Quantifying cell fate decisions for differentiation and reprogramming of a human stem cell network: landscape and biological paths.
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.
Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, New York, United States of America.
Chunhe
C
Li
Jin
J
Wang
D002454:Cell Differentiation / Q000502:physiology; D019295:Computational Biology; D053263:Gene Regulatory Networks; D005819:Genetic Markers; D006801:Humans; D007700:Kinetics; D008954:Models, Biological; D013234:Stem Cells / Q000166:cytology*
D005819:Genetic Markers