A massively parallel reporter assay library to screen short synthetic promoters in mammalian cells

Adam M. Zahm, William S. Owens, Samuel R. Himes, Braden S. Fallon, Kathleen E. Rondem, Alexa N. Gormick, Joshua S. Bloom, Sriram Kosuri, Henry Chan and Justin G. English ()
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Adam M. Zahm: University of Utah School of Medicine
William S. Owens: Octant Inc.
Samuel R. Himes: University of Utah School of Medicine
Braden S. Fallon: University of Utah School of Medicine
Kathleen E. Rondem: University of Utah School of Medicine
Alexa N. Gormick: University of Utah School of Medicine
Joshua S. Bloom: Octant Inc.
Sriram Kosuri: Octant Inc.
Henry Chan: Octant Inc.
Justin G. English: University of Utah School of Medicine

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: Abstract Cellular responses to stimuli underpin discoveries in drug development, synthetic biology, and general life sciences. We introduce a library comprising 6144 synthetic promoters, each shorter than 250 bp, designed as transcriptional readouts of cellular stimulus responses in massively parallel reporter assay format. This library facilitates precise detection and amplification of transcriptional activity from our promoters, enabling the systematic development of tunable reporters with dynamic ranges of 50−100 fold. Our library proved functional in numerous cell lines and responsive to a variety of stimuli, including metabolites, mitogens, toxins, and pharmaceutical agents, generating robust and scalable reporters effective in screening assays, biomarkers, and synthetic circuits attuned to endogenous cellular activities. Particularly valuable in therapeutic development, our library excels in capturing candidate reporters to signals mediated by drug targets, a feature we illustrate across nine diverse G-protein coupled receptors (GPCRs), critical targets in drug development. We detail how this tool isolates and defines discrete signaling pathways associated with specific GPCRs, elucidating their transcriptional signatures. With its ease of implementation, broad utility, publicly available data, and comprehensive documentation, our library will be beneficial in synthetic biology, cellular engineering, ligand exploration, and drug development.

Date: 2024
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DOI: 10.1038/s41467-024-54502-9

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