DiMeN Doctoral Training Partnership: Characterisation of a novel Joubert Syndrome (JS) model: dissecting genotype/phenotype heterogeneity in human disease towards personalised medicine

Based in Newcastle in the laboratory of Prof John Sayer (http://www.ncl.ac.uk/igm/staff/profile/john.sayer) with additional supervision from Prof Colin Johnson in Leeds (http://medhealth.leeds.ac.uk/profile/300/635/colin_anfimov_johnson) and providing a comprehensive training in human disease genetics, encompassing human disease modelling, bioinformatics and state-of-the-art cellular and molecular techniques, delivered by a multidisciplinary team at the forefront of ciliopathy research, this PhD project will fundamentally increase our understanding of ciliopathies, whilst providing training specifically tailored to the “genomic era”. Newcastle is at the forefront of recent advances in genomic medicine, for example, delivering the first genetic diagnosis as part of the Genomics England 100,000 genomes project (http://www.genomicsengland.co.uk/first-patients-diagnosed-through-the-100000-genomes-project/).

The term ciliopathy covers a wide range of disorders characterised by various combinations of cystic kidney disease, retinal degeneration and brain abnormalities in patients. Cystic kidney disease accounts for 10% of the 40,000 UK patients requiring dialysis/transplantation and there are currently no disease-modifying treatments for these conditions.

The archetypal ciliopathy is known as Joubert Syndrome (JS) which is predominantly caused by mutations in the CEP290 gene, discovered by Prof John Sayer (https://www.ncbi.nlm.nih.gov/pubmed/16682973). Prof Sayer and Dr Miles created a model of JS, carrying a Cep290 mutation analogous to that found in patients and demonstrated that this model faithfully recapitulates the human condition, more closely than any other model (https://www.ncbi.nlm.nih.gov/pubmed/24946806). Analysis of this model identified a previously unrecognized abnormality in the Hedgehog signalling pathway within the kidney. Treatment of kidney cells isolated from both the model, and more significantly, from JS patients with drugs that stimulate the Hedgehog signalling pathway restores normal function to these cells ex vivo. This indicates that diseased kidney cells from patients are not permanently disabled and that our model systems provide a means to identify potential treatments. (http://www.thejournal.co.uk/news/health/newcastle-university-scientists-made-first-7438749).

However, JS patients show a wide range of symptoms, such that i) mutations in one particular gene can cause any one of several different clinical phenotypes and ii) mutations in different genes can cause the same phenotype. Thus, knowing the mutation alone does not accurately predict the type of disease a patient will develop. We have examples of this in our clinic – patients with the same mutations present with very different symptom severity. This genotype/phenotype heterogeneity complicates efforts to understand the cause of the disease, make accurate diagnoses, and develop specific treatments.

In this project a novel model of JS will be characterised, based upon the Cep164 gene, whose discovery involved both Prof Sayer and Prof Johnson (https://www.ncbi.nlm.nih.gov/pubmed/22863007). Cep164 mutations typically cause more severe forms of JS than Cep290. By comparing the two models and cross-referencing with human genomic data, the underlying mechanisms that drive variation amongst patients will be revealed. Understanding the genotype/phenotype heterogeneity of ciliopathies naturally leads to precision, personalised medicine approaches in terms of diagnosis, prognosis and tailoring specific treatments to specific, genetically defined, groups of patients.

The project will involve a broad range of experiments including: i) characterisation of Cep164 expression patterns in mouse and human, making use of the MRC-Wellcome Trust Human Developmental Biology Resource at Newcastle (http://hdbr.org). These experiments have already been published for Cep290 (https://www.ncbi.nlm.nih.gov/pubmed/23028714) and will provide a foundation for subsequent comparisons between Cep164 and Cep290; ii) characterisation of the phenotype of Cep164 mutant mice, initially as we previously described for Cep290 (https://www.ncbi.nlm.nih.gov/pubmed/24946806); iii) Comparison of the consequences of Cep290 and Cep164 mutation at the molecular level using whole genome expression profiling (microarray) of Cep164 mutant kidneys; iv) High-resolution structural analyses targeting cilia to compare the effects of Cep164 and Cep290 mutation.

Phenotype and gene expression data will inform a detailed analysis of cilial structure and function, cross-referencing the whole-genome siRNA dataset of genes involved in ciliogenesis and ciliopathies (https://www.ncbi.nlm.nih.gov/pubmed/26167768) recently generated in Leeds. Molecular interactions highlighted in this way will be further investigated using super resolution microscopy and expertise in cilial protein interactions/localisation available in Leeds.

The data generated by comparison of these models will reveal the specific molecular pathways influencing disease progression. These data will be cross-referenced to genetic variants within JS patient exome/genome datasets to determine their contribution to heterogeneity amongst patients.