Epithelial-mesenchymal transition (EMT) is a trans-differentiation program essential for development and wound healing that is pathologically activated during cancer progression. During this process, cells undergo complex changes at the transcriptional and translational levels leading to dissolution of cell-cell junctions, loss of apical-basal polarity, and cytoskeleton reorganization. Transforming Growth Factor-β (TGF-β) is well-established in driving cancer progression through EMT induction. Remodeling of cellular junctions, including gap junctions, is critical to acquiring migratory and invasive characteristics during EMT. The gene GJA1 encodes for Connexin43 (Cx43), the most ubiquitously expressed gap junction protein where altered regulation of Cx43 is associated with cancer progression. Intriguingly, Cx43 mRNA undergoes alternative ‘internal’ translation initiation, generating N-terminally truncated isoforms, including GJA1-20k, which regulates Cx43 gap junction formation. We have previously demonstrated GJA1-20k expression is inhibited during TGF-β-induced EMT, limiting gap junction formation; however, the relationship between GJA1-20k modulation of gap junction localization and cellular invasion and migration remains unknown. Given the role GJA1-20k has in regulating gap junctions, we hypothesize that suppression of GJA1-20k expression promotes metastatic trait acquisition through limiting gap junction formation. Utilizing lentivirally transduced stable mouse mammary gland epithelial (NMuMG) and triple-negative human breast epithelial (MDA-MB-231) cells expressing GJA1-20k, or Lac Z as control, we tested effects on TGF-β-induced EMT induction and metastatic trait induction. Boyden chambers, would/scratch assays were employed to analyze cell invasion and migration respectively. We found GJA1-20k overexpression during EMT results in decreased cell invasion and migration to LacZ controls. Future directions include evaluation of GJA1-20k restoration in a metastatic breast cancer model in vivo. Investigating the underlying role of GJA1-20k in EMT-induced cell junction remodeling could be promising as a potential pharmacological target process independent of transcriptional or post-translational pathways. Ultimately, by adding novel information in the expanding and compelling field of translational control, this work could aid in developing the future of precision medicine as new therapeutic solutions to treat cancer will require limiting cancer cell’s ability to metastasize. / R01 HL132236 JWS R41 CA250874 SL R01HL132236 Diversity Supplement KLY II 23PRE1025483 AHA Predoctoral Fellowship KLY II / Doctor of Philosophy / Every organ system relies upon cell-to-cell communication to properly function and is the basis of multi-cellular life. Gap junctions are nanoscale conduits allowing the passage of small signaling molecules and ions between adjacent cells, similar to telephone tubes. Gap junctions are formed from proteins called connexins. Interestingly, it is well known that shorter pieces of connexin proteins can regulate the formation of gap junctions and are uniquely created by a process called alternative ‘internal’ translation. Changes in the amounts of short-length and full-length connexin proteins are often found in cancer cells. Cancer is the uncontrolled growth of abnormal cells. Commonly, the morphology of cancer cells, and the way they communicate with neighboring cells, is altered. Cancer progression is aided by changes in cell signaling molecules, including TGF-β which can drive cancer cells to leave primary tumor sites and grow elsewhere in the body. This is important for the cancer cells to continue dividing and eventually metastasizing (invading other organ systems). Treating cancer once it has spread to other regions of the body is difficult and is the main cause of cancer deaths worldwide. Using TGF-β to model metastatic changes in mouse and human cell lines, we studied how short-length connexin protein affects metastatic cancer cell behavior. With this information we will be able to guide the development of druggable alternative ‘internal’ translation targets, by restoring the proper communication between neighboring cells and therefore preventing spread of cancer cells.

<p>Metastasis of primary mammary tumors to vital secondary organs is the primary cause of breast cancer-associated death, with no effective treatment. Metastasis is a highly selective process that requires cancer cells to overcome multiple barriers to escape the primary tumor, survive in circulation, and eventually colonize distant secondary organs. One of the important aspects of metastatic cancers is the ability to undergo epithelial-mesenchymal transition (EMT) and the reverse process mesenchymal-epithelial transition (MET) process. Constant interconversion of tumor cells between these phenotypes creates epithelial-mesenchymal heterogeneity (EMH) and interaction between these tumor cell types and the stromal cell compartment is clearly important to metastasis. In healthy tissues, stromal cells maintain the composition and structure of the tissue through the production of extracellular matrix (ECM) proteins and paracrine signaling with epithelial cells. However, little is known about how EMH promotes changes in the ECM to promote breast cancer progression and metastasis. Cancer cells also secret exosomes, nano-size extracellular vesicles, to establish intercellular communication with distant organs in order to induce metastasis. These exosomes contain a plethora of different proteins including extracellular matrix proteins and matrix crosslinking enzymes. Fibronectin, an important ECM protein, plays an active role in tumor progression and is often crosslinked by tissue transglutaminase 2 (TGM2) to promote fibrosis in cancer. Both FN and TGM2 exist in exosomes and are expressed by heterogenous breast tumors. Although FN and TGM2 have been reported to play essential roles in cancer, their involvement in metastasis remains unclear. This work utilizes a variety of approaches to investigate the role of tumor heterogeneity and ECM proteins in promoting breast cancer metastasis. In this dissertation, we establish that mesenchymal cells expressing intracellular FN are held in a stable non-metastatic mesenchymal phenotype and produce cellular fibrils containing functionalized FN capable of supporting the growth of metastatic competent epithelial cells. We introduce a novel 3D culture system consisting of a tessellated scaffold which is capable of recapitulating cellular and matrix phenotypes <i>in vivo. </i>Further, we also demonstrate breast tumor cells secrete exosomes containing TGM2 crosslinked FN fibrils to promote premetastatic niche formation and induction of metastasis.<i> </i>Using genetic approaches, we establish TGM2 is essential and sufficient to drive metastasis. Finally, we demonstrate pharmacological inhibition of TGM2 offers a potential therapeutic strategy to treat metastatic breast cancer. Altogether, our research provides insights into the mechanism through which TGM2 promotes metastatic breast cancer. This work will help in developing new drugs to target TGM2 aimed at reducing breast cancer metastasis.<br></p>

La transition épithélio-Mésenchymateuse (TEM) est un processus de plasticité cellulaire qui existe dans le développement embryonnaire et qui permet la formation des tissus et organes. Dans la cancérogénèse, ce processus est réactivé par des facteurs de transcription dont l’action implique très probablement un remodelage de la chromatine. La cartographie exacte de ces changements épigénétiques est peu connue à l’échelle du génome entier, même si il y a eu quelques études antérieures explorant les changements de quelques loci de façon bien ciblée. Ce mémoire traite du remodelage épigénétique médié par le facteur de transcription Twist1 dans un modèle de lignée mammaire immortalisée. L’architecture de ce remodelage a été cartographiée grâce à l’utilisation des techniques de haut-Débit pour analyser la méthylation de l’ADN (DREAM) et les modifications des histones (ChIPseq). Nos résultats montrent un changement majeur du méthylome pendant la TEM avec une hyperméthylation focale et une hypométhylation globale des corps des gènes prédominant au niveau des « domaines partiellement méthylés »; ces domaines sont déjà connus dans le développement pour gagner de façon concomitante à leur hypométhylation des marques d’histone répressives. Nous avons aussi observé un remodelage des domaines de l’histone répressive H3K27me3 avec une réduction de leur taille, et surtout le quasi doublement du nombre de gènes bivalents qui accompagne la transition. Le couplage de la méthylation de l’ADN avec le profil des microRNA nous a permis d’identifier le miR-203 comme l’unique microRNA régulé par méthylation de l’ADN durant la TEM; nous avons aussi montré que l’extinction épigénétique du miR-203 est requise pour la TEM et l’acquistion des propriétés de cellules souches. Enfin, nous avons réalisé une caractérisation génétique et/ou épigénétique de deux cancers rares, les carcinomes fibrolamellaires du foie et les carcinomes du rein à translocation. Pour les carcinomes fibrolamellaires du foie, nous avons décrit la nature endocrine de cette tumeur et établi une signature épigénétique basée sur la méthylation de l’ADN pouvant servir à différencier les formes histologiques appelées « pures » des formes « mixtes ». Pour les cancers du rein à translocation, nous avons montré les bases génétiques et épigénétiques de la différence entre les formes pédiatriques et adultes, avec la découverte fréquente du gain du bras chromosomique 17q dans les formes adultes. Nous avons aussi identifié une mutation récurrente dans le gène qui remodèle la chromatine INO80D appartenant à la famille INO80. En conclusion, ce travail explore le rôle de l’étude de l’épigénome pour comprendre la reprogrammation pendant les processus physiologiques comme la TEM d’une part et le cancer d’autre part. / The epithelial-Mesenchymal transition (EMT) is a process of cellular plasticity that exists in embryonic development and which allows the formation of tissues and organs. In carcinogenesis, the process is reactivated by transcription factors whose action probably involves chromatin remodeling. The exact mapping of these epigenetic changes is poorly understood genome-Wide, although there have been some previous studies exploring changes in so few well-Targeted loci. This thesis deals with the epigenetic remodeling mediated by the transcription factor Twist1 in a model of human mammary immortalized cell line. The architecture of this remodeling has been mapped through the use of high-Throughput techniques to analyze DNA methylation (DREAM) and histone modifications (ChIPseq). Our results suggest a major change in the EMT methylome with focal hypermethylation and gene body hypomethylation predominantly within "partially methylated domains"; these areas are already known in development to gain repressive histone marks concomitantly with DNA hypomethylation. We also observed landscape remodeling of repressive histone mark H3K27me3 with a reduction in domains size, and especially the almost doubling of the number of bivalent genes. The coupling of DNA methylation with the profile of microRNA has allowed us to identify miR-203 as single microRNA regulated by DNA methylation during EMT; we have also shown that epigenetic suppression of miR-203 is both required for EMT and acquisition of stem cell properties. Finally, we performed a genetic and/or epigenetic characterization of two rare cancers, named fibrolamellar hepatocellular carcinomas and translocation renal cell carcinomas. In fibrolamellar hepatocellular carcinoma, we described the endocrine nature of this tumor and established a signature based on DNA methylation which can be used to distinguish histological forms called "pure" from "mixed" fibrolamellar hepatocellular carcinomas. Regarding translocation renal cell carcinomas, we established the genetic and epigenetic basis of differences between pediatric and adult forms, characterized by frequent gain of 17q gain chromosomal arm in adults. We also identified recurrent mutations in the chromatin remodeling gene INO80D which belongs to INO80 family. In conclusion, this work explores the impact of analyzing the epigenome to understand reprogramming during physiological processes such as EMT and cancer.

La fibrose pulmonaire idiopathique (FPI) et le syndrome de détresse respiratoire aiguë (SDRA) de l’adulte constituent des affections sévères du poumon distal, avec un pronostic sombre pour les patients. A ce jour, aucun traitement n’est réellement efficace. De manière intéressante, une hypoxie alvéolaire est retrouvée dans ces pathologies.La thérapie cellulaire utilisant des cellules souches mésenchymateuses humaines (CSMh) pourrait représenter un intérêt thérapeutique chez l’Homme. Cependant, leurs mécanismes d’action sont multiples et encore mal définis. Aussi, nous avons testé in vitro l’hypothèse selon laquelle les CSMh pourraient exercer un effet cytoprotecteur paracrine sur les cellules épithéliales alvéolaires (CEA) soumises à l’hypoxie.Dans une première étude, nous avons montré qu’une exposition prolongée à l’hypoxie telle que celle rencontrée au cours de la FPI induisait des modifications phénotypiques des CEA primaires de rat, évocatrices d’une transition épithélio-mésenchymateuse (TEM). On observe une perte progressive d’expression des marqueurs épithéliaux (TTF1, AQP5, ZO-1 et E-Cadhérine), couplée à l’apparition tardive de marqueurs mésenchymateux (α-SMA et Vimentine). Ces modifications phénotypiques s’accompagnent de l’expression dès les premières heures d’hypoxie de facteurs de transcription impliqués dans la TEM (SNAI1, TWIST1 et ZEB1) ou induits par l’hypoxie (HIF-1α et HIF-2α), et de protéines induisant la TEM (TGF-β1 et CTGF). La co-culture des CEA avec des CSMh en fond de puits prévient les modifications phénotypiques induites par l’hypoxie ainsi que l’expression des facteurs pro-TEM TWIST1, ZEB1, TGF-β1 et CTGF. Cet effet bénéfique des CSM est en partie expliqué par la sécrétion d’un facteur de croissance épithélial, le KGF.Dans une deuxième étude, nous avons confirmé que les CEA entraient en apoptose en condition hypoxique, via l’induction de deux voies de signalisations hypoxiques pro-apoptotiques. D’une part, les facteurs de transcription induits par l’hypoxie HIF sont stabilisés, et une cible pro-apoptotique, Bnip3, est induite. D’autre part, l’hypoxie induit une accumulation d’espèces réactives à l’oxygène délétère pour la cellule, perturbant l’équilibre redox de la cellule, endommageant l’ADN, et conduisant à l’apoptose. Cette accumulation pourrait résulter notamment d’une diminution de l’activité des enzymes anti-oxydantes SOD, en hypoxie. Le manque d’oxygène entraine également l’expression de CHOP, facteur de transcription pro-apoptotique impliqué dans le stress du réticulum endoplasmique, qui va13inhiber l’expression de la protéine anti-apoptotique Bcl-2. Nous avons montré que la culture des CEA en présence de milieu conditionné de CSMh (mc-CSMh) permet de prévenir partiellement l’apoptose des CEA en hypoxie, en modulant la voie de signalisation HIF, et en prévenant l’accumulation et les effets délétères des ROS. L’effet protecteur des CSM impliquerait le KGF comme observé lors de la première étude, mais également le HGF.Ces deux études indiquent que les CSMh sont susceptibles d’exercer des effets cytoprotecteurs paracrines vis-à-vis des CEA soumises à l’hypoxie aiguë ou prolongée, en limitant d’une part les modifications phénotypiques évocatrices de TEM, et d’autre part l’apoptose des CEA via la modulation des voies de signalisations hypoxiques. La sécrétion par les CSMh de KGF et de HGF, facteurs de croissance épithéliaux connus pour leurs effets bénéfiques sur les CEA, explique en partie les effets protecteurs paracrines des CSMh. Nos résultats suggèrent que les effets cytoprotecteurs des CSMh vis-à-vis des CEA pourraient contribuer aux effets bénéfiques des CSMh observés in vivo dans différents modèles animaux de fibrose induite, ou lors d’agressions alvéolaires aiguës. / Acute or chronic alveolar injuries provoke massive apoptosis of alveolar epithelial cells (AEC) that compromises an efficient repair of the alveolar epithelium and leads to lung diseases such as ARDS or IPF. These disorders are commonly associated with local alveolar hypoxia aggravating their progression through the stimulation of AEC apoptosis. Administration of allogenic mesenchymal stem cells (MSCs) has been shown to limit lung inflammation and fibrosis in murine models of alveolar injury, through a still poorly understood paracrine mechanism. In a first study, we showed that long term exposure of AEC in hypoxia leads to phenotypic alterations which looks like epithelio-mesenchymal transition (EMT). Co-culture with MSCs prevent hypoxia-induced EMT.In a second work, we studied whether MSC could protect AEC from hypoxia-induced apoptosis and the mechanisms involved. hMSC-conditioned media (hMSC-CM) significantly reduced hypoxia-induced apoptosis of AEC. Such a anti-apoptotic effect was also obtained with ROS scavenger N-acetylcystein or HIF1a inhibitor YC-1. hMSC-CM decreased the protein expression of HIF1α and HIF2α and of their pro-apoptotic target Bnip3 in hypoxic AEC. hMSC-CM also reduced ROS accumulation in hypoxic AEC by enhancing the activity of anti-oxidant enzymes and prevented the induction of CHOP, a pro-apoptotic factor induced by ROS signaling. The paracrine effect of hMSC was partly dependent on KGF and HGF secretion. hMSC prevent via a paracrine effect hypoxia-induced apoptosis of AEC by modulating hypoxic and ROS signaling.These two studies show that MSCs exert cytoprotective effects in vitro against hypoxia-induced apoptosis and EMT in AEC

La transplantation pulmonaire pour les patients avec une maladie pulmonaire en phase terminale est leur seul espoir de survie. Malheureusement, certains greffés du poumon rencontrent des difficultés après la transplantation du poumon, dont l'un est le rejet chronique du greffon pulmonaire également connu histologiquement comme la bronchiolite oblitérante et cliniquement comme syndrome de bronchiolite oblitérante. L'étiologie exacte de la BO reste mal comprise. Certaines hypothèses suggèrent l'implication des cellules épithéliales dans le processus de remodelage des voies respiratoires, conduisant à l'obstruction des voies aériennes. Un des mécanismes proposés est un processus de transition, connue sous le nom de transition épithéliale-mésenchymateuse (TEM). Lors de ce processus, les cellules perdent leurs propriétés épithéliales, acquièrent un phénotype mésenchymateux et deviennent plus mobiles et envahissantes. Cette transformation leur permet de participer activement au processus de remodelage bronchique dans la bronchiolite oblitérante. L’induction de la TEM peut être due à certains facteurs tels que l'inflammation et l'apoptose. Le principal objectif de ce travail de maîtrise est de détecter in vivo la présence de la TEM dans des biopsies transbronchiques obtenues chez des greffés et de l’associer à leurs conditions cliniques. Le deuxième objectif est d'induire la TEM in vitro dans les cellules épithéliales des petites voies aériennes à l'aide de milieux conditionnés apoptotiques et non apoptotiques produits par les cellules endothéliales microvasculaires humaines du poumon. D’autre part, nous avons évalué si des médiateurs connus pour participer au processus de TEM tels que le facteur de croissance du tissu conjonctif (CTGF)et le facteur de croissance transformant bêta (TGF-beta) ainsi que le perlecan sont présents dans les milieux conditionnés utilisés. / For patients with end-stage lung disease, lung transplantation is their only hope for survival. Unfortunately, some of the lung transplant recipients (LTRs) might face obstacles following lung transplantation, one of which is chronic lung transplant rejection also known as bronchiolitis obliterans (BO) histologically and bronchiolitis obliterans syndrome (BOS) clinically. The exact etiology behind BO development remains poorly understood. Speculations have suggested the involvement of epithelial cells in the airway remodeling process leading to airway obstruction. One of the proposed mechanisms is a transitional process, known as epithelial-mesenchymal-transition (EMT). In this process epithelial cells lose their properties and acquire mesenchymal ones causing them to be more mobile and invasive which allow them to take part of the airway remodeling process in BO. Induction of EMT can be due to several factors such as inflammation, apoptosis. In our study we try to detect in vivo the presence of EMT in transbronchial biopsies (TBB) obtained from LTRs and associates it with their clinical conditions. We also try to manipulate and induce EMT in vitro in small airway epithelial cells (SAEC) using conditioned apoptotic (SSC4h) and non apoptotic (ZVAD) media produced from human microvascular endothelial cells (HMVEC) from lung. In addition, we worked on detecting possible mediators such as connective-tissue growth factor (CTGF), transforming growth factor-beta (TGF-β), and perlecan in produced media.

La voie de signalisation du récepteur des androgènes (RA) est la principale cible thérapeutique des cancers de la prostate métastatiques. Toutefois, l'émergence de variants constitutivement actifs du RA dépourvus de leur partie C-terminale conduit à une résistance au traitement. Pendant ma thèse, j'ai montré que les variants du RA induisent une transition épithélio-mésenchymateuse (EMT) partielle, un phénomène observé lors de la progression tumorale. J'ai ensuite étudié les mécanismes conduisant à cette expression différentielle de marqueurs de l’EMT en me focalisant sur la N-cadhérine (CDH2). Le RA entier (AR-FL) et les variants du RA interagissent tous les deux au niveau des éléments de réponse aux androgènes dans l'intron1 de CDH2. Cependant, une augmentation du niveau d’acétylation des histones est observée uniquement avec les variants du RA. Mes données nous mène à un modèle où l'AR-FL réprimerait l'expression de CDH2 alors que les variants du RA induiraient son expression. / Androgen receptor (AR) pathway is the main therapeutic target for metastatic prostate cancer (Pca).However, the expression of AR variants lacking the carboxy-terminal end lowers therapy efficacy. During myphD, I showed that AR variants induce a partial epithelial-mesenchymal transition (EMT), a phenomenon observed during tumor progression. To understand the mode of action of AR variants, I explored the mechanisms leading to this differential expression of EMT markers focusing my research on N-cadherin(CDH2). While both the full length AR (AR-FL) and AR variants could interact with androgen response elements present in intron 1 of CDH2, I highlighted that they had opposite effects concerning histone modifications. Indeed, increased histone acetylation in this genomic region was observed only in the presence of AR variants. My data lead us to propose a model in which AR-FL represses CDH2 gene, while AR variants favor its expression.

Glioma, the tumor of glial cells, is one of the common types of primary central nervous system (CNS) neoplasms. Astrocytoma is the most common of all gliomas and originates from astrocytic glial cells. Astrocytoma tumors belong to two main categories: benign tumors, comprising of grade I Pilocytic astrocytoma and malignant tumors which diffusely infiltrate throughout the brain parenchyma. Diffusely infiltrating astrocytomas are graded into diffuse astrocytoma (DA; grade II), anaplastic astrocytoma (AA; grade III) and glioblastoma (GBM; grade IV) in the order of increasing malignancy. Patients with grade II astrocytoma have a median survival time of 6 to 8 years after surgical intervention. While the more aggressive grade III (AA) and grade IV (GBM) are together called malignant astrocytomas, the treatment protocols and length of survival are distinctly different between these grades. The median survival time for grade III patients is 2 to 3 years whereas patients with grade IV have a median survival of 12-15 months. GBMs have been further divided into primary GBM and secondary GBM on the basis of clinical and histopathological criteria. Primary GBM presents in an acute de novo manner with no evidence of an antecedent lower grade tumor and it accounts for >90% of all GBMs. In contrast, secondary GBM results from the progressive malignant transformation of a grade II or grade III astrocytoma. The current WHO grading system of astrocytomas is based on the histopathological characteristics of the underlying tumor tissue. Diagnoses by pathologists are dependent on specific histologic features: increased mitosis, nuclear atypia, microvascular proliferation and/or necrosis, which associate with biologically aggressive behaviour (WHO 2007). Though grading based on histology is largely reproducible and well accepted, subjectivity involved and substantial disagreement between pathologists has remained a major concern. Because of inherent sampling problems (mainly due to tumor location in the brain) and inadequate sample size available for histological evaluation, there exists a very high possibility of error in grading. Recent studies have attempted to characterize the molecular basis for the histological and prognostic differences between grade III and grade IV astrocytoma. While reports have shown the grade specific profile of gene expression, there is no molecular signature that can accurately classify grade III and grade IV astrocytoma samples. In the current work, we have identified molecular signatures for the accurate classification of grade III and grade IV astrocytoma patients by using transcriptome and miRNome data. The receptor tyrosine kinase pathway is known to be overexpressed in 88% of glioblastoma patients. The expression and activation of the receptors is reported to be deregulated by events like amplification and activating mutations. The aberrant expression of RTKs could also be due to the deregulation of miRNAs, which, in the untransformed astrocytes regulate and fine-tune the levels of the RTKs. In the current study, we have identified that tumor suppressor miRNA miR-219-5p regulates RTK pathway by targeting EGFR and PDGFRα. Part I. Transcriptome approach: Identification of a 16-gene signature for classification of malignant astrocytomas In order to obtain a more robust molecular classifier to accurately classify grade III and grade IV astrocytoma samples, we used transcriptome data from microarray study previously performed in our laboratory. The differential regulation of 175 genes identified from microarray was validated in a cohort of grade III and grade IV patients by real-time qRT-PCR. In order to identify the classification signature that can classify grade III and grade IV astrocytoma samples, we used the expression data of 175 genes for performing Prediction Analysis of Microarrays (PAM) in the training set of grade III and grade IV astrocytoma samples. PAM analysis identified the most discriminatory 16-gene expression signature for the classification of grade III and grade IV astrocytoma. The Principal Component Analysis (PCA) of 16-genes astrocytoma patient samples revealed that the expression of 16-genes could classify grade III and grade IV astrocytoma samples into two separate clusters. In the training set, the 16-gene signature was able to classify grade III and grade IV patients with an accuracy rate of 87.9% as tested by additional analysis of Cross-Validated probability by PAM. The 16-gene signature obtained in the training set was validated in the test set with diagnostic accuracy of 89%. We further validated the 16-gene signature in three independent cohorts of patient samples from publicly available databases: GSE1993, GSE4422 and TCGA datasets and the classification signature got validated with accuracy rates of 88%, 92% and 99% respectively. To address the discordance in grading between 16-gene signature and histopathology, we looked at the clinical features (age and survival) and molecular markers (CDKN2A loss, EGFR amplification and p53 mutation) that differ substantially between grade III and grade IV in discordant grade III and grade IV samples. The grading done by 16-gene signature correlated with known clinical and molecular markers that distinguish grade III and grade IV proving the utility of the 16-gene signature in the molecular classification of grade III and grade IV. In order to identify the pathways that 16 genes of the classification signature could regulate, we performed protein-protein interaction network and subsequently pathway analysis. The pathways with highest significance were ECM (extracellular matrix) and focal adhesion pathways, which are known to be involved in the epithelial to mesenchymal transition (EMT), correlating well with the aggressive infiltration of grade IV tumors. In addition to accurately classifying the grade III and grade IV samples, the 16-gene signature also demonstrated that genes involved in epithelial-mesenchymal transition play key role in distinguishing grade III and grade IV astrocytoma samples. Part II. miRNome approach microRNAs (miRNAs) have emerged as one of the important regulators of the interaction network that controls various cellular processes. miRNAs are short non-coding RNAs (mature RNA being 21-22nt long) that regulate the target mRNA by binding mostly in the 3’ UTR bringing about either translational repression or degradation of the target. miRNAs are shown to play key roles in cell survival, proliferation, apoptosis, migration, invasion and various other characteristic features that get altered in human cancers. miRNAs are characterized to have oncogenic or tumor suppressor role and the aberrant expression of miRNAs is reported in multiple human cancer types. Part A. Genome-wide expression profiling identifies deregulated miRNAs in malignant astrocytoma With an aim to identify the role of miRNAs in the development of in malignant astrocytoma, we performed a large-scale, genome-wide microRNA (miRNA) (n=756) expression profiling of 26 grade IV astrocytoma, 13 grade III astrocytoma and 7 normal brain samples. Using Significance Analysis of Microarrays (SAM), we identified several differentially regulated miRNAs between control normal brain and malignant astrocytoma, grade III and grade IV astrocytoma, grade III astrocytoma and grade IV secondary GBM, progressive pathway and de novo pathway of GBM development and also between primary and secondary GBM. Importantly, we identified a most discriminatory 23-miRNA expression signature, by using PAM, which precisely distinguished grade III from grade IV astrocytoma samples with an accuracy of 90%. We re-evaluated the grading of discordant samples by histopathology and identified that one of the discordant grade III samples had areas of necrosis and it was reclassified as grade IV GBM. Similarly, out of two discordant grade IV samples, one sample had oligo component and it was reclassified as grade III mixed oligoastrocytoma. Thus, after the revised grading, the prediction accuracy increased from 90% to 95%. The differential expression pattern of nine miRNAs was further validated by real-time RT-PCR in an independent set of malignant astrocytomas (n=72) and normal samples (n=7). Inhibition of two glioblastoma-upregulatedmiRNAs (miR-21 and miR-23a) and exogenous overexpression of two glioblastoma-downregulatedmiRNAs (miR-218 and miR-219-5p) resulted in reduced soft agar colony formation but showed varying effects on cell proliferation and chemosensitivity. Thus, we have identified the grade specific expression of miRNAs in malignant astrocytoma and identified a miRNA expression signature to classify grade III astrocytoma from grade IV glioblastoma. In addition, we have demonstrated the functional relevance of miRNA modulation and thus showed the miRNA involvement and their importance in astrocytoma development. Part B. miR-219-5p inhibits the receptor tyrosine kinase pathway by targeting mitogenic receptor kinases in glioblastoma The receptor tyrosine kinase (RTK) pathway, being one of the important growth promoting pathways, is known to be deregulated in 88% of the patients with glioblastoma. In order to understand the role of miRNAs in regulating the RTK pathway, we undertook a screening procedure to identify the potential miRNAs that could target different members of the RTK pathway. From the screening study involving bioinformatical prediction of miRNAs and subsequent experimental validation by modulation of miRNA levels in glioma cell lines, we identified miR-219-5p as a candidate miRNA. The overexpression of miR-219-5p reduced the protein levels of both EGFR and PDGFRα. We confirmed the binding of miR-219-5p to the 3’ UTRs by using reporter plasmids. We also confirmed the specificity of miR-219-5p binding sites in the 3’ UTR of EGFR by site directed mutagenesis of binding sites which abrogated the miRNA-UTR interaction. The expression of miR-219-5p was significantly downregulated in grade III as well as in grade IV astrocytoma samples in the miRNA microarray experiment and we further validated the downregulation in an independent cohort of grade III and grade IV astrocytoma patients by real-time qRT-PCR. The ectopic overexpression of miR-219-5p in glioma cell lines inhibited cell proliferation, colony formation, anchorage independent growth and the migration of glioma cells. In addition, overexpression of miR-219-5p decreased MAPK and PI3K pathways, in concordance with its ability to target EGFR and PDGFRα. Additionally, for the further characterization of miR-219-5p – EGFR interaction and its effect on MAPK and PI3K pathways, we used U87 glioma cells that stably overexpress wild-type EGFR and constitutively active ΔEGFR (both lacking 3’-UTR and thus being insensitive to miR-219-5p overexpression) along with U87 parental cells. In these cell lines with the overexpression of EGFR lacking 3’-UTR, miR-219-5p was unable to inhibit - MAPK and PI3K pathways and also glioma cell migration suggesting that these effects were indeed because of its ability to target EGFR. Further, in the glioblastoma patient cohort (TCGA dataset), we found significant negative correlation between EGFR protein levels, both total EGFR and phospho EGFR and miR-219-5p levels in the glioblastoma tissue samples suggesting a role of miR-219-5p in increasing the protein levels of EGFR in glioblastoma. In summary, we have identified and characterized miR-219-5p as the RTK regulating tumor suppressor miRNA in glioblastoma.

La glycogénose de type Ia (GSDIa) est une maladie métabolique rare causée par un déficit en glucose-6- phosphatase (G6Pase), menant à l'absence de production endogène de glucose. Cette pathologie est caractérisée par des hypoglycémies sévères, une hépatomégalie et une stéatose hépatique ainsi qu'une néphromégalie. En absence de traitement curatif, la prise en charge de cette maladie repose actuellement sur des mesures diététiques très strictes. Cependant, des complications apparaissent avec l'âge comme le développement de tumeurs hépatiques et la progression de la néphropathie vers l'insuffisance rénale. Afin d'étudier l'évolution de cette pathologie à long terme, nous avons utilisé des modèles murins originaux présentant une invalidation du gène de la sous-unité catalytique de la G6Pase spécifiquement au niveau du foie ou des reins. Dans ce travail, nous avons démontré que la déficience en G6Pase uniquement au niveau des reins est suffisante pour entrainer le développement de la pathologie rénale de la GSDIa. Les souris déficientes en G6Pase hépatique nous ont permis de mettre en évidence les effets délétères d'une consommation modérée de fructose ou de galactose et d'une alimentation riche en lipides, de type « cafétéria », sur la pathologie hépatique de la GSDIa, en particulier sur le développement tumoral. Nous avons également démontré chez ces souris l'efficacité et l'innocuité d'un traitement par thérapie génique ciblant le foie. Le transfert de gène avec un vecteur lentiviral, permettant l'intégration du transgène au génome, semble plus efficace qu'avec un vecteur AAV pour prévenir le développement de la pathologie hépatique de la GSDIa et l'apparition des tumeurs / Glycogen storage disease type Ia (GSDIa) is a rare metabolic disease caused by glucose-6-phosphatase (G6Pase) deficiency, leading to the absence of endogenous glucose production. This pathology is characterized by severe hypoglycemia, hepatomegaly, hepatic steatosis and nephromegaly. In the absence of a curative therapy, the current treatments available consist in strict dietary management. However, various complications occur with aging, such as hepatic tumor development and progressive chronic renal disease leading to renal failure. In order to study the long term pathology development, we used original mouse models, presenting an invalidation of the gene encoding the G6Pase catalytic subunit, specifically in the liver or in the kidneys. In this work, we demonstrated that renal G6Pase deficiency alone is sufficient to induce the development of the GSDIa nephropathy. Mice with liver-specific G6Pase deficiency allowed us to highlight the deleterious effects of high-fat diet, such as « fast-food » diet, as well as moderate consumption of fructose or galactose on the hepatic GSDIa pathology, particularly on tumor development. Furthermore, we demonstrated the efficiency and innocuity of gene therapies targeting the liver in these mice. Gene transfer with a lentiviral vector, allowing transgene integration into the genome, seems to be more efficient than an AAV vector in preventing the development of hepatic GSDIa pathology and tumor formation

Les cellules cancéreuses ayant des propriétés souches, appelées cellules souches cancéreuses (CSCs), sont au sommet de l'organisation hiérarchique des tumeurs et sont soupçonnées d'être responsable des rechutes et de la formation de métastases. Cependant, nous nous sommes demandé comment ces cellules sont-elles capables de supporter le stress métabolique lié à l'oncogène et de croitre dans un environnement nutritif défavorable distinct de celui d'une tumeur établie ? Nous avons mis en évidence dans ce travail le rôle de la réponse aux glucocorticoïdes dans le contrôle de la plasticité mammaire et l'induction d'une plasticité métabolique nécessaire au maintien du potentiel tumorigène des CSCs. Nous avons montré qu'en régulant la reprogrammation cellulaire via l'induction du gène MAFB, les glucocorticoïdes contrôlent le caractère souche des cellules épithéliales malignes en activant la voie de biosynthèse des hexosamines. L'efficacité anabolique de ces cellules est alors augmentée, favorisant le développement de la tumeur et des métastases. Ensemble, nos résultats suggèrent que l'inhibition de l'activité métabolique des glucocorticoïdes pourrait être une stratégie pour éliminer les CSCs et traiter les tumeurs mammaires / Cancer cells with stemness properties - generally designated cancer stem cells (CSCs) - are at the apex of the hierarchical organisation of tumours and are believed to drive tumour recurrence and metastasis formation. However, how they perform these neoplastic activities in a nutritive environment that is distinct from the one in an established tumour is unknown. Here, we unveil the prominent role of glucocorticoid activity in the control of mammary cancer cell plasticity and the induction of metabolic pliancy necessary for the tumorigenic potential of CSCs. By regulating MAFB-dependent cell reprogramming, glucocorticoids control stemness traits in malignant epithelial cells. As an integral part of this regulation, glucocorticoids activate the hexosamine biosynthetic pathway and rewire the metabolism of CSCs. The anabolic efficiency of these cells increases then, fostering tumour and metastasis development. Together, our findings suggest that inhibition of glucocorticoid metabolic activity could be an original strategy for CSC eradication and tumour treatment

Un enjeu majeur en cancérologie est de réduire le risque de développement métastatique et de rechute. La transition épithélio-mésenchymateuse (EMT), processus physiologique au cours de l'embryogenèse, est un mécanisme central de la carcinogenèse, contribuant de façon précoce à la transformation et la dissémination des cellules tumorales via l'inhibition de la surveillance cellulaire (apoptose et senescence) et l'acquisition de capacités migratoires et invasives. Une autre caractéristique des cancers est la capacité d'échapper à la réponse immunitaire, puissante barrière anti-tumorale. Mais les cellules tumorales entretiennent des relations complexes avec le système immunitaire. Alors que la propension de l'inflammation et des cellules immunitaires innées à favoriser le développement tumoral et l'échappement immunitaire, via l'induction de l'EMT et le maintien d'un microenvironnement immuno-suppresseur, a été bien étudiée, le rôle éventuel de la réponse immunitaire adaptative dans la promotion de l'EMT est quant à lui peu connu. Grâce au développement d'un modèle murin de lignée tumorale mammaire plastique surexprimant l'oncogène Her2/Neu, ce travail démontre in vivo la capacité des cellules tumorales à subir l'EMT, induite par la réponse immunitaire médiée par les lymphocytes T. La déplétion spécifique des lymphocytes T (LT) CD4 restaure le phénotype épithélial de la tumeur, indiquant que les LT CD4 médient une réponse immunitaire induisant l'EMT. En retour, l'EMT confère aux cellules tumorales la capacité de modeler l'immunité comme le recrutement de neutrophiles. Ce travail apporte un nouvel éclairage sur les interactions entre cellules tumorales et système immunitaire / Current clinical challenge in many carcinomas is to reduce the risk of metastasis development and cancer recurrence. Epithelial-mesenchymal transition (EMT), a physiological process during embryogenesis, is a central mechanism in oncogenesis. EMT induction contributes to early transformation and dissemination through inhibition of cellular surveillance (apoptosis and senescence) and increased migrative and invasive behavior. Another necessary hallmark of cancer is the ability of tumor cells to evade immune surveillance, a powerful barrier against tumor progression. But cancer cells enjoy intricate relations with the immune system. Whereas inclination of inflammation and innate immune cells to favor tumor development and immune escape, via EMT induction and immunosuppressive microenvironment maintenance, has been well investigated, the role of adaptive immune response in EMT promotion is understudied. Based on the development of a plastic murine mammary tumor cell line model overexpressing Her2/Neu oncogene, this study demonstrate in vivo that tumor cells keep an epithelial phenotype in adaptive immunodeficient mice but undergo EMT under the pressure of T-cell mediated immune response, characterized by loss of epithelial EpCAM marker and acquisition of mesenchymal features and EMT transcriptomic signature. CD4 T cell depletion but not CD8 restores the epithelial phenotype of tumors, suggesting that CD4 T cells mediate an immune response that could lead ton EMT induction. In return, EMT confers the ability of tumor cells to shape immunity like intra-tumor neutrophil infiltration. This work shed a new light on interactions between tumor cells and immune system