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Krishnan J, Torabi R, Schuppert A, Napoli ED. A modified Ising model of Barabási-Albert network with gene-type spins. J Math Biol 2020; 81:769-798. [PMID: 32897406 PMCID: PMC7519008 DOI: 10.1007/s00285-020-01518-6] [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: 08/20/2019] [Revised: 05/02/2020] [Indexed: 12/30/2022]
Abstract
The central question of systems biology is to understand how individual components of a biological system such as genes or proteins cooperate in emerging phenotypes resulting in the evolution of diseases. As living cells are open systems in quasi-steady state type equilibrium in continuous exchange with their environment, computational techniques that have been successfully applied in statistical thermodynamics to describe phase transitions may provide new insights to the emerging behavior of biological systems. Here we systematically evaluate the translation of computational techniques from solid-state physics to network models that closely resemble biological networks and develop specific translational rules to tackle problems unique to living systems. We focus on logic models exhibiting only two states in each network node. Motivated by the apparent asymmetry between biological states where an entity exhibits boolean states i.e. is active or inactive, we present an adaptation of symmetric Ising model towards an asymmetric one fitting to living systems here referred to as the modified Ising model with gene-type spins. We analyze phase transitions by Monte Carlo simulations and propose a mean-field solution of a modified Ising model of a network type that closely resembles a real-world network, the Barabási–Albert model of scale-free networks. We show that asymmetric Ising models show similarities to symmetric Ising models with the external field and undergoes a discontinuous phase transition of the first-order and exhibits hysteresis. The simulation setup presented herein can be directly used for any biological network connectivity dataset and is also applicable for other networks that exhibit similar states of activity. The method proposed here is a general statistical method to deal with non-linear large scale models arising in the context of biological systems and is scalable to any network size.
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Affiliation(s)
- Jeyashree Krishnan
- Aachen Institute for Advanced Study in Computational Engineering Science (AICES) Graduate School, RWTH Aachen University, Aachen, Germany. .,Joint Research Center for Computational Biomedicine (JRC-Combine), RWTH Aachen University, Aachen, Germany.
| | - Reza Torabi
- Department of Physics and Astronomy, University of Calgary, Calgary, AB, Canada
| | - Andreas Schuppert
- Aachen Institute for Advanced Study in Computational Engineering Science (AICES) Graduate School, RWTH Aachen University, Aachen, Germany.,Joint Research Center for Computational Biomedicine (JRC-Combine), RWTH Aachen University, Aachen, Germany
| | - Edoardo Di Napoli
- Aachen Institute for Advanced Study in Computational Engineering Science (AICES) Graduate School, RWTH Aachen University, Aachen, Germany.,Jülich Supercomputing Center, Forschungszentrum Jülich, Jülich, Germany
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2
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Rockne RC, Branciamore S, Qi J, Frankhouser DE, O'Meally D, Hua WK, Cook G, Carnahan E, Zhang L, Marom A, Wu H, Maestrini D, Wu X, Yuan YC, Liu Z, Wang LD, Forman S, Carlesso N, Kuo YH, Marcucci G. State-Transition Analysis of Time-Sequential Gene Expression Identifies Critical Points That Predict Development of Acute Myeloid Leukemia. Cancer Res 2020; 80:3157-3169. [PMID: 32414754 PMCID: PMC7416495 DOI: 10.1158/0008-5472.can-20-0354] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/06/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
Temporal dynamics of gene expression inform cellular and molecular perturbations associated with disease development and evolution. Given the complexity of high-dimensional temporal genomic data, an analytic framework guided by a robust theory is needed to interpret time-sequential changes and to predict system dynamics. Here we model temporal dynamics of the transcriptome of peripheral blood mononuclear cells in a two-dimensional state-space representing states of health and leukemia using time-sequential bulk RNA-seq data from a murine model of acute myeloid leukemia (AML). The state-transition model identified critical points that accurately predict AML development and identifies stepwise transcriptomic perturbations that drive leukemia progression. The geometry of the transcriptome state-space provided a biological interpretation of gene dynamics, aligned gene signals that are not synchronized in time across mice, and allowed quantification of gene and pathway contributions to leukemia development. Our state-transition model synthesizes information from multiple cell types in the peripheral blood and identifies critical points in the transition from health to leukemia to guide interpretation of changes in the transcriptome as a whole to predict disease progression. SIGNIFICANCE: These findings apply the theory of state transitions to model the initiation and development of acute myeloid leukemia, identifying transcriptomic perturbations that accurately predict time to disease development.See related commentary by Kuijjer, p. 3072 GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/15/3157/F1.large.jpg.
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Affiliation(s)
- Russell C Rockne
- Division of Mathematical Oncology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope Medical Center, Duarte, California.
| | - Sergio Branciamore
- Department of Diabetes Complications & Metabolism, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Jing Qi
- Department of Hematological Malignancies Translational Science, Hematology & Hematopoietic Cell Transplantation and the Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - David E Frankhouser
- Department of Diabetes Complications & Metabolism, Beckman Research Institute, City of Hope Medical Center, Duarte, California
- Department of Population Sciences, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Denis O'Meally
- Center for Gene Therapy, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Wei-Kai Hua
- Department of Hematological Malignancies Translational Science, Hematology & Hematopoietic Cell Transplantation and the Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Guerry Cook
- Department of Hematological Malignancies Translational Science, Hematology & Hematopoietic Cell Transplantation and the Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Emily Carnahan
- Department of Hematological Malignancies Translational Science, Hematology & Hematopoietic Cell Transplantation and the Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Lianjun Zhang
- Department of Hematological Malignancies Translational Science, Hematology & Hematopoietic Cell Transplantation and the Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Ayelet Marom
- Department of Hematological Malignancies Translational Science, Hematology & Hematopoietic Cell Transplantation and the Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Herman Wu
- Department of Hematological Malignancies Translational Science, Hematology & Hematopoietic Cell Transplantation and the Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Davide Maestrini
- Division of Mathematical Oncology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Xiwei Wu
- Department of Molecular Medicine; Bioinformatics Core, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Yate-Ching Yuan
- Department of Molecular Medicine; Bioinformatics Core, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Zheng Liu
- Department of Molecular and Cellular Biology; Integrative Genomics Core, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Leo D Wang
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Medical Center, Duarte, California
- Department of Pediatrics, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Stephen Forman
- Department of Hematological Malignancies Translational Science, Hematology & Hematopoietic Cell Transplantation and the Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Nadia Carlesso
- Department of Hematological Malignancies Translational Science, Hematology & Hematopoietic Cell Transplantation and the Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope Medical Center, Duarte, California
| | - Ya-Huei Kuo
- Department of Hematological Malignancies Translational Science, Hematology & Hematopoietic Cell Transplantation and the Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope Medical Center, Duarte, California.
| | - Guido Marcucci
- Department of Hematological Malignancies Translational Science, Hematology & Hematopoietic Cell Transplantation and the Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope Medical Center, Duarte, California
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Personalized disease signatures through information-theoretic compaction of big cancer data. Proc Natl Acad Sci U S A 2018; 115:7694-7699. [PMID: 29976841 DOI: 10.1073/pnas.1804214115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Every individual cancer develops and grows in its own specific way, giving rise to a recognized need for the development of personalized cancer diagnostics. This suggested that the identification of patient-specific oncogene markers would be an effective diagnostics approach. However, tumors that are classified as similar according to the expression levels of certain oncogenes can eventually demonstrate divergent responses to treatment. This implies that the information gained from the identification of tumor-specific biomarkers is still not sufficient. We present a method to quantitatively transform heterogeneous big cancer data to patient-specific transcription networks. These networks characterize the unbalanced molecular processes that deviate the tissue from the normal state. We study a number of datasets spanning five different cancer types, aiming to capture the extensive interpatient heterogeneity that exists within a specific cancer type as well as between cancers of different origins. We show that a relatively small number of altered molecular processes suffices to accurately characterize over 500 tumors, showing extreme compaction of the data. Every patient is characterized by a small specific subset of unbalanced processes. We validate the result by verifying that the processes identified characterize other cancer patients as well. We show that different patients may display similar oncogene expression levels, albeit carrying biologically distinct tumors that harbor different sets of unbalanced molecular processes. Thus, tumors may be inaccurately classified and addressed as similar. These findings highlight the need to expand the notion of tumor-specific oncogenic biomarkers to patient-specific, comprehensive transcriptional networks for improved patient-tailored diagnostics.
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Kravchenko-Balasha N, Johnson H, White FM, Heath JR, Levine RD. A Thermodynamic-Based Interpretation of Protein Expression Heterogeneity in Different Glioblastoma Multiforme Tumors Identifies Tumor-Specific Unbalanced Processes. J Phys Chem B 2016; 120:5990-7. [PMID: 27035264 DOI: 10.1021/acs.jpcb.6b01692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We describe a thermodynamic-motivated, information theoretic analysis of proteomic data collected from a series of 8 glioblastoma multiforme (GBM) tumors. GBMs are considered here as prototypes of heterogeneous cancers. That heterogeneity is viewed here as manifesting in different unbalanced biological processes that are associated with thermodynamic-like constraints. The analysis yields a molecular description of a stable steady state that is common across all tumors. It also resolves molecular descriptions of unbalanced processes that are shared by several tumors, such as hyperactivated phosphoprotein signaling networks. Further, it resolves unbalanced processes that provide unique classifiers of tumor subgroups. The results of the theoretical interpretation are compared against those of statistical multivariate methods and are shown to provide a superior level of resolution for identifying unbalanced processes in GBM tumors. The identification of specific constraints for each GBM tumor suggests tumor-specific combination therapies that may reverse this imbalance.
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Affiliation(s)
- Nataly Kravchenko-Balasha
- NanoSystems Biology Cancer Center, Division of Chemistry, Caltech , Pasadena, California 91125, United States.,Bio-Medical Sciences Department, The Faculty of Dental Medicine, The Hebrew University of Jerusalem , Jerusalem 9112001, Israel
| | - Hannah Johnson
- Signaling Programme, The Babraham Institute , Cambridge CB22 3AT, United Kingdom
| | - Forest M White
- Department of Biological Engineering, MIT , Cambridge, Massachusetts 02139, United States
| | - James R Heath
- NanoSystems Biology Cancer Center, Division of Chemistry, Caltech , Pasadena, California 91125, United States
| | - R D Levine
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine and Department of Chemistry and Biochemistry, UCLA , Los Angeles, California 90095, United States.,The Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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6
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Kravchenko-Balasha N, Simon S, Levine RD, Remacle F, Exman I. Computational surprisal analysis speeds-up genomic characterization of cancer processes. PLoS One 2014; 9:e108549. [PMID: 25405334 PMCID: PMC4236016 DOI: 10.1371/journal.pone.0108549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 08/31/2014] [Indexed: 01/18/2023] Open
Abstract
Surprisal analysis is increasingly being applied for the examination of transcription levels in cellular processes, towards revealing inner network structures and predicting response. But to achieve its full potential, surprisal analysis should be integrated into a wider range computational tool. The purposes of this paper are to combine surprisal analysis with other important computation procedures, such as easy manipulation of the analysis results – e.g. to choose desirable result sub-sets for further inspection –, retrieval and comparison with relevant datasets from public databases, and flexible graphical displays for heuristic thinking. The whole set of computation procedures integrated into a single practical tool is what we call Computational Surprisal Analysis. This combined kind of analysis should facilitate significantly quantitative understanding of different cellular processes for researchers, including applications in proteomics and metabolomics. Beyond that, our vision is that Computational Surprisal Analysis has the potential to reach the status of a routine method of analysis for practitioners. The resolving power of Computational Surprisal Analysis is here demonstrated by its application to a variety of cellular cancer process transcription datasets, ours and from the literature. The results provide a compact biological picture of the thermodynamic significance of the leading gene expression phenotypes in every stage of the disease. For each transcript we characterize both its inherent steady state weight, its correlation with the other transcripts and its variation due to the disease. We present a dedicated website to facilitate the analysis for researchers and practitioners.
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Affiliation(s)
- Nataly Kravchenko-Balasha
- NanoSystems Biology Cancer Center, Division of Chemistry, Caltech, Pasadena, California, United States of America
| | - Simcha Simon
- Software Engineering Department, The Jerusalem College of Engineering, Azrieli, Jerusalem, Israel
| | - R. D. Levine
- The Institute of Chemistry, The Hebrew University, Jerusalem, Israel
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - F. Remacle
- The Institute of Chemistry, The Hebrew University, Jerusalem, Israel
- Département de Chimie, Université de Liège, Liège, Belgium
| | - Iaakov Exman
- Software Engineering Department, The Jerusalem College of Engineering, Azrieli, Jerusalem, Israel
- * E-mail:
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Surprisal analysis characterizes the free energy time course of cancer cells undergoing epithelial-to-mesenchymal transition. Proc Natl Acad Sci U S A 2014; 111:13235-40. [PMID: 25157127 DOI: 10.1073/pnas.1414714111] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The epithelial-to-mesenchymal transition (EMT) initiates the invasive and metastatic behavior of many epithelial cancers. Mechanisms underlying EMT are not fully known. Surprisal analysis of mRNA time course data from lung and pancreatic cancer cells stimulated to undergo TGF-β1-induced EMT identifies two phenotypes. Examination of the time course for these phenotypes reveals that EMT reprogramming is a multistep process characterized by initiation, maturation, and stabilization stages that correlate with changes in cell metabolism. Surprisal analysis characterizes the free energy time course of the expression levels throughout the transition in terms of two state variables. The landscape of the free energy changes during the EMT for the lung cancer cells shows a stable intermediate state. Existing data suggest this is the previously proposed maturation stage. Using a single-cell ATP assay, we demonstrate that the TGF-β1-induced EMT for lung cancer cells, particularly during the maturation stage, coincides with a metabolic shift resulting in increased cytosolic ATP levels. Surprisal analysis also characterizes the absolute expression levels of the mRNAs and thereby examines the homeostasis of the transcription system during EMT.
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