(EN) Mitochondria are the principal intracellular organelles responsible for fuel generation; however, they are not just cell powerhouses but are involved in a range of other intracellular functions including cell metabolism, proliferation, death, and immune responses. Loss of function in mitochondria will result in oxidative stress, which is one of the underlying causal factors for a variety of diseases including cancer. Cancer cells can predominantly produce energy by glycolysis even in the presence of oxygen. This alternative metabolic behavior is known as the "Warburg Effect." Linked to this, cancer cell mitochondria can switch between glycolysis and oxidative phosphorylation (OXPHOS) for their energy requirements and survival. The electron transport chain (ETC) function is pivotal for mitochondrial respiration, which is also needed for dihydroorotate dehydrogenase (DHODH) activity that is essential for de novo pyrimidine synthesis. In our research, we have used respiration-deficient cancer cells to challenge the dogma that mitochondria with their DNA are constrained within cells in the body. Our results document that mitochondria move from normal cells within the tumor stroma to tumor cells without mitochondrial DNA (mtDNA), resulting in long-lasting recovery of mitochondrial functions and,...

<p>Liposarcoma (LPS) arises from adipocytes and is a rare malignancy among all cancer types, but represents the most common form of soft tissue sarcoma, with approximately 2,000 new cases reported annually. Clinically, liposarcomas are classified into four subtypes based on histological analysis: well-differentiated liposarcoma (WDLPS), dedifferentiated liposarcoma (DDLPS), myxoid/round cell liposarcoma, and pleomorphic liposarcoma. Although histological analysis provides useful information for identifying various liposarcoma subtypes, treatment options rely on a fundamental understanding of driver mutations and molecular mechanisms underlying tumorigenesis. This thesis focuses on elucidating important driver mutations and therapeutic targets to eradicate DDLPS. Notch signaling is an evolutionarily conserved signaling pathway essential for organ development and stem cell function. Aberrant Notch signaling underlies the tumorigenesis of many cancers including LPS. However, the specific role of Notch signaling in development of LPS remains elusive. In Chapter 2, I provide evidence demonstrating that Notch signaling plays a key role in cancer stem cells (CSCs), also referred to as tumor-initiating cells (TICs), that drive aggressive DDLPS. I used serial transplantation to enrich and generate a murine DDLPS cell line with constitutively activated Notch signaling (NICDOE). My analyses revealed that NICDOE DDLPS cells are heterogeneous and contain TICs that express cancer stem cell markers. Chapter 3 elucidates how Notch signaling regulates CSCs of LPS. I analyzed human LPS samples to establish a strong correlation between Notch signaling activation and tumor marker expression and prognosis. I further performed gene expression and metabolic analyses of NICDOE DDLPS cells. These assays revealed that NICDOE reduced mitochondrial respiration in DDLPS cells, which was associated with diminished expression of peroxisome proliferator-activated receptor gamma coactivator 1α (PGC-1α), a master regulator of mitochondrial biogenesis. CRISPR/CAS9-mediated deletion of the NICDOE cassette rescued the expression of PGC-1α and mitochondrial respiration in DDLPS cells. Similarly, overexpression of PGC-1α was sufficient to rescue mitochondrial biogenesis in DDLPS cells. Together, these data demonstrate that Notch signaling regulates CSCs, at least partially by controlling PGC-1α mediated mitochondria biogenesis.</p>

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Breast cancer is a common malignant disease affecting millions of women worldwide. Amplification of HER2 oncogene, a tyrosine kinase receptor, in breast cancer allows application of targeted therapy, but approximately one third of patients develop resistance to treatment. Relocalization of HER2 from the plasma membrane into the mitochondria was found and suggested as one of the potential causes of such resistance. Here we document that the function of mitochondrial HER2 is distinct from that of HER2 in the plasma membrane. Mitochondrial HER2 enhances cancer cell energetic metabolism, proliferation and migration in vitro, and tumour formation in vivo in mice correlating with elevated level of ROS signalling. The kinase activity of mitochondrial HER2 is unaffected, therefore I investigated its role in mitochondrial HER2 function. Moderate, endogenous levels of the kinase activity of mitochondrial HER2 drive pro-tumorigenic properties of breast cancer cells, while constitutive kinase activity sensitizes these cells to cell death and attenuates tumour formation in animal models. On the other hand, impairment of kinase activity due to mutation in the ATP binding site of mitochondrial HER2 supports adherence-independent growth in vitro and tumor growth in vivo. We propose that HER2 function in...

Cancer cells display metabolic alterations to meet the bioenergetic demands for their high proliferation rates. Succinate is a central metabolite of the tricarboxylic acid (TCA) cycle, but was also shown to act as an oncometabolite and to specifically activate the succinate receptor 1 (SUCNR1), which is expressed in several types of cancer. However, functional studies focusing on the connection between SUCNR1 and cancer cell metabolism are still lacking. In the present study, we analyzed the role of SUCNR1 for cancer cell metabolism and survival applying different signal transduction, metabolic and imaging analyses. We chose a gastric, a lung and a pancreatic cancer cell line for which our data revealed functional expression of SUCNR1. Further, presence of glutamine (Gln) caused high respiratory rates and elevated expression of SUCNR1. Knockdown of SUCNR1 resulted in a significant increase of mitochondrial respiration and superoxide production accompanied by an increase in TCA cycle throughput and a reduction of cancer cell survival in the analyzed cancer cell lines. Combination of SUCNR1 knockdown and treatment with the chemotherapeutics cisplatin and gemcitabine further increased cancer cell death. In summary, our data implicates that SUCNR1 is crucial for Gln-addicted cancer cells by limiting TCA cycle throughput, mitochondrial respiration and the production of reactive oxygen species, highlighting its potential as a pharmacological target for cancer treatment.

Breast cancer is a common malignant disease affecting millions of women worldwide. Amplification of HER2 oncogene, a tyrosine kinase receptor, in breast cancer allows application of targeted therapy, but approximately one third of patients develop resistance to treatment. Relocalization of HER2 from the plasma membrane into the mitochondria was found and suggested as one of the potential causes of such resistance. Here we document that the function of mitochondrial HER2 is distinct from that of HER2 in the plasma membrane. Mitochondrial HER2 enhances cancer cell energetic metabolism, proliferation and migration in vitro, and tumour formation in vivo in mice correlating with elevated level of ROS signalling. The kinase activity of mitochondrial HER2 is unaffected, therefore I investigated its role in mitochondrial HER2 function. Moderate, endogenous levels of the kinase activity of mitochondrial HER2 drive pro-tumorigenic properties of breast cancer cells, while constitutive kinase activity sensitizes these cells to cell death and attenuates tumour formation in animal models. On the other hand, impairment of kinase activity due to mutation in the ATP binding site of mitochondrial HER2 supports adherence-independent growth in vitro and tumor growth in vivo. We propose that HER2 function in...

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Le cancer du pancréas est l’un des plus chimiorésistants, avec un taux de survie sur 5 ans inférieur à 5%. La chimiorésistance pourrait être due à la présence de cellules initiatrices de tumeur (TICs), une petite sous-population des cellules tumorales possédant la capacité de régénérer une nouvelle tumeur. Il a été démontré que la metformine cible les TICs par un mécanisme non élucidé. Il est connu que la metformine affecte le métabolisme du carbone. Il a également été démontré que le métabolisme du carbone, plus précisément la glycine décarboxylase (GLDC), est à la fois nécessaire et suffisant à l’acquisition de propriétés d’initiation tumorale. Nous proposons que la metformine cible les cellules initiatrices de tumeur en affectant le métabolisme du carbone. Nous avons utilisé des lignées cellulaires dérivées d’un modèle murin de cancer du pancréas pour comparer l’expression génique de lésions bénignes versus malignes. Les cellules malignes surexpriment Gldc. La metformine diminue l’expression de Gldc, et la surexpression de Gldc diminue la sensibilité à la metformine dans un essai de sphères tumorales. La metformine induit une augmentation du ratio NADP+/NADPH, et la surexpression de Gldc empêche cette augmentation. Nous proposons que la metformine diminue l’expression de Gldc, ce qui cause une diminution du flux du métabolisme du carbone, et donc une diminution de la production de NADPH par ce dernier. L’augmentation du ratio NADP+/NADPH inhibe la synthèse des acides gras et la régénération de la glutathione, ce qui pourrait expliquer la diminution de la formation de sphères tumorales sous traitement metformine. / Pancreatic cancer is one of the most chemoresistant cancers, with a 5-year survival rate lesser than 5%. Chemoresistance might be due to the presence of tumor-initiating cells (TICs), a small subpopulation of tumor cells with stem-like characteristics which possess the unique ability to self-renew and to generate a new tumor. Metformin has been shown to affect TICs in various cancer types, but the mechanism through which it does so is unclear. It is known that metformin affects one-carbon metabolism. It has also been shown that one-carbon metabolism, more precisely the glycine decarboxylase (GLDC) enzyme, is both necessary and sufficient to the acquisition of tumor-initiating properties. Considering this, we propose that metformin affects TICs by targeting one-carbon metabolism. Using cell lines derived from a genetically engineered mouse model of pancreatic cancer, we compared gene expression data from cells derived from benign pancreatic neoplasia with cells derived from pancreatic ductal adenocarcinoma (PDAC), and found that PDAC cells exhibited a dramatic increase in Gldc expression. Metformin treatment decreases Gldc expression in PDAC cell lines, and Gldc overexpression greatly decreases metformin sensitivity in a tumor sphere assay. Metformin induces an increase in NADP+/NADPH ratio, which is rescued by Gldc overexpression. We propose a model in which metformin decreases Gldc expression, which causes reduced flux through mitochondrial one-carbon metabolism. This results in decreased NADPH production by this pathway. This increase in NADP+/NADPH ratio impairs fatty acid biosynthesis and glutathione regeneration. Together these effects might explain the decrease of tumor sphere formation under metformin treatment.

Στην μετα-γονιδιωματική εποχή, την εποχή της συστημικής βιολογίας, η κατανόηση της πολυπλοκότητας της κυτταρικής φυσιολογίας απαιτεί την ανάλυση της δυναμικής των δικτύων βιομοριακών αλληλεπιδράσεων σε όλα τα μοριακά επίπεδα κυτταρικής λειτουργίας. Με τη σειρά της, η λειτουργική γονιδιωματική, ένας θεμελιώδης λίθος της συστημικής βιολογίας, στοχεύει στον πολυδιάστατο χαρακτηρισμό ενός γονιδίου, συνδυάζοντας δεδομένα από τις τεχνολογίες υψηλής απόδοσης. Είναι αυτή ακριβώς η ενοποίηση όλων των μοριακών προτύπων για ένα διαταραγμένο βιολογικό σύστημα που μπορεί να δώσει πληροφορίες αναφορικά με την λειτουργία ενός αγνώστου γονιδίου. Στο πλαίσιο αυτό, η παρούσα Διπλωματική Εργασία αποτελεί μέρος της ολιστικής λειτουργικής ανάλυσης δύο αλληλεπιδρώντων, αγνώστου βιολογικού ρόλου, πρωτεϊνών, της DGCR14 και της FRA10AC1, οι οποίες έχουν απομονωθεί ως συστατικά του σωματιδίου συναρμογής και έχουν συσχετιστεί με νευρολογικές ασθένειες. Η παρούσα εργασία επικεντρώνεται στην μεταβολομική μελέτη των μοριακών επιπτώσεων της υπερέκφρασης της DGCR14 σε ένα ανθρώπινο κυτταρικό μοντέλο, τα κύτταρα HeLa, με την χρήση της αέριας χρωματογραφίας - φασματομετρία μάζας. Ωστόσο, για να επιτευχθεί αυτό, θέματα σχετικά με τις δυνατότητες ποσοτικοποίησης των πολυβηματικών ομικών αναλύσεων έπρεπε να επιλυθούν. Μια σημαντική παράμετρος αφορά στην γρήγορη αδρανοποίηση των ενζυματικών διεργασιών έτσι ώστε οι αποκτηθέντες μετρήσεις να αντικατοπτρίζουν την πραγματική κυτταρική φυσιολογία. Για τον σκοπό αυτό, ο πειραματικός σχεδιασμός πρέπει να τροποποιείται κατάλληλα έτσι ώστε οποιεσδήποτε απαιτούμενες προ-αναλυτικές διαδικασίες χειρισμού των κυττάρων να έχουν ελάχιστη επίδραση στην φυσιολογία τους. Μελετήσαμε συνεπώς την επίδραση τεσσάρων πρωτοκόλλων συλλογής προσκολλημένων κυττάρων και δύο διαφορετικών διαλυμάτων έκπλυσης στο μεταβολικό πρότυπο κυττάρων HeLa. Τα μεταβολομικά δεδομένα αξιολογήθηκαν στο πλαίσιο της καρκινικής μεταβολικής φυσιολογίας και το πρωτόκολλο με την ελάχιστη δυνατή επίδραση στην κυτταρική φυσιολογία καθορίστηκε. Μεταξύ των αποτελεσμάτων αυτής της μελέτης, πολύτιμες πληροφορίες σχετικά με την μεταβολική φυσιολογία των αθανατοποιημένων κυτταρικών σειρών προέκυψαν, οι οποίες ενίσχυσαν σημαντικά την υπάρχουσα γνώση γύρω από τον καρκινικό μεταβολισμό, σε σταθερές ή μεταβαλλόμενες περιβαλλοντικές συνθήκες. Επακόλουθα, η βελτιστοποίηση της διαδικασίας συλλογής είχε ως αποτέλεσμα την δημιουργία ενός αντιπροσωπευτικού μεταβολικού προτύπου κυττάρων HeLa πάνω στο οποίο πραγματοποιήθηκε η αξιολόγηση της υπερέκφρασης της πρωτεΐνης DGCR14 χωρίς να επισκιάζεται από πειραματικές αποκλίσεις εισαγόμενες από την διαδικασία χειρισμού των κυττάρων. Αναφορικά με τα κύτταρα που υπερεκφράζουν την DGCR14, η μεταβολομική ανάλυση εντόπισε μια αλλαγή φυσιολογίας συνδεόμενη με συγκεκριμένα μεταβολικά μονοπάτια τα οποία υποδηλώνουν έντονο μεταβολικό στρες. Για να διερευνήσουμε την συσχέτιση της υπερέκφρασης της DGCR14 με τον παραπάνω μεταβολικό φαινότυπο, χρησιμοποιήσαμε το ανακατασκευασμένο δίκτυο πρωτεϊνικών αλληλεπιδράσεων του σωματιδίου συναρμογής στον άνθρωπο και το δίκτυο πρωτεϊνικών αλληλεπιδράσεων στον άνθρωπο από την μετα-βάση δεδομένων PICKLE, προκειμένου να αντλήσουμε επιπλέον πληροφορίες για τον ρόλο της DGCR14 βάσει της θέσης της σε σχέση με άλλους κόμβους και υπερ-κόμβους. Μια πιθανή λειτουργική συσχέτιση της DGCR14 με αυτοφαγικούς και λυσοσωμικούς μηχανισμούς βρέθηκε, η οποία θα αξιολογηθεί και μελλοντικά μέσω της ανάλυσης, ξεχωριστά και συνδυαστικά, των μοριακών συνεπειών της υπερ- και υπο-έκφρασης σε όλα τα μοριακά επίπεδα κυτταρικής λειτουργίας. / In the post-genomic, systems biology era, developing a systems level understanding of a physiological process requires the analysis of biomolecular network dynamics at all molecular levels of cellular function. Likewise, functional genomics, an essential foundation of systems biology research, aims to define and analyze gene function at a global level by integrating data obtained from multiple high-throughput technologies. It is the integration of all the molecular profiles for a systematically perturbed system that can provide insight about the function of unknown genes. Along these lines, the present study is part of the systematic functional analysis of two interacting, but yet of unknown biological role, spliceosomal proteins, DGCR14 and FRA10AC1, that have both been implicated in neurological diseases. The present work focuses on studying the molecular consequences of DGCR14 overexpression in a human cell model, HeLa cells, at the metabolic level using Gas Chromatography-(ion trap) Mass Spectrometry. However, to succeed in this, issues regarding the quantification capabilities of the multistep omic analysis procedures needed to be resolved. A major concern refers to the fast quenching of any enzymatic processes, so that the acquired measurements indeed reflect the cellular physiology in vivo. To this end, the experimental design should be appropriately adjusted so that any required sample handling actions before quenching have a minimal effect on cellular physiology. Thus, we investigated the effect of four cell collection protocols and two different washing solutions on the intracellular metabolic profile measurements of a HeLa cell culture. The measurements were interpreted in the context of the known cancer cell metabolic physiology and the protocol with the minimum possible effect on cellular physiology was specified. Among the results of this study, valuable information about the metabolic physiology of the immortal cell line arise, which improved our knowledge about cancer metabolism under steady or varying environmental conditions. Subsequently, the optimization of the collection procedure enabled us to establish a representative metabolic profile of HeLa cells against which the overexpression of DGCR14 was evaluated without being obscured by the effect of the sample handling. Regarding the overexpressing cells, the metabolomic analysis detected a trend of physiological change connected to specific metabolic pathways indicating strong metabolic stress. To understand how DGCR14 overexpression generates this particular metabolic phenotype, we used the human spliceosomal complex protein-protein interaction (PPI) network and the integrated human PPI meta-database PICKLE to extract additional information about DGCR14 role based on its location with respect to other nodes and hubs. A possible functional correlation of DGCR14 to autophagic and lysosomal mechanisms was established, that will be further evaluated in the future through the analysis, separately and in combination, of the consequences of DGCR14 over- and under-expression at all molecular levels of cellular function.

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