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Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts

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. Here, we identify the succes...

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Autores principales: Ilia, Katherine, Shakiba, Nika, Bingham, Trevor, Jones, Ross D., Kaminski, Michael M., Aravera, Eliezer, Bruno, Simone, Palacios, Sebastian, Weiss, Ron, Collins, James J., Del Vecchio, Domitilla, Schlaeger, Thorsten M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9900859/
https://www.ncbi.nlm.nih.gov/pubmed/36747813
http://dx.doi.org/10.1101/2023.01.25.525529
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author Ilia, Katherine
Shakiba, Nika
Bingham, Trevor
Jones, Ross D.
Kaminski, Michael M.
Aravera, Eliezer
Bruno, Simone
Palacios, Sebastian
Weiss, Ron
Collins, James J.
Del Vecchio, Domitilla
Schlaeger, Thorsten M.
author_facet Ilia, Katherine
Shakiba, Nika
Bingham, Trevor
Jones, Ross D.
Kaminski, Michael M.
Aravera, Eliezer
Bruno, Simone
Palacios, Sebastian
Weiss, Ron
Collins, James J.
Del Vecchio, Domitilla
Schlaeger, Thorsten M.
author_sort Ilia, Katherine
collection PubMed
description 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. Here, we identify the successful reprogramming trajectories of the core pluripotency TF, OCT4, and design a genetic controller that enforces such trajectories with high precision. By combining a genetic circuit that generates a wide range of OCT4 trajectories with live-cell imaging, we track OCT4 trajectories with clonal resolution and find that a distinct constant OCT4 trajectory is required for colony formation. We then develop a synthetic genetic circuit that yields a tight OCT4 distribution around the identified trajectory and outperforms in terms of reprogramming efficiency other circuits that less accurately regulate OCT4. Our synthetic biology approach is generalizable for identifying and enforcing TF dynamics for cell fate programming applications.
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spelling pubmed-99008592023-02-07 Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts Ilia, Katherine Shakiba, Nika Bingham, Trevor Jones, Ross D. Kaminski, Michael M. Aravera, Eliezer Bruno, Simone Palacios, Sebastian Weiss, Ron Collins, James J. Del Vecchio, Domitilla Schlaeger, Thorsten M. bioRxiv Article 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. Here, we identify the successful reprogramming trajectories of the core pluripotency TF, OCT4, and design a genetic controller that enforces such trajectories with high precision. By combining a genetic circuit that generates a wide range of OCT4 trajectories with live-cell imaging, we track OCT4 trajectories with clonal resolution and find that a distinct constant OCT4 trajectory is required for colony formation. We then develop a synthetic genetic circuit that yields a tight OCT4 distribution around the identified trajectory and outperforms in terms of reprogramming efficiency other circuits that less accurately regulate OCT4. Our synthetic biology approach is generalizable for identifying and enforcing TF dynamics for cell fate programming applications. Cold Spring Harbor Laboratory 2023-01-25 /pmc/articles/PMC9900859/ /pubmed/36747813 http://dx.doi.org/10.1101/2023.01.25.525529 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Ilia, Katherine
Shakiba, Nika
Bingham, Trevor
Jones, Ross D.
Kaminski, Michael M.
Aravera, Eliezer
Bruno, Simone
Palacios, Sebastian
Weiss, Ron
Collins, James J.
Del Vecchio, Domitilla
Schlaeger, Thorsten M.
Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts
title Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts
title_full Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts
title_fullStr Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts
title_full_unstemmed Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts
title_short Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts
title_sort synthetic genetic circuits to uncover and enforce the oct4 trajectories of successful reprogramming of human fibroblasts
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9900859/
https://www.ncbi.nlm.nih.gov/pubmed/36747813
http://dx.doi.org/10.1101/2023.01.25.525529
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