O câncer diferenciado da tireoide (CDT) representa cerca de 90% das malignidades tireoidianas com incidência crescente nas últimas décadas. As modalidades de tratamento incluem tireoidectomia, terapia com 131I (com e sem r-hTSH), radio e quimioterapias. Pouco se sabe sobre os efeitos desses tratamentos em nível celular. O presente trabalho foi proposto com o intuito de avaliar em que extensão a terapia com radioiodo pode causar danos em linfócitos periféricos de pacientes com CDT precedidos ou não com r-hTSH, levando-se em consideração, efeitos agudos, tardios e dosimétricos do 131I (estudo in vivo). Um estudo in vitro também foi realizado em células-alvo de tumores tireoidianos (WRO) por meio de análise de citotoxicidade, genotoxicidade e captação do radioiodo. Para tanto, amostras sanguíneas de pacientes, divididos em 2 grupos (grupo A com r-hTSH + 131I e grupo B somente com 131I) foram coletadas antes, 24h, 1 semana, 1 mês e 1 ano após administração do 131I para análise de aberrações cromossômicas (AC). Curva dose-resposta para 131I in vitro foi elaborada para a estimativa de dose absorvida nos pacientes, comparando as frequências de dicêntricos obtidas in vitro com dados in vivo pelo programa Monte Carlo. A iodoterapia induziu um aumento no número de AC em linfócitos de pacientes com valor máximo 24h após o tratamento, com declínio gradativo ao longo do tempo, com mais danos cromossômicos no grupo B em relação ao grupo A, atingindo níveis similares aos basais 1 anos após a administração do radioido. A frequência de dicêntricos encontrada nos linfócitos de pacientes 24h após o tratamento foi equivalente àquela induzida in vitro (0,354 ± 0,153 MBq/mL para o grupo A e 0,309 ± 0,154 MBq/mL para o grupo B), que corresponde a dose absorvida de 0,8 ± 0,3 Gy e 0,7 ± 0,3 Gy para os grupos A e B, respectivamente, sem significância estatística entre os grupos. As células WRO mostraram um ciclo celular relativamente lento de 96,3h com um cariótipo instável. O ensaio genotóxico mostrou uma radiorresistência relativamente alta (0,07 a 3,70 MBq/mL), sem significância estatística com e sem r-hTSH. No entanto, o ensaio citotóxico, mostrou uma tendência à queda nas concentrações mais altas de 1,85 (p<0,05) e 3,70 MBq/mL (p<0,01) somente na presença de r-hTSH, coincidindo com nível mais alto de captação. Células WRO foram relativamente radiorresitentes também à irradiação externa de 60Co na faixa de dose de 0,2 a 8,3 Gy, com queda gradativa em função do tempo para doses mais altas (10, 20 e 40Gy). Dados obtidos mostraram pouco dano citogenético nos pacientes após a exposição terapêutica com radioiodo, o que sugere um tratamento seguro e eficaz para os pacientes dos dois grupos. Pacientes do grupo A, no entanto, obtiveram uma melhor qualidade de vida com o uso do r-hTSH. Estudos in vitro com irradiação interna (131I) e externa (60Co) com ou sem r-hTSH, apontam a necessidade de uma estratégia terapêutica alternativa para contornar a perda da habilidade das células tireoidianas (WRO) em concentrar o radioiodo, responsável pelo relativo insucesso da iodoterapia em pacientes com CDT. / Differentiated thyroid cancer (DTC) represents about 90% of thyroid malignancies with increasing incidence in the recent decades. Treatment modalities include thyroidectomy, 131I therapy (with or without r-hTSH), radio and chemiotherapy. Little is known about the effects of these treatments at the cellular level. This work was proposed in order to assess to what extent radioiodine therapy can cause damage in peripheral lymphocytes of patients with DTC, preceded or not by r-hTSH, taking into account acute, slow and dosimetric effectsof 131I (in vivo study). An in vitro study was also carried out on thyroid tumor target cells (WRO) by cytotoxicity and genotoxicity analysis and radioiodine uptake. For this, blood samples from patients divided into two groups (group A, r-hTSH + 131I and group B,131I only) were collected before, 24 hours, 1 week, 1 month and 1 year after 131I administration for aberration chromosome analysis (CA). A dose-response curve for 131I in vitro was developed for estmating the absorbed dose in patients, comparing the dicentric frequencies obtained in vitro with in vivo data by Monte Carlo program. Radioiodine therapy induced an increase in the number of CA in lymphocytes of patients peaking 24 hours after treatment, with gradual decline over time and with more chromosomal damage in group B than in group A, reaching baseline levels one year afterradioidine administration. The frequency of dicentric found inpatient lymphocytes, 24h after treatment, was equivalent to that induced in vitro (0.354 ± 0.153 MBq / mL for group A and 0.309 ± 0.154 MBq / mL for group B), which corresponds to absorbed doses of 0.8 ± 0.3 Gy and 0.7 ± 0.3 Gy for groups A and B, respectively, with no significant difference between the groups. WRO cells showed a cell cycle relatively slow: 96,3h with an unstable karyotype. The genotoxic test showed a relatively high radioresistance (0.07 to 3.70 MBq/mL), with no statistical significance, with or without r-hTSH. However, the cytotoxic assay, showed a tendency to decrease at higher concentrations of 1.85 (p <0.05) and 3.70 MBq/ml (p <0.01) only in the presence of r-hTSH, coincident with the highest level of uptake. WRO cells were also relatively radioresistant toexternal irradiation of 60Co in the range of 0.2-8.3 Gy, with a gradual decrease in function of time for higher doses (10,20 and 40Gy).The data obtained showed little cytogenetic damage in patients upon therapeutic exposure, suggesting a safe and effective treatment forboth groups of patients. Patients in group A, however, had a better quality of life by using r-hTSH. In vitro studies with internal (131I) and external (60Co)irradiation, with or without r-hTSH, point to the need for an alternative therapeutic strategy to overcome the loss of ability of thyroid cells (WRO) to concentrate radioiodine, wich is responsible for the failure of radioiodine therapy in patients with DTC.

Made available in DSpace on 2016-08-19T17:47:09Z (GMT). No. of bitstreams: 1 Antonio Alberto Carvalho.pdf: 630872 bytes, checksum: 13ecf29f7245808d06388075ae78be17 (MD5) Previous issue date: 2006-06-16 / In this study the results of the evaluation cytogenetics of 694 patients with suspected of being carriers of chromosomal abnormality, seen in Sarah Network of Hospitals for Rehabilitation - San Luis Unit, in the period from December 1996 to January 2005. / Neste estudo são apresentados os resultados da avaliação citogenética de 694 pacientes, com suspeita de serem portadores de anomalia cromossômica, atendidos na Rede Sarah de Hospitais de Reabilitação - Unidade São Luís, no período de dezembro de 1996 a janeiro de 2005.

Made available in DSpace on 2017-07-10T14:38:24Z (GMT). No. of bitstreams: 1 Dissertacao Simone Cristina Girardi.pdf: 4377774 bytes, checksum: 366158b7c208a2a4a26392aebcbc096b (MD5) Previous issue date: 2015-02-27 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Pimelodidae is a family of fishes of South America, and although several taxonomic and molecular studies have been conducted, the phylogenetic relationships among the genera are not still fully understood. In order to provide data to assist in the understanding of the relationships within this family, cytogenetic studies were performed in two species of Iheringichthys and seven species of Pimelodus from three river systems. The specimens were collected in the Piquiri River, Upper Paraná River basin; in the Iguaçu River, downstream to the Iguaçu Falls in the Middle Paraná River basin; in the Iguaçu River, Lower Iguaçu River basin and in the Ijuí River, Upper Uruguay River basin. The analysis showed the presence of 2n=56 chromosomes for all species, corroborating the hypothesis of this basal diploid number for the family. The AgNORs, confirmed by 18S rDNA-FISH, were localized in the terminal position on long arm of a chromosome pair for all analyzed species, which has been reported for all species of Pimelodidae and may indicate a basal trait for the family. The heterochromatin distribution pattern found herein is similar to those described for other Pimelodidae, and allowed us to differentiate most of the species, becoming an important marker. The location of 5S rDNA sequences in Iheringichthys species allowed their differentiation, and can be used as a taxonomic marker. In Pimelodus species, it was verified a variation in the number and position of 5S rDNA sites. In P. britskii and P. maculates, sites of 5S rDNA and 18S were found in synteny, which may indicate a derived condition for these species, considering that they are the only for pimelodids species till now studied that have this feature. The results of this study provided data that contribute to the knowledge of the evolutionary history of the species for Pimelodidae; establishing phylogenetic relationships and assisting in the identification of these species. / Pimelodidae é uma família de peixes da região Neotropical, e embora vários estudos taxonômicos e moleculares tenham sido realizados, as relações filogenéticas entre seus gêneros ainda não são totalmente compreendidas. Com o intuito de fornecer dados para auxiliar no entendimento das relações dentro desta família, foram realizados estudos citogenéticos em duas espécies de Iheringichthys e em sete espécies de Pimelodus de três sistemas hidrográficos. Os exemplares foram coletados no rio Piquiri, Bacia do Alto rio Paraná; no rio Iguaçu, jusante às Cataratas do Iguaçu na Bacia do Médio rio Paraná; no rio Iguaçu, Bacia do Baixo rio Iguaçu e no rio Ijuí, Bacia do Alto rio Uruguai. As análises mostraram a presença de 2n=56 cromossomos em todas as espécies, reforçando a hipótese de número diplóide basal para a família. As AgRONs, confirmadas pela FISH-DNAr 18S, foram localizadas na região terminal do braço longo de um par de cromossomos em todas as espécies estudadas, sendo que posição terminal desta região é observada em todas as espécies de Pimelodidae e pode indicar um caracter basal da família. O padrão de distribuição de heterocromatina encontrado é semelhante ao observado em outros Pimelodidae, e permitiu diferenciar a maioria das espécies, sendo um importante marcador. A localização das sequências de DNAr 5S nas espécies de Iheringichthys permitiu diferenciá-las, podendo ser utilizado como marcador taxonômico. Em Pimelodus, variação quanto ao número e posição de sítios do DNAr 5S foi observada. Em P. britskii e P. maculatus os sítios de DNAr 5S e 18S foram localizados em sintenia, o que pode indicar uma condição derivada para estas espécies, visto que são as únicas espécies de Pimelodidae que apresentam esta característica até o momento. Os resultados do presente estudo fornecem dados que contribuem para o conhecimento da história evolutiva das espécies de Pimelodidae, permitem estabelecer relações filogenéticas e auxiliam na identificação destas espécies.

Orientador: Danilo Moretti-Ferreira / Resumo: As ACs são alterações visíveis nos cromossomos, classificadas como numéricas e estruturais. Atualmente o grande desafio da genética clínica é classificar e associar a relevância clínica dos desequilíbrios genéticos ao fenótipo dos portadores. O trabalho tem como objetivo principal caracterizar desequilíbrio genômico sem diagnóstico sindrômico previamente descritos pelas técnicas de citogenética clássica, molecular visando apurar os pontos de quebras e genes inseridos na região cromossômica alterada por meio da citogenômica em estudos de casos. Foram feitas análises por citogenética (bandamento GTG), citogenética molecular (FISH) e citogenômica (array-CGH) em três pacientes com malformações congênitas não-sindrômicas para definição diagnóstica e maior conhecimento sobre a correlação genótipo-fenótipo. Foram redigidos estudos de casos de três pacientes portadores de MCs, atraso do desenvolvimento e deficiência intelectual. O primeiro copilado de caso trata-se de paciente do sexo feminino com anomalias esqueléticas, deficiência intelectual e atraso do desenvolvimento. O cariótipo da paciente é 46,XX[11]/47,XX,+mar[9]. A análise de array-CGH revelou dois ganhos/duplicações nas bandas cromossômicas 6p11.2q12 (10.335 Mb de tamanho) e 6q14.1q14.3 (10.765 Mb de tamanho). Por meio da técnica da FISH e os resultados do array-CGH a região duplicada 6q14.1q14.3 encontra-se inserida em um cromossomo marcador, oriundo do cromossomo 6. Os sinais clínicos descritos na paciente foram semelhan... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The ACs are visible changes in the chromosomes, classified as numerical and structural. Currently the great challenge of clinical genetics is to classify and associate the clinical relevance of genetic imbalances with the phenotype of the carriers. The main objective of this work is to characterize genomic imbalance without syndromic diagnosis previously described by the classical and molecular cytogenetic techniques, in order to determine the breakpoints and genes inserted in the chromosomal region altered by cytogenetics in case studies. Cytogenetics (GTG banding), molecular cytogenetics (FISH) and cytogenetics (array-CGH) were performed in three patients with non-syndromic congenital malformations for diagnostic definition and greater knowledge on genotype-phenotype correlation. Case studies of three patients with MCs, developmental delay and intellectual disability were written. The first case file is a female patient with skeletal anomalies, intellectual disability and developmental delay. The patient's karyotype is 46, XX [11] / 47, XX, + sea [9]. The array-CGH analysis revealed two gains / doublings in the chromosomal bands 6p11.2q12 (10,335 Mb in size) and 6q14.1q14.3 (10,765 Mb in size). Through the FISH technique and the results of the array-CGH the duplicate region 6q14.1q14.3 is inserted in a chromosome marker, coming from chromosome 6. The clinical signs described in the patient were similar to other patients with duplication of the region 6q14. The genes PGM3, M... (Complete abstract click electronic access below) / Mestre

Durante a divisão celular as Aurora-quinases (AURKA e AURKB) participam da formação e controle das fibras do fuso mitótico enquanto as isoformas proteicas (DIDO1, DIDO2 e DIDO3), originadas do splicing alternativo do gene DIDO, auxiliam na junção dos microtúbulos aos cinetócoros. Portanto, ambas são relevantes na regulação do ciclo celular. Interessantemente, a superexpressão (ou o ganho de função) das AURKs ou a baixa expressão (ou perda de função) das isoformas de DIDO estão ambos associados com amplificação dos centrossomos e à instabilidade cromossômica (CIN), com consequente aneuploidia. Dentre as doenças hematológicas com registros de CIN, a leucemia linfoide crônica (LLC) pode apresentar amplificação dos centrossomos e alteração nos níveis de expressão das AURKs acarretando aneuplodias. Apesar disso, não existem estudos avaliando a potencial associação destes genes com CIN na LLC. Avaliando seus níveis de expressão gênica em amostras de LLC de pacientes com ou sem aberrações cromossômicas, mostramos que o aumento dos níveis de AURKA e AURKB e, inversamente, a redução dos níveis das variantes de DIDO, são significativamente associados com ganhos cromossômicos e com aumento da contagem de glóbulos brancos (WBC). Claramente, amostras de LLC sem qualquer anormalidade citogenética apresentam níveis de expressão semelhantes às amostras que contêm aberrações não-numéricas. O achado de que níveis de expressão de AURKs e variantes de DIDO são completamente opostos, mostrando um padrão discreto de inter-relação, levou-nos a investigar o potencial mecanismo regulatório por trás disso. Tendo em vista que outros, anteriormente, mostraram que o cluster oncogênico miR-17~92 é significativamente hiper-regulado em células de pacientes com LLC purificadas expressando genes IGHV não mutados (em comparação com células mutadas de pacientes) e, que o miR-17 é expresso em níveis significativamente mais elevados em células IGHV não mutadas ou ZAP-70 positivas (mau prognóstico geralmente associada à CIN), resolvemos investigar o potencial de regulação negativa dos microRNAs deste cluster sobre as variantes de DIDO. Além disso, com base no mecanismo regulatório já descrito pelo qual a superexpressão de AURKA induz a transcrição do cluster miR-17~92, mediada por E2F1 (com uma correlação entre as expressões de ambas as proteínas em diferentes tipos de câncer), decidimos investigar este eixo regulatório em LLC. Notavelmente, todas as variantes de DIDO apresentam-se preditas como fortes alvos de vários microRNAs deste cluster oncogênico. Mostramos, então, que amostras de LLC com baixa expressão de DIDO, além dos já mencionados níveis elevados de AURK, exibiram níveis significativamente mais elevados do fator de transcrição E2F1 e de seu alvo transcricional, o transcrito primário do miR-17~92 (MIR17HG). Além disso, por meio do uso da linhagem de celular NTERA-2, como modelo experimental, mostramos que o siRNA nocaute para AURKA (nos níveis transcricional e proteico, como confirmado por qPCR e western blot) é acompanhada por uma significativa redução de E2F1 e também de MIR17HG. Ainda, a transfecção de células NTERA-2 com sintéticos microRNAs miméticos do cluster miR-17~92 (ou seja, 19a-miR, miR-20a e miR-92a) resultou em uma clara e significativa redução dos níveis de transcrição de todas as variantes de DIDO. Por fim, a inibição do siRNA especifico para a variante DIDO3 (mas não às outras variantes) levou a uma redução significativa dos níveis de transcrição de todas as variantes de DIDO, indicando um mecanismo adicional contribuindo para a downregulação dos transcritos de DIDO. Ao todo, nossos resultados demonstram a existência de um potencial mecanismo regulatório interconectado entre AURK e DIDO, associado à CIN e maior contagem de WBC na LLC. Mais importante, os níveis de expressão elevada de AURKs e os baixos níveis associados das variantes de DIDO são especificamente relacionados com anormalidades citogenéticas apresentando ganhos cromossomais, com destaque para o mecanismo celular específico, subjacente à CIN, observado neste grupo distinto LLC. Dado o papel central da CIN na gênese e progressão do câncer, esses achados provavelmente terão um impacto importante no prognóstico ou tratamento da LLC. / During cell cycle division Aurora kinases (AURKA and AURKB) participate in the formation and control of mitotic spindle fibers, while, protein isoforms (DIDO1, DIDO2 and DIDO3), derived by alternative splicing of the DIDO gene, assist at the junction of microtubules to kinetochores. Thus, both are relevant to cell cycle maintenance. Interestingly, overexpression (or gain of function) of AURKs or low expression (or loss of function of DIDO) are both associated with centrosomal amplification and chromosomal instability (CIN), leading to aneuploidy. Among hematological diseases with CIN records, chronic lymphocytic leukemia (CLL) can display centrosome amplification and changes in AURKs expression levels leading to aneuploidy. Despite this, there are no studies evaluating the potential association of these genes with CIN in CLL. By evaluating their gene expression levels in CLL samples from patients with or without chromosomal aberrations, we show that increased levels of AURKA and AURKB and, conversely, reduced levels of DIDO variants, are both significantly associated with chromosomal gains and with increased white blood cell (WBC) counts. Clearly, CLL samples without any cytogenetic abnormality had expression levels similar to samples mostly harboring non-numerical aberrations. The finding that the expression levels of AURKs and DIDO variants are completely opposed, showing a discrete inter-related pattern, led us to investigate the potential regulatory mechanism behind this. Given that other have previously shown that the oncogenic miR-17~92 cluster is significantly upregulated in purified CLL patient cells expressing unmutated IGHV genes (as compared to mutated patient cells), and that miR-17 is expressed at significantly higher levels in unmutated or ZAP-70 high cases (bad prognostic cases generally associated with chromosomal instability), we investigated the potential negative regulation of DIDO variants by microRNAs from this cluster. In addition, based on the already described regulatory mechanism by which AURKA overexpression induces the E2F1-mediated transcription upregulation of the miR-17~92 cluster (with an observed expression correlation of both proteins in cancer specimens); we decided to investigate this regulatory axis in CLL. Notably, we found that all DIDO variants are predicted to be heavily targeted by several miRs of this oncogenic cluster. We show that CLL samples with low DIDO expression, in addition to the already mentioned AURK high levels, displayed significant higher levels of the transcription factor E2F1 and of its transcriptional target, the miR-17~92 primary transcript (MIR17HG). Moreover, by using the NTERA-2 cell line as a model, we show that siRNA knockdown of AURKA (at the transcript and protein level, as confirmed by qPCR and western blot) is accompanied by a striking significant reduction of E2F1 and also of MIR17HG. Furthermore, transfection of NTERA-2 cells with synthetic mimics of the miR-17~92 cluster (namely, miR-19a, miR-20a and miR-92a) results in a clear and significant reduction in the transcript levels of all DIDO variants. Finally, specific siRNA inhibition of the DIDO3 variant (but not the others) led to a significant reduction in the transcript levels of all DIDO variants, indicating an additional mechanism contributing to the downregulation of DIDO transcripts. Altogether, our results demonstrate the existence of a potential interconnected regulatory mechanism between AURK and DIDO, associated with CIN and higher WBC counts in CLL. More importantly, the high expression levels of AURKs and the associated low levels of DIDO variants are specifically associated with cytogenetic abnormalities presenting chromosomal gains, highlighting the specific cellular mechanism underlying the CIN observed in this distinct CLL group. Given the central role of CIN in cancer genesis and progression, these findings will likely have an important impact on prognosis or treatment of CLL.

Le développement embryonnaire précoce des mammifères femelles s’accompagne de l’inactivation transcriptionnelle d’un de leurs deux chromosomes X. Cet évènement est initié suite à l’expression mono-allélique de l’ARN non codant Xist, qui est contrôlée par de nombreux éléments cis-régulateurs présents dans le centre d’inactivation du chromosome X (Xic) – tel son anti-sens répresseur Tsix. Mon travail de thèse a consisté à développer des approches permettant d’appréhender le paysage structural dans lequel s’exerce cette régulation. La caractérisation de l’architecture tridimensionnelle du Xic, par des techniques basées sur la capture de conformation chromosomique (3C) et l’hybridation in situ en fluorescence (FISH), m’a permis de mettre en évidence que les promoteurs respectifs de Xist et Tsix sont engagés dans des interactions physiques intimes avec des loci distaux, localisés au sein du Xic, et de montrer qu’au moins certaines de ces régions exercent un effets régulateurs à longue-distance. Les éléments du Xic contactés par les régions promotrices de Xist et de Tsix sont en outre fondamentalement différents, chacune engageant des associations chromosomiques sur plusieurs centaines de kilobases dans leur direction 5’ respective.Ce travail a également permis de révéler des propriétés insoupçonnées de l’architecture chromosomiques. En effet, le Xic apparaît scindé en plusieurs sous-régions, couvrant chacune entre 200kb et 1Mb, à l’intérieur desquelles les interactions chromosomiques sont préférentiellement établies. L’existence de ces domaines d’interaction s’intègre avec d’autres propriétés structurales du génome, tels la composition de la chromatine sous-jacente et l’association à la lamine nucléaire, mais n’apparaît pas en dépendre directement. En étudiant la dynamique de la conformation chromosomique du Xic au cours de la différenciation cellulaire, j’ai pu constater la robustesse de cette organisation, sauf sur le chromosome X inactif, qui se distingue par la perte des contacts chromosomiques préférentiels détectables sur son homologue actif.Enfin, j’ai pu mettre en évidence que la variabilité du repliement général du chromosome X amène à un instant donné chaque allèle de Tsix à contacter physiquement des jeux de séquences distales différents, suggérant que l’environnement structural instantané de chacun de ces allèles à l’orée de l’activation mono-allélique de Xist est différent. Ce travail, combinant des approches à l’échelle de la population cellulaire d’une part et de la fibre de chromatine unique d’autre part, apporte une nouvelle vision du paysage structural et régulateur dans lequel s’inscrit le contrôle de l’activité transcriptionnelle de Xist, et fourni de nouvelles perspectives concernant les principes fondamentaux de l’organisation topologique des chromosomes chez les mammifères. / Early development of female mammals is accompanied by transcriptional inactivation of one of their two X chromosomes. This event is initiated following mono-allelic expression of the Xist non-coding RNA – what is achieved by the interplay of numerous cis-regulatory elements present within the X inactivation center (Xic), such as its repressive antisense Tsix. Our work aimed at throwing light on the structural landscape that underlies such long-range regulation. Characterization of the three-dimensional architecture of the Xic, by the means of Chromosome Conformation Capture (3C)-based techniques and in situ fluorescence hybridization (FISH), revealed that the respective promoters of Xist and Tsix contact many distal genomic elements within the Xic, and that at least one of such interacting region exerts long-range cis-transcriptional control. Noticeably, Xist and Tsix promoters associate with different sets of elements in their respective 5’ direction that are spread out over several hundreds of kilobases These experiments also revealed unforeseen properties of chromatin architecture. Indeed, the Xic appears to be partitioned in several sub-regions, each spanning between 200kb and 1Mb, inside which chromosomal interactions are preferentially established. The existence of these interaction domains integrates with other structural features of the genome, such as underlying chromatin composition and association with the nuclear lamina, but does not seem to directly depend on them. By analyzing chromosome conformation of the Xic during cell differentiation we document the robustness of this organizational principle, with the noticeable exception of the inactive X chromosome that assumes a folding pattern that is more random than its active homolog. Finally we also bring evidence that variability in the folding pattern of the two X chromosomes in the same cell brings each Tsix allele in association with different sets of chromosomal partners at a given moment, suggesting that the instantaneous structural environment of each allele at the onset of mono-allelic Xist up-regulation is different.By combining approaches at the scale of cell populations on the one hand, and at the single chromatin fiber level on the other, this study provides a first vision of the structural landscape in which Xist regulation takes place, and brings new insights concerning fundamental properties of chromosome organization in mammals.

A displasia frontonasal (DFN) compreende quadros de aparência facial variável, sendo clinicamente caracterizada por dois ou mais dos seguintes sinais: hipertelorismo ocular com consequente alargamento da base nasal; fissura facial mediana afetando o nariz ou o nariz e lábio superior e, por vezes, o palato; fissura alar (uni ou bilateral); ponta nasal ausente; crânio anterior bífido oculto, e implantação em &#39;V&#39; dos cabelos na fronte. A DFN pode ser vista como um defeito de desenvolvimento que pode ocorrer por si só ou como parte do quadro clínico de várias síndromes. A maioria dos casos de DFN é esporádica, e em raras circunstâncias foram observadas alterações cromossômicas em alguns indivíduos. Até o momento, quatro genes foram relacionados à patogênese molecular de algumas das síndromes com DFN, EFNB1, associado a uma forma de DFN ligada ao X e os genes ALX1, ALX3 e ALX4, todos associados a formas de DFN com herança autossômica recessiva. Embora esteja claro haver heterogeneidade etiológica, na maioria dos casos de DFN a causa não é conhecida, dificultando o adequado aconselhamento genético aos pacientes e seus familiares. Sendo assim, realizamos estudos com diferentes estratégias metodológicas buscando melhor compreender as possíveis causas genéticas da DFN. Ao todo foram analisados 10 pacientes: um caso familial de DFN leve com herança aparentemente autossômica dominante, um caso clinicamente sugestivo de mutação em ALX1, e oito casos de DFN associada a atraso de desenvolvimento com ou sem outras anomalias, dos quais um apresentava um rearranjo de novo aparentemente balanceado entre os cromossomos 4 e 12. Optamos por realizar sequenciamento dos genes previamente relacionados a fenótipos com DFN em todos os casos; para aqueles em que não foram detectadas mutações patogênicas, realizamos análise de variações de número de cópias (CNV) por microarray de polimorfismos de base única e, para o paciente com rearranjo cromossômico, realizamos o mapeamento do ponto de quebra por hibridação in situ fluorescente. Constatamos uma mutação em heterozigose no gene ALX4 co-segregando com o fenótipo do caso familial, sendo esta a primeira descrição de alteração em tal gene causando uma forma de DFN com herança dominante, e sugerimos pela primeira vez um mecanismo de dominância negativa. No caso sugestivo de mutação em ALX1, o diagnóstico foi confirmado através da identificação de uma mutação em homozigose neste gene do paciente; este caso consiste no 3o da literatura mundial e evidencia pela primeira vez que mutações em ALX1 não necessariamente levam a atraso de desenvolvimento ou deficiência intelectual. Os estudos citogenéticos e moleculares dos pontos de quebra do paciente com rearranjo cromossômico sugeriram os genes ARAP2 e CAND1 como possíveis responsáveis por seu quadro clínico, enquanto o estudo de CNVs nos indivíduos com DFN associada a atraso de desenvolvimento apontou os genes DNAJB12 e ENOX2 como possíveis candidatos para explicar o fenótipo de dois dos pacientes. É preciso que novos estudos sejam realizados a fim de melhor compreender o significado de tais achados e a real contribuição de cada gene para o desenvolvimento craniofacial humano e para a etiologia da DFN. Para os casos em que não foram identificadas alterações conclusivas no presente estudo, embora causas ambientais não possam ser descartadas, é preciso que seja investigada também a existência de fatores genéticos e epigenéticos não detectáveis pelas metodologias utilizadas, bem como a hipótese de mosaicismo somático. Nossos resultados, além de corroborarem o envolvimento dos genes ALX1 e ALX4 em fenótipos com DFN, sugerem também novos genes candidatos: ARAP2, CAND1, DNAJB12 e ENOX2 / Frontonasal dysplasia (FND) is a rare group of disorders that comprises cases with a variety of facial appearances, and is clinically characterized by two or more of the following signs: ocular hypertelorism with consequent broadening of the nasal root; median facial cleft affecting the nose and/or upper lip and palate; clefting of the alae nasi (uni or bilateral); lack of formation of the nasal tip; anterior cranium bifidum occultum; and a V-shaped frontal hairline. FND is a developmental defect that can occur alone or as part of several syndromes. Most cases of FND are sporadic, and in rare circumstances chromosomal alterations were observed in affected individuals. To date, four genes have been related to the molecular pathogenesis of some syndromes with DFN, one (EFNB1) is associated with an X-linked form while the 3 others (ALX1, ALX3 and ALX4) are associated with autosomal recessive forms. Although it is clear that FND is etiologic heterogeneous, the causative mechanism is unknown in most cases which makes it hard to give proper genetic counseling to patients and their families. In order to get new insights into the genetic mechanisms leading to FND, we performed studies with different methodologies. Altogether, 10 patients were analyzed: a familial case of a mild form of FND with an apparently autosomal dominant inheritance pattern, a case clinically suggestive of mutation in ALX1, and eight cases of FND associated with developmental delay with or without other anomalies, one of which with an apparently balanced de novo rearrangement between chromosomes 4 and 12. We chose to sequence the genes previously associated with FND phenotypes in all cases; for those in which pathogenic mutations were not detected, we conducted an analysis of copy number variations (CNV) by single nucleotide polymorphisms microarrays; for the patient with chromosomal rearrangement, we also mapped the breakpoints by using fluorescence in situ hybridization. We found a heterozygous mutation in ALX4 co-segregating with the phenotype of the familial case; this is the first description of mutation in this gene causing a form of FND with dominant inheritance pattern, and we suggested for the first time a dominant negative mechanism. In the case suggestive of mutation in ALX1, the diagnosis was confirmed by the identification of a homozygous mutation in this gene; this is the third case of the literature and shows for the first time that mutations in ALX1 are not necessarily related to developmental delay or intellectual disability. Breakpoints cytogenetic and molecular studies done with the patient with chromosomal rearrangement suggested ARAP2 and CAND1 genes as causative candidates for his condition, while the study of CNVs in individuals with FND associated with developmental delay pointed DNAJB12 and ENOX2 genes as possible candidates to explain the phenotypes of two of the patients. Further studies are necessary to better understand the significance of such findings and the actual contribution of each of these genes to human craniofacial development and the etiology of FND. Although environmental causes cannot be ruled out, it should also be investigated the existence of genetic and epigenetic factors as well as the possibility of somatic mosaicism, among the cases negative for the molecular approaches used in our study. Our results corroborate the involvement of ALX1 and ALX4 in FND phenotypes, and suggest new candidate genes: ARAP2, CAND1, DNAJB12 and ENOX2.

<p>The common shrew, <i>Sorex araneus</i>, has one of the most variable karyotypes among mammals, displaying numerous chromosomes races throughout its distribution, which can be categorized into different karyotypic groups. The objective of this thesis was to examine the postglacial population history of Fennoscandian common shrews using autosomal microsatellites, mitochondrial DNA (mtDNA) and a Y chromosome specific microsatellite (L8Y).</p><p>Autosomal microsatellites and mtDNA revealed weak genetic structure over a hybrid zone between the karyotypically divergent Northern and Western karyotypic groups. However, the genetic structure displayed by the Y chromosome microsatellite was orders of magnitude higher. Hence, considerable chromosomal differences between the groups do not prevent female gene flow, while male gene flow is reduced (cf. Haldane's rule). Further, the results suggest that the Haldane effect may be caused by the chromosomal differences between the karyotypic groups.</p><p>No mtDNA differentiation was observed either between chromosome races or between the Northern and Western karyotypic groups in Fennoscandia. The combined pattern of karyotypic and mtDNA variation of Fennoscandian common shrews, suggest bi-directional postglacial recolonisation from a single refugium in Europe. The variation of the Y-linked microsatellite supported this conclusion. In contrast, significant mtDNA structure, discordant with the karyotypic variation, revealed that common shrews in southern Finland belong to a different lineage than remaining Fennoscandian regions, implying postglacial recolonisation from a different source.</p><p>MtDNA variation of the chromosome races in Sweden supports the hypothesis that three races of the Western karyotypic group have been formed through whole arm reciprocal translocations (WARTs), as suggested by their mutual karyotypic variation. The variation of the molecular markers supports the theory of rapid karyotypic evolution in the common shrew.</p>

The common shrew, Sorex araneus, has one of the most variable karyotypes among mammals, displaying numerous chromosomes races throughout its distribution, which can be categorized into different karyotypic groups. The objective of this thesis was to examine the postglacial population history of Fennoscandian common shrews using autosomal microsatellites, mitochondrial DNA (mtDNA) and a Y chromosome specific microsatellite (L8Y). Autosomal microsatellites and mtDNA revealed weak genetic structure over a hybrid zone between the karyotypically divergent Northern and Western karyotypic groups. However, the genetic structure displayed by the Y chromosome microsatellite was orders of magnitude higher. Hence, considerable chromosomal differences between the groups do not prevent female gene flow, while male gene flow is reduced (cf. Haldane's rule). Further, the results suggest that the Haldane effect may be caused by the chromosomal differences between the karyotypic groups. No mtDNA differentiation was observed either between chromosome races or between the Northern and Western karyotypic groups in Fennoscandia. The combined pattern of karyotypic and mtDNA variation of Fennoscandian common shrews, suggest bi-directional postglacial recolonisation from a single refugium in Europe. The variation of the Y-linked microsatellite supported this conclusion. In contrast, significant mtDNA structure, discordant with the karyotypic variation, revealed that common shrews in southern Finland belong to a different lineage than remaining Fennoscandian regions, implying postglacial recolonisation from a different source. MtDNA variation of the chromosome races in Sweden supports the hypothesis that three races of the Western karyotypic group have been formed through whole arm reciprocal translocations (WARTs), as suggested by their mutual karyotypic variation. The variation of the molecular markers supports the theory of rapid karyotypic evolution in the common shrew.

The process of evolution is of both scientific and medical interest. This thesis presents several studies using complete genomic reference sequences, comparative genomic data, and intraspecific diversity data to study the two key processes of evolution: mutation and selection. Large duplications, deletions, inversions, and translocations of DNA contribute to genomic variation both between and within species. Human chromosomes 15 and 17 contain a high percentage of dispersed, recently duplicated sequences. Examination of the relationships between these sequences showed that the majority of all duplications within each chromosome could be linked through core sequences that are prone to duplication. Comparison to orthologous sequences in other mammals allowed a reconstruction of the ancestral state of the human chromosomes, revealing that regions of rearrangement specific to the human lineage are highly enriched in chromosome-specific duplications. Comparison to copy number variation data from other studies also shows that these regions are enriched in current human structural variation. One specific region, the MAPT locus at 17q21.31, known to contain an inversion polymorphism in Europeans, was resequenced completely across both human orientation haplotypes and in chimpanzee and orangutan, revealing complex duplication structures at the inversion breakpoints, with the human region being more complex than chimpanzee or orangutan. Fluorescent in-situ hybridization analysis of human, chimpanzee, and orangutan chromosomes showed inversion polymorphisms of independent origin in all three species, demonstrating that this region has been a hotspot of genomic rearrangement for at least twelve million years. These results reveal a mechanistic relationship between sequence duplication and rearrangement in the great apes. We also generated a draft sequence of the chimpanzee genome and compared it to that of the human. Among other findings, this showed that CpG dinucleotides contribute 25% of all single base mutations, with a rate of mutation ~10-fold that of other bases, and that the male mutation rate in great apes is ~5-6 times the female rate, a higher ratio than had been observed in comparisons of primates and rodents. We detected six regions of probable recent positive selection in humans with a statistical method relying on chimpanzee sequence to control for regional variation in mutation rates. Finally, resequencing of several lines of domestic chicken and comparison to the reference chicken genome identified a number of gene deletions fixed in domestic lines and also several potential selective sweeps. Of particular interest are a missense mutation in TSHR nearly fixed in all domestic chickens and a partial deletion of SH3RF2 fixed in a high growth line. The TSHR mutation may play a role in relaxation of seasonal reproduction. A high-resolution QTL mapping experiment showed that the SH3RF2 deletion is significantly associated with increased growth. This work provides important new insights into the mechanics of evolutionary change at both the single nucleotide and structural level and identifies potential targets of natural and artificial selection in humans and chickens.