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Molecular Advances and Insights in Cancer Genomics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Oncology".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 602

Special Issue Editors


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Guest Editor
SEIKO Life Science Laboratory, SEIKO Research Institute for Education, Osaka 540-6591, Japan
Interests: non-equilibrium dynamics; single-cell early embryo development; critical gene ensemble; cell fate

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Guest Editor
Environment and Health Department, Istituto Superiore di Sanità, 00161 Rome, Italy
Interests: data analysis; complex systems; systems biology; statistical mechanics
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
Interests: biological physics; nonlinear science; biophysical chemistry

Special Issue Information

Dear Colleagues,

Cancer genomics has revolutionized tumor biology, offering new perspectives on the nature and onset of this complex pathology. Recent breakthroughs in chromatin architecture—the dynamic DNA-protein complex regulating gene expression—offer deep insights into cancer development and progression. This special topic, “Molecular Advances and Insights in Cancer Genomics”, explores these advancements and their impact on improving cancer outcomes.

High-throughput technologies like next-generation sequencing and single-cell genomics reveal genetic and epigenetic alterations driving tumor heterogeneity and clonal evolution. Integrating multi-omics—genomics, transcriptomics, proteomics, and epigenomics—provides a comprehensive molecular landscape of cancer, identifying actionable biomarkers for early detection, prognosis, and personalized treatments.

From a broader perspective, considering the genome as a dynamic system endowed with both criticality and computational capabilities provides a fundamentally new framework for understanding biological systems. This framework, grounded in complex systems biology, enhances our understanding of gene regulation and cellular responses, addressing challenges like tumor heterogeneity and resistance. Chromatin-focused techniques, such as Hi-C and single-cell CRISPR screens, combined with genome computing principles, provide vital insights into genome organization and accessibility. These advancements pave the way for more effective therapies and improved patient outcomes while simultaneously laying the foundation for a new discipline in biological statistical mechanics.

Dr. Masa Tsuchiya
Prof. Dr. Alessandro Giuliani
Prof. Dr. Kenichi Yoshikawa
Guest Editors

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Keywords

  • biochemistry
  • biophysics
  • cancer genomics
  • cell biology
  • complex networks
  • complex systems
  • data science
  • development and differentiation
  • epigenomics
  • genome computing
  • higher-order structure of chromatin
  • multi-omics integration
  • next-generation sequencing
  • proteomics
  • single-cell CRISPR screens
  • single-cell genomics
  • transcriptomics
  • tumor biology

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Published Papers (1 paper)

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Research

35 pages, 6442 KiB  
Article
Genomic-Thermodynamic Phase Synchronization: Maxwell’s Demon-like Regulation of Cell Fate Transition
by Masa Tsuchiya, Kenichi Yoshikawa and Alessandro Giuliani
Int. J. Mol. Sci. 2025, 26(10), 4911; https://doi.org/10.3390/ijms26104911 - 20 May 2025
Viewed by 73
Abstract
Dynamic criticality—the balance between order and chaos—is fundamental to genome regulation and cellular transitions. In this study, we investigate the distinct behaviors of gene expression dynamics in MCF-7 breast cancer cells under two stimuli: heregulin (HRG), which promotes cell fate transitions, and epidermal [...] Read more.
Dynamic criticality—the balance between order and chaos—is fundamental to genome regulation and cellular transitions. In this study, we investigate the distinct behaviors of gene expression dynamics in MCF-7 breast cancer cells under two stimuli: heregulin (HRG), which promotes cell fate transitions, and epidermal growth factor (EGF), which binds to the same receptor but fails to induce cell-fate changes. We model the system as an open, nonequilibrium thermodynamic system and introduce a convergence-based approach for the robust estimation of information-thermodynamic metrics. Our analysis reveals that the Shannon entropy of the critical point (CP) dynamically synchronizes with the entropy of the rest of the whole expression system (WES), reflecting coordinated transitions between ordered and disordered phases. This phase synchronization is driven by net mutual information scaling with CP entropy dynamics, demonstrating how the CP governs genome-wide coherence. Furthermore, higher-order mutual information emerges as a defining feature of the nonlinear gene expression network, capturing collective effects beyond simple pairwise interactions. By achieving thermodynamic phase synchronization, the CP orchestrates the entire expression system. Under HRG stimulation, the CP becomes active, functioning as a Maxwell’s demon with dynamic, rewritable chromatin memory to guide a critical transition in cell fate. In contrast, under EGF stimulation, the CP remains inactive in this strategic role, passively facilitating a non-critical transition. These findings establish a biophysical framework for cell fate determination, paving the way for innovative approaches in cancer research and stem cell therapy. Full article
(This article belongs to the Special Issue Molecular Advances and Insights in Cancer Genomics)
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