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Brown G. Hematopoietic and Chronic Myeloid Leukemia Stem Cells: Multi-Stability versus Lineage Restriction. Int J Mol Sci 2022; 23:13570. [PMID: 36362357 PMCID: PMC9655164 DOI: 10.3390/ijms232113570] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 07/30/2023] Open
Abstract
There is compelling evidence to support the view that the cell-of-origin for chronic myeloid leukemia is a hematopoietic stem cell. Unlike normal hematopoietic stem cells, the progeny of the leukemia stem cells are predominantly neutrophils during the disease chronic phase and there is a mild anemia. The hallmark oncogene for chronic myeloid leukemia is the BCR-ABLp210 fusion gene. Various studies have excluded a role for BCR-ABLp210 expression in maintaining the population of leukemia stem cells. Studies of BCR-ABLp210 expression in embryonal stem cells that were differentiated into hematopoietic stem cells and of the expression in transgenic mice have revealed that BCR-ABLp210 is able to veer hematopoietic stem and progenitor cells towards a myeloid fate. For the transgenic mice, global changes to the epigenetic landscape were observed. In chronic myeloid leukemia, the ability of the leukemia stem cells to choose from the many fates that are available to normal hematopoietic stem cells appears to be deregulated by BCR-ABLp210 and changes to the epigenome are also important. Even so, we still do not have a precise picture as to why neutrophils are abundantly produced in chronic myeloid leukemia.
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MESH Headings
- Mice
- Animals
- Fusion Proteins, bcr-abl/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Hematopoietic Stem Cells/metabolism
- Mice, Transgenic
- Leukemia, Myeloid, Acute/metabolism
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Affiliation(s)
- Geoffrey Brown
- Institute of Clinical Sciences, School of Biomedical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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Iglesias PA. The Use of Rate Distortion Theory to Evaluate Biological Signaling Pathways. ACTA ACUST UNITED AC 2016. [DOI: 10.1109/tmbmc.2016.2623600] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Mc Mahon SS, Lenive O, Filippi S, Stumpf MPH. Information processing by simple molecular motifs and susceptibility to noise. J R Soc Interface 2016; 12:0597. [PMID: 26333812 DOI: 10.1098/rsif.2015.0597] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Biological organisms rely on their ability to sense and respond appropriately to their environment. The molecular mechanisms that facilitate these essential processes are however subject to a range of random effects and stochastic processes, which jointly affect the reliability of information transmission between receptors and, for example, the physiological downstream response. Information is mathematically defined in terms of the entropy; and the extent of information flowing across an information channel or signalling system is typically measured by the 'mutual information', or the reduction in the uncertainty about the output once the input signal is known. Here, we quantify how extrinsic and intrinsic noise affects the transmission of simple signals along simple motifs of molecular interaction networks. Even for very simple systems, the effects of the different sources of variability alone and in combination can give rise to bewildering complexity. In particular, extrinsic variability is apt to generate 'apparent' information that can, in extreme cases, mask the actual information that for a single system would flow between the different molecular components making up cellular signalling pathways. We show how this artificial inflation in apparent information arises and how the effects of different types of noise alone and in combination can be understood.
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Affiliation(s)
- Siobhan S Mc Mahon
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Biosciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Oleg Lenive
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Biosciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Sarah Filippi
- Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
| | - Michael P H Stumpf
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Biosciences, Imperial College London, South Kensington, London SW7 2AZ, UK Institute of Chemical Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
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Mousavian Z, Díaz J, Masoudi-Nejad A. Information theory in systems biology. Part II: protein-protein interaction and signaling networks. Semin Cell Dev Biol 2015; 51:14-23. [PMID: 26691180 DOI: 10.1016/j.semcdb.2015.12.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 12/07/2015] [Indexed: 12/25/2022]
Abstract
By the development of information theory in 1948 by Claude Shannon to address the problems in the field of data storage and data communication over (noisy) communication channel, it has been successfully applied in many other research areas such as bioinformatics and systems biology. In this manuscript, we attempt to review some of the existing literatures in systems biology, which are using the information theory measures in their calculations. As we have reviewed most of the existing information-theoretic methods in gene regulatory and metabolic networks in the first part of the review, so in the second part of our study, the application of information theory in other types of biological networks including protein-protein interaction and signaling networks will be surveyed.
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Affiliation(s)
- Zaynab Mousavian
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - José Díaz
- Grupo de Biología Teórica y Computacional, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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Respiratory particle deposition probability due to sedimentation with variable gravity and electrostatic forces. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 820:3-47. [PMID: 25417014 DOI: 10.1007/978-3-319-09012-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In this chapter, we study the effects of the acceleration gravity on the sedimentation deposition probability, as well as the aerosol deposition rate on the surface of the Earth and Mars, but also aboard a spacecraft in orbit around Earth and Mars as well for particles with density ρ p = 1,300 kg/m³, diameters d p = 1, 3, 5 μm, and residence times t = 0.0272, 0.2 , respectively. For particles of diameter 1 μm we find that, on the surface of Earth and Mars the deposition probabilities are higher at the poles when compared to the ones at the equator. Similarly, on the surface of the Earth we find that the deposition probabilities exhibit 0.5 and 0.4 % higher percentage difference at the poles when compared to that of the equator, for the corresponding residence times. Moreover in orbit equatorial orbits result to higher deposition probabilities when compared to polar ones. For both residence times particles with the diameters considered above in circular and elliptical orbits around Mars, the deposition probabilities appear to be the same for all orbital inclinations. Sedimentation probability increases drastically with particle diameter and orbital eccentricity of the orbiting spacecraft. Finally, as an alternative framework for the study of interaction and the effect of gravity in biology, and in particular gravity and the respiratory system we introduce is the term information in a way Shannon has introduced it, considering the sedimentation probability as a random variable. This can be thought as a way in which gravity enters the cognitive processes of the system (processing of information) in the cybernetic sense.
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Byrne MB, Kimura Y, Kapoor A, He Y, Mattam KS, Hasan KM, Olson LN, Wang F, Kenis PJA, Rao CV. Oscillatory behavior of neutrophils under opposing chemoattractant gradients supports a winner-take-all mechanism. PLoS One 2014; 9:e85726. [PMID: 24465668 PMCID: PMC3897492 DOI: 10.1371/journal.pone.0085726] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 11/29/2013] [Indexed: 12/19/2022] Open
Abstract
Neutrophils constitute the largest class of white blood cells and are the first responders in the innate immune response. They are able to sense and migrate up concentration gradients of chemoattractants in search of primary sites of infection and inflammation through a process known as chemotaxis. These chemoattractants include formylated peptides and various chemokines. While much is known about chemotaxis to individual chemoattractants, far less is known about chemotaxis towards many. Previous studies have shown that in opposing gradients of intermediate chemoattractants (interleukin-8 and leukotriene B4), neutrophils preferentially migrate toward the more distant source. In this work, we investigated neutrophil chemotaxis in opposing gradients of chemoattractants using a microfluidic platform. We found that primary neutrophils exhibit oscillatory motion in opposing gradients of intermediate chemoattractants. To understand this behavior, we constructed a mathematical model of neutrophil chemotaxis. Our results suggest that sensory adaptation alone cannot explain the observed oscillatory motion. Rather, our model suggests that neutrophils employ a winner-take-all mechanism that enables them to transiently lock onto sensed targets and continuously switch between the intermediate attractant sources as they are encountered. These findings uncover a previously unseen behavior of neutrophils in opposing gradients of chemoattractants that will further aid in our understanding of neutrophil chemotaxis and the innate immune response. In addition, we propose a winner-take-all mechanism allows the cells to avoid stagnation near local chemical maxima when migrating through a network of chemoattractant sources.
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Affiliation(s)
- Matthew B. Byrne
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yuki Kimura
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ashish Kapoor
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yuan He
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kewin S. Mattam
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Katherine M. Hasan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Luke N. Olson
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Fei Wang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Paul J. A. Kenis
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Christopher V. Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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Gkigkitzis I. Theoretical aspects and modelling of cellular decision making, cell killing and information-processing in photodynamic therapy of cancer. BMC Med Genomics 2013; 6 Suppl 3:S3. [PMID: 24565264 PMCID: PMC3981166 DOI: 10.1186/1755-8794-6-s3-s3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background The aim of this report is to provide a mathematical model of the mechanism for making binary fate decisions about cell death or survival, during and after Photodynamic Therapy (PDT) treatment, and to supply the logical design for this decision mechanism as an application of rate distortion theory to the biochemical processing of information by the physical system of a cell. Methods Based on system biology models of the molecular interactions involved in the PDT processes previously established, and regarding a cellular decision-making system as a noisy communication channel, we use rate distortion theory to design a time dependent Blahut-Arimoto algorithm where the input is a stimulus vector composed of the time dependent concentrations of three PDT related cell death signaling molecules and the output is a cell fate decision. The molecular concentrations are determined by a group of rate equations. The basic steps are: initialize the probability of the cell fate decision, compute the conditional probability distribution that minimizes the mutual information between input and output, compute the cell probability of cell fate decision that minimizes the mutual information and repeat the last two steps until the probabilities converge. Advance to the next discrete time point and repeat the process. Results Based on the model from communication theory described in this work, and assuming that the activation of the death signal processing occurs when any of the molecular stimulants increases higher than a predefined threshold (50% of the maximum concentrations), for 1800s of treatment, the cell undergoes necrosis within the first 30 minutes with probability range 90.0%-99.99% and in the case of repair/survival, it goes through apoptosis within 3-4 hours with probability range 90.00%-99.00%. Although, there is no experimental validation of the model at this moment, it reproduces some patterns of survival ratios of predicted experimental data. Conclusions Analytical modeling based on cell death signaling molecules has been shown to be an independent and useful tool for prediction of cell surviving response to PDT. The model can be adjusted to provide important insights for cellular response to other treatments such as hyperthermia, and diseases such as neurodegeneration.
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Iglesias PA. Systems biology: the role of engineering in the reverse engineering of biological signaling. Cells 2013; 2:393-413. [PMID: 24709707 PMCID: PMC3972675 DOI: 10.3390/cells2020393] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 05/06/2013] [Accepted: 05/15/2013] [Indexed: 12/05/2022] Open
Abstract
One of the principle tasks of systems biology has been the reverse engineering of signaling networks. Because of the striking similarities to engineering systems, a number of analysis and design tools from engineering disciplines have been used in this process. This review looks at several examples including the analysis of homeostasis using control theory, the attenuation of noise using signal processing, statistical inference and the use of information theory to understand both binary decision systems and the response of eukaryotic chemotactic cells.
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Affiliation(s)
- Pablo A Iglesias
- Department of Electrical and Computer Engineering, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
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