No description available.

Les souches Saccharomyces cerevisiae présentent une forte diversité phénotypique, notamment au niveau des propriétés fermentaires parmi les souches œnologiques. Les bases moléculaires de ces différences de comportements ainsi que les mécanismes d'adaptation à l'environnement œnologique sont encore mal connues. Les variations d'expression génique contribuent à cette diversité phénotypique, cependant les réseaux et les gènes concernés sont peu décrits. Afin d'aborder ces questions, nous avons développé une approche intégrée « génétique-génomique » qui combine la cartographie de QTL en fermentation alcoolique et les profils d'expression d'une population recombinée. La recherche de QTL d'expression nous a permis de détecter 1465 eQTL correspondant à des régulations locales ou distantes dont certaines regroupées en hotspots. Nous avons déterminé qu'une duplication d'un segment chromosomique est impliquée dans le contrôle de la cinétique de fermentation. Nos données ont révélé que les perturbations d'expression concernent de nombreux réseaux métaboliques. Nous avons caractérisé plus finement les sources de variations d'expression qui affectent les systèmes de détoxification, et avons montré que les modifications de régulation de plusieurs exporteurs membranaires sont liées à des mutations dans des facteurs de transcription. Nous avons également décrypté les variations contrôlant les gènes du métabolisme de la thiamine. Nous montrons qu'une altération du senseur Thi3p, conduit à privilégier l'expression des gènes de biosynthèse de la thiamine chez la souche œnologique aux dépens d'un gène de pyruvate décarboxylase. Ces travaux nous ont ainsi permis d'accéder à une partie des bases moléculaires responsables de la diversité et de l'adaptation des souches aux conditions œnologiques. / Saccharomyces cerevisiae strains have a high phenotypic diversity, particularly in terms of fermentation properties among wine strains. The molecular bases underlying these behavior differences and the mechanisms of adaptation to the wine environment are still poorly known. Changes in gene expressions contribute to this phenotypic diversity. However, the regulatory networks and the genes involved are badly described. To address these questions, we developed an integrated “genetics-genomics” approach that combines QTL mapping in alcoholic fermentation and expression analysis of a recombinant population. The search for expression QTL allowed us to detect 1465 eQTL corresponding to local or distant regulations, several of them being grouped into hotspots. We highlighted that a duplication of a chromosomal segment is involved in the control of the fermentation kinetics. Our data showed that the expression disturbances are involved in many metabolic networks. We characterized more precisely the sources of expression variations affecting the detoxification systems, and showed that the changes in regulation of several membrane exporters are linked to mutations in transcription factors. We have also deciphered the variations controlling genes of the thiamine metabolism. We showed that an alteration of the sensor Thi3p tends to favor the expression of genes for the thiamine biosynthesis in wine strain at the expense of a gene encoding a pyruvate decarboxylase. This work allowed us to access some of the molecular bases responsible of the diversity and the strains adaptation to oenological conditions.

Clonal evolution is a multistep process characterized by progression of the disease, adverse prognosis and shortening of overall survival. The aim of the dissertation was a detailed characterization of identified changes in patients with myelodysplastic syndromes (MDS) and clonal evolution and evaluation of their prognostic impact. We performed detail cytogenomic analyses in 36/469 (8%) patients with confirmed linear clonal evolution. We described 57 primary abnormalities (32% MDS-specific) at the time of diagnosis, the most frequent was deletion of long arm of chromosome 5. We proved 156 secondary aberrations (21% MDS-specific) during the course of the clonal evolution, the most frequent were trisomies/tetrasomies of chromosome 8. We identified acquired uniparental disomies (aUPD) in 19% of patients. In MDS-specific aUPDs 4q, 11q and 17p, we proved homozygous mutations of TET2, c-CBL and TP53 genes. We found a statistically significant difference in overall survival between the groups of patients divided according to their diagnostic cytogenomic findings. In patients with clonal evolution before treatment 54% of aberrations were gains of whole chromosomes, by contrast 44% of abnormalities identified in patients with clonal evolution after treatment were monosomies or deletions. The study of clonal...

O imprinting genômico é um processo regulado epigeneticamente que faz com que os alelos sejam expressos de acordo com a sua origem parental. No cromossomo 11 (11p15.5), existem duas regiões controladoras de imprinting (ICR1 e ICR2), que controlam a expressão de genes marcados (imprinted). Os padrões de metilação dessas regiões podem ser alterados pela dissomia uniparental (DUP), que ocorre quando parte de ou um cromossomo inteiro do mesmo par de homólogos é herdado de somente um genitor. Erros mitóticos podem gerar mosaicismo com uma linhagem de células com DUP e a outra biparental. As síndromes de Silver-Russell (SSR) e Beckwith-Wiedemann (SBW) são doenças de alterações do imprinting genômico, envolvendo os cromossomos 7 (SSR) e 11 (SSR e SBW). A Hemihiperplasia Isolada (HHI) parece corresponder a uma forma mais leve da SBW.. No presente trabalho, foi realizada uma varredura in silico para busca de novos microssatélites nos cromossomos 7 e 11, e selecionados seis do tipo tetra ou pentanucleotídeos, no cromossomo 7, e 12, no cromossomo 11. O perfil de metilação nas ICRs foi verificado por três técnicas distintas: MS-MLPA, DESM-RT e por uma nova estratégia desenvolvida neste trabalho denominada DESM-QFPCR. Foram avaliados 32 pacientes com SBW, 16 HHI, 20 com SSR e seus pais, quando disponíveis, além de um paciente com fenótipo aparentemente normal com cariótipo 46,XX/46,XY e cuja placenta apresentou displasia mesenquimal placentária (DMP) a qual está associada à SBW. Os novos marcadores apresentaram alta taxa de heterozigose (média de 70%), e ausência das características indesejáveis dos dinucleotídeos predominantemente utilizados para detecção de DUP. Seis marcadores estão entre genes controlados pelas ICRs 1 e 2. A DUP paterna do cromossomo 11 (DUPpat Cr11), sempre restrita a 11p15.5, foi responsável por 13% dos casos de HHI e 19% dos de SBW. As alterações estruturais foram confirmadas por minissequenciamento quantitativo de SNPs e por MS-MLPA. Um paciente apresentou duplicação paterna abrangendo ambas as ICRs. Uma deleção não descrita anteriormente no gene CDKN1C foi observada em uma paciente e sua mãe. Para os pacientes com DUPpat Cr11, foram investigados microssatélites em 13 autossomos e nos cromossomos sexuais para detecção de mosaicismo global. Apenas o paciente com DMP apresentou mosaicismo [células androgenéticas (25-30%) e biparentais], sugerindo evento de dupla fertilização. Nos pacientes com SSR, foi observada hipometilação na ICR1 em 25% dos casos. Para a SBW, foi observada hipermetilação na ICR1 e hipometilação na ICR2 em 6% e 42% dos casos, respectivamente. Os casos com DUPpat Cr11 apresentaram alteração de metilação em ambas as ICRs. As frequências de alterações (epi) genéticas encontradas foram semelhantes às previamente descritas na literatura para as SBW, SSR e HHI. Neste trabalho, foi desenvolvida uma nova técnica para estudo de metilação do DNA de ICRs e testados marcadores microssatélites inéditos na região 11p15, que quando comparados com metodologias mais tradicionais de avaliação, como DESM-RT e MS-MLPA, mostraram elevada correlação dos resultados. Os achados mostram a complexidade da etiologia das doenças estudadas no presente trabalho e os dados moleculares serão imprescindíveis para o aconselhamento genético adequado para cada caso em particular e suas famílias. / Genomic imprinting is a epigenetically regulated process where the alleles are expressed in terms of their parental origin. On chromosome 11 (11p15.5) there are two regions controlling imprinting (ICR1 and ICR2), which control imprinted gene expression. The methylation patterns in these regions may be altered by uniparental disomy (UPD), which occurs when part or whole chromose is inherited from only one parent. Mitotic errors can lead to mosaicism with a cell line with DUP and other, biparental. The Silver-Russell syndrome (SRS) and Beckwith-Wiedemann syndrome (BWS) are diseases of abnormal genomic imprinting, involving chromosomes 7 (SSR) and 11 (SRS and BWS). The Isolated Hemihiperplasia (IHH) seems to correspond to a milder form of the SBW. In the present study, we performed an in silico scan to search for new microsatellites on chromosomes 7 and 11, and selected six tetra- and/or pentanucleotides on chromosome 7, and 12 on chromosome 11. The pattern of methylation in ICRs was verified by three different techniques: MS-MLPA, DESM-RT and a new strategy developed in this work called DESM-QFPCR. We evaluated 32 patients with BWS, HHI 16, with 20 SSR and their parents, when available, and one patient with apparently normal phenotype with karyotype 46, XX/46, XY and whose placenta showed placental mesenchymal dysplasia (PMD) which is associated with SBW. The new markers showed a high heterozygosity rate (average 70%), and absence of undesirable characteristics of dinucleotides, predominantly used for detection of DUP. Six markers spans genes controlled by the ICRs 1 and 2. The paternal UPD for chromosome 11 (UPDpat Cr11), all restricted to 11p15.5, was responsible for 13% of cases of HHI and 19% of the SBW. Structural changes were confirmed by quantitative SNaPshot sequencing of SNPs and MS-MLPA. One patient had paternal duplication encompassing both ICRs. A not previously described deletion in the gene CDKN1C was observed in one patient and her mother. For patients with DUPpat Cr11, microsatellites were investigated in 13 autosomes and sex chromosomes to detect wide mosaicism. Only patients with DMP showed mosaicism [androgenetic cells (25-30%) and biparental], suggesting double fertilization. In patients with SRS, ICR1 hypomethylation was observed in 25% of cases. For BWS, ICR1 hypermethylation and in ICR2 hypomethylation were observed 6% and 42% of cases, respectively. All cases with UPDpat Cr11 presented abnormal methylation in both ICRs. The (epi) genetic change frequencies were similar to those previously described in the literature for BWS, SRR andIHH. In the present work, we developed a new technique to study DNA methylation of ICRs and tested novel microsatellite markers in the 11p15 region, which showed high correlation of results, when compared with more traditional methods such as RT-DESM and MS-MLPA. The results show the complex etiology of these diseases and the molecular data are essential for appropriate patient and families genetic counseling.

O imprinting genômico é um processo regulado epigeneticamente que faz com que os alelos sejam expressos de acordo com a sua origem parental. No cromossomo 11 (11p15.5), existem duas regiões controladoras de imprinting (ICR1 e ICR2), que controlam a expressão de genes marcados (imprinted). Os padrões de metilação dessas regiões podem ser alterados pela dissomia uniparental (DUP), que ocorre quando parte de ou um cromossomo inteiro do mesmo par de homólogos é herdado de somente um genitor. Erros mitóticos podem gerar mosaicismo com uma linhagem de células com DUP e a outra biparental. As síndromes de Silver-Russell (SSR) e Beckwith-Wiedemann (SBW) são doenças de alterações do imprinting genômico, envolvendo os cromossomos 7 (SSR) e 11 (SSR e SBW). A Hemihiperplasia Isolada (HHI) parece corresponder a uma forma mais leve da SBW.. No presente trabalho, foi realizada uma varredura in silico para busca de novos microssatélites nos cromossomos 7 e 11, e selecionados seis do tipo tetra ou pentanucleotídeos, no cromossomo 7, e 12, no cromossomo 11. O perfil de metilação nas ICRs foi verificado por três técnicas distintas: MS-MLPA, DESM-RT e por uma nova estratégia desenvolvida neste trabalho denominada DESM-QFPCR. Foram avaliados 32 pacientes com SBW, 16 HHI, 20 com SSR e seus pais, quando disponíveis, além de um paciente com fenótipo aparentemente normal com cariótipo 46,XX/46,XY e cuja placenta apresentou displasia mesenquimal placentária (DMP) a qual está associada à SBW. Os novos marcadores apresentaram alta taxa de heterozigose (média de 70%), e ausência das características indesejáveis dos dinucleotídeos predominantemente utilizados para detecção de DUP. Seis marcadores estão entre genes controlados pelas ICRs 1 e 2. A DUP paterna do cromossomo 11 (DUPpat Cr11), sempre restrita a 11p15.5, foi responsável por 13% dos casos de HHI e 19% dos de SBW. As alterações estruturais foram confirmadas por minissequenciamento quantitativo de SNPs e por MS-MLPA. Um paciente apresentou duplicação paterna abrangendo ambas as ICRs. Uma deleção não descrita anteriormente no gene CDKN1C foi observada em uma paciente e sua mãe. Para os pacientes com DUPpat Cr11, foram investigados microssatélites em 13 autossomos e nos cromossomos sexuais para detecção de mosaicismo global. Apenas o paciente com DMP apresentou mosaicismo [células androgenéticas (25-30%) e biparentais], sugerindo evento de dupla fertilização. Nos pacientes com SSR, foi observada hipometilação na ICR1 em 25% dos casos. Para a SBW, foi observada hipermetilação na ICR1 e hipometilação na ICR2 em 6% e 42% dos casos, respectivamente. Os casos com DUPpat Cr11 apresentaram alteração de metilação em ambas as ICRs. As frequências de alterações (epi) genéticas encontradas foram semelhantes às previamente descritas na literatura para as SBW, SSR e HHI. Neste trabalho, foi desenvolvida uma nova técnica para estudo de metilação do DNA de ICRs e testados marcadores microssatélites inéditos na região 11p15, que quando comparados com metodologias mais tradicionais de avaliação, como DESM-RT e MS-MLPA, mostraram elevada correlação dos resultados. Os achados mostram a complexidade da etiologia das doenças estudadas no presente trabalho e os dados moleculares serão imprescindíveis para o aconselhamento genético adequado para cada caso em particular e suas famílias. / Genomic imprinting is a epigenetically regulated process where the alleles are expressed in terms of their parental origin. On chromosome 11 (11p15.5) there are two regions controlling imprinting (ICR1 and ICR2), which control imprinted gene expression. The methylation patterns in these regions may be altered by uniparental disomy (UPD), which occurs when part or whole chromose is inherited from only one parent. Mitotic errors can lead to mosaicism with a cell line with DUP and other, biparental. The Silver-Russell syndrome (SRS) and Beckwith-Wiedemann syndrome (BWS) are diseases of abnormal genomic imprinting, involving chromosomes 7 (SSR) and 11 (SRS and BWS). The Isolated Hemihiperplasia (IHH) seems to correspond to a milder form of the SBW. In the present study, we performed an in silico scan to search for new microsatellites on chromosomes 7 and 11, and selected six tetra- and/or pentanucleotides on chromosome 7, and 12 on chromosome 11. The pattern of methylation in ICRs was verified by three different techniques: MS-MLPA, DESM-RT and a new strategy developed in this work called DESM-QFPCR. We evaluated 32 patients with BWS, HHI 16, with 20 SSR and their parents, when available, and one patient with apparently normal phenotype with karyotype 46, XX/46, XY and whose placenta showed placental mesenchymal dysplasia (PMD) which is associated with SBW. The new markers showed a high heterozygosity rate (average 70%), and absence of undesirable characteristics of dinucleotides, predominantly used for detection of DUP. Six markers spans genes controlled by the ICRs 1 and 2. The paternal UPD for chromosome 11 (UPDpat Cr11), all restricted to 11p15.5, was responsible for 13% of cases of HHI and 19% of the SBW. Structural changes were confirmed by quantitative SNaPshot sequencing of SNPs and MS-MLPA. One patient had paternal duplication encompassing both ICRs. A not previously described deletion in the gene CDKN1C was observed in one patient and her mother. For patients with DUPpat Cr11, microsatellites were investigated in 13 autosomes and sex chromosomes to detect wide mosaicism. Only patients with DMP showed mosaicism [androgenetic cells (25-30%) and biparental], suggesting double fertilization. In patients with SRS, ICR1 hypomethylation was observed in 25% of cases. For BWS, ICR1 hypermethylation and in ICR2 hypomethylation were observed 6% and 42% of cases, respectively. All cases with UPDpat Cr11 presented abnormal methylation in both ICRs. The (epi) genetic change frequencies were similar to those previously described in the literature for BWS, SRR andIHH. In the present work, we developed a new technique to study DNA methylation of ICRs and tested novel microsatellite markers in the 11p15 region, which showed high correlation of results, when compared with more traditional methods such as RT-DESM and MS-MLPA. The results show the complex etiology of these diseases and the molecular data are essential for appropriate patient and families genetic counseling.

No description available.

Le caryotype moléculaire permet d’identifier un CNV chez 10-14% des individus atteints de déficience intellectuelle et/ou de malformations congénitales. C’est pourquoi il s’agit maintenant de l’analyse de première intention chez ces patients. Toutefois, le rendement diagnostique n’est pas aussi bien défini en contexte prénatal et l’identification de CNVs de signification clinique incertaine y est particulièrement problématique à cause du risque d’interruption de grossesse. Nous avons donc testé 49 fœtus avec malformations majeures et un caryotype conventionnel normal avec une micropuce CGH pangénomique, et obtenu un diagnostic dans 8,2% des cas. Par ailleurs, des micropuces à très haute résolution combinant le caryotype moléculaire et le génotypage de SNPs ont récemment été introduites sur le marché. En plus d’identifier les CNVs, ces plateformes détectent les LOHs, qui peuvent indiquer la présence d’une mutation homozygote ou de disomie uniparentale. Ces anomalies pouvant être associées à la déficience intellectuelle ou à des malformations, leur détection est particulièrement intéressante pour les patients dont le phénotype reste inexpliqué. Cependant, le rendement diagnostique de ces plateformes n’est pas confirmé, et l’utilité clinique réelle des LOHs n’est toujours pas établie. Nous avons donc testé 21 enfants atteints de déficience intellectuelle pour qui les méthodes standards d’analyse génétique n’avaient pas résulté en un diagnostic, et avons pu faire passer le rendement diagnostique de 14,3% à 28,6% grâce à l’information fournie par les LOHs. Cette étude démontre l’utilité clinique d’une micropuce CGH pangénomique chez des fœtus avec malformations, de même que celle d’une micropuce SNP chez des enfants avec déficience intellectuelle. / Molecular karyotyping identifies a CNV in 10-14% of individuals affected with intellectual disability and/or congenital abnormalities. Therefore, it is now the first-tier analysis for these patients. However, the diagnostic yield is not as clear in the prenatal context, and the risk of pregnancy termination makes the detection of variants of uncertain clinical significance particularly problematic. We tested 49 fetuses with major malformations and a normal karyotype, using a pangenomic CGH array, and obtained a diagnosis in 8.2% of cases. Furthermore, high-resolution microarrays combining molecular karyotyping and SNP genotyping were recently introduced on the market. In addition to identifying CNVs, these platforms detect LOHs, which can indicate the presence of a homozygous mutation or of uniparental disomy. Since these abnormalities can be associated with intellectual disability or congenital abnormalities, their detection is of particular interest for patients whose phenotype remains unexplained. However, the diagnostic yield obtained with these platforms is not confirmed, and the real clinical value of LOH detection is not yet established. We tested 21 children affected with intellectual disability for whom standard genetic analyses failed to provide a diagnosis, and were able to increase the diagnostic yield from 14.3% to 28.6% as a result of the information provided by LOHs. This study shows the clinical usefulness of pangenomic CGH arrays in fetuses with malformation(s), as well as that of SNP arrays in children with intellectual disability.

Ce travail de thèse se propose d’étudier le retard de croissance intra-utérin sous l’angle de la cytogénétique placentaire, avec deux approches distinctes et complémentaires. La première approche visera à réévaluer l’influence des anomalies chromosomiques limitées au placenta sur la croissance fœtale, car des études précédentes ont rapporté des résultats contradictoires à ce sujet. La première partie de ce travail permettra en outre d’étudier l’incidence et l’influence de la disomie uniparentale chez les fœtus issus des grossesses compliquées d’une anomalie chromosomique limitée au placenta. La deuxième approche de notre travail s’intéressera à la longueur de structures chromosomiques particulières, les télomères, au niveau placentaire. Il a récemment été décrit que la longueur des télomères des cellules placentaires était réduite au terme des grossesses compliquées d’un retard de croissance intra-utérin. La longueur télomérique placentaire n’a jamais été évaluée au cours de ces grossesses et pourrait potentiellement être utilisée comme biomarqueur placentaire du retard de croissance intra-utérin. La deuxième partie de ce travail nous permettra également d’évaluer le nombre de copies des régions chromosomiques portant les gènes codant pour les principales sous-unités du complexe enzymatique télomérase et de rechercher la présence d’agrégats télomériques au niveau placentaire en cas de retard de croissance intra-utérin. / This thesis proposes to study intrauterine growth restriction in terms of cytogenetics of placenta, with two distinct and complementary approaches. The first approach will be to reassess the influence of confined placental mosaicism on fetal growth, as previous studies have reported conflicting results on this issue. The first part of this work will also study the influence of fetal uniparental disomy in case of confined placental mosaicism. The second approach of our work will focus on the length of terminal chromosomal structures, telomeres, at the placental level. It has recently been reported that telomere length was reduced in placental cells collected at term in pregnancies complicated by intrauterine growth restriction. Placental telomere length has never been evaluated in ongoing pregnancies and it could potentially be used as a placental biomarker of intrauterine growth restriction. The second part of this work will also focus on the copy number of chromosomal regions carrying genes encoding the main subunits of the telomerase enzyme complex and will look for the presence of placental telomeric aggregates in case of intrauterine growth restriction.