Ciliopathies are a group of heterogeneous diseases associated with ciliary dysfunction. Diseases in this group display considerable phenotypic variation within individual diseases as well as overlapping phenotypes among clinically distinct diseases. In particular, mutations in CEP290 cause phenotypically diverse ciliopathies ranging from isolated retinal degeneration, nephronophthisis (NPHP), and Bardet-Biedl Syndrome (BBS) to the neonatal lethal Meckel-Gruber syndrome (MKS). However, the underlying mechanisms of the variable expressivity in ciliopathies are not well understood. This thesis focuses on evaluating the molecular and biological processes behind the retinal degeneration and obesity observed in cilia disorders with respect to CEP290 and other ciliopathy genes using the zebrafish and mouse model systems. CEP290 is the most frequently mutated gene underlying the non-syndromic blinding disorder, Leber's congenital amaurosis (LCA). We first aimed to characterize the function of various CEP290 domains and to characterize a zebrafish model aimed at progressing towards future therapy for patients with CEP290 LCA. To this end, an antisense oligonucleotide [Morpholino(MO)] was used for gene knockdown. We showed that cep290 MO-injected embryos have reduced Kupffer's vesicle size and delays in melanosome transport, two phenotypes that are observed upon knockdown of BBS genes in zebrafish. More importantly, the embryos had a statistically significant reduction in visual function, and this vision impairment caused by the disruption of cep290 can be rescued by expressing only the N-terminal region of the human CEP290 protein. These data indicate a specific region of the CEP290 protein, which is necessary for visual function. We examined the contribution of BBS genes to the clinical variability of CEP290-associated ciliopathies. We demonstrated that the BBSome binds to the N-terminal region of CEP290 and co-localizes with CEP290 to the centriolar satellite in ciliated cells and to the connecting cilium of photoreceptor cells. We further showed that the BBSome is required for proper localization of CEP290 in these structures. Genetic interactions were tested using Cep290rd16, a Cep290 hypomorphic allele with an in-frame deletion of 299 residues, and Bbs4 null mutant mouse lines. Additional loss of Bbs4 alleles in Cep290rd/rd mutants results in increased body weight and accelerated photoreceptor degeneration compared to mice without Bbs4 mutations. Furthermore, double heterozygous mice (Cep290+/rd16; Bbs4+/-) have increased body weight compared to single heterozygous animals. Our data indicated that genetic interactions between the BBSome components and CEP290 underlie the variable expression and overlapping phenotypes of ciliopathies caused by CEP290 mutations. Finally, this work was extended to other cilia disorders through the characterization of genetic interactions between CEP290 and other ciliopathy genes. We found that different NPHP and MKS proteins interact with CEP290 via its different regions, suggesting the central role of CEP290 in CEP290 biological/cellular functions. To characterize the functional interaction between these proteins, we used in vitro systems to double knockdown CEP290 with other NPHP and MKS genes and showed that depletion of a certain combination set of these proteins disrupted the localization of proteins into the cilia. The data indicated that the phenotypic variability of human ciliopathies is associated with different degree of compromise of cilia function.

Hundreds of individually rare, but collectively common Mendelian disorders result in visual impairment. One of these disorders is a heterogeneous syndromic form of retinal degeneration, Bardet-Biedl Syndrome (BBS). This disease is an autosomal recessive disorder characterized by retinal degeneration, obesity, learning disabilities, congenital anomalies, and an increased incidence of hypertension and diabetes. Typically, individuals with BBS experience vision loss during childhood leading to blindness by the third decade of life. At least fourteen genes (BBS1-BBS14) are reported to individual cause BBS. This thesis focuses on one of these genes, BBS3, with the overall goal of characterizig the function of BBS3 in terms of both syndromic and non-syndromic retinal degeneration using the zebrafish and mouse model systems. A member of the Ras family of small GTP-binding proteins, BBS3 is postulated to play a role in vesicular transport. A second highly conserved transcript of BBS3, BBS3L, has been identified and is expressed predominantly in the mouse and zebrafish eye. The eye-specific expression of BBS3L facilitates the dissection of BBS function in the retina independent of alterations to other tissues. To this end a Bbs3L knockout mouse was generated and histological analysis at 9 months reveals disorganization of the inner segments, indicative of retinal degeneration. To further evaluate the functional effects of BBS3 deficiency in the eye, an antisense oligonucleotide (Morpholino) approach was utilized to knockdown bbs3 gene expression in zebrafish. Consistent with an eye specific role, knockdown of bbs3L results in mislocalization of the photopigment green cone opsin and reduced visual function, but not abnormalities of the Kupffer's vesicle or delays in intracellular trafficking of melanosomes, both cardinal features of BBS in the zebrafish. To dissect the individual functions of BBS3 and BBS3L, in vitro transcribed wild-type human BBS3 or BBS3L RNA was co-injected with the bbs3 morpholinos. BBS3L RNA, but not BBS3 RNA, restores green opsin localization and vision. Moreover, only BBS3 RNA is sufficient to rescue melanosome transport, a cardinal feature of BBS in the zebrafish. Bbs3L knockout mice as well as a zebrafish bbs3 knockdown model demonstrate that BBS3L is both necessary and sufficient for retinal function and organization. This work was extended to humans by characterizing the A89V missense mutation in BBS3 that results in non-syndromic retinal degeneration. To evaluate the in vivo function of the A89V missense mutation in non-syndromic retinal degeneration and BBS, rescue experiments were performed in the zebrafish. Unlike wild-type BBS3L RNA, BBS3L A89V RNA does not rescue the vision defect seen with loss of bbs3 in zebrafish; however, BBS3 A89V RNA is able to suppress the cardinal zebrafish BBS phenotype of melanosome transport, similar to wild-type BBS3 RNA. These data demonstrate that the BBS3L A89V mutation identified in patients with non-syndromic retinal degeneration is critical and specific for the vision defect.

Thesis (Ph.D.)--Memorial University of Newfoundland, 2001. / Bibliography: leaves 197-218.

Bardet-Biedl syndrome (BBS) is a pleiotropic and genetically heterogeneous disorder, and a well-known ciliopathy. Nineteen different genes have been reported for BBS, mutations in which cause characteristic phenotypes including retinal degeneration, obesity, polydactyly, renal abnormalities, hypogenitalism and cognitive impairment. Protein products of eleven BBS genes are part of two major complexes: the BBSome complex and a CCT/CTRiC/BBS complex. The CCT/CTRiC/BBS complex assists in the formation of the BBSome complex, which in turn traffics numerous receptor proteins to the cilia. However, the precise mechanism by which BBSome ciliary trafficking activity is regulated is not fully understood. In fact, a complete picture of the cellular functions of BBS proteins is still missing, and gaps remain in our understanding of the pleiotropy and heterogeneity of the disease. With the aim of bridging those gaps, this thesis project was designed to identify tissue specific cargoes of the BBSome and to characterize their BBS-related functions. To this end, we generated a transgenic LAP-BBS4 mouse, which expresses the transgene in various tissues including brain, eye, testis, heart, kidney, and adipose tissue. We found that despite tissue specific variable expression, LAP-BBS4 was able to complement the deficiency of Bbs4 and rescue all the BBS phenotypes in the Bbs4 null mice. The finding provides an encouraging prospective for gene therapy for BBS related phenotypes and potentially for other ciliopathies. We also utilized the transgenic mice to search for tissue specific BBSome cargo proteins and identified CEP131 as a novel BBSome interacting protein. Using in vitro cell culture models we show that CEP131 interacts with the BBSome through BBS4. CEP131 is not involved in BBSome assembly, but accumulation of the BBSome in cilia is enhanced upon CEP131 depletion. Our in vitro data implicate CEP131 as a negative regulator of ciliary BBSome trafficking. Finally, we show that cep131 knockdown in zebrafish embryos results in typical BBS phenotypes including Kupffer's vesicle abnormalities and melanosome transport delay. This finding confirms the association of CEP131 with the BBS pathway. Overall, the work performed for this thesis provides further insight into the regulation of BBSome ciliary trafficking and suggests CEP131 as a BBS candidate gene.

Thesis (M.Sc.)--Memorial University of Newfoundland, 2004. / Restricted until May 2005. Bibliography: leaves 62-68.

Thesis advisor: John Wing / Thesis advisor: Stephen Wicks / Molecular biology and genetics, single nucleotide polymorphism genetic mapping, phenotypic assays including behavioral assessment, and fluorescent microscopy of GFP-tagged proteins were used to study ciliary defects in the nematode Caenorhabditis elegans. Mammalian cilia are multifunctional. Some of the physiological roles in which they are involved include sensing developmental signaling molecules and ligands as well as creating flows of mucus and cerebrospinal fluid that function as flow meters and mechanosensors. Due to the multifunctional nature of cilia, it is not surprising that many human diseases can be caused by ciliary defects. Bardet-Biedl Syndrome is a rare genetic ciliopathy characterized by retinal degeneration, polydactyly, obesity, cystic kidneys, mental retardation, and many other ailments. We have identified osm- 12/bbs-7 to be a C. elegans homologue of human BBS7, a gene known to cause Bardet-Biedl Syndrome when mutated. With the help of Michel Leroux’s group, I showed the BBS-7 protein to be localized to the base of cilia and to undergo intraflagellar transport along the ciliary axoneme. Our findings suggest that BBS- 7 plays a role in the assembly and/or functioning of the IFT complex. I also performed a mutagenesis and phenotypic screen for animals defective in the uptake of DiI into a subset of their ciliated neurons in order to identify new components involved in ciliogenesis and IFT. I describe an extended bulked segregant analysis (BSA) mapping methodology, which can save time and resources by filtering out alleles of previously known genes without performing time-consuming interval mapping. In addition, I identified one of the 11 dyefilling defective alleles from the screen to be a novel allele of dyf-3, which encodes a protein required for sensory cilia formation. / Thesis (PhD) — Boston College, 2008. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

In recent years, microarray technology has revealed the widespread presence of submicroscopic deletions and duplications throughout the human genome termed copy number variants (CNVs). CNVs have a profound effect on gene expression and are an important source of normal genetic variation. In addition, a small proportion of CNVs contribute to genetically simple and complex disease. This thesis focuses on the identification of pathogenic CNVs contributing to the etiology of diseases with "missing heritability" using a well-planned study design individually tailored to each disease cohort to optimize CNV detection and interpretation. We performed a genome-wide analysis for CNVs in five disease cohorts with genetic etiology: autism, age-related macular degeneration (AMD), glaucoma, clubfoot, and Bardet-Biedl syndrome (BBS). Our results indicate that CNVs likely account for a proportion of cases for each disease cohort reported in this thesis. Approximately 20% of our cohort of individuals with autism from trio pedigrees harbors a CNV known to confer risk to develop autism and we identified other novel and rare variants that may play a role in autism pathogenesis. We also characterized a duplication of 2p25.3 identified in two male half-siblings with autism and determined that their mother was somatic mosaic for the duplication. Our work provides evidence that this novel CNV disrupting the genes PXDN and MYT1L are the autism-causing mutation in this pedigree. A comparative cases experimental design was used in the study of AMD and glaucoma. While no common "risk CNVs" were identified for either eye disorder, we did identify several rare overlapping CNVs disrupting genes known to play a role in the eye that may confer risk to disease in a small proportion of individuals. In a fourth genetically complex disease, clubfoot, we identified a duplication of 17q23.2 disrupting the genes TBX4, NACA2, and BRIP1 that segregates with the autosomal dominant clubfoot phenotype in a large pedigree with 16 affected individuals. In addition, the duplication is within the linkage interval identified for this family. We also applied microarray technology to analyze the genomes of individuals with BBS, an autosomal recessive disorder, for the presence of CNVs in known BBS genes as well as CNVs that elucidate novel candidate genes for BBS. From 34 BBS patients with an unidentified mutation, we observed one CNV, a heterozygous deletion of BBS10, unmasking a BBS10 frameshift mutation. A promising BBS candidate gene also emerged from our studies, implicated by an intragenic deletion of the gene MARK3 predicted to result in a frameshift and premature truncation of the protein. Functional studies utilizing antisense morpholino gene knockdown in the zebrafish provide additional evidence that MARK3 is a BBS gene as knockdown of zebrafish mark3 results in a Kupffer's Vesicle defect and a melanosome transport delay, two cardinal BBS phenotypes in the zebrafish. In addition to identifying CNVs involved in disease, the work outlined in this thesis provides valuable insight into the study design and interpretation of a genome-wide analysis of CNV. This includes the appropriate use of controls and publicly available control databases, methods for enriching for CNVs in a patient cohort to maximize efficiency and discovery, and the importance of analyzing all patient cohorts with heritable disease for the presence of CNVs disrupting known disease genes and CNVs that implicate novel genetic candidates. As the reliability and resolution of CNV detection continue to improve, allowing detection of > 1,000 CNVs in each individual genome, it becomes more important than ever to have a well-defined study design for both the detection and interpretation of CNVs.

The identification of disease genes (genes that when mutated cause human diseases) is an important and challenging problem. Proper diagnosis, prevention, as well as care for patients require an understanding of disease pathophysiology, which is best understood when the underlying causative gene(s) or genetic element(s) are identified. While the availability of the sequenced human genome helped to lead to the discovery of more than 1,900 disease genes, the rate of disease gene discovery is still occurring at a slow pace. The use of genetic linkage methods have successfully led to the identification of numerous disease genes. However, linkage studies are ultimately restricted by available meioses (clinical samples) which result in numerous candidate disease genes. This thesis addresses candidate gene prioritizations in disease gene discovery as applied toward a genetically heterogeneous disease known as Bardet-Biedl Syndrome (BBS). Specifically, the integration of various functional information and the development of a novel comparative genomic approach (Computational Orthologous Prioritization - COP) that led to the identification of BBS3 and BBS11. Functional data integration and application of the COP method may be helpful toward the identification of other disease genes.

Neonatal hydrocephalus is a common neurological disorder leading to expansion of the cerebral ventricles. This disease is associated with significant morbidity and mortality and is often fatal if left untreated. Hydrocephalus was first described over 2500 years ago by Hippocrates, the father of medicine, and remains poorly understood today. Current therapies still rely on invasive procedures developed over 60 years ago that are associated with high failure and complication rates. Thus, the identification of molecular mechanisms and the development of non-invasive medical treatments for neonatal hydrocephalus are high priorities for the medical and scientific communities. The prevailing doctrine in the field is that hydrocephalus is strictly a "plumbing problem" caused by impaired cerebrospinal fluid (CSF) flow. Recently, animal models with impaired cilia have provided insight into the mechanisms involved in communicating (non-obstructive) hydrocephalus. However, as a result of a poor understanding of hydrocephalus, no animal studies to date have identified an effective non-invasive treatment. The goal of this thesis project is to investigate the molecular mechanisms underlying this disease and to identify a non-invasive, highly effective treatment strategy. In Chapter 2, we utilize a novel animal model with idiopathic hydrocephalus, mimicking the human ciliopathy Bardet-Biedl Syndrome (BBS), to examine the role of cilia in hydrocephalus. We find that these mice develop communicating hydrocephalus prior to the development of ependymal "motile" cilia, suggesting that this phenotype develops as a result of dysfunctional "primary" cilia. Primary cilia are non-motile and play a role in cellular signaling. These results challenge the current dogma that dysfunctional motile cilia underlies neonatal hydrocephalus and implicate a novel role for primary cilia and cellular signaling in this disease. Chapter 3 focuses on identifying the link between primary cilia and neonatal hydrocephalus. In this chapter, we report that disrupting the molecular machinery within primary cilia leads to faulty PDGFRα signaling and the loss of a particular class of neural progenitor cells called oligodendrocyte precursor cells (OPCs). We find that the loss of OPCs leads to neonatal hydrocephalus. Importantly, we identify the molecular mechanism underlying both the loss of OPCs and the pathogenesis of neonatal hydrocephalus. Chapter 4 explores the therapeutic potential of targeting the defective cellular signaling pathways to treat neonatal hydrocephalus. By targeting the faulty signaling, we restore normal development of oligodendrocyte precursor cells, and curtail the development of hydrocephalus. This work challenges the predominant view of hydrocephalus being strictly a "plumbing problem" treatable solely by surgical diversion of CSF. Here, we propose that hydrocephalus is a neurodevelopmental disorder that can be ameliorated by non-invasive means. Importantly, we introduce novel molecular targets and a non-invasive treatment strategy for this devastating disorder. To our knowledge, we are the first to successfully treat neonatal hydrocephalus in any model organism by targeting neural progenitor cells.

Cilia are finger-like projections that extend from the surface of most cells. These microtubule-based structures serve important mechanical or sensory functions. Motile cilia have been implicated in fluid movement whereas the non-motile primary cilia have been shown to play a role in sensory signal transduction. There exists a dichotomy in the field that primary cilia have only sensory function and motile cilia only have mechanical function. The central question of this thesis project is "what are the structural and functional components of airway motile cilia and are these cilia sensory?" In Chapter 2, the role of Bardet-Biedl Syndrome (BBS) proteins in maintaining the structure and function of airway motile cilia is examined. We found that BBS proteins localize to the cilium and to ciliary-related structures in human airway epithelia. Using mutant mice we found that BBS proteins play an essential role in motile cilia structure and the loss of BBS proteins results in reduced ciliary beat. These proteins have previously been shown to play a role in primary cilia structure and function, and our studies indicate a novel function for BBS proteins. Chapter 3 examines the sensory role of motile cilia. Our data show that bitter taste receptors and components of the bitter taste signal transduction pathway localize to the motile cilia or to the ciliated cells. Ciliated cells also show an increase in intracellular calcium in response to bitter compounds, accompanied by a corresponding increase in cilia beat. The increase in intracellular calcium originates at the ciliated cells and is propagated to adjacent cells. Chapter 4 delves into the possibility that every motile ciliated cell also contains a single, primary cilium. Using immunostaining and Smoothened as a marker for primary cilia, we found that every group of motile cilia contains a single Smoothened-positive cilium. Furthermore, downstream components of the Sonic Hedgehog pathway are also present in ciliated cells. Chapter 6 is a summary chapter including possible explanations for observed outcomes and plans for future experiments. Our results indicate that the divide between primary and motile cilia may not be as great as has been previously thought.