The sound of silence: Transgene silencing in mammalian cell engineering

Alan Cabrera; Hailey I Edelstein; Fokion Glykofrydis; Kasey S Love; Sebastian Palacios; Josh Tycko; Meng Zhang; Sarah Lensch; Cara E Shields; Mark Livingston; Ron Weiss; Huimin Zhao; Karmella A Haynes; Leonardo Morsut; Yvonne Y Chen; Ahmad S Khalil; Wilson W Wong; James J Collins; Susan J Rosser; Karen Polizzi; Michael B Elowitz; Martin Fussenegger; Isaac B Hilton; Joshua N Leonard; Lacramioara Bintu; Kate E Galloway; Tara L Deans

doi:10.1016/j.cels.2022.11.005

The sound of silence: Transgene silencing in mammalian cell engineering

Cell Syst. 2022 Dec 21;13(12):950-973. doi: 10.1016/j.cels.2022.11.005.

Authors

Alan Cabrera¹, Hailey I Edelstein^#², Fokion Glykofrydis^#³, Kasey S Love^#⁴, Sebastian Palacios^#⁴, Josh Tycko^#⁵, Meng Zhang^#⁶, Sarah Lensch⁷, Cara E Shields⁸, Mark Livingston⁹, Ron Weiss¹⁰, Huimin Zhao⁶, Karmella A Haynes⁸, Leonardo Morsut³, Yvonne Y Chen¹¹, Ahmad S Khalil¹², Wilson W Wong¹³, James J Collins¹⁴, Susan J Rosser¹⁵, Karen Polizzi¹⁶, Michael B Elowitz¹⁷, Martin Fussenegger¹⁸, Isaac B Hilton¹⁹, Joshua N Leonard², Lacramioara Bintu⁷, Kate E Galloway²⁰, Tara L Deans²¹

Affiliations

¹ Department of Bioengineering, Rice University, Houston, TX 77005, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
² Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; The Eli and Edythe Broad CIRM Center, Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.
³ Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033-9080, USA.
⁴ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
⁵ Department of Genetics, Stanford University, Stanford, CA 94305, USA.
⁶ Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, Urbana, IL 61801, USA.
⁷ Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
⁸ Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA.
⁹ Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA.
¹⁰ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
¹¹ Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA; Parker Institute for Cancer Immunotherapy Center at UCLA, Los Angeles, CA 90095, USA.
¹² Biological Design Center and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
¹³ Biological Design Center and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
¹⁴ Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033-9080, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
¹⁵ School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
¹⁶ Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK.
¹⁷ Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
¹⁸ Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland; Faculty of Science, University of Basel, Mattenstrasse 26, Basel 4058, Switzerland.
¹⁹ Department of Bioengineering, Rice University, Houston, TX 77005, USA.
²⁰ Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
²¹ Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA. Electronic address: [email protected].

^# Contributed equally.

Abstract

To elucidate principles operating in native biological systems and to develop novel biotechnologies, synthetic biology aims to build and integrate synthetic gene circuits within native transcriptional networks. The utility of synthetic gene circuits for cell engineering relies on the ability to control the expression of all constituent transgene components. Transgene silencing, defined as the loss of expression over time, persists as an obstacle for engineering primary cells and stem cells with transgenic cargos. In this review, we highlight the challenge that transgene silencing poses to the robust engineering of mammalian cells, outline potential molecular mechanisms of silencing, and present approaches for preventing transgene silencing. We conclude with a perspective identifying future research directions for improving the performance of synthetic gene circuits.

Keywords: genome engineering; mammalian synthetic biology; synthetic gene circuit stability; transgene silencing.

Publication types

Review
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural

MeSH terms

Animals
Cell Communication
Gene Regulatory Networks*
Genetic Engineering*
Mammals / genetics
Transgenes / genetics

Abstract

Publication types

MeSH terms

Grants and funding