<p>Microarray-based comparative genomic hybridization (array-CGH) has emerged as a versatile platform with a wide range of applications in molecular genetics. This thesis focuses on the development of array-CGH with a specific aim to approach disease-related questions through improved strategies in array construction and enhanced resolution of analysis. In <b>paper I</b>, we applied an array covering 11 Mb of 22q, encompassing the <i>NF2</i> locus, for deletion detection in sporadic schwannoma. Hemizygous deletions and tumor heterogeneity were identified. Array-CGH was established as a reliable platform for detection of DNA dosage alterations. <b>Paper II</b> described the construction of the<i> NF2</i> gene-specific microarray for high-resolution scanning of deletions in the <i>NF2</i> locus. We report a novel PCR-based non-redundant strategy for microarray fabrication, which considerably improved the sensitivity and reliability of deletion detection. <b>Paper III</b> reported the first tiling-path array comprehensively covering a human chromosome. The usefulness of the 22q-array was demonstrated by applying it to detect DNA dosage-alterations in 22q-associated disorders. In <b>paper IV</b>, we optimized array-CGH protocols for deletion detection in 22q11 deletion-syndrome. We showed that genomic and cDNA clones are not optimal for analysis of 22q11 locus and that PCR-based non-redundant strategy is reliable for deletion detection in such regions. In <b>paper V</b>, we utilized the 22q-array for understanding the genetic basis of schwannomatosis. Two commonly deleted regions were identified within the <i>IGL</i> and the <i>GSTT1/CABIN1</i> loci. Further investigations using high-resolution arrays, bioinformatic analysis and mutational screening were performed. Missense mutations, specific to the schwannomatosis- and NF2 samples, were identified in the <i>CABIN1 </i>gene. <b>Paper VI</b> described the first array-CGH study for comprehensive and high-resolution profiling of deletions spanning the 17q11 locus. Both typical and atypical deletions were identified in NF1 samples. Bioinformatic analysis revealed novel segmental duplications, which can potentially mediate 17q11 deletions.</p>

Microarray-based comparative genomic hybridization (array-CGH) has emerged as a versatile platform with a wide range of applications in molecular genetics. This thesis focuses on the development of array-CGH with a specific aim to approach disease-related questions through improved strategies in array construction and enhanced resolution of analysis. In <b>paper I</b>, we applied an array covering 11 Mb of 22q, encompassing the NF2 locus, for deletion detection in sporadic schwannoma. Hemizygous deletions and tumor heterogeneity were identified. Array-CGH was established as a reliable platform for detection of DNA dosage alterations. <b>Paper II</b> described the construction of the NF2 gene-specific microarray for high-resolution scanning of deletions in the NF2 locus. We report a novel PCR-based non-redundant strategy for microarray fabrication, which considerably improved the sensitivity and reliability of deletion detection. <b>Paper III</b> reported the first tiling-path array comprehensively covering a human chromosome. The usefulness of the 22q-array was demonstrated by applying it to detect DNA dosage-alterations in 22q-associated disorders. In <b>paper IV</b>, we optimized array-CGH protocols for deletion detection in 22q11 deletion-syndrome. We showed that genomic and cDNA clones are not optimal for analysis of 22q11 locus and that PCR-based non-redundant strategy is reliable for deletion detection in such regions. In <b>paper V</b>, we utilized the 22q-array for understanding the genetic basis of schwannomatosis. Two commonly deleted regions were identified within the IGL and the GSTT1/CABIN1 loci. Further investigations using high-resolution arrays, bioinformatic analysis and mutational screening were performed. Missense mutations, specific to the schwannomatosis- and NF2 samples, were identified in the CABIN1 gene. <b>Paper VI</b> described the first array-CGH study for comprehensive and high-resolution profiling of deletions spanning the 17q11 locus. Both typical and atypical deletions were identified in NF1 samples. Bioinformatic analysis revealed novel segmental duplications, which can potentially mediate 17q11 deletions.

Indiana University-Purdue University Indianapolis (IUPUI)

Indiana University-Purdue University Indianapolis (IUPUI) / Neurofibromatosis type 1 (NF1) is a neurocutaneous disorder that affects roughly 1 in 3500 individuals. In addition to physical features (e.g., neurofibromas), developmental disorders are also common that can affect cognition, learning, attention and social function. The NF1 gene encodes neurofibromin, a GTPase activating protein (GAP)-like protein that negatively regulates Ras GTPase activation. Mutation at the NF1 locus increases the output of MAPK and PI3K signal transduction from the cellular membrane to the nucleus. Similar to humans, Nf1+/- mice show spatial learning abnormalities that are potentially correlated with increases in GABA-mediated inhibition and deficits in long-term potentiation in the hippocampus. Here, we demonstrate for the first time that Nf1+/- mice exhibit a selective loss of long-term social learning / memory and increased GABAergic inhibition in the basolateral amygdala, a critical brain region for regulating social behaviors. Next, utilizing a genetic intercross, we show that the co-deletion of p21-activated kinase type 1 (Pak1-/-), which positively regulates MAPK activation, restores Nf1+/--dependent MAPK hyperactivation in neurons cultured from the frontal cortex. We found that the co-deletion of Pak1 in Nf1+/- mice (Nf1+/- / Pak1-/-) also restores the deficits in long-term social learning / memory seen in Nf1+/- mice and normalizes the increases in GABA-mediated inhibition in the BLA, as compared to Nf1+/- mice. Together, these findings establish a role for Nf1 and Pak1 genes in the regulation of social learning in Nf1-deficient mice. Furthermore, proteomic studies identify dysregulation of F-actin and microtubule dynamics in the prefrontal cortex, and implicate proteins associated with vesicular release as well as neurite formation and outgrowth (e.g., LSAMP, STXBP1, DREB). In the BLA, disintegrin and metalloproteinase domain-containing protein 22 (ADAM22) was identified, and ADAM22 may play a role in the regulation of AMPA receptors. Finally, due to the increased co-occurrence of NF1 and autism, these findings may also have important implications for the pathology and treatment of NF1-related social deficits and some forms of autism.

Cochlear implants (CIs) and auditory brainstem implants (ABIs) are prostheses for hearing used in patients with profound hearing impairment. A CI requires an operational cochlear nerve to function in contrast to an ABI. ABIs were initially designed for adult patients with neurofibromatosis type 2 (NF2), suffering from bilateral vestibular schwannomas. Now ABIs are also used for patients, both adults and children, with congenital cochlear malformations, cochlear nerve hypoplasia/aplasia, and cochlear ossification. The aims of this thesis are to evaluate hearing outcome in patients implanted with a CI after long-term deafness. An extended period of deafness has earlier been considered as a contraindication for CI surgery. Further, we analyzed if electrically evoked auditory brainstem responses (eABRs) can predict CI outcome and pinpoint the optimal selection of treatment such as CI or ABI. We also disclose our experiences from ABI surgery in Uppsala, such as implant use, hearing outcome, complications, and satisfaction among the patients. Finally, we evaluated the results and benefits of ABIs in non-NF2 pediatric patients. Results show that patients with an extended deafness period and durations over 20 years can achieve speech understanding and benefit from CIs. Patients with long-term deafness and limited years of hearing before deafness did not perform as well as those with shorter deafness duration and longer hearing experience did. eABR seems to have a definite role in the diagnostic armamentarium, to better consider alternative surgical strategies such as ABI. No eABR waveform predicted a poor CI outcome. There was no correlation between speech perception and eABR waveform latencies or eABR waveform quality. A majority of the ABI patients used their ABIs and benefited from them for at least some period. ABI assisted voice control in a majority of the full-time users and they reported improved understanding of speech with the implant switched on. No severe complications from ABI surgery or ABI stimulation were noted. The patients were generally satisfied, even if their hearing remained very limited. All pediatric patients but one used the implant continuously and benefited from it.

La neurofibromatose de type 1 (NF1) est un syndrome de prédisposition tumorale causée par une mutation perte-de-fonction du gène suppresseur de tumeurs NF1. Près de la moitié des patients atteints de NF1 développent un type de tumeurs bénignes des gaines des nerfs périphériques appelés neurofibromes plexiformes. Ces tumeurs sont majoritairement constituées de cellules de Schwann présentant une inactivation somatique du deuxième allèle NF1. Les neurofibromes plexiformes peuvent se transformer en tumeurs malignes dénommées MPNST (Malignant Peripheral Nerve Sheath Tumor) qui sont des sarcomes extrêmement agressifs, résistants aux thérapies actuelles et représentant la première cause de mortalité des patients NF1. A ce jour, les acteurs à l’origine de cette transformation maligne ne sont pas clairement établis. Leur identification représente donc un enjeu majeur pour une prise en charge appropriée des patients et le développement de nouvelles molécules thérapeutiques. Dans ce contexte, le travail mené au cours de ma thèse a eu pour objectifs la recherche et la caractérisation de nouvelles voies de signalisations impliquées dans la tumorigenèse NF1. D’une part, une approche orientée par les travaux antérieurs au laboratoire a permis de montrer l’implication de la voie WNT dans la tumorigenèse NF1. D’autre part, une approche génomique plus large a conduit à la mise en évidence de l’inactivation du répresseur transcriptionnel PRC2 (Polycomb Repressive Complex 2) dans près de la moitié des MPNST. La génération de modèles cellulaires in vitro a facilité l’exploration des gènes surexprimés lors de la perte de fonction du PRC2. Elle a également permis d’entreprendre un crible lentiCRISPR pan-génomique à la recherche des gènes essentiels à la survie des cellules tumorales mutées pour le PRC2. / Neurofibromatosis type 1 (NF1) is a tumor predisposition syndrome caused by loss-offunction mutations in the NF1 tumor suppressor gene. Almost half of NF1 patients develop a specific type of benign peripheral nerve sheath tumor called plexiform neurofibromas. These tumors are mainly composed of Schwann cells in which the second NF1 allele is inactivated. Plexiform neurofibromas can give rise to malignant tumors called MPNST that are extremely aggressive sarcomas, resistant to therapy and which represents the first cause of early demise of NF1 patients. The molecular mechanisms underlying this malignant transformation remain enigmatic. Their identification is crucial for appropriate management of NF1 patients and development of new therapies. The goal of my PhD was to identify and characterize new signaling pathways involved in NF1 tumorigenesis. On the one hand, we highlighted the involvement of WNT pathway in NF1 tumorigenesis. On the other hand, a larger genomic approach led to the identification of the transcriptional repressor PRC2 (Polycomb Repressive Complex 2) inactivation in almost half of MPNST. We have generated various cell models, which facilitated the exploration of genes aberrantly expressed consequently to PRC2 loss-offunction. These models also allowed performing a pan-genomic lentiCRISPR screen searching for essential genes for PRC2-mutated tumor cells survival.

Made available in DSpace on 2016-01-26T12:51:17Z (GMT). No. of bitstreams: 1 joaorobertoantonio_tese.pdf: 4793958 bytes, checksum: 56e42b3687617eb1ad6580c037e8fee1 (MD5) Previous issue date: 2001-08-30 / Neurofibromatosis (NF) is a neuroectodermal abnormality composed of a set of conditions having clinical manifestations which mainly affect the skin, eyes, bones, nervous system and eventually have repercussions on other internal organs. Its inheritance pattern is normally autosomally dominant and it has been considered one of the most frequent genetic diseases in the human race with a high penetration and variable expressiveness. This work studies the genetical-clinical aspects, makes a quantitative evaluation of the mastocytes and the extracellular matrix in neurofibromas in a group of thirty patients diagnosed with NF-1 and makes a comparison with a control group of ten normal individuals. The genetical-clinical evaluation confirmed the diagnosis of type 1 NF (NF-1) in all the patients. The main characteristics were neurofibromas, caféau-lait spots (CLS), Lisch nodules and axial or inguinal freckles. The multiple neurofibromas and Lisch nodules were considered to be exclusive to NF-1. Macrocephaly, in isolation, was not sufficient for the diagnosis of NF-1 and the other characteristics observed were considered complications. With the tissue from biopsies of both normal skin and neurofibromas of these patients, ten histologic sections were obtained. These were stained using hematoxylin-eosine, Gömöri trichrome, pricrosirius-hematoxylin, silver and iron-hematoxylin impregnation to evaluate the components of the extracellular matrix and staining using Toluidine blue to count the mastocytes. There was a significant increase in the number of mastocytes and the extracellular matrix was altered compared to the normal skin. This alteration was seen by the high cellularity associated with an increased density of fibrous components, specifically collagen type III, the scarcity or almost nonexistence of amorphous fundamental substance and the lack of elastic tissue. These findings seem to have an important role in the formation of neurofibromas and can help in the treatment of NF. / A Neurofibromatose (NF), é uma anormalidade neuroectodérmica constituída por um conjunto de condições com manifestações clínicas que comprometem principalmente a pele, olhos, ossos, sistema nervoso e, eventualmente, com repercussões aos outros órgãos internos. Seu padrão de herança é autossômica dominante e tem sido considerada uma das mais freqüente na espécie humana com penetrância elevada e expressividade variável. No presente trabalho, estudou-se os aspectos genético-clínicos, realizou-se a avaliação quantitativa dos mastócitos e da matriz extracelular em neurofibromas de um grupo de 30 pacientes diagnosticados como NF-1 e comparou-se com o grupo controle constituído de 10 indivíduos normais. A avaliação genético-clínica confirmou o diagnóstico de NF-1 em todos os pacientes. As características principais ou major foram os neurofibromas, MCCL, nódulo de Lisch e sardas axilares ou inguinais. Os neurofibromas múltiplos e os nódulos de Lisch foram considerados exclusivos de NF-1. A macrocefalia, quando isoladamente, não demonstrou ser suficiente para o diagnóstico de NF1 e as outras características foram consideradas como complicações. Em material obtido de biópsias de pele normal e de neurofibromas desses pacientes, realizou-se 10 cortes histológicos os quais foram submetidos às técnicas de coloração pela hematoxilina-eosina, tricrômio de gomori, tricrômio do pricrosirius-hematoxilina, impregnação pela prata e hematoxilinaférrica para a avaliação dos componentes da matriz extracelular e pela coloração com o azul de toluidina para a contagem de mastócitos. Houve diferença significativa no número dos mastócitos que encontraram-se aumentados e, quanto a matriz extracelular, apresentou-se alterada em comparação com a pele normal pela alta celularidade associada à elevada densidade dos componentes fibrosos, particularmente do colágeno tipo III, com escassez ou quase ausência de substância fundamental amorfa e ausência de material elástico. Tais achados parecem ter um papel significativo na formação dos neurofibromas e podem colaborar na terapêutica da NF.

Merlin is a tumour suppressor protein that is frequently mutated or downregulated in cancer. Biallelic Merlin inactivation is causative of tumour formation, including schwannoma, meningioma and ependymoma. These tumours can occur sporadically or as part of the genetic condition Neurofibromatosis type 2 (NF2) and cause significant morbidity. The current treatment options are restricted to surgery and radiotherapy, which are invasive and may cause further tumour development. The activity of both the E3 ubiquitin ligase complex Cullin 4 really interesting new gene (RING) E3 ubiquitin ligase- DNA damage binding protein (DDB1) and Cullin 4 associated factor 1 (CRL4-DCAF1) and Kinase suppressor of RAS 1 (KSR1) have been shown to be upregulated in schwannoma to drive tumour growth. KSR1 has also been shown to interact with components of the CRL4-DCAF1 complex. We investigated the expression, interaction and therapeutic potential of targeting these proteins in Merlin deficient schwannoma and meningioma using a primary human cell model and relevant cell lines. We found that DCAF1 and KSR1 protein were overexpressed in schwannoma and meningioma and confirmed that targeting both DCAF1 and KSR1 in meningioma had additive effects on proliferation. We also identified that CRL4-DCAF1 facilitates KSR1 dependent RAF/Mitogen-activated protein kinase (MAPK)/ Extracellular signal regulated kinase (ERK) kinase (MEK)/ERK pathway activity. We showed MLN3651, a neddylation inhibitor that targets ubiquitin ligase activity, reduced proliferation and activated apoptosis in Merlin-deficient tumours. We also showed that Merlin-positive tumours were less sensitive to MLN3651 than Merlin-deficient tumours; therefore, MLN3651 sensitivity may be CRL4-DCAF1-dependent. Finally, combination of MLN3651 and the MEK1/2 inhibitor AZD6244 had additive effects, particularly in meningioma. Combinatorial therapy activated the Hippo pathway, inhibited RAF/MEK/ERK pathway activity and proliferation demonstrating that targeting the activity and downstream pathways of both DCAF1 and KSR1 represents an attractive novel therapeutic strategy in Merlin-deficient tumours.

No description available.

Contexte : Le schwannome vestibulaire (SV) est une tumeur bénigne de la gaine du nerf vestibulaire. La plupart des SV présentent une inactivation somatique bi-allèlique du gène suppresseur de tumeur NF2. L’inactivation congénitale du gène NF2 est impliquée dans le développement de la Neurofibromatose de type 2, une maladie génétique autosomique dominante prédisposant au développement de tumeurs multiples du système nerveux central et en particulier de schwannomes vestibulaires bilatéraux. Le traitement des schwannomes vestibulaires repose sur la chirurgie ou la radiothérapie délivrée en conditions stéréotaxiques. La réduction de la dose d’irradiation des schwannomes vestibulaires a permis d’améliorer le pronostic fonctionnel auditif tout en garantissant un taux de réponse satisfaisant. Pourtant de nombreux patients présenteront une surdité neurosensorielle progressive. Afin de poursuivre cette réduction de dose d’irradiation, des modèles biologiques fidèles récapitulant le statut d’inactivation du gène NF2 et la surdité neurosensorielle sont nécessaires à l’élaboration d’une approche préclinique.Problématique : Nous avons proposé de développer des systèmes modèles in-vitro et in-vivo compatibles avec l’étude de la radiosensibilité des schwannomes vestibulaires en combinaison avec des thérapies ciblant les voies de signalisation spécifiquement activées par la perte de fonction NF2.Méthodes : Les lignées cellulaires humaines de schwannomes vestibulaires NF2 (HEI_193, HEI_182), et de cellules de Schwann vestibulaire contrôle (HEI_286) ont été cultivées en essai clonogénique afin de déterminer le nombre d’unité formatrices de colonies à doses croissantes d’inhibiteur mTOR (Rapamycine), PI3K (GDC_0941), mTOR et PI3K (BEZ_235) pour déterminer le 50% d’inhibition de croissance (GI50%) puis en combinaison à doses croissantes de radiation gamma (Co60). La lignée cellulaire murine inactivée pour nf2 (SC4#9) a été utilisée pour réaliser des greffes syngéniques orthotopiques. La croissance des tumeurs a été suivie par IRM et bioluminescence et l’audition déterminée par potentiels évoqués auditifs. L’analyse histologique des cochlées a été réalisée par coloration en hématoxyline et éosine puis par fluorescence après clarification cochléaire. Des volumes complets ont été obtenus par microscopie confocale à balayage laser.Résultats : Les essais clonogéniques réalisés en Agarose ont identifié une radiorésistance relative des lignées humaines de schwannomes mutées pour NF2 par comparaison au contrôle humain non muté. Cette résistance identifiée en réponse à l’exposition à une dose unique d’irradiation gamma peut être contournée par l’inhibition de la voie mTOR au moment de l’irradiation restituant une sensibilité comparable au contrôle humain non muté. Une tendance à un bénéfice de l’association d’une inhibition mTOR à un inhibiteur PI3 kinase a été retrouvée à une dose maximum d’irradiation. Un modèle murin de schwannome vestibulaire qui récapitule la croissance dans l’angle ponto-cérébelleux et la perte d’audition a été développé par injection stéréotaxique dans le paquet acoustico faciale. Le suivi de croissance de ce schwannome a été caractérisé par IRM et bio-luminescence in-vivo. Enfin un protocole de clarification cochléaire a été adapté aux mammifères murins pour permettre l’étude histologique de cochlées intactes compatible avec l’étude de l’otoxicité des schwannomes et/ou de leur traitement .Conclusion : Les modèles décrits dans cette thèse permettent l’évaluation pré-clinique de stratégies thérapeutiques combinant thérapie ciblée et irradiation gamma en dose unique. L’amélioration des connaissances des mécanismes participant à l’ototoxicité des schwannomes et de leur traitement permettra d’améliorer le ciblage moléculaire afin de réduire les effets auditifs secondaires de la radiochirurgie. / Context: Vestibular schwannomas (VS) are benign neoplasm arising from the Schwann cells of the vestibular nerve. Most of sporadic VS carry a bi-allelic inactivation of the tumor suppressor gene NF2. Congenital inactivation of the NF2 gene is linked to the onset of Neurofibromatosis type 2 (NF2), a genetic condition predisposing to the development of multiple benign tumor of the central nervous system with bilateral VS as a hallmark. Treatment of VS is either surgical or by use of radiation therapy delivered in stereotactic condition. A significant dose reduction has led to improving the hearing outcomes while maintaining good tumor control. Meanwhile a significant number of treated patients will develop a progressive sensorineural hearing loss (SNHL). Laboratory models that faithfully recapitulate NF2 gene inactivation and SNHL are needed to pursue the reduction of the dose delivered.Aim: We aimed at developing new models in-vitro and in-vivo for the study of vestibular schwannoma radio sensitivity in combination with selected compounds that selectively target the pathways activated secondary to NF2 loss of function.Methodes: Human vestibular schwannoma cell lines (HEI_193, HEI_182) and control human Schwann cell line (HEI_286) were used in clonogenic assay to determine the number of colony forming unit (CFU) spontaneously and at increasing dosing of mTOR inhibitor (Rapamycin), PI3 kinase inhibitor (GDC_0941), PI3K-mTOR dual inhibitor (BEZ_235) to determine the 50% growth inhibitory threshold (GI50%) then in combination with increasing radiation regimen of gamma radiation emitted by a source of Co60. The mouse cell line inactivated for nf2 (SC4#9) was used to generate orthotropic syngrafts. The growth of the tumor was monitored using MRI and bioluminescence imaging and hearing was tested by recording auditory brainstem responses. Pathology of the cochlea were obtained from paraffin embedded sections and then using fluorescence confocal microscopy of whole mounted transparent cochleae.Results: Soft agar clonogenic assays were used and identified a resistance to radiation therapy in human cell lines of VS inactivated for NF2 when compared to the non-mutated control. This radiation resistance could be overcome by pre-exposure to the mTOR inhibitor Rapamycin allowing a return to the radiosensibility of non-mutated control. There was a tendency toward a beneficial effect when using a dual inhibition of the mTOR and PI3 kinase at a maximum dose of exposure to radiation. A mouse model of VS has been developed by stereotactic seeding of nf2 deficient cell line SC4#9 targeting the cochleo-vestibular nerve complex. It recapitulates the growth in the suitable micro-environment and secondary SNHL. The growth has been characterized using MRI and in-vivo bioluminescence imaging. Hearing loss was confirmed using sequential ABR. Last a protocol for the clarification of whole mounted cochleae has been adapted to species of rodents suitable for the pathological study of ototoxic change secondary to VS and/or its treatment.Conclusion: The models presented in this thesis may be used for the preclinical evaluation of combined therapeutic approaches with single dose gamma radiation. A better understanding of the mechanisms involved in ototoxicity secondary to VS and of its treatment would improve the molecular targeting in order to warrant better auditory outcomes.