Ciliopathies are phenotypically and genetically very heterogeneous disorders. Although next generation sequencing (NGS) technologies has revolutionized gene discovery in this field, it remains enigmatic, how similar ciliary lesions result in highly organ-specific phenotypes. Many ciliopathies affect the kidneys, but also occur in combination with skeletal dysplasia. This proposal focuses on the clinical and molecular characterization of patients presenting with specific combined renal and skeletal dysplasia phenotypes. We identified two large consanguineous Turkish families presenting with a novel type of acromesomelic dysplasia (AMD). Furthermore, we have recruited more than 30 cases from a large asphyxiating thoracic dysplasia (ATD) cohort who are negative for all known disease genes. The first aim of the project will identify causative genes for these putative novel ciliopathies by a combination of panel and whole exome sequencing. Candidate genes will be thoroughly characterized by a stepwise approach in patient-derived primary cells, cell lines of chondrogenic and nephrogenic differentiation, organ culture, and zebrafish models. The second aim of the project will define the relationship between known and novel ciliopathy genes, in particular intraflagellar transport (IFT) components, to developmental signaling pathways. This will be achieved by combining screening of trans-differentiated primary cells for signaling defects with in vivo analyses. We will generate genetically tailored zebrafish models of the above disease phenotypes by targeting disease-associated IFT componentsusing TALEN and CRISPR/cas technology, to obtain a spectrum of null alleles, hypomorphic variants, and disease-associated point mutations. This will provide the molecular basis to study variability of developmental phenotypes in vivo and to validate common and organ-specific pathogenic factors. The third aim will examine the role of natriuretic peptide (NP)/cGMP-dependent signaling in ciliopathies. Preliminary data revealed reduced cGMP levels in Mainzer-Saldino syndrome patient-derived primary cells. We will therefore investigate ciliary functions in cell models, and generate a zebrafish model of AMD by targeting Npr2 and Cnp. In these animals, we will screen for signaling defects known or hypothesized to cause organ-specific pathology. With these complementary strategies, we aim to unravel tissue-specific ciliary molecular mechanisms in skeleto- and nephrogenesis, which may eventually lead to targeted therapeutic approaches.