Automation of high-throughput workflow for arrayed CRISPR activation library screening

Yang, C.-C.; Deshpande, A. J.; Jackson, M.; Adams, P. D.; Pasquale, E. B.; Murad, R.; Yin, J.-A.; Wu, Y.; Beketova, A.; Huang, C.-T.

doi:10.1101/2025.11.10.687722

bioRxiv · 10.1101/2025.11.10.687722

Automation of high-throughput workflow for arrayed CRISPR activation library screening

Yang, C.-C.·Deshpande, A. J.·Jackson, M.·Adams, P. D.·Pasquale, E. B.·Murad, R.·Yin, J.-A.·Wu, Y.·Beketova, A.·Huang, C.-T.

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Abstract

CRISPR-mediated gene activation (CRISPRa) is among the most efficient and reliable strategies for mimicking sustained activation of endogenous promoters and their corresponding genes at physiological levels. By leveraging guide-RNA (gRNA) library design, CRISPRa screens can be applied on a whole-genome scale and are compatible with both arrayed and pooled formats, depending on assay requirements. Compared with conventional arrayed CRISPRa libraries that use single or dual gRNAs and often require multiple gRNA candidates per target, a recently developed CRISPRa library (termed T. gonfio) incorporates four tandem gRNAs per lentivector per target, thereby reducing library complexity and representing the smallest arrayed genome-wide CRISPRa library. To streamline genome-wide arrayed CRISPRa screening, this study developed a high-throughput automated workflow using the Biomek i7 Hybrid liquid-handling platform, integrated with multiple peripheral instruments. The workflow comprises three pipelines: lentiviral library transduction, cell library passaging, and assay processing. These pipelines together establish and maintain the transduced cell library for extended screening times. This enables assay processing at desired extended time points and improves the likelihood of identifying phenotypes that require longer time to develop, making the workflow suitable even for rapidly proliferating cell models. In a pilot arrayed screen using a T. gonfio mini-library targeting kinases and phosphatases, activation of the EPHA2 receptor promoter induced a growth reduction phenotype in the HEK293 cell model. This phenotype was recapitulated in a parallel pooled CRISPRa screen using the same mini-library and further validated in a co-culture assay.

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Yang, C.-C., Deshpande, A. J., Jackson, M., Adams, P. D., Pasquale, E. B., Murad, R., Yin, J.-A., Wu, Y., Beketova, A., Huang, C.-T.. 2025-11-12. Automation of high-throughput workflow for arrayed CRISPR activation library screening. https://doi.org/10.1101/2025.11.10.687722

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