Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 4 uppsatser.

Dissertation (Ph.D.)--University of South Florida, 2005. / Includes vita. Includes bibliographical references. Also available online in PDF format.

Τα τελευταία χρόνια πολλές ερευνητικές ομάδες εστίασαν στην ταυτοποίηση γονιδίων που ενέχονται σε διάφορες βιολογικές διεργασίες και η Δροσόφιλα αποτέλεσε τον ιδανικό οργανισμό-μοντέλο λόγω της διαθεσιμότητας πολλών γενετικών εργαλείων. Η ανάπτυξη της τεχνολογίας της RNA παρεμβολής ευνόησε ιδιαίτερα την ευρείας κλίμακας γενετική ανάλυση στη Δροσόφιλα. Εκμεταλλευόμενοι τα διαθέσιμα εργαλεία πραγματοποιήσαμε μία μελέτη σάρωσης βασισμένη σε RNAi για γονίδια που εμπλέκονται στη μορφογένεση του συστήματος των σωματικών μυών και του επιθηλίου του φτερού της Drosophila melanogaster. Συνολικά, εξετάσαμε 321 γονίδια με συστημική ή ιστοειδική RNAi σιώπηση στο μεσόδερμα ή με συνδυασμό και των δύο και ταυτοποιήσαμε 58 γονίδια άγνωστης λειτουργίας τα οποία χρειάζονται για την ανάπτυξη και ομοιόσταση του εμβρυϊκού/προνυμφικού μυϊκού συστήματος. Περιέργως, στις μισές σχεδόν περιπτώσεις δεν παρατηρήσαμε φαινότυπο θνησιμότητας πλήρους διεισδυτικότητας, γεγονός που υποδεικνύει ότι ο αριθμός των γονιδίων που συμμετέχουν στη συγκεκριμένη διεργασία είναι μεγαλύτερος από αυτόν που έχει προβλεφθεί με βάσει τα αποτελέσματα μίας ευρείας κλίμακας μελέτης σάρωσης με RNAi στο μυϊκό σύστημα που ολοκληρώθηκε πρόσφατα. Επιπλέον, μελετήσαμε 242 γονίδια με ιστοειδική σιώπηση στα επιθήλια και ταυτοποιήσαμε 32, τα οποία είναι απαραίτητα για τη βιωσιμότητα, και 24, τα οποία είναι αναγκαία για τη μορφοποίηση του ενήλικου φτερού. Από τα γονίδια που έδωσαν θετικό αποτέλεσμα επιλέξαμε ένα το οποίο είναι απαραίτητο και για τις δύο διεργασίες, το chd64. Το chd64 κωδικοποιεί μία πρωτεΐνη που αποτελείται από μία δομική περιοχή με ομολογία στις καλπονίνες (CH) και ένα μοτίβο CLIK23 και παρουσιάζει 42% και 43% ταυτότητα με τις τρανσγελίνες 2 και 3 των θηλαστικών αντιστοίχως. Οι τρανσγελίνες συνιστούν μία οικογένεια πρωτεϊνών που εμφανίζουν υψηλό βαθμό συντήρησης και συμμετέχουν στο σχηματισμό δεσμίδων και στη σταθεροποίηση των ινιδίων ακτίνης. Το γονιδίωμα της Δροσόφιλας εμπεριέχει τρεις διαφορετικούς γενετικούς τόπους: CG4694 ή Mp20, CG14996 ή Chd64 and CG5023, σε πλήρη αναλογία με τα γονιδιώματα των θηλαστικών. Τα προκαταρκτικά αποτελέσματα μας έδειξαν ότι από τα γονίδια που κωδικοποιούν τις τρεις τρανσγελίνες της Δροσόφιλας μόνο το Chd64 είναι απαραίτητο για τη βιωσιμότητα και τη σωστή ανάπτυξη των μυϊκών και επιθηλιακών ιστών. Για να μελετήσουμε τη λειτουργία του γονιδίου ήταναπαραίτητο: α) να διερευνήσουμε το πρότυπο έκφρασης του και β) να αξιολογήσουμε τα αποτελέσματα της απώλειας λειτουργίας του σε διαφορετικούς ιστούς. Έτσι, δημιουργήσαμε διαγονιδιακές μύγες που έφεραν τυχαίες ενθέσεις ενός γενωμικού τμήματος του γονιδίου συζευγμένου με GFP που επέτρεπε την παρατήρηση του ενδογενούς προτύπου έκφρασης του γονιδίου σε ζωντανό οργανισμό κατά τη διάρκεια της ανάπτυξης. Ταυτόχρονα, δημιουργήσαμε ένα αντίσωμα έναντι ολόκληρης της πρωτεΐνης Chd64. Επιπλέον, προμηθευτήκαμε δύο UAS:chd64IR στελέχη και πολλά διαφορετικά GAL4 στελέχη με σκοπό να μελετήσουμε την επίδραση της μειορρύθμισης του chd64 σε διαφορετικούς ιστούς. Τέλος, δημιουργήσαμε δύο ελλείψεις που απομακρύνουν το chd64. Τα δεδομένα που έχουμε ως τώρα δείχνουν ότι το chd64 εκφράζεται έντονα στον εμβρυϊκό/προνυμφικό πεπτικό σωλήνα, στα αιμοκύτταρα, στην τραχεία, στο νευρικό σύστημα, στα περιτραχειακά κύτταρα Inka, στους εμβρυϊκούς δίσκους, στους σιελογόνους αδένες, στην επιδερμίδα και στα τενόντια κύτταρα. Επιπλέον, διαπιστώσαμε έκφραση του γονιδίου στα θυλακοκύτταρα και μισχοειδή κύτταρα των ωοθυλακίων. Σε όλους τους παραπάνω κυτταρικούς τύπους η πρωτεΐνη συσσωρεύεται στο κυτταρόπλασμα και στην περιφέρεια του κυττάρου. Λεπτομερέστερη ανάλυση των μεγάλων κυττάρων των σιελογόνων αδένων έδειξε ότι η πρωτεΐνη εντοπίζεται σε μεβρανικές δομές που αντιστοιχούν στο ενδοπλασματικό δίκτυο και στο φλοιό του κυττάρου, όπου συνεντοπίζεται με την ακτίνη. Οι μελέτες απώλειας λειτουργίας έδειξαν ότι έκφραση του chd64 είναι απαραίτητη για τη βιωσιμότητα και τη μορφολογία ή/και λειτουργικότητα των μαλπιγγιανών σωληναρίων. Συγκεκριμένα, διαπιστώσαμε ότι η αναστολή της ζυγωτικής έκφρασης του γονιδίου οδηγεί σε διόγκωση των μαλπιγγιανών σωληναρίων και σχετίζεται με τη μη φυσιολογική υποκυτταρική κατανομή της DE-καδερίνης. Ωστόσο, ο τρόπος δράσης του γονιδίου στην προαναφερθείσα διαδικασία παραμένει άγνωστος. Η απομάκρυνση της μητρικής προέλευσης Chd64 πρωτεΐνης και η εκτενέστερη εξέταση της διαδικασίας καθορισμού και της πολικότητας των κυττάρων που συγκροτούν τα μαλπιγγιανά σωληνάρια σε αγρίου τύπου και μεταλλαγμένο γενετικό υπόβαθρο με τη χρήση κατάλληλων μαρτύρων θα μας δώσουν νέες πληροφορίες σχετικά με τη λειτουργία του γονίδιου σε ολόκληρο τον οργανισμό. / In the past years many research groups have focused in the identification of genes that are involved in distinct biological processes and Drosophila has provided the ideal model-organism due to the availability of several genetic tools. The introduction of RNAi technology has greatly facilitated the conduction of many large scale genetic analyses in Drosophila. Taking advantage of the available tools we conducted an RNAi-based screen for genes involved in the morphogenesis of the somatic muscle system and wing epithelium of Drosophila melanogaster. Collectively, we tested 321 genes with either systemic or tissue-specific RNAi silencing in the mesoderm or a combination of both and discovered 58 novel genes which are required for proper development and homeostasis of the embryonic/larval muscular system. Surprisingly, in almost half of the cases we did not observe a lethal phenotype of complete penetrance arguing that the number of genes involved in the particular process is greater than the one estimated based on the results of a recently completed genome-wide scale RNAi-based muscle screen. In addition, we tested 242 genes by tissue-specific gene inactivation in the epithelia and identified 32 that are required for adult viability and 24 that are indispensible for proper adult wing morphogenesis. Among our positive hits we selected one that is required for both processes for further examination, namely chd64. Chd64 encodes a protein that consists of a calponin-homology (CH) domain and a CLIK23 motif and exhibits 42% and 43% identity with the mammalian transgelins 2 and 3 respectively. Transgelins comprise a highly conserved family of proteins that have been implicated in the bundling and stabilization of actin filaments. The Drosophila genome bears three distinct loci: CG4694 or Mp20, CG14996 or Chd64 and CG5023 by complete analogy to the mammalian genomes. Our initial results showed that out of the three genes that code for the fly transgelins only chd64 is required for viability and the proper development of muscle and epithelial tissues. In order to gain insight into the function of chd64 it was crucial to: a) explore the expression pattern of the gene and b) evaluate the effects of chd64 loss of function in diverse tissues. Thus, we generated transgenic flies that bear random insertions of a GFP-tagged genomic fragment for the gene that allowed us to visualize the endogenous gene expression pattern in the living organism throughout development. Meanwhile, we developed an antibody against the full-length Chd64 protein. Inaddition, we obtained two different UAS:chd64IR strains and many tissue specific GAL4 strains in order to explore the effects of chd64 knock-down in the specific tissues. Finally we generated two deletions that remove chd64. Our data so far indicate that chd64 is largely expressed in the embryonic/larval gut, hemocytes, trachea, nervous system, peritracheal Inka cells, imaginal discs, salivary glands, epidermis and tendon cells. In addition, we observed chd64 expression in the follicle and stalk cells of egg chambers. In all the above mentioned cell types the protein is accumulated in the cytoplasm and periphery. More detailed analysis using the large salivary gland cells shows that Chd64 is specifically localized in some membranous structures of the cytoplasm corresponding to the ER and in the cell cortex where it colocalises with actin. Our loss of function studies demonstrate that chd64 expression is indispensable for viability and for the normal morphology and/or function of malpighian tubules. We specifically observed that the ablation of chd64 zygotic expression results in the appearance of bloated tubules and is involved in the abnormal subcellular distribution of DE-cadherin. However the mode of the gene’s action in the above mentioned procedure remains unknown. Consequently, we conclude that chd64 exhibits a complicated expression pattern during development and is required for viability. Removal of the maternally derived Chd64 protein and further examination of malpighian tubule cell specification and polarity using specific markers in wild type and mutant backgrounds will provide a novel insight on the gene’s functions in the whole organism.

O carrapato bovino Rhipicephalus (Boophilus) microplus é o principal vetor da riquétsia Anaplasma marginale, o agente etiológico da anaplasmose, uma doença que acomete os rebanhos e causa sérios prejuízos econômicos à pecuária no Brasil. Estabelecemos em nosso laboratório o cultivo da linhagem de células BME26 que são originárias do R. (B.) microplus e também a infecção dessas células por A. marginale, um patógeno que é naturalmente transmitido pelo carrapato. Detectamos que a expressão gênica da defensina e da ixodidina nas células é aumentada frente à infecção por A. marginale, embora nenhuma alteração da expressão gênica da microplusina foi constatada. As células foram expostas a microorganismos inativados por calor e LPS, sendo que a expressão gênica da microplusina é aumentada frente a todos os estímulos. Na exposição das células BME26 com a bactéria Microccocus luteus, a expressão gênica da defensina e da ixodidina não foi alterada e no estimulo com leveduras a expressão gênica da ixodidina foi reprimida. Frente à infecção por A. marginale detectamos, aumento expressão da defensina e ixodidina. Os genes da microplusina e defensina foram silenciadas por RNAi em células infectadas por A. marginale, mas não houve alteração no número de riquétsias / The cattle tick Rhipicephalus (Boophilus) microplus is the main vector of the rickettsia Anaplasma marginale, the etiological agent of anaplasmosis, a disease that affects cattle and causes serious economic losses to the Brazilian cattle industry. We established in our laboratory the embryonic cell culture line BME26 from R. (B.) microplus and infection by A. marginale, a pathogen naturally transmitted by R. (B.) microplus. We verified that defensin and ixodidin gene expression increased in these cells after an infection by A. marginale and no alteration in microplusin gene expression was detected. The BME26 cells were exposed to heat-inactivated microorganims or to LPS, microplusin gene expression increased after all stimuli. After exposure of BME26 cells to Micrococcus luteus, expression levels of defensin and ixodidin did not change and ixodidin gene expression reduced after exposure of these cells to yeast. In the infection by A. marginale we detected defensin and ixodidin gene expression. Also, microplusin and defensin genes were silenced by RNA interference (RNAi) in A. marginale-infected BME26 cells, but we did not observe alteration in the number of MSP4 rickettsias

L’incidence du cancer du rein et sa mortalité associée se sont accrues au cours des dernières années. Le type de cancer rénal le plus fréquent est celui nommé Cancer Rénal à Cellules Claires (CRCC) où le plus souvent, le gène suppresseur de tumeur Von Hippel Lindau (VHL) est inactivé. Malgré une détection plus précoce, l’évolution de la pathologie demeure incertaine, en particulier quand les patients développent des métastases ou acquièrent une résistance au traitement (25-30% des patients). De nouvelles thérapies ciblant des kinases (Sunitinib, Sorafenib ou Temsirolimus) bien que très prometteuses conduisent très souvent à l’acquisition de résistance. Dans ce contexte, il est urgent de développer de nouveaux modèles prédictifs de la réponse des patients aux traitements et d'identifier de nouvelles cibles thérapeutiques.Ma thèse de science visait trois objectifs complémentaires : 1) Identifier par criblage chimio-génomique des kinases comme cibles thérapeutiques combinées. 2) Etablir deux modèles de culture 3D de cancer du rein qui intègrent le microenvironnement d’une tumeur: les sphéroïdes et la culture organotypique de coupe de tissus. 3) Etudier la chimio-sensibilité de ces modèles à une combinaison de molécules identifiées dans le criblage.Un criblage cellulaire a été réalisé sur la plateforme de Criblage de Molécules BioActives (CEA- Grenoble). Il a consisté à tester 80 molécules inhibitrices de protéine-kinases en combinaison avec l’extinction génique par interférence ARN (shRNAs lentiviraux) de 36 cibles potentielles connues pour leur implication dans divers cancers. La lignée cellulaire choisie (786-O) est dérivée d’une tumeur rénale à cellules claires radio et chimio-résistante et dépourvue de VHL. Parmi les touches qui compromettent la viabilité des cellules 786-O, la combinaison choisie pour son efficacité cible deux kinases importantes dans le contrôle de la survie cellulaire et de la réparation de l’ADN CK2 et ATM. Le statut VHL des cellules module de façon dramatique leur sensibilité à cette combinaison, l’association de ces deux inhibiteurs étant plus efficace sur les cellules 786-O (VHL -) que sur les mêmes cellules dans lesquelles VHL a été réintroduit (VHL+). Au sein d’une tumeur, les différents niveaux d’oxygénation constituent une variation environnementale supplémentaire créant des susceptibilités ou des résistances aux traitements thérapeutiques. Pour déterminer l’impact de nos molécules dans ce contexte, nous avons testé la viabilité des cellules 786-O VHL+ et VHL- dans des conditions normoxiques (21% O2) ou hypoxiques (1,5% O2), en présence des molécules seules ou en combinaison. En normoxie, une diminution synergique de la viabilité des cellules 786-O VHL- est observée en présence de la combinaison, alors que cet effet n’a pas lieu sur les cellules 786-O VHL+. Cette synergie est potentialisée en condition hypoxique. Au niveau mécanistique, les voies de signalisation de stress cellulaires sont d’avantage activées dans les cellules VHL- en présence de la combinaison de molécules comparé au traitement avec chacune des molécules seules. Dans les sphéroïdes tumoraux multicellulaires reproduisant l’organisation d’une micro-tumeur, nos résultats montrent que notre combinaison de molécules induit d’avantage l’apoptose des cellules VHL- que les molécules seules, alors que les cellules VHL+ ne sont sensibles à aucun des traitements.Ces résultats montrent que l’action de nos molécules combinées est clairement plus efficace dans un modèle 3-D. Ils démontrent également qu’il est possible d’objectiver une pharmaco-modulation de la viabilité de cultures organotypiques de tumeur du rein par des combinaisons d’inhibiteurs chimiques de protéine-kinases. Les perspectives de ce travail sont la validation de cette combinaison sur des tumeurs humaines et l’exploitation des cultures organotypiques comme test personnalisé de réponse aux traitements. / Renal cell carcinoma accounts for 3% of all malignant diseases in adults making it the 10th most common cancer in France. The most frequent type of Kidney cancer is Clear Cell Renal Cell Carcinoma (CCRCC). Almost all CCRCC show an inactivation of the Von Hippel Lindau tumour suppressor gene (VHL). Between 25-30% of the patients will develop metastatic renal cell carcinoma (mRCC) by the time they are diagnose or become unresponsive to all treatments and in these cases, the disease has a rapid progression. Over the past years, kinase-targeted therapies (Sunitinib, Sorafenib, Temsirolimus) have become the mainstay of treatment for mRCC, however, most, if not all, patients acquire resistance to these approaches over time.In this context my PhD had 3 goals: a) to find a new combinatory targeted therapy through a High Throughput Screening; b) to establish 3D models mimicking the real environment of the tumours (spheroids, Tissue Slice Culture); c) to validate the Hits through different molecular and cellular biology studies.We conducted a synthetic lethal screen on the CMBA platform (CEA-Grenoble), choosing 36 potential genes targets and 80 kinases inhibitors drugs. Each of the target gene was silenced by a transduction with shRNA Lentivirus into the 786-O cell line derived from ccRCC that lacks the tumour suppressor VHL, is radio- and chemo-therapy resistant, has increased mobility and is highly metastatic. Among the hit combinations that affect cell viability, one of them was chosen because it targets two important kinases involved in cell survival and DNA repair: CK2 and ATM. Moreover, this combination is specifically more active in the 786-O VHL- cells than in 786-O VHL+ cell line. We evaluated the effect of our drugs on the viability of our 786-O VHL+ and VHL- cells in normoxic (21% O2) or hypoxic (1.5% O2) conditions that reflect different environments that are present in a tumour. Surprisingly, in normoxia, we found a synergetic effect of the drug mix only on the 786-O VHL- cells but not on 786-O VHL+ cells. Furthermore, this effect was even stronger in conditions of Hypoxia (up to 20% of synergism).Mechanistically, an up-regulation of the stress pathways was much stronger in the VHL- cells in the presence of the combination than with the drugs alone. No apoptosis was detected in this 2D models. In Multi-Cellular Tumour Spheroid (MCTS) where the organization of a micro-tumour is reproduced, our drugs are even more effective in inducing cell apoptosis than in 2D monolayers of 786-O VHL- cells. These results also demonstrate that pharmaco-modulation of viability of renal tumour organotypic culture by chemical combination targeting protein kinases can be studied. Perspectives of this work are the validation of this drug combination on human renal tumours and the use of organotypic culture as a test for personalized treatment response.

Chez la femme, le cancer du sein est le cancer le plus fréquemment diagnostiqué. Différents traitements sont disponibles selon le sous-type tumoral. Cependant, certaines patientes sont réfractaires à ces thérapies et restent vulnérables lors de récidives. Le cancer a longtemps été défini par une division aberrante des cellules, mais aujourd'hui, il est évident que la résistance à la mort cellulaire programmée est un paramètre majeur dans l'étiologie de la maladie.Les cyclines de type D régulent le cycle cellulaire en permettant la transition de la phase G1 à la phase S. Pour cela, elles activent les kinases dépendantes des cyclines 4/6 (CDK4/6) qui phosphorylent les protéines du rétinoblastome ce qui libère le facteur de transcription E2F. La Cycline D1 (CycD1) nucléaire est donc centrale dans le contrôle du cycle. Son gène est amplifié dans les cancers humains et la moitié des patientes atteintes d'un cancer du sein ont une surexpression de CycD1. Par l’activation de CDK4, CycD1 est essentielle à l'apparition et à la progression tumorale. Ainsi, des inhibiteurs spécifiques de CDK4/6 ont été développés contre le cancer du sein. Malheureusement, certaines patientes restent insensibles à ce traitement. À ce titre, le ciblage spécifique de CycD1 pourrait représenter une alternative clinique. En effet, en plus de la régulation du cycle, CycD1 est également impliquée, indépendamment de CDK4, dans la survie des cellules cancéreuses. Cependant, aucun mécanisme de l'impact de CycD1 dans le maintien tumoral n'a été établi pour démontrer ce potentiel thérapeutique. En outre, CycD1 a été décrite dans les organes à l’âge adulte pour réguler le métabolisme du glucose et l'hématopoïèse. Par conséquent, pour éviter tout effet secondaire indésirable, nous avons décidé d’évaluer l’implication potentielle de CycD1 dans les organes adultes. Grâce au Tandem-HTRF, basé sur le transfert d'énergie entre deux anticorps, nous avons révélé la dynamique inattendue de CycD1 dans chaque organe adulte. De plus, nous avons montré que l’altération de l'expression de CycD1 conduit à une diminution des capacités de survie des cellules saines post-mitotiques.Au vu de ces limitations, nous avons développé une nouvelle approche d'ARN interférence spécifique des cellules cancéreuses appelée TAG-RNAi. Cette technologie permet de cibler CycD1 uniquement dans la tumeur afin d'épargner les cellules saines. Cette approche innovante consiste à cibler un tag présent uniquement sur l’ARNm de CycD1 des cellules cancéreuses. Ainsi, nous avons découvert que le ciblage spécifique de CycD1 induit une régression rapide et spontanée des tumeurs dépendantes des oncogènes RAS ou ERBB2. Par protéomique in vivo, j'ai découvert que lors de stress pro-apoptotiques, CycD1 cytoplasmique interagit avec la procaspase-3 et bloque son activation pour empêcher l'apoptose des cellules. Ces travaux démontrent la valeur clinique du ciblage spécifique de CycD1 dans les cancers afin d'améliorer l'efficacité des chimiothérapies.Par conséquent, il restait à déterminer comment appliquer le TAG-RNAi contre CycD1 uniquement dans les cellules cancéreuses des patientes. Puisque le tag exotique présent sur le gène Ccnd1 chez la souris nous a permis de cibler spécifiquement les cellules cancéreuses, nous avons pensé que des mutations retrouvées dans les cancers humains représentaient une option de ciblage. Ainsi, nous avons étendu le concept TAG-RNAi aux mutations somatiques caractéristiques des cancers pour cibler avec succès l'expression des mutants KRAS-G12V ou BRAF-V600E comme exemples. L'idée est donc d'identifier les mutations de Ccnd1 chez les patientes afin d'appliquer le TAG-RNAi comme une thérapie personnalisée afin d’éviter les effets secondaires. Enfin, l'expression de CycD1 représente un nouveau biomarqueur pour le cancer et les troubles liés à l'âge: de faibles taux prédisposent aux maladies dégénératives tandis que des taux élevés indiquent une susceptibilité accrue au cancer. / Breast cancer is the most frequently diagnosed cancer in women. This cancer is the leading cause of death in women aged from 35 to 65 years old. Different treatments are now available depending on tumor subtypes. However, some patients are still refractory to these therapies and are at risk of disease relapse. Cancer research has long focused on aberrant cancer cell division but today it is evident that the resistance to programmed cell death is also a major characteristic of the disease.D-type cyclins regulate cell cycle by allowing the transition from the G1-phase to the S-phase. These regulatory subunits activate the Cyclin-Dependent Kinases 4/6 (CDK4/6) that phosphorylate the retinoblastoma proteins which then release the E2F transcription factors. Nuclear Cyclin D1 (CycD1) is therefore central in the control of division. The Ccnd1 gene is amplified in human cancers and half of breast cancer patients bare an overexpression of CycD1. CycD1 is required for mammary carcinoma onset and progression in a CDK4 kinase-dependent manner. Hence, specific CDK4/6 inhibitors have been developed and authorized in the clinics against breast cancer. Unfortunately, some patients remain insensitive to this treatment. In this frame, the specific targeting of CycD1 could represent a strategic alternative in clinics to overcome these pitfalls. Indeed, in addition to cell cycle regulation with CDK4, CycD1 is also involved in CDK4-independent features of cancer cells like cell survival. However, to date, no clear mechanism for the impact of CycD1 in tumor maintenance is established to demonstrate the therapeutic value of its targeting.Moreover, recent studies have demonstrated the participation of CycD1 in adult organs to regulate glucose metabolism and hematopoiesis. As a consequence, to avoid any undesirable side effects, we decided to gauge the potential CycD1 implication in post-mitotic organs body-wide. We set up a new hypersensitive technology named Tandem-HTRF based on the energy transfer between two antibodies to reveal the unexpected dynamics of CycD1 expression in adult organ. Then, we discovered that alterations of CycD1 expression induced dramatic functional consequences on the survival capacities of healthy adult post-mitotic cells.Based on these limitations, we developed a novel RNAi approach specific to cancer cells named TAG-RNAi. This technology allows the silencing of CycD1 in cancer cells only to spare healthy cells. This innovative approach consists in the targeting of a mRNA tag only present on CycD1 from cancer cells. Using this technique, we found that the specific silencing of CycD1 induces a rapid and spontaneous regression of tumors driven by the RAS or ERBB2 oncogenes. Then, thanks to a proteomics screening in vivo, I discovered that under pro-apoptotic stresses the cytoplasmic CycD1 interacts with the procaspase-3 protein and blocks its activation to prevent cancer cell apoptosis. Altogether, my work demonstrates the clinical value of the specific targeting of CycD1 in cancers to increase the efficacy of chemotherapeutic treatments.Hence, it remained to be determined how to apply in patients RNAi against CycD1 only in cancer cells. Because the exotic tagging of its gene was instrumental in mice cancer models, we reasoned that human cancer mutations could represent such a specific tag. We have extended the concept of TAG-RNAi to somatic mutations characteristic of human cancers to successfully target the expression of KRAS-G12V or BRAF-V600E mutants as examples. The idea is therefore to identify Ccnd1 mutations in cancer patients in order to apply TAG-RNAi as a custom therapeutic approach that will manage side effects. More unanticipated, CycD1 expression represents a new biomarker for both cancer and age-related disorders: low CycD1 levels predispose to degenerative complications while high CycD1 levels indicate increased susceptibility to cancer and resistance to treatment.

RNA interference (RNAi) is an evolutionarily conserved, sequence-specific gene silencing pathway found in eukaryotes, in which 21-nucleotide, small interfering RNAs (siRNAs) guide destruction of a corresponding target mRNA. RNAi is a natural mechanism for both genome surveillance and gene regulation. Moreover, siRNAs can be transfected into cultured mammalian cells, causing the sequence-specific ‘knock down’ of an mRNA. My work in the Zamore lab has centered around the Drosophilain vitro system and cultured mammalian cells to study the RNA interference (RNAi) pathway. small interfering RNAs (siRNAs) are incorporated into the RNA-induced silencing complex (RISC), which culminates in the cleavage of a complementary target mRNA. Previous work proved that certain structural features of siRNAs are essential for RNAi in flies, including the requirement for 5´ phosphates and 3´ hydroxyl groups. In cultured mammalian cells, the requirement for a 5´ phosphate also holds true, but we found no evidence to support the necessity for 3´ hydroxyls in either system. In addition, siRNAs can act as single strands entering the pathway downstream of double-stranded siRNAs, both of which are competent in directing the cleavage of its cognate mRNA at a single site. While these key features are a requirement for functional siRNAs, alone they do not determine the efficiency to which an siRNA can enter the RISC. In fact, both strands of an siRNA can enter RISC to a different degree as determined by the stabilities of the 5´ ends of the siRNA strand, a phenomenon termed ‘functional asymmetry’. This characteristic is also reflected in another class of small RNAs involved in gene silencing known as microRNAs (miRNAs), which are processed from long hairpin RNA structures into mature, single-stranded non-coding RNAs. The asymmetric loading of siRNAs suggests that miRNAs are initially generated from siRNA-like duplexes cleaved from the stem of the hairpins. The strand whose 5´ end is less tightly paired will be processed into the mature miRNA, while the other strand is destroyed. By applying the rules of siRNA asymmetry it is possible to predict which side of the stem will be processed into the mature miRNA, a finding verified experimentally by our lab and others. This discovery also has additional implications in designing highly effective siRNAs and in reducing siRNA off-target effects. We used these results to design siRNAs that target the single nucleotide polymorphism in superoxide dismutase that causes the familial form of amyotrophic lateral sclerosis (ALS), but leave the wild-type mRNA intact and functional. Our experiments have helped define the ‘rules’ for creating SNP-specific siRNAs. In particular, we found that only siRNAs with a purine:purine mismatch to the allele not intended for destruction show good discrimination. The placement of the mismatch in a tiled set of siRNAs shows that mismatches located in the 5´ region of the siRNA, a region shown to be responsible for siRNA binding, can not discriminate between alleles. In contrast, mismatches in the 3´ region of the siRNA, the region contributing to catalysis, discriminate between wild-type and mutant alleles. This work is an important step in creating allele-specific siRNAs as therapeutics for dominant negative genetic diseases. But how does RISC cleave its target? By isolating both the 5´ and 3´ cleavage products produced by RISC in the Drosophila in vitro system, we discovered that RISC acts as a Mg2+-dependent endonuclease that cleaves a single phosphodiester bond in the mRNA target, leaving 5´ phosphate and 3´ hydroxyl groups. These findings were a critical step in the demonstration that Argonaute, a protein known to be a component of RISC, is the RNAi endonuclease.

RNA silencing is an evolutionary conserved sequence-specific mechanism of regulation of gene expression. RNA interference (RNAi), a type of RNA silencing in animals, is based on recognition and endonucleolytic cleavage of target mRNA complimentary in sequence to 21-nucleotide (nt) small RNA guides, called small interfering RNAs (siRNAs). Another class of 21-nt small RNAs, called micro RNAs (miRNAs), is endogenously encoded in eukaryotic genomes. Both production of siRNAs from long double-stranded RNA (dsRNA) and biogenesis of miRNAs from hairpin structures are governed by the ribonuclease III enzyme Dicer. Although produced as duplex molecules, siRNAs and miRNAs are assembled into effector complex, called the RNA-induced silencing complex (RISC), as single-strands. A member of the Argonaute family of small RNA-binding proteins lies at the core of all known RNA silencing effector complexes. Plants and animals contain multiple Argonaute paralogs. In addition to endonucleolytic cleavage, Argonaute proteins can direct translational repression/destabilization of mRNA or transcriptional silencing of DNA sequences by the siRNAdirected production of silent heterochromatin. The Schizosaccharomyces pombe genome encodes only one of each of the three major classes of proteins implicated in RNA silencing: Dicer (Dcr1), RNA-dependent RNA polymerase (RdRP; Rdp1), and Argonaute (Ago1). These three proteins are required for silencing at centromeres and for the initiation of transcriptionally silent heterochromatin at the mating-type locus. That only one Dicer, RdRP and Argonaute is expressed in S. pombe might reflect the extreme specialization of RNA silencing pathways regulating targets only at the transcriptional level in this organism. We decided to test if classical RNAi can be induced in S. pombe. We introduced a dsRNA hairpin corresponding to a GFP transgene. GFP silencing triggered by dsRNA reflected a change in the steady-state concentration of GFP mRNA, but not in the rate of GFP transcription. RNAi in S. pombe required dcr1, rdp1, and ago1, but did not require chp1, tas3, or swi6, genes required for transcriptional silencing. We concluded that the RNAi machinery in S. pombecould direct both transcriptional and posttranscriptional silencing using a single Dicer, RdRP, and Argonaute protein. Our findings suggest that, in spite of specialization in distinct siRNA-directed silencing pathways, these three proteins fulfill a common biochemical function. In Drosophila, miRNA and RNAi pathways are both genetically and biochemically distinct. Dicer-2 (Dcr-2) generates siRNAs, whereas the Dicer-1 (Dcr-1)/Loquacious complex produces miRNAs. Argonaute proteins can be divided by sequence similarity into two classes: in flies, the Ago subfamily includes Argonaute1 (Ago1) and Argonaute2 (Ago2), whereas the Piwi subfamily includes Aubergine, Piwi and Argonaute 3. siRNAs and miRNAs direct posttranscriptional gene silencing through effector complexes containing Ago1 or Ago2. The third class of small RNAs, called repeat-associated small interfering RNAs (rasiRNAs), is produced endogenously in the Drosophilagerm line. rasiRNAs mediate silencing of endogenous selfish genetic elements such as retrotransposons and repetitive sequences to ensure genomic stability. We examined the genetic requirements for biogenesis of rasiRNAs in both male and female germ line of Drosophilaand silencing of 8 different selfish elements, including tree LTR retrotransposons, two non-LTR retrotransposons, and three repetitive sequences. We find that biogenesis of rasiRNAs is different from that of miRNAs and siRNAs. rasiRNA production appears not to require Dicer-1 or Dicer-2. rasiRNAs lack the 2´,3´ hydroxy termini characteristic of animal siRNA and miRNA. While siRNAs derive from both the sense and antisense strands of their dsRNA precursors, rasiRNAs accumulate in antisense polarity to their corresponding target mRNAs. Unlike siRNAs and miRNAs, rasiRNAs function through the Piwi, rather than the Ago, Argonaute protein subfamily. We find that rasiRNAs silence their target RNAs posttranscriptionally: mutations that abrogate rasiRNA function dramatically increase the steady-state mRNA level of rasiRNA targets, but do not alter their rate of transcription, measured by nuclear run-on assay. Our data suggest that rasiRNAs protect the fly germ line through a silencing mechanism distinct from both the miRNA and RNAi pathways.

Les polérovirus infectent une large gamme de plantes d’intérêt économique. Ils sont transmis par un insecte vecteur, le puceron, selon le mode circulant non-multipliant. Le virus, acquis par le puceron lors de l’ingestion de sève sur une plante infectée, traverse l’épithélium des cellules intestinales puis celui des glandes salivaires par un mécanisme de transcytose impliquant des récepteurs encore inconnus. Le récepteur de l’éphrine (Eph) est une protéine membranaire dont un domaine est capable de se lier dans la levure aux protéines structurales des polérovirus. En développant des techniques basées sur l’ARN interférence, nous avons montré que l’acquisition orale d’ARN double brin ciblant Eph chez le puceron Myzus persicae permet de réduire de manière reproductible l’internalisation des polérovirus dans le corps du puceron. Les pucerons ainsi traités transmettent le virus avec une efficacité réduite. Eph pourrait donc assurer la fonction de récepteur des polérovirus chez M. persicae. / Poleroviruses infect a wide range of economically important plants. They are transmitted in a circulative and non-propagative mode by an insect vector, the aphid. The virus particles are acquired by aphids when ingesting the sap from an infected plant and cross successively the epithelia of the midgut and the salivary gland cells by a transcytosis mechanism that relies on the presence of unknown receptors.The ephrin receptor (Eph) is a membrane protein which contains a domain able to bind in yeast to the structural proteins of poleroviruses. By developing methods based on RNA interference, we have shown that oral acquisition of double-stranded RNA targeting Eph in the aphid Myzus persicae can reproducibly reduce polerovirus internalization into the aphid's body. Such treated aphids transmit the virus to plants with a lower efficiency. Eph could therefore function as a receptor for poleroviruses in M. persicae.

L'aggravation actuelle du risque lié au paludisme résulte du développement du phénomène de résistance de souches de Plasmodium falciparum aux molécules antipaludiques. Une telle situation et l’absence de vaccin efficace nécessitent le développement de nouvelles stratégies antiparasitaires. Jusqu’à présent, les mécanismes moléculaires qui contrôlent le cycle parasitaire sont méconnus. Chez la plupart des eucaryotes, les protéine kinases sont impliquées dans des fonctions cellulaires essentielleset constituent une cible privilégiée pour la conception de nouveaux médicaments. Dans cecadre, nous nous sommes intéressés à la voie de transduction de l’AMP cyclique et en particulier à la sous-unité catalytique de la protéine kinase AMPc dépendante (PfPKAc)dont le rôle essentiel reste mal défini chez P. falciparum. Deux approches complémentaires ont été choisies pour étudier cette kinase :1) au niveau biochimique par le clonage, l’expression, la purification et la caractérisation enzymatique de la PfPKAc. L’objectif était d’obtenir une enzyme active in vitro de façon à pourvoir mesurer les constantes enzymatiques de la PfPKAc et conduire les premiers essais d’inhibitions.2) au niveau cellulaire en analysant les conséquences de l’inhibition par des ARN interférents spécifiques des transcrits de la PfPKAc. Le développement parasitaire mais également le transcriptome global ont été étudiés de manière à préciser les voies métaboliques liées à cette kinase plasmodiale.L’ensemble de ces études précise la compréhension de la voie de transduction de l’AMP cyclique et de la PfPKA qui pourrait conduire au développement de nouvelles voies thérapeutiques. / Nowadays, the increase of risks associated with malaria results from the development of resistance of Plasmodium falciparum strains to antimalarial drugs. This situation and the lack of an effective vaccine require the development of new antimalarial strategies. Untilnow, molecular mechanisms controlling the life cycle of malaria parasites, are still poorly understood. In most eukaryotes, protein kinases are implicated in essential cellular functions and represent attractive targets for the development of new drugs. In this context, we focused on the signaling pathway implicating cAMP and particularly the catalytic subunit of cAMP-dependent protein kinase (PfPKAc), whose function is still unclear in P. falciparum. Two complementary strategies were chosen to study this kinase:1) at the biochemical level by the cloning, expression, purification and enzymatic characterization of the PfPKAc. The objective was to obtain an in vitro active PfPKAc to evaluate the kinetic constants of PfPKAc and to conduct the first inhibition studies.2) at the cellular level by studying the consequences of PfPKAc transcripts inhibition byspecific interfering RNAs. The parasite growth but also the overall transcriptome werestudied to specify the metabolic pathways associated with this plasmodial protein kinase.All of these studies improve the understanding of cAMP transduction pathway and PfPKA,which could allow the development of new therapeutic approaches.