No description available.

KRAS is a gene that plays a very important role in the initiation and development of several types of cancer. In particular, 90% of human pancreatic cancers are due to KRAS mutations. KRAS is difficult to target directly and a promising therapeutic path is its indirect inactivation by targeting one of its Synthetic Lethal Partners (SLPs). A gene G is a Synthetic Lethal Partner of KRAS if the simultaneous perturbation of KRAS and G leads to cell death. In the past, efforts to identify KRAS SLPs with high-throughput RNAi screens have been performed. These studies have reported only few top-ranked SLPs. To our knowledge, these screens have never been considered in combination for further examination. This thesis employs integrative analysis of the published screens, utilizing additional, independent data aiming at the detection of more robust therapeutic targets. To this aim, RankSLP, a novel statistical analysis approach was implemented, which for the first time i) consistently integrates existing KRAS-specific RNAi screens, ii) consistently integrates and normalizes the results of various ranking methods, iii) evaluates its findings with the use of external data and iv) explores the effects of random data inclusion. This analysis was able to predict novel SLPs of KRAS and confirm some of the existing ones.

Caenorhabditis elegans possui quatro genes de kpcs (kex2/subtilisin-like proprotein convertases): kpc-1, kpc-2/egl-3, kpc-3/aex-5, kpc-4/bli-4. Em C. elegans, dois dos quatro polipeptídeos de vitelogenina encontrados dentro dos ovócitos, YP115 e YP88, se originam a partir de um precursor polipeptídico (VIT-6) clivado pós-traducionalmente após o motivo RGKR. Nematóides transgênicos foram produzidos com construções repórteres transcricionais de GFP. Foi verificada expressão de kpc-1 tanto em neurônios quanto em células musculares e intestinais. Esses dados, aliados aos dados da literatura para os outros genes kpc de C. elegans, sugerem o envolvimento de KPC-1 no processamento de VIT-6, que é secretada por células intestinais. Ensaios de Western-blot compararam o processamento de VIT-6 em nematóides selvagens, mutantes e knock-down por RNAi para os diferentes genes kpc. A análise de nematóides mutantes e knock-down por RNAi combinado para os outros três genes de convertase de C. elegans confirmou a redundância da atividade dessas enzimas no processamento de VIT-6. / Four kpc genes are found in the Caenorhabditis elegans genome: (kex2/subtilisin-like proprotein convertases): kpc-1, kpc-2/egl-3, kpc-3/aex-5, kpc-4/bli-4. Two of the four vitellogenin polypeptides, YP115 and YP88, originate from a precursor, VIT-6. VIT-6 is cleaved post-translationally after the RGKR motif. Transgenic worms carrying GFP transcription reporter constructs were produced. Expression of kpc-1 has been localized to neurons as well as muscular and intestinal cells. These data, together with the ones available from the literature for the other kpc genes, suggest the involvement of KPC-1 in the processing of VIT-6, which is secreted from intestinal cells. Western-blot analysis compared the pattern of VIT-6 processing in wild-type, mutants and RNAi-treated worms for the other kpcs. Analysis of worms treated by combined RNAi confirmed the redundancy of KPCs in VIT-6 processing.

Les interactions hôte-pathogène sont un jeu vaste et complexe entre agent pathogène et hôtepour la victoire de la bataille de la pathogenèse. Plusieurs organismes modèles sont étudiéspour illustrer les mécanismes impliqués dans ces interactions. Dans ma thèse, j'ai utilisé lesplanaires comme un organisme modèle pour explorer les interactions hôte-pathogène. Comme les différents organismes modèles peuvent mettre enévidence les différentes caractéristiques de l'immunité, j'ai décidé de tirer avantage del'absence de connaissances sur l'immunité des planaires en explorant l'inexplorée. Dans monprojet, j'ai infecté les planaires avec 16 bactéries pathogènes : les planaires y sont très résistantes. Pour en explorer lemécanisme j'ai effectué un profilage du transcriptome à partir deplanaires infectées, suivie par un criblage par ARN interférence des gènes up-régulés. J'aidécouvert les gènes qui régissent la résistance antibactérienne dans les planaires, et de façonintéressante, le criblage a permis de mettre en évidence un gène, MORN2, dont la fonctionimmunologique était complètement inconnue. L'induction et l'extinction de l'expression de MORN2dans les macrophages ont révélé que MORN2 contrôle l'internalisation, la réplication et letrafic des bactéries à l'intérieur de la cellule. Dans mon étude, j'ai démontré que MORN2 estun composant de la phagocytose associée à LC3 et qu'il peut surmonter le blocage de lafusion phagolysosomale imposée par les bactéries pathogènes. Ainsi ma thèse met en avantl'importance d'utiliser des organismes modèles inhabituels afin de dévoiler des mécanismesinexplorées et des molécules impliquées dans les interactions hôte-pathogène. / Host-pathogen interaction is a vast and complex interplay between pathogen and hostto conquer the battle of pathogenesis. Several model organisms are being studied to illustratethe mechanisms involved in these interactions. In my thesis I have used planarians as a modelorganism to explore host-pathogen interactions. As different model organismscan highlight different features of immunity I decided to take advantage of lack of knowledgeabout planarian immunity and get benefits from exploring unexplored. In my project I haveinfected planarians with 16 pathogenic bacteria and I found that in contrary to othercommonly used model organisms such as Drosophila, C. elegans and zebrafish the planariansare highly resistant to bacterial infections. To explore the mechanism behind this resistance Iperformed infection induced transcriptome profiling followed by RNA interference screeningof up-regulated gens. I discovered genes governing antibacterial resistance in planarians andinterestingly the screening highlighted a gene MORN2 of which the immunological functionwas completely unknown. The human ortholog of MORN2 is then further assessed for itsantimicrobial function. Induced expression and down regulation of MORN2 in macrophagesrevealed that MORN2 controls uptake, replication and trafficking of bacteria inside the cell.In my study I demonstrated that MORN2 is a component of LC3-associated phagocytosis andit can overcome phagosome maturation blockage imposed by pathogenic bacteria. Thus mythesis propounds the importance of using unusual model organisms to unveil unexploredmechanisms and molecules involved in host-pathogen interactions.

A região N-terminal de OTI-VIT-1 foi expressa e os polipeptídeos recombinantes foram purificados. OTI-VIT-1 pode ser homólogo da vitelina YP170B de C. elegans. Foram identificados um intron na região 5´ e dois na região 3´ do gene Oti-vit-1. Antissoro monoespecífico para PVIT1HisC confirmou que o gene Oti-vit-1 codifica VT1. O polipeptídeo recombinante P40-H, correspondente à região N-terminal da proteína OTI-VIT-6 interage com um polipeptídeo de aproximadamente 100 kDa (P100) presente em extratos proteicos totais de O. tipulae. Estudamos também o papel da Proteína Microssômica Transportadora de Triglicerídeos (MTP) na biossíntese de Vitelogenina do nematoide C. elegans. Ensaios de RNAi em C. elegans, utilizando parte da sequência do gene da MTP (Cel-dsc-4) foram realizados nas linhagens N2 e DH1033. Microscopia de fluorescência de vermes adultos da linhagem DH1033, submetidos a RNAi, mostrou acúmulo de YP170B::GFP no interior dos enterócitos. Este acúmulo sugere a participação da MTP na secreção de VTG. Análise imunológica da vitelogenina nestes mesmos vermes não detectaram alterações no processamento de CEL-VIT-6, sugerindo que o mesmo ocorra não só no pseudoceloma, mas também no interior dos enterócitos. / The N-terminal region of OTI-VIT-1 was expressed and the recombinant polypeptides were purified. OTI-VIT-1 may be homologous to the vitellin YP170B from C. elegans. We identified an intron in the 5 \'region and two in 3\' region from Oti-vit-1. Monospecific antisera to PVIT1HisC confirmed that the gene Oti-vit-1 encodes VT1. The recombinant polypeptide P40-H, corresponding to the N-terminal region of the protein OTI-VIT-6, interacts with a polypeptide of approximately 100 kDa (P100) present in total protein extracts of O. tipulae. The role of microsomal triglyceride transfer protein (MTP) in the biosynthesis of vitellogenin was studied in the nematode C. elegans. Trials of RNAi in C. elegans, using the sequence of the MTP gene (Cel-dsc-4) were performed in the strains N2 and DH1033. Fluorescence microscopy of adult worms of strain DH1033, subjected to RNAi, showed accumulation of YP170B:: GFP within the enterocytes. This accumulation suggests the involvement of MTP in the secretion of VTG. Analysis using anti-vitellogenin immune serum did not detect changes in the processing of CEL-VIT-6, suggesting that it occurs not only in pseudocoelom but also within the enterocytes.

O agente etiológico da Febre Maculosa das Montanhas Rochosas (RMSF), conhecida no Brasil como Febre Maculosa Brasileira, é a bactéria Rickettsia rickettsii. Essa bactéria é transmitida ao homem pela picada de diferentes espécies de carrapatos ixodídeos. No Brasil, os vetores são Amblyomma cajennense e A. aureolatum. As taxas de prevalência de R. rickettsii nas populações de carrapatos de áreas endêmicas para RMSF são baixas, em geral abaixo de 1%. Essa baixa prevalência parece estar associada a menores taxas reprodutivas e de sobrevivência de linhagens infectadas, sugerindo que R. rickettsii seja patogênica também para os seus vetores. Infecções experimentais demonstraram que 80-100% dos indivíduos de uma colônia de A. aureolatum mantida em laboratório são infectados por R. rickettsii, enquanto apenas 10-60% de A. cajennense adquirem a bactéria. Esses dados indicam que as respostas dessas duas espécies de carrapatos à infecção sejam diferentes, resultando em diferentes taxas de prevalência da bactéria. Dessa maneira, a caracterização molecular das interações entre carrapatos do gênero Amblyomma e a bactéria R. rickettsii é importante, podendo gerar informações não somente para o esclarecimento acerca dos mecanismos de patogenicidade de R. rickettsii para os carrapatos, mas também para um melhor entendimento dos mecanismos responsáveis pela aparente restringência de A. cajennense à infecção. Assim, os objetivos do presente estudo foram: (i) analisar os efeitos da infecção por R. rickettsii sobre o perfil de expressão gênica de carrapatos A. cajennense por hibridação subtrativa por supressão (SSH), (ii) validar os dados de SSH por reação em cadeia de polimerase quantitativa precedida por transcrição reversa (RT-qPCR) e (iii) caracterizar funcionalmente dois genes com expressão induzida pela infecção por RNA de interferência (RNAi). Após a análise bioinformática dos dados de SSH, 44 sequências únicas foram obtidas, das quais 36 representam genes com expressão induzida e 8 genes com expressão reprimida pela infecção. A indução dos genes codificadores da subunidade I da citocromo c oxidase (COX1), da subunidade IV da NADH desidrogenase, de uma proteína com domínio de inibidor de serina-proteases Kunitz-type (papilina-like), identificados por SSH, e de um peptídeo antimicrobiano (hebraeína), foi confirmada por RT-qPCR. O silenciamento gênico da hebraeína e da papilina-like não teve nenhum efeito na aquisição de R. rickettsii pelo vetor, indicando que, isoladamente, não são responsáveis pela proteção de A. cajennense contra a infecção. Os dados gerados pelo presente estudo abrem perspectivas para que outros genes sejam avaliados quanto ao seu papel na aquisição de R. rickettsii, os quais, no futuro, podem ser considerados como alvos para o desenvolvimento de vacinas. / The etiologic agent of the Rocky Mountain Spotted Fever (RMSF), also known as Brazilian Spotted Fever in Brazil, is the bacterium Rickettsia rickettsii. This rickettsia is transmitted to humans by the bite of various tick species. In Brazil, Amblyomma cajennense and A. aureolatum are known as vectors. The prevalence rates of R. rickettsii infected ticks in RMSF endemic areas are low, oscillating around 1%. These low prevalence rates seems to be associated with lower reproductive and survival rates of infected ticks, suggesting that R. rickettsii is also pathogenic to its vectors. Experimental infections with R. rickettsii have demonstrated that 80 to 100% of A. aureolatum ticks from a laboratory colony acquire this bacterium, whereas only 10 to 60% of A. cajennense ticks become infected. These results indicate that the responses of these two tick species against infection are different, resulting in different prevalence rates of the bacterium. Therefore, the elucidation of the interactions between ticks of the genera Amblyomma and the bacterium R. rickettsii at a molecular level is important to provide information to better understand the mechanisms of pathogenicity of R. rickettsii against ticks as well as for the elucidation of the mechanisms responsible for the apparent refractoriness of A. cajennense against infection. Therefore, the objectives of the current study were: (i) analyze the effets of the infection with R. rickettsii on the gene expression of ticks A. cajennense by suppression subtractive hybridization (SSH), (ii) validate SSH data by reverse transcription quantitative polymerase chain reaction (RT-qPCR), and (iii) functionally characterize two genes induced by infection using RNA interference (RNAi). After bioinformatics analysis of SSH data, 44 unique sequences were obtained, among which 36 represent genes with expression induced and 8 repressed genes by infection. The induction of genes encoding subunit I of cytochrome c oxidase (COX1), the NADH dehydrogenase subunit IV, a protein containing Kunitz-type inhibitor domain (papilin-like), identified by SSH, and an antimicrobial peptide (hebraein), was confirmed by RT-qPCR. The effects of knockdown of hebraein and papilin-like encoding genes had no effect on the acquisition of R. rickettsii by the vector. Data of the current study may be used to evaluate the role of other genes in acquisition of R. rickettsii, which, in the future, may be considered as target for vaccine development.

KRAS is a gene that plays a very important role in the initiation and development of several types of cancer. In particular, 90% of human pancreatic cancers are due to KRAS mutations. KRAS is difficult to target directly and a promising therapeutic path is its indirect inactivation by targeting one of its Synthetic Lethal Partners (SLPs). A gene G is a Synthetic Lethal Partner of KRAS if the simultaneous perturbation of KRAS and G leads to cell death. In the past, efforts to identify KRAS SLPs with high-throughput RNAi screens have been performed. These studies have reported only few top-ranked SLPs. To our knowledge, these screens have never been considered in combination for further examination. This thesis employs integrative analysis of the published screens, utilizing additional, independent data aiming at the detection of more robust therapeutic targets. To this aim, RankSLP, a novel statistical analysis approach was implemented, which for the first time i) consistently integrates existing KRAS-specific RNAi screens, ii) consistently integrates and normalizes the results of various ranking methods, iii) evaluates its findings with the use of external data and iv) explores the effects of random data inclusion. This analysis was able to predict novel SLPs of KRAS and confirm some of the existing ones.

Weltweit hat das duktale Adenokarzinom des Pankreas (PDAC) unter den Krebserkrankungen die schlechteste Prognose. Aufgrund der unspezifischen Symptome wird die Erkrankung meist erst in einem lokal fortgeschrittenem Stadium diagnostiziert, wenn eine kurative Tumorresektion nicht mehr möglich ist und es bereits zur Metastasierung gekommen ist. Trotz intensiver klinischer Forschung wird mit bisherigen Therapieansätzen wie zum Beispiel Gemcitabin (auch in Kombination mit nab-Paclitaxel) nur eine geringfügige Verbesserung des medianen Überlebens erzielt. Diese Therapieresistenz gegenüber Gemcitabin wurde in in vitro Versuchen mit verschiedenen humanen PDAC-Zelllinien bestätigt. Die zusätzlich behandelte nichttumorigene Pankreasdukt-Zelllinie HDPE-E6E7 zeigte hingegen eine starke Sensitivität gegenüber dem Chemotherapeutikum. Ursächlich beteiligt an der generellen Resistenz dieser Tumore gegenüber Chemo- und Strahlentherapie sind verschiedene Apoptose-Evasionsmechanismen. Diese sind vor allem durch ein Ungleichgewicht pro- und antiapoptotischer Faktoren bedingt (Lowe 2004). Zusätzlich fördern KRAS-Mutationen, die nahezu universell in allen PDACs vorliegen, die Proliferation der Tumorzellen und unterstützen die Apoptose-Dysregulation durch eine verstärkte Expression antiapoptotischer Proteine. Nach umfangreichen Literaturrecherchen (Werner 2011a, Werner 2011b) wurden verschiedenste PDAC-Zelllinien hinsichtlich ihrer Expression von Apoptose-assoziierten Genen analysiert. Untersucht wurden diesbezüglich verschiedene humane PDAC-Zelllinien, aber auch Primärzellkulturen (PaCaDD-Zellen), die in unserem Labor per Outgrowth-Methode aus Patiententumorgewebe etabliert wurden. Ergänzend wurden murine Zelllinien analysiert, die aus einem genetischen PDAC-Mausmodell (KRASG12D; P53R172H; PDX1 CRE) stammen. Normiert bezüglich der Expression der HDPE-E6E7-Zellen wurde eine vielfältige, sehr heterogene Dysregulation von verschiedenen, mit der Apoptose assoziierten Proteinen festgestellt. Per siRNA-basiertem Knockdown wurden verschiedene Kandidatengene hinsichtlich ihrer funktionellen Bedeutung für die Zellproliferation und Apoptose-Induktion näher charakterisiert. In einem dynamischen Prozess wurde eine multimodale Therapie entwickelt, bei der fünf antiapoptotische Zielgene (BCLXL, FLIP, MCL1L, SURVIVIN und XIAP) kombiniert mit KRAS als zentralem Onkogen simultan in ihrer Expression inhibiert wurden. Ziel war es, hierdurch sowohl die extrinsische als auch intrinsische Apoptose zu normalisieren und eine möglicherweise durch Caspase-Inhibitoren blockierte Signaltransduktion zu ermöglichen. Ein zusätzlicher Knockdown von KRAS sollte einer Gegenregulierung dieser Therapie vorbeugen und die gesteigerte Proliferation der Tumorzellen unterbinden. Dieser so genannte SGS6-Therapieansatz zeigte in vitro in allen fünf getesteten humanen sowie in zwei murinen Zelllinien eine starke Apoptose-Induktion und Verminderung der Zellzahl. Durch Zweit-siRNAs wurde die spezifische Wirksamkeit der Knockdowns bestätigt und zelluläre off-target-Effekte wurden ausgeschlossen. Auch in vivo wurde in einem subkutanen Allograftmodell mit dem SGS6-Therapiekonzept eine starke Tumorreduktion erzielt. Die analoge Untersuchung der nichttumorösen Pankreasdukt-Zelllinie HDPE-E6E7 zeigte, dass die SGS6-Therapie deutlich spezifischer für die Krebszellen war verglichen zur Behandlung mit Gemcitabin.

RNA-bindande proteiner (RBP:er) har framträtt som kritiska regulatorer i post-transkriptionell genreglering, och deras dysreglering bidrar till cancerpatogenes. CAPRIN1, ett cytoplasmiskt protein, har identifierats som ett onkofetalt RBP med potentiell betydelse i hepatocellulärt karcinom (HCC), en mycket malign form av levercancer med dålig prognos. Detta examensarbete syftade till att använda gensredigeringsteknologier som CRISPR-interferens (CRISPRi) och RNA-interferens (RNAi) för att störa CAPRIN1-uttryck i HCC-cellinjer och analysera dess effekter på cellproliferation och mängden av CAPRIN1:s främsta RNA-mål. CRISPRi-konstruktioner som riktade sig mot transkriptionsstartstället (TSS) av CAPRIN1 designades och validerades, men trots lyckad kloning och uttryck av guideRNA:er (gRNA:er) resulterade CRISPRi-medierad gensläckning (KD) inte i någon signifikant minskning av CAPRIN1-uttryck. Ineffektiviteten hos CRISPRi tillskrevs låg transfektionseffektivitet, vilket bekräftades av fluorescensmikroskopi med EGFP-expressande plasmider i HepG2- och Huh7-celler. Detta kräver ytterligare optimering av elektroporationsparametrar eller utforskning av alternativa leveransmetoder. I kontrast uppnådde RNAi-medierad KD en betydande minskning av CAPRIN1-uttryck, vilket visade hög KD-effektivitet (90%) enligt RT-qPCR. Denna nivå av gensläckning gav en robust modell för vidare analyser. Efterföljande RT-qPCR av sex topp-RNA-mål identifierade av RAPseq visade varierande svar, med oväntad uppreglering av MYC och Cyclin D2, vilket går emot litteratur som antyder att deras stabilitet beror på CAPRIN1. Denna diskrepans kan förklaras av betydande standardavvikelse i uttrycksnivåerna, vilket understryker behovet av att upprepa experimenten samt genomföra en transkriptomanalys med RNA-seq för att identifiera meningsfulla mål såsom långa icke-kodande RNA (lncRNA:er). Ytterligare, MTT-proliferationstester, visade ökad cellproliferation efter CAPRIN1-KD, även om experimentella inkonsekvenser såsom ojämna cellantal begränsade slutsatsernas pålitlighet. För att erhålla tillförlitliga resultat behöver dock MTT-testet upprepas för att säkerställa konsistens med den positiva kontrollen och samla in statistiskt signifikanta data.Sammanfattningsvis, trots att CRISPRi-försöket stötte på betydande utmaningar, kan gRNA-designen och klonade plasmider användas i framtida studier när elektroporationsprotokollet har optimerats. Dessutom visade den framgångsrika RNAi-medierade KD av CAPRIN1 en alternativ metod som kan antas för vidare studier med andra RBP-kandidater. Framtida studier bör syfta till att optimera elektroporationssystemet, validera KD på proteinnivå och använda RNA-seq för en omfattande analys av CAPRIN1:s inverkan på transkriptomet i HCC-cellinjer. Dessa ansträngningar kommer att förbättra förståelsen av CAPRIN1:s regulatoriska mekanismer och dess potential som terapeutiskt mål vid HCC. / RNA-binding proteins (RBPs) play a crucial role in post-transcriptional gene regulation, and their dysregulation is implicated in cancer pathogenesis. CAPRIN1, a cytoplasmic activation/proliferation-associated protein, identified as an oncofetal RBP with potential significance in hepatocellular carcinoma (HCC), is a worthy candidate to be studied. Objective: This project aimed to establish a protocol for silencing RBPs gene expression via CRISPR interference (CRISPRi) technology using CAPRIN1 as a case study, as the roles of CAPRIN1 in tumorigenesis remains unknown. Results: Despite successful cloning of the designed gRNAs, CRISPRi-mediated knockdown did not reduce CAPRIN1 expression, attributed to low transfection efficiency as indicated by fluorescence microscopy. RNAi-mediated knockdown, however, achieved substantial reduction in CAPRIN1 expression (90%). Subsequent analysis of CAPRIN1 top RNA interactors showed substantial standard deviations, highlighting the need for repeating the experiments. The MTT assay showed uneven initial seeding densities, necessitating further repetitions of the assay. Conclusions: The study highlights the challenges associated with CRISPi-mediated knockdown, especially in transfecting HepG2 cells with large plasmids using electroporation. However, the designed gRNAs and cloned plasmids have the potential to be used in future studies, provided that the transfection process is further optimized. RNAi proved to be an effective alternative for gene silencing, achieving high knockdown efficiency and enabling subsequent analysis of CAPRIN1 target RNAs. Prioritizing further optimization of CRISPRi transfection protocols in upcoming projects will facilitate the adoption of this workflow for investigating other RBP candidates. Additionally, performing a comprehensive RNA-seq analysis could provide a deeper understanding of CAPRIN1’s role in HCC.

No description available.