Gestational diabetes (GDM) is a disorder of glucose metabolism arising for the first time in pregnancy and spontaneously receding after birth. The issue of GDM is very topical since, according to the latest update of diagnostic criteria, up to 17% of pregnant women is threatened by this disorder. The incidence of GDM correlates with the increasing prevalence of overweight/obesity and metabolic syndrome. It is proved that women who have had gestational diabetes have an enormously increased risk of developing type 2 diabetes mellitus (DM2T). The risk accosiated with a gestational diabetes pregnancy stretches beyond the host, and can affect the fetus both directly (e. g. macrosomia development), and epigenetically (increases susceptibility to obesity, DM2T development or cardiovascular disease). Significant influence on the development of GDM (or DM2T) is a body composition that is directly related to lifestyle (nutritional intake and physical activity) and genetic role i salso involved. Early intervention may help delay the risk of developing DM2T and other metabolic complications. In this diploma thesis we monitored metabolic profiles of glucose and lipids and body composition based on anthropometric examination and questionnaires of nutritional income and physical activity. For the complex...

Au cours du vieillissement, l’organisme subit de nombreuses altérations, dont une perte de masse et de fonction musculaire appelée sarcopénie. Ses causes sont multifactorielles. Elle est partiellement liée à une altération de la stimulation de la synthèse protéique musculaire post-prandiale, et certains facteurs tels que le stress oxydant, l’inflammation et la résistance à l’insuline, responsables de nombreux dysfonctionnements métaboliques, accélèrent ce phénomène. Or, ces dérégulations peuvent être induites par une alimentation trop riche en sucres ajoutés, caractéristique des habitudes alimentaires actuelles et qui pourrait donc accélérer le vieillissement. Pourtant, à ce jour, peu d'études ont étudié les effets combinés du vieillissement et d'un régime riche en sucres ajoutés, et à notre connaissance, aucune ne s’est intéressée à la sarcopénie. Ainsi, notre objectif au cours de cette thèse a été de déterminer si un régime riche en sucres ajoutés était capable d'accélérer la sarcopénie. Il était également intéressant d'étudier les effets combinés du vieillissement et de ce régime sur d'autres tissus qui semblent particulièrement exposés, le foie, et le cerveau. Enfin, nous avons également voulu analyser les effets préventifs d'un mélange de micronutriments à la fois in vivo et in vitro. Pour cela, des rats âgés de 16 mois ont été nourris durant 5 mois avec un régime contrôle ou un régime composé à 62% de saccharose, supplémenté ou non en rutine, vitamine A, vitamine E, vitamine D, zinc, et sélénium. En outre, nous avons également inclut un groupe de témoins adultes (8 mois), nourris avec un régime contrôle. Par ailleurs, les effets anti-inflammatoires des micronutriments ont été testés in vitro.Nous avons pu constater que le régime riche en saccharose a accéléré la perte de masse musculaire liée à l’âge en altérant la synthèse protéique musculaire post prandiale, vraisemblablement via l’altération de la sensibilité à l’insuline plutôt que par une augmentation du stress oxydant et de l'inflammation, qui ont été peu affectés par le régime. Il a également entraîné un gain de masse grasse et une augmentation marquée des triglycérides hépatiques et plasmatiques, qui pourraient en partie s’expliquer par une modification de l’activité des enzymes du métabolisme lipidique dans le foie. Au niveau cérébral, la surconsommation de fructose a entraîné une diminution de la concentration protéique qui ne semble pas due à un défaut de synthèse protéique. La supplémentation en micronutriments n’a que partiellement contrecarré les effets du saccharose puisqu’elle n’a pas eu d’effet sur la masse maigre mais a permis de limiter la prise de masse grasse, notamment en inhibant la lipogenèse hépatique. Elle a également restauré la synthèse protéique diminuée au cours du vieillissement dans le cerveau. In vitro, elle a permis de réduire l'inflammation induite expérimentalement.Ainsi, cette thèse a permis de montrer qu’un régime riche en sucres ajoutés accélère la sarcopénie chez le rat âgé mais entraîne également des altérations au niveau hépatique et cérébral. La prévention par les micronutriments testés reste malgré tout limitée. / With aging, several alterations occur, including a loss of muscle mass and function, called sarcopenia. Many factors are responsible for the development of sarcopenia, but some factors as inflammation, oxidative stress and insulin resistance, which have many deleterious effects during aging, can reduce meal-induced stimulation of muscle protein synthesis which was shown to partly explain age-related muscle mass loss. Those factors can be induced by a diet rich in added sugar, characteristic of current dietary habits. Although this kind of diet could accelerate aging features, little is known about combined effect of aging and high sugar diet, particularly on sarcopenia. Thus, the purpose of this work was to determine whether high chronic intake of added sugars could accelerate sarcopenia. We also interested in the combined effect of added sugars and aging on other exposed tissues: liver and brain. Finally, we assessed the preventive effects of a micronutrient supplementation both in vivo and in vitro.In order to do that, for 5 months, 16 month old rats were starch fed or sucrose fed (62% sucrose), with or without micronutrients supplementation (rutin, vitamin A, vitamin E, vitamin D, selenium and zinc). Additionally, an adult control group of 8 month old rats was included. Besides, anti-inflammatory effects of micronutrients were tested in vitro.We showed that high sucrose diet accelerated age-related muscle mass loss by impairing postprandial protein synthesis, likely through decreased insulin sensitivity since inflammation and oxidative stress were only slightly affected by high sucrose diet. This diet also resulted in fat mass gain and increased plasma and liver triglycerides, by modulating the activity of enzymes involved in liver lipid metabolism. In the brain, high sucrose consumption led to decreased protein concentration independently of protein synthesis alteration. Micronutrients supplementation only partially reversed high sucrose diet effects: it did not act on lean body mass but prevented fat mass gain, by inhibiting hepatic lipogenesis. It also restored brain protein synthesis, which was reduced by aging. In vitro, it reduced experimentally induced inflammation.Thus, this work showed that a high sucrose diet accelerates sarcopenia in old rats but also induces liver and brain alterations. Prevention by micronutrients remained limited.

Le rat Lou/C, issu de la souche Wistar, reste maigre tout au long de sa vie. Le but de ce travail était de caractériser la balance énergétique du rat Lou/C et d’établir quel(s) étai(en)t le(s) tissu(s) thermogène(s) impliqué(s) dans la dissipation de l’énergie alimentaire ingérée en excès. Si la quantité d’énergie ingérée, rapportée par unité de masse corporelle, n’était pas différente entre les deux souches de rats, la dépense énergétique du Lou/C était supérieure au repos, suite à un repas et lors de l’exercice physique. Le rat Lou/C montrait également une hyperactivité locomotrice spontanée volontaire bien supérieure à celle du Wistar. De façon inattendue, le tissu adipeux brun (BAT) des Lou/C était peu actif, comme l'ont montré des approches fonctionnelles in vivo, biochimiques in vitro ou moléculaires. L'absence d'activation du BAT du rat Lou/C n’était pas liée à une déficience du tissu puisqu’il était aisément activable par une exposition prolongée au froid. La forte activité physique spontanée du Lou/C ne s’accompagnait pas de l’activation de processus thermogènes particuliers des mitochondries isolées de BAT ou de muscle squelettique. En revanche, nous avons mis en évidence un mécanisme potentiel de découplage des oxydations phosphorylantes mitochondriales dans le foie des Lou/C. Contre toute attente, le rat Lou/C disposait de capacités de synthèse des acides gras équivalentes à celles du Wistar dans le foie et supérieures dans le tissu adipeux blanc avec de fortes capacités d’oxydation de ces substrats dans ces tissus, suggérant un possible cycle futile entre la synthèse des acides gras et leur oxydation dans le foie et le tissu adipeux blanc. Le rat Lou/C représente donc un modèle original de régulation de la balance énergétique qui n’est pas basé sur l’activité thermogène du BAT. Le muscle squelettique, le foie et le tissu adipeux blanc du Lou/C pourraient participer à un métabolisme actif des lipides et contribuer à la dissipation accrue de l’énergie ingérée en excès. / Lou/C rat, an inbred strain of Wistar origin, remains lean throughout life. Our study aimed to characterize the energy balance of Lou/C rats and determine the tissue(s) that could be implicated in the dissipation of excess energy intake. Food intake, expressed per unit body mass, was not different between the two strains of rats but resting metabolic rate, diet-induced thermogenesis and exercise-associated energy expenditure were higher in the Lou/C strain. Moreover, the spontaneous activity of Lou/C rats was amazingly higher than that of Wistar rats. Unexpectedly, the thermogenic brown adipose tissue (BAT) of Lou/C rats was not over-stimulated as demonstrated by functional in vivo, biochemical in vitro or molecular approaches. Nevertheless, Lou/C BAT was not deficient as it could easily be stimulated by prolonged cold exposure. The high spontaneous activity of Lou/C rats was not correlated with an activation of specific thermogenic processes in isolated mitochondria of BAT or skeletal muscle. However, oxidation and phosphorylation were partly uncoupled in liver mitochondria of Lou/C rats. Unexpectedly, Lou/C rats displayed similar capacities for fatty acid synthesis in liver but higher capacities in white adipose tissue than Wistar rats, in association with high capacities for oxidation of these substrates in these tissues. These results suggested a possible mechanism of futile cycling between fatty acid synthesis and oxidation in liver and white adipose tissue. Lou/C rats therefore represent an original model of regulation of energy balance that is not based on the thermogenic activity of BAT. Skeletal muscle, liver and white adipose tissue of Lou/C rats could contribute to a higher lipid metabolism and the dissipation of excess energy intake.

Le réticulum endoplasmique et la mitochondrie sont deux organites majeurs impliqués dans la régulation du métabolisme glucido-lipidique. Ces structures interagissent au niveau de points de contact étroits appelés Mitochondria-Associated Endoplasmique Reticulum Membranes (MAMs). Les MAMs sont une zone de communication et d’échanges, de lipides et de calcium entre autre, indispensables à l’activité des deux organites et au maintien de l’homéostasie cellulaire. Des connexions physiques sont assurées par l’interaction de protéines complémentaires, comme le canal anionique voltage-dépendant (VDAC)-1, la protéine chaperonne (Grp)-75 et le récepteur de l'inositol 1,4,5-triphosphate (IP3R)-1, constituant un complexe impliqué dans le transfert de calcium. D’autres acteurs comme les mitofusines 1 et 2 (MFN1/2) assurent également un rapprochement entre les deux organites et semblent jouer un rôle dans les échanges des lipides. Récemment, les MAMs sont apparues comme un nouveau carrefour de la signalisation de l’insuline dans le foie. Le monoxyde d’azote (NO) participe également au contrôle de la réponse à l’insuline hépatique et a une action spécifique sur la mitochondrie. Mes travaux de thèse ont montré que le NO à des concentrations physiologiques module les interactions entre le RE et la mitochondrie dans le foie et que son action sur les MAMs implique la voie de signalisation sGC/cGMP/PKG. J’ai également démontré que la modulation des MAMs par le NO semble jouer un rôle clé dans la régulation de la voie de signalisation à l’insuline (projet1). Par ailleurs, j’ai exploré l’importance des MAMs dans la régulation du métabolisme lipidique. Pour cela, j’ai modulé l’expression protéique de Grp75 et Mfn2 sur un modèle d’hépatocarcinome humain (Huh7). Mes résultats ont montré qu’une surexpression des deux protéines améliore les MAMs et la β-oxydation mitochondriale mais conduit à une accumulation intracellulaire de lipides. Ceci serait dû à un défaut de sécrétion des lipides dans les lipoprotéines VLDL et pourrait impliquer l’apparition d’un stress mitochondrial et une altération des échanges de phospholipides entre les deux organites (projet 2). Par conséquence mon travail confirme le rôle physiologique des MAMs et éclaire les mécanismes d’actions de cette plateforme cellulaire dans la régulation du métabolisme glucido-lipidique hépatique. A plus long terme ces connaissances participeront peut-être à l’identification de potentielles cibles thérapeutiques afin de prévenir la stéatose et la résistance à l’insuline hépatiques et leurs complications / The endoplasmic reticulum and mitochondria are two major organelles involved in the regulation of glucose and lipid metabolism. These structures interact at close contact points called Mitochondria-Associated Endoplasmic Reticulum Membranes (MAMs). MAMs constitute an area of communication and exchange, of lipids and calcium among others, essential for the activity of both organelles and the maintenance of cellular homeostasis. Physical connections are ensured by the interaction of complementary proteins, such as the voltage-dependent anionic channel (VDAC)-1, the chaperone protein (Grp)-75 and the inositol 1,4,5-triphosphate receptor (IP3R)-1, constituting a complex involved in calcium transfer. Other actors such as mitofusins 1 and 2 (MFN1/2) also connect the two organelles and are involved in lipid exchanges. Recently, MAMs have emerged as a new carrefour for insulin signaling in the liver. Nitric oxide (NO) also helps control the response to hepatic insulin and has a specific action on mitochondria. My thesis work showed that NO at physiological concentrations modulates the interactions between RE and mitochondria in the liver and that its action on MAMs involves the sGC/cGMP/PKG signalling pathway. I also demonstrated that NO modulation of MAMs plays a key role in regulating the insulin signaling pathway (project 1). In addition, I explored the importance of MAMs in the regulation of lipid metabolism. For that purpose, protein expression of Grp75 and Mfn2 was modulated in a human hepatocarcinoma model (Huh7). Results showed that overexpression of both proteins improves MAMs and mitochondrial β-oxidation but leads to intracellular lipid accumulation. This could be due to a defect in lipid secretion in VLDL lipoproteins and could imply the appearance of mitochondrial stress and an alteration of phospholipid exchanges between the two organelles (project 2). Consequently, my work confirms the physiological role of MAMs and sheds light on the mechanisms of action of this cellular platform in the regulation of glucose and lipid metabolism in the liver. In the longer term, this knowledge may contribute to the identification of potential therapeutic targets to prevent steatosis and hepatic insulin resistance and their complications

<p>Regulation of metabolism in mammalian cells is achieved through a complex interplay between cellular signaling, metabolic reactions, and transcriptional changes. The modeling of metabolic fluxes in a cell requires the knowledge of all these mechanisms, some of which may be unknown. A cybernetic approach provides a framework to model these complex interactions through the implicit accounting of such regulatory mechanisms, assuming a biological “goal”. The goal-oriented control policies of cybernetic models have been used to predict metabolic phenomena ranging from complex substrate uptake patterns and dynamic metabolic flux distributions to the behavior of gene knockout strains. The premise underlying the cybernetic framework is that the regulatory processes affecting metabolism can be mathematically formulated as a cybernetic objective through variables that constrain the network to achieve a specified biological “goal”. </p><p>Cybernetic theory builds on the perspective that regulation is organized towards achieving goals relevant to an organism’s survival or displaying a specific phenotype in response to a stimulus. While cybernetic models have been established by prior work carried out in bacterial systems, we show its applicability to more complex biological systems with a predefined goal. We have modeled eicosanoid, a well-characterized set of inflammatory lipids derived from arachidonic acid, metabolism in mouse bone marrow derived macrophage (BMDM) cells stimulated by Kdo2-Lipid A (KLA, a chemical analogue of Lipopolysaccharide found on the surface of bacterial cells) and adenosine triphosphate (ATP, a danger signal released in response to surrounding cell death) using cybernetic control variables. Here, the cybernetic goal is inflammation; the hallmark of inflammation is the expression of cytokines which act as autocrine signals to stimulate a pro-inflammatory response. Tumor necrosis factor (TNF)-α is an exemplary pro-inflammatory marker and can be designated as a cybernetic objective for modeling eicosanoid—prostaglandin (PG) and leukotriene (LK)—metabolism. Transcriptomic and lipidomic data for eicosanoid biosynthesis and conversion were obtained from the LIPID Maps database. We show that the cybernetic model captures the complex regulation of PG metabolism and provides a reliable description of PG formation using the treatment ATP stimulation. We then validated our model by predicting an independent data set, the PG response of KLA primed ATP stimulated BMDM cells.</p><p>The process of inflammation is mediated by the production of multiple cytokines, chemokines, and lipid mediators each of which contribute to specific individual objectives. For such complex processes in mammalian systems, a cybernetic objective based on a single protein/component may not be sufficient to capture all the biological processes thereby necessitating the use of multiple objectives. The choice of the objective function has been made by intuitive considerations in this thesis. If objectives are conjectured, an argument can be made for numerous alternatives. Since regulatory effects are estimated from unregulated kinetics, one encounters the risk of multiplicity in this regard giving rise to multiple models. The best model is of course that which is able to predict a comprehensive set of perturbations. Here, we have extended our above model to also capture the dynamics of LKs. We have used migration as a biological goal for LK using the chemoattractant CCL2 as a key representative molecule describing cell activation leading to an inflammatory response where a goal composed of multiple cybernetic objectives is warranted. Alternative model objectives included relating both branches of the eicosanoid metabolic network to the inflammatory cytokine TNF-α, as well as the simple maximization of all metabolic products such that each equally contributes to the inflammatory system outcome. We were again able to show that all three cybernetic objectives describing the LK and PG branches for eicosanoid metabolism capture the complex regulation and provide a reliable description of eicosanoid formation. We performed simulated drug and gene perturbation analyses on the system to identify differences between the models and propose additional experiments to select the best cybernetic model.</p><p>The advantage to using cybernetic modeling is in its ability to capture system behavior without the same level of detail required for these interactions as standard kinetic modeling. Given the complexity of mammalian systems, the cybernetic goal for mammalian cells may not be based solely on survival or growth but on specific context dependent cellular responses. In this thesis, we have laid the groundwork for the application of cybernetic modeling in complex mammalian systems through a specific example case of eicosanoid metabolism in BMDM cells, illustrated the case for multiple objectives, and highlighted the extensibility of the cybernetic framework to other complex biological systems.</p>

No description available.

<p dir="ltr">Cancer biological mechanisms are a vastly researched area in the field, yet they are not well understood in the various contexts in which cancer is found. Cancerous tumors often exist in harsh, stressful environments for normal cells, but cancer cells can thrive in these conditions. The tumor microenvironment (TME) typically has low oxygen levels (hypoxia), high acidity, and low nutrition. Exposure to the TME leads to many metabolic changes in the cells, enabling cancer to continue proliferating and migrating. However, these metabolic changes are not well understood, especially at the single-cell level. The ability to monitor cells in real time to determine the physical characteristics they undergo is critical to understanding the impact of these metabolic changes. Conventional methods focus on determining the genomic and proteomic changes in large numbers of cells, which may be overlooked if the changes are homogeneous across samples. In this work, we demonstrate the power of using multiple imaging techniques in combination with biochemical methods to visualize metabolic changes and determine the causes in various cancer cells under extreme hypoxia conditions.</p><p dir="ltr">The changes in the microtubule network that occur under hypoxia at the single-cell level are not widely researched. The use of confocal fluorescence microscopy can determine microtubule polymerization in conjunction with eGFP-transfected EB3, a protein that assists in microtubule polymerization. We have determined that hypoxic HeLa cells produce finger-like protrusions when exposed to hypoxia that help with cell migration and, ultimately, cancer cell metastasis. The formation of these protrusions is facilitated by localized mitochondria activities in the protrusions.</p><p dir="ltr">The metabolic changes in lipid droplets (LDs) under hypoxia at the single-cell level remain an elusive topic. The use of stimulated Raman spectroscopy (SRS) and coherent anti-Stokes Raman scattering (CARS) can determine the quantity and spatial-temporal distribution of LDs in cancer cells. We have found that LDs redistribute to the endoplasmic reticulum (ER) and increase in intensity in hypoxic MIA PaCa-2 and A549 cells. Time-lapse CARS microscopy revealed a release-accumulate process of these LDs on ER in hypoxia. We also studied the impact of carbon sources on LD formation and found that MIA PaCa2 cells prefer direct lipid uptake while glucose is also essential to reduce lipotoxicity. The use of hyperspectral stimulated Raman scattering (hSRS) also reveals that the content of the LDs changes to include less cholesteryl ester and a decrease in lipid saturation level.</p><p dir="ltr">Collectively, these findings shed new light on the understanding of cytoskeleton dynamics and lipid metabolism in hypoxic conditions. The discoveries made within this research would lead to better treatment strategies for effective treatment of hypoxia-resistant cancer cells.</p>

<p dir="ltr">Regulation of complex biological processes aims to achieve goals essential for an organism's survival or to exhibit specific phenotypes in response to stimuli. This regulation can occur at several levels, such as cellular metabolism, signaling pathways, gene transcription, mRNA translation into proteins, and post-translational modifications. Systems biology approaches can facilitate integrating mechanistic knowledge and high-throughput omics data to develop quantitative models that can help improve our understanding of regulations at various levels. However, computational modeling of biological processes is challenging due to the vast details of various processes with unknown mechanisms. The cybernetic modeling approach accounts for unknown control mechanisms by defining a biological goal that the system aims to optimize and subsequently mathematically formulates the cybernetic goal.</p><p dir="ltr">This thesis aims to develop a mathematical framework that integrates a cybernetic model with novel information-theoretic methods to study the inflammatory response in mammalian macrophage cells. The inflammatory response of the body is a protective mechanism that fights off infecting pathogens by inducing the production of immune signaling proteins called cytokines and chemokines, as well as specific lipids known as eicosanoids. However, excessive levels of cytokines and eicosanoids may result in chronic inflammatory diseases such as hyper-inflammation syndrome, COVID-19, and asthma. Only a few studies have focused on quantitative modeling of the role of lipid metabolism in inflammation. One key lipid is Arachidonic acid (AA), which during inflammation, gets converted into inflammatory lipids called eicosanoids. Previous models utilize Michaelis-Menten kinetics or assume the linear form and can, at best, include control at the gene expression level only. The distinguishing feature of a cybernetic model is that by defining a cybernetic objective, it can account for control at multiple levels, including transcriptional, translational, and post-translational modifications.</p><p dir="ltr">The following paragraphs address a specific research problem, outline the approaches to investigate it, and summarize the key findings.</p><p dir="ltr">First, we studied the cellular response to inflammatory stimuli that produce eicosanoids—prostanoids (PRs) and leukotrienes (LTs)—and signaling molecules—cytokines and chemokines—by macrophages. A few studies suggest that targeting eicosanoid metabolism could be a promising new approach to regulating cytokine storm in COVID-19 infection. We developed a cybernetic model combined with novel information-theoretic approaches to study the integrated system of eicosanoids and cytokines. Our cybernetic model formulates a cybernetic goal, which requires the causal relationship between the eicosanoid and cytokine secretion processes; however, this causal relationship is unknown due to insufficient mechanistic information. We developed novel information-theoretic approaches (discussed later in detail) to understand the causality between eicosanoids and cytokines. The causality result from information theory suggests that Arachidonic acid (AA) may be the cause for initiating the secretion of cytokine TNF. The model captured the data for all experimental conditions, including control, treatment with Adenosine triphosphate (ATP), (3-deoxy-d-manno-octulosonic acid) 2-lipid A (Kdo2-Lipid A, abbreviated as KLA), and a combined treatment of ATP and KLA in mouse bone marrow-derived macrophages (BMDM). The model explains the dynamics of metabolites for all experimental conditions, validating the hypothesis. It also enhanced our understanding of enzyme dynamics by predicting their profiles. The results indicated that the dominant metabolites are PGD2 (a PR) and LTB4 (an LT), aligning with their corresponding known prominent biological roles during inflammation. Based on the causality and cybernetic model result and using heuristic arguments, we also infer that AA overproduction can lead to increased secretion of cytokines/chemokines. Consequently, a potential clinical implication of this study is that modulating eicosanoid levels could lower TNFα expression, suggesting eicosanoids could be a viable strategy for managing hyperinflammation.</p><p dir="ltr">Second, we studied the dynamics of the anti-inflammatory lipid mediators from eicosapentaenoic acid (EPA) metabolism, which can be beneficial in reducing the severity of diseases such as cancer and cardiovascular effects and promoting visual and neurological development. This study employed a cybernetic model to study the enzyme competition between AA and EPA metabolism in murine macrophages. The cybernetic model adequately captured the experimental data for control non-supplemented and EPA-supplemented conditions in RAW 264.7 macrophages. The cybernetic variables provide insights into the competition between AA and EPA for the COX enzyme. Predictions from our model suggest that the system undergoes a switch from a predominantly pro-inflammatory state in control to an anti-inflammatory state with EPA supplementation. A potential application of this study is utilizing the model estimation of the ratio of concentrations required for the switch to occur as 2.2, which aligns with the experimental observations and falls within the recommended range of 1-5 needed to promote anti-inflammatory response.</p><p dir="ltr">Third, we focused on predicting novel causal connections between AA and cytokines using time series analysis as mechanistic information connecting AA and cytokines is unknown. In this work, we developed Time delay Renyi Symbolic Transfer Entropy (TDRSTE), a novel model-free information-theoretic metric. We computed it from high-throughput omics datasets for bivariate non-stationary time series to quantify causal time delays. The TDRSTE method adequately estimated time delay for the synthetic dataset, captured causality for the real-world biological dataset of the AA metabolic network with a prediction accuracy of 80.6%, where it correctly identified 25 out of 31 connections, and detected novel connections between non-stationary lipidomics and transcriptomics profiles for eicosanoids and cytokines, respectively. The results indicate that AA may initiate the secretion of cytokines like TNFα, IL1α, IL18, and IL10. Conversely, cytokines such as IL6 and IL1β may have an early causal impact on AA. These findings suggest a potential causal link between AA and cytokines, paving the way for further exploration with more extensive experimental data in future investigations.</p><p dir="ltr">This thesis develops a theoretical framework that integrates the cybernetic modeling technique with novel information-theoretic approaches to study the inflammatory response in mouse macrophages. As described in previous paragraphs, the success of the cybernetic framework in capturing the dynamic behavior of multiple processes serves to validate the idea that regulation is driven toward achieving cellular goals. The cybernetic framework can be applied to better understand the mechanisms underlying the normal and diseased states and to predict the behavior of the system given a perturbation.</p>

[ES] El equilibrio de la homeostasis de proteínas es esencial para asegurar la funcionalidad celular. La expresión de proteínas propensas a plegarse mal induce la formación de agregados tóxicos que alteran el correcto funcionamiento de estos sistemas de control, lo que conduce a un desequilibrio de la homeostasis de proteínas, y por consiguiente a una afectación patológica. Varias enfermedades neurodegenerativas, como la enfermedad de Huntington (EH), Parkinson, Alzheimer, entre otras, tienen en común esta marca patológica molecular. Especialmente, la EH pertenece a un grupo de patologías producidas por proteínas que contienen expansiones de poliQs (varias ataxias espinocerebelosas, la atrofia muscular bulbar y espinal y la atrofia dentatorubro-pálidoluisiana), que hacen que estos péptidos sean propensos a la agregación, y causen los problemas que hemos descrito. A pesar de que estas enfermedades son genéticas, y se conoce su causa molecular, se cree que la presencia de variantes alélicas en otros genes puede exacerbar o ralentizar la agregación de proteínas con poliQs. Por tanto, la identificación de estos genes permitirá profundizar en los mecanismos moduladores de la dinámica de agregación de poliQs e identificar dianas terapéuticas frente a la toxicidad de poliQs. También es ampliamente conocido que el ARN que porta tripletes CAG tiene carácter patogénico. En este trabajo hemos desarrollado modelos, empleando C. elegans, que muestran signos indirectos de que están expresando transcritos CAG patogénicos, puesto que los tejidos diana están alterados. Usamos uno de estos modelos, que perturba la función de las neuronas GABAérgicas del gusano, para realizar un cribado de 85 compuestos farmacológicos, que nos llevó a identificar cuatro compuestos que reducían los defectos motores en estos animales. Además de poliQs y transcritos CAG, también se producen péptidos derivados de una traducción no canónica, conocida como traducción RAN. En relación a esto, hemos profundizado en la identificación y modelización de estos péptidos en C. elegans mediante la expresión de expansiones CAG fusionadas a proteínas fluorescentes para su detección in vivo. Además hemos empleado otros modelos ya existentes, para caracterizar potenciales dianas terapéuticas, como AMPK, la cual puede ser activada por diferentes sustancias. Sin embargo, algunas sustancias, como la metformina o el salicilato, son pleiotrópicas. Por tanto, hemos caracterizado la activación sinérgica de AMPK, mediante metformina y salicilato, para reducir el estrés por agregados de poliQs, con lo que podríamos evitar que otras dianas resulten activadas. Por último, hemos demostrado que este tratamiento sinérgico reduce la toxicidad inducida por la α -sinucleína implicada en la enfermedad de Parkinson. Por otro lado, hemos caracterizado en C. elegans un nuevo alelo que potencia la la agregación de poliQs, vlt10, en el gen unc-1. Nuestros resultados sugieren que la mutación unc-1(vlt10) perturba la sinapsis eléctrica entre las neuronas sensoriales IL2 y ASJ, induciendo un exceso de señalización hormonal que requiere la función de la sulfotransferasa SSU-1. También hemos demostrado que la diana de esta señal es un receptor nuclear llamado NHR-1. En este mismo capítulo, hemos identificado otra ruta de señalización hormonal, mediada por otro receptor nuclear (DAF-12), que tiene un papel protector. Se desconoce qué hormona modula la actividad de NHR-1. Sin embargo, hemos identificado que algunos de los genes regulados por NHR-1 están relacionados con el metabolismo lipídico. Además, hemos observado que la disrupción de unc-1 induce la acumulación de lípidos en los gusanos, pero a la vez estos animales contienen menos ácidos grasos totales. Esto sugiere que las grasas juegan un papel fundamental en la modulación de la agregación de poliQs, y quizás señala posibles dianas terapéuticas contra enfermedades causadas / [CA] L'equilibri de l'homeòstasi de proteïnes és essencial per a assegurar la funcionalitat cel·lular. L'expressió de proteïnes propenses a plegar-se malament indueix la formació d'agregats tòxics i altera el correcte funcionament dels sistemes de control, cosa que condueix a un desequilibri de l'homeòstasi de proteïnes, i per consegüent a una afectació patològica. Diverses malalties neurodegeneratives, com la malaltia de Huntington (MH), Parkinson i Alzheimer, entre altres, tenen en comú aquesta signatura patològica. Especialment, la MH pertany a un grup de patologies produïdes per proteïnes que contenen expansions de poliQs (s'inclouen diverses atàxies espinocerebel·loses 1, 2, 3, 6, 7 i 17, l'atròfia muscular bulbar i espinal, i l'atròfia dentatorúbrica-pàl·lidaluisiana), que fan que aquests pèptids siguen propensos a l'agregació, i causen els problemes que hem descrit. Malgrat que aquestes malalties són genètiques i es coneix la seva causa molecular, es creu que la presència de variants al·lèliques en gens pot incrementar o alentir l'agregació de proteïnes amb poliQs. Per tant, la identificació de gens modificadors permet aprofundir en els mecanismes moduladors de la dinàmica d'agregació de poliQs ens permet trobar dianes terapèutiques enfront de la toxicitat de poliQs. També és àmpliament conegut que l'ARN que contenen expansions CAG té caràcter patogènic. Per tant, hem desenvolupat models, utilitzant C. elegans, en els quals es mostren signes indirectes que expressen transcrits patogènics, ja que els teixits diana revelen una funcionalitat alterada. Utilitzant aquests models, que alteren la funció de les neurones GABAèrgiques del cuc, hem realitzat un cribratge de 85 compostos farmacològics, que ens va portar a identificar quatre compostos que reduïen els defectes motors en aquests animals. A més de poliQs i l'ARN que conté expansions de CAG, es produeixen pèptids derivats d'una traducció no canònica, coneguda com a traducció RAN. En relació amb això, hem aprofundit en la identificació i modelització d'aquests pèptids en C. elegans mitjançant l'expressió d'expansions CAG fusionades a proteïnes fluorescents per a la seva detecció in vivo. A més hem emprat models ja generats, per a caracteritzar potencials dianes terapèutiques, com AMPK puga ser activat per diversos fàrmacs. No obstant això, alguns activadors, com la metformina o el salicilat, són substàncies pleiotròpiques. Per tant, hem caracteritzat l'activació sinèrgic de AMPK, mitjançant metformina i salicilat, per a reduir l'estrés induït per agregats de poliQs i s'evita l'activació de dianes no desitjades. I finalment, hem demostrat que aquest tractament sinèrgic podria ser utilitzat per a reduir proteïnes tòxiques com la α-sinucleína, causant de la malaltia de Parkinson. D'altra banda, hem caracteritzat un nou modulador de l'agregació de poliQs, vlt10, en el gen unc-1, que produeix un augment d'agregació de poliQs. Els nostres resultats suggereixen que la mutació unc-1(vlt10) pertorba la sinapsi elèctrica entre les neurones sensorials IL2 i ASJ, induint un excés de senyalització hormonal que requereix la funció de la sulfotransferasa SSU-1. També hem demostrat que la diana d'aquest senyal és un receptor nuclear anomenat NHR-1. En el mateix capítol, hem identificat una altra ruta de senyalització hormonal, mitjançada per un altre receptor nuclear (DAF-12), que té un paper protector. Es desconeix l'hormona que modula l'activitat de NHR-1. No obstant això, hem identificat que alguns del genes regulats per NHR-1 estan relacionats amb el metabolisme lipídic. els resultats han sigut confirmats. També hem observat que la disrupció de unc-1 indueix l'acumulació de lípids en els cucs, però simultàniament aquests animals contenen menys àcids grassos totals. Això suggereix que els greixos juguen un paper fonamental en la modulació de l'agregació de poliQs, i potser assenyala / [EN] The balance of protein homeostasis is essential to ensure cellular functionality. The expression of proteins that are prone to misfolding induces the formation of toxic aggregates, which leads to an imbalance in protein homeostasis and pathological consequences. Several neurodegenerative diseases, such as Huntington disease (HD), Parkinson, Alzheimer, among others, have this molecular pathological mark in common. HD belongs to a group of pathologies produced by proteins that contain expansions of polyQs (several spinocerebellar ataxias 1, 2, 3, 6, 7 and 17, bulbar and spinal muscular atrophy and the dentatorubral-pallidoluysian atrophy), which make these peptides prone to aggregation, and cause the problems described above. Although these diseases are genetic, and their molecular cause is known, it is believed that the presence of allelic variants in other genes can exacerbate or slow the polyQ aggregation. Therefore, the identification of these genes will allow delving into the modulating mechanisms of the polyQ aggregation dynamics and find therapeutic targets against the polyQ toxicity. In addition, RNA that contains CAG triplets is pathogenic. In this work we have developed models using C. elegans that show indirect signs of pathogenic transcript expression since altered functionality was observed in target tissues. We use a model, which disturbs the function of the worm's GABAergic neurons, to screen for 85 pharmacological compounds, which led us to identify four compounds that reduced motor defects in these animals. In addition to polyQs and CAG transcripts, also are produced peptides derived from a non-canonical translation, known as RAN translation. In this regard, we have delved into the identification and modelling of these peptides in C. elegans through the expression of CAG expansions fused to fluorescent proteins to investigate them in vivo. Furthermore, we have used models previously generated to characterize potential therapeutic targets, such as AMPK. This enzyme can be activated using different compounds. However, some activators, such as metformin or salicylate, are pleiotropic substances. Therefore, in the second chapter of this thesis, we have characterised the synergistic activation of AMPK, using metformin and salicylate, to reduce the stress induced by polyQ aggregates and prevent possible unwanted targets from being activated. Finally, we have shown that this synergistic treatment could be used to reduce α-synuclein toxicity, which is involved in Parkinson disease. On the other hand, we have characterised a new allele that enhances polyQ aggregation, vlt10, in the unc-1 gene. Our results suggest that the unc-1(vlt10) mutation disturbs the electrical synapse between sensory neurons IL2 and ASJ, inducing an excess of hormonal signalling that requires the function of the sulfotransferase SSU-1. We have also shown that the target of this signal is the nuclear receptor NHR-1. In the same chapter, we have identified another hormonal signalling pathway, mediated by another nuclear receptor (DAF-12), which has a protective role. It is unknown which hormone modulates the activity of NHR-1. However, we have identified several genes that regulate lipid metabolism and whose expression could be modulated by NHR-1. In addition, we have observed that the disruption of unc-1 induces the accumulation of lipids in worms, but at the same time these animals contain less total fatty acids. Thus, our results suggest that the metabolism of fats play a key role in modulating polyQs aggregation, highlighting potential therapeutic targets against diseases caused by aggregation-prone proteins. / Gómez Escribano, AP. (2021). Modelos de toxicidad inducidos por microsatélites CAG y caracterización de dianas terapéuticas en C. elegans [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/166783

INTRODUÇÃO: A esteato-hepatite não alcóolica (NASH) é considerada problema de saúde pública, dada sua crescente incidência e seu possível papel na carcinogênese hepato-celular. Terapias atuais envolvem alterações de dieta e estilo de vida, mas têm seu resultado prejudicado pela baixa aderência dos pacientes. Abordagens farmacológicas ainda são precárias. Uma grande dificuldade no manejo de NASH reside no limitado entendimento de sua fisiopatologia, que parece envolver complexas alterações metabólicas e inflamatórias. Ácidos graxos poli-insaturados ômega-3 (AGPIs n-3) são reconhecidos por suas propriedades moduladoras do metabolismo lipídico e da inflamação, e estão diminuídos em pacientes com NASH. O uso clínico de AGPIs n-3 tem mostrado benefício no controle da esteatose e na produção de marcadores da resposta metabólica e inflamatória em NASH, embora com algumas observações contraditórias. A compreensão de mecanismos moleculares modulados por AGPIs n-3 em NASH podem ser úteis para identificar alvos moleculares que auxiliem no desenho de intervenção farmacológica efetiva. Nesse sentido, ciências ômicas são particularmente úteis para a compreensão de mecanismos moleculares com alto valor translacional para a prática clínica e podem contribuir para a identificação desses alvos. OBJETIVO: O presente estudo avaliou a resposta proteômica hepática e lipidômica plasmática de pacientes com NASH perante o tratamento com AGPIs n-3. MÉTODO: As avaliações proteômicas e lipidômicas foram desenvolvidas por espectometria de massas e/ou cromatografia gasosa em amostras de biópsias hepáticas e plasma coletadas de pacientes envolvidos em estudo preliminar, realizado no Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo. O referido estudo envolveu pacientes adultos, de ambos os sexos e com diagnóstico de NASH tratados diariamente, durante 6 meses, com 3 cápsulas contendo mistura de óleo de linhaça e óleo de peixe [0,315 g AGPIs: sendo 0,065 g de ácido eicosapentaenoico (EPA), 0,050 g de docosahexaenoico (DHA) e 0,2 g alfa linolênico (ALA) por cápsula]. Pacientes, após o tratamento com AGPIs n-3, que apresentaram altas concentrações plasmáticas de ALA e/ou DHA e/ou baixas de ácido araquidônico (AA) mostraram melhora parcial das alterações de histologia hepática. No presente estudo, avaliamos as vias proteômicas e marcadores lipidômicos resultantes do tratamento com AGPIs n-3. Isto foi feito por meio da comparação, antes (grupo AT) e depois do tratamento (grupo DT), de pools de tecido hepático (análise por interactoma) e amostras de plasma (OPLS-DA). RESULTADOS: Foram identificadas proteínas hepáticas, exclusivamente e/ou alteradamente expressas, no grupo DT, relacionadas com vias de matriz celular, metabolismo lipídico, de estresse oxidativo, e de retículo endoplasmático e respiração celular. Com excessão da via de matriz celular, a análise do interactoma revelou alteração funcional significativa das vias moduladas por essas proteínas. Em conjunto, essas alterações foram sugestivas de diminuição de lipotoxicidade, estresse oxidativo e respiração anaeróbia, e aumento de respiração aeróbia após tratamento com AGPIs n-3. Estas modificações são marcadores potenciais de melhora de função de retículo endoplasmático e mitocondrial. Em adição, após o tratamento com AGPIs n-3, o perfil lipidômico plasmático mostrou-se alterado com significativo aumento de glicerofosfolípides, ALA e EPA, e diminuição de ácido araquidônico (n-6) e da razão AGPIs n-6/n-3. Estes dados são concordantes com potencial melhora das funções de retículo endoplasmático e mitocondriais. CONCLUSÃO: O tratamento com AGPIs n-3 em pacientes com NASH influenciou favoravelmente o perfil proteômico hepático e lipidômico sistêmico. Em conjunto, essas alterações sugerem melhora da função de retículo endoplasmático e mitocondrial, com potencial impacto na homeostase celular, por meio da modulação de diferentes vias biológicas / INTRODUCTION: Non-alcoholic steatohepatitis (NASH) is considered a public health problem, given its increasing incidence and its possible role in hepatocellular carcinogenesis. Current therapies involve diet and lifestyle changes, but its applicability suffers from low patients adherence. Pharmacological approaches are still missing. A main difficulty in the NASH management lies in the limited understanding of its pathophysiology, which seems to involve complex metabolic and inflammatory disturbances. Omega-3 polyunsaturated fatty acids (n-3 PUFAs) are recognized for its modulatory properties on lipid metabolism and inflammation and are decreased in patients with NASH. The clinical use of these PUFAs has shown benefit in controlling steatosis and the production of metabolic and inflammatory response markers in NASH, despite some conflicting reports. Understanding mechanisms modulated by n-3 PUFAs in NASH may be useful for identifying molecular targets that could assist in the design of effective pharmacologic interventions. In this sense, omics sciences are particularly useful for understanding molecular mechanisms with high translational value to clinical practice and may contribute to the identification of these targets. AIM: This study evaluated the liver proteomic and plasma lipidomics responses of patients with NASH towards treatment with n-3 PUFAs. METHODS: The proteomic and lipidomic evaluations were studied by mass spectrometry and / or gas chromatography in samples from liver biopsies and plasma collected from patients enrolled in a preliminary clinical trial of the Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo. This study involved adult patients of both sexes diagnosed with NASH treated daily for 6 months, with 3 capsules containing a mixture of linseed and fish oils [0.315 g PUFAs: 0.065 g eicosapentaenoic acid (EPA) , 0.050 g docosahexaenoic (DHA) and 0.2 g alpha linolenic acid (ALA) per capsule]. Patients, after treatment with n-3 PUFAs, with higher concentrations of ALA and DHA and lower arachidonic acid (AA) showed improvement of liver histology alterations. In the present study we evaluated the proteomics pathways and lipidomics markers resulted from treatment with PUFAs n-3. This was performed by comparing, before (BT group) and after (AT group) treatment, liver tissue pools (analysis interactome) and plasma samples (OPLS-DA). RESULTS: It was identified, in a way exclusive and altered, the expressed liver proteins in AT group, related to pathways of cellular matrix, lipid metabolism, oxidative and endoplasmic reticulum stress and cellular respiration. With the exception of cell matrix, the analysis of the interactome revealed substantial functional alterations of the pathways modulated by these proteins. Together, these changes were suggestive of decreased lipotoxicity, oxidative stress and anaerobic respiration and increased aerobic respiration following treatment with PUFAs n-3. These modifications are potential markers of endoplasmic reticulum and mitochondrial functions improvement. In addition, after treatment with n-3 PUFAs, the lipidomics profile was modified, with significant increase in glycerophospholipids, ALA and EPA and decrease of arachidonic acid (AA) and n-6/n-3 AGPIs ratio. These findings are concordant with potential improvement of reticulum endoplasmic and mitochondrial functions. CONCLUSION: In patients with NASH the treatment with n-3 PUFAs favorably influenced hepatic proteomic and systemic lipidomics profiles. Together, these changes suggest improved endoplasmic reticulum and mitochondrial functions, with potential impact on cellular homeostasis through the modulation of different biological pathways