Bayesian modeling suggests that IL-12 (p40), IL-13 and MCP-1 drive murine cytokine networks in vivo

BackgroundCytokine-hormone network deregulations underpin pathologies ranging from autoimmune disorders to cancer, but our understanding of these networks in physiological/pathophysiological states remains patchy. We employed Bayesian networks to analyze cytokine-hormone interactions in vivo using murine lactation as a dynamic, physiological model system.ResultsCirculatory levels of estrogen, progesterone, prolactin and twenty-three cytokines were profiled in post partum mice with/without pups. The resultant networks were very robust and assembled about structural hubs, with evidence that interleukin (IL)-12 (p40), IL-13 and monocyte chemoattractant protein (MCP)-1 were the primary drivers of network behavior. Network structural conservation across physiological scenarios coupled with the successful empirical validation of our approach suggested that in silico network perturbations can predict in vivo qualitative responses. In silico perturbation of network components also captured biological features of cytokine interactions (antagonism, synergy, redundancy).ConclusionThese findings highlight the potential of network-based approaches in identifying novel cytokine pharmacological targets and in predicting the effects of their exogenous manipulation in inflammatory/immune disorders.

[1]  Paul D. W. Kirk,et al.  Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements , 2011, BMC Bioinformatics.

[2]  B. Fleischer,et al.  Trypanosoma cruzi induces strong IL‐12 and IL‐18 gene expression in vivo: correlation with interferon‐gamma (IFN‐γ) production , 1997, Clinical and experimental immunology.

[3]  M. Karin,et al.  Signal transduction by tumor necrosis factor and its relatives. , 2001, Trends in cell biology.

[4]  M. Hollingsworth,et al.  Molecular pathology of early pancreatic cancer. , 2010, Cancer biomarkers : section A of Disease markers.

[5]  Ron S. Kenett,et al.  Encyclopedia of statistics in quality and reliability , 2007 .

[6]  D. Pe’er Bayesian Network Analysis of Signaling Networks: A Primer , 2005, Science's STKE.

[7]  G. Mantovani,et al.  Oxytocin both increases proliferative response of peripheral blood lymphomonocytes to phytohemagglutinin and reverses immunosuppressive estrogen activity. , 2010, In vivo.

[8]  Marco Grzegorczyk,et al.  An introduction to Gaussian Bayesian networks. , 2010, Methods in molecular biology.

[9]  James J. Walker,et al.  Uterine and serum cytokine arrays in the mouse during estrus. , 2007, Animal reproduction science.

[10]  J. Mestecky,et al.  Homeostasis of the Mucosal Immune System , 2001 .

[11]  Peter Norvig,et al.  Artificial Intelligence: A Modern Approach , 1995 .

[12]  P. Sfikakis,et al.  Anti-TNF agents for Behçet's disease: analysis of published data on 369 patients. , 2011, Seminars in arthritis and rheumatism.

[13]  P. Brandtzaeg The mucosal immune system and its integration with the mammary glands. , 2010, The Journal of pediatrics.

[14]  M. Russo,et al.  Hormonal regulation of cytokine release by human fetal membranes at term gestation: effects of oxytocin, hydrocortisone and progesterone on tumour necrosis factor-alpha and transforming growth factor-beta 1 output. , 2002, Journal of reproductive immunology.

[15]  C. Brightling,et al.  Expression and activation of the oxytocin receptor in airway smooth muscle cells: Regulation by TNFα and IL-13 , 2010, Respiratory research.

[16]  R. Ness,et al.  Inflammation and Endometrial Cancer: A Hypothesis , 2005, Cancer Epidemiology Biomarkers & Prevention.

[17]  T. Wagner,et al.  Endogenous human growth hormone (GH) modulates the effect of gonadotropin-releasing hormone on pituitary function and the gonadotropin response to the negative feedback effect of testosterone in adult male transgenic mice bearing human GH gene. , 1988, Endocrinology.

[18]  David Maxwell Chickering,et al.  Learning Bayesian Networks: The Combination of Knowledge and Statistical Data , 1994, Machine Learning.

[19]  Judea Pearl,et al.  Bayesian Networks , 1998, Encyclopedia of Social Network Analysis and Mining. 2nd Ed..

[20]  F. Bucchieri,et al.  IL-13 receptor α 2: A regulator of IL-13 and IL-4 signal transduction in primary human fibroblasts , 2006 .

[21]  L. Arnaud,et al.  Systemic perturbation of cytokine and chemokine networks in Erdheim-Chester disease: a single-center series of 37 patients. , 2011, Blood.

[22]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[23]  R. D'Amato,et al.  Inhibition of angiogenesis in vivo by interleukin 12. , 1995, Journal of the National Cancer Institute.

[24]  W. Karmaus,et al.  Review: Immune Markers in Breast Milk and Fetal and Maternal Body Fluids: A Systematic Review of Perinatal Concentrations , 2011, Journal of human lactation : official journal of International Lactation Consultant Association.

[25]  T. Jenssen,et al.  A literature network of human genes for high-throughput analysis of gene expression , 2001, Nature Genetics.

[26]  W. Tulalamba,et al.  Prolactin alters the mRNA expression of osteoblast-derived osteoclastogenic factors in osteoblast-like UMR106 cells , 2011, Molecular and Cellular Biochemistry.

[27]  E. Crivellato The role of angiogenic growth factors in organogenesis. , 2011, The International journal of developmental biology.

[28]  R. Tribe,et al.  Cytokine Networks and the Regulation of Uterine Function in Pregnancy and Parturition , 2008, Journal of neuroendocrinology.

[29]  D. Pe’er,et al.  Principles and Strategies for Developing Network Models in Cancer , 2011, Cell.

[30]  R. Frydman,et al.  Cytokines, implantation and early abortion: re‐examining the Th1/Th2 paradigm leads to question the single pathway, single therapy concept , 2003, American journal of reproductive immunology.

[31]  M. Norcross,et al.  Regulation of interleukin-12 expression in human monocytes: selective priming by interferon-gamma of lipopolysaccharide-inducible p35 and p40 genes. , 1995, Blood.

[32]  Albert-László Barabási,et al.  Controllability of complex networks , 2011, Nature.

[33]  P. Baiardi,et al.  Determinants of Risk Infection During Therapy with Anti TNF-Alpha Blocking Agents in Rheumatoid Arthritis , 2012, The open rheumatology journal.

[34]  Dirk Husmeier,et al.  Bayesian integration of biological prior knowledge into the reconstruction of gene regulatory networks with Bayesian networks. , 2007, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

[35]  K. Sachs,et al.  Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data , 2005, Science.

[36]  James J. Walker,et al.  Murine serum cytokines throughout the estrous cycle, pregnancy and post partum period. , 2006, Animal reproduction science.

[37]  Xujing Wang,et al.  Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data , 2011, BMC Bioinformatics.

[38]  M. Ramos-Casals,et al.  Cardiovascular Risk in Systemic Autoimmune Diseases: Epigenetic Mechanisms of Immune Regulatory Functions , 2011, Clinical & developmental immunology.

[39]  P. Bohjanen,et al.  Evaluating posttranscriptional regulation of cytokine genes. , 2012, Methods in molecular biology.

[40]  P. M. Reber Prolactin and immunomodulation. , 1993, The American journal of medicine.

[41]  A. Barabasi,et al.  Network medicine : a network-based approach to human disease , 2010 .

[42]  J Mestecky Homeostasis of the mucosal immune system: human milk and lactation. , 2001, Advances in experimental medicine and biology.

[43]  P. Brandtzaeg Mucosal immunity: integration between mother and the breast-fed infant. , 2003, Vaccine.

[44]  Melanie I. Stefan,et al.  Molecules for memory: modelling CaMKII , 2007, BMC Systems Biology.

[45]  E. Ginns,et al.  Deficiency in Mouse Oxytocin Prevents Milk Ejection,but not Fertility or Parturition , 1996, Journal of neuroendocrinology.

[46]  T. Insel,et al.  Oxytocin is required for nursing but is not essential for parturition or reproductive behavior. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[47]  E. Peeva,et al.  Prolactin alters the mechanisms of B cell tolerance induction. , 2009, Arthritis and rheumatism.

[48]  G. Lanfranchi,et al.  Reconstruction and functional analysis of altered molecular pathways in human atherosclerotic arteries , 2009, BMC Genomics.

[49]  Zoubin Ghahramani,et al.  A Bayesian approach to reconstructing genetic regulatory networks with hidden factors , 2005, Bioinform..

[50]  R. Russell,et al.  Structural systems biology: modelling protein interactions , 2006, Nature Reviews Molecular Cell Biology.

[51]  Nir Friedman,et al.  Data Analysis with Bayesian Networks: A Bootstrap Approach , 1999, UAI.

[52]  D. Armstrong,et al.  Regulation of lipid metabolism and progesterone production in rat corpora lutea and ovarian interstitial elements by prolactin and luteinizing hormone. , 1969, Endocrinology.

[53]  J. Zhu,et al.  An integrative genomics approach to the reconstruction of gene networks in segregating populations , 2004, Cytogenetic and Genome Research.

[54]  John Quackenbush,et al.  Seeded Bayesian Networks: Constructing genetic networks from microarray data , 2008, BMC Systems Biology.

[55]  Eugene R. Tracy,et al.  A Bayesian network approach to feature selection in mass spectrometry data , 2010, BMC Bioinformatics.

[56]  E. Ginns,et al.  Oxytocin and milk removal are required for post-partum mammary-gland development. , 1997, Genes and function.

[57]  Michal Linial,et al.  Using Bayesian Networks to Analyze Expression Data , 2000, J. Comput. Biol..

[58]  P. Scuffham,et al.  A mixed treatment comparison of the short-term efficacy of biologic disease modifying anti-rheumatic drugs in established rheumatoid arthritis , 2011, Current medical research and opinion.

[59]  P. Brandtzaeg The secretory immunoglobulin system: regulation and biological significance. Focusing on human mammary glands. , 2002, Advances in experimental medicine and biology.

[60]  F. Balkwill,et al.  The cytokine network. , 1989, Immunology today.

[61]  Radford M. Neal Pattern Recognition and Machine Learning , 2007, Technometrics.

[62]  Peter A. Flach,et al.  Hierarchical Bayesian Networks: A Probabilistic Reasoning Model for Structured Domains , 2002 .

[63]  S. Oertelt-Prigione The influence of sex and gender on the immune response. , 2012, Autoimmunity reviews.

[64]  N. Horseman,et al.  Defective mammopoiesis, but normal hematopoiesis, in mice with a targeted disruption of the prolactin gene , 1997, The EMBO journal.

[65]  E. Bluman,et al.  Human natural killer cells produce abundant macrophage inflammatory protein-1 alpha in response to monocyte-derived cytokines. , 1996, The Journal of clinical investigation.

[66]  Suresh K. Bhavnani,et al.  How cytokines co-occur across asthma patients: From bipartite network analysis to a molecular-based classification , 2011, J. Biomed. Informatics.

[67]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[68]  E. Bröcker,et al.  Interleukin‐13 selectively induces monocyte chemoattractant protein‐1 synthesis and secretion by human endothelial cells. Involvement of IL‐4Rα and Stat6 phosphorylation , 1997, Immunology.

[69]  P. Kelly,et al.  Immune system development and function in prolactin receptor-deficient mice. , 1999, Journal of immunology.

[70]  L. Penny Monocyte chemoattractant protein 1 in luteolysis. , 2000, Reviews of reproduction.

[71]  M. Bachmann,et al.  Averting inflammation by targeting the cytokine environment , 2010, Nature Reviews Drug Discovery.

[72]  D. Flint,et al.  Control of Milk Secretion and Apoptosis DuringMammary Involution , 1999, Journal of Mammary Gland Biology and Neoplasia.

[73]  Daniel P. Downes,et al.  Monocyte Chemotactic Protein-1 Promotes Inflammatory Vascular Repair of Murine Carotid Aneurysms via a Macrophage Inflammatory Protein-1&agr; and Macrophage Inflammatory Protein-2–Dependent Pathway , 2011, Circulation.

[74]  Ian H. Witten,et al.  The WEKA data mining software: an update , 2009, SKDD.

[75]  S. Akira,et al.  IL-18, although antiallergic when administered with IL-12, stimulates IL-4 and histamine release by basophils. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[76]  G. Roda,et al.  Cytokine Networks in Ulcerative Colitis , 2011 .

[77]  Juliette van Steenwinckel,et al.  Neurochemokines: a menage a trois providing new insights on the functions of chemokines in the central nervous system , 2011, Journal of neurochemistry.

[78]  Douglas A Lauffenburger,et al.  Lyapunov exponents and phase diagrams reveal multi-factorial control over TRAIL-induced apoptosis , 2011, Molecular systems biology.

[79]  M. Černá,et al.  Immunomodulatory role of prolactin in diabetes development. , 2009, Autoimmunity reviews.

[80]  Sze Ma,et al.  Recent development in pleiotropic effects of statins on cardiovascular disease through regulation of transforming growth factor-beta superfamily. , 2011, Cytokine & growth factor reviews.

[81]  A. Buckley Prolactin, a lymphocyte growth and survival factor , 2001, Lupus.

[82]  Philip N Benfey,et al.  Reconstructing regulatory network transitions. , 2011, Trends in cell biology.

[83]  A. Migliore,et al.  INDIRECT COMPARISON OF THE EFFECTS OF ANTI-TNF BIOLOGICAL AGENTS IN PATIENTS WITH ANKYLOSING SPONDYLITIS BY MEANS OF A MIXED TREATMENT COMPARISON PERFORMED ON EFFICACY DATA FROM PUBLISHED RANDOMISED, CONTROLLED TRIALS. , 2014, Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research.

[84]  R. Ransohoff,et al.  TNF-alpha microinjection upregulates chemokines and chemokine receptors in the central nervous system without inducing leukocyte infiltration. , 2003, Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research.

[85]  K. Aziz,et al.  Molecular markers for cancer prognosis and treatment: have we struck gold? , 2012, Cancer letters.

[86]  C. Wilde,et al.  Metabolic adaptations in mouse mammary gland during a normal lactation cycle and in extended lactation. , 1987, Quarterly journal of experimental physiology.

[87]  N. Orsi Cytokine networks in the establishment and maintenance of pregnancy , 2008, Human fertility.

[88]  Peter Norvig,et al.  Artificial intelligence - a modern approach, 2nd Edition , 2003, Prentice Hall series in artificial intelligence.