Expression, Diagnosis and Deep Phenotyping of Ciliopathy Genes

Abstract

Primary cilia are solitary, highly conserved organelles present on almost all mammalian cells. Acting as an antenna to detect and transduce extracellular signals, they are essential during development and maintaining cellular homeostasis. Ciliopathies are a group of rare disorders caused by dysfunction of cilia, and often affect multiple organs such as the brain, retina, kidney and liver. Ciliopathies are poorly understood due to the large degree of genetic and phenotypic heterogeneity and overlapping phenotypes associated with each disorder. Ciliary proteins have various roles in the cilium. ARL3 and ARL2BP are involved in protein trafficking, mutations can cause retinitis pigmentosa and Joubert syndrome. CEP120 is involved in centriole biogenesis, mutations are known to cause Joubert and Jeune syndrome. TULP3 is involved in IFT-A trafficking and Hedgehog signalling (Hh), mutations can cause cystic kidney and liver disease. Phenotypes that mimic ciliopathies are also seen in other syndromes such as Poretti-Boltshauser syndrome (PTBHS). However, PTBHS is exclusively caused by mutations in LAMA1 which is not associated with the cilium. Therefore understanding the expression patterns of known ciliopathy causing genes, genetically diagnosing patients with ciliopathy phenotypes, and investigating these genes at a molecular level is essential in understanding the pathomechanism of ciliopathies. The expression pattern of ARL3 and CEP120 was investigated in developing human tissues to better understand the expression of these genes and the role they play in the organs affected by their mutations. Whole genome/exome sequencing (WGS/WES) was used in combination with data provided by The Genomics England 100,000 Genomes Project to genetically diagnose rare disease patients with ciliopathy phenotypes. Novel, pathogenic variants were identified in three genes (LAMA1, TULP3, ARL2BP) in six unrelated individuals with various clinical characteristics. In vitro deep phenotyping was performed on cellular models of ciliary genes identified by WGS/WES analyses. A potential shared pathomechanism of disease was investigated by molecular analysis of ciliary gross morphology, protein content, and effects on Hh signalling.