Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths

Chunhe Li and Jin Wang

PLOS Computational Biology, 2013, vol. 9, issue 8, 1-14

Abstract: Cellular reprogramming has been recently intensively studied experimentally. We developed a global potential landscape and kinetic path framework to explore a human stem cell developmental network composed of 52 genes. We uncovered the underlying landscape for the stem cell network with two basins of attractions representing stem and differentiated cell states, quantified and exhibited the high dimensional biological paths for the differentiation and reprogramming process, connecting the stem cell state and differentiated cell state. Both the landscape and non-equilibrium curl flux determine the dynamics of cell differentiation jointly. Flux leads the kinetic paths to be deviated from the steepest descent gradient path, and the corresponding differentiation and reprogramming paths are irreversible. Quantification of paths allows us to find out how the differentiation and reprogramming occur and which important states they go through. We show the developmental process proceeds as moving from the stem cell basin of attraction to the differentiation basin of attraction. The landscape topography characterized by the barrier heights and transition rates quantitatively determine the global stability and kinetic speed of cell fate decision process for development. Through the global sensitivity analysis, we provided some specific predictions for the effects of key genes and regulation connections on the cellular differentiation or reprogramming process. Key links from sensitivity analysis and biological paths can be used to guide the differentiation designs or reprogramming tactics.Author Summary: Cellular differentiation and reprogramming have been extensively studied using experimental methods. We developed a landscape and kinetic path approach to explore the global stability of a stem cell developmental network. The cell fates are quantified by the basins of attractions of the underlying landscape. The developmental process can be quantitatively described and uncovered by the biological paths on the landscape from the progenitor state to the differentiation state. This allows us to trace the underlying detailed kinetic process and obtain the recipe for engineering differentiation and reprogramming. By quantifying the landscape topography by the barrier heights and dynamic transition speed, we can evaluate the stability and kinetics of cell fate decision making process of the development and reprogramming. The global sensitivity analysis provided predictions about the effects of the key genes and regulation links of the network on the stability of differentiation and reprogramming process. This can be tested in the experiments. Results from sensitivity analysis and biological paths acquired can be used to guide the differentiation designs or reprogramming tactics.

Date: 2013
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (1)

Downloads: (external link)
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003165 (text/html)
https://journals.plos.org/ploscompbiol/article/fil ... 03165&type=printable (application/pdf)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1003165

DOI: 10.1371/journal.pcbi.1003165

Access Statistics for this article

More articles in PLOS Computational Biology from Public Library of Science
Bibliographic data for series maintained by ploscompbiol ().