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Characterization and mitigation of gene expression burden in mammalian cells

Author

Listed:
  • Timothy Frei

    (ETH Zürich)

  • Federica Cella

    (Istituto Italiano di Tecnologia-IIT
    University of Genoa)

  • Fabiana Tedeschi

    (Istituto Italiano di Tecnologia-IIT)

  • Joaquín Gutiérrez

    (ETH Zürich)

  • Guy-Bart Stan

    (Imperial College London)

  • Mustafa Khammash

    (ETH Zürich)

  • Velia Siciliano

    (Istituto Italiano di Tecnologia-IIT)

Abstract

Despite recent advances in circuit engineering, the design of genetic networks in mammalian cells is still painstakingly slow and fraught with inexplicable failures. Here, we demonstrate that transiently expressed genes in mammalian cells compete for limited transcriptional and translational resources. This competition results in the coupling of otherwise independent exogenous and endogenous genes, creating a divergence between intended and actual function. Guided by a resource-aware mathematical model, we identify and engineer natural and synthetic miRNA-based incoherent feedforward loop (iFFL) circuits that mitigate gene expression burden. The implementation of these circuits features the use of endogenous miRNAs as elementary components of the engineered iFFL device, a versatile hybrid design that allows burden mitigation to be achieved across different cell-lines with minimal resource requirements. This study establishes the foundations for context-aware prediction and improvement of in vivo synthetic circuit performance, paving the way towards more rational synthetic construct design in mammalian cells.

Suggested Citation

  • Timothy Frei & Federica Cella & Fabiana Tedeschi & Joaquín Gutiérrez & Guy-Bart Stan & Mustafa Khammash & Velia Siciliano, 2020. "Characterization and mitigation of gene expression burden in mammalian cells," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-18392-x
    DOI: 10.1038/s41467-020-18392-x
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    Citations

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    Cited by:

    1. Shunsuke Kawasaki & Hiroki Ono & Moe Hirosawa & Takeru Kuwabara & Shunsuke Sumi & Suji Lee & Knut Woltjen & Hirohide Saito, 2023. "Programmable mammalian translational modulators by CRISPR-associated proteins," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Anna-Maria Makri Pistikou & Glenn A. O. Cremers & Bryan L. Nathalia & Theodorus J. Meuleman & Bas W. A. Bögels & Bruno V. Eijkens & Anne Dreu & Maarten T. H. Bezembinder & Oscar M. J. A. Stassen & Car, 2023. "Engineering a scalable and orthogonal platform for synthetic communication in mammalian cells," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. Kirill Sechkar & Harrison Steel & Giansimone Perrino & Guy-Bart Stan, 2024. "A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    4. Sebastián Sosa-Carrillo & Henri Galez & Sara Napolitano & François Bertaux & Gregory Batt, 2023. "Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    5. Ross D. Jones & Yili Qian & Katherine Ilia & Benjamin Wang & Michael T. Laub & Domitilla Del Vecchio & Ron Weiss, 2022. "Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    6. Andras Gyorgy, 2023. "Competition and evolutionary selection among core regulatory motifs in gene expression control," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    7. Chenrui Qin & Yanhui Xiang & Jie Liu & Ruilin Zhang & Ziming Liu & Tingting Li & Zhi Sun & Xiaoyi Ouyang & Yeqing Zong & Haoqian M. Zhang & Qi Ouyang & Long Qian & Chunbo Lou, 2023. "Precise programming of multigene expression stoichiometry in mammalian cells by a modular and programmable transcriptional system," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    8. Stanislav Anastassov & Maurice Filo & Ching-Hsiang Chang & Mustafa Khammash, 2023. "A cybergenetic framework for engineering intein-mediated integral feedback control systems," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    9. Roberto Di Blasi & Mara Pisani & Fabiana Tedeschi & Masue M. Marbiah & Karen Polizzi & Simone Furini & Velia Siciliano & Francesca Ceroni, 2023. "Resource-aware construct design in mammalian cells," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    10. Carlos Barajas & Hsin-Ho Huang & Jesse Gibson & Luis Sandoval & Domitilla Vecchio, 2022. "Feedforward growth rate control mitigates gene activation burden," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    11. Yuanli Gao & Lei Wang & Baojun Wang, 2023. "Customizing cellular signal processing by synthetic multi-level regulatory circuits," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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