Nothing is perfect, and this includes the ability to maintain homeostasis within the cell with age. Factors such as aging, chemicals, and gene dysfunction disrupt cellular homeostasis, leading to increased stress and compromising the ability of animals to maintain a healthy lifespan. Dysregulated homeostasis can be detrimental on an organismal level, impacting locomotion, and on a cellular level causing proteins to misfold and become aggregates, which are toxic to cells. Toxic protein aggregation and loss of locomotory function are key hallmarks of several age-related diseases. My Ph.D. work examined the collapse of homeostasis on electrotaxis, the age-associated increase in proteotoxicity, the decline in longevity, and neuronal and muscle health. On a behavioural level I demonstrated that loss of various components of the MT-UPR, ER-UPR, and HSR modulated the speed of animals. Additionally, I found that activation of stress responses due to chemicals and exercise reduced and increased the speed of animals respectively. On a cellular level I elucidated potential mechanisms by which Mesencephalic Astrocyte Derived Neurotrophic Factor (MANF) affects the stress response to maintain homeostasis and prevent protein aggregation. I observed the novel localization and role of MANF in lysosomes to potentially act as a critical regulator of the stress response to maintain proteostasis, neuronal health and longevity, thereby bringing balance to the cell. Furthermore, the broad tissue expression of MANF revealed its localization to muscles. This supports the ability of MANF to act as more than a neurotrophic factor as it was found to be required for muscular health in animals in an age-dependent manner. Overall, my Ph.D. research has provided new insights into the stress response and behaviour and the precise role of MANF in mediating stress response signaling to promote organismal and cellular fitness. / Dissertation / Doctor of Science (PhD) / Cellular perturbations or stress disrupt homeostasis, activating multiple stress responses. Activation of the stress response can determine the fate of an organism and is crucial to its health. Although the stress response pathways are generally understood, little is known about how the stress responses preserve animal behaviour or how they are regulated to promote organismal survival. My work has provided a basis for how stress responses affect behaviour positively and negatively in animals. I found that the stress response required mesencephalic astrocyte derived neurotrophic factor (MANF) to promote organismal survival. My thesis determined that MANF acts as more than a neurotrophic factor. MANF was found to not only be essential in neuronal health but also longevity and muscle health. Overall, this thesis demonstrated the impact of stress response on behaviour and the potential mechanism by which MANF is cytoprotective in whole organisms.

Protein folding is the process in which polypeptides in their non-native states attain the unique folds of their native states. Adverse environmental conditions and genetic predisposition challenge the folding process and accelerate the production of proteotoxic misfolded proteins. Misfolded proteins are selectively recognized and removed from the cell by processes of protein quality control (PQC). In PQC molecular chaperones of the Heat shock protein 70 kDa (Hsp70) family play important roles by recognizing and facilitating the removal of misfolded proteins. Hsp70 function is dependent on cofactors that regulate the intrinsic ATPase activity of the chaperone. In this thesis I have used yeast genetic, cell biological and biochemical experiments to gain insight into the regulation of Hsp70 function in PQC by nucleotide-exchange factors (NEFs). Study I shows that the NEF Fes1 is a key factor essential for cytosolic PQC. A reverse genetics approach demonstrated that Fes1 NEF activity is required for the degradation of misfolded proteins associated with Hsp70 by the ubiquitin-proteasome system. Specifically, Fes1 association with Hsp70-substrate complexes promotes interaction of the substrate with downstream ubiquitin E3 ligase Ubr1. The consequences of genetic removal of FES1 (fes1Δ) are the failure to degrade misfolded proteins, the accumulation of protein aggregates and constitutive induction of the heat-shock response. Taken the experimental data together, Fes1 targets misfolded proteins for degradation by releasing them from Hsp70. Study II describes an unusual example of alternative splicing of FES1 transcripts that leads to the expression of the two alternative splice isoforms Fes1S and Fes1L. Both isoforms are functional NEFs but localize to different compartments. Fes1S is localized to the cytosol and is required for the efficient degradation of Hsp70-associated misfolded proteins. In contrast, Fes1L is targeted to the nucleus and represents the first identified nuclear NEF in yeast. The identification of distinctly localized Fes1 isoforms have implications for the understanding of the mechanisms underlying nucleo-cytoplasmic PQC. Study III reports on the mechanism that Fes1 employs to regulate Hsp70 function. Specifically Fes1 carries an N-terminal domain (NTD) that is conserved throughout the fungal kingdom. The NTD is flexible, modular and is required for the cellular function of Fes1. Importantly, the NTD forms ATP-sensitive complexes with Hsp70 suggesting that it competes substrates of the chaperone during Fes1-Hsp70 interactions. Study IV reports on methodological development for the efficient assembly of bacterial protein-expression plasmids using yeast homologous recombination cloning and the novel vector pSUMO-YHRC. The findings support the notion that Fes1 plays a key role in determining the fate of Hsp70-associated misfolded substrates and thereby target them for proteasomal degradation. From a broader perspective, the findings provide information essential to develop models that describe how Hsp70 function is regulated by different NEFs to participate in protein folding and degradation. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.</p>

A key prerequisite for cellular and organismal health is a functional proteome. A variety of human protein misfolding diseases are associated with the occurrence of amyloid protein aggregates, such as amyotrophic lateral sclerosis (ALS) or Huntington’s disease. The proteins involved in disease manifestation all contain aggregation-prone sequences of low compositional complexity. Such sequences are also known as prion-like, because of their sequence similarity to yeast prions. Yeast prion proteins are a specific subset of amyloid forming proteins with distinct physio-chemical and functional features, which give them transmissible properties. The aggregation properties of yeast prions and disease-related prion-like proteins reside in structurally independent, prion-forming domains (PrDs). These domains are highly enriched for uncharged polar amino acids, such as glutamine (Q) and asparagine (N). These compositional features can be used to predict prion-like proteins bioinformatically. To investigate the prevalence of prion-like proteins across different organisms, we analyzed a range of eukaryotic proteomes. Our analysis revealed that the slime mold D. discoideum contains the highest number of prion-like N/Q-rich proteins of all organisms. Based on this finding, we hypothesized that D. discoideum could be a valuable model system to study protein homeostasis (proteostasis) and the molecular basis of protein misfolding diseases. To explore how D. discoideum manages its highly aggregation-prone proteome, we analyzed the behavior of several well-characterized misfolding-prone marker proteins (variants of the disease-causing exon 1 of the huntingtin protein as well as wildtype and variant versions of the Q/N-rich yeast prion Sup35NM). Intriguingly, these proteins did not form cytosolic aggregates in D. discoideum, as they do in other organisms. Aggregates, however, formed as a result of heat stress, which indicates that the tested proteins have the capacity to aggregate, but are kept under tight control under normal conditions. Furthermore, when the stress level was reduced, the stress-induced aggregates dissolved, suggesting that D. discoideum has evolved mechanisms to reverse aggregation after a period of acute stress. Together, these findings reveal an unusual resilience of D. discoideum to aggregation-prone proteins, which very likely results from specific adaptations in its proteostasis network. By studying these specific adaptations, we could get important insight into the strategies that nature employs to control and maintain a highly aggregation-prone proteome. So far, our experimental investigations have revealed evidence for three specific adaptations. First, we identified the disaggregase Hsp101 as a key player in the acute stress response of D. discoideum. A functional analysis of Hsp101 in yeast and D. discoideum revealed that it supports thermotolerance. Second, we found evidence for an important role of the nucleus and nucleolus in proteostasis. We discovered that a small fraction of highly aggregation-prone proteins accumulated in the nucleus or nucleolus of D. discoideum cells. The magnitude of this nuclear accumulation could be increased by proteasome impairment, which suggests that the ubiquitin-proteasome system (UPS) is involved. This finding is consistent with previous studies in other organisms and hints at the possibility that D. discoideum disposes of aggregation-prone proteins by degrading them in the nucleus/nucleolus. Third and finally, we found that cells containing nuclear accumulations are asymmetrically distributed in the multicellular developmental stage (slug), suggesting that D. discoideum employs cell-sorting mechanisms to dispose of cells with accumulated protein damage. Although our current understanding of proteostasis in D. discoideum is preliminary, we have gained important insight into the molecular mechanisms and cellular pathways that D. discoideum uses to counteract protein aggregation. Findings from this work will inform similar comparative studies in other organisms and will impact our molecular understanding of protein misfolding diseases and aging. / Eine wesentliche Voraussetzung für die Gesundheit von Zellen und Organismen ist ein funktionales Proteom. Eine Reihe von humanen Protein- Missfaltungs-Erkrankungen, wie Chorea Huntington und Amyotrophe Lateralsklerose (ALS) werden mit dem Auftreten von amyloiden Protein- Aggregaten in Verbindung gebracht. Sämtliche Proteine, die in der Pathogenese dieser Krankheiten eine Rolle spielen, enthalten aggregations-anfällige Sequenzen mit geringer Sequenzkomplexität. Solche Sequenzen werden als Prion-ähnlich bezeichnet, da sie in ihrer Zusammensetzung den Prionen aus der Hefe S. cerevisiae gleichen. Die Prion-Proteine der Hefe gehören zu einer Unterart von amyloid-aggregierenden Proteinen, die durch bestimmte physikochemische und funktionelle Eigenschaften einen infektiösen Charakter erhalten. Die Aggregations-Eigenschaften von Hefeprionen und aggregationsanfällige Proteinen, die mit Erkrankungen in Verbindung gebracht werden, basieren auf strukturell unabhängigen, Prion-bildenden Domänen (prion domain, PrD). Diese Domänen sind angereichert mit polaren Aminosäuren wie Glutamin und Asparagin. Diese Zusammensetzung kann dazu verwendet werden prion-ähnliche Proteine bioinformatisch vorherzusagen. Um die Verbreitung von Prion-ähnlichen Proteinen in verschiedenen Organismen zu untersuchen, analysierten wir eine Reihe von eukaryotischen Proteomen. Unsere Analyse zeigte, dass der Schleimpilz D. discoideum die höchste Anzahl von Prion-ähnlichen N/Q-reichen Proteinen aufzeigt. Aufgrund dieser Erkenntnisse erstellten wir die Hypothese, dass D. discoideum ein nützlicher Modellorganismus sein könnte, um Protein Homöostase (Proteostase) sowie die molekulare Basis von Proteins-Missfaltungs-Erkrankungen zu ergründen. Um zu analysieren, wie D. discoideum mit seinem höchst aggregations-anfälligen Proteom umgehen kann, untersuchten wir das Verhalten mehrerer bereits charakterisierter aggregations-anfälliger Marker-Proteine in D. discoideum. Hierbei verwendeten wir Varianten des krankheits-erzeugenden Exon 1 des humanen Huntingtin Protein sowie den wild-typ und Varianten des N/Q-reichen Hefe Prions Sup35. Interessanterweise bildeten diese Proteine, anders als in anderen Organismen, keine zytosolischen Aggregate in D. discoideum aus. Aggregate wurden jedoch unter Hitzestress-Bedingungen gebildet. Dies deutet darauf hin, dass die getesteten Proteine durchaus das Vermögen zu aggregieren besitzen, jedoch unter normalen Wachstumsbedingungen streng kontrolliert werden. Wenn, darüberhinaus das Stress- Level gesenkt wurde, kam es zur Auflösung der stress-induzierten Aggregate. Dies deutet darauf hin, dass D. discoideum Mechanismen entwickelt hat, um Aggregate nach Perioden von akutem Stress wieder aufzulösen. Zusammengenommen enthüllen diese Erkenntnisse eine ungewöhnliche Widerstandsfähigkeit gegenüber aggregations-anfälligen Proteinen. Diese beruht höchstwahrscheinlich auf spezifischen Modifikationen im Proteostase Netzwerk. Durch die Analyse dieser spezifischen Anpassungen könnten wichtige Einblicke in die Strategien gewährt werden, welche die Natur benutzt, um ein höchst aggregations-anfälliges Proteom zu erhalten und zu kontrollieren. Bisher erbrachten unsere Experimente Anhaltspunkte für drei spezifische Anpassungen. Erstens zeigten wir, dass die Disaggregase Hsp101 eine Schlüsselrolle in der akuten Stressantwort in D. discoideum einnimmt. Eine funktionale Analyse von Hsp101 in D. discoideum und Hefe zeigte, dass die Disaggregase Thermotoleranz fördert. Zweitens haben wir Anhaltspunkte, dass der Nukleus und der Nukleolus eine wichtige Rolle in der Proteostase einnehmen. Eine geringe Fraktion der überaus aggregations-anfälligen Proteine akkumuliert im Nukleus oder Nukleolus von D. discoideum. Das Ausmaß der nuklearen Akkumulation konnte erhöht werden, wenn das Proteasom beeinträchtigt wird. Dies deutet darauf hin, dass das Ubiquitin-Proteasom-System involviert sein könnte. Diese Beobachtung ist im Einklang mit jüngsten Berichten aus anderen Organismen und daraus folgt, dass D. discoideum möglicherweise aggregations-anfällige Proteine durch Abbau im Nukleus entsorgt. Drittens konnten wir feststellen, dass Zellen, die nukleare Akkumulationen enthalten, asymmetrisch in der multizellulären Entwicklungs-Struktur des Pseudoplasmodiums verteilt sind. Dies deutet darauf hin, dass D. discoideum möglicherweise den Zellsortierungsmechanismus während der Entwicklung nutzen kann, um Zellen mit angereicherten Protein-Schäden zu beseitigen. Auch wenn das gegenwärtige Verständnis der Proteostase in D. discoideum nur vorläufig ist, haben wir wichtige Einblicke in die molekularen Mechanismen und zellulären Prozesse erhalten, die D. discoideum verwendet, um Protein-Aggregation zu verhindern. Die Ergebnisse dieser Arbeit werden ähnliche vergleichende Studien in anderen Organismen beeinflussen und Auswirkungen auf unser molekulares Verständnis über Protein-Missfaltungs-Erkrankungen und das Altern haben.

One of the greatest risk factors for disease is advanced age. As the human lifespan has increased, so too have the burdens of caring for an increasingly older population suffering from rising rates of cardiovascular disease, kidney disease, diabetes, and dementia. The need for improving medical technology and developing new therapies for age-related diseases is manifest. Yet our understanding of the processes of aging and how to attenuate the effects of aging remains incomplete. Various studies have established calorie restriction as a robust method for extending lifespan in laboratory organisms; however the mechanism is a topic of much debate. Advancing our understanding of calorie restriction holds promise for illuminating biochemical processes involved in the aging process. One of the best explanations for the lifespan extension benefits of calorie restriction is that it improves cellular protein homeostasis (proteostasis), but because proteostasis is dynamic, it can be difficult to measure. We developed a novel combined omics methodology integrating kinetic proteomics, and applied it to a mouse model placed on calorie restriction. Our unbiased approach integrating just three measurements (kinetic proteomics, quantitative proteomics, and transcriptomics) enabled us to characterize the synthesis and degradation of thousands of proteins, and determine that calorie restriction largely alters proteostasis by slowing global protein synthesis post-transcriptionally. Validating our omics approach, we were able to replicate many previous results found in the literature, demonstrating the differential regulation of various protein ontologies in response to the nutrient stress of calorie restriction. Moreover, we were able to detect differential degradation of the large and small ribosomal subunits under calorie restriction, and proposed a model in which the rate of protein synthesis could be attenuated by the depletion of the large ribosomal subunit relative to the small subunit. The flexibility of our dynamic combined omics approach was demonstrated by the expansion of measurements to include nucleic acids and lipids. Flux measurements of DNA, ribosomal RNA, and lipids yielded cellular division rates, ribosome turnover, and lipid metabolism insights, respectively. We also adapted this approach to two-dimensional tissue imaging by DESI-MS in a proof-of-concept study to demonstrate its utility for studying regional differences in metabolism. The future integration of metabolomics and lipidomics into our combined omics approach would be facile, and add unprecedented depth to systems-wide studies involving cellular metabolism. Applied to the regulation of cellular homeostasis in humans, this has the potential to open new avenues for elucidating the etiology of aging, understanding the pathology of age-related diseases, and identifying novel targets for therapeutics.

Small Heat Shock Proteins (sHSP) are molecular chaperones that play protective roles in cell survival and have been shown to possess chaperone activity. As such, mutations in this family of proteins result in a wide variety of diseases from cancers to cardiomyopathies. The sHSPs Beta-2 (HspB2) and alpha-beta crystalline (CryAB) are two of the ten human sHSPs and are both expressed in cardiac and skeletal muscle cells. A heart that cannot properly recover or defend against stressors such as extreme heat or cold, oxidative/reductive stress, and heavy metal-induced stress will constantly struggle to maintain efficient function. Accordingly, CryAB is required for myofibril recovery from ischemia/reperfusion (I/R) and HspB2 is required I/R recovery as well as efficient cardiac ATP production. Despite these critical roles, little is known about the molecular function of these chaperones. We have identified over two hundred HspB2-binding partners through both yeast two-hybrid and copurification approaches, including interactions with myofibril and mitochondrial proteins. There is remarkable overlap between the two approaches (80%) suggesting a high confidence level in our findings. The sHSP, CryAB, only binds a subset of the HspB2 interactome, showing that the HspB2 interactome is specific to HspB2 and supporting non-redundant roles for sHSPs. We have confirmed a subset of these binding partners as HspB2 clients via in vitro chaperone activity assays. In addition, comparing the binding patterns and activity of sHSP variants in comparison to wild type can help to elucidate how variants participate in causing disease. Accordingly, we have used Y2H and in vitro chaperone activity assays to compare the disease-associated human variants R120GCryAB and A177PHspB2 to wild type and have identified differences in binding and chaperone function. These results not only provide the first molecular evidence for non-redundancy of the sHSPs, but provides a useful resource for the study of sHSPs in mitochondrial and myofibril function.

Every cell consists of carefully orchestrated biomolecules such as lipids, carbohydrates, and proteins. To maintain internal stability (homeostasis), cells maintain the right amount of these molecules at the right time and at the right place. This process is especially true for proteins since they are the foundation functional units within the cell. Proteins form structures and perform chemistry that bestows cells overarching functional roles. Cells maintain protein homeostasis (proteostasis) by modulating synthesis, folding, and degradation processes (turnover) to maintain the abundance levels for all proteins. This is the foundational kinetic model of proteostasis that is covered in this work, and it comprises protein abundance and turnover essential for protein homeostasis. When proteostasis is lost, cells may also fail to perform their internal cellular functions which will impact their external role. The sustained loss of proteostasis leads to disease. In the area of proteomics, we seek out the mechanisms of proteome change that result in the loss of normal proteostasis that are associated with disease states. As biochemists we explore the role of different proteins within biological systems and disease states. Predominantly, these studies involve isolating proteins (generally one at time) to measure abundance levels, function, and structure. In more recent years, technological advances in liquid chromatography and mass spectrometry (LC-MS) ushered in the golden age of proteomics. With LC-MS we can explore thousands of proteins in a single experiment to measure their expression levels. This work covers the fundamentals of this process as well as examples of LC-MS based proteomics for biomarker discovery and individual protein dynamics. In a sense, these experiments are like taking a snapshot of what proteins are found within a biological system at a given moment. However, cells are not static systems, rather they are dynamic systems in which proteins are being created and destroyed to maintain proteostasis. In this regard, LC-MS has recently become a powerful tool to explore protein turnover for thousands of proteins. Combined with protein abundance measurements, protein turnover yields a dynamic image of the internal state of the cell. This work applies the ideas within the kinetic model of proteostasis to explore the changes in protein homeostasis associated with Apolipoprotein E (ApoE) isoforms. ApoE isoforms are a genetic risk factor of ongoing research because of their role in disease and longevity. This work reviews some of the proposed mechanisms associated with ApoE genotype, and the LC-MS experiment we created to measure both proteome wide abundance and turnover changes associated with ApoE genotype. Our findings not only provide evidence that unifies previous ApoE studies, and it provides a benchmark for how to incorporate both quantitative and kinetic proteomics to monitor proteostasis.

Introdução: A hipertensão pulmonar tromboembólica crônica (HPTEC) está incluída no grupo 4 da Classificação Internacional de Hipertensão Pulmonar (HP). É caracterizada pela persistência de obstrução por trombos sanguíneos na circulação pulmonar, associada à presença de HP, após três meses de anticoagulação efetiva. O tratamento de escolha é a cirurgia de tromboendarterectomia pulmonar (TEAP), mas alguns dos mecanismos fisiopatológicos envolvidos nesta forma de hipertensão ainda permanecem incertos. O redirecionamento dos fluxos sanguíneos pulmonares e a hipóxia exercem papel importante na HPTEC, como também em casos de hipertensão pulmonar residual, após a cirurgia de TEAP. Entretanto, existem poucos dados sobre as respostas das células endoteliais pulmonares a essas mudanças de fluxo e de oxigenação, surgindo a necessidade do estudo da proteostase celular nesta doença. Objetivo: (A) Caracterização morfológica das células em culturas provenientes de artéria pulmonar de pacientes com HPTEC submetidos à TEAP. (B) Avaliação da resposta das células endoteliais, a partir da análise de proteínas envolvidas na proteostase celular, quando submetidas a diferentes níveis de stress mecânico e à hipóxia. Método: Trombos extraídos por TEAP foram processados, as células retiradas foram cultivadas, marcadas com CD31 e submetidas a stress mecânico por vinte e quatro horas, constituindo o grupo HPTEC. A proteostase celular foi avaliada pela medida de proteínas expressas por essas células, tanto em culturas quanto pela análise imuno-histoquímica do tecido vascular pulmonar. Como grupo controle foram utilizadas células endoteliais pulmonares humanas de linhagem (CE) e tecido de artérias pulmonares de doadores de transplante de pulmão. As culturas de ambos os grupos também foram colocadas em hipóxia e analisada a expressão indireta de óxido nítrico (NO) por meio da medida de nitrato. Resultado: as células do grupo HPTEC com morfologia endotelial foram marcadas positivamente com CD31 e apresentaram características semelhantes às do grupo CE. Em relação ao stress mecânico, na condição estática as células HPTEC expressaram menor quantidade de óxido nítrico sintase endotelial (eNOS). Quando submetidas a stress de alta intensidade (shear stress >= 15 dynes/cm2), as reduções ficaram ainda mais evidentes, sinalizando uma disfunção endotelial. Na análise de outras proteínas, como GRP94, GRP78, HSP70, as respostas também foram menores no alto fluxo. Na avaliação imunohistoquímica da camada íntima do vaso pulmonar, a HSP70 apresentava-se diminuída, corroborando os achados das culturas. Os valores de NO foram inferiores no grupo HPTEC quando se comparam hipóxia e normóxia. Conclusão: (A) A avaliação morfológica mostrou que as culturas de células HPTEC eram endoteliais. (B) A análise funcional revelou que estas células apresentaram redução de resposta, o que caracteriza alteração da proteostase, que se tornou mais evidente quando foram submetidas a shear stress de alta magnitude. A hipóxia reduziu a produção de NO, entretanto sem diferenciar os grupos celulares estudados / Introduction: Chronic Thromboembolic Pulmonary Hypertension (CTEPH) is included in group 4 of the International Classification of Pulmonary Hypertension (PH). It is characterized by persistent obstruction by blood clots in the pulmonary circulation, associated with the presence of PH, after 3 months of effective anticoagulation. The treatment of choice is pulmonary endarterectomy (PEA). However, some of the pathophysiological mechanisms involved in this form of hypertension still remain uncertain. The redirection of pulmonary blood flow and hypoxia play an important role in CTEPH, and also, in cases of residual pulmonary hypertension after PEA surgery. Nevertheless, there is insufficient data from the pulmonary endothelial cell responses to this flow and oxygenation changes, reflecting the need to further study of cellular proteostasis in this disease. Objective: (A) Morphological characterization of cells in cultures from the pulmonary artery of CTEPH patients submitted to PEA. (B) Evaluation of the response of endothelial cells, through the analysis of proteins involved in cellular proteostasis, when submitted to different levels of mechanical stress and hypoxia. Method: Thrombus extracted by PEA were processed and the cells removed were cultured, marked with CD31 and submitted to mechanical stress for 24 hours and constituted the group CTEPH. Cellular proteostasis was measured by the quantification of the proteins expressed in cultures and in pulmonary vascular tissue by immunohistochemistry analysis. As a control group, the human pulmonary endothelial cells (EC) and pulmonary artery tissue from lung transplant donors were used. Cultures of both groups were also placed in hypoxia and the indirect expression of nitric oxide (NO) was analyzed by nitrate measurement. Results: The cells with endothelial morphology from the CTEPH group were positively marked with CD31 and presented similar characteristics as the EC group. Regarding mechanical stress, in the static condition, the CTEPH cells expressed a lesser amount of endothelial nitric oxide synthase (eNOS). When submitted to high flow (shear stress > 15 dynes / cm2) the reductions became even more evident, signaling an endothelial dysfunction. In the analysis of other proteins, such as GRP94, GRP78, HSP70, responses were also lower in high shear stress. In the immunohistochemistry analysis of the intimal layer of the pulmonary vessel HSP70 was diminished, corroborating with the findings of the cultures. The NO values were lower in the CTEPH group when compared hypoxia and normoxia. Conclusion: (A) Morphological evaluation showed that cultures of CTEPH cells were endothelial. (B) Functional analysis revealed that these cells had reduced response, which characterizes proteostasis alterations, which became more evident when they underwent shear stress of high magnitude. Hypoxia reduced NO production, however without differentiating the cell groups studied

Critical illness associated muscle weakness and muscle dysfunction in intensive care unit (ICU) patients lead to severe morbidity and mortality as well as significant adverse effect on quality of life. Immobilization, mechanical ventilation, neuromuscular blocking agents, corticosteroids, and sepsis have been implicated as important risk factors, but the underlying molecular and cellular mechanisms remain unclear.  A unique porcine ICU model was employed to investigate the effect of these risk factors on the expression profiles, gene expression and contractile properties of limb and diaphragm muscle, in the early phase of ICU stay. This project has focused on unraveling the underlying molecular and cellular pathways or networks in response to ICU and critical illness interventions. Upregulation of heat shock proteins indicated to play a protective role despite number of differentially transcribed gene groups that would otherwise have a negative effect on muscle fiber structure and function in response to immobilization and mechanical ventilation.  Mechanical ventilation appears to play a critical role in development of diaphragmatic dysfunction. Impaired autophagy, chaperone expression and protein synthesis are indicated to play a pivotal role in exacerbating muscle weakness in response to the combined effect of risk factors in ICU. These results may be of therapeutic importance in alleviating critical illness associated muscle weakness.

Upon ageing, a progressive disruption of protein homeostasis often leads to extensive protein aggregation and neurodegeneration. It is therefore important to study at the proteome level the origins and consequences of such disruption, which so far have remained elusive. Addressing this problem has recently become possible by major advances in mass spectrometry-based (MS) proteomics, which allows the identifications and quantification of thousands of proteins in a variety of biological samples. In the first part of this thesis, I analyse proteome-wide MS data for the nematode worm C. elegans upon ageing, in wild type (WT), long-lived and short-lived mutant strains. By comparing the total abundance and the soluble abundance for nearly 4000 proteins, I provide extensive evidence that proteins are expressed in adult worms at levels close to their solubility limits. With the use of sequence-based prediction tools, I then identify specific physico-chemical properties associated with this age-related protein homeostasis impairment. The results that I obtained reveal that the total intracellular protein content remains constant, in spite of the fact that the proteome undergoes wide remodeling upon ageing, resulting into severe protein homeostasis disruption and widespread protein aggregation. These results suggest a protein-dependent decrease in solubility associated with the protein homeostasis failure. In the second part of the thesis, I determine and classify potential interactions of misfolded protein oligomers with other proteins. This phenomenon is widely believed to give rise to cytotoxicity, although the mechanisms by which this happens are not fully understood. To address this question, I process and analyse MS data from structurally different oligomers (toxic type A and nontoxic type B) of the protein HypF-N, incubated in vitro with proteins extracted from murine cell cultures. I find that more than 2500 proteins are pulled down with the misfolded oligomers. These results indicate that the two types of oligomers interact with the same pool of proteins and differ only in the degree of binding. Functional annotation analysis on the groups reveals a preference of the oligomers to bind proteins in specific biological pathways and categories, including in particular mitochondrial membrane proteins, RNA-binding proteins and molecular chaperones. Overall, in this study I complement the powerful and high-throughput experimental approach of MS proteomics with bioinformatics analyses and prediction algorithms to define the physical, chemical and biological features of protein homeostasis disruption upon ageing and the interactome of misfolded oligomers.

La maladie de Huntington (MH) est une maladie neurodégénérative causée par une extension de répétitions du codon CAG dans le gène de la Huntingtine (Htt). Cette maladie est caractérisée par la mort des neurones striataux et la présence d’agrégats de Htt mutée (mHtt). De plus, au cours de la MH, les astrocytes, qui sont essentiels au bon fonctionnement neuronal, changent d’état et deviennent réactifs. La réactivité astrocytaire est caractérisée par des changements morphologiques et transcriptomiques mais l’impact fonctionnel de cette réactivité reste peu compris.Afin d’étudier le rôle des astrocytes réactifs dans la MH, nous avons utilisé des vecteurs viraux récemment développés par notre équipe, qui induisent ou bloquent la réactivité astrocytaire in vivo en ciblant la voie JAK2-STAT3. Nous avons montré que les astrocytes réactifs diminuent le nombre et la taille des agrégats de mHtt majoritairement présents dans les neurones. Ceci est associé à l’amélioration de plusieurs altérations neuronales observées dans ces modèles. Une analyse transcriptomique réalisée sur des astrocytes réactifs révèle des changements majeurs d’expression de gènes liés aux systèmes de protéostasie. De plus, l’activité du lysosome et du protéasome est augmentée dans les astrocytes réactifs de souris modèles de la MH. Nous montrons également que les astrocytes réactifs éliminent plus efficacement leurs propres agrégats de mHtt, suggérant qu’au cours de la MH, ces cellules pourraient dégrader plus efficacement la mHtt provenant des neurones. De plus, certaines protéines chaperonnes sont induites dans les astrocytes réactifs. En particulier, la co-chaperonne DNAJB1/Hsp40 est surexprimée dans les astrocytes réactifs et est retrouvée dans les exosomes isolés à partir de striata de souris MH. Des expériences de gain et perte de fonction suggèrent que cette chaperonne est impliquée dans les effets bénéfiques des astrocytes réactifs sur l’agrégation de la mHtt et l’état des neurones. Les astrocytes réactifs pourraient donc libérer des protéines anti-agrégantes qui favorise l’élimination de la mHtt dans les neurones.Notre étude montre que les astrocytes peuvent, en devenant réactifs au cours de la MH, acquérir des propriétés bénéfiques pour les neurones et favoriser, via un dialogue complexe avec les neurones, l’élimination des agrégats de mHtt. / Huntington’s disease (HD) is a hereditary neurodegenerative disease caused by an expansion of CAG codons in the Huntingtin gene. It is characterized by the death of striatal neurons and the presence of mutant Huntingtin (mHtt) aggregates. In pathological conditions, as in HD, astrocytes change and become reactive. Astrocyte reactivity is characterized by morphological and significant transcriptomic changes. Astrocytes are essential for the proper functioning of neurons but the functional changes associated with reactivity are still unclear.To better understand the roles played by reactive astrocytes in HD, we took advantage of our recently developed viral vectors that infect selectively astrocytes in vivo and either block or induce reactivity, through manipulation of the JAK2-STAT3 pathway. We used these vectors in two complementary mouse models of HD and found that reactive astrocytes decrease the number and the size of mHtt aggregates that mainly form in neurons. Reduced mHtt aggregation was associated with improvement of neuronal alterations observed in our mouse models of HD. A genome-wide transcriptomic analysis was performed on acutely sorted reactive astrocytes and revealed an enrichment in genes linked to proteolysis. Lysosomal and proteosomal activities were also increased in reactive astrocytes in HD mice. Moreover, we show that reactive astrocytes degrade more efficiently their own mHtt aggregates, suggesting that these cells could siphon mHtt away from neurons. Alternatively, several chaperones were induced in reactive astrocytes. In particular, the co-chaperone DNAJB1/Hsp40 was upregulated in reactive astrocytes and was present in exosomal fraction from HD mouse striatum. Loss and gain of function experiments suggest that this chaperone is involved in the beneficial effects of reactive astrocytes on mHtt aggregation and neuronal status. Therefore, reactive astrocytes could release anti-aggregation proteins that could promote mHtt clearance in neurons.Overall, our data show that astrocytes, by becoming reactive in HD, develop a protective response that involves complex bidirectional signaling with neurons to reduce mHtt aggregation.