One of the pathological hallmarks of Alzheimer's disease (AD) is the amyloid plaque deposition in aging brains by aggregation of amyloid-β (Aβ) peptides. In this study, the effect of chloroplast derived myelin basic protein (MBP) fused with cholera toxin subunit B (CTB) was investigated in advanced diseased stage of human and mouse AD brains. The CTB-fusion protein in chloroplasts facilitates transmucosal delivery in the gut by the natural binding ability of CTB pentameric form with GM1 receptors on the intestinal epithelium. Further, bioencapsulation of the MBP within plant cells confers protection from enzymes and acids in the digestive system. Here, 12-14 months old triple transgenic AD mice were fed with CTB-MBP bioencapsulated in the plant cells for 3 months. A reduction of 67.3% and 33.3% amyloid levels in hippocampal and cortical regions, respectively were observed by immunostaining of brain sections with anti- Aβ antibody. Similarly, 70% decrease in plaque number and 40% reduction of plaque intensity was observed through thioflavin S (ThS) staining that specifically stains amyloid in the AD brain. Furthermore, ex vivo 3xTg AD mice brain sections showed up to 45% reduction of ThS stained amyloid levels when incubated with enriched CTB-MBP in a concentration dependent manner. Similarly, incubation of enriched CTB-MBP with ex vivo postmortem human brain tissue sections with advanced stage of AD resulted up to 47% decrease of ThS stained amyloid plaque intensity. Lastly, lyophilization of plant material facilitates dehydration and long term storage of capsules at room temperature, in addition to increasing CTB-MBP concentration by 17 fold. These observations offer a low cost solution for treatment of even advanced stages of the AD by facilitating delivery of therapeutic proteins to central nervous system to address other neurodegenerative disease.

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Background: Amyloid β (Aβ)-directed immunotherapy has shown promising results in preclinical and early clinical Alzheimer’s disease (AD) trials, but successful translation to late clinics has failed so far. Compelling evidence suggests that post-translationally modified Aβ peptides might play a decisive role in onset and progression of AD and first clinical trials targeting such Aβ variants have been initiated. Modified Aβ represents a small fraction of deposited material in plaques compared to pan-Aβ epitopes, opening up pathways for tailored approaches of immunotherapy. Here, we generated the first monoclonal antibodies that recognize L-isoaspartate-modified Aβ (isoD7-Aβ) and tested a lead antibody molecule in 5xFAD mice. Methods: This work comprises a combination of chemical and biochemical techniques as well as behavioral analyses. Aβ peptides, containing L-isoaspartate at position 7, were chemically synthesized and used for immunization of mice and antibody screening methods. Biochemical methods included anti-isoD7-Aβ monoclonal antibody characterization by surface plasmon resonance, immunohistochemical staining of human and transgenic mouse brain, and the development and application of isoD7-Aβ ELISA as well as different non-modified Aβ ELISA. For antibody treatment studies, 12 mg/kg anti-isoD7-Aβ antibody K11_IgG2a was applied intraperitoneally to 5xFAD mice for 38 weeks. Treatment controls implemented were IgG2a isotype as negative and 3D6_IgG2a, the parent molecule of bapineuzumab, as positive control antibodies. Behavioral studies included elevated plus maze, pole test, and Morris water maze. Results: Our advanced antibody K11 showed a KD in the low nM range and > 400fold selectivity for isoD7-Aβ compared to other Aβ variants. By using this antibody, we demonstrated that formation of isoD7-Aβ may occur after formation of aggregates; hence, the presence of the isoD7-modification differentiates aged Aβ from newly formed peptides. Importantly, we also show that the Tottori mutation responsible for early-onset AD in a Japanese pedigree is characterized by massively accelerated formation of isoD7-Aβ in cell culture. The presence of isoD7-Aβ was verified by K11 in post mortem human cortex and 5xFAD mouse brain tissue. Passive immunization of 5xFAD mice resulted in a significant reduction of isoD7-Aβ and total Aβ in brain. Amelioration of cognitive impairment was demonstrated by Morris water maze, elevated plus maze, pole, and contextual fear conditioning tests. Interestingly, despite the lower abundance of the isoD7-Aβ epitope, the application of anti-isoD7-Aβ antibodies showed comparable treatment efficacy in terms of reduction of brain amyloid and spatial learning but did not result in an increase of plasma Aβ concentration as observed with 3D6 treatment. Conclusions: The present study demonstrates, for the first time, that the antibody-mediated targeting of isoD7- modified Aβ peptides leads to attenuation of AD-like amyloid pathology. In conjunction with previously published data on antibodies directed against pGlu-modified Aβ, the results highlight the crucial role of modified Aβ peptides in AD pathophysiology. Hence, the results also underscore the therapeutic potential of targeting modified amyloid species for defining tailored approaches in AD therapy.

Neuroimaging data, often high-dimensional and collected across multiple imaging modalities, is a valuable tool for studying the underlying mechanisms of how the human brain structures, functions, and thus impacts cognition. This dissertation aims to address the challenges of analyzing high-dimensional neuroimaging data, such as the missing data issue in multimodal fusion, the preservation of underlying hierarchical structure between mediators and exposure-by-mediator interactions in model selection with high-dimensional potential mediators, and the false discovery rate control for mediator selection from a high-dimensional candidate set. The first part of this dissertation aims to address the commonly occurring missing data issue during multimodal fusion. Recent advances in multimodal imaging acquisition techniques have allowed us to measure different aspects of brain structure and function. Multimodal fusion, such as linked independent component analysis (LICA), is a popular approach to integrate complementary information. However, these methods are severely limited by the common occurrence of missing data in brain imaging. In the first chapter, we propose a Full Information LICA algorithm (FI-LICA) to handle the missing data problem during multimodal fusion under the LICA framework. Built upon the principle of full information from complete cases, our method utilizes all available information to recover the missing latent information. Our simulation experiments show the ideal performance of FI-LICA compared to current practices. Further, applying to multimodal data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) study, FI-LICA demonstrates better performance in classifying current diagnosis and in predicting the transition of participants with mild cognitive impairment (MCI) to AD, thereby highlighting the practical utility of our proposed method. The second part of this dissertation aims to preserve the underlying hierarchical structure between mediators and exposure-by-mediator interactions during model selection in the high-dimensional mediator settings. In mediation analysis, the exposure often influences the mediating effect, i.e., there is an interaction between exposure and mediator on the dependent variable. When the mediator is high-dimensional, it is necessary to identify non-zero mediators (M) and exposure-by-mediator (X-by-M) interactions. Although several high-dimensional mediation methods can naturally handle X-by-M interactions, research is scarce in preserving the underlying hierarchical structure between the main effects and the interactions. To fill the knowledge gap, in the second chapter, we develop the XMInt procedure to select M and X-by-M interactions in the high-dimensional mediators setting while preserving the hierarchical structure. Our proposed method employs a sequential regularization-based forward-selection approach to identify the mediators and their hierarchically preserved interaction with exposure. Our numerical experiments show promising selection results. Furthermore, we apply our method to ADNI morphological data and examine the role of cortical thickness and subcortical volumes on the effect of amyloid-beta accumulation on cognitive performance, which could be helpful in understanding the brain compensation mechanism. The third part of this dissertation aims to control the false discovery rate (FDR) when selecting mediators from a high-dimensional candidate set. Specifically, we formulate a multiple-hypothesis testing framework for mediator selection from a high-dimensional candidate set and propose a method, which extends the recent development in FDR-controlled variable selection with knockoff, to select mediators with FDR control. We show that the proposed method and algorithm achieve finite sample FDR control. We present extensive simulation results to demonstrate the power and finite sample performance compared with the existing method. Lastly, we demonstrate the method by analyzing data from the Adolescent Brain Cognitive Development (ABCD) study, in which the proposed method selects several resting-state functional magnetic resonance imaging connectivity markers as mediators for the relationship between adverse childhood events and the crystallized composite score in the NIH toolbox.

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.

A neurodegeneração é um processo onde ocorre morte celular progressiva. O tráfego neuronal anterógrado e retrógado, e entre os compartimentos é essencial para a viabilidade celular. As proteínas Rabs pertencem à família de pequenas GTPases, com funções de tráfego de vesículas e organelas, para realizarem sua função as proteínas Rab podem recrutar proteínas motoras como as KIF 1B e KIF 5, responsáveis pelo transporte anterógrado mitocondrial. A associação do distúrbio do tráfego intracelular com doenças neurodegenerativas tem sido tema de estudos recentes. Com isso o objetivo do presente trabalho é analisar a expressão das proteínas Rab, bem como estudar as proteínas motoras que podem contribuir para o esclarecimento sobre os distúrbios no tráfego intracelular que antecedem a formação de agregados proteicos envolvidos em neurodegeneração. Para tanto, utilizou-se o modelo de tratamento com rotenona para indução de agregados em Ratos Lewis idosos que foram expostos a rotenona durante 4 semanas, em seguida foram avaliados os níveis de expressão das proteínas Rab no hipocampo, substância negra e locus coeruleus, por western blotting. Foram analisados também os níveis de expressão das proteínas motoras KIF1B e KIF5 antes e durante a formação de agregados proteicos, em culturas de células, de ratos Lewis neonatos, do hipocampo, substância negra e locus coeruleus tratadas com rotenona por 24 horas ou 48 horas nas concentrações de 0,1nM, 0, 3nM e 0,5nM. Foi observado diminuição dos níveis de expressão das proteínas Rab 1 nas regiões do hipocampo e locus coeruleus. Houve aumento de expressão das Rab 4,5 e 6 no hipocampo, porém na substância negra a expressão da Rab 1 aumentou e da Rab 6 diminuiu. Já no locus coeruleus in vivo a Rab 6 aumentou, mas as Rab 1, 5 e 11 diminuíram sua expressão. Já a expressão da KIF 5 aumentou com o tratamento de 0,1nM de rotenona e diminuiu após 0,5nM do xenobiótico por 48 horas in vitro, na mesma região. Na substância negra aumentaram as KIFs 1B e 5 após o tratamento com 0,5nM por 48 horas in vitro, mas diminuíram as KIF 1B e 5 após o tratamento com 0,3nM por 24 horas e KIF 5 após o tratamento com 0,1nM por 48 horas. Esses resultados permitem concluir que a expressão de proteínas importantes para o tráfego mitocondrial e de vesículas encontram-se alteradas e fazem parte dos eventos intracelulares que antecedem a neurodegeneração / Neurodegeneration is a process that leads to progressive cell death. The anterograde and retrograde neuronal traffic as well as the traffic between compartments are essential for cell viability. The Rab proteins belong to the small GTPases family with function of vesicles and organelle trafficking. Rab proteins can recruit motor proteins such as KIF 1B and KIF 5 that are responsible for anterograde mitochondrial transport. The association of intracellular traffic disturb with neurodegenerative diseases have been theme of recent studies. Thereat the objective of this study is analyze the expression of Rab and motor proteins that can contribute for the understanding about the disturb of the intracellular traffic that precedes protein aggregation involved in neurodegeneration. For this purpose it was employed the model of rotenone treatment for induction of aggregation in aged Lewis rats that were exposed to rotenone during 4 weeks in order to evaluate Rabs expression. The levels of motor proteins KIF 1B and KIF 5 expression were evaluated before and during the formation of protein aggregates in hippocampus, substantia nigra and locus coeruleus cell cultures of neonates Lewis rats, exposed to rotenone for 24 hours or 48 hours in the concentrations of 0.1nM, 0.3nM or 0.5nM. It was observed decreased levels of Rab 1 expression in hippocampus and locus coeruleus. Rabs 4,5 and 6 were increased in the hippocampus, but in the substantia nigra the expression of Rab 1 increased and Rab 6 decreased. In the locus coeruleus the Rab 6 increased, but Rabs 1, 5 and 11 decreased. The expression of KIF 5 increased after 0.1nM of rotenone and decreased after the exposure to 0.5nM of for 48 hours in cultured cell from the locus coeruleus. In the substantia nigra the KIF1B and KIF 5 increased after treatment with 0.5nM for 48 hours in vitro, but these protein decreased after treatment with 0.3nM for 24 hours in vitro, and KIF 5 after treatment with 0.1nM for 48 hours. These results allow us conclude that the expression of important proteins for the mitochondrial and vesicles traffic are altered and participate of intracellular events that precede the neurodegeneration