Nika Shakiba, Postdoctoral Fellow, MIT
Cell fate programming can be achieved through the forced overexpression of key transcription factors (TFs), directing cells to new states. The ability to program cell fate not only provides novel insights into the nature of cell state plasticity, but also has implications for regenerative medicine. Perhaps the most prominent example of cell programming is the process of “reprogramming”, whereby somatic cells are induced to a pluripotent stem cell state through the forced overexpression of four key TFs. While reprogramming has been extensively studied, there remains an opportunity to apply engineering principles to predictably control the cell state of somatic cells as they navigate the reprogramming process, thereby resulting in high-efficiency and high-fidelity cell fate transitions. Here, we hypothesize that the process of reprogramming human somatic cells, which is traditionally hindered by low efficiencies, can be improved by guiding cells on a trajectory of TF overexpression in which factor stoichiometry follows an optimized route. To do this, we first apply a barcode-based lineage tracing strategy to uncover the ideal reprogramming route of successful human cells and next develop a synthetic genetic circuit for tunable and dynamic control over TF expression to track the predicted ideal trajectory. Our results reveal a “sweet spot” of TF expression throughout reprogramming and in pluripotency while demonstrating a dose-dependent effect of TF expression on reprogramming efficiency. Furthermore, by applying a negative-feedback approach, we develop a novel genetic circuit with two key design properties – the elimination of endogenous TF expression and tunable exogenous expression – enabling full temporal control over TF levels. Our combined lineage tracing and synthetic biology approach serves as a powerful tool for cell fate programming broadly, providing key insights into the role of TF manipulations on driving cell fate as well as how cell trajectories can be predictably controlled using a novel synthetic genetic circuit design.
Dr. Nika Shakiba is currently a postdoctoral fellow in Prof. Ron Weiss’ Lab for Mammalian Synthetic Biology in the Department of Biological Engineering at Massachusetts Institute of Technology (MIT). She will be joining the University of British Columbia (UBC) in Vancouver as an Assistant Professor in July 2020. Her work in synthetic biology uses engineering principles to control the behavior of stem cells through the design, construction, and optimization of decision-making genetic circuits. Dr. Shakiba completed her doctoral training in Prof. Peter Zandstra’s Stem Cell Bioengineering lab at the University of Toronto, where she focused on uncovering the role of heterogeneity and clonal competition in the reprogramming process. Her independent research program seeks to apply a combined systems and synthetic biology approach to reverse- and forward-engineer the role of cell competition in developmental and stem cell systems.