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Ilia K, Shakiba N, Bingham T, Jones RD, Kaminski MM, Aravera E, Bruno S, Palacios S, Weiss R, Collins JJ, Del Vecchio D, Schlaeger TM. Synthetic genetic circuits to uncover the OCT4 trajectories of successful reprogramming of human fibroblasts. SCIENCE ADVANCES 2023; 9:eadg8495. [PMID: 38019912 PMCID: PMC10686568 DOI: 10.1126/sciadv.adg8495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
Reprogramming human fibroblasts to induced pluripotent stem cells (iPSCs) is inefficient, with heterogeneity among transcription factor (TF) trajectories driving divergent cell states. Nevertheless, the impact of TF dynamics on reprogramming efficiency remains uncharted. We develop a system that accurately reports OCT4 protein levels in live cells and use it to reveal the trajectories of OCT4 in successful reprogramming. Our system comprises a synthetic genetic circuit that leverages noise to generate a wide range of OCT4 trajectories and a microRNA targeting endogenous OCT4 to set total cellular OCT4 protein levels. By fusing OCT4 to a fluorescent protein, we are able to track OCT4 trajectories with clonal resolution via live-cell imaging. We discover that a supraphysiological, stable OCT4 level is required, but not sufficient, for efficient iPSC colony formation. Our synthetic genetic circuit design and high-throughput live-imaging pipeline are generalizable for investigating TF dynamics for other cell fate programming applications.
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Affiliation(s)
- Katherine Ilia
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nika Shakiba
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3 Canada
| | - Trevor Bingham
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard University, Boston, MA 02115, USA
| | - Ross D. Jones
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3 Canada
| | - Michael M. Kaminski
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz-Association, Berlin 10115, Germany
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Medizinische Klinik m.S. Nephrologie und Intensivmedizin, Berlin 10117, Germany
- Berlin Institute of Health, Berlin 13125, Germany
| | - Eliezer Aravera
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Simone Bruno
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
| | - Sebastian Palacios
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - James J. Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Domitilla Del Vecchio
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
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Wang NB, Lende-Dorn BA, Adewumi HO, Beitz AM, Han P, O'Shea TM, Galloway KE. Proliferation history and transcription factor levels drive direct conversion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.26.568736. [PMID: 38077004 PMCID: PMC10705288 DOI: 10.1101/2023.11.26.568736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The sparse and stochastic nature of reprogramming has obscured our understanding of how transcription factors drive cells to new identities. To overcome this limit, we developed a compact, portable reprogramming system that increases direct conversion of fibroblasts to motor neurons by two orders of magnitude. We show that subpopulations with different reprogramming potentials are distinguishable by proliferation history. By controlling for proliferation history and titrating each transcription factor, we find that conversion correlates with levels of the pioneer transcription factor Ngn2, whereas conversion shows a biphasic response to Lhx3. Increasing the proliferation rate of adult human fibroblasts generates morphologically mature, induced motor neurons at high rates. Using compact, optimized, polycistronic cassettes, we generate motor neurons that graft with the murine central nervous system, demonstrating the potential for in vivo therapies.
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Affiliation(s)
- Nathan B Wang
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | | | - Honour O Adewumi
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Adam M Beitz
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | - Patrick Han
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | - Timothy M O'Shea
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Kate E Galloway
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
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