Charles University, Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Daniel Diviš Supervisors: Prof. Dr. Florence Apparailly, Directrice de Recherche Prof. PharmDr. Petr Pávek, Ph.D. (formal tutor) Title of diploma thesis: The role of miR-150 in the physiopathology of oligoarticular juvenile idiopathic arthritis Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatoid disease affecting children, and its pathological mechanisms are still poorly understood. Innate and adaptive immunity including myeloid cells play a major role in these processes. Epigenetic deregulations along with non-coding microRNAs have been reported in many inflammatory diseases. Moreover, preliminary results obtained by the research group of Prof. Florence Apparailly showed accumulation of intermediate monocytes along with the high expression of miR-150 in the synovial fluid of children affected by oligoarticular JIA. Based on these findings a hypothesis has been postulated suggesting that miR-150 could have a role in the pathogenesis of this disease and in the regulation of monocyte differentiation and function. To study the impact of miR-150 on monocytes from the peripheral blood of healthy donors, transfection experiments were performed to neutralize miR-150. The...

Oligodendroglial tumours originate from oligodendrocytes usually arising in the white matter and could be classified into grade-II oligodendrogliomas (OD) and anaplastic oligodendrogliomas (AOD, grade-III) according to the 2016 World Health Organization (WHO) grading scheme. ODs1 could be diagnosed by pathological and immunohistochemical analyses, however recent evidence suggests that they could be better diagnosed on the basis of defined genetic entities, such as the combined loss of chromosome 1p and 19q arms and IDH mutation. 1p/19q co-deletion is molecular hallmark of ODs and is clinically associated with better prognosis, response to chemo/radio-therapy and overall survival. Typical oligodendroglial histological features are strongly associated with 1p/19q loss and IDH mutation, which is critically important as diagnostic point of view. The examining of exclusive molecular signatures and transcriptome expression profiles added to histological class could compliment the classification of OD subtypes. In this regard, microRNAs (miRNAs, miRs) profiles could serve classifier signatures for tumour subsets. MiRNAs are 22nt short non-coding RNAs which are expressed endogenously and regulate diverse cellular process through negative control on gene expression at the posttranscriptional level by direct or imperfect interaction with their target mRNAs. MiRNAs are involved in regulating human tumorigenesis acting as either tumour suppressors or oncogenes. During the passage of tumorigenesis miRNA expression level is significantly increased or decreased compared to corresponding normal tissue. The same is observed with their mRNAs. Therefore, transcriptome profiling of human tumours could identify signatures associated with progression, diagnosis, prognosis and response to therapy. However, until recently the information regarding the expression of miRNAs and mRNA in oligodendroglial tumours is scarce. In this study we performed miRNA and mRNA differential expression profiling between grade II and grade III ODs using microarray based expression profiling platforms (723 transcripts and 41,000 genes, respectively). 7 cases for OD grade-II, and 7 for AOD grade-III, and 15 non neoplastic white matter (nnWM) samples were used after microdissection with no previous history of treatment. We performed a systematic evaluation of miRNAs and mRNAs expressions and determined miRNAs and putative target genes that are differentially expressed in grade III AOD, but not in grade II OD and in non-neoplastic white matter (nnWM). 1 ODs when used with ,,s\" will represent both OD and AOD. 50 miRNAs were overexpressed and 43 were down regulated in AOD-III, whereas 7 miRNAs showed significant reduction in expressions in OD-II group. 3 miRNAs were commonly down regulated in comparisons of both groups. The hsa-miR-23a was strongly upregulated and hsamiR-27a was strongly downregulated in AOD-III. The functions of hsa-miR-23a and hsa-miR- 27a were tested in human adult fibroblasts for cell proliferation assay and apoptosis detection. Cells treated with pre-miR-23a and pre-miR-27a showed 20% reduction in cell proliferation as compared with controls. Further, the functional relevance of miRNAs to their target mRNAs was validated for each group, using real time qPCR. 10 key-miRNAs from AOD were subjected to validation by qPCR. We were able to confirm 7 miRNAs (p? 0.05). Among these, 5 miRs (miR- 193a-3p, miR-24, miR-27a, miR-30a-5p and miR-30c) showed reduced expression whose target genes (CCND1, HDAC2, PDGFA and RAB-26) were upregulated. Whereas, 2 miRNAs likewise miR-301b and miR-378 were overexpressed whose target genes BCL2, FGF2, CD44 and PPP4R4 confirmed by qPCR (p? 0.05). Bioinformatics based gene ontology (GO), and networking analysis revealed that differential expression and targets are attributed to differentiation of embryonic stem cells, cell adhesion, angiogenesis and neurogenesis, resistance to apoptosis, protein-protein interactions and cell proliferation. It was possible to identify and validate miRNAs and their mRNA-targets potentially involved in the progression of oligodendrogliomas particularly in grade III-AOD. Collectively, this analysis provides new insights to malignant progression of oligodendroglial tumours and could compliment WHO-2016 diagnosis scheme and may provide predictive outcome in patients as well as decision to therapy. / Oligodendrogliomas originários de oligodendrócitos que geralmente surgem na substância branca podendo ser classificados em grau oligodendroglioma (II-OD), e anaplastic oligodendrogliomas (grau III-AOD). Os ODs2 podem ser diagnosticados por análises patológicas e imuno-histoquímicas, porém evidências recentes sugerem que poderiam ser melhor diagnosticados com base em assinaturas moleculares, como a deleção combinada dos cromossomas 1p e 19q - marcadores moleculares dos OD associados clinicamente a um melhor prognóstico, resposta à terapia e melhor sobrevida. As características histológicas típicas dos oligodendrogliomas também estão fortemente associadas à deleção de 1p/19q, que é criticamente importante como ponto de vista diagnóstico. Assim, os subtipos de gliomas podem ser fortemente diferenciados não somente em relação ao seu perfil histológico mas também com base em seu perfil de expressão genica e suas assinaturas moleculares exclusivas. Os microRNAs (miRNAs, miRs) emergiram como assinaturas moleculares para os diferentes graus. Os miRNAs são RNAs não codificantes, contendo em torno de 22 nucleótidos. São expressos endogenamente e regulam diversos processos celulares através do controle negativo da expressão gênica em nivel pós-transcricional e por interacção directa ou imperfeita com o RNAm-alvo. Os miRNAs estão envolvidos na regulação da tumorigenese humana atuando como supressores de tumour ou oncogenes. Durante o processo da tumorigenese o nível de expressão dos miRNAs é aumentado ou diminuído significativamente em comparação com tecido normal correspondente. O perfil de expressão de miRNA de tumores humanos poderia identificar assinaturas associadas com progressão, diagnóstico, prognóstico e resposta à terapia. Contudo, até recentemente a informação sobre a expressão de miRNAs em oligodendrogliomas é escassa. Neste estudo, avaliamos o perfil de expressão diferencial de miRNA e RNAm em ODs graus II e III usando plataformas de perfis de expressão baseadas em microarray (723 transcritos e 41.000 genes, respectivamente). Foram utilizados 14 casos de ODs microdissecados, sendo 7 OD grau II, e 7 AOD grau III (anaplasicos) sem histórico prévio de tratamento, além de 15 amostras de substancia branca não neoplásica (nnSB). Por meio de avaliações sistemáticas foram determinados miRNAs e mRNAs expressos em AOD grau III, mas não em OD grau II e em substancias brancas não neoplásicas (nnSB). 2 ODs when used with ,,s\" will represent both OD and AOD. Assim, foram encontrados 50 miRNAs com alta expressão e 43 miRNAs com baixa expressão em AOD-III, enquanto que 7 miRNAs apresentaram expressões reduzidas no grupo OD-II. Na comparação entre os dois grupos, 3 miRNAs apresentaram baixa expressão. A hsa-miR-23a mostrou alta expressão e a hsa-miR-27a apresentou uma diminuição de expressão importante em AOD III. A atividade dos hsa-miR-23a e hsa-miR-27a foram testadas em células de fibroblastos adultos humanos usando ensaios de proliferação celular e detecção de apoptose. As células tratadas com pre-miR-23a e pre-miR-27a mostraram 20% redução de proliferação celular em comparação com os controles. Para cada grupo, a relevância funcional dos miRNAs e seus mRNAs alvos foi validada utilizando qPCR. Dos 10 miRNAs submetidos a validação em grau III, foi possivel confirmar 7 miRNA(p<0,05). Entre esses, 5 miRs (miR-193a-3p, miR-24, miR- 27a, miR-30a-5p e miR-30c) mostraram expressão reduzida, cujos genes alvos (CCND1, HDAC2, PDGFA e RAB-26) apresentavam alta expressão. Enquanto que, 2 miRNAs como miR-301b e miR-378 apresentaram alta expressão cujos genes alvo BCL2, FGF2, CD44 e PPP4R4 foram confirmados por qPCR (p<0,05). Ferramentas de bioinformática (Gene Ontology) e a análises em rede revelaram que a expressão diferencial e os alvos são atribuídos à diferenciação de células-tronco embrionárias, adesão de celular, angiogênese e neurogênese, resistência à apoptose, interações proteína-proteína e proliferação celular. Foi possível identificar e validar miRNAs e RNAm-alvos potencialmente envolvidos na progressão de oligodendrogliomas. Coletivamente, esta análise fornece novos achados relacionados a progressão maligna de tumores oligodendrogliais e poderia facilitar o diagnóstico preciso e mais restritivo, o desfecho preditivo em pacientes, bem como auxiliar na decisão da terapia.

A reverse transcription reaction allows the production of complementary DNA (cDNA) using an RNA template and relies on polymerases displaying reverse transcriptase (RT) activity. This process, with major applications in both research and in medical diagnostics, is often limited by the nature of the RTs available. RNA secondary structure can prove problematic where mesophilic retroviral RTs are used while the alternative approach, using thermophilic DNA polymerases with RT activity, often results in error-prone cDNA production. <br /> This project recognised the need to study other possible sources of thermophilic RTs and outlines the study of four previously uncharacterised Group II Intronencoded proteins (IEP), with RT domains, from thermophilic bacteria. While cloning of the IEP genes and their expression on a small scale proved successful, difficulties were encountered when attempting purification. Despite a lack of overall purity, samples containing IEPs from Thermosinus carboxydivorans and Petrotoga mobilis were shown to have RT activity but characterisation of these IEPs was not carried out. However, an IEP from Bacillus caldovelox proved to be an excellent candidate for characterisation as successful purification was achieved. Enzyme engineering was also performed, fusing a Sac7d domain onto the C-terminus of this protein. These enzymes were shown to have optimum RT activity at 54ºC with activity still being displayed at 76ºC. Other studies on these enzymes showed that, unlike the retroviral RTs, the IEPs displayed no DNA-dependent DNA polymerase activity. The Sac7d fusion protein was also studied in terms of possible enhancements to the RT activity of an IEP. However, preliminary studies showed that, although this domain did not prove to be detrimental to the enzyme, it had little effect on improving the processivity of the RTs. <br /> Although this class of RT looks promising in terms of use as an alternative thermophilic RT, the IEPs studied in this report did incur major limitations during cDNA synthesis, which included lower than expected optimum reaction temperatures, very low fidelity and an inability to synthesise cDNA using complex RNA templates.

La progression naturelle des tumeurs consiste en une extension locale, puis à distance (métastase) par migration de cellules dans le sang et la lymphe vers des sites secondaires. Il est donc primordial de pouvoir détecter des cellules tumorales circulantes en plus de l’analyse morphologique et de l’immunocytochimie. De plus, deux technologies (cytométrie en flux et RT-PCR quantitative en temps réel) sont adaptées pour une analyse automatisée, rapide et sensible d’une très faible quantité de cellules. Le but de notre travail a été de mettre au point des systèmes de détection pour l’identification de cellules cancéreuses dans les épanchements péritonéaux et dans le sang. L’étude des biomarqueurs moléculaires apparaît comme une approche complémentaire intéressante pour améliorer l'efficacité du diagnostic dans ce type d'échantillons biologiques. Nous nous sommes intéressés à la mise en évidence de nouveaux marqueurs tumoraux qui pourront être utilisés pour le diagnostic précoce et le pronostic des cancers en utilisant les nouvelles techniques de biologie moléculaire. Il est probable que l'utilisation de multiples marqueurs moléculaires puisse permettre d’évoquer plus particulièrement certains types de cancers. Nous avons pu mettre en place une technique de PCR quantitative en temps réel, nettement plus sensible que la cytologie classique, et nous avons appliqué cette technique à l'étude de marqueurs tumoraux dans les liquides d’épanchement, mais aussi dans le sang pour rechercher et doser l’ARN messager. Nos résultats montrent que la cytométrie en flux adaptée à des lignées cellulaires ne l’est pas pour des prélèvements cliniques. Par la PCR quantitative, il a été possible de quantifier le niveau d’expression des marqueurs tumoraux étudiés en utilisant des plasmides de référence qui ont été préparés pour chaque gène. Plusieurs marqueurs permettent de différencier des épanchements malins et des épanchements bénins, mais surtout les antigènes CLDN4 et Ep-CAM étaient significativement plus élevés (68% et 57%, respectivement) chez les patients avec épanchements malins. L’ARN messager circulant de la CLDN4 était détectable et significativement plus élevée dans les sérums de patients atteints de cancer du sein (64% p<0,05). Les résultats indiquent que l'utilisation d'une combinaison de marqueurs comportant laclaudine 4 est plus susceptible de détecter des cellules malignes et d'être utiles pour le suivi de patients / The natural progression of tumors is a local extension, and remotely (metastasis) by migrating cells in the blood and the lymph to secondary sites. It is therefore essential to detect circulating tumor cells in addition to morphological analysis and immunocytochemistry. In addition, two technologies (flow cytometry and RT-PCR in real time) are suitable for a rapid and sensitive automated analysis of a very small quantity of cells. The aim of our work was to develop detection systems for identification of cancer cells in peritoneal effusions and blood. The study of molecular biomarkers appears as an attractive complementary approach to improve the efficiency of diagnosis in this type of biological samples. We are interested in the identification of new tumor markers that can be used for early diagnosis and prognosis of cancer using new techniques of molecular biology. It is likely that the use of multiple molecular markers can help to raise some specific types ofcancers. We were able to develop a quantitative PCR technique in real time, significantly more sensitive than conventional cytology, and we applied this technique to the study of tumor markers in effusions, but also in blood for detecting messenger RNA. Our results show that flow cytometry well-adapted to cell lines, is not unusable for clinical specimens. For quantitative PCR, it was possible to quantify the expression levels of tumor markers using reference plasmids prepared for each gene. Several markers can differentiate malignant and benign effusions, but especially CLDN4 and Ep-CAM antigens were significantly higher (68% and 57% respectively) in patients with malignant effusions.The circulating CLDN4 mRNA was detectable and significantly higher in the sera of patients with breast cancer (64% p <0.05). The results indicate that using a combination of markers including claudin 4 is more likely to detect malignant cells and be useful for monitoring patients

Orientador: Andrigo Barboza De Nardi / Resumo: A medicina comparativa torna-se cada vez mais importante para obtenção de estudos aprofundados em diversas áreas incluindo a oncologia, possibilitando melhor conhecimento da genética do câncer e desenvolvimentos de novas terapias. A expressão do IGF2BP-1 tem sido correlacionada com lesões pré-neoplásicas e neoplasias de maior agressividade, além de estar correlacionada com mau prognóstico em pacientes oncológicos com melanomas, sarcomas e carcinomas. A proposta geral desta pesquisa é identificar a expressão do IGF2BP-1 em linhagens celulares de osteossarcoma (OSA) canino e murino, bem como correlacionar sua expressão com o comportamento celular e avaliar a intensidade de marcação desta proteína através de imuno-histoquímica em amostras de OSA canino. Os resultados deste ensaio demonstraram que o IGF2BP-1 reduziu o potencial de formação de colônias, aumentou o potencial de invasão e migração celular e gerou aumento da expressão dos genes ABCG2, AXIN2, BTrCP, VEGF, CD133 e C-MYC em células de OSA murinho. A expressão deste gene em células de cão aumentou a formação de colônias, reduziu o potencial de invasão e migração celular e o silenciamento parcial do IGF2BP-1 gerou redução da expressão dos genes CCND1, CD133, CMYC e FZD6 em células de OSA canino. O silenciamento parcial do IGF2BP-1 gerou aumento dos genes AXIN-2 e VEGF em células de OSA canino. A imuno-histoquímica é um método eficaz para detecção do IGF2BP-1 em amostras de OSA canino evidenciando marcação citoplasmática f... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

Oligodendroglial tumours originate from oligodendrocytes usually arising in the white matter and could be classified into grade-II oligodendrogliomas (OD) and anaplastic oligodendrogliomas (AOD, grade-III) according to the 2016 World Health Organization (WHO) grading scheme. ODs1 could be diagnosed by pathological and immunohistochemical analyses, however recent evidence suggests that they could be better diagnosed on the basis of defined genetic entities, such as the combined loss of chromosome 1p and 19q arms and IDH mutation. 1p/19q co-deletion is molecular hallmark of ODs and is clinically associated with better prognosis, response to chemo/radio-therapy and overall survival. Typical oligodendroglial histological features are strongly associated with 1p/19q loss and IDH mutation, which is critically important as diagnostic point of view. The examining of exclusive molecular signatures and transcriptome expression profiles added to histological class could compliment the classification of OD subtypes. In this regard, microRNAs (miRNAs, miRs) profiles could serve classifier signatures for tumour subsets. MiRNAs are 22nt short non-coding RNAs which are expressed endogenously and regulate diverse cellular process through negative control on gene expression at the posttranscriptional level by direct or imperfect interaction with their target mRNAs. MiRNAs are involved in regulating human tumorigenesis acting as either tumour suppressors or oncogenes. During the passage of tumorigenesis miRNA expression level is significantly increased or decreased compared to corresponding normal tissue. The same is observed with their mRNAs. Therefore, transcriptome profiling of human tumours could identify signatures associated with progression, diagnosis, prognosis and response to therapy. However, until recently the information regarding the expression of miRNAs and mRNA in oligodendroglial tumours is scarce. In this study we performed miRNA and mRNA differential expression profiling between grade II and grade III ODs using microarray based expression profiling platforms (723 transcripts and 41,000 genes, respectively). 7 cases for OD grade-II, and 7 for AOD grade-III, and 15 non neoplastic white matter (nnWM) samples were used after microdissection with no previous history of treatment. We performed a systematic evaluation of miRNAs and mRNAs expressions and determined miRNAs and putative target genes that are differentially expressed in grade III AOD, but not in grade II OD and in non-neoplastic white matter (nnWM). 1 ODs when used with ,,s\" will represent both OD and AOD. 50 miRNAs were overexpressed and 43 were down regulated in AOD-III, whereas 7 miRNAs showed significant reduction in expressions in OD-II group. 3 miRNAs were commonly down regulated in comparisons of both groups. The hsa-miR-23a was strongly upregulated and hsamiR-27a was strongly downregulated in AOD-III. The functions of hsa-miR-23a and hsa-miR- 27a were tested in human adult fibroblasts for cell proliferation assay and apoptosis detection. Cells treated with pre-miR-23a and pre-miR-27a showed 20% reduction in cell proliferation as compared with controls. Further, the functional relevance of miRNAs to their target mRNAs was validated for each group, using real time qPCR. 10 key-miRNAs from AOD were subjected to validation by qPCR. We were able to confirm 7 miRNAs (p? 0.05). Among these, 5 miRs (miR- 193a-3p, miR-24, miR-27a, miR-30a-5p and miR-30c) showed reduced expression whose target genes (CCND1, HDAC2, PDGFA and RAB-26) were upregulated. Whereas, 2 miRNAs likewise miR-301b and miR-378 were overexpressed whose target genes BCL2, FGF2, CD44 and PPP4R4 confirmed by qPCR (p? 0.05). Bioinformatics based gene ontology (GO), and networking analysis revealed that differential expression and targets are attributed to differentiation of embryonic stem cells, cell adhesion, angiogenesis and neurogenesis, resistance to apoptosis, protein-protein interactions and cell proliferation. It was possible to identify and validate miRNAs and their mRNA-targets potentially involved in the progression of oligodendrogliomas particularly in grade III-AOD. Collectively, this analysis provides new insights to malignant progression of oligodendroglial tumours and could compliment WHO-2016 diagnosis scheme and may provide predictive outcome in patients as well as decision to therapy. / Oligodendrogliomas originários de oligodendrócitos que geralmente surgem na substância branca podendo ser classificados em grau oligodendroglioma (II-OD), e anaplastic oligodendrogliomas (grau III-AOD). Os ODs2 podem ser diagnosticados por análises patológicas e imuno-histoquímicas, porém evidências recentes sugerem que poderiam ser melhor diagnosticados com base em assinaturas moleculares, como a deleção combinada dos cromossomas 1p e 19q - marcadores moleculares dos OD associados clinicamente a um melhor prognóstico, resposta à terapia e melhor sobrevida. As características histológicas típicas dos oligodendrogliomas também estão fortemente associadas à deleção de 1p/19q, que é criticamente importante como ponto de vista diagnóstico. Assim, os subtipos de gliomas podem ser fortemente diferenciados não somente em relação ao seu perfil histológico mas também com base em seu perfil de expressão genica e suas assinaturas moleculares exclusivas. Os microRNAs (miRNAs, miRs) emergiram como assinaturas moleculares para os diferentes graus. Os miRNAs são RNAs não codificantes, contendo em torno de 22 nucleótidos. São expressos endogenamente e regulam diversos processos celulares através do controle negativo da expressão gênica em nivel pós-transcricional e por interacção directa ou imperfeita com o RNAm-alvo. Os miRNAs estão envolvidos na regulação da tumorigenese humana atuando como supressores de tumour ou oncogenes. Durante o processo da tumorigenese o nível de expressão dos miRNAs é aumentado ou diminuído significativamente em comparação com tecido normal correspondente. O perfil de expressão de miRNA de tumores humanos poderia identificar assinaturas associadas com progressão, diagnóstico, prognóstico e resposta à terapia. Contudo, até recentemente a informação sobre a expressão de miRNAs em oligodendrogliomas é escassa. Neste estudo, avaliamos o perfil de expressão diferencial de miRNA e RNAm em ODs graus II e III usando plataformas de perfis de expressão baseadas em microarray (723 transcritos e 41.000 genes, respectivamente). Foram utilizados 14 casos de ODs microdissecados, sendo 7 OD grau II, e 7 AOD grau III (anaplasicos) sem histórico prévio de tratamento, além de 15 amostras de substancia branca não neoplásica (nnSB). Por meio de avaliações sistemáticas foram determinados miRNAs e mRNAs expressos em AOD grau III, mas não em OD grau II e em substancias brancas não neoplásicas (nnSB). 2 ODs when used with ,,s\" will represent both OD and AOD. Assim, foram encontrados 50 miRNAs com alta expressão e 43 miRNAs com baixa expressão em AOD-III, enquanto que 7 miRNAs apresentaram expressões reduzidas no grupo OD-II. Na comparação entre os dois grupos, 3 miRNAs apresentaram baixa expressão. A hsa-miR-23a mostrou alta expressão e a hsa-miR-27a apresentou uma diminuição de expressão importante em AOD III. A atividade dos hsa-miR-23a e hsa-miR-27a foram testadas em células de fibroblastos adultos humanos usando ensaios de proliferação celular e detecção de apoptose. As células tratadas com pre-miR-23a e pre-miR-27a mostraram 20% redução de proliferação celular em comparação com os controles. Para cada grupo, a relevância funcional dos miRNAs e seus mRNAs alvos foi validada utilizando qPCR. Dos 10 miRNAs submetidos a validação em grau III, foi possivel confirmar 7 miRNA(p<0,05). Entre esses, 5 miRs (miR-193a-3p, miR-24, miR- 27a, miR-30a-5p e miR-30c) mostraram expressão reduzida, cujos genes alvos (CCND1, HDAC2, PDGFA e RAB-26) apresentavam alta expressão. Enquanto que, 2 miRNAs como miR-301b e miR-378 apresentaram alta expressão cujos genes alvo BCL2, FGF2, CD44 e PPP4R4 foram confirmados por qPCR (p<0,05). Ferramentas de bioinformática (Gene Ontology) e a análises em rede revelaram que a expressão diferencial e os alvos são atribuídos à diferenciação de células-tronco embrionárias, adesão de celular, angiogênese e neurogênese, resistência à apoptose, interações proteína-proteína e proliferação celular. Foi possível identificar e validar miRNAs e RNAm-alvos potencialmente envolvidos na progressão de oligodendrogliomas. Coletivamente, esta análise fornece novos achados relacionados a progressão maligna de tumores oligodendrogliais e poderia facilitar o diagnóstico preciso e mais restritivo, o desfecho preditivo em pacientes, bem como auxiliar na decisão da terapia.

Ascochyta blight, caused by Ascochyta rabiei (Pass.) Labrousse, is one of the most destructive diseases of chickpea (Cicer arietinum L.) worldwide. Despite the existence of highly resistant uncultivated genotypes, attempts to develop cultivars with a high level of durable resistance have been unsuccessful. This study investigated the chickpea defence response to A. rabiei using a functional genomics approach, which has the capacity to improve the overall understanding of the coordinated defence response at a molecular level. An existing cDNA library was used to generate a resource of Expressed Sequence Tags (ESTs) that, after clustering, comprised 516 unigenes. The unigenes were functionally annotated resulting in the identification of 20 specific defence-related unigenes, as well as numerous transcripts with possible involvement in the coordination of defence responses. To explore the expression patterns of the defence-related unigenes in an A. rabiei resistant and susceptible genotype, the unigenes were employed as probes in microarrays. Resulting expression data was analysed to identify differentially expressed unigenes over a time-course after infection. Comparison of the expression profiles from the resistant and susceptible genotype identified three putative genes that were exclusively up-regulated in the resistant genotype, thus may be involved in an effective defence response. Considering that a defence response can involve hundreds of genes, the entire set of chickpea unigenes were used to construct large-scale microarrays. To supplement the chickpea probes, 156 putative defence-related grasspea (Lathyrus sativus L.) ESTs and 41 lentil (Lens culinaris Med.) Resistance Gene Analogs (RGAs) were also included. Expression profiles for three chickpeas and one wild relative were generated over a time course. 97 differentially expressed ESTs were identified using a robust experimental system that included confirmation by quantitative RT-PCR. The results indicated that genes involved in the active defence response were similar to those governed by R-gene mediated resistance, including the production of reactive oxygen species and the hypersensitive response, down-regulation of 'housekeeping' gene expression, and expression of pathogenesis-related proteins. The comparison between resistant and susceptible genotypes identified certain gene expression 'signatures' that may be predictiv e of resistance. To further characterise the regulation of potential defence-related genes, the microarray was used to study expression profiles of the three chickpea genotypes (excluding the wild relative) after treatment with the defence signalling compounds, ethylene (E), salicylic acid (SA), and jasmonate (JA). 425 ESTs were differentially expressed, and comparison between genotypes revealed the presence of a wider range of inducible defence responses in resistant genotypes. Linking the results with the previous microarray results indicated the presence of other pathogen-specific signalling mechanisms in addition to E, SA and JA. The lower arsenal of defence-related gene expression observed in the susceptible genotype may be a result of 'breaks' in the pathways of defence-related gene activation. To draw together the findings of all experiments, a model was constructed for a hypothetical mechanism of chickpea resistance to A. rabiei. The model was synthesised based on the evidence gathered in this study and previously documented defence mechanisms in chickpea, and identified signal transduction as a key to resistance.

Reduction of cardiac myocyte loss and repair of the vasculature post myocardial infarction are important therapeutic goals because the potential for intrinsic repair is limited. Preclinical and limited clinical data support the possibility that bone marrow-derived mesenchymal stem cells may be a suitable cell type for cellular therapy. The goal of this research was to determine the effectiveness of using MSCs from aged mice in cellular therapy for the treatment of AMI. The central hypothesis for this research was that therapeutic potential of mesenchymal stem cells decreases with age. This research utilized global gene expression analysis to investigate molecular differences in MSCs harvested from three different age groups of mice. Microarray analysis was performed to investigate changes in gene expression with respect to aging. Furthermore, both in vitro and in vivo experiments were completed to analyze the functional and molecular characteristics of the MSCs. The data identified age-related defects in mouse MSCs as well as determined the molecular basis for these deficiencies. This study indicates that MSCs from 26m mice are severely deficient in the induction of angiogenesis and cardiac repair due to defective paracrine factor secretion caused by decreased expression of growth factor/cytokine genes. Hypoxia attenuates the deficiency in the aged mice, whereas in young mice low oxygen promotes secretion of paracrine growth factors. It was determined a dysfunction in HIF-1 alpha signaling was present in MSCs from 26m mice and is regulated by the PI3K/Akt signaling in MSCs. Furthermore, two novel and important and novel aspects of this study were the discovery that cell cycle regulation gene expression decreases with age and MSCs have increased insulin resistance with age. Increased insulin resistance in this cell type with aging is likely to have profound effects on the clinical outcomes of using these cells therapeutically. Likewise, loss of cell cycle regulation during proliferation could also lead to undesirable clinical effects. Gaining insight to the repair potential of these cells with respect to age will help to better define future trials of autologous stem cells not only for heart disease but for all of the many applications proposed for these cells.

Drought is a major constraint for attaining economic yield in tree crops. As an initial step to understand molecular response to water-deficit-stress in trees, gene expression in response to water stress was quantified using real-time RT-PCR. The specific objectives established for this to were I. to identify and characterize the genes induced by drought stress in Aleppo pine (Pinus halepensis) and II to identify and quantify the differentially expressed genes in different populations of Loblolly pine (Pinus taeda.L) due to water deficit (chapter III). Results of these studies may be used to identify candidate genes for future breeding programs against water-deficit-stress.

Les Norovirus (NoV), appartenant à la famille des Caliciviridae, sont une cause majeure dépidémies et de cas sporadiques de gastroentérites hautement contagieuses chez lhomme. Leur transmission emprunte la voie fécale-orale et ils sont à l'origine dune part importante des toxi-infections humaines d'origine alimentaire, en particulier dues à la consommation de mollusques bivalves. Ils possèdent un génome constitué dARN monocaténaire de polarité positive et sont classeés par analyse de proximité génétique en cinq génogroupes, contenant chacun plusieurs génotypes. Un problème majeur réside dans lincapacité à multiplier facilement les NoV en culture de cellules. La RT-PCR est devenue la méthode de choix pour leur détection dans les échantillons de matières fécales, les denrées alimentaires et les prélèvements effectués dans lenvironnement. Il est important de disposer de techniques à la fois sensibles et permettant également la détection dun large panel de NoV. La quantification de la charge virale est possible par lutilisation des techniques de RT-PCR en temps réel et est primordiale pour non seulement déterminer le niveau de contamination dun prélèvement, mais également pour étudier et caractériser la pathogénie de linfection à NoV. Des NoV ont été détectés dans diverses espèces animales, dont lespèce bovine. Ces découvertes ont soulevé d'importantes questions sur une éventuelle transmission zoonotique et l'existence d'un réservoir animal pour les NoV. La caractérisation moléculaire des deux prototypes de NoV bovins, nommément le virus Newbury2 et le virus Jena, a révélé qu'ils étaient génétiquement proches et associés aux NoV humains. Parmi les hypothèses évoquées, les animaux pourraient être soit des porteurs passifs de NoV, soit infectés de manière active par ces virus, responsables dès lors d'une zoonose. Caractériser les NoV circulant chez lhomme et les espèces animales est intéressant dans le but détudier leurs voies de transmission et léventuel passage inter-espèce de ces virus. Un mécanisme important d'évolution des NoV est la recombinaison, dun grand intérêt dans létude des NoV, générant des modifications du génome viral aboutissant à la création dun génome « chimère » à partir de deux génomes parentaux différents. Elle crée ainsi de la variation génétique et par là lémergence de nouveaux virus. En effet, il est bien documenté que la recombinaison se produit souvent parmi les NoV et contribue à la diversité génétique de ces virus ainsi quà lapparition de nouvelles épidémies. La prévalence des souches de NoV recombinants peut être sous-estimée par le fait que la caractérisation des NoV est habituellement basée sur le séquençage partiel du gène de lARN polymérase-ARN dépendante uniquement, alors quidéalement il faudrait séquencer différentes parties du génome, principalement lARN polymérase-ARN dépendante et la protéine de capside, pour identifier de tels virus. Il est important de déterminer précisément l'implication exacte de la recombinaison sur lévolution des NoV afin de comprendre les mécanismes dévolution des souches et l'avantage sélectif conféré pour certaines dentre elles. Etudier ce mécanisme permettra de mieux comprendre lavantage sélectif observé pour certains NoV et aidera à élucider les voies de transmission des NoV. Létude de ces deux points (transmission zoonotique et virus recombinants) est primordiale. En effet, le franchissement de la barrière despèce affecterait à la fois l'épidémiologie et l'évolution de ces virus, et compliqueraient également la capacité au développement dun vaccin ou dun traitement. Dans d'autres espèces animales, comme les chevaux ou les oiseaux, aucun NoV na été détecté à ce jour mais ces dernières années, des NoV ont été décrits dans de nombreuses espèces animales (chien, lion, mouton). Cela laisse donc présager dune gamme despèce cible encore plus étendue. Ce travail sinscrit dans le cadre de létude des voies de transmission des NoV avec comme objectif, après la mise au point de méthodes rapides et sensibles de détection et de quantification, dapporter un éclaircissement aux questions importantes relatives à lévolution des NoV et à leur catégorie dhôte. Dans un premier temps, la RT-PCR conventionnelle a été utilisée afin de détecter les NoV dans les espèces humaine et bovine. Ensuite, une RT-PCR utilisant la technologie SYBR Green a été développée et utilise un contrôle interne constitué dARN ajouté au même tube. Ce test est capable de détecter des NoV humains et bovins appartenant aux génogroupes I, II et III et permet de faire la distinction entre les NoV et le contrôle interne par lanalyse des courbes de dissociation. Une dilution 10 fois des échantillons sest révélée la méthode de choix pour lever les inhibitions. Afin de pouvoir confirmer directement le résultat et de permettre la quantification des NoV, une RT-PCR en temps réel utilisant la technologie TaqMan a été développée. Elle utilise un contrôle interne dARN et un standard dARN. De façon très intéressante, cette méthode peut détecter les NoV humains appartenant au génogroupes I, II et bovins du génogroupe III. Les inhibitions furent efficacement levées par une dilution 10 fois de léchantillon ou lajout de sérum albumine bovine au mix de RT-PCR. Ces deux RT-PCR en temps réel ont montré une sensibilité supérieure comparée à la RT-PCR conventionnelle. Avec pour objectif de comprendre les voies de transmission des NoV, la situation en Belgique a été investiguée et des NoV humains et bovins ont été détectés et analysés par séquençage partiel. Des NoV appartenant à différents génogroupes ont été détectés : GI et GII chez lhomme et GIII chez les bovins. Par analyse de la proximité génétique, les NoV bovins se sont révélés de génotype GIII.2 et les NoV humains de différents génotypes, mais majoritairement de génotype GII.4. Ces analyses ont permis également lidentification dune co-infection et de deux recombinants naturels, ces derniers étant proches de génotypes différents en fonction de la région du génome analysée (polymérase ou capside). L'identification de zones privilégiées pour la recombinaison dans la région située à la jonction de l'ORF (open reading frame) 1 et de lORF2 confirme l'importance de cette région dans ce phénomène. Afin détudier lévolution des NoV bovins, un NoV bovin détecté en Belgique fut séquencé complètement (Bo/B309/2003/BE) et comparé à la souche originale Newbury2 (isolée dans les années 80). Dune part, cette études a permis daboutir à la mise au point et la validation doutils permettant la détection et létude les NoV humains et animaux, tant pour leur pathogénie, que leur évolution ou leurs voies de transmission. Dautre part, basée sur le panel déchantillons recueillis durant cette étude, lanalyse phylogénétique des NoV détectés va dans le sens des études réalisées dans dautres pays tendant à montrer que les NoV bovins constituent un groupe de virus distincts, différents des NoV humains. Cela suggère que les NoV bovins ne représentent pas un risque pour la santé humaine. Néanmoins, la possibilité dune infection zoonotique ou dun réservoir animal ne peut pas être exclue vu la proximité de séquence entre les NoV humains et animaux et aussi la relation étroite et proche entre les populations humaines et les élevages danimaux. La détection dune co-infection et de deux recombinants naturels démontre les possibilités dévolution des NoV et limportance dune analyse complète de leur génome pour leur caractérisation. Ce travail a été pionnier dans létude des NoV au laboratoire et a ouvert la voie à dautres sujets de recherche sur les NoV et à de nouvelles thèses de doctorat, notamment sur létude de linteraction NoV-hôte (NoV dans lespèce bovine) et létude de la recombinaison des NoV in vitro (NoV murins).