A synthetic transcription platform for programmable gene expression in mammalian cells

William C W Chen; Leonid Gaidukov; Yong Lai; Ming-Ru Wu; Jicong Cao; Michael J Gutbrod; Gigi C G Choi; Rachel P Utomo; Ying-Chou Chen; Liliana Wroblewska; Manolis Kellis; Lin Zhang; Ron Weiss; Timothy K Lu

doi:10.1038/s41467-022-33287-9

A synthetic transcription platform for programmable gene expression in mammalian cells

Nat Commun. 2022 Oct 18;13(1):6167. doi: 10.1038/s41467-022-33287-9.

Authors

William C W Chen^#^{1

2

3

4

5}, Leonid Gaidukov^#^{6

7}, Yong Lai^#^{6

8}, Ming-Ru Wu^{6

9}, Jicong Cao⁶, Michael J Gutbrod^{10

11}, Gigi C G Choi^{6

12}, Rachel P Utomo^{6

13}, Ying-Chou Chen^{6

8

14}, Liliana Wroblewska¹⁵, Manolis Kellis^{10

11}, Lin Zhang¹⁶, Ron Weiss^{6

7}, Timothy K Lu^{17

18

19}

Affiliations

¹ Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. William.Chen@usd.edu.
² Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. William.Chen@usd.edu.
³ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. William.Chen@usd.edu.
⁴ Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA. William.Chen@usd.edu.
⁵ Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, 57069, USA. William.Chen@usd.edu.
⁶ Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
⁷ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
⁸ Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
⁹ Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA.
¹⁰ Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
¹¹ Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA.
¹² Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China.
¹³ Department of Biochemistry, Wellesley College, Wellesley, MA, 02481, USA.
¹⁴ Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan.
¹⁵ Pfizer Inc., Cambridge, MA, 02139, USA.
¹⁶ Pfizer Inc., Andover, MA, 01810, USA.
¹⁷ Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. tim@lugroup.org.
¹⁸ Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. tim@lugroup.org.
¹⁹ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. tim@lugroup.org.

^# Contributed equally.

Abstract

Precise, scalable, and sustainable control of genetic and cellular activities in mammalian cells is key to developing precision therapeutics and smart biomanufacturing. Here we create a highly tunable, modular, versatile CRISPR-based synthetic transcription system for the programmable control of gene expression and cellular phenotypes in mammalian cells. Genetic circuits consisting of well-characterized libraries of guide RNAs, binding motifs of synthetic operators, transcriptional activators, and additional genetic regulatory elements express mammalian genes in a highly predictable and tunable manner. We demonstrate the programmable control of reporter genes episomally and chromosomally, with up to 25-fold more activity than seen with the EF1α promoter, in multiple cell types. We use these circuits to program the secretion of human monoclonal antibodies and to control T-cell effector function marked by interferon-γ production. Antibody titers and interferon-γ concentrations significantly correlate with synthetic promoter strengths, providing a platform for programming gene expression and cellular function in diverse applications.

Publication types

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

MeSH terms

Animals
Antibodies, Monoclonal / genetics
Gene Expression
Gene Regulatory Networks
Humans
Interferon-gamma* / genetics
Mammals / genetics
Synthetic Biology
Transcription Factors* / metabolism
Transcription, Genetic

Substances

Interferon-gamma
Transcription Factors
Antibodies, Monoclonal

Abstract

Publication types

MeSH terms

Substances

Grants and funding