Computational identification of small molecules for increased gene expression by synthetic circuits in mammalian cells

M. Pisani, F. Calandra, A. Rinaldi, F. Cella, F. Tedeschi, I. Boffa, D. Vozzi, N. Brunetti-Pierri, A. Carissimo, F. Napolitano and V. Siciliano ()
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M. Pisani: Istituto Italiano di Tecnologia-IIT
F. Calandra: Istituto Italiano di Tecnologia-IIT
A. Rinaldi: Istituto Italiano di Tecnologia-IIT
F. Cella: Istituto Italiano di Tecnologia-IIT
F. Tedeschi: Istituto Italiano di Tecnologia-IIT
I. Boffa: Telethon Institute of Genetics and Medicine (TIGEM)
D. Vozzi: Istituto Italiano di Tecnologia-IIT
N. Brunetti-Pierri: Telethon Institute of Genetics and Medicine (TIGEM)
A. Carissimo: Consiglio Nazionale delle Ricerche (CNR)
F. Napolitano: University of Sannio
V. Siciliano: Istituto Italiano di Tecnologia-IIT

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract Engineering mammalian cells with synthetic circuits drives innovation in next-generation biotherapeutics and industrial biotechnology. However, applications often depend on cellular productivity, which is constrained by finite cellular resources. Here, we harness computational biology to identify drugs that boost productivity without additional genetic modifications. We perform RNA-sequencing on cells expressing an incoherent feed-forward loop (iFFL), a genetic circuit that enhances operational capacity. To find drugs that mimic this effect, we use DECCODE (Drug Enhanced Cell COnversion using Differential Expression), an unbiased method that matches our transcriptional data with thousands of drug-induced profiles. Among the compound candidates, we select Filgotinib, that enhances expression of both transiently and stably expressed genetic payloads across various experimental scenarios and cell lines, including AAV and lentivirus transduction. Our results reveal cell-specific responses, underscoring the context dependency of small-molecule treatments. Altogether, we present a versatile tool for biomedical and industrial applications requiring enhanced productivity from engineered cells.

Date: 2025
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DOI: 10.1038/s41467-025-62529-9

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