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Koncz G, Jenei V, Tóth M, Váradi E, Kardos B, Bácsi A, Mázló A. Damage-mediated macrophage polarization in sterile inflammation. Front Immunol 2023; 14:1169560. [PMID: 37465676 PMCID: PMC10351389 DOI: 10.3389/fimmu.2023.1169560] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/07/2023] [Indexed: 07/20/2023] Open
Abstract
Most of the leading causes of death, such as cardiovascular diseases, cancer, dementia, neurodegenerative diseases, and many more, are associated with sterile inflammation, either as a cause or a consequence of these conditions. The ability to control the progression of inflammation toward tissue resolution before it becomes chronic holds significant clinical potential. During sterile inflammation, the initiation of inflammation occurs through damage-associated molecular patterns (DAMPs) in the absence of pathogen-associated molecules. Macrophages, which are primarily localized in the tissue, play a pivotal role in sensing DAMPs. Furthermore, macrophages can also detect and respond to resolution-associated molecular patterns (RAMPs) and specific pro-resolving mediators (SPMs) during sterile inflammation. Macrophages, being highly adaptable cells, are particularly influenced by changes in the microenvironment. In response to the tissue environment, monocytes, pro-inflammatory macrophages, and pro-resolution macrophages can modulate their differentiation state. Ultimately, DAMP and RAMP-primed macrophages, depending on the predominant subpopulation, regulate the balance between inflammatory and resolving processes. While sterile injury and pathogen-induced reactions may have distinct effects on macrophages, most studies have focused on macrophage responses induced by pathogens. In this review, which emphasizes available human data, we illustrate how macrophages sense these mediators by examining the expression of receptors for DAMPs, RAMPs, and SPMs. We also delve into the signaling pathways induced by DAMPs, RAMPs, and SPMs, which primarily contribute to the regulation of macrophage differentiation from a pro-inflammatory to a pro-resolution phenotype. Understanding the regulatory mechanisms behind the transition between macrophage subtypes can offer insights into manipulating the transition from inflammation to resolution in sterile inflammatory diseases.
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Affiliation(s)
- Gábor Koncz
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Viktória Jenei
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Márta Tóth
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Eszter Váradi
- Institute of Genetics, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Balázs Kardos
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Bácsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- ELKH-DE Allergology Research Group, Debrecen, Hungary
| | - Anett Mázló
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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2
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Pensotti A, Bertolaso M, Bizzarri M. Is Cancer Reversible? Rethinking Carcinogenesis Models-A New Epistemological Tool. Biomolecules 2023; 13:biom13050733. [PMID: 37238604 DOI: 10.3390/biom13050733] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
A growing number of studies shows that it is possible to induce a phenotypic transformation of cancer cells from malignant to benign. This process is currently known as "tumor reversion". However, the concept of reversibility hardly fits the current cancer models, according to which gene mutations are considered the primary cause of cancer. Indeed, if gene mutations are causative carcinogenic factors, and if gene mutations are irreversible, how long should cancer be considered as an irreversible process? In fact, there is some evidence that intrinsic plasticity of cancerous cells may be therapeutically exploited to promote a phenotypic reprogramming, both in vitro and in vivo. Not only are studies on tumor reversion highlighting a new, exciting research approach, but they are also pushing science to look for new epistemological tools capable of better modeling cancer.
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Affiliation(s)
- Andrea Pensotti
- Research Unit of Philosophy of Science and Human Development, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Systems Biology Group Lab, Department of Experimental Medicine, Sapienza University, 00185 Rome, Italy
| | - Marta Bertolaso
- Research Unit of Philosophy of Science and Human Development, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Mariano Bizzarri
- Systems Biology Group Lab, Department of Experimental Medicine, Sapienza University, 00185 Rome, Italy
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Ahn JH, Song EJ, Jung DH, Kim YJ, Seo IS, Park SC, Jung YS, Cho ES, Mo SH, Hong JJ, Cho JY, Park JH. The sesquiterpene lactone estafiatin exerts anti-inflammatory effects on macrophages and protects mice from sepsis induced by LPS and cecal ligation puncture. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 99:153934. [PMID: 35172258 DOI: 10.1016/j.phymed.2022.153934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/05/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Previously, we found that the water extract of Artermisia scoparia Waldst. & Kit suppressed the cytokine production of lipopolysaccharide (LPS)-stimulated macrophages and alleviated carrageenan-induced acute inflammation in mice. Artemisia contains various sesquiterpene lactones and most of them exert immunomodulatory activity. PURPOSE In the present study, we investigated the immunomodulatory effect of estafiatin (EST), a sesquiterpene lactone derived from A. scoparia, on LPS-induced inflammation in macrophages and mouse sepsis model. STUDY DESIGN AND METHODS Murine bone marrow-derived macrophages (BMDMs) and THP-1 cells, a human monocytic leukemia cell line, were pretreated with different doses of EST for 2 h, followed by LPS treatment. The gene and protein expression of pro-inflammatory cytokines interleukin (IL)-6, tumor necrosis factor (TNF)-α, and inducible nitric oxide synthase (iNOS) were measured by quantitative real-time polymerase chain reaction (qPCR) and Western blot analysis. The activation of nuclear factor kappa B (NF-κB) and mitogen-activated protein kinases (MAPKs) was also evaluated at the level of phosphorylation. The effect of EST on inflammatory cytokine production, lung histopathology, and survival rate was assessed in an LPS-induced mice model of septic shock. The effect of EST on the production of cytokines in LPS-stimulated peritoneal macrophages was evaluated by in vitro and ex vivo experiments and protective effect of EST on cecal ligation and puncture (CLP) mice was also assessed. RESULTS The LPS-induced expression of IL-6, TNF-α, and iNOS was suppressed at the mRNA and protein levels in BMDMs and THP-1 cells, respectively, by pretreatment with EST. The half-maximal inhibitory concentration (IC50) of EST on IL-6 and TNF-α production were determined as 3.2 μM and 3.1 μM in BMDMs, 3 μM and 3.4 μM in THP1 cells, respectively. In addition, pretreatment with EST significantly reduced the LPS-induced phosphorylation p65, p38, JNK, and ERK in both cell types. In the LPS-induced mice model of septic shock, serum levels of IL-6, TNF-α, IL-1β, CXCL1, and CXCL2 were lower in EST-treated mice than in the control animals. Histopathology analysis revealed that EST treatment ameliorated LPS-induced lung damage. Moreover, while 1 of 7 control mice given lethal dose of LPS survived, 3 of 7 EST-treated (1.25 mg/kg) mice and 5 of 7 EST-treated (2.5 mg/kg) mice were survived. Pretreatment of EST dose-dependently suppressed the LPS-induced production of IL-6, TNF-α and CXCL1 in peritoneal macrophages. In CLP-induced mice sepsis model, while all 6 control mice was dead at 48 h, 1 of 6 EST-treated (1.25 mg/kg) mice and 3 of 6 EST-treated (2.5 mg/kg) mice survived for 96 h. CONCLUSION These results demonstrated that EST exerts anti-inflammatory effects on LPS-stimulated macrophages and protects mice from sepsis. Our study suggests that EST could be developed as a new therapeutic agent for sepsis and various inflammatory diseases.
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Affiliation(s)
- Jae-Hun Ahn
- Laboratory Animal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Eun-Jung Song
- Laboratory Animal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Do-Hyeon Jung
- Laboratory Animal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Yeong-Jun Kim
- Laboratory Animal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - In-Su Seo
- Laboratory Animal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Seong-Chan Park
- Laboratory Animal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea
| | - You-Seok Jung
- Laboratory Animal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Eun-Seo Cho
- Department of Food Science & Technology, Chonnam National University, Gwangju, Republic of Korea.
| | - Sang Hyun Mo
- Department of Food Science & Technology, Chonnam National University, Gwangju, Republic of Korea.
| | - Jung Joo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk 28116, Republic of Korea.
| | - Jeong-Yong Cho
- Department of Food Science & Technology, Chonnam National University, Gwangju, Republic of Korea.
| | - Jong-Hwan Park
- Laboratory Animal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea.
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Searching for unifying laws of general adaptation syndrome: Comment on "Dynamic and thermodynamic models of adaptation" by Gorban et al. Phys Life Rev 2021; 37:97-99. [PMID: 33845448 DOI: 10.1016/j.plrev.2021.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 01/03/2023]
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Bui TT, Lee D, Selvarajoo K. ScatLay: utilizing transcriptome-wide noise for identifying and visualizing differentially expressed genes. Sci Rep 2020; 10:17483. [PMID: 33060728 PMCID: PMC7566603 DOI: 10.1038/s41598-020-74564-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 09/28/2020] [Indexed: 01/10/2023] Open
Abstract
Differential expressed (DE) genes analysis is valuable for understanding comparative transcriptomics between cells, conditions or time evolution. However, the predominant way of identifying DE genes is to use arbitrary threshold fold or expression changes as cutoff. Here, we developed a more objective method, Scatter Overlay or ScatLay, to extract and graphically visualize DE genes across any two samples by utilizing their pair-wise scatter or transcriptome-wide noise, while factoring replicate variabilities. We tested ScatLay for 3 cell types: between time points for Escherichia coli aerobiosis and Saccharomyces cerevisiae hypoxia, and between untreated and Etomoxir treated Mus Musculus embryonic stem cell. As a result, we obtain 1194, 2061 and 2932 DE genes, respectively. Next, we compared these data with two widely used current approaches (DESeq2 and NOISeq) with typical twofold expression changes threshold, and show that ScatLay reveals significantly larger number of DE genes. Hence, our method provides a wider coverage of DE genes, and will likely pave way for finding more novel regulatory genes in future works.
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Affiliation(s)
- Thuy Tien Bui
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology & Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Daniel Lee
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Kumar Selvarajoo
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology & Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore. .,Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.
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6
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Attractor Concepts to Evaluate the Transcriptome-wide Dynamics Guiding Anaerobic to Aerobic State Transition in Escherichia coli. Sci Rep 2020; 10:5878. [PMID: 32246034 PMCID: PMC7125300 DOI: 10.1038/s41598-020-62804-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/19/2020] [Indexed: 01/14/2023] Open
Abstract
For any dynamical system, like living organisms, an attractor state is a set of variables or mechanisms that converge towards a stable system behavior despite a wide variety of initial conditions. Here, using multi-dimensional statistics, we investigate the global gene expression attractor mechanisms shaping anaerobic to aerobic state transition (AAT) of Escherichia coli in a bioreactor at early times. Out of 3,389 RNA-Seq expression changes over time, we identified 100 sharply changing genes that are key for guiding 1700 genes into the AAT attractor basin. Collectively, these genes were named as attractor genes constituting of 6 dynamic clusters. Apart from the expected anaerobic (glycolysis), aerobic (TCA cycle) and fermentation (succinate pathways) processes, sulphur metabolism, ribosome assembly and amino acid transport mechanisms together with 332 uncharacterised genes are also key for AAT. Overall, our work highlights the importance of multi-dimensional statistical analyses for revealing novel processes shaping AAT.
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7
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Selvarajoo K. Large‐scale‐free network organisation is likely key for biofilm phase transition. ENGINEERING BIOLOGY 2019. [DOI: 10.1049/enb.2019.0012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Kumar Selvarajoo
- Computational and Systems Biology, Biotransformation Innovation Platform (BioTrans), Agency for Science Technology & Research (A*STAR) 61 Biopolis Drive Proteos 13873 Singapore
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8
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Zou Y, Bui TT, Selvarajoo K. ABioTrans: A Biostatistical Tool for Transcriptomics Analysis. Front Genet 2019; 10:499. [PMID: 31214245 PMCID: PMC6555198 DOI: 10.3389/fgene.2019.00499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 05/07/2019] [Indexed: 11/13/2022] Open
Abstract
Here we report a bio-statistical/informatics tool, ABioTrans, developed in R for gene expression analysis. The tool allows the user to directly read RNA-Seq data files deposited in the Gene Expression Omnibus or GEO database. Operated using any web browser application, ABioTrans provides easy options for multiple statistical distribution fitting, Pearson and Spearman rank correlations, PCA, k-means and hierarchical clustering, differential expression (DE) analysis, Shannon entropy and noise (square of coefficient of variation) analyses, as well as Gene ontology classifications.
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Affiliation(s)
- Yutong Zou
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Thuy Tien Bui
- Biotransformation Innovation Platform (BioTrans), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Kumar Selvarajoo
- Biotransformation Innovation Platform (BioTrans), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
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9
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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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10
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The GABA A Receptor α2 Subunit Activates a Neuronal TLR4 Signal in the Ventral Tegmental Area that Regulates Alcohol and Nicotine Abuse. Brain Sci 2018; 8:brainsci8040072. [PMID: 29690521 PMCID: PMC5924408 DOI: 10.3390/brainsci8040072] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/04/2018] [Accepted: 04/18/2018] [Indexed: 01/06/2023] Open
Abstract
Alcoholism initiates with episodes of excessive alcohol drinking, known as binge drinking, which is one form of excessive drinking (NIAAA Newsletter, 2004) that is related to impulsivity and anxiety (Ducci et al., 2007; Edenberg et al., 2004) and is also predictive of smoking status. The predisposition of non-alcohol exposed subjects to initiate binge drinking is controlled by neuroimmune signaling that includes an innately activated neuronal Toll-like receptor 4 (TLR4) signal. This signal also regulates cognitive impulsivity, a heritable trait that defines drug abuse initiation. However, the mechanism of signal activation, its function in dopaminergic (TH+) neurons within the reward circuitry implicated in drug-seeking behavior [viz. the ventral tegmental area (VTA)], and its contribution to nicotine co-abuse are still poorly understood. We report that the γ-aminobutyric acidA receptor (GABAAR) α2 subunit activates the TLR4 signal in neurons, culminating in the activation (phosphorylation/nuclear translocation) of cyclic AMP response element binding (CREB) but not NF-kB transcription factors and the upregulation of corticotropin-releasing factor (CRF) and tyrosine hydroxylase (TH). The signal is activated through α2/TLR4 interaction, as evidenced by co-immunoprecipitation, and it is present in the VTA from drug-untreated alcohol-preferring P rats. VTA infusion of neurotropic herpes simplex virus (HSV) vectors for α2 (pHSVsiLA2) or TLR4 (pHSVsiTLR4) but not scrambled (pHSVsiNC) siRNA inhibits signal activation and both binge alcohol drinking and nicotine sensitization, suggesting that the α2-activated TLR4 signal contributes to the regulation of both alcohol and nicotine abuse.
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A systems biology approach to overcome TRAIL resistance in cancer treatment. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:142-154. [DOI: 10.1016/j.pbiomolbio.2017.02.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 02/21/2017] [Accepted: 02/21/2017] [Indexed: 11/20/2022]
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12
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Tsuchiya M, Giuliani A, Hashimoto M, Erenpreisa J, Yoshikawa K. Self-Organizing Global Gene Expression Regulated through Criticality: Mechanism of the Cell-Fate Change. PLoS One 2016; 11:e0167912. [PMID: 27997556 PMCID: PMC5173342 DOI: 10.1371/journal.pone.0167912] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/22/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A fundamental issue in bioscience is to understand the mechanism that underlies the dynamic control of genome-wide expression through the complex temporal-spatial self-organization of the genome to regulate the change in cell fate. We address this issue by elucidating a physically motivated mechanism of self-organization. PRINCIPAL FINDINGS Building upon transcriptome experimental data for seven distinct cell fates, including early embryonic development, we demonstrate that self-organized criticality (SOC) plays an essential role in the dynamic control of global gene expression regulation at both the population and single-cell levels. The novel findings are as follows: i) Mechanism of cell-fate changes: A sandpile-type critical transition self-organizes overall expression into a few transcription response domains (critical states). A cell-fate change occurs by means of a dissipative pulse-like global perturbation in self-organization through the erasure of initial-state critical behaviors (criticality). Most notably, the reprogramming of early embryo cells destroys the zygote SOC control to initiate self-organization in the new embryonal genome, which passes through a stochastic overall expression pattern. ii) Mechanism of perturbation of SOC controls: Global perturbations in self-organization involve the temporal regulation of critical states. Quantitative evaluation of this perturbation in terminal cell fates reveals that dynamic interactions between critical states determine the critical-state coherent regulation. The occurrence of a temporal change in criticality perturbs this between-states interaction, which directly affects the entire genomic system. Surprisingly, a sub-critical state, corresponding to an ensemble of genes that shows only marginal changes in expression and consequently are considered to be devoid of any interest, plays an essential role in generating a global perturbation in self-organization directed toward the cell-fate change. CONCLUSION AND SIGNIFICANCE 'Whole-genome' regulation of gene expression through self-regulatory SOC control complements gene-by-gene fine tuning and represents a still largely unexplored non-equilibrium statistical mechanism that is responsible for the massive reprogramming of genome expression.
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Affiliation(s)
- Masa Tsuchiya
- Systems Biology Program, School of Media and Governance, Keio University, Fujisawa, Japan
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, Rome, Italy
| | - Midori Hashimoto
- Graduate School of Frontier Science, the University of Tokyo, Kashiwa, Japan
| | | | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
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Bizzarri M, Cucina A. SMT and TOFT: Why and How They are Opposite and Incompatible Paradigms. Acta Biotheor 2016; 64:221-39. [PMID: 27283400 DOI: 10.1007/s10441-016-9281-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 05/23/2016] [Indexed: 01/02/2023]
Abstract
The Somatic Mutation Theory (SMT) has been challenged on its fundamentals by the Tissue Organization Field Theory of Carcinogenesis (TOFT). However, a recent publication has questioned whether TOFT could be a valid alternative theory of carcinogenesis to that presented by SMT. Herein we critically review arguments supporting the irreducible opposition between the two theoretical approaches by highlighting differences regarding the philosophical, methodological and experimental approaches on which they respectively rely. We conclude that SMT has not explained carcinogenesis due to severe epistemological and empirical shortcomings, while TOFT is gaining momentum. The main issue is actually to submit SMT to rigorous testing. This concern includes the imperatives to seek evidence for disproving one's hypothesis, and to consider the whole, and not just selective evidence.
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Affiliation(s)
- Mariano Bizzarri
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy.
- Systems Biology Group Lab, Sapienza University of Rome, Via Antonio Scarpa 14, 00161, Rome, Italy.
| | - Alessandra Cucina
- Department of Surgery "Pietro Valdoni", Sapienza University of Rome, Via A. Scarpa 14, 00161, Rome, Italy
- Azienda Policlinico Umberto I, Viale del Policlinico 155, 00161, Rome, Italy
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Selvarajoo K. Can the second law of thermodynamics hold in cell cultures? Front Genet 2015; 6:262. [PMID: 26300913 PMCID: PMC4528183 DOI: 10.3389/fgene.2015.00262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/24/2015] [Indexed: 12/02/2022] Open
Affiliation(s)
- Kumar Selvarajoo
- Institute for Advanced Biosciences, Keio University Tsuruoka, Japan ; Systems Biology Program, Graduate School of Media and Governance, Keio University Fujisawa, Japan
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15
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Tsuchiya M, Giuliani A, Hashimoto M, Erenpreisa J, Yoshikawa K. Emergent Self-Organized Criticality in Gene Expression Dynamics: Temporal Development of Global Phase Transition Revealed in a Cancer Cell Line. PLoS One 2015; 10:e0128565. [PMID: 26067993 PMCID: PMC4465832 DOI: 10.1371/journal.pone.0128565] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 04/28/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The underlying mechanism of dynamic control of the genome-wide expression is a fundamental issue in bioscience. We addressed it in terms of phase transition by a systemic approach based on both density analysis and characteristics of temporal fluctuation for the time-course mRNA expression in differentiating MCF-7 breast cancer cells. METHODOLOGY In a recent work, we suggested criticality as an essential aspect of dynamic control of genome-wide gene expression. Criticality was evident by a unimodal-bimodal transition through flattened unimodal expression profile. The flatness on the transition suggests the existence of a critical transition at which up- and down-regulated expression is balanced. Mean field (averaging) behavior of mRNAs based on the temporal expression changes reveals a sandpile type of transition in the flattened profile. Furthermore, around the transition, a self-similar unimodal-bimodal transition of the whole expression occurs in the density profile of an ensemble of mRNA expression. These singular and scaling behaviors identify the transition as the expression phase transition driven by self-organized criticality (SOC). PRINCIPAL FINDINGS Emergent properties of SOC through a mean field approach are revealed: i) SOC, as a form of genomic phase transition, consolidates distinct critical states of expression, ii) Coupling of coherent stochastic oscillations between critical states on different time-scales gives rise to SOC, and iii) Specific gene clusters (barcode genes) ranging in size from kbp to Mbp reveal similar SOC to genome-wide mRNA expression and ON-OFF synchronization to critical states. This suggests that the cooperative gene regulation of topological genome sub-units is mediated by the coherent phase transitions of megadomain-scaled conformations between compact and swollen chromatin states. CONCLUSION AND SIGNIFICANCE In summary, our study provides not only a systemic method to demonstrate SOC in whole-genome expression, but also introduces novel, physically grounded concepts for a breakthrough in the study of biological regulation.
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Affiliation(s)
- Masa Tsuchiya
- Systems Biology Program, School of Media and Governance, Keio University, Fujisawa, Japan
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, Rome, Italy
| | - Midori Hashimoto
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
| | | | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
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Simeoni O, Piras V, Tomita M, Selvarajoo K. Tracking global gene expression responses in T cell differentiation. Gene 2015; 569:259-66. [PMID: 26028587 DOI: 10.1016/j.gene.2015.05.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/28/2015] [Accepted: 05/26/2015] [Indexed: 12/24/2022]
Abstract
Upon receiving antigens from the innate immune cells, CD4(+) T cells differentiate into distinct effector cells. To probe the global responses of distinct effector cells, we analyzed transcriptome-wide expressions of Th1, Th2, Treg and Th17 using Pearson correlation, entropy and principal component analyses, with Th0 as a control. Although the global response of Th0 was quite distinct from Th17, surprisingly, it was highly similar to Th1, Th2 and Treg. Moreover, 8 major temporal groups consisting of 5704 differentially expressed genes were revealed for both Th0 and Th17. Gene functional enrichment analysis showed immune responses and metabolic processes were mainly activated between Th0 and Th17, while genes related to cell cycle and replication were differentially regulated. Moreover, we found the upregulation of several novel genes for Th0 and Th17. Overall, we deduce that Th0 is globally similar to Th1, Th2 and Treg. Our results indicate that Th0 is a differentiated state and, therefore, may not be used as a control cell type.
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Affiliation(s)
- Oriane Simeoni
- ENSEIRB-MATMECA, Bordeaux Institute of Technology, Talence, France; Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Vincent Piras
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Kumar Selvarajoo
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.
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17
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The reduction of gene expression variability from single cells to populations follows simple statistical laws. Genomics 2015; 105:137-44. [DOI: 10.1016/j.ygeno.2014.12.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 12/31/2022]
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18
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Transcriptome-wide variability in single embryonic development cells. Sci Rep 2014; 4:7137. [PMID: 25409746 PMCID: PMC4238013 DOI: 10.1038/srep07137] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 11/04/2014] [Indexed: 11/23/2022] Open
Abstract
Molecular heterogeneity of individual molecules within single cells has been recently shown to be crucial for cell fate diversifications. However, on a global scale, the effect of molecular variability for embryonic developmental stages is largely underexplored. Here, to understand the origins of transcriptome-wide variability of oocytes to blastocysts in human and mouse, we examined RNA-Seq datasets. Evaluating Pearson correlation, Shannon entropy and noise patterns (η2vs.μ), our investigations reveal a phase transition from low to saturating levels of diversity and variability of transcriptome-wide expressions through the development stages. To probe the observed behaviour further, we utilised a stochastic transcriptional model to simulate the global gene expressions pattern for each development stage. From the model, we concur that transcriptome-wide regulation initially begins from 2-cell stage, and becomes strikingly variable from 8-cell stage due to amplification and quantal transcriptional activity.
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19
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Tsuchiya M, Hashimoto M, Takenaka Y, Motoike IN, Yoshikawa K. Global genetic response in a cancer cell: self-organized coherent expression dynamics. PLoS One 2014; 9:e97411. [PMID: 24831017 PMCID: PMC4022610 DOI: 10.1371/journal.pone.0097411] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/18/2014] [Indexed: 12/19/2022] Open
Abstract
Understanding the basic mechanism of the spatio-temporal self-control of genome-wide gene expression engaged with the complex epigenetic molecular assembly is one of major challenges in current biological science. In this study, the genome-wide dynamical profile of gene expression was analyzed for MCF-7 breast cancer cells induced by two distinct ErbB receptor ligands: epidermal growth factor (EGF) and heregulin (HRG), which drive cell proliferation and differentiation, respectively. We focused our attention to elucidate how global genetic responses emerge and to decipher what is an underlying principle for dynamic self-control of genome-wide gene expression. The whole mRNA expression was classified into about a hundred groups according to the root mean square fluctuation (rmsf). These expression groups showed characteristic time-dependent correlations, indicating the existence of collective behaviors on the ensemble of genes with respect to mRNA expression and also to temporal changes in expression. All-or-none responses were observed for HRG and EGF (biphasic statistics) at around 10–20 min. The emergence of time-dependent collective behaviors of expression occurred through bifurcation of a coherent expression state (CES). In the ensemble of mRNA expression, the self-organized CESs reveals distinct characteristic expression domains for biphasic statistics, which exhibits notably the presence of criticality in the expression profile as a route for genomic transition. In time-dependent changes in the expression domains, the dynamics of CES reveals that the temporal development of the characteristic domains is characterized as autonomous bistable switch, which exhibits dynamic criticality (the temporal development of criticality) in the genome-wide coherent expression dynamics. It is expected that elucidation of the biophysical origin for such critical behavior sheds light on the underlying mechanism of the control of whole genome.
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Affiliation(s)
- Masa Tsuchiya
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, School of Media and Governance, Keio University, Fujisawa, Japan
- * E-mail: (MT); (KY)
| | - Midori Hashimoto
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
| | - Yoshiko Takenaka
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Ikuko N. Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
- * E-mail: (MT); (KY)
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20
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Piras V, Selvarajoo K. Beyond MyD88 and TRIF Pathways in Toll-Like Receptor Signaling. Front Immunol 2014; 5:70. [PMID: 24605113 PMCID: PMC3932418 DOI: 10.3389/fimmu.2014.00070] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 02/08/2014] [Indexed: 12/04/2022] Open
Affiliation(s)
- Vincent Piras
- Institute for Advanced Biosciences , Keio University, Tsuruoka , Japan ; Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa , Japan
| | - Kumar Selvarajoo
- Institute for Advanced Biosciences , Keio University, Tsuruoka , Japan ; Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa , Japan
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21
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Busch H, Boerries M, Bao J, Hanke ST, Hiss M, Tiko T, Rensing SA. Network theory inspired analysis of time-resolved expression data reveals key players guiding P. patens stem cell development. PLoS One 2013; 8:e60494. [PMID: 23637751 PMCID: PMC3630159 DOI: 10.1371/journal.pone.0060494] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 02/27/2013] [Indexed: 01/07/2023] Open
Abstract
Transcription factors (TFs) often trigger developmental decisions, yet, their transcripts are often only moderately regulated and thus not easily detected by conventional statistics on expression data. Here we present a method that allows to determine such genes based on trajectory analysis of time-resolved transcriptome data. As a proof of principle, we have analysed apical stem cells of filamentous moss (P. patens) protonemata that develop from leaflets upon their detachment from the plant. By our novel correlation analysis of the post detachment transcriptome kinetics we predict five out of 1,058 TFs to be involved in the signaling leading to the establishment of pluripotency. Among the predicted regulators is the basic helix loop helix TF PpRSL1, which we show to be involved in the establishment of apical stem cells in P. patens. Our methodology is expected to aid analysis of key players of developmental decisions in complex plant and animal systems.
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Affiliation(s)
- Hauke Busch
- ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany.
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22
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Selvarajoo K, Giuliani A. Finding Self-organization from the Dynamic Gene Expressions of Innate Immune Responses. Front Physiol 2012; 3:192. [PMID: 22701431 PMCID: PMC3371675 DOI: 10.3389/fphys.2012.00192] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/22/2012] [Indexed: 11/26/2022] Open
Affiliation(s)
- Kumar Selvarajoo
- Institute for Advanced Biosciences, Keio University Tsuruoka, Yamagata, Japan
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23
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Selvarajoo K. Understanding multimodal biological decisions from single cell and population dynamics. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:385-99. [DOI: 10.1002/wsbm.1175] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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24
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Piras V, Hayashi K, Tomita M, Selvarajoo K. Enhancing apoptosis in TRAIL-resistant cancer cells using fundamental response rules. Sci Rep 2011; 1:144. [PMID: 22355661 PMCID: PMC3216625 DOI: 10.1038/srep00144] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 10/14/2011] [Indexed: 12/21/2022] Open
Abstract
The tumor necrosis factor related apoptosis-inducing ligand (TRAIL) induces apoptosis in malignant cells, while leaving other cells mostly unharmed. However, several carcinomas remain resistant to TRAIL. To investigate the resistance mechanisms in TRAIL-stimulated human fibrosarcoma (HT1080) cells, we developed a computational model to analyze the temporal activation profiles of cell survival (IκB, JNK, p38) and apoptotic (caspase-8 and -3) molecules in wildtype and several (FADD, RIP1, TRAF2 and caspase-8) knock-down conditions. Based on perturbation-response approach utilizing the law of information (signaling flux) conservation, we derived response rules for population-level average cell response. From this approach, i) a FADD-independent pathway to activate p38 and JNK, ii) a crosstalk between RIP1 and p38, and iii) a crosstalk between p62 and JNK are predicted. Notably, subsequent simulations suggest that targeting a novel molecule at p62/sequestosome-1 junction will optimize apoptosis through signaling flux redistribution. This study offers a valuable prospective to sensitive TRAIL-based therapy.
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Affiliation(s)
- Vincent Piras
- Institute for Advanced Biosciences, Keio University,
Tsuruoka, 997-0035, Japan
- Systems Biology Program, Graduate School of Media and
Governance, Keio University, Fujisawa, 252-8520,
Japan
- These authors contributed equally to this work
| | - Kentaro Hayashi
- Institute for Advanced Biosciences, Keio University,
Tsuruoka, 997-0035, Japan
- Systems Biology Program, Graduate School of Media and
Governance, Keio University, Fujisawa, 252-8520,
Japan
- These authors contributed equally to this work
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University,
Tsuruoka, 997-0035, Japan
- Systems Biology Program, Graduate School of Media and
Governance, Keio University, Fujisawa, 252-8520,
Japan
| | - Kumar Selvarajoo
- Institute for Advanced Biosciences, Keio University,
Tsuruoka, 997-0035, Japan
- Systems Biology Program, Graduate School of Media and
Governance, Keio University, Fujisawa, 252-8520,
Japan
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25
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Güttsches AK, Löseke S, Zähringer U, Sonnenborn U, Enders C, Gatermann S, Bufe A. Anti-inflammatory modulation of immune response by probiotic Escherichia coli Nissle 1917 in human blood mononuclear cells. Innate Immun 2011; 18:204-16. [PMID: 21382908 DOI: 10.1177/1753425910396251] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Escherichia coli Nissle 1917 (EcN) bears a defect in its LPS biosynthesis leading to truncated variable oligosaccharide-antigen chains and a semi-rough phenotype. It is effectively inactivated by complement factors due to resolved serum resistance and is, therefore, safe as a probiotic strain, i.e. for the treatment of inflammatory gastrointestinal diseases. It is unknown whether the modification of LPS in EcN contributes to its probiotic properties. Purified LPS from EcN and wild-type LPS from uropathogenic E. coli W536 together with raw lysates of both strains were analyzed for their gene expression activity with human PBMCs measured by microarrays. Comparing the two LPS molecules and the two lysate variants with each other, respectively, no differences of transcriptional patterns were observed. However, when comparing LPS with lysate patterns, pro-inflammatory cytokine IL-12p40 was up-regulated by both LPS molecules and anti-inflammatory IL-10 by both lysates. The higher the lysate concentration, the higher IL-10 release from PBMCs, clearly exceeding LPS induced IL-12p40 release. Furthermore, inflammatory chemokine CCL24 (eotaxin) was down-regulated by lysates and quantitative real-time PCR revealed that EcN compared to wild-type LPS was 8 times stronger in down-regulation of CCL24. We conclude that truncated LPS may down-regulate CCL24-mediated inflammation and that EcN lysate contains as yet unidentified factors which preferably induce anti-inflammatory activity. Both effects may contribute to the probiotic properties of EcN.
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Collective dynamics of specific gene ensembles crucial for neutrophil differentiation: the existence of genome vehicles revealed. PLoS One 2010; 5:e12116. [PMID: 20725638 PMCID: PMC2920325 DOI: 10.1371/journal.pone.0012116] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 07/16/2010] [Indexed: 12/16/2022] Open
Abstract
Cell fate decision remarkably generates specific cell differentiation path among the multiple possibilities that can arise through the complex interplay of high-dimensional genome activities. The coordinated action of thousands of genes to switch cell fate decision has indicated the existence of stable attractors guiding the process. However, origins of the intracellular mechanisms that create “cellular attractor” still remain unknown. Here, we examined the collective behavior of genome-wide expressions for neutrophil differentiation through two different stimuli, dimethyl sulfoxide (DMSO) and all-trans-retinoic acid (atRA). To overcome the difficulties of dealing with single gene expression noises, we grouped genes into ensembles and analyzed their expression dynamics in correlation space defined by Pearson correlation and mutual information. The standard deviation of correlation distributions of gene ensembles reduces when the ensemble size is increased following the inverse square root law, for both ensembles chosen randomly from whole genome and ranked according to expression variances across time. Choosing the ensemble size of 200 genes, we show the two probability distributions of correlations of randomly selected genes for atRA and DMSO responses overlapped after 48 hours, defining the neutrophil attractor. Next, tracking the ranked ensembles' trajectories, we noticed that only certain, not all, fall into the attractor in a fractal-like manner. The removal of these genome elements from the whole genomes, for both atRA and DMSO responses, destroys the attractor providing evidence for the existence of specific genome elements (named “genome vehicle”) responsible for the neutrophil attractor. Notably, within the genome vehicles, genes with low or moderate expression changes, which are often considered noisy and insignificant, are essential components for the creation of the neutrophil attractor. Further investigations along with our findings might provide a comprehensive mechanistic view of cell fate decision.
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27
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Felli N, Cianetti L, Pelosi E, Carè A, Liu CG, Calin GA, Rossi S, Peschle C, Marziali G, Giuliani A. Hematopoietic differentiation: a coordinated dynamical process towards attractor stable states. BMC SYSTEMS BIOLOGY 2010; 4:85. [PMID: 20553595 PMCID: PMC2904736 DOI: 10.1186/1752-0509-4-85] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 06/16/2010] [Indexed: 01/06/2023]
Abstract
Background The differentiation process, proceeding from stem cells towards the different committed cell types, can be considered as a trajectory towards an attractor of a dynamical process. This view, taking into consideration the transcriptome and miRNome dynamics considered as a whole, instead of looking at few 'master genes' driving the system, offers a novel perspective on this phenomenon. We investigated the 'differentiation trajectories' of the hematopoietic system considering a genome-wide scenario. Results We developed serum-free liquid suspension unilineage cultures of cord blood (CB) CD34+ hematopoietic progenitor cells through erythroid (E), megakaryocytic (MK), granulocytic (G) and monocytic (Mo) pathways. These cultures recapitulate physiological hematopoiesis, allowing the analysis of almost pure unilineage precursors starting from initial differentiation of HPCs until terminal maturation. By analyzing the expression profile of protein coding genes and microRNAs in unilineage CB E, MK, G and Mo cultures, at sequential stages of differentiation and maturation, we observed a coordinated, fully interconnected and scalable character of cell population behaviour in both transcriptome and miRNome spaces reminiscent of an attractor-like dynamics. MiRNome and transcriptome space differed for a still not terminally committed behaviour of microRNAs. Conclusions Consistent with their roles, the transcriptome system can be considered as the state space of a cell population, while the continuously evolving miRNA space corresponds to the tuning system necessary to reach the attractor. The behaviour of miRNA machinery could be of great relevance not only for the promise of reversing the differentiated state but even for tumor biology.
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Affiliation(s)
- Nadia Felli
- Department of Hematology, Oncology and Molecular Medicine Istituto Superiore di Sanità, Rome, Italy
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28
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Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations. Immunobiology 2010; 215:724-36. [PMID: 20580463 DOI: 10.1016/j.imbio.2010.05.012] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 05/20/2010] [Indexed: 12/15/2022]
Abstract
In order to address fundamental questions associated with the relationships between mononuclear phagocytes and other myeloid and lymphoid cell populations, we have taken advantage of the growing body of expression data available in the public domain. We collated a large number of published expression studies on mouse haemopoietic cell lineages comprising 304 cell samples from 29 independent experiments performed on a single microarray platform (Affymetrix MOE430-2). The data were subjected to network-based cluster analysis using Biolayout Express(3D). Genes with related function clustered together in distinct regions of the graph reaffirming many known associations between gene expression and role in specific pathways and defining most major cell types of the immune system. Promoters of genes within individual clusters were distinguished by over-representation of regulatory motifs recognised by specific transcription factors. However, these data indicate that commonly used myeloid subpopulation markers, such as CD11c (Itgax), do not correlate with expression of other genes, and further bring into question their use in defining myeloid cell lineage, activation (M1 vs. M2) and antigen-presenting cell function. In particular, there were few mRNA markers that clearly distinguished classical dendritic cells (DC) from macrophages, other than low expression of genes required for phagocytic activity. Bone marrow-derived DC, grown in GM-CSF, were clearly identified as phagocytes and distinguished from isolated lymphoid tissue DC. Thus, through pooling datasets from public data and examining the gene expression clusters within, we can learn a great deal about the transcriptional networks that underpin the differences in functional activities between cell populations of the immune system.
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29
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Hume DA, Summers KM, Raza S, Baillie JK, Freeman TC. Functional clustering and lineage markers: insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations. Genomics 2010; 95:328-38. [PMID: 20211243 DOI: 10.1016/j.ygeno.2010.03.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 03/01/2010] [Accepted: 03/02/2010] [Indexed: 12/24/2022]
Abstract
Very large microarray datasets showing gene expression across multiple tissues and cell populations provide a window on the transcriptional networks that underpin the differences in functional activity between biological systems. Clusters of co-expressed genes provide lineage markers, candidate regulators of cell function and, by applying the principle of guilt by association, candidate functions for genes of currently unknown function. We have analysed a dataset comprising pure cell populations from hemopoietic and non-hemopoietic cell types (http://biogps.gnf.org). Using a novel network visualisation and clustering approach, we demonstrate that it is possible to identify very tight expression signatures associated specifically with embryonic stem cells, mesenchymal cells and hematopoietic lineages. Selected examples validate the prediction that gene function can be inferred by co-expression. One expression cluster was enriched in phagocytes, which, alongside endosome-lysosome constituents, contains genes that may make up a 'pathway' for phagocyte differentiation. Promoters of these genes are enriched for binding sites for the ETS/PU.1 and MITF families. Another cluster was associated with the production of a specific extracellular matrix, with high levels of gene expression shared by cells of mesenchymal origin (fibroblasts, adipocytes, osteoblasts and myoblasts). We discuss the limitations placed upon such data by the presence of alternative promoters with distinct tissue specificity within many protein-coding genes.
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Affiliation(s)
- David A Hume
- The Roslin Institute, Roslin Biocentre, Roslin, Midlothian, UK.
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30
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Giuliani A. Collective motions and specific effectors: a statistical mechanics perspective on biological regulation. BMC Genomics 2010; 11 Suppl 1:S2. [PMID: 20158873 PMCID: PMC2822530 DOI: 10.1186/1471-2164-11-s1-s2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The interaction of a multiplicity of scales in both time and space is a fundamental feature of biological systems. The complementation of macroscopic (entire organism) and microscopic (molecular biology) views with a mesoscopic level of analysis able to connect the different planes of investigation is urgently needed. This will allow to both obtain a general frame of reference for rationalizing the burden of data coming from high throughput technologies and to derive effective operational views on biological systems. RESULTS The network paradigm in which microscopic level elements (nodes) are each other related by functional links so giving rise to both global (entire network) and local (specific) behavior is a promising metaphor to try and develop a statistical mechanics inspired approach for biological systems. Here we show the application of this paradigm to different systems going from yeast metabolism to murine macrophages response to immune stimulation. CONCLUSIONS The need to complement the purely molecular view with mesoscopic approaches is evident in all the studied examples that in turn demonstrate the untenability of the simple ergodic approach dominant in molecular biology in which the data coming from huge ensemble of cells are considered as relative to a single 'average' cell.
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Affiliation(s)
- Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanità, Viale Regina Elena 299, Roma, Italy.
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31
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Lelièvre JM, Le Bourhis D, Breton A, Hayes H, Servely JL, Vignon X. Heat-induced and spontaneous expression of Hsp70.1Luciferase transgene copies localized on Xp22 in female bovine cells. BMC Res Notes 2010; 3:17. [PMID: 20180997 PMCID: PMC2832894 DOI: 10.1186/1756-0500-3-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 01/22/2010] [Indexed: 12/03/2022] Open
Abstract
Background Expression of several copies of the heat-inducible Hsp70.1Luciferase (LUC) transgene inserted at a single X chromosome locus of a bull (Bos taurus) was assessed in females after X-chromosome inactivation (XCI). Furthermore, impact of the chromosomal environment on the spontaneous expression of these transgene copies before XCI was studied during early development in embryos obtained after in vitro fertilization (IVF), when the locus was carried by the X chromosome inherited from the bull, and after somatic cell nuclear transfer (SCNT) cloning, when the locus could be carried by the inactive Xi or the active Xa chromosome in a female donor cell, or by the (active) X in a male donor cell. Findings Transgene copies were mapped to bovine Xp22. In XXLUC female fibroblasts, i.e. after random XCI, the proportions of late-replicating inactive and early-replicating active XLUC chromosomes were not biased and the proportion of cells displaying an increase in the level of immunostained luciferase protein after heat-shock induction was similar to that in male fibroblasts. Spontaneous transgene expression occurred at the 8-16-cell stage both in transgenic (female) embryos obtained after IVF and in male and female embryos obtained after SCNT. Conclusions The XLUC chromosome is normally inactivated but at least part of the inactivated X-linked Hsp70.1Luciferase transgene copies remains heat-inducible after random XCI in somatic cells. Before XCI, the profile of the transgenes' spontaneous expression is independent of the epigenetic origin of the XLUC chromosome since it is similar in IVF female, SCNT male and SCNT female embryos.
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Affiliation(s)
- Jean-Marc Lelièvre
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy en Josas, France.
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