This qualitative study investigated the remembered lived experiences of six individuals who were diagnosed with Usher syndrome, the effect that the progressive condition had upon their lives, and their experiences with vocational rehabilitation. Usher syndrome is an autosomal recessive condition that presents as deafness or hearing loss with comorbid retinitis pigmentosa sometimes with vestibular areflexia. The participants recalled details of their own reaction to the diagnoses as well as the reactions of their parents. Themes were identified in their responses that included independent dependence, Usher support, parental reaction, lowered expectations, hope, and ongoing change. The participants, three men and three women, reported periods of adjustment and sadness as well as hopes for their future, career accomplishments, and social interactions.

Retinitis Pigmentosa (RP) refers to a group of inherited retinal dystrophies resulting from progressive photoreceptor degeneration and accumulation of intra-retinal pigment-like deposits. X-linked forms of RP are frequently caused by mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene. The RPGR transcript undergoes complex alternative splicing to express both constitutive (RPGR^ex1-19) and RPGR^ORF15 variants. Although RPGR is thought to play a role in ciliary function, little is known about the physiological significance of expressing two distinct groups of variants. This study compares Rpgr^ex1-19 and Rpgr^ORF15 expression in developing photoreceptors using immunoblot analysis and immunohistochemistry, assesses ciliary affinity in adult photoreceptors by protein fractionation, examines Rpgr function in transgenic mouse models and identifies a novel Rpgr^ORF15 binding partner using a yeast two-hybrid screen. Our data reveal that Rpgr expression undergoes dynamic temporal regulation during retinal development and indicates variability in ciliary localization of Rpgr variants in adult photoreceptors. Utilization of distinct Rpgr variants during stages of photoreceptor development suggests independent roles. Further examination of Rpgr function using transgenic mouse models over-expressing either the Rpgr^ex1-19 or Rpgr^ORF15 variant reveals that despite normal ciliary localization, an excess of RPGR^ex1-19 results in atypical accumulation of Rpgr in photoreceptor outer segments, abnormal photoreceptor morphology and severe retinal degeneration. The data indicate that the constitutive variant cannot substitute for Rpgr function in photoreceptors and suggest that proper maintenance of the Rpgr isoform ratio is critical to photoreceptor viability. Using mouse retinal cDNA in a yeast two-hybrid screen with the C-terminus of the Rpgr^ORF15 variant, we identified a novel variant of whirlin as an interacting partner. Mutations in whirlin result in Usher syndrome, a disorder characterized by hearing loss and RP. RT-PCR and immunoblot analysis were used to confirm the presence of selected candidate partners in the retina and interaction was confirmed by pull-down assays and co-immunoprecipitation from retinal homogenate. Immunohistochemistry showed co-localization of RPGR and whirlin within photoreceptors and identified isoform specific localization of whirlin. These findings indicate that whirlin binds Rpgr^ORF15 and that this novel isoform may be required for photoreceptor function, thus providing a potential mechanism for the RP phenotype observed in Usher syndrome.

No description available.

Le syndrome de Usher (USH) est une maladie transmise selon le mode autosomique récessif caractérisée par l’association d’une surdité congénitale (HL) et d’une rétinite pigmentaire (RP), et dans certains cas, d’une aréflexie vestibulaire. Une hétérogénéité clinique et génétique est reconnue. Environ 10 % des cas USH restent non résolus après analyse moléculaire exhaustive des différents gènes. Ces cas incluent les patients qui ne portent aucune mutation dans un des gènes USH connus ainsi que les patients porteurs d’une seule mutation dans un gène USH. Au cours de cette thèse, nous nous sommes intéressés à l’étude des patients porteurs d’une seule mutation dans les gènes USH2A et PCDH15.Dans la première partie de la thèse, nous avons analysé une cohorte de patients avec un phénotype USH2A bien défini : 5 patients pour lesquels une seule mutation à l’état hétérozygote avait été identifiée dans le gène USH2A et un patient porteur d’un variant silencieux en trans d’une mutation non-sens.Pour les 5 patients, nous avons émis l’hypothèse que la seconde mutation, restant à être identifiée, pourrait se trouver dans des régions introniques profondes. Pour cela, nous avons développé une approche de séquençage à haut débit (NGS) de l’ADN pour identifier les variants introniques profonds dans le gène USH2A et évaluer leurs conséquences sur l’épissage. Comme preuve de concept et pour valider l’approche, y compris le pipeline bio-informatique et l’évaluation des outils de prédiction de l’épissage, nous avons analysé un patient porteur d’un pseudoexon (PE) connu dans le gène USH2A. Ensuite, les 5 patients ont été étudiés en utilisant le pipeline défini, ce qui a conduit à l’identification de 3 nouveaux variants introniques profonds chez 4 d’entre eux. Tous les variants ont été prédits comme pouvant avoir un impact sur l’épissage et aboutir à l’insertion de PE. Ces prédictions ont été validées par les essais minigènes. Grâce à cette étude, nous présentons une stratégie innovante pour identifier les mutations introniques profondes, lorsque l’analyse des transcrits n’est pas possible. Par ailleurs, le pipeline bio-informatique développé fonctionne indépendamment de la taille du gène analysé, ce qui permet l’application possible de cette approche à n’importe quel gène. Par ailleurs, un oligonucléotide antisens de type morpholino (AMO) a été évalué in vitro afin de rétablir l’altération d’épissage induite par une des mutations identifiées. Les résultats ont montré un taux d’exclusion élevé du transcrit aberrant et suggèrent une application possible en thérapie moléculaire. Nous avons ensuite effectué des études sur le variant USH2A c.1377T>A, un variant silencieux afin d’évaluer son effet sur l’épissage. L’analyse de l’ARN issu de cellules nasales du patient a montré que ce variant conduit au saut de l’exon 8 dans les transcrits USH2A. Ceci a été confirmé par un essai minigène. En outre, des études préliminaires ont été réalisées en utilisant des outils de prédictions et des essais minigènes pour évaluer l’implication des éléments cis-régulateurs dans le défaut d’épissage observé chez le patient. Dans la deuxième partie de la thèse, nous avons analysé une patiente USH1, pour laquelle une seule mutation avait été identifiée dans le gène PCDH15. Dans ce cas, nous avons combiné la culture des cellules épithéliales nasales avec l’analyse des transcrits PCDH15. Celle-ci a été réalisée par séquençage de cinq RT-PCR chevauchantes. Grâce à cette analyse, nous avons réussi à délimiter une région d’intérêt dans le transcrit, dont l’amplification a échoué exclusivement pour l’allèle porteur de la mutation non identifiée. D’autres analyses ont été effectuées dans la région génomique correspondante par capture ciblée couplée au séquençage NGS et LongRange PCR suivi de séquençage Sanger. Cependant, aucun variant candidat n’a été identifié à ce jour. Nous suggérons l’implication de mécanismes moléculaires complexes qui restent à être caractérisés. / Usher syndrome (USH) is an autosomal recessive disorder characterized by the association of sensorineural hearing loss (HL) and retinitis pigmentosa (RP), and in some cases, vestibular areflexia. Clinical and genetic heterogeneity are recognised. Indeed, three clinical types can be caused by mutations in one of the 10 known genes and USH2A represents the most frequently involved gene.Approximately 10 % of the USH cases remain genetically unsolved after extensive molecular analysis of the different genes, which includes sequencing of the exons and their intronic boundaries, combined to large rearrangements screening by array CGH. These unsolved cases include patients who do not carry any mutation in any of the known USH genes and patients who carry a single USH mutation. During this thesis we focalised on the study of patients carrying a single mutation in USH2A and PCDH15 gene.First, we have analysed a cohort of well-defined USH2A patients: five patients, for whom a single USH2A heterozygous mutation had been identified and one patient carrying a silent variant in trans to a nonsense mutation. For the 5 patients, we supposed that the second mutation remaining to be found could be localised deep in the introns. Indeed, a deep intronic mutation resulting in the inclusion of a pseudoexon (PE 40) in USH2A transcripts had been identified, following RNA analysis from nasal cells. Unfortunately, analysing USH2A transcripts still represent a challenging approach in a diagnostic settings and it is not always possible. To circumvent this issue, we have developed a DNA-Next Generation Sequencing (NGS) approach to identify deep intronic variants in USH2A and evaluate their consequences on splicing. As a proof of concept and to validate this approach, including the bioinformatics pipeline and the assessment of splicing predictor tools, the patient carrying the PE 40 was analysed at first. Then, the 5 patients were studied using the defined pipeline, which led to the identification of 3 distinct novel deep intronic variants in 4 of them. All were predicted to affect splicing and resulted in the insertion of PEs, as shown by minigene assays. Through this study, we present a new and attractive strategy to identify deep intronic mutations, when RNA analyses are not possible. In addition, the bioinformatics pipeline developed is independent of the gene size, implying the possible application of this approach to any disease-linked gene. Moreover, an antisense morpholino oligonucleotide (AMO) tested in vitro for its ability to restore the splicing alterations caused by one of the identified mutation provided high inhibition rates. These results are indicative of a potential application for molecular therapy.In the second case, we have performed studies on the USH2A c.1377T>A silent variant to investigate its effect on splicing. Analysis of RNA from nasal cells of patients showed that this variant led to the skipping of exon 8 in USH2A transcripts. This was confirmed by minigene assay. Moreover, preliminary studies have been performed using prediction tools and minigene assays to assess the involvement of cis-acting elements in causing the aberrant splicing.In the second part of the thesis, we have analysed an USH1 patient, for whom only one mutation had been identified in the PCDH15 gene. In this case, we combined nasal epithelial cells culture with the analysis of the PCDH15 transcripts. This was performed by sequencing five overlapping RT-PCRs. Through this analysis, we were able to delimit a region within the transcript, which failed to be amplified exclusively in the allele carrying the unidentified mutation. Further analyses have been performed in the corresponding genomic region by NGS-target capture and LongRange PCR associated with Sanger sequencing. However, no evident mutation has been identified so far. Therefore, we suggest the involvement of complex molecular mechanisms that remain to be characterised.

Deafness is the most common sensory deficit in humans, affecting 278 million people worldwide. Non-syndromic hearing loss (NSHL), hearing loss not associated with other symptoms, is the most common type of hearing loss and most NSHL in developed countries is due to a genetic cause. The inner ear is a remarkably complex organ, and as such, there are estimated to be hundreds of genes with mutations that can cause hearing loss. To date, 62 of these genes have been identified. This extreme genetic heterogeneity has made comprehensive genetic testing for deafness all but impossible due to low-throughput genetic testing methods that sequence a single gene at a time. The human genome project was completed in 2003. Soon after, genomic technologies, including massively parallel sequencing, were developed. MPS gives the ability to sequence millions or billions of DNA base-pairs of the genome simultaneously. The goal of my thesis work was to use these newly developed genomic technologies to create a comprehensive genetic testing platform for deafness and use this platform to answer key scientific questions about genetic deafness. This platform would need to be relatively inexpensive, highly sensitive, and accurate enough for clinical diagnostics. In order to accomplish this goal we first determined the best methods to use for this platform by comparing available methods for isolation of all exons of all genes implicated in deafness and massively parallel sequencers. We performed this pilot study on a limited number of patient samples, but were able to determine that solution-phase targeted genomic enrichment (TGE) and Illumina sequencing presented the best combination of sensitivity and cost. We decided to call this platform and diagnostic pipeline OtoSCOPE®. Also during this study we identified several weaknesses with the standard method for TGE that we sought to improve. The next aim was to focus on these weaknesses to develop an improved protocol for TGE that was highly reproducible and efficient. We developed a new protocol and tested the limits of sequencer capacity. These findings allowed us to translate OtoSCOPE® to the clinical setting and use it to perform comprehensive genetic testing on a large number of individuals in research studies. Finally, we used the OtoSCOPE® platform to answer crucial questions about genetic deafness that had remained unanswered due to the low-throughput genetic testing methods available previously. By screening 1,000 normal hearing individuals from 6 populations we determined the carrier frequency for non-DFNB1 recessive deafness-causing mutations to be 3.3%. Our findings will also help us to interpret variants uncovered during analysis of deafness genes in affected individuals. When we used OtoSCOPE® to screen 100 individuals with apparent genetic deafness, we were able to provide a genetic diagnosis in 45%, a large increase compared to previous gene-by-gene sequencing methods. Because it provides a pinpointed etiological diagnosis, genetic testing with a comprehensive platform like OtoSCOPE® could provide an attractive alternative to the newborn hearing screen. In addition, this research lays the groundwork for molecular therapies to restore or reverse hearing loss that are tailored to specific genes or genetic mutations. Therefore, a molecular diagnosis with a comprehensive platform like OtoSCOPE® is integral for those affected by hearing loss.

La vue et l'ouïe font intervenir des cellules capables de rapidement traduire une onde, lumineuse ou sonore, en un message électrochimique transmissible au cerveau. La fonction de ces cellules sensitives repose sur leurs morphologies uniques. Les mutations de onze gènes sont la cause des syndromes Usher, associant cécité et surdité. Les protéines Usher sont indispensables à l'architecture de ces deux types cellulaires ; elles forment des complexes dont les interactions clés sont maintenues principalement par des domaines PDZ. L'une des protéines centrales de ce réseau est la Whirline, une protéine multi-domaine contenant trois domaines PDZ. Pour comprendre les bases moléculaires des syndromes Usher, nous nous sommes concentrés sur la caractérisation biochimique et biophysique de la Whirline. Nous avons identifié un nouveau domaine HHD2 de la Whirline dont nous avons obtenue la structure à haute résolution et déterminé le comportement en solution, isolé et avec les domaines adjacents. Nous avons ensuite caractérisé un supramodule transitoire entre deux domaines PDZ, maintenu par des extensions structurées de chacun des domaines. Nous avons résolu la structure de la conformation compacte unique de ce complexe et étudié son équilibre avec un ensemble de conformations étendues. Nous avons enfin caractérisé in vitro le réseau d'interaction des domaines PDZ de la Whirline avec les protéines Usher. L'ensemble de nos résultats sur la structure modulaire et l'interactome de la Whirline permet de mieux comprendre le rôle de la Whirline dans les différents complexes Usher et d'expliquer les conséquences de ses mutations sur les mécanismes moléculaires de l'audition et de la vision. / Vision and hearing rely on the capacity of cells to rapidly transduce electromagnetic waves or sound waves into chemical messages that are transmissible to the brain. The function of these sensory cells requires unique morphologies. The mutations of eleven genes are responsible for Usher syndromes, associating blindness and deafness. The Usher proteins are pivotal to the architecture of the photoreceptor and hearing cells. They form complexes in which the critical interactions are mainly maintained by PDZ domains. One of these central proteins is Whirlin, a multi-domain protein encompassing three PDZ domains. To understand the molecular basis of the Usher syndromes, we focused our project on the biochemical and biophysical characterization of Whirlin. We identified a new HHD2 domain on Whirlin, for which we solved the structure at high resolution and determined the behavior in solution, isolated or with adjacent domains. We then identified a transient supramodule between two PDZ domains, maintained by PDZ structured extensions. We determined the structure of the compact and unique conformation of this tandem and we characterized its equilibrium with an ensemble of more extended conformations. Finally, we characterized in vitro the network of interaction of the PDZ domains of Whirlin, with the majority of the Usher proteins. Our results on the modular structure and the interactome of Whirlin get insight into the role of Whirlin in the numerous complexes formed by the Usher proteins and allow to better explain the consequences of its mutation on the molecular mechanisms of hearing and vision.

Human histidyl-tRNA synthetase (HARS) is an aminoacyl-tRNA synthetase (AARS) that catalyzes the attachment of the amino acid histidine to histidyl-tRNA (tRNAHis) in a two-step reaction that is essential for protein translation. Currently, two human diseases, Usher Syndrome IIIB (USH3B) and an inherited peripheral neuropathy, Charcot Marie Tooth Syndrome (CMT), have been linked genetically to single point mutations in the HARS gene. The recessive HARS USH3B mutation encodes an Y454S substitution localized at the interface between the anticodon-binding domain and the catalytic domain of the opposing subunit. Patients with Usher Syndrome IIIB lose their sight and hearing during their second decade of life, and clinicians have observed that the onset of deafness and blindness may be episodic and correlate with febrile illness. Furthermore, some young USH3B patients present with a fatal form of acute respiratory distress. In addition to the single HARS mutation linked to Usher Syndrome, eight other mutations in the HARS gene are associated with CMT, an inherited peripheral neuropathy. Peripheral neuropathies are associated with progressive and length-dependent damage of the motor and sensory neurons that transmit information to the spinal cord. The age of onset and phenotypic severity of CMT linked to HARS is highly variable. When expressed in a yeast model system, the HARS variants are dominantly lethal, and confer defects in axonal guidance and locomotor deficiencies when expressed in C.elegans. Here, the biochemical characterization of the HARS USH3B and three peripheral neuropathy variants are described. The approaches included enzyme kinetic analysis with purified HARS enzymes to monitor catalytic deficiencies, differential scanning fluorimetry (DSF) to evaluate structural instability, and cellular models to detect physiological effects of axonal outgrowth by CMT variants. The results suggest that Usher Syndrome IIIB is unlikely to be a consequence of a simple loss of aminoacylation function, while HARS-linked peripheral neuropathy variants all share common catalytic defects in aminoacylation. The HARS system represents a notable example in which two different complex human diseases arise from distinct mutations in the same parent gene. By understanding the biochemical basis of these inherited mutations and their link to Usher Syndrome and CMT, it may be possible to develop mechanism-based therapies to improve the quality of life of patients afflicted with them.

Le syndrome d’Usher (USH) cause une surdité-cécité chez l’homme. Au moins neuf gènes responsables ont été identifiés. L’origine de l’atteinte auditive a été dévoilée par l’analyse de souris mutantes, mais les causes de la cécité sont encore obscures. Néanmoins, unes des protéines de Usher, la myosine VIIa, a été impliquée dans le transport intracellulaire dans les photorécepteurs. Pour mieux comprendre le rôle dans la rétine, j’ai étudié l’un de ses partenaires, la spectrine βV. Nous avons conclu que cette spectrine, en collaboration avec les protéines USH1, est impliquée dans le trafic cellulaire: elle couple les moteurs (myosine VIIA, kinesine II et le complexe dynéine/dynactine) à leurs cargos en route vers le segment externe des photorécepteurs. La combinaison d’études comparatives dans les cellules ciliées (CC) de l'oreille interne de grenouille et de souris, de tests biochimiques et d’analyses phylogénétiques indique que le transport vers et depuis la surface apicale des cellules est la fonction ancestrale de cette spectrine. Chez les mammifères, une pression évolutive a engendré le recrutement de la spectrine βV à la paroi latérale des CC externes auditives, probablement pour participer à une nouvelle fonction: l’électromotilité. Enfin, j’ai étudié l’origine de la surdité dans le syndrome d’Usher III. Le seul gène causal connu est CLRN1, qui code pour la clarine-1. Nous avons conclu que la clarine-1 est nécessaire à la maturation et le maintien des touffes ciliaires des CC. De plus, la clarine-1 est essentielle pour le regroupement des canaux calciques voltage-dépendants au voisinage immédiat de la machinerie exocytotique de la synapse à ruban des CC internes. / Usher syndrome (USH) causes a combined deafness-blindness in humans. At least nine causative genes are known. While the analysis of USH knockout mice has shed light on the origin of the auditory deficit, the causes of vision loss are still unclear. Nevertheless, USH1B protein, myosin VIIa, appears to contribute to intracellular traffic in photoreceptor cells. To better understand the role of this myosin in the retina, I studied the functions of its interacting partner, spectrin βV. We found that spectrin V, along with USH1 proteins, participates in intracellular transport by coupling motor proteins (myosin VIIa, kinesin II, dynein/dynactin complex) to the cargoes en route towards the outer segment of photoreceptor cells. Evidence from comparative studies in frog and mouse inner ear, biochemical assays and phylogenetic analyses point to cargo trafficking to and from the apical cell region, as the likely ancestral function of this spectrin. Our analyses also suggest that evolutionary pressures in the mammalian lineage drove the recruitment of spectrin βV to the lateral wall of auditory outer hair cells, probably to support a new function: electromotility. Finally, I explored the origin of hearing loss in Usher syndrome of type III (USH3). So far, the only causal gene known is CLRN1, which codes for clarin-1. The comparative characterization of two Clrn1 mouse mutants revealed that clarin-1 is required for the maturation and maintenance of the hair bundle in the hair cells. Moreover, our results indicate that clarin-1 is also essential to cluster the voltage-gated Ca2+ channels in close proximity to the exocytotic machinery of the ribbon synapse of inner hair cells.

Les photorécepteurs sont des neurones très spécifiques dédiés à la phototransduction et reposant sur une machinerie cellulaire très complexe. La dépolarisation permanente dans le noir des photorécepteurs déclenche une transmission synaptique constante et extrêmement spécifique qui requièrent une quantité d'énergie considérable. Les photorécepteurs peuvent dégénérer lorsque la phototransduction ou l'apport énergétique sont altérés. Le syndrome d'Usher conduit à une surdité et une cécité. La recherche du rôle des protéines usher dans les photorécepteurs a été freinée par l'absence de phénotype rétinien dans les modèles. De la même façon, la compréhension des mécanismes moléculaires conduisant à l'atteinte des cônes dans la rétinopathie diabétique a été entravée par l'absence de symptômes vasculaires et neuronaux dans les modèles. Durant ma thèse, j'ai caractérisé deux modèles animaux des syndromes Usher et HANAC. Des atteintes neuronales ont été démontrées par électrorétinogramme et par l'observation de changements morphologiques des cellules. Dans les modèles Usher, j'ai également montré une neuroprotection des photorécepteurs par plusieurs stratégies. Dans le modèle HANAC, les atteintes neuronales étaient associées à une tortuosité vasculaire anormale une augmentation de la perméabilité vasculaire et l'expression accrue de VEGF. Les évaluations phénotypiques de ces trois modèles fournissent un nouvel aperçu de la physiopathologie des dégénérescences des cônes dans le syndrome d'Usher et dans les maladies vasculaires complexes. Ce travail ouvre surtout la voie au développement et à l'évaluation de nouvelles stratégies thérapeutiques pour ces maladies menant à la cécité. / Photoreceptors are very specific neurons dedicated to phototransduction, which relies on very complex machinery. The maintained depolarization in darkness triggers a constant and thus very specific type of synaptic transmission. These require high energy need. As a consequence, photoreceptors can degenerate in various hereditary retinal diseases when phototransduction or energy consumption are altered. The Usher syndrome is such a hereditary disease leading to both deafness and blindness. If Usher proteins are involved in the mechanotransduction in hair cells, investigating their role in photoreceptors has been hamperedby the lack of a retinal phenotype in murine models. Similarly, understanding themolecular mechanisms of cone dysfunction in diabetic retinopathy has beenhampered by the lack of vascular and neuronal symptoms and neuronal models. During my PhD, I have developed animal models of Usher and HANAC syndromes both leading to cone photoreceptor dysfunction and damage. Cone dysfunction was demonstrated by electroretinogram recording and by morphological changes, retinal gliosis and microglial activation. In the Usher models, I also demonstrated photoreceptor neuroprotection by different strategies. In the HANAC model, neuronal dysfunction was associated as in diabetic retinopathy to blood vessel tortuosity, blood vessel permeability and incresead VEGF expression levels. These phenotypic evaluations of mouse models provide new insights into the physiopathology of cone photoreceptor degeneration in Usher syndrome and in complex vascular diseases. It also open the way for the development and assessment of new therapeutic strategies for these diseases leading to blindness.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20789号 / 医博第4289号 / 新制||医||1025(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 山田 亮, 教授 大森 孝一, 教授 高田 穣 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM