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Heredia-Torrejón M, Montañez R, González-Meneses A, Carcavilla A, Medina MA, Lechuga-Sancho AM. VUS next in rare diseases? Deciphering genetic determinants of biomolecular condensation. Orphanet J Rare Dis 2024; 19:327. [PMID: 39243101 PMCID: PMC11380411 DOI: 10.1186/s13023-024-03307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 08/06/2024] [Indexed: 09/09/2024] Open
Abstract
The diagnostic odysseys for rare disease patients are getting shorter as next-generation sequencing becomes more widespread. However, the complex genetic diversity and factors influencing expressivity continue to challenge accurate diagnosis, leaving more than 50% of genetic variants categorized as variants of uncertain significance.Genomic expression intricately hinges on localized interactions among its products. Conventional variant prioritization, biased towards known disease genes and the structure-function paradigm, overlooks the potential impact of variants shaping the composition, location, size, and properties of biomolecular condensates, genuine membraneless organelles swiftly sensing and responding to environmental changes, and modulating expressivity.To address this complexity, we propose to focus on the nexus of genetic variants within biomolecular condensates determinants. Scrutinizing variant effects in these membraneless organelles could refine prioritization, enhance diagnostics, and unveil the molecular underpinnings of rare diseases. Integrating comprehensive genome sequencing, transcriptomics, and computational models can unravel variant pathogenicity and disease mechanisms, enabling precision medicine. This paper presents the rationale driving our proposal and describes a protocol to implement this approach. By fusing state-of-the-art knowledge and methodologies into the clinical practice, we aim to redefine rare diseases diagnosis, leveraging the power of scientific advancement for more informed medical decisions.
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Affiliation(s)
- María Heredia-Torrejón
- Inflammation, Nutrition, Metabolism and Oxidative Stress Research Laboratory, Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cadiz, Spain
- Mother and Child Health and Radiology Department. Area of Clinical Genetics, University of Cadiz. Faculty of Medicine, Cadiz, Spain
| | - Raúl Montañez
- Inflammation, Nutrition, Metabolism and Oxidative Stress Research Laboratory, Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cadiz, Spain.
- Department of Molecular Biology and Biochemistry, University of Malaga, Andalucía Tech, E-29071, Málaga, Spain.
| | - Antonio González-Meneses
- Division of Dysmorphology, Department of Paediatrics, Virgen del Rocio University Hospital, Sevilla, Spain
- Department of Paediatrics, Medical School, University of Sevilla, Sevilla, Spain
| | - Atilano Carcavilla
- Pediatric Endocrinology Department, Hospital Universitario La Paz, 28046, Madrid, Spain
- Multidisciplinary Unit for RASopathies, Hospital Universitario La Paz, 28046, Madrid, Spain
| | - Miguel A Medina
- Department of Molecular Biology and Biochemistry, University of Malaga, Andalucía Tech, E-29071, Málaga, Spain.
- Biomedical Research Institute and nanomedicine platform of Málaga IBIMA-BIONAND, E-29071, Málaga, Spain.
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, E-28029, Madrid, Spain.
| | - Alfonso M Lechuga-Sancho
- Inflammation, Nutrition, Metabolism and Oxidative Stress Research Laboratory, Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cadiz, Spain
- Division of Endocrinology, Department of Paediatrics, Puerta del Mar University Hospital, Cádiz, Spain
- Area of Paediatrics, Department of Child and Mother Health and Radiology, Medical School, University of Cadiz, Cadiz, Spain
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Tsuchiya M, Giuliani A, Brazhnik P. From Cell States to Cell Fates: Control of Cell State Transitions. Methods Mol Biol 2024; 2745:137-162. [PMID: 38060184 DOI: 10.1007/978-1-0716-3577-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
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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Affiliation(s)
- Masa Tsuchiya
- SEIKO Life Science Laboratory, SEIKO Research Institute for Education, Osaka, Japan
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, Rome, Italy
| | - Paul Brazhnik
- Academy of Integrated Science, Virginia Tech, Blacksburg, VA, USA
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Tsuchiya M, Brazhnik P, Bizzarri M, Giuliani A. Synchronization between Attractors: Genomic Mechanism of Cell-Fate Change. Int J Mol Sci 2023; 24:11603. [PMID: 37511359 PMCID: PMC10380305 DOI: 10.3390/ijms241411603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
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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Affiliation(s)
- Masa Tsuchiya
- SEIKO Life Science Laboratory, SEIKO Research Institute for Education, Osaka 540-6591, Japan
| | - Paul Brazhnik
- Academy of Integrated Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Mariano Bizzarri
- Systems Biology Group, Department of Experimental Medicine, University La Sapienza, 00163 Roma, Italy
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, 00161 Rome, Italy
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Tsuchiya M, Giuliani A, Zimatore G, Erenpreisa J, Yoshikawa K. A Unified Genomic Mechanism of Cell-Fate Change. Results Probl Cell Differ 2022; 70:35-69. [PMID: 36348104 DOI: 10.1007/978-3-031-06573-6_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The purpose of our studies is to elucidate the nature of massive control of the whole genome expression with a particular emphasis on cell-fate change. The whole genome expression is coordinated by the emergence of a critical point (CP: a peculiar set of biphasic genes) with the genome acting as an integrated dynamical system. In response to stimuli, the genome expression self-organizes into local sub-, near-, and super-critical states, each exhibiting distinct collective behaviors with its center of mass acting as a local attractor, coexisting with the whole genome attractor (GA). The CP serves as the organizing center of cell-fate change, and its activation makes local perturbation to spread over the genome affecting GA. The activation of CP is in turn elicited by genes with elevated temporal variance (oscillating-mode genes), normally in charge to keep genome expression at pace with microenvironment fluctuations. When oscillation exceeds a given threshold, the CP synchronizes with the GA driving genome expression state transition. The expression synchronization wave invading the entire genome is fostered by the fusion-splitting dynamics of silencing pericentromere-associated heterochromatin domains and the consequent folding-unfolding transitions of transcribing euchromatin domains. The proposed mechanism is a unified step toward a time-evolutional transition theory of biological regulation.
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Affiliation(s)
- Masa Tsuchiya
- SEIKO Life Science Laboratory, SEIKO Research Institute for Education, Osaka, Japan.
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, Rome, Italy.
| | | | | | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
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Zimatore G, Tsuchiya M, Hashimoto M, Kasperski A, Giuliani A. Self-organization of whole-gene expression through coordinated chromatin structural transition. BIOPHYSICS REVIEWS 2021; 2:031303. [PMID: 38505632 PMCID: PMC10903504 DOI: 10.1063/5.0058511] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/20/2021] [Indexed: 03/21/2024]
Abstract
The human DNA molecule is a 2-m-long polymer collapsed into the micrometer space of the cell nucleus. This simple consideration rules out any "Maxwell demon"-like explanation of regulation in which a single regulatory molecule (e.g., a transcription factor) finds autonomously its way to the particular target gene whose expression must be repressed or enhanced. A gene-by-gene regulation is still more contrasting with the physical reality when in the presence of cell state transitions involving the contemporary expression change of thousands of genes. This state of affair asks for a statistical mechanics inspired approach where specificity arises from a selective unfolding of chromatin driving the rewiring of gene expression pattern. The arising of "expression waves" marking state transitions related to chromatin structural reorganization through self-organized critical control of whole-genome expression will be described in the present paper. We adopt as a model system the gene expression time course of a cancer cell (MCF-7) population exposed to an efficient stimulus causing a state transition in comparison with an ineffective stimulus. The obtained results will be put into the perspective of biological adaptive systems living on the edge of chaos.
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Affiliation(s)
- Giovanna Zimatore
- eCampus University, 22060 Novedrate, Como, Italy and CNR-IMM Bologna, Italy
| | - Masa Tsuchiya
- SEIKO Life Science Laboratory, SEIKO Research Institute for Education, Osaka 540-659, Japan
| | - Midori Hashimoto
- Japan Fisheries Research and Education Agency, Kanagawa 236-8648, Japan
| | - Andrzej Kasperski
- Institute of Biological Sciences, Department of Biotechnology, University of Zielona Góra, ul. Szafrana 1, 65-516 Zielona Góra, Poland
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, 00161 Rome, Italy
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Krigerts J, Salmina K, Freivalds T, Zayakin P, Rumnieks F, Inashkina I, Giuliani A, Hausmann M, Erenpreisa J. Differentiating cancer cells reveal early large-scale genome regulation by pericentric domains. Biophys J 2021; 120:711-724. [PMID: 33453273 PMCID: PMC7896032 DOI: 10.1016/j.bpj.2021.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/30/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
Finding out how cells prepare for fate change during differentiation commitment was our task. To address whether the constitutive pericentromere-associated domains (PADs) may be involved, we used a model system with known transcriptome data, MCF-7 breast cancer cells treated with the ErbB3 ligand heregulin (HRG), which induces differentiation and is used in the therapy of cancer. PAD-repressive heterochromatin (H3K9me3), centromere-associated-protein-specific, and active euchromatin (H3K4me3) antibodies, real-time PCR, acridine orange DNA structural test (AOT), and microscopic image analysis were applied. We found a two-step DNA unfolding after 15-20 and 60 min of HRG treatment, respectively. This behavior was consistent with biphasic activation of the early response genes (c-fos - fosL1/myc) and the timing of two transcriptome avalanches reported in the literature. In control, the average number of PADs negatively correlated with their size by scale-free distribution, and centromere clustering in turn correlated with PAD size, both indicating that PADs may create and modulate a suprachromosomal network by fusing and splitting a constant proportion of the constitutive heterochromatin. By 15 min of HRG treatment, the bursting unraveling of PADs from the nucleolus boundary occurred, coinciding with the first step of H3K4me3 chromatin unfolding, confirmed by AOT. The second step after 60 min of HRG treatment was associated with transcription of long noncoding RNA from PADs and peaking of fosL1/c-myc response. We hypothesize that the bursting of PAD clusters under a critical silencing threshold pushes the first transcription avalanche, whereas the destruction of the PAD network enables genome rewiring needed for differentiation repatterning, mediated by early response bivalent genes.
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Affiliation(s)
- Jekabs Krigerts
- Latvian Biomedicine Research and Study Centre, Riga, Latvia; University of Latvia, Riga, Latvia
| | | | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedicine Research and Study Centre, Riga, Latvia
| | - Felikss Rumnieks
- Latvian Biomedicine Research and Study Centre, Riga, Latvia; University of Latvia, Riga, Latvia
| | - Inna Inashkina
- Latvian Biomedicine Research and Study Centre, Riga, Latvia
| | - Alessandro Giuliani
- Environment and Health Department, Italian National Institute of Health, Rome, Italy
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, Heidelberg, Germany.
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Erenpreisa J, Salmina K, Anatskaya O, Cragg MS. Paradoxes of cancer: Survival at the brink. Semin Cancer Biol 2020; 81:119-131. [PMID: 33340646 DOI: 10.1016/j.semcancer.2020.12.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/17/2022]
Abstract
The fundamental understanding of how Cancer initiates, persists and then progresses is evolving. High-resolution technologies, including single-cell mutation and gene expression measurements, are now attainable, providing an ever-increasing insight into the molecular details. However, this higher resolution has shown that somatic mutation theory itself cannot explain the extraordinary resistance of cancer to extinction. There is a need for a more Systems-based framework of understanding cancer complexity, which in particular explains the regulation of gene expression during cell-fate decisions. Cancer displays a series of paradoxes. Here we attempt to approach them from the view-point of adaptive exploration of gene regulatory networks at the edge of order and chaos, where cell-fate is changed by oscillations between alternative regulators of cellular senescence and reprogramming operating through self-organisation. On this background, the role of polyploidy in accessing the phylogenetically pre-programmed "oncofetal attractor" state, related to unicellularity, and the de-selection of unsuitable variants at the brink of cell survival is highlighted. The concepts of the embryological and atavistic theory of cancer, cancer cell "life-cycle", and cancer aneuploidy paradox are dissected under this lense. Finally, we challenge researchers to consider that cancer "defects" are mostly the adaptation tools of survival programs that have arisen during evolution and are intrinsic of cancer. Recognition of these features should help in the development of more successful anti-cancer treatments.
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Affiliation(s)
| | - Kristine Salmina
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | | | - Mark S Cragg
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
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Dual Function Molecules and Processes in Cell Fate Decision: A Preface to the Special Issue. Int J Mol Sci 2020; 21:ijms21249601. [PMID: 33339424 PMCID: PMC7766797 DOI: 10.3390/ijms21249601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/04/2020] [Indexed: 11/17/2022] Open
Abstract
A lot of water has passed under the bridge since 1999, when C [...].
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Proietti S, Cucina A, Pensotti A, Fuso A, Marchese C, Nicolini A, Bizzarri M. Tumor reversion and embryo morphogenetic factors. Semin Cancer Biol 2020; 79:83-90. [DOI: 10.1016/j.semcancer.2020.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 07/09/2020] [Accepted: 09/01/2020] [Indexed: 12/20/2022]
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