A incidência de melanomas tem crescido mundialmente. Apesar de representar um potencial problema de saúde pública pela sua incidência crescente, melanomas ainda se apresentam como tumores de difícil tratamento, especialmente quando diagnosticados em estadios avançados. A taxa de resposta a quimioterapia não ultrapassa 30% de resposta clínica objetiva nestes casos. As bases moleculares da quimiorresistência não são ainda completamente esclarecidas e seu conhecimento será útil para o delineamento de estratégias de quimiossensibilização. Em estudos anteriores, observamos que o tratamento de linhagem de células de melanoma metastático humano com o quimioterápico cisplatina induz o acúmulo de proibitina nas células sobreviventes. Proibitina é uma molécula expressa ubiquamente na maioria das células. Há evidências de que a forma nuclear esteja envolvida com o processo de morte celular e inibição de E2F1 enquanto a forma citoplasmática parece atuar como chaperona mitocondrial, garantindo sua homeostasia. O objetivo deste projeto foi avaliar a compartimentalização subcelular e a expressão de proibitina, após tratamento com 25 M de cisplatina por 24 horas em diferentes linhagens de melanoma metastático humano; e, o efeito de sua subexpressão, usando-se small interference (si) RNA. Nós mostramos que nas linhagens de melanoma humano LB373Mel, SKMel 37 e Mel 85, a proibitina foi encontrada predominantemente no citoplasma, associada, pelo menos em parte, com a mitocôndria. Após tratamento com cisplatina, uma porção da proibitina também foi encontrada no núcleo, como pode ser detectado utilizando-se anticorpo monoclonal (clone II-14-1). Experimentos de knockdown de proibitina por siRNA obtiveram sucesso em duas de três linhagens. Nessas duas linhagens (LB373Mel e Mel 85), o bloqueio do acúmulo de proibitina após tratamento com cisplatina levou à quimiossensibilização. A quimiossensibilização à cisplatina não foi observada na linhagem SKMel 37, que foi capaz de acumular proibitina mesmo quando tratada com siRNA específico para proibitina. A conclusão deste projeto é que a expressão de proibitina é parte da resposta celular que leva a sobrevivência de células de melanoma expostas à cisplatina / The incidence of melanomas has grown world-wide. Besides representing a potential problem of public health for its increasing incidence, melanomas are tumors of difficult treatment, especially when diagnosed in advanced phases. The clinical objective response rate does not exceed 30% in these cases. The molecular bases of chemoresistance are not completely clarified and their understanding will be useful for the delineation of chemosensitization strategies. In previous studies, we observed that the treatment of a human metastatic melanoma cell line with the chemotherapeutic agent cisplatin induced the accumulation of prohibitin in the surviving cells. Prohibitin is ubiquitously expressed molecule in most cells. There is evidence that the nuclear form is involved with the process of cell death and inhibition of E2F1, while the cytoplasmic form seems to act as mitochondrial chaperone, guaranteeing its homeostasis. The aim of this project was to evaluate the subcellular compartmentalization and protein expression profile of prohibitin, after treatment with 25M of cisplatin for 24 hours in different human metastatic melanoma cell line, and the effect of its underexpression, using siRNA. We showed that, in human melanoma cell lines, LB373Mel, SKMel 37 and Mel 85, prohibitin was found predominantly in the cytoplasm, associated at least in part with the mitochondria. Upon cisplatin treatment, a fraction of prohibitin was also found in the nucleus, as detected by using a monoclonal antibody (clone II-14-10). Knockdown experiments were successful in two out of three cell lines. In these two cell lines (LB373Mel and Mel 85) blockage of the accumulation of prohibitin upon cisplatin treatment led to chemosensitization. Chemosensitization to cisplatin was not observed for SKMel 37 cells, which accumulated prohibitin even when treated with prohibitin specific siRNA oligonucleotides. Altogether, we concluded that expression of prohibitin is part of the cellular response that leads to cell survival in melanoma cells exposed to cisplatin

Orientador: Maria Cristina Cintra Gomes Marcondes / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-26T00:25:10Z (GMT). No. of bitstreams: 1 Tomasin_Rebeka_D.pdf: 4368331 bytes, checksum: 33a1f49902e0d1a423b1a4b7ebe757e9 (MD5) Previous issue date: 2014 / Resumo: Câncer é um nome genérico para um grupo de mais de cem doenças que compartilham algumas características. Talvez a característica mais marcante das neoplasias malignas seja a rápida proliferação de células anormais para além de suas fronteiras usuais, invasão de tecidos adjacentes e finalmente dispersão para órgãos distantes. Anualmente, cerca de oito milhões de pessoas morrem devido ao câncer e outros doze milhões de novos casos são diagnosticados. Dentre os eventos associados à progressão neoplásica, destacam-se as metástases e a caquexia. Metástases são tumores em sítios secundários, sendo responsáveis por cerca de 90% do total de mortes por câncer. Já a caquexia, uma síndrome paraneoplásica, é caracterizada por extensa espoliação de gordura e massa magra, fadiga e alterações metabólicas, prejudicando a qualidade de vida e a sobrevida de cerca de 50-85% dos pacientes, dependendo do tipo de tumor. Com relação às terapias, o grande desafio ainda é combater o tumor sem prejudicar o hospedeiro, o que acredita-se ser possível através de terapias-alvo para genes específicos e/ou tratamentos coadjuvantes, incluindo aqueles que empregam suplementação e/ou drogas derivadas de produtos naturais, que muitas vezes tem menor efeito tóxico ao hospedeiro. Desse modo, este trabalho teve dois objetivos: (1) avaliar a ação da administração oral de Aloe vera e mel sobre o tecido tumoral e o hospedeiro portador de carcinosarcoma de Walker 256; e (2) identificação de genes supressores de metástase através de screen funcional in vivo empregando-se biblioteca de shRNA em modelo de câncer de mama triplo negativo. Em relação ao primeiro objetivo, os resultados sugerem que a associação entre Aloe vera e mel pode modular a proteólise e o estresse oxidativo de maneira diferencial preservando o hospedeiro em detrimento do tecido tumoral. Ainda, o tratamento com Aloe vera e mel parece ser capaz de diminuir a propensão metastática das células tumorais in vivo, através de aumento na expressão de caderina-E e redução na expressão de caderina-N, bem como inibição da angiogênese. Outros experimentos sugerem que os efeitos antitumorais observados in vivo estão, em parte, relacionados à ação imunomodulatória de alguns componentes da Aloe vera. Com relação ao segundo objetivo, foram identificados dezenas de candidatos a genes supressores de metástase. Dentre esses genes, que estão sendo validados, Mnat1, Snd1, Cul5, Gabbr1, Rorb, Adk, Ccnd3, Gdnf, Nr1d1, Ptprs e Ltah4 são os genes-candidatos de maior confiabilidade por cumprirem um ou mais dos seguintes requisitos: (a) diminuição significativa do nível de DNA e RNA em canceres de mama humanos agressivos, sendo assim relacionados à pior prognostico, (b) papel biológico sugestivo, (c) fenótipo marcante durante o screen ou ainda (d) decréscimo significativo na expressão em linhagens de câncer de mama mais agressivas / Abstract: Cancer is a generic name for a group of over a hundred diseases which share some features. The most remarkable feature in cancer disease is the fast proliferation of abnormal cells beyond their usual boundaries, invasion of surrounding tissues and finally spread to distant organs. Every year, cancer is responsible for over eight million deaths and twelve million new cases are diagnosed. Among all the events associated with the neoplastic progression, metastasis and cachexia are major issues. Metastases, which are tumours growing in secondary sites, account for 90% of all cancer deaths. Cachexia, a paraneoplastic syndrome, is characterized by severe fat and lean mass waste, fatigue and metabolic alterations, jeopardizing the quality of life and reducing the survival of about 50-85% of the cancer patients, depending on the tumour type. Regarding to the therapies, the biggest challenge is still fighting the tumour without harming the host, which is believed to be possible by targeted therapies to specific genes and/or adjuvant treatments, including supplementation and drugs derived from natural compounds, which usually have lower side effects in the host. Knowing these points, this work had two aims: (1) evaluate the effects of Aloe vera and honey in both tumour and host tissues in Walker 256-tumour bearing rats; and, (2) identification of metastasis suppressor genes using a functional in vivo shRNA screen in a triple negative breast cancer syngeneic model. Regarding to the first aim, the results suggested that the combination of Aloe vera and honey selectively modulate proteolysis and oxidative stress, damaging the tumour tissue while protected the host. Moreover, the Aloe vera and honey treatment apparently decreases the metastatic potential in vivo, by simultaneous increase in E-cadherin and decrease in N-cadherin expression, while decreased tumour vascularization. Finally, our results suggested the antitumoral effects observed in vivo are, at least partially, related to the immunomodulatory activity of some Aloe vera¿s compounds. Regarding to the second aim, dozens of putative metastasis suppressor genes were identified. High confidence candidates, which would be further analysed are Mnat1, Snd1, Cul5, Gabbr1, Rorb, Adk, Ccnd3, Gdnf, Nr1d1, Ptprs e Ltah4. Their selection was based on meeting the following requirements: (a) significant decrease at DNA or RNA level in highly aggressive human breast cancer carcinomas and thus, worse prognosis, (b) suggestive biological role, (c) occurrence of a remarkable phenotype during the screen, and (d) significant decrease in expression in more aggressive cancer cell lines / Doutorado / Biologia Celular / Doutora em Biologia Celular e Estrutural

Asparagine (N)-linked glycosylation occurs on 90% of membrane and secretory proteins and drives folding and trafficking along the secretory pathway. The N-glycan can be attached to an N-X-T/S-Y (X,Y ≠ P) consensus site by one of two oligosaccharyltransferase (OST) STT3 enzymatic isoforms either during protein translation (co-translational) or after protein translation has completed (post-translational). While co-translational N-glycosylation is both rapid and efficient, post-translational N-glycosylation occurs on a much slower time scale and, due to competition with protein degradation and forward trafficking, could be detrimental to the success of a peptide heavily reliant on post-translational N-glycosylation. In evidence, mutations in K+ channel subunits that shift N-glycosylation kinetics have been directly linked to cardiac arrhythmias. My thesis work focuses on identifying primary sequence factors that affect the rate of N-glycosylation. To identify the molecular determinants that dictate whether a consensus site acquires its initial N-glycan during or after protein synthesis, I used short (~ 100-170 aa) type I transmembrane peptides from the KCNE family (E1-E5) of K+ channel regulatory subunits. The lifetime of these small membrane proteins in the ER translocon is short, which places a significant time constraint on the co-translational N-glycosylation machinery and increases the resolution between co- and post-translational events. Using rapid metabolic pulse-chase experiments described in Chapter II, I identified several molecular determinants among native consensus sites in the KCNE family that favor co-translational N-glycosylation: threonine containing-consensus sites (NXT), multiple N-terminal consensus sites, and long C-termini. The kinetics could also be shifted towards post-translational N-glycosylation by converting to a serine containing-consensus site (NXS), reducing the number of consensus sites in the peptide, and shortening the C-termini. In Chapter III, I utilized an E2 scaffold peptide to examine the N-glycosylation kinetics of the middle X residue in an NXS consensus site. I found that large hydrophobic and negatively charged residues hinder co-translational N-glycosylation, while polar, small hydrophobic, and positively charged residues had the highest N-glycosylation efficiencies. Poorly N-glycosylated NXS consensus sites with large hydrophobic and negatively charged X residues had a significantly improved co-translational N-glycosylation efficiency upon conversion to NXT sites. Also in Chapter III, I adapted a siRNA knockdown strategy to definitively identify the OST STT3 isoforms that perform co- and post-translational N-glycosylation for type I transmembrane substrates. I found that the STT3A isoform predominantly performs co-translational N-glycosylation while the STT3B isoform predominantly performs post-translational N-glycosylation, in agreement with the roles of these enzymatic subunits on topologically different substrates. Taken together, these findings further the ability to predict the success of a consensus site by primary sequence alone and will be helpful for the identification and characterization of N-glycosylation deficiency diseases.

Small RNA silencing pathways regulate development, viral defense, and genomic integrity in all kingdoms of life. An Argonaute (Ago) protein, guided by a tightly bound, small RNA or DNA, lies at the core of these pathways. Argonaute uses its small RNA or DNA to find its target sequences, which it either cleaves or stably binds, acting as a binding scaffold for other proteins. We used Co-localization Single-Molecule Spectroscopy (CoSMoS) to analyze target binding and cleavage by Ago and its guide. We find that both eukaryotic and prokaryotic Argonaute proteins re-shape the fundamental properties of RNA:RNA, RNA:DNA, and DNA:DNA hybridization: a small RNA or DNA bound to Argonaute as a guide no longer follows the well-established rules by which oligonucleotides find, bind, and dissociate from complementary nucleic acid sequences. Counter to the rules of nucleic acid hybridization alone, we find that mouse AGO2 and its guide bind to microRNA targets 17,000 times tighter than the guide without Argonaute. Moreover, AGO2 can distinguish between microRNA-like targets that make seven base pairs with the guide and the products of cleavage, which bind via nine base pairs: AGO2 leaves the cleavage products faster, even though they pair more extensively. This thesis presents a detailed kinetic interrogation of microRNA and RNA interference pathways. We discovered sub-domains within the previously defined functional domains created by Argonaute and its bound DNA or RNA guide. These sub-domains have features that no longer conform to the well-established properties of unbound oligonucleotides. It is by re-writing the rules for nucleic acid hybridization that Argonautes allow oligonucleotides to serve as specificity determinants with thermodynamic and kinetic properties more typical of RNA-binding proteins than that of RNA or DNA. Taken altogether, these studies further our understanding about the biology of small RNA silencing pathways and may serve to guide future work related to all RNA-guided endonucleases.

Organisms employ sophisticated mechanisms to silence foreign nucleic acid, such as viruses and transposons. Evidence exists for pathways that sense copy number, unpaired DNA, or aberrant RNA (e.g., dsRNA), but the mechanisms that distinguish “self” from “non-self” are not well understood. Our studies on transgene silencing in C. elegans have uncovered an RNA surveillance system in which the PIWI protein, PRG-1, uses a vast repertoire of piRNAs to recognize foreign transcripts and to initiate epigenetic silencing. Partial base pairing by piRNAs is sufficient to guide PRG-1 targeting. PRG-1 in turn recruits RdRP to synthesize perfectly matching antisense siRNAs (22G-RNAs) that are loaded onto worm-specific Argonaute (WAGO) proteins. WAGOs collaborate with chromatin factors to maintain epigenetic silencing (RNAe). Since mismatches are allowed during piRNA targeting, piRNAs could—in theory— target any transcript expressed in the germline, but germline genes are not subject to silencing by RNAe. Moreover, some foreign sequences are expressed and appear to be adopted as “self.” How are “self” transcripts distinguished from foreign transcripts? We have found that another Argonaute, CSR-1, and its siRNAs—also synthesized by RdRP—protect endogenous genes from silencing by RNAe. We refer to this pathway as RNA-mediated gene activation (RNAa). Reducing CSR-1 or PRG-1 or increasing piRNA targeting can shift the balance towards expression or silencing, indicating that PRG-1 and CSR-1 compete for control over their targets. Thus worms have evolved a remarkable nucleic acids immunity mechanism in which opposing Argonaute pathways generate and maintain epigenetic memories of self and non-self nucleotide sequences.

La protéine du TGF-[bêta]1 est une protéine multifonctionnelle qui agit dans plusieurs types cellulaires. Son action varie selon le type de cellulaire. Bien qu'elle ait un rôle inhibiteur chez les astrocytes normaux, elle posséderait un rôle principalement activateur de nombreuses voies carcinogéniques chez les tumeurs astrocytaires primaires malignes. L'isoforme du TGF-[bêta]1 est celle qui est la plus impliquée dans ces processus. Elle joue un rôle dans l'activation des voies d'invasion tissulaire et d'angiogenèse, mais inhibe des mécanismes d'apoptose et d'immunosuppression.La présente étude vise à évaluer l'effet de l'inhibition de la protéine du TGF-[bêta]1 sur le modèle cellules de glioblastome F98/Fischer sur la prolifération et la migration cellulaire. Pour ce faire, un inhibiteur sélectif au récepteur a d'abord été utilisé. Par la suite, des techniques d'inhibitions nucléotidiques (oligoantisens, siRNA, shRNA) ont été testées. Nous avons d'abord validé l'utilisation du modèle F98/Fischer dans l'étude des fonctions du TGF-[bêta]1 et de l'inhibition de la production de cette protéine. Nous avons observé la production importante de TGF-[bêta]1 par les cellules F98 avec des essais immunologiques (Western, ELISA). Avec l'essai ELISA, nous avons observé la production considérable de TGF-[bêta]1 actif d'emblée.La présence de notre protéine d'intérêt a été détectée dans le cerveau de rat Fischer implanté avec les cellules F98 contrairement aux animaux sains qui ne montrent aucune trace de TGF-[bêta]1. Ensuite, nous avons tenté de mettre au point une approche nucléotidique pour inhiber la production du TGF-[bêta]1. Pour les oligoantisens et les siRNA qui ont été couplés avec le vecteur liposomale Metafecten, nous n'avons pas réussi à obtenir de diminution significative du TGF-[bêta]1 dans les surnageants des cultures de F98 . Pour l'approche au shRNA/lentivirus, nous n'avons pas réussi à former de bactéries contenant la construction recherchée. Par la suite, nous avons testé sur notre modèle cellulaire un inhibiteur pharmacologique sélectif, le SB-431642, du récepteur permettant la phosphoryllation de la voie instracellulaire Smad, le T[bêta]R-I. Les essais de prolifération (WST-1) ont permis de constater un ralentissement dans la croissance des F98 traitées au SB-431542. Un essai immunologique western a permis de constater que la production de VEGF était d'ailleurs influencée par cette inhibition du TGF-[bêta]1. L'utilisation d'un vecteur luciférase couplé à un élément de réponse Smad a permis de constater que la voie du TGF-[bêta]1 était bel et bien affectée à la baisse par cet inhibiteur. En effet, le dosage luminescent de la luciférase a permis de noter une diminution significative de sa quantité. L'activité d'un tel vecteur est proportionnelle à l'activité Smad intracellulaire. Nous avons aussi testé cet inhibiteur sur le modèle de croissance tumorale tridimensionnelle de sphéroïdes F98.La croissance des sphéroïdes a été ralentie par la présence de l'inhibiteur et l'invasion de la matrice de collagène observée chez les sphéroïdes contrôles a été freinée par l'ajout de SB-431542. Bien que certains de nos essais n'aient pas donné les résultats escomptés, l'utilisation de l'inhibiteur SB-431542 nous a permis de voir l'implication à du TGF-[bêta]1 dans les mécanismes de progression tumorale chez la lignée cellulaire F98, tel que la prolifération et la migration cellulaire. Ces résultats sont le préalable à d'éventuels essais avec le modèle d'étude animal, le rat Fischer avec l'utilisation de cellules de glioblastomes F98.

BACKGROUND: Scythe/BAT3 is a member of the BAG protein family whose role in apoptosis has been extensively studied. However, since the developmental defects observed in Bat3-null mouse embryos cannot be explained solely by defects in apoptosis, we investigated whether BAT3 is also involved in cell-cycle progression. METHODS/PRINCIPAL FINDINGS: Using a stable-inducible Bat3-knockdown cellular system, we demonstrated that reduced BAT3 protein level causes a delay in both G1/S transition and G2/M progression. Concurrent with these changes in cell-cycle progression, we observed a reduction in the turnover and phosphorylation of the CDK inhibitor p21, which is best known as an inhibitor of DNA replication; however, phosphorylated p21 has also been shown to promote G2/M progression. Our findings indicate that in Bat3-knockdown cells, p21 continues to be synthesized during cell-cycle phases that do not normally require p21, resulting in p21 protein accumulation and a subsequent delay in cell-cycle progression. Finally, we showed that BAT3 co-localizes with p21 during the cell cycle and is required for the translocation of p21 from the cytoplasm to the nucleus during the G1/S transition and G2/M progression. CONCLUSION: Our study reveals a novel, non-apoptotic role for BAT3 in cell-cycle regulation. By maintaining a low p21 protein level during the G1/S transition, BAT3 counteracts the inhibitory effect of p21 on DNA replication and thus enables the cells to progress from G1 to S phase. Conversely, during G2/M progression, BAT3 facilitates p21 phosphorylation by cyclin A/Cdk2, an event required for G2/M progression. BAT3 modulates these pro- and anti-proliferative roles of p21 at least in part by regulating cyclin A abundance, as well as p21 translocation between the cytoplasm and the nucleus to ensure that it functions in the appropriate intracellular compartment during each phase of the cell cycle. / Dissertation

Dissertation (Ph.D.)--University of South Florida, 2009. / Includes vita. Includes bibliographical references. Also available online.

Dissertation (Ph.D.)--University of South Florida, 2009. / Title from PDF of title page. Document formatted into pages; contains 149 pages. Includes vita. Includes bibliographical references.

Short noncoding RNAs play roles in regulating nearly every biological process, in nearly every organism, yet the exact function and importance of these molecules remains a subject of some debate. In order to gain a better understanding of the contexts in which these regulators have evolved, I have undertaken a variety of approaches to study the evolutionary history of the components that make up these pathways, in the form of two main research efforts. In the first chapter, I have used a combination of population genetics and molecular evolution techniques to show that proteins involved in the piRNA pathway are rapidly evolving, and that different components of the pathway seem to be evolving rapidly on different timescales. These rapidly evolving piRNA pathway proteins can be loosely separated into two groups. The first group appears to evolve quickly at the species level, perhaps in response to transposons that invade across species lines, while the second group appears to evolve quickly at the level of individual populations, perhaps in response to transposons that are paternally present yet novel to the maternal genome. In the second chapter of my research, I have used molecular evolution techniques and carefully devised controls to show that the binding sites of well-conserved miRNAs are among the most slowly changing short motifs in the genome, consistent with a conserved function for these short RNAs in regulatory pathways that are ancient and extremely slow to change. I have additionally discovered a major flaw in an existing approach to motif turnover calculations, which may lead to systematic biases in the published literature toward the false inference of increased regulatory complexity over time. I have implemented a revised approach to motif turnover that addresses this flaw.