Le but de mon projet est de créer et d’appliquer des outils pour l’analyse de la biologie des systèmes musculaires en utilisant différentes données OMICS. Ce projet s’intéresse plus particulièrement à la dysferlinopathie due la déficience d’une protéine appelée dysferline qui est exprimée principalement dans les muscles squelettiques et cardiaque. La perte du dysferline due à la mutation (autosomique-récessive) du gène DYSF entraîne une dystrophie musculaire progressive (LGMD2B, MM, DMAT). Nous avons déjà développé des outils bio-informatiques qui peuvent être utilisés pour l’analyse fonctionnelle de données OMICS, relative à la dyspherlinopathie. Ces derniers incluent le test dit «gene set enrichment analysis», test comparant les profils OMICS d’intérêts aux données OMICS musculaires préalablement publiées ; et l’analyse des réseaux impliquant les diffèrent(e)s protéines et transcrits entre eux/elles. Ainsi, nous avons analysé des centaines de données omiques publiées provenant d’archives publiques. Les outils informatiques que nous avons développés sont CellWhere et MyoMiner. CellWhere est un outil facile à utiliser, permettant de visualiser sur un graphe interactif à la fois les interactions protéine-protéine et la localisation subcellulaire des protéines. Myominer est une base de données spécialisée dans le tissu et les cellules musculaires, et qui fournit une analyse de co-expression, aussi bien dans les tissus sains que pathologiques. Ces outils seront utilisés dans l'analyse et l'interprétation de données transcriptomiques pour les dyspherlinopathies mais également les autres pathologies neuromusculaires. / The aim of this project was to build and apply tools for the analysis of muscle omics data, with a focus on Dysferlin deficiency. This protein is expressed mainly in skeletal and cardiac muscles, and its loss due to mutation (autosomal-recessive) of the DYSF gene, results in a progressive muscular dystrophy (Limb Girdle Muscular Dystrophy type 2B (LGMD2B), Miyoshi myopathy and distal myopathy with tibialis anterior onset (DMAT)). We have developed various tools and pipelines that can be applied towards a bioinformatics functional analysis of omics data in muscular dystrophies and neuromuscular disorders. These include: tests for enrichment of gene sets derived from previously published muscle microarray data and networking analysis of functional associations between altered transcripts/proteins. To accomplish this, we analyzed hundreds of published omics data from public repositories. The tools we developed are called CellWhere and MyoMiner. CellWhere is a user-friendly tool that combines protein-protein interactions and protein subcellular localizations on an interactive graphical display (https://cellwhere-myo.rhcloud.com). MyoMiner is a muscle cell- and tissue-specific database that provides co-expression analyses in both normal and pathological tissues. Many gene co-expression databases already exist and are used broadly by researchers, but MyoMiner is the first muscle-specific tool of its kind (https://myominer-myo.rhcloud.com). These tools will be used in the analysis and interpretation of transcriptomics data from dysferlinopathic muscle and other neuromuscular conditions and will be important to understand the molecular mechanisms underlying these pathologies.

Submitted by Erika Demachki (erikademachki@gmail.com) on 2014-09-18T17:39:38Z No. of bitstreams: 2 merged.pdf: 2827460 bytes, checksum: 84c579b817b24021e72bdea116e8ab88 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Jaqueline Silva (jtas29@gmail.com) on 2014-09-18T21:39:12Z (GMT) No. of bitstreams: 2 merged.pdf: 2827460 bytes, checksum: 84c579b817b24021e72bdea116e8ab88 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-09-18T21:39:12Z (GMT). No. of bitstreams: 2 merged.pdf: 2827460 bytes, checksum: 84c579b817b24021e72bdea116e8ab88 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-03-31 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Intellectual disability is a signal comprising a set of clinically and genetically heterogeneous disorders in which the development and/or function of the brain is compromised. This deficiency is characterized by significant limitations both in intellectual functioning and in adaptive behavior and is observed begins before 18 years of age. It is characterized by a high degree of variable expression, and the expression of a wide range of phenotypes, ranging from various genetic syndromes known to characteristics non-syndromic and psychological and/or psychiatric disorders. The etiology is still poorly understood and about half of the cases are unclear. In recent years, the chromosomal analysis by microarray has revolutionized the evaluation of patients with developmental delay or intellectual disability. By this method, the genome of a patient is examined to detect gains or losses of genetic material that are usually too small to be detected by chromosome banding studies. Genomic deletions and duplications have an important role in characterizing genetic diseases, including many neurological disorders and neural development. Identifying these changes may contribute to the clinical management of affected individuals and assist their families, and furthermore, can provide information on the processes of development and brain function. In this context the main objective of this study was identified possible submicroscopic genomic changes associated with intellectual disability, using a platform Chromosomal Microarray high resolution in patients referred by doctors of public health from Goiás state and had initially a normal karyotype. Thus 15 patients with intellectual disabilities were tested by high resolution HD CytoScan Array (Affymetrix) tecnology which detected the presence of 33 variations in the number of genome copies in 10 (66.7%) of the probands. Nineteen microduplications (57.6%) and 14 microdeletions (42.4%) were observed, and 17 CNVs (51.5%) were neutral, 7 (21.2%) pathogenic, 5 (15.15%) potentially pathogenic and 4 (12.12%) of uncertain significance. Five patients showed no change in the number of copies. In this study, we could propose a genetic etiology for the phenotype of 8 patients and thus the diagnostic yield of the platform used was 53.3%. Although modest, this study was significant because this technology was first employed in the state of Goiás and thus, could contribute more genetic information about this complex and heterogeneous neurological sign of great importance to global public health. / A deficiência intelectual é um sinal que compreende um conjunto de distúrbios clinica e geneticamente heterogêneos em que o desenvolvimento e/ou a função do cérebro é comprometida. Esta deficiência é caracterizada por limitações significativas tanto no funcionamento intelectual quanto no comportamento adaptativo e se inicia antes dos 18 anos de idade. É caracterizada por um elevado grau de expressividade variável, e pela manifestação de uma grande gama de fenótipos, variando de diversas síndromes genéticas conhecidas a características não sindrômicas e desordens psicológicas e/ou psiquiátricas. A etiologia ainda é mal compreendida e cerca de metade dos casos não são esclarecidos. A análise cromossômica por microarray tem revolucionado, nos últimos anos, a avaliação de pacientes com atraso no desenvolvimento ou deficiência intelectual. Por este método, o genoma de um paciente é examinado para a detecção de ganhos ou perdas de material genético que, normalmente, são muito pequeno para serem detectados por estudos cromossômicos com bandamento G. Deleções e duplicações genômicas têm um papel importante na caracterização de doenças genéticas, incluindo muitas desordens neurológicas e do desenvolvimento neural. A identificação dessas alterações pode contribuir para a manejo clínico dos indivíduos afetados e auxiliar suas famílias, e além disso, pode também fornecer informações sobre os processos do desenvolvimento e funcionamento do cérebro. Neste contexto o objetivo principal deste estudo foi identificar possíveis alterações genômicas submicroscópicas associadas à deficiência intelectual, utilizando uma plataforma de Chromosomal Microarray de alta resolução, em pacientes referenciados por médicos da rede pública de saúde do Estado de Goiás e que tenham apresentado inicialmente um cariótipo normal. Desta forma foram testados 15 pacientes com deficiência intelectual, pela tecnologia de alta resolução CytoScan HD Array (Affymetrix) que detectou a presença de 33 variações no número de cópias genômicas em 10 (66,7%) dos probandos. Foram observadas 19 microduplicações (57,6%) e 14 microdeleções (42,4%), sendo que 17 CNVs (51,5%) eram neutras, 7 (21,2 %) patogênicas, 5 (15,15%) potencialmente patogênicas e 4 (12,12%) de significado incerto. Cinco pacientes não apresentaram nenhuma alteração no número de cópias. Neste estudo foi possível propor uma etiologia genética para o fenótipo de 8 pacientes e dessa forma o rendimento diagnóstico, a título de pesquisa, da plataforma utilizada foi de 53,3%. Este estudo foi relevante já que esta tecnologia foi empregada pela primeira vez no estado de Goiás e com isso, pudemos contribuir com mais informação genética sobre esse complexo e heterogêneo sinal neurológico de grande importância para a saúde pública mundial.

Os microRNAs são pequenos RNAs, não-codificantes que funcionam como reguladores a nível pós-transcricional da expressão gênica. Nos últimos anos, novas evidências demonstram o papel importante dos microRNAs na regulação e desenvolvimento do sistema imune. Apesar da função de poucos microRNAs ser conhecida, a sua expressão alterada vêm sendo associada a patogênese de diversas doenças autoimunes, incluindo a artrite reumatóide (AR). Recentemente a expressão desregulada de uma série de microRNAs está sendo descrita em pacientes com AR, e o papel patogênico de apenas uma parte deles foi investigada em modelos animais. A artrite reumatóide é uma doença autoimune sistêmica caracterizada por um intenso processo inflamatório na sinóvia, podendo causar destruição óssea e articular. Os linfócitos T apresentam papel importante na indução, manutenção e progressão da doença. A artrite induzida por colágeno é um modelo animal amplamente utilizado por suas características fisiopatológicas muito similares à doença em humanos. A linhagem de camundongos DBA-1/J desenvolve a doença após imunização e booster com colágeno do tipo II, enquanto que a linhagem DBA-2/J se mostra refratária. Isso confere um sistema modelo de susceptibilidade/resistência à artrite, que pode ser estudado em diferentes abordagens. O objetivo do nosso estudo foi identificar o perfil transcricional e as redes de interação entre um grupo de microRNAs e seus respectivos alvos nos timócitos e linfócitos T CD3+ periféricos nos camundongos da linhagem DBA-1/J e DBA-2/J. Para a avaliação da expressão gênica, utilizou-se a tecnologia de microarrays. O uso de programas de análise e para a construção das redes foi imprescindível. Os resultados encontrados evidenciam uma expressão diferenciada de mRNAs e microRNAs em timócitos e linfócitos T CD3+ periféricos entre as duas linhagens utilizadas. Novos microRNAs foram encontrados nos diferentes estágios de desenvolvimento do linfócito T. Nas redes de interação microRNA-RNAm obtidas, genes importantes associados aos processos de sistema imune, adesão e diferenciação celular, apoptose, recombinação, ativação de linfócitos T e resposta inflamatória, foram encontrados como potenciais alvos. Além disso, em uma perspectiva clínica, baseados nos resultados obtidos em camundongo, nos encontramos a expressão do miR-505 nos linfócitos T de pacientes com AR. Nossos resultados contribuem para a melhor compreensão dos mecanismos molecular envolvidos na resistência/susceptibilidade a CIA. / MicroRNAs (miRNAs) are small non-coding RNA molecules that modulate the expression of multiple protein-encoding genes at the post-transcriptional level. During the last several years, evidence has emerged to show their critical role for the regulation and development of immune system. Although the function of most mammalian miRNAs has yet to be determined, their aberrant expression has been associated with several autoimmune conditions, including rheumatoid arthritis (RA). Recently, the deregulated expression of a dozen miRNAs has been reported in patients with RA, and the pathogenic role of only a few of these has been investigated in experimental mouse models. RA is a systemic autoimmune disorder mainly characterized by the inflammation of synovial tissue that can lead to destruction of bone and cartilage. The role of effectors T cells in induction, maintenance and progression of the disease is now becoming better understood. Collagen-induced arthritis is an animal model widely studied due to its similarities to human disease. The DBA-1/J mouse strain develops arthritis after immunization process and booster with Type II collagen, and the DBA-2/J strain is refractory to the disease induction. This offers an useful susceptibility/resistance model-system to study RA. The aim of this study was to identify the expression profiles and interaction networks between a set of microRNAs and their mRNA targets in thymocytes and peripheral CD3+ T lymphocytes in DBA-1/J and DBA-2/J mice strain. For this purpose we used the microarray technology to evaluate the expression of the miRNAs and mRNAs as possible targets involved in this process. The use of bioinformatics software to reconstruct the networks was essential. The results show differential expression of mRNAs and miRNAs in thymocytes and peripheral CD3+ T lymphocytes between both strains. New miRNAs were found during all the stages of T cells development. The microRNA-mRNA interaction networks obtained in this study showed that important genes related to apoptose, immune system, recombination, cell adhesion and differentiation, inflammatory process and T cell activation were found as potential targets. In addition, in a clinical prospects, based on the results obtained in mice, we found the expression of the miRNA miR-505 in T cells of RA patients. Our results contribute to a better understand of the molecular mechanisms evolved in the resistance/susceptibility to CIA.

Neste trabalho realizamos um programa de seqüenciamento em larga escala de cDNAs obtidos de bibliotecas construídas a partir de mRNA de células de B. emersonii submetidas ao choque térmico e ao estresse por cádmio. Obtivemos 6350 seqüências expressas (ESTs) de alta qualidade, que representam 2326 seqüências únicas putativas (unigenes) do fungo. Destes unigenes putativos, 1282 genes foram classificados em pelo menos uma das categorias do Consórcio Gene Ontology (GO). A análise do transcriptoma parcial de B. emersonii determinado até o momento permitiu a identificação de 78 unigenes codificando chaperones moleculares de todas as famílias conhecidas. Para avaliarmos a expressão global dos genes em resposta a estresses ambientais, como o choque térmico e o cádmio, realizamos ensaios de microarranjos de DNA nestas condições de estresse. Observamos que em resposta ao choque térmico, B. emersonii induz a expressão de genes que codificam proteínas relacionadas com o enovelamento de proteínas e com a proteólise, o que seria esperado em condições de temperaturas elevadas, assim como genes que codificam proteínas com propriedades antioxidantes, além de proteínas envolvidas no metabolismo de nucleotídeos e no metabolismo de carboidratos. Em resposta ao estresse por cádmio, verificou-se a indução de genes que codificam principalmente proteínas com propriedades antioxidantes, proteínas envolvidas no metabolismo de aminoácidos, proteínas relacionadas com o transporte celular e proteínas envolvidas no enovelamento de proteínas e proteólise. Uma das conseqüências do estresse por cádmio é o aumento do estresse oxidativo e proteínas antioxidantes têm um papel fundamental na resposta a este tipo de estresse. Dentre os genes observados durante o seqüenciamento das ESTs de B. emersonii, observamos dez genes codificando proteínas distintas da família Hsp70. Nove genes hsp70 são expressos em pelo menos um dos estágios do desenvolvimento do fungo e sete apresentam uma indução significativa após o choque térmico. Estes dados sugerem que estes genes desempenham um papel importante durante o desenvolvimento e em resposta ao estresse térmico em B. emersonii. Outro dado interessante obtido neste trabalho foi o enriquecimento de ESTs que continham íntrons em sua seqüência nas bibliotecas de estresse. Portanto, o choque térmico e o estresse por cádmio em B. emersonii diminuem a eficiência de processamento dos íntrons permitindo sua caracterização. O cDNA da proteína Hsp17 foi o que apresentou o maior número de ESTs seqüenciadas nas bibliotecas de estresse. Experimentos de Northern blot indicaram que o gene hsp17 possui um nível de expressão muito baixo durante o ciclo de vida de B. emersonii, no entanto, como esperado sua expressão aumenta drasticamente quando as células de esporulação ou germinação são submetidas a choque térmico. Os níveis da proteína Hsp17 acompanham os níveis do seu mRNA, indicando que o controle da expressão do gene hsp17 deve ocorrer em nível de transcrição. / In this work we realized a large scale, sequencing program of cDNAs libraries obtained from mRNA of B. emersonii cells submitted to heat shock and cadmium stress. A total of 6350 high quality expressed sequence tags (ESTs) were obtained, representing 2326 unique putative genes (unigenes) of this fungus. From these putative unigenes, 1282 genes were classified at least in one of the three Gene Ontology Consortium (GO) categories. The analysis of the partial transcriptome of B. emersonii, determined until now, allowed the identification of 78 unigenes encoding molecular chaperones of all known protein families. To evaluate the global expression of the genes in response to environmental stresses, such as heat shock and cadmium, DNA microarray assays were performed. We observed that in response to heat shock B. emersonii induces the expreession of genes encoding proteins related to protein folding and proteolysis, as expected under high temperature conditions, as well as genes encoding proteins with antioxidant properties and proteins involved in nucleotide and carbohydrate metabolism. In response to cadmium stress, we mainly verified the induction of genes for proteins with antioxidant properties, proteins involved in amino acid metabolism, proteins related to cellular transport and proteins related to protein folding and proteolysis. One of the consequences of the exposure to cadmium is the increase of oxidative stress, and antioxidant proteins have a fundamental role in the response to this kind of injury. Amongst the genes observed during the B. emersonii EST sequencing program, ten genes encoding distinct proteins from the Hsp70 family were observed. Nine of them are expressed at least in one stage of the fungus development and seven genes presented a significant induction during heat shock treatment. These data suggest that the hsp70 genes perform an important role during development and in response to heat stress in B. emersonii. Another interesting result from this work was the enrichment of ESTs containing introns in the stress libraries. Thus, heat shock and cadmium stress decrease the efficiency of intron processing in B. emersonii, allowing for intron characterization. The cDNA for the Hsp17 protein presented the highest number of ESTs sequenced from the stress libraries. Northern blot experiments indicated that the hsp17 gene is expressed at very low levels throughout the life cycle of B. emersonii, however, as expected its expression increases drastically when sporulation or germination cells are submitted to heat shock. Hsp17 protein levels accompany its mRNA levels, indicating that the control of expression of the hsp17 gene occurs at a transcriptional level.

A cutícula dos insetos é composta principalmente por uma variedade de proteínas que interagem com filamentos de quitina, um polímero de N-acetilglicosamina, para formar um envoltório rígido que protege e dá forma ao organismo. O crescimento dos insetos depende da renovação periódica da cutícula, que se desprende durante a apólise e é digerida enquanto a epiderme sintetiza uma nova cutícula substituta. Tal renovação caracteriza a muda e metamorfose e é coordenada por hormônios, com destaque para os ecdisteróides. O atual trabalho objetivou caracterizar a expressão diferencial de genes do tegumento (cutícula e epiderme subjacente), além de elucidar aspectos de regulação e função no contexto da muda e metamorfose, com foco nos genes codificadores de proteínas estruturais e enzimas cuticulares. Para este fim, utilizamos o tegumento de fases específicas da muda pupal-adulta, isto é, de pupas (Pw), de pupas em apólise (Pp) e de adultas faratas (Pbl) para análises de microarrays de cDNA. As análises dos microarrays mostraram 761 e 1173 genes diferencialmente expressos nos tegumentos de adultas faratas (Pbl) em comparação com pupas (Pw) ou pupas em apólise (Pp), respectivamente. A categorização destes genes, segundo os critérios do Gene Ontology, distinguiu totalmente o tegumento de adultas faratas (Pbl) dos tegumentos de pupas (Pw) ou pupas em apólise (Pp) tanto em relação ao critério Processo Biológico quanto em relação à Função molecular, evidenciando grande mudança na expressão gênica durante a construção do exoesqueleto definitivo nas adultas faratas (Pbl). Os microarrays mostraram aumento estatisticamente significante da expressão de 24 genes cuticulares no tegumento de adultas faratas. Este resultado foi validado por RT-PCR em tempo real (qRT-PCR) para 23 destes genes (AmelCPR3, AmelCPR4, AmelCPR6, AmelCPR14, AmelCPR15, AmelCPR17, AmelCPR23, AmelCPR24, AmelCPR25, AmelCPR28, AmelCPR29, AmelCPR30, apd-1, apd-2, apd-3, CPLCP1, Am-C, Am-D, AmelTwdl1, AmelTwdl2, GB12449, GB12811 e GB11550), e por RT-PCR semiquantitativa para o gene Amlac2. Além disto, a maior expressão de outros 2 genes cuticulares (AmelCPR1 e AmelCPR2) em adultas faratas foi demonstrada por qRT-PCR. Estes genes cuticulares positivamente regulados no tegumento de adultas faratas (Pbl) devem estar envolvidos com a formação e diferenciação do exoesqueleto definitivo. O aumento da expressão gênica neste período da muda (Pbl) é regulado pela variação do título de ecdisteróides e ocorre enquanto o título deste hormônio decai, após ter atingido o pico indutor da apólise na fase de desenvolvimento precedente (Pp). Ao contrário, as análises por qRT-PCR mostraram que 2 outros genes cuticulares (AmelCPF1 e AmelCPR1) são negativamente regulados no tegumento de adultas faratas em comparação com pupas, sugerindo que são específicos de cutícula pupal. Estes genes foram inibidos pelo aumento dos níveis de ecdisteróides, que induz a apólise. Vinte e um entre os 24 genes cuticulares diferencialmente expressos nos microarrays codificam proteínas pertencentes às famílias CPF, CPR, Apidermina, CPLCP, Análoga a peritrofina e Tweedle. Os outros 3 genes diferencialmente expressos (GB12449, GB12811, GB11550) não tinham sido ainda caracterizados como genes cuticulares. Dois deles, GB12449 e GB12811, foram sequenciados para validação da predição e para a caracterização das respectivas estruturas genômicas. Experimentos de hibridação in situ com sonda fluorescente (FISH) nos permitiram localizar altos níveis de transcritos destes genes no citoplasma de células da epiderme de adultas faratas, sugerindo fortemente sua natureza cuticular e envolvimento na construção do exoesqueleto definitivo. O presente estudo consiste na primeira análise global de expressão de genes do tegumento de uma espécie de himenóptero social. Os resultados apresentados levaram à identificação de genes com expressão associada à muda pupal-adulta e formação do exoesqueleto definitivo. Este trabalho contribui com novos dados moleculares para o aprofundamento do conhecimento da metamorfose de A. mellifera. / The insect cuticle is mainly composed of proteins that interact with chitin filaments to form a rigid structure that protects and shapes the organism. Insects grow through the periodic renewal of the cuticle, which is shed at each apolysis episode, and subsequently digested while the epidermis synthesizes the cuticle of the next stage. These molting events are coordinated by hormones, mainly ecdysteroids. The current work aimed to characterize differential gene expression in the integument (cuticle and underlying epidermis) during the ecdysteroid-regulated pupal-to-adult molt. Special attention was given to the structure and expression of genes encoding proteins and enzymes involved in cuticle formation and differentiation. To achieve these goals, we used thoracic integument of newly-ecdysed pupae (Pw), pupae in apolysis (Pp) and pharate adults (Pbl) in cDNA microarray analyses. The microarray analysis showed 761 and 1173 differentially expressed genes in the pharate adult integument (Pbl) in comparison to pupae (Pw) or pupae in apolysis (Pp), respectively. Gene Ontology terms for Biological Process and Molecular Function completely distinguished the integument of pharate adults (Pbl) from the integument of pupae (Pw) or pupae in apolysis (Pp). The microarray analysis discriminated 24 cuticular genes with a significant expression increase in the pharate adult integument. This was validated by real time RT-PCR analysis (qRT-PCR) for 23 of these genes (AmelCPR3, AmelCPR4, AmelCPR6, AmelCPR14, AmelCPR15, AmelCPR17, AmelCPR23, AmelCPR24, AmelCPR25, AmelCPR28, AmelCPR29, AmelCPR30, apd-1, apd-2, apd-3, CPLCP1, Am-C, Am-D, AmelTwdl1, AmelTwdl2, GB12449, GB12811 and GB11550), and by semiquantitative RT-PCR for Amlac2. In addition, the increased expression of other two cuticular genes (AmelCPR1 and AmelCPR2) was confirmed by qRT-PCR. These up-regulated cuticular genes in pharate adult integument apparently are involved in adult cuticle formation and differentiation, which occurs while the ecdysteroids titers decay, after reaching the peak that induces apolysis in the preceding phase (Pp). In contrast, two cuticular genes (AmelCPF1 e AmelCPR1) were confirmed by qRT-PCR analysis as negatively regulated in the integument of pharate adults compared to pupae, suggesting that they are specific to pupal cuticle. Therefore, these genes were inhibited by the increasing ecdysteroid levels that induce apolysis. Twenty one of the 24 cuticular genes differentially expressed in the microarrays encode proteins belonging to the CPF, CPR, Apidermin, CPLCP, Analogous to peritrofins and Tweedle families. The other three differentially expressed genes (GB12449, GB12811, GB11550) had not yet been assigned as cuticular genes. Two of them (GB12449 and GB12811) were sequenced, thus allowing prediction validation and gene structure characterization. In situ hybridization experiments using fluorescent probe (FISH) localized high expression of these genes in the pharate adult epidermis, strongly suggesting their involvement in the construction of the adult exoskeleton. This study is the first global gene expression analysis of the integument from a social hymenopteran species. The expression of genes in the integument was associated to the molting process and to the adult exoskeleton formation. This work contributes with new molecular data for a deeper understanding of A. mellifera metamorphosis.

La compréhension des mécanismes qui contrôlent l'expression des gènes est un enjeu majeur pour la recherche médicale. Elle nécessite un ensemble d'approches pangénomiques telles que les puces à ADN et plus récemment le séquençage à très haut débit qui génèrent une masse toujours plus grande de données numériques à traiter. Au cours de ma thèse, j'ai développé plusieurs outils informatiques innovants pour faciliter leur exploitation. Ainsi, j'ai créé une librairie R (AgiND) qui vérifie la qualité des données de puces à ADN Agilent et permet de les normaliser. Le nombre croissant d'expériences stockées dans Gene Expression Omnibus a motivé la mise en place du projet TBrowser. Une méthode originale DBF-MCL a été créée pour extraire des signatures transcriptionnelles annotées par l'intégration de diverses sources d'information. Stockées dans une base de données, elles sont accessibles à travers une interface Java, un service web SOAP et une librairie R/Bioconductor (RTools4TB). Enfin, un pipeline d'analyse dédié au ChIP-seq a été implémenté. Tous ces outils ont servi pour l'étude de diverses maladies dans le cadre de collaborations. / Understanding the mechanisms that control gene expression is a major challenge for medical research. This requires using a large set of pangenomic approaches such as those using DNA microarrays and high-throughput sequencing that generate an ever growing mass of digital data. During my thesis, I have developed several computer-based tools to facilitate their processing and analysis. I have created a R library (AgiND) that controls the quality of Agilent DNA microarray data and allows their statistical normalization. The growing number of experiences stored in Gene Expression Omnibus has motivated the development of the TBrowser project. An original method, DBF-MCL, was created to extract annotated transcriptional signatures by integrating various sources of information. Stored in a database, these signatures are accessible using a Java interface, a SOAP web service and a R/Bioconductor library (RTools4TB). Finally, a pipeline dedicated to the ChIP-seq analyses has been implemented. All these tools were used to study various diseases in collaborations.

The majority of genetic differences between species and individuals have been hypothesised to impact on the regulation, rather than the structure, of genes. As the details of genetic variation are uncovered by the various genome sequencing projects, understanding the functional effects on gene regulation will be key to uncovering the molecular mechanisms underying the genesis and inheritance of common phenotypes, such as complex human disease and commercially important traits in plants and animals. Unlike coding sequence polymorphisms, genetic variants affecting gene expression will reside in the transcriptional machinery and its regulatory inputs. As these are largely specific to cell- or tissue-types, we would expect that regulatory variants will also affect final mRNA levels in a tissue specific manner. Genetic variation between individuals may therefore be more complex than the sum total of sequence differences between them. Demonstrating this hypothesis is the main focus of this thesis. We use microarrays to measure mRNA levels of approximately 22,000 transcripts in inbred and recombinant inbred strains of mice, and present compelling evidence that the genetic influences on these levels are tissue-specific in at least 85% of cases. We uncover two loci which apparently influence transcript levels of multiple genes in a tissue-specific manner. We also present evidence that failure of microarray data normalisation may cause spurious linkage of expression phenotypes leading to erroneous biological conclusions, and detail a novel, extensible mathematical framework for performing tailored normalisation which can remove such systematic bias. The wider context of these results is then discussed.

Sonic hedgehog (Shh) is a secreted morphogen involved in patterning a wide range of structures in the developing embryo. When cells receive the Shh signal a cascade of effects begin which in turn regulate downstream target genes. The genes controlled by Sonic hedgehog provide messages instructing cells how to differentiate or when to divide. Disruption of the hedgehog signalling cascade leads to a number of developmental disorders and plays a key role in the formation of a range of human cancers. Patched, the receptor for Shh, acts as a tumour suppressor and is mutated in naevoid basal cell carcinoma syndrome (NBCCS). NBCCS patients display a susceptibility to tumour formation, particularly for basal cell carcinoma (BCC). The discovery of Patched mutations in sporadic BCCs and other tumour types further highlights the importance of this pathway to human cancer. The identification of genes regulated by hedgehog is crucial for understanding how disruption of this pathway leads to neoplastic transformation. It is assumed that the abnormal expression of such genes plays a large role in directing cells to divide at inappropriate times. Only a small number of genes controlled by Shh have been described in vertebrate tissues. In the work presented in this thesis a Sonic hedgehog responsive embryonic mouse cell line, C3H/10T1/2, was used as a model system for hedgehog target gene discovery. Known downstream target genes were profiled to determine their induction kinetics, building up a body of knowledge on the response to Shh for this cell type. During this work, it was discovered that C3H/10T1/2 cells do not become fully competent to respond to Shh stimulation until the cells reach a critical density, a factor that had to be taken into account when determining timepoints of interest for further investigation. Several techniques were employed to identify genes that show expression changes between Shh stimulated and control cells. In one of these techniques, RNA from cell cultures activated with Shh was used to interrogate cDNA microarrays, and this provided many insights into the downstream transcriptional consequences of hedgehog stimulation. Microarrays consist of thousands of spots of DNA of known sequence gridded onto glass slides. Experiments using this technology allow the expression level of thousands of genes to be measured simultaneously. Independent stimulation methods combined with northern blotting were used to investigate individual genes of interest, allowing genuine targets to be confirmed and false positives eliminated. This resulted in the identification of eleven target genes. Seven of these are induced by Sonic hedgehog (Thrombomodulin (Thbd), Glucocorticoid induced leucine zipper (Gilz), Brain factor 2 (Bf2), Nuclear receptor subfamily 4, group A, member 1 (Nr4a1), Insulin-like growth factor 2 (Igf2), Peripheral myelin protein 22 (Pmp22), Lim and SH3 Protein 1 (Lasp1)), and four are repressed (Secreted frizzled related proteins 1 and 2 (Sfrp1 and Sfrp2), Macrophage inflammatory protein-1 gamma (Mip-1?), and Anti-mullerian hormone (Amh)). The majority of these represent novel downstream genes not previously reported as targets of Shh. The new target genes have a diverse range of functions, and include transcriptional regulators and molecules known to be involved in regulating cell growth or apoptosis. The corroboration of genes previously implicated in hedgehog signalling, along with the finding of novel targets, demonstrates both the validity and power of the C3H/10T1/2 system for Shh target gene discovery. The identification of novel Sonic hedgehog responsive genes provides candidates whose abnormal expression may be decisive in initiating tumour formation and future studies will investigate their role in development and disease. It is expected that such findings will provide vital clues to the aetiology of various human cancers, and that an understanding of their roles may ultimately provide greater opportunities in the future design of anti-tumour therapies.

<p>The main objective of the reported study was to investigate how biomedical ontologies, logically structured representations of various aspects of the biomedical reality, can help researchers in analyzing experimental data. The dissertation reports two attempts to construct tools for the analysis of high-throughput experimental results using explicit domain knowledge representations. Furthermore, integrative efforts made by the community of Open Biomedical Ontologies (OBO), in which the author has participated, are reported, and a framework for consistently connecting the Gene Ontology (GO) with the Taxonomy of Species is proposed and discussed.</p>

Renewable fibers produced by forest trees provide excellentraw material of high economic value for industrialapplications. Despite this, the genes and corresponding enzymesinvolved in wood fiber biosynthesis in trees are poorlycharacterized. This thesis describes a functional genomicsapproach for the identification of carbohydrate-active enzymesinvolved in secondary cell wall (wood) formation in hybridaspen. First, a 3' target amplification method was developed toenable microarray-based gene expression analysis on minuteamounts of RNA. The amplification method was evaluated usingboth a smaller microarray containing 192 cDNA clones and alarger microarray containing 2995 cDNA clones that werehybridized with targets isolated from xylem and phloem.Moreover, a gene expression study of phloem differentiation wasperformed to show the usefulness of the amplificationmethod. A microarray containing 2995 cDNA clones representing aunigene set of a cambial region EST library was used to studygene expression during wood formation. Transcript populationsfrom thin tissue sections representing different stages ofxylem development were hybridized onto the microarrays. It wasdemonstrated that genes encoding lignin and cellulosebiosynthetic enzymes, as well as a number of genes withoutassigned function, were differentially expressed across thedevelopmental gradient. Microarrays were also used to track changes in geneexpression in the developing xylem of transgenic, GA-20 oxidaseoverexpressing hybrid aspens that had increased secondarygrowth. The study revealed that a number of genes encoding cellwall related enzymes were upregulated in the transgenic trees.Moreover, most genes with high transcript changes could beassigned a role in the early events of xylogenesis. Ten genes encoding putative cellulose synthases (CesAs) wereidentified in our ownPopulusESTdatabase. Full length cDNA sequences wereobtained for five of them. Expression analyses performed withreal-time PCR and microarrays in normal wood undergoingxylogenesis and in tension wood revealed xylem specificexpression of four putative CesA isoenzymes. Finally, an approach combining expressionprofiling,bioinformatics as well as EST and full length sequencing wasadopted to identify secondary cell wall related genes encodingcarbohydrate-active enzymes, such as glycosyltransferases andglycoside hydrolases. As expected, glycosyltransferasesinvolved in the carbohydrate biosynthesis dominated thecollection of the secondary cell wall related enzymes that wereidentified. Key words:Populus, xylogenesis, secondary cell wall,cellulose, hemicellulose, microarrays, transcript profiling,carbohydrate-active enzyme, glycosyltransferase, glycosidehydrolase