Shibin Mathew1, Sankaramanivel Sundararaj1, Hikaru Mamiya1, Ipsita Banerjee2. 1. Department of Chemical and Petroleum Engineering, University of Pittsburgh, PA 15261, Department of Bioengineering and McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA. 2. Department of Chemical and Petroleum Engineering, University of Pittsburgh, PA 15261, Department of Bioengineering and McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USADepartment of Chemical and Petroleum Engineering, University of Pittsburgh, PA 15261, Department of Bioengineering and McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USADepartment of Chemical and Petroleum Engineering, University of Pittsburgh, PA 15261, Department of Bioengineering and McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
Abstract
MOTIVATION: Maintenance of the self-renewal state in human embryonic stem cells (hESCs) is the foremost critical step for regenerative therapy applications. The insulin-mediated PI3K/AKT pathway is well appreciated as being the central pathway supporting hESC self-renewal; however, the regulatory interactions in the pathway that maintain cell state are not yet known. Identification of these regulatory pathway components will be critical for designing targeted interventions to facilitate a completely defined platform for hESC propagation and differentiation. Here, we have developed a systems analysis approach to identify regulatory components that control PI3K/AKT pathway in self-renewing hESCs. RESULTS: A detailed mathematical model was adopted to explain the complex regulatory interactions in the PI3K/AKT pathway. We evaluated globally sensitive processes of the pathway in a computationally efficient manner by replacing the detailed model by a surrogate meta-model. Our mathematical analysis, supported by experimental validation, reveals that negative regulators of the molecules IRS1 and PIP3 primarily govern the steady state of the pathway in hESCs. Among the regulators, negative feedback via IRS1 reduces the sensitivity of various reactions associated with direct trunk of the pathway and also constraints the propagation of parameter uncertainty to the levels of post receptor signaling molecules. Furthermore, our results suggest that inhibition of negative feedback can significantly increase p-AKT levels and thereby, better support hESC self-renewal. Our integrated mathematical modeling and experimental workflow demonstrates the significant advantage of computationally efficient meta-model approaches to detect sensitive targets from signaling pathways. AVAILABILITY AND IMPLEMENTATION: FORTRAN codes for the PI3K/AKT pathway and the RS-HDMR implementation are available from the authors upon request.
MOTIVATION: Maintenance of the self-renewal state in human embryonic stem cells (hESCs) is the foremost critical step for regenerative therapy applications. The insulin-mediated PI3K/AKT pathway is well appreciated as being the central pathway supporting hESC self-renewal; however, the regulatory interactions in the pathway that maintain cell state are not yet known. Identification of these regulatory pathway components will be critical for designing targeted interventions to facilitate a completely defined platform for hESC propagation and differentiation. Here, we have developed a systems analysis approach to identify regulatory components that control PI3K/AKT pathway in self-renewing hESCs. RESULTS: A detailed mathematical model was adopted to explain the complex regulatory interactions in the PI3K/AKT pathway. We evaluated globally sensitive processes of the pathway in a computationally efficient manner by replacing the detailed model by a surrogate meta-model. Our mathematical analysis, supported by experimental validation, reveals that negative regulators of the molecules IRS1 and PIP3 primarily govern the steady state of the pathway in hESCs. Among the regulators, negative feedback via IRS1 reduces the sensitivity of various reactions associated with direct trunk of the pathway and also constraints the propagation of parameter uncertainty to the levels of post receptor signaling molecules. Furthermore, our results suggest that inhibition of negative feedback can significantly increase p-AKT levels and thereby, better support hESC self-renewal. Our integrated mathematical modeling and experimental workflow demonstrates the significant advantage of computationally efficient meta-model approaches to detect sensitive targets from signaling pathways. AVAILABILITY AND IMPLEMENTATION: FORTRAN codes for the PI3K/AKT pathway and the RS-HDMR implementation are available from the authors upon request.
Authors: Amanda B McLean; Kevin A D'Amour; Karen L Jones; Malini Krishnamoorthy; Michael J Kulik; David M Reynolds; Alan M Sheppard; Huiqing Liu; Ying Xu; Emmanuel E Baetge; Stephen Dalton Journal: Stem Cells Date: 2007-01 Impact factor: 6.277
Authors: Amar M Singh; David Reynolds; Timothy Cliff; Satoshi Ohtsuka; Alexa L Mattheyses; Yuhua Sun; Laura Menendez; Michael Kulik; Stephen Dalton Journal: Cell Stem Cell Date: 2012-03-02 Impact factor: 24.633
Authors: Alexander D Malkin; Robert P Sheehan; Shibin Mathew; William J Federspiel; Heinz Redl; Gilles Clermont Journal: PLoS Comput Biol Date: 2015-10-15 Impact factor: 4.475