Host organisms evolved antiviral responses, which can recognize the viral infection and deal with it. One of the frequent signs of viral infection in a cell is appearance of double-stranded RNA (dsRNA). One of the pathways responding to dsRNA is RNA interference (RNAi), which functions as the key antiviral defence system in invertebrates and plants. Mammals, however, utilize for antiviral defence a different dsRNA-sensing pathway called the interferon response. RNAi functions only in mammalian oocytes and early embryonal stages although its enzymatic machinery is present in all somatic cells, where it is employed in the microRNA pathway. A previous study indicated that the functionality of RNAi in mouse oocytes functions due to an oocyte-specific isoform of protein Dicer (DicerO ), which is truncated at the N-terminus. In my thesis, I aimed to assess whether DicerO processes RNAi substrates more efficiently in vitro than the full-length Dicer (DicerS ), which is found in somatic cells. Therefore, I developed Dicer purification protocol for obtaining both recombinant mouse Dicer isoforms of high purity. I examined their activity in a non-radioactive cleavage assay using RNA substrates with structural features characteristic of RNAi substrates. My results suggest that recombinant DicerO and DicerS do not...

Doctor of Philosophy / Department of Biology / Susan J. Brown / RNA interference (RNAi) is a natural gene-silencing phenomenon triggered by dsRNA (dsRNA). While RNAi is an endogenous process that plays essential roles in regulating gene expression it can also be harnessed as a tool for the study of gene function. Introducing dsRNA that is homologous to target mRNA into a cell triggers the RNAi response causing the destruction of the homologous mRNA and a loss of function phenotype. In some organisms, such as the nematode Caenorhabditis elegans, once dsRNA is introduced into the body cavity, the RNAi effect is seen throughout the organism because the dsRNA is taken up by individual cells and is then spread from cell to cell. This process has been termed the systemic RNAi response. For other organisms, such as the fruit fly Drosophila melanogaster, introduction of dsRNA into the body cavity does not result in a systemic RNAi response. This may be due to the cell’s inability to take up dsRNA or spread that dsRNA from cell to cell. For other organisms, including mammals, introduction of dsRNA into the body cavity does not result in a systemic RNAi response because the immune response causes dsRNA destruction before it can be utilized in the RNAi pathway. For organisms that do not exhibit a systemic RNAi response, complex genetic methods are needed to introduce dsRNA into cells to induce the RNAi response. Therefore, one of the challenges in utilizing RNAi as a genetic tool is introducing the dsRNA into individual cells. In recent years, systemic RNAi responses have been documented in both model and non-model organisms, making RNAi an accessible genetic tool. The red flour beetle, Tribolium castaneum is an emerging model organism that has a robust systemic RNAi response. However, the mechanism of systemic RNAi and the specific parameters required to obtain a strong systemic RNAi response in this organism have not been thoroughly investigated. The aim of this work is to provide data that can allow RNAi to be better utilized as a genetic tool in Tribolium and to use this information as a basis for the use of RNAi in other insects in which it can be performed. Specifically we provide data on the essential parameters necessary to achieve an effective systemic response in Tribolium, we describe differences in the systemic RNAi response between Drosophila and Tribolium, we analyze the conservation and function of RNAi machinery genes in Tribolium and we provide information on the genes critical for a systemic RNAi response in Tribolium.

Doctor of Philosophy / Department of Biochemistry / Subbarat Muthukrishnan / The extracellular matrices of cuticle and peritrophic matrix of insects are composed mainly of chitin complexed with proteins, some of which contain chitin-binding domains. This study is focused on the identification and functional characterization of genes encoding proteins that possess one or more copies of the six-cysteine-containing ChtBD2 domain (Peritrophin A motif =CBM_14 =Pfam 01607) in the red flour beetle, Tribolium castaneum. A bioinformatics search of T. castaneum genome yielded previously characterized chitin metabolic enzymes and several additional proteins. Using phylogenetic analyses, the exon-intron organization of the corresponding genes, domain organization of proteins, and temporal and tissue-specificity of expression patterns, these proteins were classified into three large families. The first family includes 11 proteins essentially made up of 1 to 14 repeats of the peritrophin A domain. Transcripts for these proteins are expressed only in the midgut and only during feeding stages of development. We therefore denote these proteins as “Peritrophic Matrix Proteins” or PMPs. The genes of the second and third families are expressed in cuticle-forming tissues throughout all stages of development but not in the midgut. These two families have been denoted as “Cuticular Proteins Analogous to Peritrophins 3” or CPAP3s and “Cuticular Proteins Analogous to Peritophins 1” or CPAP1s based on the number of ChtBD2 domains that they contain. Unlike other cuticular proteins studied so far, TcCPAP1-C protein is localized predominantly in the exocuticle and could contribute to the unique properties of this cuticular layer. RNA interference (RNAi), which down-regulates transcripts for any targeted gene, results in lethal and/or abnormal phenotypes for some, but not all, of these genes. Phenotypes are often unique and are manifested at different developmental stages, including embryonic, pupal and/or adult stages. The experiments presented in this dissertation reveal that while the vast majority of the CPAP3 genes serve distinct and essential functions affecting survival, molting or normal cuticle development. However, a minority of the CPAP1 and PMP family genes are indispensable for survival under laboratory conditions. Some of the non-essential genes may have functional redundancy or may be needed only under special circumstances such as exposure to stress or pathogens.

O adenocarcinoma ductal pancreático (PDAC, pancreatic ductal adenocarcinoma), o tipo mais prevalente de câncer do pâncreas, é uma neoplasia extremamente agressiva e com elevado índice de letalidade. Há uma necessidade premente de identificação de vulnerabilidades no PDAC que possam ser exploradas como alvos terapêuticos, e a utilização de modelos pré-clínicos que recapitulem a complexidade biológica e heterogeneidade clínica da doença é um aspecto central para a realização dessa tarefa. Os xenotransplantes de tecido tumoral derivado de pacientes (PDX, patient-derived tumor tissue xenografts), realizados em camundongos imunodeficientes, replicam com grande similaridade as principais características do tumor original e, assim, constituem uma ferramenta valiosa para o teste de drogas e estudos funcionais. Neste trabalho, 17 amostras cirúrgicas de PDAC humano foram implantadas subcutaneamente em camundongos nude atímicos. Sete tumores (41%) foram enxertados com sucesso e têm sido mantidos em sucessivas gerações de animais receptores. O exame histológico de seis desses xenoenxertos identificou características morfológicas compatíveis com os padrões reconhecidos no PDAC humano, assim como uma consistente similaridade de seu status de diferenciação histológica em relação aos perfis verificados nos tumoresoriginais. O cultivo in vitro de células derivadas de um dos xenotumores resultou em uma nova linhagem de câncer de pâncreas, com morfologia e cinética de crescimento comparáveis às de outras linhagens celulares de câncer pancreático. O potencial tumorigênico dessa nova linhagem foi validado in vivo, com uma consistente formação de tumores após inoculação em camundongos nude. A fim de aproveitar esse recurso para a investigação de potenciais alvos terapêuticos no PDAC, um rastreamento de vulnerabilidades moleculares foi realizado por meio de silenciamento gênico em larga-escala com RNA de interferência (RNAi). Uma biblioteca lentiviral de 4492 shRNAs (short hairpin RNAs), alvejando cerca de 350 genes envolvidos na regulação epigenética, foi empregada para a triagem de genes de suscetibilidade nas células derivadas de PDX, e em outras cinco linhagens tumorais pancreáticas (AsPC-1, BxPC-3, Capan-1, MIA PaCa-2 e PANC-1). Inicialmente, foi realizada uma série de experimentos preliminares, visando à amplificação e controle de qualidade da biblioteca de silenciamento, à produção de vetores lentivirais e à padronização das condições experimentais para a transdução e seleção das células-alvo. Apenas três das linhagens avaliadas (AsPC-1, MIA PaCa-2 e PANC-1) mostraram-se permissíveis à transdução pelos vetores lentivirais, e foram assim utilizadas no screening de alvos epigenéticos. A análise dos dados obtidos nesse ensaio está em curso e os resultados serão utilizados para a definição de potenciais alvos candidatos. Em conclusão, recursos valiosos para apoiar a pesquisa sobre o câncer de pâncreas foram desenvolvidos. A coleção de PDXs estabelecida, bem como a linhagem celular recém-derivada, constituem uma fonte permanente e estável de células de PDAC para análises moleculares e estudos funcionais que busquem elucidar aspectos da doença ainda pouco compreendidos. Adicionalmente, os reagentes gerados e a expertise adquirida com os ensaiosrealizados com a biblioteca de shRNAs contra alvos epigenéticos serão de grande utilidade em futuras investigações para identificar genes com funções importantes na manutenção do fenótipo tumoral, e consequentemente com potencial para serem explorados terapeuticamente. / Pancreatic ductal adenocarcinoma (PDAC), the most prevalent type of pancreatic cancer, is a highly aggressive and lethal neoplasm. There is a pressing need to identify vulnerabilities in PDAC suited to be exploited as therapeutic targets, and the use of preclinical models recapitulating the biological complexity and clinical heterogeneity of the disease is central to this task. Patient-derived tumor tissue xenografts (PDX), established in immunodeficient mice, replicate with great similarity the main characteristics of the original tumor and thus constitute a valuable tool for drug testing and functional studies. In this work, 17 surgical samples of human PDAC were implanted subcutaneously in athymic nude mice. Seven tumors (41%) were successfully grafted and have been maintained through successive generations of recipient animals. Histological examination of six of these xenografts identified morphological characteristics compatible with the recognized patterns of human PDAC, as well as a consistent similarity of their histological differentiation status in relation to the profiles verified in the original tumors. In vitro culture of cells derived from one of these xenografts resulted in a new pancreatic cancer cell line, with morphology and growth kinetics comparable to those of other pancreatic tumor cells. The tumorigenic potential of this freshly derived cell line was validated in vivo, with a consistent tumor formation following inoculation into nude mice. To take advantage ofthis resource to investigate potential therapeutic targets in PDAC, a screening of molecular vulnerabilities was performed through large-scale gene silencing with RNA interference (RNAi). A lentiviral library containing 4492 short hairpin RNAs (shRNAs), targeting about 350 genes involved in epigenetic regulation, was employed for the search of susceptibility genes in the PDX-derived cells and in other five pancreatic tumor cell lines (AsPC-1, BxPC -3, Capan-1, MIA PaCa-2 and PANC-1). Initially, a series of preliminary experiments were carried out aiming at the amplification and quality control of the silencing library, production of lentiviral vectors and adjustment of the experimental conditions for transduction and selection of the target cells. Only three of the cell lines evaluated (AsPC-1, MIA PaCa-2 and PANC-1) were permissible for transduction by the lentiviral vectors, and were accordingly used in the screening of epigenetic targets. The analysis of data obtained in this trial is ongoing and the results will be used for definition of potential candidate targets. In conclusion, valuable resources to support research on pancreatic cancer have been developed. The established collection of PDXs as well as the newly derived cell line constitutes a permanent and stable source of PDAC cells for molecular analyzes and functional studies seeking to elucidate aspects of this disease that are still poorly understood. Additionally, both the reagents generated and the expertise gained from the RNAi assay against epigenetic targets will have inordinate usefulness in future investigations to identify genes with major functions in maintaining the malignant phenotype, and consequently with the potential to be exploited therapeutically.

The Gram-negative bacterium Photorhabdus luminescens is a pathogen of insects. It is able to secrete a variety of toxins and effectors against its host in order to escape its immune defences. The model insect Manduca sexta is able to mount a variety of humoral and cellular responses against pathogen attack. Ultimately these prove ineffective against P. luminescens. The pre-treatment of M. sexta with Escherichia coli provides protection against the pathogenesis of P. luminescens. Here, I use RNA interference and Fluorescence-assisted cell sorting techniques to investigate interactions between pathogen and host to further elucidate the roles of various host factors in mounting the immune response. I also investigate the nutrient requirements of the bacteria for pathogenesis. I show data that peptidoglycan recognition protein (PGRP) is essential for the up-regulation of antimicrobial peptides, an important immune defence. I also show that P. luminescens has a requirement for two types of iron during pathogenesis of M. sexta. And lastly I show that P. luminescens is able to avoid phagocytosis, another important immune defence.

Les éléments transposables (ET) sont des parasites génomiques présents dans tous les génomes, dont une partie présente une structure similaire à celle de certains virus. Dans les cellules ovariennes d'insecte, l'abondance des transcrits d’ET est contrôlée par ARN interférence (ARNi), et plus particulièrement par la voie piARN (Piwi-interacting RNA). Une autre voie d'ARNi, la voie siARN (Small interfering RNA), constitue l'une des principales réponses immunitaires des insectes contre les infections virales, et est aussi dédiée au contrôle somatique des ET. Ces deux voies d'ARNi sont dirigées par des effecteurs moléculaires distincts et décrites comme indépendantes. Cependant, des similitudes structurales et de mécanisme de contrôle entre les ET et les virus suggèrent la possibilité d’une interaction. Nous avons utilisé la drosophile comme modèle et infecté l'organisme avec le virus Sindbis (SINV), un arbovirus (Arthropod-Borne virus), ou le virus Sigma (SV), un virus spécifique de drosophile. À l'aide d'un séquençage à haut débit, nous avons caractérisé les répertoires d'ARN et de petits ARN interférents produits par les drosophiles infectées, à partir des tissus de carcasses ou d'ovaires. Globalement, nos résultats démontrent un impact de l'infection virale sur les quantités de transcrits d’ET via la modulation des répertoires piARN et siARN, et représentent la première démonstration des effets d’infections virales sur l’activité des ET. Plus précisément, l’infection par SINV favorise une diminution globale des quantités de transcrits d’ET alors que l’infection par SV réactive de nombreux ET. Nos données suggèrent que la modulation résulte de substrats d'ARN partagés et de trans-régulateurs communs des voies de l'ARNi. Ces résultats ouvrent un nouvel axe de recherche en génomique, suggérant que les épidémies virales ou les infections chroniques peuvent avoir un impact sur l'activité des ET, et donc sur le taux de diversification génétique ultérieure / Transposable elements (TEs) are genomic parasites that are found in all genomes, a part of which display structure similarity to some viruses. In insect ovarian cells, TE transcript abundance is controlled by RNA interference (RNAi) machinery and more particularly by the piRNA pathway (Piwi-interacting RNA). Another RNAi pathway, named siRNA pathway (Small interfering RNA), is one of the key insect immune responses against viral infections and is also dedicated to TE somatic control. These two interfering RNA pathways are led by distinct molecular effectors and described as independent. However, similarities in structure and control mechanisms across TEs and viruses suggest that an interplay may exist. We used Drosophila as a model, and infected the organism with Sindbis virus (SINV), an arbovirus (Arthropod-Borne virus), or Sigma virus (SV), a Drosophila-specific virus. Using high-throughput sequencing, we characterized the RNA and small-RNA repertoires produced by Drosophila flies from carcass or ovary tissues. Overall, our results demonstrate an impact of viral infection on TE transcript amounts via modulation of the piRNA and siRNA repertoires and represent the first demonstration of the effects of viral infection on TE activity. More precisely, SINV infection promotes a global decrease of TE transcript levels while SV infection reactivates many TEs. Our data suggest that the modulation results from shared RNA substrates and common trans-regulators of the small RNA pathways. These results open new avenue of research in genomics, suggesting that viral epidemics or chronic infections can impact TE activity and thus the rate of subsequent genetic diversification

Le cilié Paramecium tetraurelia est un modèle intéressant pour l'étude de la diversité et de l'évolution des voies d'ARN interférence (ARNi) chez les eucaryotes. L'une des voies d'ARNi végétatives peut être induite en nourrissant les paramécies de bactéries produisant un ARN double-brin (ARNdb) homologue à un gène donné, dont l'expression est inactivée de manière post-transcriptionnelle par la production de siARN de 23 nt. Un crible de mutagénèse a permis d'obtenir des mutants mendéliens déficients pour l'ARNi, dont les génomes ont été séquencés afin d'identifier sans a priori des gènes impliqués dans cette voie. 6 gènes ont été identifiés: un Dicer, deux ARN polymérases ARN-dépendantes (RDR1 et 2), une nucléotidyl-transférase (CID1) et deux gènes codant de nouvelles protéines (PDS1 et 2). Pour étudier leur rôle dans la biosynthèse ou l'action des siARN, ces derniers ont été séquencés à partir de cellules sauvages ou mutantes, nourries d'un ARNdb homologue à un gène non essentiel. L'analyse bio-informatique a montré que des siARN dits 'primaires' sont produits à partir de l'ARNdb bactérien, tandis que des siARN dits 'secondaires' sont produits à partir de la totalité de l'ARNm endogène ciblé, et sont majoritairement de polarité anti-sens. Alors que la production des siARN primaires dépend de tous les gènes étudiés, les résultats n'impliquent que RDR2 dans celle des siARN secondaires. Enfin, j'ai montré que certains clusters de siARN endogènes dépendent de RDR1 et de CID1, tandis que d'autres dépendent de RDR2. La paramécie produit également des siARN antisens aux ARN ribosomaux bactériens, suggérant de nouvelles hypothèses quant à la fonction naturelle de cette voie. / The ciliate Paramecium tetraurelia is an interesting model to study the diversity and evolution of RNA interference (RNAi) pathways. One of the vegetative RNAi pathways is induced by feeding cells with bacteria producing double-stranded RNA (dsRNA) homologous to a given gene, which is then post-transcriptionally silenced through the production of 23-nt siRNAs. A forward genetic screen allowed us to obtain Mendelian mutants deficient in dsRNA-induced RNAi, and mutated genes were identified by whole-genome resequencing. 6 genes were identified: one Dicer, two RNA-dependent RNA polymerases (RDR1 et 2), one nucleotidyl-transferase (CID1) and two genes encoding novel poteins (PDS1 and 2). To study their roles in siRNA biosynthesis or action, we sequenced small RNAs from wild-type or mutants cells fed with a dsRNA homologous to a non-essential endogenous gene. Bioinformatic analyses showed that 'primary' siRNAs are produced from the bacterial dsRNA trigger, while 'secondary' siRNAs, predominantly of antisense polarity, are produced from the whole length of the targeted endogenous mRNA. While primary siRNA production requires all of the genes studied, the results only implicate RDR2 in the production of secondary siRNAs. Finally, I showed that some clusters of endogenous siRNAs depend on RDR1 and CID1, whereas others depend on RDR2. Paramecium was also shown to produce siRNAs that are antisense to bacterial ribosomal RNAs, suggesting new hypotheses about the possible natural functions of this pathway.

Aujourd'hui la recherche en biologie dispose d'une masse d'informations génomiques considérable qu'il faut comprendre fonctionnellement pour faire émerger de nouveaux concepts, qui formeront le berceau de nouvelles thérapies. Ces études mettent en jeu des mécanismes contrôlés à l'échelle moléculaire et nécessitent le traitement d'informations à haut-débit et de manière parallèle. Les travaux pluridisciplinaires présentés ont permis de mettre au point une technologie miniaturisée de culture de cellules en gouttes matricées sur supports solides, pour tester l'action des molécules sur le comportement de cellules.<br />Après avoir mis au point un démonstrateur macroscopique validé par des transfections de molécules nucléiques, nous avons développé un protocole de fabrication de substrats miniaturisés capable de maintenir 100 nano-gouttes par cm² à l'aide d'un différentiel de tension de surface. Un robot de dispense de pico-gouttes a été intégré pour réaliser les gouttes de culture cellulaire de manière automatique. Le comportement des cellules au sein des gouttes est évalué par microscopie en fluorescence à haut-contenu après fixation. Chaque cellule de chaque goutte est caractérisée par des dizaines de paramètres de manière individuelle.<br />Cette nouvelle approche analytique a été appliquée dans le cadre d'un projet multipartenaire de criblage de siRNA visant à étudier l'impact de gènes sur la chimiorésistance de glioblastomes. Par ailleurs nous avons montré l'utilisation de la spectrométrie de masse comme méthode de phénotypage multiparamétrique. Cette technologie de puce à cellules est particulièrement adaptée à l'étude à haut-débit des comportements fins de cultures cellulaires.

Insects encounter many microorganisms in nature and to survive they have developed counter measures against the invading pathogens. In Drosophila melanogaster research on insect immunity has mainly been focused on infections by bacteria and fungi. We have explored the immune response against natural infections of the parasite Octosporea muscaedomesticae and the Drosophila C virus as compared to natural infections of bacteria and fungi. By using Affymetrix Drosophila GeneChips, we were able to obtain 48 genes uniquely induced after parasitic infection. It was also clearly shown that natural infections led to different results than when injecting the pathogens. In order to search for the ultimate role of the lepidopteran protein hemolin, we used RNA interference (RNAi). We could show that injection of double stranded RNA (dsRNA) of Hemolin in pupae of Hyalophora cecropia led to embryonic malformation and lethality and that there was a sex specific difference. We continued the RNAi investigation of hemolin in another lepidopteran species, Antheraea pernyi, and discovered that hemolin was induced by dsRNA per se. A similar induction of hemolin was seen after infection with baculovirus and we therefore performed in vivo experiments on baculovirus infected pupae. We could show that a low dose of dsHemolin prolonged the period before the A. pernyi pupae showed any symptoms of infection, while a high dose led to a more rapid onset of symptoms. By performing in silico analysis of the hemolin sequence from A. pernyi in comparison with other Hemolin sequences, it was possible to select a number of sites that either by being strongly conserved or variable could be important targets for future studies of hemolin function.

Nucleic acids are macromolecules in cells for storing and transferring genetic information. Moreover, nucleic acids, especially RNAs, can fold into well-defined 3D structures and catalyze biochemical reactions. As ubiquitous biological molecules in all living systems, nucleic acids are important drug targets, and they can also be used in diagnostics and therapeutics. Structural information of nucleic acids provides the foundation for DNA and RNA function studies. X-ray crystallography has been a useful tool for structural studies of bio-macromolecules at atomic level. There are two major problems in macromolecular crystal structure determination: phasing and crystallization. Although selenium derivatization is routinely used for solving novel protein structures through the MAD phasing technique, the phase problem is still a critical issue in nucleic acid crystallography. The covalent selenium-derivatization of nucleic acids has been proven to be a useful strategy for solving the phase problem in nucleic acid X-ray crystallography. Besides the facilitation of nucleic acid crystallography, there is also a wide range of other applications for selenium-derivatized nucleic acids (SeNA). The investigation presented in this dissertation mainly focuses on the following research subjects (1) Synthesis and characterization of selenium-derivatized nucleic acids for X-ray crystallography, especially phosphoroselenoate RNAs. They are generated and used for crystallization. (2) Application of selenium-derivatized RNA for RNA interference. Phosphoroselenoate RNAs are tested for RNAi activities. (3) Synthesis and characterization of the uridine 5’-triphosphate modified with selenium at position 4. (4) Facile synthesis and antitumor activities of selenium modified deoxyribonucleosides. MeSe-thymidine nucleosides have shown antitumor activity in cell assays.