Periodic Reporting for period 1 - SCilS (Studying Ciliary Signaling in Development and Disease)
Reporting period: 2020-01-01 to 2021-12-31
Characterising novel ciliary signalling concepts in development and homeostasis (WP2). ESR5 targets the molecular mechanisms balancing the output of ciliary TGFβ/BMP signalling, and has scrutinized a key module in this process using patient cells, stem cell models and siRNA approaches in order to continue evaluating its role in signalling in health and disease. ESR6 has made progress in studying the interplay between primary cilia and metabolic rewiring in Polycystic Kidney Disease, and acquired skills in evaluating cilium morphology under diverse stress conditions, and the use of cilium gene ablation models (cells and mice) to distinguish the specific response of ciliary processes to cellular stress. ESR7 has provided novel insights into the role of Dlg1 and Kif13B in regulating the ciliary length and signalling capacity in kidney epithelial cells. To assess this by proximity proteomics, she successfully carried out a secondment in Nijmegen (with P1) to acquire expertise in this technique and generate relevant datasets that await further analysis. ESR8 is targeting the neuronal cilia and neurodevelopmental processes that are defective in Joubert syndrome using iPSC-derived cell lines and organoids as models. She was able to validate that the neurons cultured in the lab are ciliated, and generated iPSC homozygous knockouts of neuronal ciliopathy genes. Also, the next steps in initiating differentiated iNeurons for microelectrode arrays (MEAs) and cerebral organoid generation were initiated successfully, including acquiring expertise with several analysis methods. ESR9 is evaluating ciliary pathways and ontologies following a computational approach. In close collaboration with ESR13, she has devised a socioaffinity-like metric, which was applied to PubMed to extract disease/gene associations and (more importantly) to rank them according to the weight/uniqueness of evidence.
Determining the biomedical consequences of disrupted ciliary signalling in ciliopathies (WP3). Based on comparative transcriptomic analyses, ESR10, who is analysing altered signalling pathways in patients with renal ciliopathies, characterized an abnormal inflammatory response in urine and urinary renal epithelial cells (URECs) from patients with the renal ciliopathy, nephronophthisis (NPH), as well as in the kidneys of mouse models. ESR11 is focusing on therapeutic approaches for renal ciliopathies to characterize the effects of new molecules and their mechanism of action. Two specific compounds, including a prostaglandin-derived molecule, have a broad positive effect on ciliogenesis in URECs of patients with mutations in NPHP genes. ESR12 is focusing on ciliary signalling in cardiovascular development and disease, and characterized two new candidate genes involved in chronic heart disease using zebrafish transgenic lines. The goal of ESR13 is to provide an online system for the study of affinity proteomics data analysis to study edgetic effects resulting from mutations in ciliopathy genes. The "socioaffinity" metric to query single-wash affinity proteomics data as well as datasets when data for both wild-type and mutation(s) are available was improved. ESR14 is using zebrafish to model ciliopathy disease, and generated CRISPR knockout zebrafish lines of two ciliary genes with a potential role in cardiac regeneration. Using a novel automated medium throughput platform, she is evaluating the cardiac regeneration kinetics of mutant larvae generated after genetic ablation of cardiomyocytes.
Network wide training (WP4) is provided for the fellows in the form of six complimentary skills courses and four research training courses (all compulsory for the ESRs). These SCilS training events are not running exactly to schedule, due to COVID-19 pandemic, however we have been able to complete over 60% of the network-wide training to date. The events scheduled to take place in 2020 and in Q1-Q3 of 2021 were all organized online.