Obesity is associated with reduced skeletal muscle insulin sensitivity, a major risk factor for development of type II diabetes. These metabolic diseases are commonly associated with an accumulation of mitochondrial dysfunction, which is speculated to contribute toward insulin resistance. High-fat diets reduce human skeletal muscle insulin sensitivity and mitochondrial function. Conversely, endurance training increases insulin sensitivity and enhances mitochondrial performance. Recent evidence in mice has found that central mechanisms of mitochondrial quality control, autophagy and mitophagy, may be suppressed in response to excess fat intake, but upregulated following endurance exercise training. These data may provide a mechanism for dietary and exercise-mediated regulation of mitochondrial quality and metabolic function. The current study investigated the impact of an acute high-fat diet on skeletal muscle autophagy and mitophagy in sedentary, healthy, non-obese college age males'. The expression of skeletal muscle autophagy and mitophagy protein markers were analyzed in response to a high-fat meal before and after a 5-day high-fat diet. Next, we examined the differences in skeletal muscle autophagy and mitophagy protein markers, and associations with skeletal muscle metabolic flexibility between endurance-trained male runners' and sedentary, healthy, non-obese males' following an overnight fast and in response to a high-fat meal. Autophagy markers' indicated reduced autophagy activity in response to a high-fat meal and following a high-fat diet, which exacerbated the high-fat meal response. However, these data could not be confirmed due to methodological limitations. Mitophagy markers were not significantly affected by the high-fat meal or diet. There were no significant differences in the expression of autophagy protein markers between endurance-trained and sedentary groups', but mitophagy markers were significantly elevated in endurance-trained runners'. Metabolic flexibility was not significantly different between groups' following an overnight fast or in response to a high-fat meal, and was not associated with the expression of autophagy and mitophagy protein markers. In conclusion, autophagy may be suppressed by a 5-day high-fat diet, but further analysis is required for confirmation. Endurance-trained male runners show increased markers of mitophagy, which were not associated with improved metabolic flexibility while fasted or following a high-fat meal. / Ph. D.

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No description available.

The diverse outcomes of ubiquitination primarily relate to the flexibility of ubiquitin in forming homo- or heterotypic chains on each of its seven lysine residues which in turn stimulate distinct downstream signaling pathways. These ubiquitin signals must be selectively initiated on the substrate protein and subsequently decoded to facilitate the desired cellular function. These initiation and decoding steps often involve additional post-translational modifications and ubiquitin receptor proteins, but the enzymes and ubiquitin chains involved for many ubiquitinated substrates are not clear. Here, I have explored the initiation and decoding of ubiquitin signals, focusing on lysine-11 (K11) linked polyubiquitin chains and their role in protein degradation. I established in vitro assays to understand how K11-chains are decoded and whether these chains act as a signal for proteasome-mediated degradation. Pure homotypic K11-chains did not bind the proteasome or its associated ubiquitin binding proteins, but did bind to the mitophagy ubiquitin receptors, MyosinVI and TAX1BP1. Heterotypic K11/K48 linkages not only bound the proteasome but also stimulated degradation of the cell cycle substrate, cyclin B1. To further explore the functions of K11-chains I focused on the hypoxia inducible transcription factor (HIF) pathway, as K11-ubiquitination had been implicated in proteasome-independent degradation of the transcription factor. I established an in vitro assay to initiate HIF ubiquitination, via prolyl hydroxylation, and determine the type of ubiquitin chains involved. Recombinant HIF isoforms were rapidly hydroxylated when incubated with cell extracts. Moreover, the levels of iron and small molecule metabolites within the lysates regulated HIF hydroxylation. However, this hydroxylation was insufficient to reproducibly promote HIF ubiquitination or determine the ubiquitin chains involved. While the nature of the polyubiquitin chains formed in the HIF pathway remain elusive, my studies identify distinct roles for homotypic and heterotypic K11-polyubiquitination in proteasome-mediated degradation.

Le gène gec1/gabarapl1 (glandular epithelial cell 1/gabarap like 1), identifié au sein de notre équipe, est un gène apparenté à la famille atg8 (autophagy related gene 8) et  la  sous-­‐famille  gabarap  (GABAA  receptor  associated  protein)  incluant  les  gènes  gabarap, gabarapl1, gabarapl2 et gabarapl3. Les protéines codées par ces gènes présentent de très fortes identités de séquences et des structures similaires. Le gène gabarapl1 est exprimé préférentiellement dans le SNC dans lequel il est le transcrit de la famille atg8 le plus fortement exprimé. Des études fonctionnelles ont démontré que la protéine GABARAPL1 intervient dans le trafic intracellulaire de récepteurs, et plus particulièrement  du  récepteur  GABAA  et  du  récepteur  aux  κ-­‐opioïdes,  via  son  interaction avec les microtubules. Cependant, le rôle de cette protéine ne se limite probablement  pas  au  seul  transport  de  ces  récepteurs.  Notre  équipe  a  d’ailleurs  récemment démontré que GABARAPL1 est impliquée dans le processus d’autophagie, un mécanisme de dégradation cellulaire. Dans  le  cadre  de  ma  thèse,  j’ai  eu  trois  objectifs :  (1)  l’étude  de  la  spécificité  d’anticorps anti-­‐GABARAPL1 commerciaux disponibles, (2) la cartographie détaillée de l’expression de GABARAPL1 dans le cerveau murin et (3) l’étude de la surexpression de GABARAPL1 dans un modèle neuronal in vitro en conditions de stress mitochondriaux. Etant donné la forte homologie entre GABARAPL1 et GABARAP, aucun anticorps spécifique  commercial  n’était  disponible  lorsque  nous  avons  débuté  mon  projet  de  recherche. Nous avons donc, dans un premier temps, étudié la spécificité des différents anticorps commerciaux anti-­‐GABARAPL1 disponibles et identifié un anticorps capable de détecter de façon spécifique cette protéine in vitro et in vivo. Grâce  à  cet  anticorps  spécifique,  nous  avons  ensuite  entrepris  l’étude  de  l’expression in vivo de la protéine GABARAPL1 dans le SNC de souris chez l’adulte et au cours du développement embryonnaire. Nous avons ainsi démontré que GABARAPL1 est exprimée dans les neurones immatures et les fibres neuronales à partir du 11e jour de  développement  et  son  expression  augmente  progressivement  jusqu’à  un  taux  maximal observé chez l’adulte. Chez l’adulte, GABARAPL1 est exprimée uniquement dans  les  neurones  et  plus  particulièrement  dans  ceux  impliqués  dans  les  fonctions  motrices et neuroendocrines. De plus, nous avons noté que le marquage ponctiforme de  GABARAPL1  co-­‐localise  partiellement  avec  p62  dans  des  cultures  neuronales  primaires, confirmant son association aux vésicules autophagiques in vivo. Pour caractériser la fonction cellulaire de GABARAPL1, nous avons surexprimé cette protéine dans des cellules neuronales SK-­‐N-­‐BE(2). L’étude de ce nouveau modèle neuronal a montré que la surexpression de DsRed-­‐GABARAPL1 semble potentialiser la réponse  autophagique  des  cellules,  ce  qui  permet  une  induction  plus  précoce  suite  à  des traitements induisant l’autophagie. De plus, la surexpression de GABARAPL1 inhibe la mort des cellules soumises à des stress ciblant les mitochondries (CCCP), ce qui  suggère  que  GABARAPL1  pourrait  protéger  les  neurones  contre  certains  stress  aggravant la progression des maladies neurodégénératives. L’ensemble  de  ces  travaux  a  permis  d’identifier  un  outil  spécifique  à  l’immunodétection de GABARAPL1, de cartographier son expression dans le SNC murin au cours du développement et chez l’adulte et finalement, de démontrer un rôle protecteur  de  GABARAPL1  contre  la  mort  neuronale  induite  par  un  stress  mitochondrial. / The gec1/gabarapl1 gene (glandular epithelial cell 1/gabarap like 1), identified within our team, is a gene related to the atg8 (autophagy related gene 8) family and the gabarap  (GABAA  receptor-­‐associated  protein)  subfamily  of  genes  including  gabarap,  gabarapl1, gabarapl2 and gabarapl3. The protein products of these genes present a very  strong  sequence  identity  and  are  structurally  similar.  The  gabarapl1  gene  is  expressed preferentially in the central nervous system, in which it is the most highly expressed  transcript  of  the  atg8  family.  Functional  studies  have  shown  that  the  GABARAPL1 protein is involved in intracellular trafficking of receptors, in particular the  GABAA  receptor  and  the  κ-­‐opioid  receptor,  via  its  interaction  with  cytoskeletal  elements. The role of this protein, however, is clearly not limited to the transport. Our team has also recently shown that GABARAPL1 is involved in the autophagic process, a cellular degradation mechanism. My  thesis  objectives  were  three-­‐tiered:  (1)  the  study  of  the  specificity  of  anti-­‐GABARAPL1 antibodies, (2) the detailed mapping of GABARAPL1 expression in the mouse  brain  and  (3)  the  study  of  GABARAPL1  overexpression  under  conditions  of  mitochondrial stress in an in vitro neuronal model. Given the high homology between GABARAPL1 and GABARAP, no commercially available  specific  antibody  was  available  when  we  started  my  research  project.  As  such, we conducted a study on the specificity of different commercially available anti-­‐GABARAPL1 antibodies and identified an antibody that specifically recognized this protein in vitro and in vivo experiments. With this specific antibody, we then undertook a study of the in vivo expression of the GABARAPL1 protein in the adult mouse central nervous system and throughout embryonic development. In this study, we demonstrate that GABARAPL1 is expressed in immature neurons and neural fibers in the embryo from the 11th day of embryonic development and its expression gradually increases to a maximum in adults. In adults, GABARAPL1 is expressed in neurons, in particular, in those involved in motor control and  neuroendocrine  functions.  The  punctate  labeling  of  GABARAPL1  partially  co-­‐localizes with p62 in primary neuronal cultures, confirming its association with autophagic vesicles in vivo. To  characterize  the  cellular  function  of  GABARAPL1,  we  overexpressed  this  protein in neuronal SK-­‐N-­‐BE (2) cells. The study of our neuronal cell model revealed that  overexpression  of  DsRed-­‐GABARAPL1  appears  to  prime  cells  for  autophagy,  resulting in an earlier induction of autophagy after treatments that induce this processes.  In  addition,  overexpression  of  this  protein  delays  cell  death  in  a  CCCP-­‐induced mitochondrial stress model, suggesting that GABARAPL1 could protect neurons  against  certain  stresses  known  to  contribute  to  the  development  of  neurodegenerative diseases. Together,  this  work  has  identified  a  specific  tool  for  the  immunodetection  of  GABARAPL1, produced a detailed map of GABARAPL1 expression in the developing and  adult  murine  central  nervous  system  and  finally,  demonstrated  a  protective  role  for GABARAPL1 against neuronal death induced by mitochondrial stress.

Pancreatic cancer is one of the deadliest types of malignant diseases. Asymptomatic early tumour stages, tumour heterogeneity, cancer cell plasticity and unusually dense pancreatic stroma are responsible for the poor prognosis attributed to late diagnosis and therapy resistance. Therefore, targeting of a pivotal element common for any cell type within the tumour, e.g. mitochondria, may bring significant improvement. In this work, we demonstrate mitochondrial targeting of metformin, an anti-diabetic drug associated with reduced risk of developing pancreatic cancer, substantially increases accumulation of the compound in mitochondria. In consequence, we show that mitochondrially targeted metformin, MitoMet, eliminates pancreatic cancer cells in more than 1000-fold lower concentration than used for its parental compound. Following interaction with respiratory complex I (CI), MitoMet inhibits mitochondrial respiration, activates AMP-activated protein kinase pathway and causes depolarization of mitochondrial membrane potential in pancreatic cancer cells. Moreover, MitoMet induces cell cycle arrest and apoptosis, which is partially mediated via increased level of reactive oxygen species (ROS), and suppresses pancreatic tumour growth in vivo. Interestingly, SMAD4-deficient pancreatic cancer cells manifest...

Dues à leur importance croissante dans la dégénérescence musculaire, les mitochondries sont de plus en plus étudiées en relation à diverses myopathies. Leurs mécanismes de contrôle de qualité sont reconnus pour leur rôle important dans la santé mitochondrial. Dans cette étude, nous tentons de déterminer si le déficit de mitophagie chez les souris déficiente du gène Parkin causera une exacerbation des dysfonctions mitochondriales normalement induite par la doxorubicine. Nous avons analysé l’impact de l’ablation de Parkin en réponse à un traitement à la doxorubicine au niveau du fonctionnement cardiaque, des fonctions mitochondriales et de l’enzymologie mitochondriale. Nos résultats démontrent qu’à l’état basal, l’absence de Parkin n’induit pas de pathologie cardiaque mais est associé à des dysfonctions mitochondriales multiples. La doxorubicine induit des dysfonctions respiratoires, du stress oxydant mitochondrial et une susceptibilité à l’ouverture du pore de transition de perméabilité (PTP). Finalement, contrairement à notre hypothèse, l’absence de Parkin n’accentue pas les dysfonctions mitochondriales induites par la doxorubicine et semble même exercer un effet protecteur. / Mitochondria are becoming the focus of many studies because of their increasingly important role in cellular damage and related myopathies. Their endogenous quality control mechanisms are recognized for their crucial role in mitochondrial health. In our study, we attempted to determine if the deficit of mitophagy in Parkin deficient mice would cause an exacerbation of mitochondrial dysfunctions usually induced by doxorubicin. We have analyzed the impact of the ablation of Parkin in response to treatment with doxorubicin at the level of cardiac functions, mitochondrial functions as well as mitochondrial enzymology. Our results demonstrated that at baseline, the absence of Parkin didn’t induce cardiac pathologies but was associated with many mitochondrial dysfunctions. Doxorubicin induced respiratory dysfunctions, mitochondrial oxidative stress as well as greater susceptibility to permeability transition pore (PTP) opening. Finally, contrary to our hypothesis, the absence of Parkin, didn’t exacerbate mitochondrial dysfunctions induced by doxorubicin and seemed to have a protective effect.

La maladie de Parkinson (MP) est une pathologie neurodégénérative fréquente. Différents mécanismes moléculaires ont été mis en cause, dont une dysfonction mitochondriale. Des mutations du gène LRRK2, codant la protéine leucine-rich repeat kinase 2, sont responsables de formes autosomiques dominantes. La substitution la plus fréquente, G2019S, confère à la protéine un gain de fonction. LRRK2 semble réguler l’homéostasie mitochondriale, rôle initialement attribué aux protéines Parkine et PINK1, qui régulent en particulier la mitophagie. Nous avons étudié le rôle de LRRK2 et de son variant LRRK2-G2019S dans la régulation de la mitophagie dépendante de PINK1/Parkine. Nous avons également évalué l’effet de l’activité kinase sur ce processus dans un modèle cellulaire et dans des fibroblastes de patients. Nous avons exploré l’effet de LRRK2 sur la régulation d’interactions protéiques essentielles dans la mitophagie. Enfin, nous avons comparé l’efficacité de la mitophagie dans les formes familiales de la MP liées aux gènes LRRK2 et PARK2. Nous avons montré que LRRK2 et son variant LRRK2 G2019S retardent la mitophagie. Au travers de son activité kinase, LRRK2 compromet des interactions protéiques clefs impliquant Parkine et la GTPase Drp1. Nous avons mis en évidence un défaut de ce processus dans les fibroblastes de patients porteurs de mutations du gène PARK2. Ce défaut est également retrouvé dans les fibroblastes de patients porteurs de la substitution G2019S, dans lesquels il est corrigé par l’inhibition de l’activité kinase de la protéine. Ces résultats mettent en évidence un rôle de LRRK2 et de sa substitution pathogène dans la mitophagie dépendante de la voie PINK1/Parkine. / Parkinson’s disease (PD) is a frequent neurodegenerative disorder. Different molecular mechanisms are suspected, among which mitochondrial dysfunction stands out. Mutations in LRRK2, encoding leucine-rich repeat kinase 2 (LRRK2), cause autosomal dominant PD forms. The most frequent G2019S substitution leads to a gain of function. LRRK2 seems to modulate mitochondrial homeostasis, initially associated with Parkin and PINK1 proteins, which regulate in particular mitophagy. Here, we explored the involvement of LRRK2 and its kinase activity in the regulation of PINK1/Parkin-dependent mitophagy, and evaluated the consequence of the G2019S substitution, both in a cell line (COS7) and in primary fibroblasts from PD patients. In particularly, we studied the impact of LRRK2 on the regulation of protein-protein interactions essential for mitophagy initiation. We also compared the efficiency of PINK1/Parkin-dependent mitochondrial clearance in familial PD forms linked to LRRK2 and PARK2. Our results show that LRRK2 and its LRRK2 G2019S variant delay mitophagy. Moreover, these proteins compromised key interactions involving Parkin and the GTPase dynamin related protein 1 (Drp1) on the outer mitochondrial membrane. We confirmed a defect in this process in fibroblasts from patients with PARK2 mutations and found a similar alteration in fibroblasts from patients with the G2019S substitution. Inhibition of LRRK2 kinase activity restored mitophagy induction in cells from LRRK2 patients, but not in cells from PARK2 patients. Altogether, these results highlight a role of LRRK2 and its pathogenic substitution in the regulation of PINK1/Parkin-dependent mitophagy.

The evolution and adaptation of microorganisms is so rapid it can be seen in the time frame of days. The root cause for their evolution comes from selective environmental pressures that see organisms with beneficial mutations survive otherwise deadly encounters or outperform members of its population who fail to adapt. This does not always result in strict improvement of the individual as in the case of antibiotic resistant bacteria who often display fitness tradeoffs to avoid death (see Reviews [1-3]). For example, when an ampicillin resistance gene (ampC) containing plasmid that is occasionally found in the wild was transformed into S. typhimurium the bacteria had slower growth and impaired invasiveness [4]. In another example, capreomycin use with mycobacteria resulted in lower binding of the drug to the ribosome through mutations in rRNA methylase TlyA 16S rRNA, which decreases the overall fitness of the mycobacteria [5]. The evolutionary interactomes between bacteria and antibiotics do not end there, as antibiotic resistant bacteria often accumulate compensatory mechanisms to regain fitness. These range in effect with some altering individual cellular pathways and others having systemic affects [1]. My work has focused on the intersection of diabetes and related antibiotic resistant bacterial infections. Diabetes is one of the leading health issues in the United States, with over 10% of the adult population and over 26% of the elderly diagnosed (American Diabetes Association) [6]. Herein I further characterize the molecular pathways involved in diabetes, through the study of PAS kinase (PASK) function. PAS kinase is a serine-threonine protein kinase which regulates the pathways disrupted in diabetes, namely triglyceride accumulation, metabolic rate (respiration), adiposity and insulin production and sensitivity [7-9]. In this study I specifically focus on the effects of PAS kinase and its substrate, USF1/Cbf1p, and how their altered metabolic deficiencies can be suppressed using yeast cells. Through this study I further characterized the molecular function of USF1/Cbf1p through the identification of putative co-transcriptional regulators, identify novel genes involved in the regulation of respiration, and uncover a function or a previous uncharacterized protein, Pal1p. Part of the diabetes healthcare challenge results from the wide range of diseases that are associated with diabetes, including obesity [10, 11], renal failure [12, 13], neuropathies and neurodegeneration [14, 15], endocrine dysfunctions [16, 17], and cancers [18]. In addition, diabetes is a leading cause of lower limb amputations, due to poor circulation and the prevalence of ulcers [19-21], many of which are antibiotic resistant [22-25]. Phage therapy, based on the administration of bacterial viruses, is a viable option for the treatment of these diseases, with our lab recently isolating bacteriophages for several clinical cases. In the second half of my thesis, I present the study of the adaptation of bacteriophages to their hosts as well as report contributions of local ecology to their evolution.

No description available.