Analysis of GPCR properties of Frizzled receptors and establishment of the "in vitro" platform for screening of Frizzled agonists/antagonists as potential therapeutic agents

Morphogens of the Wnt protein family are the secreted lipoglycoprotein ligands which initiate several pathways heavily involved in the coordination of various developmental stages of organisms in the majority of animal species. Deregulation of these pathways in the adult leads to formation and sustaining of multiple types of cancer. The latter notion is reinforced by the fact that the very discovery of the first Wnt ligand was due to its role as the causative factor of carcinogenic transformation (Nusse and Varmus, 1982). Nowadays our knowledge on Wnt signaling has "moved with the times" and these pathways were identified to be often crucial for tumor formation, its interactions with the microenvironment, and promotion of the metastases (Huang and Du, 2008; Zerlin et al., 2008; Jessen, 2009). Thus the relevance of the pathway as the target for drug development has further increased in the light of modern paradigms of the complex cancer treatments which target also spreading and growth- promoting factors of tumors by specific and highly efficient substances (Pavet et al., 2010). Presently the field of the Wnt-targeting drug research is almost solely dominated by assays based on transcriptional activation induced by the signaling. This approach resulted in development of a number of promising substances (Lee et al., 2011). Despite its effectiveness, the method nevertheless suffers from several drawbacks. Among the major ones is the fact that this approach is prone to identify compounds targeting rather downstream effectors of the pathway, which are indiscriminately used by all the subtypes of the Wnt signaling. Additionally, proteins which are involved in several signaling cascades and not just the Wnt pathway turn out as targets of the new compounds. These issues increase risks of side effects due to off-target interactions and blockade of the pathway in healthy cells. In the present work we put forward a novel biochemical approach for drug development on the Wnt pathway. It targets Frizzleds (Fzs) - a family of 7-transmbembrane proteins which serve as receptors for Wnt ligands. They offer unique properties for the development of highly specific and effective drugs as they control all branches of the Wnt signaling. Recent advances in the understanding of the roles of heterotrimeric G proteins downstream from Fzs (Katanaev et al., 2005; Liu et al., 2005; Jernigan et al., 2010) suggest application of enzymatic properties of these effectors to monitor the receptor-mediated events. We have applied this knowledge in practice and established a specific and efficient method based on utilization of a novel high-throughput format of the GTP-binding assay to follow the activation of Fzs. This type of assay is a robust and well-established technology for the research and screenings on the GPCRs (Harrison and Traynor, 2003). The conventional method of detection involves the radioactively labeled non-hydrolysable GTP analog [35S]GTPyS. Its application in the large-scale screenings is however problematic which promoted development of the novel non-radioactive GTP analog GTP-Eu. The new molecule employs phenomenon of the time-resolved fluorescence to provide sensitivity comparable to the conventional radioactive substance. Initially GTP-Eu was tested only in one of many possible types of GTP-binding assays (Frang et al., 2003). In the present work we expand these limits by demonstrating the general comparability of the novel label with the radioactive method in various types of assays. We provide a biochemical characterization of GTP-Eu interactions with heterotrimeric and small GTPases and a comparative analysis of the behavior of the new label in the assays involving heterotrimeric G protein effectors. These developments in the GTP-binding assay were then applied to monitor G protein activation by the Fz receptors. The data obtained in mammalian cultured cell lines provides for the first time an unambiguous biochemical proof for direct coupling of Fzs with G proteins. The specificity of this interaction has been confirmed by the experiments with the antagonists of Fz and by the pertussis toxin-mediated deactivation. Additionally we have identified the specificity of Wnt3a towards several members of the Fz family and analyzed the properties of human Fz-1 which was found to be the receptor coupled to the Gi/o family of G proteins. Another process playing significant role in the functioning of every GPCR is endocytosis. This phenomenon can also be employed for drug screenings on GPCRs (Bickle, 2010). In the present work we have demonstrated that Drosophila Fz receptors are involved in an unusual for many GPCRs manifestation of the receptor-mediated internalization. Through combination of biochemical approaches and studies on Drosophila as the model organism we have shown that direct interactions of the Fzs and the α-subunit of the heterotrimeric G protein Go with the small GTPase Rab5 regulate internalization of the receptor in early endosomes. We provide data uncovering the decisive role of this self-promoted endocytosis in formation of a proper signaling output in the canonical as well as planar cell polarity (PCP) pathways regulated by Fz. The results of this work thus establish a platform for the high-throughput screening to identify substances active in the cancer-related Wnt pathways. This methodology has been adjusted and applied to provide the important insights in Fz functioning and will be instrumental for further investigations on the Wnt-mediated pathways.

Highly parallel genetic approaches in Mendelian and complex diseases

The recent advance in high-throughput sequencing and genotyping protocols allows rapid investigation of Mendelian and complex diseases on a scale not previously been possible. In my thesis research I took advantage of these modern techniques to study retinitis pigmentosa (RP), a rare inherited disease characterized by progressive loss of photoreceptors and leading to blindness; and hypertension, a common condition affecting 30% of the adult population. Firstly, I compared the performance of different next generation sequencing (NGS) platforms in the sequencing of the RP-linked gene PRPF31. The gene contained a mutation in an intronic repetitive element, which presented difficulties for both classic sequencing methods and NGS. We showed that all NGS platforms are powerful tools to identify rare and common DNA variants, also in case of more complex sequences. Moreover, we evaluated the features of different NGS platforms that are important in re-sequencing projects. The main focus of my thesis was then to investigate the involvement of pre-mRNA splicing factors in autosomal dominant RP (adRP). I screened 5 candidate genes in a large cohort of patients by using long-range PCR as enrichment step, followed by NGS. We tested two different approaches: in one, all target PCRs from all patients were pooled and sequenced as a single DNA library; in the other, PCRs from each patient were separated within the pool by DNA barcodes. The first solution was more cost-effective, while the second one allowed obtaining faster and more accurate results, but overall they both proved to be effective strategies for gene screenings in many samples. We could in fact identify novel missense mutations in the SNRNP200 gene, encoding an essential RNA helicase for splicing catalysis. Interestingly, one of these mutations showed incomplete penetrance in one family with adRP. Thus, we started to study the possible molecular causes underlying phenotypic differences between asymptomatic and affected members of this family. For the study of hypertension, I joined a European consortium to perform genome-wide association studies (GWAS). Thanks to the use of very informative genotyping arrays and of phenotipically well-characterized cohorts, we could identify a novel susceptibility locus for hypertension in the promoter region of the endothelial nitric oxide synthase gene (NOS3). Moreover, we have proven the direct causality of the associated SNP using three different methods: 1) targeted resequencing, 2) luciferase assay, and 3) population study. - Le récent progrès dans le Séquençage à haut Débit et les protocoles de génotypage a permis une plus vaste et rapide étude des maladies mendéliennes et multifactorielles à une échelle encore jamais atteinte. Durant ma thèse de recherche, j'ai utilisé ces nouvelles techniques de séquençage afin d'étudier la retinite pigmentale (RP), une maladie héréditaire rare caractérisée par une perte progressive des photorécepteurs de l'oeil qui entraine la cécité; et l'hypertension, une maladie commune touchant 30% de la population adulte. Tout d'abord, j'ai effectué une comparaison des performances de différentes plateformes de séquençage NGS (Next Generation Sequencing) lors du séquençage de PRPF31, un gène lié à RP. Ce gène contenait une mutation dans un élément répétable intronique, qui présentait des difficultés de séquençage avec la méthode classique et les NGS. Nous avons montré que les plateformes de NGS analysées sont des outils très puissants pour identifier des variations de l'ADN rares ou communes et aussi dans le cas de séquences complexes. De plus, nous avons exploré les caractéristiques des différentes plateformes NGS qui sont importantes dans les projets de re-séquençage. L'objectif principal de ma thèse a été ensuite d'examiner l'effet des facteurs d'épissage de pre-ARNm dans une forme autosomale dominante de RP (adRP). Un screening de 5 gènes candidats issus d'une large cohorte de patients a été effectué en utilisant la long-range PCR comme étape d'enrichissement, suivie par séquençage avec NGS. Nous avons testé deux approches différentes : dans la première, toutes les cibles PCRs de tous les patients ont été regroupées et séquencées comme une bibliothèque d'ADN unique; dans la seconde, les PCRs de chaque patient ont été séparées par code barres d'ADN. La première solution a été la plus économique, tandis que la seconde a permis d'obtenir des résultats plus rapides et précis. Dans l'ensemble, ces deux stratégies se sont démontrées efficaces pour le screening de gènes issus de divers échantillons. Nous avons pu identifier des nouvelles mutations faux-sens dans le gène SNRNP200, une hélicase ayant une fonction essentielle dans l'épissage. Il est intéressant de noter qu'une des ces mutations montre une pénétrance incomplète dans une famille atteinte d'adRP. Ainsi, nous avons commencé une étude sur les causes moléculaires entrainant des différences phénotypiques entre membres affectés et asymptomatiques de cette famille. Lors de l'étude de l'hypertension, j'ai rejoint un consortium européen pour réaliser une étude d'association Pangénomique ou genome-wide association study Grâce à l'utilisation de tableaux de génotypage très informatifs et de cohortes extrêmement bien caractérisées au niveau phénotypique, un nouveau locus lié à l'hypertension a été identifié dans la région promotrice du gène endothélial nitric oxide sinthase (NOS3). Par ailleurs, nous avons prouvé la cause directe du SNP associé au moyen de trois méthodes différentes: i) en reséquençant la cible avec NGS, ii) avec des essais à la luciférase et iii) une étude de population.

Human synthetic lethal inference as potential anti-cancer target gene detection

Background: Two genes are called synthetic lethal (SL) if mutation of either alone is not lethal, but mutation of both leads to death or a significant decrease in organism's fitness. The detection of SL gene pairs constitutes a promising alternative for anti-cancer therapy. As cancer cells exhibit a large number of mutations, the identification of these mutated genes' SL partners may provide specific anti-cancer drug candidates, with minor perturbations to the healthy cells. Since existent SL data is mainly restricted to yeast screenings, the road towards human SL candidates is limited to inference methods. Results: In the present work, we use phylogenetic analysis and database manipulation (BioGRID for interactions, Ensembl and NCBI for homology, Gene Ontology for GO attributes) in order to reconstruct the phylogenetically-inferred SL gene network for human. In addition, available data on cancer mutated genes (COSMIC and Cancer Gene Census databases) as well as on existent approved drugs (DrugBank database) supports our selection of cancer-therapy candidates.Conclusions: Our work provides a complementary alternative to the current methods for drug discovering and gene target identification in anti-cancer research. Novel SL screening analysis and the use of highly curated databases would contribute to improve the results of this methodology.

Incidence and outcomes of respiratory viral infections in lung transplant recipients: a prospective study.

BACKGROUND: The incidence and outcomes of respiratory viral infections in lung transplant recipients (LTR) are not well defined. The objective of this prospective study conducted from June 2008 to March 2011 was to characterise the incidence and outcomes of viral respiratory infections in LTR. METHODS: Patients were seen in three contexts: study-specific screenings covering all seasons; routine post-transplantation follow-up; and emergency visits. Nasopharyngeal specimens were collected systematically and bronchoalveolar lavage (BAL) was performed when clinically indicated. All specimens underwent testing with a wide panel of molecular assays targeting respiratory viruses. RESULTS: One hundred and twelve LTR had 903 encounters: 570 (63%) were screening visits, 124 (14%) were routine post-transplantation follow-up and 209 (23%) were emergency visits. Respiratory viruses were identified in 174 encounters, 34 of these via BAL. The incidence of infection was 0.83 per patient-year (95% CI 0.45 to 1.52). The viral infection rates upon screening, routine and emergency visits were 14%, 15% and 34%, respectively (p<0.001). Picornavirus was identified most frequently in nasopharyngeal (85/140; 60.7%) and BAL specimens (20/34; 59%). Asymptomatic viral carriage, mainly of picornaviruses, was found at 10% of screening visits. Infections were associated with transient lung function loss and high calcineurin inhibitor blood levels. The hospitalisation rate was 50% (95% CI 30% to 70.9%) for influenza and parainfluenza and 16.9% (95% CI 11.2% to 23.9%) for other viruses. Acute rejection was not associated with viral infection (OR 0.4, 95% CI 0.1 to 1.3). CONCLUSIONS: There is a high incidence of viral infection in LTR; asymptomatic carriage is rare. Viral infections contribute significantly to this population's respiratory symptomatology. No temporal association was observed between infection and acute rejection.

Iowa EHDI News, Spring 2006

The purpose of the newsletter is to communicate with parents and professionals about newborn hearing screening in Iowa. We will share information about: Hearing screenings Intervention Resources available for parents and professionals “Best practices” by hospitals, AEAs (Area Education Agencies), or private practive audiology offices System goals Family stories Highlights from the EHDI Advisory Committee Updates on Iowa’s EHDI program It is important to point out that we are a diverse team of individuals working together to ensure that all newborns and toddlers with hearing loss are identified as early as possible and provided with timely and appropriate audiological, educational and medical intervention. Each newsletter will introduce you to various team members of the EHDI system in Iowa.

Welcome To Medicare Physical Exam, September 2007

Medicare will cover a one-time preventive physical exam within the first six months that you have Part B. This benefit is for all Medicare beneficiaries including those under age 65. How much does the exam cost? You pay 20% of the Medicare approved amount after you meet the yearly Part B deductible ($131 for 2007). Since this exam may be your first Medicare-covered service, you could meet your entire Part B deductible for the year. Medicare will cover the exam if performed by a physician, physician assistant, nurse practitioner, or clinical nurse specialist. What should I expect during the exam? The “Welcome to Medicare Physical” will include the following: 1. A review of your medical and social history. 2. A review of your potential risk factors for depression. 3. A review of your functional ability and level of safety. 4. Blood pressure, height, weight and vision test 5. An electrocardiogram (EKG) 6. Education and counseling on the above five items. 7. A written plan explaining screenings and other recommended preventive services. All seven elements must be documented in order for the physical to be covered by Medicare. The exam does not include clinical laboratory tests. Medicare will pay for a one-time ultrasound screening for abdominal aortic aneurysms for beneficiaries who are at risk (has a family history or a man age 65 to 75 who has smoked at least 100 cigarettes in his lifetime.) Only Medicare beneficiaries who receive a referral from the Welcome to Medicare physical exam will be covered for this benefit. There is no Part B deductible, but you or your supplemental insurance will be responsible for the coinsurance. What should I take to the exam? You should bring the following when you go to your “Welcome to Medicare” physical exam: • Medical records, including immunization records (if you are seeing a doctor for the first time) • Family health history • A list of current prescription drugs, how often you take them, and why.

Iowa EHDI News, Spring 2008

The purpose of the newsletter is to communicate with parents and professionals about newborn hearing screening in Iowa. We will share information about: Hearing screenings Intervention Resources available for parents and professionals “Best practices” by hospitals, AEAs (Area Education Agencies), or private practive audiology offices System goals Family stories Highlights from the EHDI Advisory Committee Updates on Iowa’s EHDI program It is important to point out that we are a diverse team of individuals working together to ensure that all newborns and toddlers with hearing loss are identified as early as possible and provided with timely and appropriate audiological, educational and medical intervention. Each newsletter will introduce you to various team members of the EHDI system in Iowa.

Iowa EHDI News, Summer 2008

The purpose of the newsletter is to communicate with parents and professionals about newborn hearing screening in Iowa. We will share information about: Hearing screenings Intervention Resources available for parents and professionals “Best practices” by hospitals, AEAs (Area Education Agencies), or private practive audiology offices System goals Family stories Highlights from the EHDI Advisory Committee Updates on Iowa’s EHDI program It is important to point out that we are a diverse team of individuals working together to ensure that all newborns and toddlers with hearing loss are identified as early as possible and provided with timely and appropriate audiological, educational and medical intervention. Each newsletter will introduce you to various team members of the EHDI system in Iowa.

Iowa EHDI News, Fall 2008

The purpose of the newsletter is to communicate with parents and professionals about newborn hearing screening in Iowa. We will share information about: Hearing screenings Intervention Resources available for parents and professionals “Best practices” by hospitals, AEAs (Area Education Agencies), or private practive audiology offices System goals Family stories Highlights from the EHDI Advisory Committee Updates on Iowa’s EHDI program It is important to point out that we are a diverse team of individuals working together to ensure that all newborns and toddlers with hearing loss are identified as early as possible and provided with timely and appropriate audiological, educational and medical intervention. Each newsletter will introduce you to various team members of the EHDI system in Iowa.

Iowa EHDI News, Winter 2008

The purpose of the newsletter is to communicate with parents and professionals about newborn hearing screening in Iowa. We will share information about: Hearing screenings Intervention Resources available for parents and professionals “Best practices” by hospitals, AEAs (Area Education Agencies), or private practive audiology offices System goals Family stories Highlights from the EHDI Advisory Committee Updates on Iowa’s EHDI program It is important to point out that we are a diverse team of individuals working together to ensure that all newborns and toddlers with hearing loss are identified as early as possible and provided with timely and appropriate audiological, educational and medical intervention. Each newsletter will introduce you to various team members of the EHDI system in Iowa.

Iowa EHDI News, Winter 2009

The purpose of the newsletter is to communicate with parents and professionals about newborn hearing screening in Iowa. We will share information about: Hearing screenings Intervention Resources available for parents and professionals “Best practices” by hospitals, AEAs (Area Education Agencies), or private practive audiology offices System goals Family stories Highlights from the EHDI Advisory Committee Updates on Iowa’s EHDI program It is important to point out that we are a diverse team of individuals working together to ensure that all newborns and toddlers with hearing loss are identified as early as possible and provided with timely and appropriate audiological, educational and medical intervention. Each newsletter will introduce you to various team members of the EHDI system in Iowa.

Iowa EHDI News, Winter 2010

The purpose of the newsletter is to communicate with parents and professionals about newborn hearing screening in Iowa. We will share information about: Hearing screenings Intervention Resources available for parents and professionals “Best practices” by hospitals, AEAs (Area Education Agencies), or private practive audiology offices System goals Family stories Highlights from the EHDI Advisory Committee Updates on Iowa’s EHDI program It is important to point out that we are a diverse team of individuals working together to ensure that all newborns and toddlers with hearing loss are identified as early as possible and provided with timely and appropriate audiological, educational and medical intervention. Each newsletter will introduce you to various team members of the EHDI system in Iowa.

Iowa EHDI News, Summer 2009

The purpose of the newsletter is to communicate with parents and professionals about newborn hearing screening in Iowa. We will share information about: Hearing screenings Intervention Resources available for parents and professionals “Best practices” by hospitals, AEAs (Area Education Agencies), or private practive audiology offices System goals Family stories Highlights from the EHDI Advisory Committee Updates on Iowa’s EHDI program It is important to point out that we are a diverse team of individuals working together to ensure that all newborns and toddlers with hearing loss are identified as early as possible and provided with timely and appropriate audiological, educational and medical intervention. Each newsletter will introduce you to various team members of the EHDI system in Iowa.

Iowa EHDI News, Summer 2010

The purpose of the newsletter is to communicate with parents and professionals about newborn hearing screening in Iowa. We will share information about: Hearing screenings Intervention Resources available for parents and professionals “Best practices” by hospitals, AEAs (Area Education Agencies), or private practive audiology offices System goals Family stories Highlights from the EHDI Advisory Committee Updates on Iowa’s EHDI program It is important to point out that we are a diverse team of individuals working together to ensure that all newborns and toddlers with hearing loss are identified as early as possible and provided with timely and appropriate audiological, educational and medical intervention. Each newsletter will introduce you to various team members of the EHDI system in Iowa.

Iowa EHDI News, Spring 2009

The purpose of the newsletter is to communicate with parents and professionals about newborn hearing screening in Iowa. We will share information about: Hearing screenings Intervention Resources available for parents and professionals “Best practices” by hospitals, AEAs (Area Education Agencies), or private practive audiology offices System goals Family stories Highlights from the EHDI Advisory Committee Updates on Iowa’s EHDI program It is important to point out that we are a diverse team of individuals working together to ensure that all newborns and toddlers with hearing loss are identified as early as possible and provided with timely and appropriate audiological, educational and medical intervention. Each newsletter will introduce you to various team members of the EHDI system in Iowa.