A Unified Genomic Mechanism of Cell-Fate Change

Tsuchiya, Masa; Giuliani, Alessandro; Zimatore, Giovanna; Erenpreisa, Jekaterina; Yoshikawa, Kunio

doi:10.1007/978-3-031-06573-6_2

Cited by 8 publications

(16 citation statements)

References 83 publications

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“…The arising of "expression waves" marking state transitions related to chromatin structural reorganization through self-organised critical control of whole-genome expression explains the regulation of biological adaptive systems, including the early embryo, living on the edge of chaos [27][28][29] and using explorative adaptation, which is particularly evident in cancer [14,30].…”

Section: Biphasic Temporal Expression Of Ap-1 Response In Various Str...mentioning

confidence: 99%

Self-organisation of early stress response in the biology of cancer

Erenpreisa,

Salmina,

Vainshelbaum

et al. 2024

Postepy Biochem

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The early stress response by AP-1 (FOS/JUN), supported by upregulation of c-Myc and involved in cell-fate changes and adaptation to hostile environments, is increased in cancer. The review shows the biphasic character of this response with negative feed-back typically lasting a few hours as a feature of the genome regulation by self-organising criticality. It involves rapid splitting of the pericentromeric heterochromatin clusters, opening of the active chromatin, and a massive transcription acceleration wave. Phylostratigraphic analysis revealed that AP-1 genes evolved in the Cambrian explosion ~500 Mya integrating the protein interaction networks of reproduction including proto-placenta intertwined with cytokine and immunity pathways, sex determination, oocyte maturation, and embryonal stemness. The peak of this response as part of accelerated cell senescence led by AP-1 and IL-1β was found in breast cancer cell-line resistant to doxorubicin. Adaptability of aggressive cancer to treatments can be explained by emergent stress response evolutionarily protecting reproduction

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Section: Biphasic Temporal Expression Of Ap-1 Response In Various Str...mentioning

confidence: 99%

Self-organisation of early stress response in the biology of cancer

Erenpreisa,

Salmina,

Vainshelbaum

et al. 2024

Postepy Biochem

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“…Through considerable research over the past several decades, c-SOC has become an important topic in many scientific research domains, such as brain research and social science [7,8]. In genomics, our own findings [9][10][11][12][13][14][15][16] revealed that self-organized criticality (SOC) is also a plausible, physically motivated, candidate framework for massive, coordinated gene expression regulation.…”

Section: Introductionmentioning

confidence: 99%

“…The occurrence of SOC in cell-fate changes has been demonstrated using a mean-field approach that exploits the average characteristics of groups of genes instead of dealing with noisy expressions of individual genes. This technique is grounded in the existence of the Coherent Stochastic Behavior (CSB; see more in [9][10][11][12][13][14][15][16]) of gene expressions within sufficiently large gene groups. While individual genes within a given group display stochasticity, the group's average expressions (centers of mass, CMs) quickly converge to certain values after the size of the group becomes sufficiently large.…”

Section: Introductionmentioning

confidence: 99%

“…Below, we list several essential key points that are important for understanding the self-organized critical (SOC) control of genome expression in cell-fate transitions (see more in [13,15].…”

Section: Introductionmentioning

confidence: 99%

“…The paper is organized as follows: Section 2 describes how, at the critical transition, OM genes dynamically modulate the synchronization of the CP and GA; this was conducted through the application of the Expression Flux Analysis (EFA: [15,16]) on time series genome expression data. Section 3 provides a potential mechanism for the synchronization between the CP and GA, and Section 4 gives a discussion of the biological basis of a potential unified SOC mechanism for the reversion of cancer cell-fate change, while Section 5 reports general conclusions.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Synchronization between Attractors: Genomic Mechanism of Cell-Fate Change

Tsuchiya

Brazhnik

Bizzarri

et al. 2023

IJMS

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Herein, we provide a brief overview of complex systems theory approaches to investigate the genomic mechanism of cell-fate changes. Cell trajectories across the epigenetic landscape, whether in development, environmental responses, or disease progression, are controlled by extensively coordinated genome-wide gene expression changes. The elucidation of the mechanisms underlying these coherent expression changes is of fundamental importance in cell biology and for paving the road to new therapeutic approaches. In previous studies, we pointed at dynamic criticality as a plausible characteristic of genome-wide transition dynamics guiding cell fate. Whole-genome expression develops an engine-like organization (genome engine) in order to establish an autonomous dynamical system, capable of both homeostasis and transition behaviors. A critical set of genes behaves as a critical point (CP) that serves as the organizing center of cell-fate change. When the system is pushed away from homeostasis, the state change that occurs at the CP makes local perturbation spread over the genome, demonstrating self-organized critical (SOC) control of genome expression. Oscillating-Mode genes (which normally keep genome expression on pace with microenvironment fluctuations), when in the presence of an effective perturbative stimulus, drive the dynamics of synchronization, and thus guide the cell-fate transition.

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