1
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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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2
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Polyploidy and Myc Proto-Oncogenes Promote Stress Adaptation via Epigenetic Plasticity and Gene Regulatory Network Rewiring. Int J Mol Sci 2022; 23:ijms23179691. [PMID: 36077092 PMCID: PMC9456078 DOI: 10.3390/ijms23179691] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Polyploid cells demonstrate biological plasticity and stress adaptation in evolution; development; and pathologies, including cardiovascular diseases, neurodegeneration, and cancer. The nature of ploidy-related advantages is still not completely understood. Here, we summarize the literature on molecular mechanisms underlying ploidy-related adaptive features. Polyploidy can regulate gene expression via chromatin opening, reawakening ancient evolutionary programs of embryonality. Chromatin opening switches on genes with bivalent chromatin domains that promote adaptation via rapid induction in response to signals of stress or morphogenesis. Therefore, stress-associated polyploidy can activate Myc proto-oncogenes, which further promote chromatin opening. Moreover, Myc proto-oncogenes can trigger polyploidization de novo and accelerate genome accumulation in already polyploid cells. As a result of these cooperative effects, polyploidy can increase the ability of cells to search for adaptive states of cellular programs through gene regulatory network rewiring. This ability is manifested in epigenetic plasticity associated with traits of stemness, unicellularity, flexible energy metabolism, and a complex system of DNA damage protection, combining primitive error-prone unicellular repair pathways, advanced error-free multicellular repair pathways, and DNA damage-buffering ability. These three features can be considered important components of the increased adaptability of polyploid cells. The evidence presented here contribute to the understanding of the nature of stress resistance associated with ploidy and may be useful in the development of new methods for the prevention and treatment of cardiovascular and oncological diseases.
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3
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Rocha RP, Koçillari L, Suweis S, De Filippo De Grazia M, de Schotten MT, Zorzi M, Corbetta M. Recovery of neural dynamics criticality in personalized whole-brain models of stroke. Nat Commun 2022; 13:3683. [PMID: 35760787 PMCID: PMC9237050 DOI: 10.1038/s41467-022-30892-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/16/2022] [Indexed: 01/13/2023] Open
Abstract
The critical brain hypothesis states that biological neuronal networks, because of their structural and functional architecture, work near phase transitions for optimal response to internal and external inputs. Criticality thus provides optimal function and behavioral capabilities. We test this hypothesis by examining the influence of brain injury (strokes) on the criticality of neural dynamics estimated at the level of single participants using directly measured individual structural connectomes and whole-brain models. Lesions engender a sub-critical state that recovers over time in parallel with behavior. The improvement of criticality is associated with the re-modeling of specific white-matter connections. We show that personalized whole-brain dynamical models poised at criticality track neural dynamics, alteration post-stroke, and behavior at the level of single participants. The authors investigate the influence of brain injury (strokes) on the criticality of neural dynamics using directly measured connectomes and whole-brain models. They show that lesions engender a sub-critical state that recovers over time in parallel with behavior.
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Affiliation(s)
- Rodrigo P Rocha
- Departamento de Física, Centro de Ciências Físicas e Matemáticas, Universidade Federal de Santa Catarina, 88040-900, Florianópolis, SC, Brazil. .,Department of Physics, School of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil. .,Padova Neuroscience Center, Università di Padova, Padova, Italy.
| | - Loren Koçillari
- Padova Neuroscience Center, Università di Padova, Padova, Italy.,Laboratory of Neural Computation, Istituto Italiano di Tecnologia, 38068, Rovereto, Italy.,Dipartimento di Fisica e Astronomia, Università di Padova and INFN, via Marzolo 8, I-35131, Padova, Italy
| | - Samir Suweis
- Padova Neuroscience Center, Università di Padova, Padova, Italy.,Dipartimento di Fisica e Astronomia, Università di Padova and INFN, via Marzolo 8, I-35131, Padova, Italy
| | | | - Michel Thiebaut de Schotten
- Brain Connectivity and Behaviour Laboratory, BCBlab, Sorbonne Universities, Paris, France.,Groupe d'Imagerie Neurofonctionnelle, Institut des Maladies Neurodégénératives-UMR 5293, CNRS, CEA University of Bordeaux, Bordeaux, France
| | - Marco Zorzi
- IRCCS San Camillo Hospital, Venice, Italy.,Dipartimento di Psicologia Generale, Università di Padova, Padova, Italy
| | - Maurizio Corbetta
- Padova Neuroscience Center, Università di Padova, Padova, Italy.,Dipartimento di Neuroscienze, Università di Padova, Padova, Italy.,Venetian Institute of Molecular Medicine (VIMM), Fondazione Biomedica, Padova, Italy
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4
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Azadifar S, Rostami M, Berahmand K, Moradi P, Oussalah M. Graph-based relevancy-redundancy gene selection method for cancer diagnosis. Comput Biol Med 2022; 147:105766. [DOI: 10.1016/j.compbiomed.2022.105766] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/12/2022] [Accepted: 06/18/2022] [Indexed: 11/26/2022]
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5
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Knoch TA. How Genomes Emerge, Function, and Evolve: Living Systems Emergence-Genotype-Phenotype-Multilism-Genome/Systems Ecology. Results Probl Cell Differ 2022; 70:103-156. [PMID: 36348106 DOI: 10.1007/978-3-031-06573-6_4] [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] [Indexed: 06/16/2023]
Abstract
What holds together the world in its innermost, what life is, how it emerges, functions, and evolves, has not only been an epic matter of endless romantic sunset poetry and philosophy, but also manifests explicitly in its perhaps most central organization unit-genomes. Their 3D architecture and dynamics, including the interaction networks of regulatory elements, obviously co-evolved as inseparable systems allowing the physical storage, expression, and replication of genetic information. Since we were able to fill finally the much-debated centennial gaps in their 3D architecture and dynamics, now entire new perspectives open beyond epigenetics reaching as far as a general understanding of living systems: besides the previously known DNA double helix and nucleosome structure, the latter compact into a chromatin quasi-fibre folded into stable loops forming stable multi-loop aggregates/rosettes connected by linkers, creating hence the again already known chromosome arms and entire chromosomes forming the cell nucleus. Instantly and for the first time this leads now to a consistent and cross-proven systems statistical mechanics genomics framework elucidating genome intrinsic function and regulation including various components. It balances stability/flexibility ensuring genome integrity, enabling expression/regulation of genetic information, as well as genome replication/spread. Furthermore, genotype and phenotype are multiplisticly entangled being evolutionarily the outcome of both Darwinian natural selection and Lamarckian self-referenced manipulation-all embedded in even broader genome ecology (autopoietic) i(!)n- and environmental scopes. This allows formulating new meta-level functional semantics of genomics, i.e. notions as communication of genes, genomes, and information networks, architectural and dynamic spaces for creativity and innovation, or genomes as central geno-/phenotype entanglements. Beyond and most fundamentally, the paradoxical-seeming local equilibrium substance stability in its entity though far from a universal heat-death-like equilibrium is solved, and system irreversibility, time directionality, and thus the emergence of existence are clarified. Consequently, real deep understandings of genomes, life, and complex systems in general appear in evolutionary perspectives as well as from systems analyses, via system damage/disease (its repair/cure and manipulation) as far as the understanding of extraterrestrial life, the de novo creation and thus artificial life, and even the raison d'etre.
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Affiliation(s)
- Tobias A Knoch
- Biophysical Genomics, TAKnoch Joined Operations Administrative Office, Mannheim, Germany.
- Human Ecology and Complex Systems, German Society for Human Ecology (DGH), TAKnoch Joined Operations Administrative Office, Mannheim, Germany.
- TAK Renewable Energy UG, TAKnoch Joined Operations Administrative Office, Mannheim, Germany.
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6
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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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7
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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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8
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Erenpreisa J, Krigerts J, Salmina K, Gerashchenko BI, Freivalds T, Kurg R, Winter R, Krufczik M, Zayakin P, Hausmann M, Giuliani A. Heterochromatin Networks: Topology, Dynamics, and Function (a Working Hypothesis). Cells 2021; 10:1582. [PMID: 34201566 PMCID: PMC8304199 DOI: 10.3390/cells10071582] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022] Open
Abstract
Open systems can only exist by self-organization as pulsing structures exchanging matter and energy with the outer world. This review is an attempt to reveal the organizational principles of the heterochromatin supra-intra-chromosomal network in terms of nonlinear thermodynamics. The accessibility of the linear information of the genetic code is regulated by constitutive heterochromatin (CHR) creating the positional information in a system of coordinates. These features include scale-free splitting-fusing of CHR with the boundary constraints of the nucleolus and nuclear envelope. The analysis of both the literature and our own data suggests a radial-concentric network as the main structural organization principle of CHR regulating transcriptional pulsing. The dynamic CHR network is likely created together with nucleolus-associated chromatin domains, while the alveoli of this network, including springy splicing speckles, are the pulsing transcription hubs. CHR contributes to this regulation due to the silencing position variegation effect, stickiness, and flexible rigidity determined by the positioning of nucleosomes. The whole system acts in concert with the elastic nuclear actomyosin network which also emerges by self-organization during the transcriptional pulsing process. We hypothesize that the the transcriptional pulsing, in turn, adjusts its frequency/amplitudes specified by topologically associating domains to the replication timing code that determines epigenetic differentiation memory.
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Affiliation(s)
- Jekaterina Erenpreisa
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Jekabs Krigerts
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Bogdan I. Gerashchenko
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, National Academy of Sciences of Ukraine, 03022 Kyiv, Ukraine;
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia;
| | - Reet Kurg
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia;
| | - Ruth Winter
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Matthias Krufczik
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Pawel Zayakin
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
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9
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Ren K, Wang L, Wang L, Du Q, Cao J, Jin Q, An G, Li N, Dang L, Tian Y, Wang Y, Sun J. Investigating Transcriptional Dynamics Changes and Time-Dependent Marker Gene Expression in the Early Period After Skeletal Muscle Injury in Rats. Front Genet 2021; 12:650874. [PMID: 34220936 PMCID: PMC8248501 DOI: 10.3389/fgene.2021.650874] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/07/2021] [Indexed: 12/21/2022] Open
Abstract
Following skeletal muscle injury (SMI), from post-injury reaction to repair consists of a complex series of dynamic changes. However, there is a paucity of research on detailed transcriptional dynamics and time-dependent marker gene expression in the early stages after SMI. In this study, skeletal muscle tissue in rats was taken at 4 to 48 h after injury for next-generation sequencing. We examined the transcriptional kinetics characteristics during above time periods after injury. STEM and maSigPro were used to screen time-correlated genes. Integrating 188 time-correlated genes with 161 genes in each time-related gene module by WGCNA, we finally identified 18 network-node regulatory genes after SMI. Histological staining analyses confirmed the mechanisms underlying changes in the tissue damage to repair process. Our research linked a variety of dynamic biological processes with specific time periods and provided insight into the characteristics of transcriptional dynamics, as well as screened time-related biological indicators with biological significance in the early stages after SMI.
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Affiliation(s)
- Kang Ren
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China.,Department of Basic Medicine, Changzhi Medical College, Changzhi, China
| | - Liangliang Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Liang Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Qiuxiang Du
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Jie Cao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Qianqian Jin
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Guoshuai An
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Na Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Lihong Dang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Yingjie Tian
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Yingyuan Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Junhong Sun
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China
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10
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Xenakis MN, Kapetis D, Yang Y, Gerrits MM, Heijman J, Waxman SG, Lauria G, Faber CG, Westra RL, Lindsey PJ, Smeets HJ. Hydropathicity-based prediction of pain-causing NaV1.7 variants. BMC Bioinformatics 2021; 22:212. [PMID: 33892629 PMCID: PMC8063372 DOI: 10.1186/s12859-021-04119-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background Mutation-induced variations in the functional architecture of the NaV1.7 channel protein are causally related to a broad spectrum of human pain disorders. Predicting in silico the phenotype of NaV1.7 variant is of major clinical importance; it can aid in reducing costs of in vitro pathophysiological characterization of NaV1.7 variants, as well as, in the design of drug agents for counteracting pain-disease symptoms. Results In this work, we utilize spatial complexity of hydropathic effects toward predicting which NaV1.7 variants cause pain (and which are neutral) based on the location of corresponding mutation sites within the NaV1.7 structure. For that, we analyze topological and scaling hydropathic characteristics of the atomic environment around NaV1.7’s pore and probe their spatial correlation with mutation sites. We show that pain-related mutation sites occupy structural locations in proximity to a hydrophobic patch lining the pore while clustering at a critical hydropathic-interactions distance from the selectivity filter (SF). Taken together, these observations can differentiate pain-related NaV1.7 variants from neutral ones, i.e., NaV1.7 variants not causing pain disease, with 80.5\documentclass[12pt]{minimal}
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\begin{document}$$\%$$\end{document}% specificity [area under the receiver operating characteristics curve = 0.872]. Conclusions Our findings suggest that maintaining hydrophobic NaV1.7 interior intact, as well as, a finely-tuned (dictated by hydropathic interactions) distance from the SF might be necessary molecular conditions for physiological NaV1.7 functioning. The main advantage for using the presented predictive scheme is its negligible computational cost, as well as, hydropathicity-based biophysical rationalization. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04119-2.
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Affiliation(s)
- Makros N Xenakis
- Department of Toxicogenomics, Section Clinical Genomics, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands. .,Research School for Mental Health and Neuroscience (MHeNS), Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands.
| | - Dimos Kapetis
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Via Celoria 11, 20133, Milan, Italy
| | - Yang Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN, 47907, USA.,Purdue Institute for Integrative Neuroscience, West Lafayette, IN, 47907, USA
| | - Monique M Gerrits
- Department of Clinical Genetics, Maastricht University Medical Center, PO box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Jordi Heijman
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
| | - Stephen G Waxman
- Department of Neurology and Center for Neuroscience and Regeneration Research, Yale University School of Medicine, New Haven, CT, 06510, USA.,Rehabilitation Research Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Giuseppe Lauria
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Via Celoria 11, 20133, Milan, Italy.,Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Via G.B. Grassi 74, 20157, Milan, Italy
| | - Catharina G Faber
- Department of Neurology, Maastricht University Medical Center, PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Ronald L Westra
- Department of Data Science and Knowledge Engineering, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
| | - Patrick J Lindsey
- Department of Toxicogenomics, Section Clinical Genomics, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands.,Research School for Oncology and Developmental Biology (GROW), Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
| | - Hubert J Smeets
- Department of Toxicogenomics, Section Clinical Genomics, Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands.,Research School for Mental Health and Neuroscience (MHeNS), Maastricht University, PO Box 616, 6200 MD, Maastricht, The Netherlands
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11
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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] [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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12
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Fiorentino J, Torres-Padilla ME, Scialdone A. Measuring and Modeling Single-Cell Heterogeneity and Fate Decision in Mouse Embryos. Annu Rev Genet 2020; 54:167-187. [PMID: 32867543 DOI: 10.1146/annurev-genet-021920-110200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cellular heterogeneity is a property of any living system; however, its relationship with cellular fate decision remains an open question. Recent technological advances have enabled valuable insights, especially in complex systems such as the mouse embryo. In this review, we discuss recent studies that characterize cellular heterogeneity at different levels during mouse development, from the two-cell stage up to gastrulation. In addition to key experimental findings, we review mathematical modeling approaches that help researchers interpret these findings. Disentangling the role of heterogeneity in cell fate decision will likely rely on the refined integration of experiments, large-scale omics data, and mathematical modeling, complemented by the use of synthetic embryos and gastruloids as promising in vitro models.
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Affiliation(s)
- Jonathan Fiorentino
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany; .,Institute of Functional Epigenetics (IFE) and Institute of Computational Biology (ICB), Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany; .,Faculty of Biology, Ludwig-Maximilians Universität, D-82152 Planegg-Martinsried, Germany
| | - Antonio Scialdone
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany; .,Institute of Functional Epigenetics (IFE) and Institute of Computational Biology (ICB), Helmholtz Zentrum München, D-85764 Neuherberg, Germany
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13
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Brash DE. Rethinking Causation for Data-intensive Biology: Constraints, Cancellations, and Quantized Organisms: Causality in complex organisms is sculpted by constraints rather than instigators, with outcomes perhaps better described by quantized patterns than rectilinear pathways. Bioessays 2020; 42:e1900135. [PMID: 32484248 PMCID: PMC7518294 DOI: 10.1002/bies.201900135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 03/19/2020] [Indexed: 12/22/2022]
Abstract
Complex organisms thwart the simple rectilinear causality paradigm of "necessary and sufficient," with its experimental strategy of "knock down and overexpress." This Essay organizes the eccentricities of biology into four categories that call for new mathematical approaches; recaps for the biologist the philosopher's recent refinements to the causation concept and the mathematician's computational tools that handle some but not all of the biological eccentricities; and describes overlooked insights that make causal properties of physical hierarchies such as emergence and downward causation straightforward. Reviewing and extrapolating from similar situations in physics, it is suggested that new mathematical tools for causation analysis incorporating feedback, signal cancellation, nonlinear dependencies, physical hierarchies, and fixed constraints rather than instigative changes will reveal unconventional biological behaviors. These include "eigenisms," organisms that are limited to quantized states; trajectories that steer a system such as an evolving species toward optimal states; and medical control via distributed "sheets" rather than single control points.
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Affiliation(s)
- Douglas E Brash
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, 06520-8040, USA
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14
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Tsuchiya M, Giuliani A, Yoshikawa K. Cell-Fate Determination from Embryo to Cancer Development: Genomic Mechanism Elucidated. Int J Mol Sci 2020; 21:E4581. [PMID: 32605138 PMCID: PMC7369777 DOI: 10.3390/ijms21134581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022] Open
Abstract
Elucidation of the genomic mechanism that guides the cell-fate change is one of the fundamental issues of biology. We previously demonstrated that whole genome expression is coordinated by the emergence of a critical point at both the cell-population and single-cell levels through the physical principle of self-organized criticality. In this paper, we further examine the genomic mechanism that determines the cell-fate changes from embryo to cancer development. The state of the critical point, acting as the organizing center of the cell fate, determines whether the genome resides in a super- or sub-critical state. In the super-critical state, a specific stochastic perturbation can spread over the entire system through the "genome engine", an autonomous critical-control genomic system, whereas in the sub-critical state, the perturbation remains at a local level. The cell-fate changes when the genome becomes super-critical. We provide a consistent framework to develop a time-evolutional transition theory for the biological regulation of the cell-fate change.
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Affiliation(s)
- Masa Tsuchiya
- SEIKO Life Science Laboratory, SRI, Osaka 540-659, Japan
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, 00161 Rome, Italy;
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan;
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15
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Spadafora C. Transgenerational epigenetic reprogramming of early embryos: a mechanistic model. ENVIRONMENTAL EPIGENETICS 2020; 6:dvaa009. [PMID: 32704385 PMCID: PMC7368376 DOI: 10.1093/eep/dvaa009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 05/10/2023]
Abstract
The notion that epigenetic information can be transmitted across generations is supported by mounting waves of data, but the underlying mechanisms remain elusive. Here, a model is proposed which combines different lines of experimental evidence. First, it has been shown that somatic tissues exposed to stressing stimuli release circulating RNA-containing extracellular vesicles; second, epididymal spermatozoa can take up, internalize and deliver the RNA-containing extracellular vesicles to oocytes at fertilization; third, early embryos can process RNA-based information. These elements constitute the building blocks upon which the model is built. The model proposes that a continuous stream of epigenetic information flows from parental somatic tissues to the developing embryos. The flow can cross the Weismann barrier, is mediated by circulating vesicles and epididymal spermatozoa, and has the potential to generate epigenetic traits that are then stably acquired in the offspring. In a broader perspective, it emerges that a natural 'assembly line' operates continuously, aiming at passing the parental epigenetic blueprint in growing embryos.
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Affiliation(s)
- Corrado Spadafora
- Institute of Translational Pharmacology, National Research Council (CNR), 100 Via del Fosso del Cavaliere, 00133 Rome, Italy
- Correspondence address. Institute of Translational Pharmacology, National Research Council (CNR), 100 Via del Fosso del Cavaliere, 00133 Rome, Italy. Tel: +39 0649917536; Fax: +39 064457529; E-mail: ;
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16
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Erenpreisa J, Giuliani A. Resolution of Complex Issues in Genome Regulation and Cancer Requires Non-Linear and Network-Based Thermodynamics. Int J Mol Sci 2019; 21:E240. [PMID: 31905791 PMCID: PMC6981914 DOI: 10.3390/ijms21010240] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/22/2019] [Accepted: 12/27/2019] [Indexed: 02/06/2023] Open
Abstract
The apparent lack of success in curing cancer that was evidenced in the last four decades of molecular medicine indicates the need for a global re-thinking both its nature and the biological approaches that we are taking in its solution. The reductionist, one gene/one protein method that has served us well until now, and that still dominates in biomedicine, requires complementation with a more systemic/holistic approach, to address the huge problem of cross-talk between more than 20,000 protein-coding genes, about 100,000 protein types, and the multiple layers of biological organization. In this perspective, the relationship between the chromatin network organization and gene expression regulation plays a fundamental role. The elucidation of such a relationship requires a non-linear thermodynamics approach to these biological systems. This change of perspective is a necessary step for developing successful 'tumour-reversion' therapeutic strategies.
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Affiliation(s)
- Jekaterina Erenpreisa
- Cancer Research Division, Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Alessandro Giuliani
- Environmental and Health Department, Istituto Superiore di Sanità, 00161 Rome, Italy;
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17
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Po A, Giuliani A, Masiello MG, Cucina A, Catizone A, Ricci G, Chiacchiarini M, Tafani M, Ferretti E, Bizzarri M. Phenotypic transitions enacted by simulated microgravity do not alter coherence in gene transcription profile. NPJ Microgravity 2019; 5:27. [PMID: 31799378 PMCID: PMC6872750 DOI: 10.1038/s41526-019-0088-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/28/2019] [Indexed: 02/07/2023] Open
Abstract
Cells in simulated microgravity undergo a reversible morphology switch, causing the appearance of two distinct phenotypes. Despite the dramatic splitting into an adherent-fusiform and a floating-spherical population, when looking at the gene-expression phase space, cell transition ends up in a largely invariant gene transcription profile characterized by only mild modifications in the respective Pearson's correlation coefficients. Functional changes among the different phenotypes emerging in simulated microgravity using random positioning machine are adaptive modifications-as cells promptly recover their native phenotype when placed again into normal gravity-and do not alter the internal gene coherence. However, biophysical constraints are required to drive phenotypic commitment in an appropriate way, compatible with physiological requirements, given that absence of gravity foster cells to oscillate between different attractor states, thus preventing them to acquire a exclusive phenotype. This is a proof-of-concept of the adaptive properties of gene-expression networks supporting very different phenotypes by coordinated 'profile preserving' modifications.
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Affiliation(s)
- Agnese Po
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanità, Rome, Italy
| | | | - Alessandra Cucina
- Department of Surgery “Pietro Valdoni”, Sapienza University, Rome, Italy
- Azienda Policlinico Umberto I, Rome, Italy
| | - Angela Catizone
- Department of Anatomy, Histology, Forensic-Medicine and Orthopedics, Sapienza University, Rome, Italy
| | - Giulia Ricci
- Department of Experimental Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, Naples, Italy
| | | | - Marco Tafani
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | | | - Mariano Bizzarri
- Department of Experimental Medicine, Sapienza University, Rome, Italy
- Systems Biology Group Lab, Sapienza University, Rome, Italy
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18
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Hordijk W, Altenberg L. Developmental structuring of phenotypic variation: A case study with a cellular automata model of ontogeny. Evol Dev 2019; 22:20-34. [PMID: 31509336 DOI: 10.1111/ede.12315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Developmental mechanisms not only produce an organismal phenotype, but they also structure the way genetic variation maps to phenotypic variation. Here, we revisit a computational model for the evolution of ontogeny based on cellular automata, in which evolution regularly discovered two alternative mechanisms for achieving a selected phenotype, one showing high modularity, the other showing morphological integration. We measure a primary variational property of the systems, their distribution of fitness effects of mutation. We find that the modular ontogeny shows the evolution of mutational robustness and ontogenic simplification, while the integrated ontogeny does not. We discuss the wider use of this methodology on other computational models of development as well as real organisms.
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Affiliation(s)
- Wim Hordijk
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria
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19
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Bizzarri M, Giuliani A, Pensotti A, Ratti E, Bertolaso M. Co-emergence and Collapse: The Mesoscopic Approach for Conceptualizing and Investigating the Functional Integration of Organisms. Front Physiol 2019; 10:924. [PMID: 31427981 PMCID: PMC6690009 DOI: 10.3389/fphys.2019.00924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/09/2019] [Indexed: 11/13/2022] Open
Abstract
The fall of reductionist approaches to explanation leaves biology with an unescapable challenge: how to decipher complex systems. This entails a number of very critical questions, the most basic ones being: "What do we mean by 'complex'?" and "What is the system we should look for?" In complex systems, constraints belong to a higher level that the molecular one and their effect reduces and constrains the manifold of the accessible internal states of the system itself. Function is related but not deterministically imposed by the underlying structure. It is quite unlikely that such kind of complexity could be grasped by current approaches focusing on a single organization scale. The natural co-emergence of systems, parts and properties can be adopted as a hypothesis-free conceptual framework to understand functional integration of organisms, including their hierarchical or multilevel patterns, and including the way scientific practice proceeds in approaching such complexity. External, "driving" factors - order parameters and control parameters provided by the surrounding microenvironment - are always required to "push" the components' fate into well-defined developmental directions. In the negative, we see that in pathological processes such as cancer, organizational fluidity, collapse of levels and dynamic heterogeneity make it hard to even find a level of observation for a stable explanandum to persist in scientific practice. Parts and the system both lose their properties once the system is destabilized. The mesoscopic approach is our proposal to conceptualizing, investigating and explaining in biology. "Mesoscopic way of thinking" is increasingly popular in the epistemology of biology and corresponds to looking for an explanation (and possibly a prediction) where "non-trivial determinism is maximal": the "most microscopic" level of organization is not necessarily the place where "the most relevant facts do happen." A fundamental re-thinking of the concept of causality is also due for order parameters to be carefully and correctly identified. In the biological realm, entities have relational properties only, as they depend ontologically on the context they happen to be in. The basic idea of a relational ontology is that, in our inventory of the world, relations are somehow prior to the relata (i.e., entities).
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Affiliation(s)
- Mariano Bizzarri
- Systems Biology Group Lab, Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Alessandro Giuliani
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Emanuele Ratti
- Reilly Center for Science, Technology, and Values, University of Notre Dame, Notre Dame, IN, United States
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20
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Piras V, Chiow A, Selvarajoo K. Long‐range order and short‐range disorder in
Saccharomyces cerevisiae
biofilm. ENGINEERING BIOLOGY 2019. [DOI: 10.1049/enb.2018.5008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Vincent Piras
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS Université Paris‐Sud, Université Paris‐Saclay avenue de la Terrasse 91198 Gif‐sur‐Yvette Cedex France
| | - Adam Chiow
- Department of Pharmaceutical Engineering Singapore Institute of Technology 10 Dover Drive Singapore 138683 Singapore
| | - Kumar Selvarajoo
- Biotransformation Innovation Platform (BioTrans) Agency for Science, Technology & Research A∗STAR 61 Biopolis Drive, Proteos Singapore 138673 Singapore
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21
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Ghorbani M, Jonckheere EA, Bogdan P. Gene Expression Is Not Random: Scaling, Long-Range Cross-Dependence, and Fractal Characteristics of Gene Regulatory Networks. Front Physiol 2018; 9:1446. [PMID: 30459629 PMCID: PMC6232942 DOI: 10.3389/fphys.2018.01446] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 09/24/2018] [Indexed: 11/30/2022] Open
Abstract
Gene expression is a vital process through which cells react to the environment and express functional behavior. Understanding the dynamics of gene expression could prove crucial in unraveling the physical complexities involved in this process. Specifically, understanding the coherent complex structure of transcriptional dynamics is the goal of numerous computational studies aiming to study and finally control cellular processes. Here, we report the scaling properties of gene expression time series in Escherichia coli and Saccharomyces cerevisiae. Unlike previous studies, which report the fractal and long-range dependency of DNA structure, we investigate the individual gene expression dynamics as well as the cross-dependency between them in the context of gene regulatory network. Our results demonstrate that the gene expression time series display fractal and long-range dependence characteristics. In addition, the dynamics between genes and linked transcription factors in gene regulatory networks are also fractal and long-range cross-correlated. The cross-correlation exponents in gene regulatory networks are not unique. The distribution of the cross-correlation exponents of gene regulatory networks for several types of cells can be interpreted as a measure of the complexity of their functional behavior.
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Affiliation(s)
| | | | - Paul Bogdan
- Electrical Engineering Department, University of Southern California, Los Angeles, CA, United States
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22
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Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks. Sci Rep 2018; 8:10885. [PMID: 30022075 PMCID: PMC6052111 DOI: 10.1038/s41598-018-29077-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 06/27/2018] [Indexed: 02/06/2023] Open
Abstract
Co-expression networks are essential tools to infer biological associations between gene products and predict gene annotation. Global networks can be analyzed at the transcriptome-wide scale or after querying them with a set of guide genes to capture the transcriptional landscape of a given pathway in a process named Pathway Level Coexpression (PLC). A critical step in network construction remains the definition of gene co-expression. In the present work, we compared how Pearson Correlation Coefficient (PCC), Spearman Correlation Coefficient (SCC), their respective ranked values (Highest Reciprocal Rank (HRR)), Mutual Information (MI) and Partial Correlations (PC) performed on global networks and PLCs. This evaluation was conducted on the model plant Arabidopsis thaliana using microarray and differently pre-processed RNA-seq datasets. We particularly evaluated how dataset × distance measurement combinations performed in 5 PLCs corresponding to 4 well described plant metabolic pathways (phenylpropanoid, carbohydrate, fatty acid and terpene metabolisms) and the cytokinin signaling pathway. Our present work highlights how PCC ranked with HRR is better suited for global network construction and PLC with microarray and RNA-seq data than other distance methods, especially to cluster genes in partitions similar to biological subpathways.
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23
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Giuliani A, Tsuchiya M, Yoshikawa K. Self-Organization of Genome Expression from Embryo to Terminal Cell Fate: Single-Cell Statistical Mechanics of Biological Regulation. ENTROPY 2017; 20:e20010013. [PMID: 33265103 PMCID: PMC7512190 DOI: 10.3390/e20010013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/18/2022]
Abstract
A statistical mechanical mean-field approach to the temporal development of biological regulation provides a phenomenological, but basic description of the dynamical behavior of genome expression in terms of autonomous self-organization with a critical transition (Self-Organized Criticality: SOC). This approach reveals the basis of self-regulation/organization of genome expression, where the extreme complexity of living matter precludes any strict mechanistic approach. The self-organization in SOC involves two critical behaviors: scaling-divergent behavior (genome avalanche) and sandpile-type critical behavior. Genome avalanche patterns—competition between order (scaling) and disorder (divergence) reflect the opposite sequence of events characterizing the self-organization process in embryo development and helper T17 terminal cell differentiation, respectively. On the other hand, the temporal development of sandpile-type criticality (the degree of SOC control) in mouse embryo suggests the existence of an SOC control landscape with a critical transition state (i.e., the erasure of zygote-state criticality). This indicates that a phase transition of the mouse genome before and after reprogramming (immediately after the late 2-cell state) occurs through a dynamical change in a control parameter. This result provides a quantitative open-thermodynamic appreciation of the still largely qualitative notion of the epigenetic landscape. Our results suggest: (i) the existence of coherent waves of condensation/de-condensation in chromatin, which are transmitted across regions of different gene-expression levels along the genome; and (ii) essentially the same critical dynamics we observed for cell-differentiation processes exist in overall RNA expression during embryo development, which is particularly relevant because it gives further proof of SOC control of overall expression as a universal feature.
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Affiliation(s)
- Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, 00161 Rome, Italy
| | - Masa Tsuchiya
- SEIKO Life Science Laboratory, SRI, Osaka 540-659, Japan
- Systems Biology Program, School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
- Correspondence:
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
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24
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Giuliani A. The application of principal component analysis to drug discovery and biomedical data. Drug Discov Today 2017; 22:1069-1076. [PMID: 28111329 DOI: 10.1016/j.drudis.2017.01.005] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 01/22/2023]
Abstract
There is a neat distinction between general purpose statistical techniques and quantitative models developed for specific problems. Principal Component Analysis (PCA) blurs this distinction: while being a general purpose statistical technique, it implies a peculiar style of reasoning. PCA is a 'hypothesis generating' tool creating a statistical mechanics frame for biological systems modeling without the need for strong a priori theoretical assumptions. This makes PCA of utmost importance for approaching drug discovery by a systemic perspective overcoming too narrow reductionist approaches.
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Affiliation(s)
- Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanità, Roma, Italy.
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