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From Cell States to Cell Fates: Control of Cell State Transitions

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Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2745))

Abstract

We examine the coordinated behavior of thousands of genes in cell fate transitions through genome expression as an integrated dynamical system using the concepts of self-organized criticality and coherent stochastic behavior. To quantify the effects of the collective behavior of genes, we adopted the flux balance approach and developed it in a new tool termed expression flux analysis (EFA). Here we describe this tool and demonstrate how its application to specific experimental genome-wide expression data provides new insights into the dynamics of the cell-fate transitions. Particularly, we show that in cell fate change, specific stochastic perturbations can spread over the entire system to guide distinct cell fate transitions through switching cyclic flux flow in the genome engine. Utilization of EFA enables us to elucidate a unified genomic mechanism for when and how cell-fate change occurs through critical transitions.

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Abbreviations

atRA:

all-trans retinoic acid

CM:

center of mass

CP:

critical point

CSB:

coherent stochastic behavior

CV:

coefficient of variation

DMSO:

dimethyl sulfoxide

EFA:

expression flux analysis

EGF:

epidermal growth factor

GA:

genome attractor

HRG:

Heregulin

nrmsf:

normalized root mean square fluctuation

PAD:

pericentromeric-associated domain

PCA:

principal component analysis

SOC:

self-organized criticality

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Acknowledgements

MT sincerely thanks Prof. Mariano Bizzarri for his editorial work, Prof. Kenichi Yoshikawa for his supports on cell-fate project over the years, and the following institution and individuals who helped complete this research project: the SEIKO Life Science Laboratory, Osaka, Japan, his family (particularly, his daughters: Drs. Kimiko and Kazumi Tsuchiya, and Dr. Harry Taylor), and Dr. Daisaku Ikeda.

Author information

Authors and Affiliations

  1. SEIKO Life Science Laboratory, SEIKO Research Institute for Education, Osaka, Japan

    Masa Tsuchiya

  2. Environment and Health Department, Istituto Superiore di Sanitá, Rome, Italy

    Alessandro Giuliani

  3. Academy of Integrated Science, Virginia Tech, Blacksburg, VA, USA

    Paul Brazhnik

Authors
  1. Masa Tsuchiya
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  2. Alessandro Giuliani
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  3. Paul Brazhnik
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Editor information

Editors and Affiliations

  1. Department of Experimental Medicine, Sapienza University, Rome, Italy

    Mariano Bizzarri

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© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Tsuchiya, M., Giuliani, A., Brazhnik, P. (2024). From Cell States to Cell Fates: Control of Cell State Transitions. In: Bizzarri, M. (eds) Systems Biology. Methods in Molecular Biology, vol 2745. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3577-3_9

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  • DOI: https://doi.org/10.1007/978-1-0716-3577-3_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3576-6

  • Online ISBN: 978-1-0716-3577-3

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