Microphthalmia, anophthalmia, and coloboma (MAC) are distinct abnormalities demonstrating a continuum of developmental eye defects that contribute to 15-20% of blindness and severe vision deficiencies in children worldwide. The genetic etiology of MAC is large, complex and encompasses the whole developmental biology of the eye. Understanding how the eye develops will aid in identifying genes and developmental pathways involved in MAC. Although investigation of the genetic architecture of congenital anomalies is growing exponentially, much work remains to be accomplished to understand the complex, genetically heterogeneous congenital anomalies, which significantly impact childhood vision. With an interest in elucidating the mechanisms that are involved in eye morphogenesis, I have characterized a SRY-Box transcription factor, Sox11, during zebrafish ocular development. The SRY (sex determining region Y)-box 11 (sox11) gene, codes for a transcription factor which functions as a regulator of cell fate, survival, and differentiation in the embryonic and adult nervous system. By titrating the levels of sox11 gene function in developing zebrafish embryos I have investigated the role of Sox11 during ocular morphogenesis and retinal neurogenesis. Chapter 1 of this dissertation provides a review of vertebrate eye development with a focus on emerging roles of SoxC proteins during vertebrate ocular morphogenesis. Chapter 2 presents data demonstrating that knockdown of both paralogs of sox11 in zebrafish results in microphthalmia, coloboma, as well as a specific deficit in mature rod photoreceptors. Additionally, we demonstrate for the first time that Sox11 regulates early ocular and photoreceptor development in part by maintaining proper levels of Hedgehog (Hh) signaling. Deficiency of Sox11 results in elevated Sonic Hedgehog a (Shha) transcript levels, which in turn leads to improper patterning of the optic vesicle into the proxio-distal territories. Furthermore, the data indicate that alterations in SOX11 gene dosage or mutation within the SOX11 coding region are potentially disease causing and contribute to human ocular defects like MAC and rod dysfunction. Chapter 3 presents data indicating that sox11 gene function is required during the critical period of neurulation (4-10 hours post fertilization) to guide choroid fissure closure and proper ocular morphogenesis to occur in the developing zebrafish. Chapter 4 is a technical report on the progress towards generating stable sox11a/b knockout zebrafish lines using the CRISPR/Cas9 genome editing approach. Transient F0 injected embryos and F0 adults carry mutations in the sox11a/b target site in addition to displaying ocular abnormalities similar to those previously reported in sox11 morphants. F1 juveniles are ready to be screened for establishment of mutagenesis efficiency and germ line transmission. Finally, in Chapter 5 I discuss how the results of each chapter demonstrate the functional requirement of Sox11 for ocular development. Furthermore, I discuss the implications of this work in the field of developmental biology and how the current data will shape future investigations. My dissertation incorporates human genetics, biochemical analyses, and zebrafish reverse genetic analyses, and will help in better understanding the exact role of Sox11 during eye development at the cellular and molecular level. Moreover, by identifying Sox11 targets belonging to the Hh pathway, as well as novel targets of Sox11 regulation, these studies may also contribute to our understanding of the function of Sox11in development and disease pathogenesis.

Organ formation is an important step during development of an organism that combines different scales from the molecular to the tissue level. Many organogenesis phenomena involve epithelial morphogenesis, where sheets of cells undergo rearrangements to form complex architectures – organ precursors, which subsequently develop into mature organs. Timely development of the characteristic architectures of the organ precursors is crucial for successful organogenesis and is determined by the choice of epithelial rearrangements that organise the constituent cells in space and time. However, for many organogenesis events the cellular dynamics underlying such epithelial rearrangements remain elusive. In the work presented here, I investigated the morphogenesis of the hemispherical retinal neuroepithelium (RNE), that serves as an organ precursor of the neural retina. Formation of RNE is an important event in vertebrates that shapes the optic cup and sets the stage for subsequent eye development. I investigated RNE morphogenesis in the developing zebrafish embryo by visualising and investigating the cellular dynamics of the process in vivo. My findings show that the zebrafish RNE is shaped by the combined action of two different epithelial rearrangements – basal shrinkage of the neuroepithelial cells and involution of cells at the rim of the developing optic cup. The basal shrinkage of the neuroepithelial cells bends the neuroepithelial sheet and starts the process of invagination. However, my results show that the major player in RNE morphogenesis is rim involution. Rim involution translocates prospective RNE cells to their designated location in the invaginating layer and contributes to RNE invagination. My work unravelled the so far unknown mechanism of rim involution. I show that the rim cells involute by collective epithelial migration using directed membrane protrusions and dynamic cell-matrix contacts. If rim migration is perturbed, the prospective RNE cells cannot reach the invaginating layer. As a result, these migration-defective cells attain the RNE fate at an ectopic location and disrupt the tissue architecture. Therefore, rim migration coordinates the cellular location with the timing of RNE fate determination and orchestrates RNE morphogenesis in space and time. Overall, my work highlights how morphogenetic processes shape the organ precursor architecture and ensure timely organ formation. These findings provide important insights not only for eye development but also for epithelial morphogenesis and organogenesis in many other systems. / Für die Entwicklung eines Organismus ist die Bildung von Organen (Organogenese) von zentraler Bedeutung. Organogenese umfasst Prozesse auf allen Ebenen der Längenskala: von der molekularen Ebene, der Gewebeebene, bis hin zur Ebene des ganzen Organismus. Viele Phänomene der Organogenese beinhalten dabei Veränderungen von Epithelien, bei der sich Schichten von Zellen zu komplexen Strukturen - Organvorläufern - umwandeln. Diese entwickeln sich später zu vollständigen Organen. Die rechtzeitige Entwicklung der charakteristischen Architektur der Organvorläufer ist entscheidend für eine erfolgreiche Organogenese und wird durch die Wahl der epithelialen Umwandlungsprozessen bestimmt, welche die Zellen in Raum und Zeit koordinieren müssen. Für viele dieser Prozesse ist jedoch genau diese zugrundeliegende Zelldynamik unklar. In der hier vorgestellten Arbeit untersuchte ich die Bildung des hemisphärischen retinalen Neuropepithels (RNE). Das RNE ist der Organvorläufer der neuralen Retina, weshalb dessen korrekte Bildung die Voraussetzung für die korrekte Entwicklung der Augen ist. Ich untersuchte die RNE-Morphogenese in sich entwickelnden Zebrafisch-Embryos durch Visualisierung und Untersuchung der zellulären Dynamik der beteiligten Prozesse in vivo. Meine Ergebnisse zeigen, dass das RNE in Zebrafischen durch die kombinierte Umwandlung von zwei verschiedenen Epithelien geformt wird. Zum einen findet eine Verkleinerung des basalen Prozesses der neuroepithelialen Zellen statt, zum anderen die Involution von Randzellen. Die basale Verkleinerung der neuroepithelialen Zellen verbiegt die neuroepitheliale Schicht und führt zur Einstülpung des RNE. Meine Ergebnisse zeigten allerdings, dass Involution von Randzellen noch bedeutsamer für die RNE-Morphogenese ist. Die involution von Randzellen transportiert potenzielle RNE-Zellen in das Neuroepithel und trägt zur RNE-Einstülpung bei. Die Bedeutung meiner Arbeit liegt darin, den bisher unbekannten Mechanismus der Randzell-Involution entdeckt zu haben. Ich zeigte, dass die Randzellen sich aktiv durch kollektive epitheliale Migration bewegen indem sie gerichtete Membranforsätze und dynamische Zell zu Matrix Kontakte etablieren. Wird die Migration der Randzellen inhibiert, so führt dies dazu, dass diese Zellen die eingestülpte RNE Schicht nicht erreichen. Sie landen dann an den falschen Positionen, wo sie die Gewerbearchitektur stören können. Daher koordiniert die Randzellmigration die Position der Zellen und orchestriert die RNE-Morphogenese in Raum und Zeit. Insgesamt zeigt meine Arbeit, wie morphogenetische Prozesse die Organvorläuferarchitektur prägen und eine rechtzeitige Organbildung sicherstellen. Diese Erkenntnisse sind sowohl für das Verständnis der Augenentwicklung, als auch für das der epithelialen Morphogenese und Organogenese in anderen Systemen von großer Bedeutung.

Gene regulatory networks, underlying the molecular regulation of eye development are conserved across many animal phyla. Genes from the Pax family of transcription factors are one of the most conserved members through the evolution, regulating the development of crucial parts of eye, including the photoreceptor cells. Pax transcription factors are considered to be regulators of opsins, molecules providing the conversion of the light stimulus into the electrochemical signalisation in the photoreceptors cells. In this thesis, pax6 and pax2/5/8 transcription factors are investigated as potential regulators of eye development in Platynereis dumerilii. pax6 and pax2/5/8 transcription factors are tested as potential regulators of the r-opsin in Platynereis, based on the observed early expression onsets of these genes. Wild-type expression analysis of pax6 and pax2/5/8 using the whole mount RNA in-situ hybridization is provided, accompanied by the initial analysis of the Platynereis pax6 knockout line. pax6 heterozygote mutants are shown to be viable and able to reproduce, however, homozygote mutation of pax6 in Platynereis is lethal. Our data suggest that transcription factors pax2/5/8, otx and six3 are not regulated by the pax6 in Platynereis. Concerning the r-opsin present in the Platynereis eyes, pax6...

Organ formation is an important step during development of an organism that combines different scales from the molecular to the tissue level. Many organogenesis phenomena involve epithelial morphogenesis, where sheets of cells undergo rearrangements to form complex architectures – organ precursors, which subsequently develop into mature organs. Timely development of the characteristic architectures of the organ precursors is crucial for successful organogenesis and is determined by the choice of epithelial rearrangements that organise the constituent cells in space and time. However, for many organogenesis events the cellular dynamics underlying such epithelial rearrangements remain elusive. In the work presented here, I investigated the morphogenesis of the hemispherical retinal neuroepithelium (RNE), that serves as an organ precursor of the neural retina. Formation of RNE is an important event in vertebrates that shapes the optic cup and sets the stage for subsequent eye development. I investigated RNE morphogenesis in the developing zebrafish embryo by visualising and investigating the cellular dynamics of the process in vivo. My findings show that the zebrafish RNE is shaped by the combined action of two different epithelial rearrangements – basal shrinkage of the neuroepithelial cells and involution of cells at the rim of the developing optic cup. The basal shrinkage of the neuroepithelial cells bends the neuroepithelial sheet and starts the process of invagination. However, my results show that the major player in RNE morphogenesis is rim involution. Rim involution translocates prospective RNE cells to their designated location in the invaginating layer and contributes to RNE invagination. My work unravelled the so far unknown mechanism of rim involution. I show that the rim cells involute by collective epithelial migration using directed membrane protrusions and dynamic cell-matrix contacts. If rim migration is perturbed, the prospective RNE cells cannot reach the invaginating layer. As a result, these migration-defective cells attain the RNE fate at an ectopic location and disrupt the tissue architecture. Therefore, rim migration coordinates the cellular location with the timing of RNE fate determination and orchestrates RNE morphogenesis in space and time. Overall, my work highlights how morphogenetic processes shape the organ precursor architecture and ensure timely organ formation. These findings provide important insights not only for eye development but also for epithelial morphogenesis and organogenesis in many other systems. / Für die Entwicklung eines Organismus ist die Bildung von Organen (Organogenese) von zentraler Bedeutung. Organogenese umfasst Prozesse auf allen Ebenen der Längenskala: von der molekularen Ebene, der Gewebeebene, bis hin zur Ebene des ganzen Organismus. Viele Phänomene der Organogenese beinhalten dabei Veränderungen von Epithelien, bei der sich Schichten von Zellen zu komplexen Strukturen - Organvorläufern - umwandeln. Diese entwickeln sich später zu vollständigen Organen. Die rechtzeitige Entwicklung der charakteristischen Architektur der Organvorläufer ist entscheidend für eine erfolgreiche Organogenese und wird durch die Wahl der epithelialen Umwandlungsprozessen bestimmt, welche die Zellen in Raum und Zeit koordinieren müssen. Für viele dieser Prozesse ist jedoch genau diese zugrundeliegende Zelldynamik unklar. In der hier vorgestellten Arbeit untersuchte ich die Bildung des hemisphärischen retinalen Neuropepithels (RNE). Das RNE ist der Organvorläufer der neuralen Retina, weshalb dessen korrekte Bildung die Voraussetzung für die korrekte Entwicklung der Augen ist. Ich untersuchte die RNE-Morphogenese in sich entwickelnden Zebrafisch-Embryos durch Visualisierung und Untersuchung der zellulären Dynamik der beteiligten Prozesse in vivo. Meine Ergebnisse zeigen, dass das RNE in Zebrafischen durch die kombinierte Umwandlung von zwei verschiedenen Epithelien geformt wird. Zum einen findet eine Verkleinerung des basalen Prozesses der neuroepithelialen Zellen statt, zum anderen die Involution von Randzellen. Die basale Verkleinerung der neuroepithelialen Zellen verbiegt die neuroepitheliale Schicht und führt zur Einstülpung des RNE. Meine Ergebnisse zeigten allerdings, dass Involution von Randzellen noch bedeutsamer für die RNE-Morphogenese ist. Die involution von Randzellen transportiert potenzielle RNE-Zellen in das Neuroepithel und trägt zur RNE-Einstülpung bei. Die Bedeutung meiner Arbeit liegt darin, den bisher unbekannten Mechanismus der Randzell-Involution entdeckt zu haben. Ich zeigte, dass die Randzellen sich aktiv durch kollektive epitheliale Migration bewegen indem sie gerichtete Membranforsätze und dynamische Zell zu Matrix Kontakte etablieren. Wird die Migration der Randzellen inhibiert, so führt dies dazu, dass diese Zellen die eingestülpte RNE Schicht nicht erreichen. Sie landen dann an den falschen Positionen, wo sie die Gewerbearchitektur stören können. Daher koordiniert die Randzellmigration die Position der Zellen und orchestriert die RNE-Morphogenese in Raum und Zeit. Insgesamt zeigt meine Arbeit, wie morphogenetische Prozesse die Organvorläuferarchitektur prägen und eine rechtzeitige Organbildung sicherstellen. Diese Erkenntnisse sind sowohl für das Verständnis der Augenentwicklung, als auch für das der epithelialen Morphogenese und Organogenese in anderen Systemen von großer Bedeutung.

Glaucoma is a heterogeneous group of diseases that is currently considered to be the leading cause of irreversible blindness worldwide. Of the identified risk factors, elevated intraocular pressure remains the only modifiable risk factor that can be targeted clinically. Ocular hypertension is often a result of dysregulation of aqueous humour fluid dynamics in the anterior eye segment. Aqueous humour drainage is regulated by structures located in the anterior chamber of the eye. In some circumstances dysregulation occurs due to developmental abnormalities of these structures. The malformation of structures in the anterior segment is thought to be due to a defect in the differentiation and/or migration of the periocular mesenchyme during development. Unique to vertebrates, the neural crest cell (NCC) population contributes to the periocular mesenchyme and is instrumental to the proper development of structures in the anterior segment. For many years our laboratory has examined the role of the Activating Protein-2 (AP-2) transcription factors that are expressed in the neural crest and vital during the development of the eye. The purpose of this research project is to investigate the role of AP-2β in the NCC population during the development of the anterior segment of the eye. Conditional deletion of AP-2β expression in the NCC population demonstrated that mutants have dysgenesis of structures in the anterior segment including defects of the corneal endothelium, corneal stroma, ciliary body and a closed iridocorneal angle. Loss of retinal ganglion cells and their axons was also observed, likely due to the disruption of aqueous outflow, suggesting the development of glaucoma. The data generated from this research project will be critical in elucidating the role of AP-2β in the genetic cascade dictating the development of the anterior eye segment in addition to providing scientific research with a novel model of glaucomatous optic neuropathy. / Thesis / Master of Science (MSc)

O formato, posição e alinhamento corretos dos componentes oculares são definidos através de uma série de mudanças morfológicas complexas durante sua embriogênese. A retina se origina de células da vesícula óptica do tubo neural enquanto as células precursoras do cristalino surgem do ectoderma que reveste o ápice da vesícula óptica. Este ectoderma é delimitado molecularmente como pre-placoidal, sofre uma série de eventos morfogênicos durante o seu desenvolvimento inicial para formar o placóide do cristalino e, posteriormente, a vesícula do cristalino. O placóide do cristalino surge a partir do espessamento do ectoderma pre-placoidal. Posteriormente, o placóide invagina para formar a vesícula do cristalino. Durante a invaginação do placóide, as células da ectoderme que circundam o placóide (células periplacodais) também se movem para fechar a abertura do cristalino que invaginou e reconstruir o ectoderma da superfície. Aqui, nos concentramos em dois processos do desenvolvimento do olho. Nós investigamos o papel da matriz extracelular no espessamento do placóide do cristalino e a dinâmica da emissão de protrusões de membrana pelas células periplacodais durante a invaginação do placóide. A matriz extracelular desempenha papel relevante na morfogênese placodal. Por exemplo, a Fibronectina na matriz extracelular entre a vesícula óptica e o ectoderma pré-placoidal é necessária para a formação de placóide do cristalino. No entanto, a dinâmica da arquitetura de Fibronectina durante a formação do placóide é desconhecida. Assim, nosso primeiro objetivo aqui foi investigar a arquitetura da Fibronectina e da Laminina, dois importantes componentes da matriz extracelular, durante o espessamento do placóide do cristalino através de imagens confocais em 3D. Nossos dados sugerem que um padrão de Fibronectina e Laminina difuso e pontuado é restrito à região do placóide. Este padrão é mantido durante o espessamento e invaginação do placóide. Encontramos um padrão similar de Laminina na região do placóide de embrião de camundongo, sugerindo a conservação desta arquitetura neste contexto. Também demonstramos que a inibição mediada por Noggin (inibidor da sinalização de BMP), que interrompe o desenvolvimento do olho, afeta a organização da Fibronectina e da Laminina, sugerindo que a sinalização de BMP regula a organização da matriz extracelular durante o desenvolvimento do placóide do cristalino. Nosso segundo objetivo foi analisar a emissão de 5 protrusões celulares finas por células periplacodais correlacionando com o movimento de invaginação. Aqui, nós investigamos a dinâmica e composição do citoesqueleto dessas protrusões para entender sua função durante o desenvolvimento do olho. Observamos uma grande quantidade de protrusões em células periplacodais de embriões de galinha e de camundongo. Nossos resultados de quantificação com protrusões de embriões de galinha não mostraram correlação entre comprimento e direção de emissão ou com meia-vida. Nós também analisamos a diversidade na composição do citoesqueleto, uma vez que encontramos protrusões positivas para Cofilina e Tubulina. Estes dados sugerem uma população heterogênea de protrusões finas de membrana periplacodais. Finalmente, também identificamos essas protrusões em outras superfícies ectodérmicas de embriões de galinha e de camundongo, sugerindo que elas desempenham um papel no desenvolvimento de ectoderme superficial. / The correct shape, position and alignment of optic components are defined through a series of complex morphological changes during the embryogenesis of the eye. The retina originates from the neural tube´s optic vesicle while the lens precursor cells arise from the ectoderm that overlie the apex of the optic vesicle. This ectoderm is molecularly delimited as preplacodal and undergoes a series of morphogenic events during its initial development to form the lens placode and subsequently the lens vesicle. The lens placode arises from the thickening of the pre-placodal ectoderm. Subsequently, the placode invaginates to form the vesicle of the lens. During the invagination of the placode, the ectodermal cells that surround the placode (peri-placodal cells) also move to close the opening of the lens that invaginated and reconstruct the surface ectoderm. Here we focus on two processes of eye development. We investigated the role of the extracellular matrix in the lens placode thickening and the dynamics of the emission of membrane protrusions by the peri-placodal cells during the lens placode invagination. The extracellular matrix plays a relevant role in placodal morphogenesis. For example, Fibronectin in the extracellular matrix between the optic vesicle and the preplacodal ectoderm is required for the formation of lens placode. However, the dynamics of the Fibronectin architecture during placode formation is unknown. Thus, our first aim here was to investigate the architecture of Fibronectin and Laminin, two important components of the extracellular matrix, during thickening of lens placode through confocal 3D images. Our data suggest that both Fibronectin and Laminin present a diffuse and punctate pattern restricted to the placodal region. This pattern is maintained during thickening and invagination of the placode. We found a similar pattern of Laminin in the placodal region of the mouse embryo, suggesting the conservation of this architecture in this context. We also demonstrate that Noggin-mediated inhibition of BMP signalling, which disrupts the development of the eye, affects the organization of Fibronectin and Laminin, suggesting that BMP signalling regulates the organization of the extracellular matrix during the lens placode development. Our second objective was to analyse the emission of thin cellular protrusions by peri-placodal cells correlating with the lens invagination movement. Here we investigated the dynamics and 3 composition of the cytoskeleton of these protrusions to understand their function during the development of the eye. We observed a large number of protrusions in peri-satellite cells of chicken and mouse embryos. Our quantification results with chicken embryo protrusions showed no correlation between length and direction of emission or with half-life. We also analysed the diversity in the composition of the cytoskeleton, and we found protrusions positive for Cofilin and Tubulin. These data suggest a heterogeneous population of periplacodal protrusions. Finally, we have also identified these protrusions on other ectodermal surfaces of chicken and mouse embryos, suggesting that they play a role in the development of surface ectoderm.

When a multicellular organism suffers damages to tissues/organs it heals itself by either substituting the lost cellular matrix by scar formation or by regenerating the lost tissue. Regeneration likely occurs by a recapitulation of the developmental process that formed the organ. Many processes regulating organ development are based on epithelial-mesenchymal interactions and a strict control of organ specific stem/progenitor cells. Elucidation of the molecular basis of these processes is therefore vital in order to develop novel therapies in regenerative medicine. The LIM homebox gene Lhx2 is interesting in this context since Lhx2 has been shown to be important for the formation of several organs by regulating epithelial-mesenchymal interactions and progenitor cell function. Targeted inactivation of Lhx2 leads to a lethal anemia due to malformed liver and severe neural abnormalities such as hypoplasia of the forebrain and anophtalmia. Thus, elucidation of the mechanisms of the function of Lhx2 in different organ systems would give important insights into the molecular mechanisms regulating epithelial-mesenchymal interactions and stem/progenitor cell function. To elucidate the function of Lhx2 in the hematopoietic system Lhx2 was initially expressed in hematopoietic progenitor cells derived from ES cells differentiated in vitro using retroviral vectors. This approach led to the generation of hematopoietic stem cell (HSC)-like cell lines suggesting that Lhx2 could impact HSC function. However neither the specificity nor the efficiency of the Lhx2-induced phenotype could be determined using this approach. To be able to elucidate the function of Lhx2 in the hematopoietic system, an ES cell line with inducible Lhx2 expression was generated. Lhx2 expression induces self-renewal of a distinct hematopoietic progenitor cell from which HSC-like cell lines were established. Down-regulation of Lhx2 in these HSC-like cell lines leads to a rapid loss of stem cell character, providing a good model to study the molecular function of Lhx2 in hematopoietic stem/progenitor cells. A global gene expression analysis was performed comparing the Lhx2+ stem cell population to the Lhx2- differentiated progeny. This approach identified genes putatively linked to self-renewal/differentiation of HSCs. A considerable proportion of the genes showed an overlapping gene expression pattern with Lhx2 expression in tissue of non-hematopoietic origin suggesting that Lhx2 function in stem/progenitor cells partly overlap with Lhx2 function during organ development. In order to define other Lhx2-dependent progenitor cell populations and to generate a tool to analyze the function of Lhx2 in organ development a new transgenic mouse model was generated. By using a specific part of the Lhx2 promoter to drive expression of Cre recombinase in vivo (Lhx2-Cre mice) we have been able to define the first eye committed progenitor cells in the forebrain. By using the Lhx2-Cre mice it will be possible to distinguish the function of genes during eye development from their function in the patterning of the forebrain e.g. the eye field transcription factors. Conditional inactivation of Lhx2 in these eye specific progenitor cells causes an immediate developmental arrest. The transgene is also active in Lhx2-/- embryonic forebrain, but re-expression of Lhx2 in Lhx2-/- progenitor cells only promote formation of retinal pigment epithelium cells. Analysis of genes expressed by the Lhx2+ stem cell population allowed us to define novel genes putatively linked to Lhx2 function in eye development. Thus, we have defined the progenitor cells in the forebrain committed to eye development and the expansion and patterning of these progenitors are dependent on Lhx2. Although commitment to eye development is Lhx2-independent, Lhx2 might be important for the acquisition of the oligopotent fate of these progenitor cells.

Le syndrome CHARGE est une maladie génétique rare dont l’acronyme désigne les principales anomalies initialement identifiées pour décrire ce syndrome : colobome, problèmes cardiaques, atrésie des choanes, retard mental et de développement, anomalies génitales et défauts aux oreilles. Les patients présentent des combinaisons hautement variables d’anomalies et ce même entre individus d’une même famille. La principale cause de ce syndrome est une mutation du gène CHD7, mais de nouveaux gènes dont la mutation peut également engendrer ce syndrome, tel FAM172A , ont récemment été identifiés. Le modèle murin Toupee porte une mutation dans le gène Fam172a et présente les principales caractéristiques du syndrome CHARGE. Fait intéressant, si FVBToupee présente dans une forte proportion le colobome oculaire, 55% des individus B6ToupeeTg/Tg et 16% des individus B6ToupeeTg/+ présentent de la microphtalmie et de l’anophtalmie. Ces anomalies oculaires ont tout d’abord été caractérisées. Les études menées ont notamment permis d’identifier que chez B6Toupee la microphtalmie et l’anophtalmie sont beaucoup plus fréquentes dans l’œil droit et qu’elles se déclinent en plusieurs degrés variables d’atteinte au globe oculaire. Par la suite, l’étude comparative des modèles ToupeeTg/Tg et Chd7Gt/+a été réalisée dans les fonds génétiques FVB et C57Bl/6. Des différences significatives de pénétrance de même que des divergences phénotypiques ont permis de déterminer que l’identité du gène à l’origine du syndrome CHARGE et que le fond génétique modulent tous deux le développement phénotypique du syndrome CHARGE. Finalement, l’étude de doubles hétérozygotes FVBToupeeTg/+ ;Chd7Gt/+ a permis de confirmer une interaction génétique modérée entre Fam172a et Chd7 tandis que l’investigation de la mortalité néonatale chez Chd7Gt/+ a permis de suspecter des problèmes d’alimentation. / CHARGE syndrome is a rare genetic disease for which the acronym stands for the main characteristics initially identified to describe the syndrome: coloboma, heart problems, choanal atresia, retarded growth and development, genital anomalies and ear defects. Patients present highly variable combinations of anomalies, even between members of the same family. The main cause of this syndrome is a mutation in the CHD7 gene, but new genes whose mutation can also give rise to this syndrome, such as FAM172A, were recently identified. The Fam172a gene is mutated in the Toupee mouse model, which presents the main characteristics of CHARGE syndrome. Interestingly, while FVBToupee animals present coloboma in a strong proportion, 55% of B6ToupeeTg/Tg individuals and 16% of B6ToupeeTg/+ individuals present microphthalmia and anophthalmia. First, detailed characterization of these ocular anomalies revealed that microphthalmia and anophthalmia are much more frequent in the right eye of B6Toupee mice, with varying degrees of severity. Then, comparative analysis of ToupeeTg/Tg and Chd7Gt/+models in FVB and C57Bl/6 genetic backgrounds further revealed significant differences in penetrance and phenotypic presentation, suggesting that the identity of the causative gene and the genetic background both modulate phenotypic outcome of CHARGE syndrome. Finally, characterization of FVBToupeeTg/+;Chd7Gt/+ double heterozygotes confirmed a moderate genetic interaction between Fam172a and Chd7 while investigations of Chd7Gt/+ neonatal mortality allowed to suspect feeding problems.

<p dir="ltr">The primary purpose of this thesis is to propose and demonstrate BioGRNsemble, a modular and flexible approach for inferencing gene regulatory networks from RNA-Seq data. Integrating the GENIE3 and GRNBoost2 algorithms, this ensembles-of-ensembles method attempts to balance the outputs of both models through averaging, before providing a trimmed-down gene regulatory network consisting of transcription and target genes. Using a Drosophila Eye Dataset, we were able to successfully test this novel methodology, and our validation analysis using an online database determined over 3500 gene links correctly detected, albeit out of almost 530,000 predictions, leaving plenty of room for improvement in the future.</p>