CRISParray: an arrayed CRISPRi screening platform for drug target discovery and validation

With the advent of new therapies such anti-sense oligos (ASOs) and mRNA, the frontiers of the druggable genome are being expanded. On paper, any gene can be considered as a target for new therapies. This new reality brings new hope to patients around the world suffering from diseases which were, until recently, not considered addressable. 

While the pool of potential drug targets has radically changed, the drug discovery process still suffers high attrition rates. With new tools to develop novel therapies for a wide range of diseases, the first step to improve is target selection. This crucial step is often guided by single parameter readout approaches, characterizing target perturbations solely in their ability to affect the monitored parameter. These strategies are extremely scalable and allow the interrogation of tens of thousands of genes simultaneously. Unfortunately, they result in an oversimplification of complex physio-pathologies, suboptimal target selection and late-stage failures. To solve this and to better inform the target selection process, we have established a scalable target screening platform that delivers multi-parameter readouts enabling a comprehensive characterization of each candidate thanks to the complementarity of these read-outs. We use CRISPR interference to conduct loss-of-function studies in a high-throughput arrayed workflow. In this workflow, sgRNAs are delivered to CRISPRi competent cells in 96-well plates. Real-time cellular monitoring is used for cellular phenotyping and RNA-sequencing for each well is used to characterize the molecular phenotype of target silencing. This approach enables us to identify the pathways in which targeted genes are involved and thus gain insights into their functions without the need for prior knowledge of said functions. This unique platform is highly flexible towards combinatory perturbations and compatible with high content imagery screening and can support the industry in the early stage of target discovery and validation. 

Authors

Eric de Bony, Wim Tripsteen, Xin Wang, Nurten Yigit, Ramiro Martinez, Fien Gysens, Pieter Mestdagh

Organisations

University of Ghent, Center for Medical Genetics of Ghent (CMGG)

Presenting author

Eric de Bony, Postdoc, University of Ghent
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