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

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 PolizziMichael B. Elowitz, Martin Fussenegger, Isaac B. Hilton, Joshua N. Leonard, Lacramioara Bintu, Kate E. Galloway, Tara L. Deans^*

^*Corresponding author for this work

Chemical and Biological Engineering

Research output: Contribution to journal › Review article › peer-review

45 Scopus citations

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.

Original language	English (US)
Pages (from-to)	950-973
Number of pages	24
Journal	Cell Systems
Volume	13
Issue number	12
DOIs	https://doi.org/10.1016/j.cels.2022.11.005
State	Published - Dec 21 2022

Funding

Funding for this work was supported in part by the National Institutes of Health grants 1DP2CA250006-01 (T.L.D.), 1R01GM129011 (W.W.W.), R01EB029483 (W.W.W.), 1R01EB026510 (J.N.L.), R21EB030772 (I.B.H.), R35GM143532 (I.B.H.), R35GM143033 (K.E.G.), R35GM138256 (L.M.), 4K00DK126120-03 (J.T.), R01EB029483 (A.S.K.), R35GM128947 (L.B.), R01EB030946 (R.W.), R01EB025256 (R.W.), 1UM1HG009402 (H.Z.), U54DK107965 (H.Z.), R21CA232244 (K.A.H.), 1RC2DK120535-01A1 (J.J.C.), and 1 U01 DK 127420 -01 (M.B.E.), the National Science Foundation grants CBET-2034495 (L.M.), CBET-2145528 (L.M.), 2141064 (K.S.L.), EF-1921677 (A.S.K.), and EF-2021552 under subaward UWSC10142 (M.B.E.). Further support was also provided by the Biotechnology and Biological Sciences Research Council (BBSRC) BB/S006206/1 (K.P.) and BB/M018040/1 (S.J.R.), ElectroGene 785800 (M.F.), the SNF (M.F.), the Paul Allen Foundation (W.W.W.), AOFSR FA9550-22-1-0316 (K.E.G.), the Wellcome Sanger Institute LEAP 21-275 (L.M.), the Parker Institute for Cancer Immunotherapy (Y.Y.C.), the W.H. Coulter Department of Biomedical Engineering at Emory University (C.E.S.), and the DoD Vannevar Bush Faculty Fellowship N00014-20-1-2825 (A.S.K.). M.B.E. is a Howard Hughes Medical Institute investigator. The authors listed with equal contribution are listed in the author list in alphabetical order.

Keywords

genome engineering
mammalian synthetic biology
synthetic gene circuit stability
transgene silencing

ASJC Scopus subject areas

Pathology and Forensic Medicine
Histology
Cell Biology

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10.1016/j.cels.2022.11.005

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Cabrera, A., Edelstein, H. I., Glykofrydis, F., Love, K. S., Palacios, S., Tycko, J., Zhang, M., Lensch, S., Shields, C. E., Livingston, M., Weiss, R., Zhao, H., Haynes, K. A., Morsut, L., Chen, Y. Y., Khalil, A. S., Wong, W. W., Collins, J. J., Rosser, S. J., ... Deans, T. L. (2022). The sound of silence: Transgene silencing in mammalian cell engineering. Cell Systems, 13(12), 950-973. https://doi.org/10.1016/j.cels.2022.11.005

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title = "The sound of silence: Transgene silencing in mammalian cell engineering",

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",

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

note = "Publisher Copyright: {\textcopyright} 2022 The Authors",

year = "2022",

month = dec,

day = "21",

doi = "10.1016/j.cels.2022.11.005",

language = "English (US)",

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Cabrera, A, Edelstein, HI, Glykofrydis, F, Love, KS, Palacios, S, Tycko, J, Zhang, M, Lensch, S, Shields, CE, Livingston, M, Weiss, R, Zhao, H, Haynes, KA, Morsut, L, Chen, YY, Khalil, AS, Wong, WW, Collins, JJ, Rosser, SJ, Polizzi, K, Elowitz, MB, Fussenegger, M, Hilton, IB, Leonard, JN, Bintu, L, Galloway, KE & Deans, TL 2022, 'The sound of silence: Transgene silencing in mammalian cell engineering', Cell Systems, vol. 13, no. 12, pp. 950-973. https://doi.org/10.1016/j.cels.2022.11.005

TY - JOUR

T1 - The sound of silence

T2 - Transgene silencing in mammalian cell engineering

AU - Cabrera, Alan

AU - Edelstein, Hailey I.

AU - Glykofrydis, Fokion

AU - Love, Kasey S.

AU - Palacios, Sebastian

AU - Tycko, Josh

AU - Zhang, Meng

AU - Lensch, Sarah

AU - Shields, Cara E.

AU - Livingston, Mark

AU - Weiss, Ron

AU - Zhao, Huimin

AU - Haynes, Karmella A.

AU - Morsut, Leonardo

AU - Chen, Yvonne Y.

AU - Khalil, Ahmad S.

AU - Wong, Wilson W.

AU - Collins, James J.

AU - Rosser, Susan J.

AU - Polizzi, Karen

AU - Elowitz, Michael B.

AU - Fussenegger, Martin

AU - Hilton, Isaac B.

AU - Leonard, Joshua N.

AU - Bintu, Lacramioara

AU - Galloway, Kate E.

AU - Deans, Tara L.

PY - 2022/12/21

Y1 - 2022/12/21

N2 - 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.

AB - 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.

KW - genome engineering

KW - mammalian synthetic biology

KW - synthetic gene circuit stability

KW - transgene silencing

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DO - 10.1016/j.cels.2022.11.005

M3 - Review article

C2 - 36549273

AN - SCOPUS:85144481170

SN - 2405-4712

VL - 13

SP - 950

EP - 973

JO - Cell Systems

JF - Cell Systems

IS - 12

ER -

The sound of silence: Transgene silencing in mammalian cell engineering

Abstract

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Keywords

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