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Imaging Cell Lineage with a Synthetic Digital Recording System


Edmonds, KeHuan Kuo (2022) Imaging Cell Lineage with a Synthetic Digital Recording System. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/a4m3-m603.


In multicellular organisms, the lineage history and spatial organization of cells both play pivotal roles in cell fate determination during development, homeostasis, and disease. Investigating lineage relationships alongside cell state and space would provide a fundamental understanding of these biological processes. Current lineage tracking approaches rely on the progressive accumulation of either naturally-occurring somatic mutations or experimentally introduced markers. In most cases, these marks are then read out by sequencing, discarding the spatial information of the cells. To address this vital gap in our toolkit, we developed a new synthetic lineage tracking system that allows us to image single-cell lineage history. This system, termed integrase-editable memory by engineered mutagenesis with optical in situ readout (intMEMOIR), uses serine integrases to stochastically and irreversibly edit a synthetic memory array, generating up to 59,049 different outcomes that can be unambiguously distinguished by fluorescence in situ hybridization (FISH). We evaluated the reconstruction accuracy of our system in mouse embryonic stem (mES) cells and disentangled the relative contribution of lineage and space to cell fate determination in Drosophila brain development, establishing the foundation for an expandable synthetic microscopy-readable system. In this thesis, Chapter 1 introduces the importance of cell lineage and spatial organization to cell fate determination, and includes a brief history of the existing technologies of the lineage tracking field. Chapter 2 describes our characterization and demonstration of the intMEMOIR system. Finally, Chapter 3 discusses design principles for robust, serine-integrase-based recording systems and suggests future directions for intMEMOIR.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:synthetic biology; lineage recording; intMEMOIR; serine integrase; developmental biology; in situ readout
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Biology
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Elowitz, Michael B.
Thesis Committee:
  • Hay, Bruce A. (chair)
  • Elowitz, Michael B.
  • Lois, Carlos
  • Sternberg, Paul W.
  • Cai, Long
Defense Date:22 October 2021
Record Number:CaltechTHESIS:11272021-193744399
Persistent URL:
Related URLs:
URLURL TypeDescription is adapted for Ch. 2., analyses, code, and sequences for Ch. 2., analyses, code, and sequences for Ch. 3.
Edmonds, KeHuan Kuo0000-0002-7317-2669
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:14434
Deposited By: KeHuan Edmonds
Deposited On:20 Jan 2022 17:02
Last Modified:27 Jan 2022 20:24

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