available experimental results on the global structure of this region in aqueous solution, our results reveal the dominant interactions, at an atomic precision, in its structural ensemble as well as the influence of its neighboring regions. We have also characterized the stability and the growth of nanotube-like structures that could occur during the aggregation of the amyloid region of huntingtin. Moreover, we have developed, in collaboration with a group of experimentalists, a precise model describing the main membrane interactions of huntingtin N-terminal, which serves as a membrane anchor that controls the localization of huntingtin in the cell. Secondly, this thesis is on the refinement of a coarse-grained model (sOPEP) and on the development of a new all-atom model (aaOPEP) that are both based on the coarse-grained OPEP force field, commonly used to study protein folding and amyloid protein aggregation. The goal behind the optimization of these models is to improve the de novo structure prediction of the PEP-FOLD method. These three models -- OPEP, sOPEP and aaOPEP -- are now also implemented in a new molecular dynamics software that we have developed specifically to greatly ease their future developments.

This thesis work describes the role of Rab proteins in amyloid processing and clearance in different cell pathways. It also describes an experimental approach used to analyze the expression effects of Rab10 in amyloid beta production. Since the main theory behind neurodegeneration in Alzheimer's disease claims that high levels of amyloid beta 42 (Aβ42) molecules trigger widespread neuronal death, control of Aβ42 has been a main target in Alzheimer's disease research. In addition, several studies show increased levels of particular Rab proteins in Alzheimer's pathogenesis. However, no review consolidates current findings in neurodegeneration of Alzheimer's with Rab protein dysfunction. The first chapter of this thesis aims to address this need by providing a current review of Rab proteins associated with APP and neurodegeneration. The second chapter constitutes an experimental approach used to characterize the effects of Rab10 and Sar1A GTPases in APP and amyloid processing. We found that Rab10 expression does not affect APP production but significantly changes Aβ generation, particularly the toxic Aβ42 and Aβ42:40 ratio. On the other hand, we found no significant effect of Sar1A expression on either APP or amyloid beta generation. These findings partially confirm the work done by Kauwe et al (2015) and provide preliminary evidence for two potential targets for protective effects in neurodegeneration.

Diss. (sammanfattning) Umeå : Umeå universitet, 2009. / Härtill 4 uppsatser.

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