Diss. (sammanfattning) Uppsala : Uppsala universitet, 2008.

From the yeast genome completed in 1996 to the 12 Drosophilagenomes published earlier this year; little more than a decade has provided an incredible amount of genomic data. Yet even with this mountain of genetic information the regulatory networks that control gene expression remain relatively undefined. In part, this is due to the enormous amount of non-coding DNA, over 98% of the human genome, which needs to be made sense of. It is also due to the large number of transcription factors, potentially 2,000 such factors in the human genome, which may contribute to any given network directly or indirectly. Certainly, one of the central limitations has been the paucity of transcription factor (TF) specificity data that would aid in the prediction of regulatory targets throughout a genome. The general lack of specificity data has hindered the prediction of regulatory targets for individual TFs as well as groups of factors that function within a common regulatory pathway. A large collection of factor specificities would allow for the combinatorial prediction of regulatory targets that considers all factors actively expressed in a given cell, under a given condition. Herein we describe substantial improvements to a previous bacterial one-hybrid system with increased sensitivity and dynamic range that make it amenable for the high-throughput analysis of sequence-specific TFs. Currently we have characterized 108 (14.3%) of the predicted TFs in Drosophilathat fall into a broad range of DNA-binding domain families, demonstrating the feasibility of characterizing a large number of TFs using this technology. To fully exploit our large database of binding specificities, we have created a GBrowse-based search tool that allows an end-user to examine the overrepresentation of binding sites for any number of individual factors as well as combinations of these factors in up to six Drosophila genomes (veda.cs.uiuc.edu/cgi-bin/gbrowse/gbrowse/Dmel4). We have used this tool to demonstrate that a collection of factor specificities within a common pathway will successfully predict previously validated cis-regulatory modules within a genome. Furthermore, within our database we provide a complete catalog of DNA-binding specificities for all 84 homeodomains in Drosophila. This catalog enabled us to propose and test a detailed set of recognition rules for homeodomains and use this information to predict the specificities of the majority of homeodomains in the human genome.

Hox genes encode a conserved family of homeodomain containing transcription factors essential for metazoan development. The establishment of overlapping Hox expression domains specifies tissue identities along the anterior-posterior axis during early embryogenesis and is regulated by chromatin architecture and retinoic acid (RA). Here we present the role nucleosome positioning plays in hox activation during embryogenesis. Using four stages of early embryo development, we map nucleosome positions at 37 zebrafish hox promoters. We find nucleosome arrangement to be progressive, taking place over several stages independent of RA. This progressive change in nucleosome arrangement on invariant sequence suggests that trans-factors play an important role in organizing nucleosomes. To further test the role of trans-factors, we created hoxb1b and hoxb1a mutants to determine if the loss of either protein effected nucleosome positions at the promoter of a known target, hoxb1a. Characterization of these mutations identified hindbrain segmentation defects similar to targeted deletions of mouse orthologs Hoxa1 and Hoxb1 and zebrafish hoxb1b and hoxb1a morpholino (MO) loss-of-function experiments. However, we also identified differences in hindbrain segmentation as well as phenotypes in facial motor neuron migration and reticulospinal neuron formation not previously observed in the MO experiments. Finally, we find that nucleosomes at the hoxb1a promoter are positioned differently in hoxb1b-/- embryos compared to wild-type. Together, our data provides new insight into the roles of hoxb1b and hoxb1a in zebrafish hindbrain segmentation and reticulospinal neuron formation and indicates that nucleosome positioning at hox promoters is dynamic, depending on sequence specific factors such as Hox proteins.

No description available.

Os craniofaringiomas são os tumores mais frequentes da região hipotálamohipofisária na faixa etária pediátrica. Apesar de serem histologicamente benignos, sua tendência infiltrativa e seu comportamento agressivo resultam em significante morbimortalidade. Histologicamente podem ser divididos em dois subtipos: adamantinomatosos e papilíferos. A patogênese dos craniofaringiomas é pouco compreendida. Mutações no gene CTNNB1, que codifica a proteína beta-catenina, são a única alteração molecular conhecida até o momento implicada na tumorigênese dos craniofaringiomas adamantinomatosos. Tais mutações afetam o sítio de degradação da beta-catenina, que passa a se acumular no citoplasma e no núcleo, ativando excessivamente a via de sinalização WNT, através da ligação aos fatores de transcrição da família LEF/TCF, levando a tumorigênese. Recentemente foi descoberto um novo mecanismo de determinação da linhagem celular hipofisária regulado pela beta-catenina, através do qual ela interage diretamente com o PROP1 para determinar a diferenciação celular hipofisária. De acordo com esse modelo, o complexo protéico PROP1/beta- catenina atua simultaneamente como repressor do HESX1 e ativador do PIT1, dependendo dos co-fatores associados. Pacientes com mutações germinativas inativadoras no PROP1 desenvolvem hipopituitarismo e podem apresentar aumento hipofisário com imagens de ressonância nuclear magnética (RNM) da região selar muitas vezes semelhantes àquelas dos craniofaringiomas, com hiperssinal em T1. Por outro lado, camundongos com expressão persistente do Prop1 exibem defeitos na regulação da proliferação celular hipofisária, incluindo cistos da bolsa de Rathke, hiperplasia adenomatosa e tumores, sugerindo que mutações com ganho de função no PROP1 também poderiam contribuir para a patogênese de tumores hipofisários em seres humanos. A semelhança entre as imagens de RNM dos pacientes com craniofaringiomas e daqueles com aumento hipofisário devido a mutações inativadoras no PROP1, e o fato de que camundongos transgênicos com expressão persistente do Prop1 apresentam aumento da susceptibilidade a tumores hipofisários, deram base a nossa hipótese de que uma desregulação na expressão do PROP1 em humanos poderia estar envolvida na patogênese dos craniofaringiomas adamantinomatosos. Esse trabalho teve como objetivo avaliar a presença de mutação somática no exon 3 do CTNNB1 e avaliar a expressão desse gene e do gene PROP1 em craniofaringiomas adamantinomatosos. Foram obtidas 14 amostras desse tipo de tumor por meio da ressecção terapêutica. As amostras foram submetidas à extração do RNA e posterior transcrição reversa para obtenção de cDNA. A partir do cDNA foi realizada PCR e sequenciamento do exon 3 do CTNNB1 em todas as amostras. Porém, a avaliação por PCR em tempo real foi realizada apenas em 12 amostras, devido à qualidade inadequada de 2 amostras para submissão a essa metodologia. Foram encontradas mutações missense, em heterozigose em 9 das 14 amostras, sendo 5 previamente descritas e 2 ainda não descritas em craniofaringiomas adamantinomatosos. Hiperexpressão do CTNNB1 foi encontrada em 7 amostras, sendo 5 com mutação e 2 sem mutação no CTNNB1.A hiperexpressão variou de 2,5 a 6,2 vezes maior que o pool de hipófise normal. Contudo, a expressão do PROP1 foi indetectável em todas as amostras. Concluímos que o aumento da expressão do CTNNB1 presente em 58% das amostras sugere o envolvimento também da hiperexpressão desse gene na etiopatogenia do craniofaringioma adamantinomatoso, enquanto a ausência de expressão do PROP1 afasta a participação desse gene na etiopatogenia do craniofaringioma adamantinomatoso / Craniopharyngiomas are the the commonest tumors to involve the hypothalamo-pituitary regions in childhood population. Histologically they are benign, and can be divided in two primary subtypes: the adamantinomatous and the papillary. Although histologically benign, their infiltrative tendency and aggressive behavior can result in great morbidity. The pathogenesis of craniopharyngiomas is poorly understood. To date, beta-catenin gene (CTNNB1) mutations have been identified only in the adamantinomatous subtype. These mutations affect the degradation target box of beta-catenin that accumulates in the cytoplasm and the nucleus increasing the transcriptional activity of WNT pathway through interaction with the transcription factors of LEF/TCF family, leading to tumorigenesis. Recently, an interaction between beta-catenin and PROP1 was described as a new mecanism for beta-catenindependent regulation of pituitary cell-lineage determination. According to this novel model, the PROP1/beta-catenin proteic complex would act as a binary switch to simultaneously repress the transcription factor HESX1 and to activate expression of transcription factor PIT1, depending on the associated cofactors. Patients with loss-of-function mutations in PROP1 present combined pituitary hormonal deficiency generally associated with pituitary enlargement and the magnetic resonance imaging (MRI) of the sellar region in these patients sometimes resembles that of the craniopharyngiomas, with T1 hyperintense signal. On the other hand, transgenic mice with persistent Prop1 expression exhibit defects consistent with misregulation of pituitary cell proliferation, including adenomatous hyperplasia with formation of Rathke\'s cleft cysts and tumors suggesting that misregulation of PROP1 expression in human could contribute to pathogenesis of pituitary tumors. The similarity between the MRI images of craniopharyngiomas patients and that of patients with loss-of-function mutations in PROP1, associated with the fact that transgenic mice with persistent Prop1 expression exhibit increased susceptibility to pituitary tumors gave rise to our hypothesis that a misregulation of PROP1 expression could be involved in the pathogenesis of adamantinomatous craniopharyngiomas. The aim of this study was to analyze the presence of somatic mutations in exon 3 of CTNNB1 and the expression pattern of this gene and the PROP1 gene in adamantinomatous craniopharyngiomas. Fourteen samples were obtained from therapeutic surgery and submitted to RNA extraction and reverse transcription in order to produce the cDNA. The cDNA was used as a template to CTNNB1 exon 3 PCR reaction followed by direct sequencing of all samples. However, the real-time RT-PCR analysis was realized only in 12 samples, since 2 of them had an insufficient quality for this method. Missence, heterozygous mutations were found in 9 out of 14 samples; five were previously described and 2 not yet described in adamantinomatous craniopharyngiomas. Overexpression of CTNNB1 was found in 7 samples, which them 5 with CTNNB1 mutation 2 whitout. The overexpression ranged from 2.5 to 6.2 fold more than pituitary normal pool. However, the PROP1 expression was undetectable in all the samples. We could conclude that the amount of 58% CTNNB1 overexpressed samples suggest also a role of this overexpression in the pathogenesis of adamantinomatous craniopharingiomas, while the undetectable levels of PROP1 exclude a role of this gene in the pathogenesis of adamantinomatous craniopharingiomas

Diss. (sammanfattning) Umeå : Umeå universitet, 2008. / Härtill 4 uppsatser.

Os craniofaringiomas são os tumores mais frequentes da região hipotálamohipofisária na faixa etária pediátrica. Apesar de serem histologicamente benignos, sua tendência infiltrativa e seu comportamento agressivo resultam em significante morbimortalidade. Histologicamente podem ser divididos em dois subtipos: adamantinomatosos e papilíferos. A patogênese dos craniofaringiomas é pouco compreendida. Mutações no gene CTNNB1, que codifica a proteína beta-catenina, são a única alteração molecular conhecida até o momento implicada na tumorigênese dos craniofaringiomas adamantinomatosos. Tais mutações afetam o sítio de degradação da beta-catenina, que passa a se acumular no citoplasma e no núcleo, ativando excessivamente a via de sinalização WNT, através da ligação aos fatores de transcrição da família LEF/TCF, levando a tumorigênese. Recentemente foi descoberto um novo mecanismo de determinação da linhagem celular hipofisária regulado pela beta-catenina, através do qual ela interage diretamente com o PROP1 para determinar a diferenciação celular hipofisária. De acordo com esse modelo, o complexo protéico PROP1/beta- catenina atua simultaneamente como repressor do HESX1 e ativador do PIT1, dependendo dos co-fatores associados. Pacientes com mutações germinativas inativadoras no PROP1 desenvolvem hipopituitarismo e podem apresentar aumento hipofisário com imagens de ressonância nuclear magnética (RNM) da região selar muitas vezes semelhantes àquelas dos craniofaringiomas, com hiperssinal em T1. Por outro lado, camundongos com expressão persistente do Prop1 exibem defeitos na regulação da proliferação celular hipofisária, incluindo cistos da bolsa de Rathke, hiperplasia adenomatosa e tumores, sugerindo que mutações com ganho de função no PROP1 também poderiam contribuir para a patogênese de tumores hipofisários em seres humanos. A semelhança entre as imagens de RNM dos pacientes com craniofaringiomas e daqueles com aumento hipofisário devido a mutações inativadoras no PROP1, e o fato de que camundongos transgênicos com expressão persistente do Prop1 apresentam aumento da susceptibilidade a tumores hipofisários, deram base a nossa hipótese de que uma desregulação na expressão do PROP1 em humanos poderia estar envolvida na patogênese dos craniofaringiomas adamantinomatosos. Esse trabalho teve como objetivo avaliar a presença de mutação somática no exon 3 do CTNNB1 e avaliar a expressão desse gene e do gene PROP1 em craniofaringiomas adamantinomatosos. Foram obtidas 14 amostras desse tipo de tumor por meio da ressecção terapêutica. As amostras foram submetidas à extração do RNA e posterior transcrição reversa para obtenção de cDNA. A partir do cDNA foi realizada PCR e sequenciamento do exon 3 do CTNNB1 em todas as amostras. Porém, a avaliação por PCR em tempo real foi realizada apenas em 12 amostras, devido à qualidade inadequada de 2 amostras para submissão a essa metodologia. Foram encontradas mutações missense, em heterozigose em 9 das 14 amostras, sendo 5 previamente descritas e 2 ainda não descritas em craniofaringiomas adamantinomatosos. Hiperexpressão do CTNNB1 foi encontrada em 7 amostras, sendo 5 com mutação e 2 sem mutação no CTNNB1.A hiperexpressão variou de 2,5 a 6,2 vezes maior que o pool de hipófise normal. Contudo, a expressão do PROP1 foi indetectável em todas as amostras. Concluímos que o aumento da expressão do CTNNB1 presente em 58% das amostras sugere o envolvimento também da hiperexpressão desse gene na etiopatogenia do craniofaringioma adamantinomatoso, enquanto a ausência de expressão do PROP1 afasta a participação desse gene na etiopatogenia do craniofaringioma adamantinomatoso / Craniopharyngiomas are the the commonest tumors to involve the hypothalamo-pituitary regions in childhood population. Histologically they are benign, and can be divided in two primary subtypes: the adamantinomatous and the papillary. Although histologically benign, their infiltrative tendency and aggressive behavior can result in great morbidity. The pathogenesis of craniopharyngiomas is poorly understood. To date, beta-catenin gene (CTNNB1) mutations have been identified only in the adamantinomatous subtype. These mutations affect the degradation target box of beta-catenin that accumulates in the cytoplasm and the nucleus increasing the transcriptional activity of WNT pathway through interaction with the transcription factors of LEF/TCF family, leading to tumorigenesis. Recently, an interaction between beta-catenin and PROP1 was described as a new mecanism for beta-catenindependent regulation of pituitary cell-lineage determination. According to this novel model, the PROP1/beta-catenin proteic complex would act as a binary switch to simultaneously repress the transcription factor HESX1 and to activate expression of transcription factor PIT1, depending on the associated cofactors. Patients with loss-of-function mutations in PROP1 present combined pituitary hormonal deficiency generally associated with pituitary enlargement and the magnetic resonance imaging (MRI) of the sellar region in these patients sometimes resembles that of the craniopharyngiomas, with T1 hyperintense signal. On the other hand, transgenic mice with persistent Prop1 expression exhibit defects consistent with misregulation of pituitary cell proliferation, including adenomatous hyperplasia with formation of Rathke\'s cleft cysts and tumors suggesting that misregulation of PROP1 expression in human could contribute to pathogenesis of pituitary tumors. The similarity between the MRI images of craniopharyngiomas patients and that of patients with loss-of-function mutations in PROP1, associated with the fact that transgenic mice with persistent Prop1 expression exhibit increased susceptibility to pituitary tumors gave rise to our hypothesis that a misregulation of PROP1 expression could be involved in the pathogenesis of adamantinomatous craniopharyngiomas. The aim of this study was to analyze the presence of somatic mutations in exon 3 of CTNNB1 and the expression pattern of this gene and the PROP1 gene in adamantinomatous craniopharyngiomas. Fourteen samples were obtained from therapeutic surgery and submitted to RNA extraction and reverse transcription in order to produce the cDNA. The cDNA was used as a template to CTNNB1 exon 3 PCR reaction followed by direct sequencing of all samples. However, the real-time RT-PCR analysis was realized only in 12 samples, since 2 of them had an insufficient quality for this method. Missence, heterozygous mutations were found in 9 out of 14 samples; five were previously described and 2 not yet described in adamantinomatous craniopharyngiomas. Overexpression of CTNNB1 was found in 7 samples, which them 5 with CTNNB1 mutation 2 whitout. The overexpression ranged from 2.5 to 6.2 fold more than pituitary normal pool. However, the PROP1 expression was undetectable in all the samples. We could conclude that the amount of 58% CTNNB1 overexpressed samples suggest also a role of this overexpression in the pathogenesis of adamantinomatous craniopharingiomas, while the undetectable levels of PROP1 exclude a role of this gene in the pathogenesis of adamantinomatous craniopharingiomas

Le récepteur hypophysaire de la GnRH (RGnRH) joue un rôle crucial dans le contrôle de la fonctionde reproduction. Dans le promoteur distal du Rgnrh, j’ai caractérisé un élément de réponsebifonctionnel répondant aux protéines LIM à homéodomaine ISL1/LHX3 et à GATA2. D’autre part,deux motifs TAAT situés dans la région plus proximale confèrent à ce gène la capacité de répondreaux facteurs Paired-like PROP1 et OTX2. Tous ces facteurs, exprimés précocement au cours del’ontogenèse hypophysaire, pourraient participer à l’émergence de l’expression du Rgnrh. Hors del’hypophyse, j’ai découvert que le Rgnrh est exprimé au cours du développement postnatal dansl’hippocampe de rat, où il module la plasticité synaptique. Par ailleurs, j’ai identifié deux nouveauxsites d’expression, la rétine et la glande pinéale. Ces résultats mettent en lumière l’importancefonctionnelle de ce récepteur et de son ligand et les rôles multiples qu’il ont acquis au cours del’évolution des Vertébrés. / In the pituitary, the GnRH receptor (GnRHR) plays a crucial role in the neuroendocrine control ofreproductive function. Within the distal region of the Gnrhr promoter, I have characterized abifunctional response element modulated by the LIM homeodomain proteins ISL1/LHX3 and byGATA2. Besides, in the proximal region of the promoter, two TAAT motifs conferred response toPaired-like factors PROP1 and OTX2. All these factors are expressed during pituitary ontogenesis andcould participate in the onset and regulation of Gnrhr expression. Outside of the pituitary, I havediscovered that the Gnrhr was expressed during postnatal development in the rat hippocampus, whereit modulated synaptic plasticity. Furthermore, I have identified two novel sites of Gnrhr expression, theretina and the pineal gland. Altogether, these data highlight the functional importance of this receptorand its ligand as well as the multiple roles they have acquired during vertebrate evolution.

No description available.

No / The Lhx2 transcription factor plays essential roles in morphogenesis and patterning of ectodermal derivatives as well as in controlling stem cell activity. Here, we show that during murine skin morphogenesis, Lhx2 is expressed in the hair follicle (HF) buds, whereas in postnatal telogen HFs Lhx2(+) cells reside in the stem cell-enriched epithelial compartments (bulge, secondary hair germ) and co-express selected stem cell markers (Sox9, Tcf4 and Lgr5). Remarkably, Lhx2(+) cells represent the vast majority of cells in the bulge and secondary hair germ that proliferate in response to skin injury. This is functionally important, as wound re-epithelization is significantly retarded in heterozygous Lhx2 knockout (+/-) mice, whereas anagen onset in the HFs located closely to the wound is accelerated compared with wild-type mice. Cell proliferation in the bulge and the number of Sox9(+) and Tcf4(+) cells in the HFs closely adjacent to the wound in Lhx2(+/-) mice are decreased in comparison with wild-type controls, whereas expression of Lgr5 and cell proliferation in the secondary hair germ are increased. Furthermore, acceleration of wound-induced anagen development in Lhx2(+/-) mice is inhibited by administration of Lgr5 siRNA. Finally, Chip-on-chip/ChIP-qPCR and reporter assay analyses identified Sox9, Tcf4 and Lgr5 as direct Lhx2 targets in keratinocytes. These data strongly suggest that Lhx2 positively regulates Sox9 and Tcf4 in the bulge cells, and promotes wound re-epithelization, whereas it simultaneously negatively regulates Lgr5 in the secondary hair germ and inhibits HF cycling. Thus, Lhx2 operates as an important regulator of epithelial stem cell activity in the skin response to injury.