Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets

Journal of Biomedical Informatics

Volumn 46, Issue 6, 2013, Pages 1030-1043

  Formanowicz, Dorota ^a   Kozak, Adam ^b   Głowacki, Tomasz ^b   Radom, Marcin ^b   Formanowicz, Piotr ^b,c  

^a POZNAN UNIVERSITY OF MEDICAL SCIENCES   (Poland)

^b POZNAN UNIVERSITY OF TECHNOLOGY   (Poland)

^c INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

Author keywords

Biological systems; Hemojouvelin synthesis; Modeling; Petri nets; T invariants

Indexed keywords

BIOLOGICAL ENTITIES; BIOLOGICAL PHENOMENA; FUNDAMENTAL PROPERTIES; GRAPHICAL REPRESENTATIONS; INHERENT COMPLEXITY; MATHEMATICAL METHOD; T-INVARIANTS; THEORY OF PETRI NETS;

DIFFERENTIAL EQUATIONS; MODELS; PETRI NETS;

BIOLOGICAL SYSTEMS;

BONE MORPHOGENETIC PROTEIN; HEMOJUVELIN; HEPCIDIN; IRON; MATRIPTASE; SMAD1 PROTEIN; SMAD5 PROTEIN; SMAD8 PROTEIN;

ARTICLE; BIOLOGICAL PHENOMENA AND FUNCTIONS CONCERNING THE ENTIRE ORGANISM; BIOLOGY; HEMOCHROMATOSIS; HOMEOSTASIS; HORMONE SYNTHESIS; HUMAN; IRON METABOLISM; MATHEMATICAL MODEL; PETRI NET; PRIORITY JOURNAL; PROTEIN INTERACTION;

BIOLOGICAL SYSTEMS; HEMOJOUVELIN SYNTHESIS; MODELING; PETRI NETS; T-INVARIANTS;

BONE MORPHOGENETIC PROTEINS; GPI-LINKED PROTEINS; HEPCIDINS; HUMANS; MODELS, BIOLOGICAL; SMAD PROTEINS;

EID: 84888200386     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2013.07.013     Document Type: Article

References (49)

1. Babitt J.L., Huang F.W., Xia Y., Sidis T.A., Samad Y., Campagna J.A., et al. Bone morphogenetic protein signaling by hemojuvelin regulates hepcidin expression. Nat Genet 2006, 38:531-539.
2. Babitt J.L., Huang F.W., Xia Y., Sidis Y., Andrews N.C., Lin H.Y. Modulation of bone morphogenetic protein signaling in vivo regulates systemic iron balance. J Clin Invest 2007, 117:1933-1939.
3. Calinski T., Harabasz J. A dendrite method for cluster analysis. Commun Stat 1974, 3(1):1-27.
4. Chao D.Y., Wang D.T. Two theoretical and practical aspects of knitting technique: invariants and a new class of Petri net. IEEE Trans Syst Man Cybern B: Cybern 1997, 27:962-977.
5. Cheng Y., Zak O., Aisen P., Harrison S.C., Walz T. Structure of the human transferrin receptor-transferrin complex. Cell 2004, 116:1052-1060.
6. Collins J.F., Wessling-Resnick M., Knutson M.D. Hepcidin regulation of iron transport. J Nutr 2008, 138:2284-2288.
7. D'Alessio F., Hentze M.W., Muckenthaler M.U. The hemochromatosis proteins HFE, TfR2, and HJV form a membrane-associated protein complex for hepcidin regulation. J Hepatol 2012, 57:1052-1060.
8. David R., Alla Discrete H. Continuous and hybrid Petri nets 2010, Springer-Verlag, Berlin, Heidelberg.
9. De Domenico I., Ward D.M., Kaplan J. Hepcidin regulation: ironing out the details. J Clin Invest 2007, 117:1755-1758.
10. Enns C.A., Ahmed R., Zhang A-S. Neogenin interacts with matriptase-2 to facilitate hemojuveline clevage. J Cell Biol 2012, 287:35104-35117.
11. Formanowicz D., Formanowicz P. A overall view of the process of the regulation of human iron metabolism. Biotechnologia 2011, 92:193-207.
12. Formanowicz D., Kozak A., Formanowicz P. A Petri net based model of oxidative stress in atherosclerosis. Found Comput Dec Sci 2012, 37:59-78.
13. Formanowicz D., Sackmann A., Formanowicz P., Błazewicz J. Petri net based model of the body iron homeostasis. J Biomed Inform 2007, 40:476-485.
14. Formanowicz D., Sackmann A., Kozak A., Błazewicz J., Formanowicz P. Some aspects of the anemia of chronic disorders modeled and analyzed by petri net based approach. Bioprocess Biosyst Eng 2011, 34:581-595.
15. Formanowicz P. On the border between biology, mathematics and computer science. Biotechnologia 2011, 92:217-220.
16. Ganz T. Hepcidin and iron regulation, 10 years later. Blood 2011, 117:4425-4433.
17. Grafahrend-Belau E., Schreiber F., Heiner M., Sackmann A., Junker B.H., Grunwald S., et al. Modularization of biochemical networks based on classification of Petri net T-invariants. BMC Bioinformatics 2008, 90.
18. Heiner M., Herajy M., Liu F., Rohr C., Schwarick M. Snoopy - a unifying Petri net tool. Lect Notes Comput Sci 2012, 7347:398-407.
19. Kaufman L., Rousseeuw P.J. Finding groups in data: an introduction to cluster analysis 1990, John Wiley and Sons, New York.
20. Kielbassa J., Bortfeldt R., Schuster S., Koch I. Modeling of the u1 snrnp assembly pathway in alternative splicing in human cells using Petri nets. Comput Biol Chem 2009, 33:46-61.
21. Klipp E., Liebermeister W., Wierling C., Kowald A., Lehrach H., Herwig R. Systems biology: a textbook 2009, Wiley-VCH, Weinheim.
22. Knutson M.D. Into the matrix: regulation of the iron regulatory hormone hepcidin by matriptase-2. Nutr Rev 2009, 65:284-288.
23. Modeling in systems biology: the Petri net approach 2011, Springer, London. I. Koch, W. Reisig, F. Schreiber (Eds.).
24. Lee D.H., Zhou L.J., Zhou Z., Xie J.X., Jung J.U., Liu Y., et al. Neogenin inhibits HJV secretion and regulates BMP-induced hepcidin expression and iron homeostasis. Blood 2010, 115:3136-3145.
25. Lin L., Valore E.V., Nemeth E., Goodnough J.B., Gabayan V., Ganz T. Iron-transferrin regulates hepcidin synthesis in primary hepatocyte culture through hemojuvelin and BMP2/4. Blood 2007, 110:2182-2189.
26. Maurer E., Gütschow M., Stirnberg M. Matriptase-2 (TMPRSS6) is directly up-regulated by hypoxia inducible factor-1: identification of a hypoxia-responsive element in the TMPRSS6 promoter region. Biol Chem 2012, 393:535-540.
27. Murata T. Petri nets: properties, analysis and aplications. Proc IEEE 1989, 90:541-580.
28. Dingle N.J., Knottenbelt W.J., Suto T. Pipe2: a tool for the performance evaluation of generalised stochastic Petri nets. ACM SIGMETRICS PER 2009, 36:34-39.
29. Oliveira J.S., Bailey C.G., Jones-Oliveira J.B., Dixon DA. An algebraic-combinatorial model for the identification and mapping of biochemical pathways. Bull Math Biol 2011, 63:1163-1196.
30. Papanikolaou G., Samuels M.E., Ludwig E.H., MacDonald M.L., Franchini P.L., Dubn++ M.P., et al. Mutations in HFE2 cause iron overload in chromosome 1q-linked juvenile hemochromatosis. Nat Genet 2004, 36:77-82.
31. Pigeon C., Ilyin G., Courselaud B., Leroyer P., Turlin B., Brissot P., et al. A new mouse liver-specific gene, encoding a protein homologous to human antimicrobial peptide hepcidin, is overexpressed during iron overload. J Biol Chem 2001, 276:7811-7819.
32. Ramsay A.J., Hooper J.D., Folgueras A.R., Velasco G., Lopez-Otin C. Matriptase-2 (TMPRSS6): a proteolitic regulator of iron homeostasis. Haematology 2009, 94:840-849.
33. Reisig W. Petri nets: an introduction 1985, Springer-Verlag, BerlinHeidelberg.
34. Bortfeldt R.H., Schuster S., Koch I. Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach. Stud Health Technol Inform 2011, 162:244-247.
35. Rodrigez Martinez A., Niemela O., Parkkila S. Hepatic and extrahepatic expression of the new iron regulatory protein hemojuvelin. Haematology 2004, 89:1441-1445.
36. Sylvain S. Invariants and other structural properties of biochemical models as a constraint satisfaction problem. Algorithms Mol Biol 2012, 7:15-24.
37. Sackmann A., Formanowicz D., Formanowicz P., Koch I., Błażewicz J. An analysis of Petri net based model of the human body iron homeostasis process. Comput Biol Chem 2007, 31:1-10.
38. Sackmann A., Heiner M., Koch I. Application of Petri net based analysis techniques to signal transduction pathway. BMC Bioinformatics 2006, 482.
39. Silvestri L., Pagani A., Camaschella C. Furin-mediated release of soluble hemojuvelin: a new link between hypoxia and iron homeostasis. Blood 2008, 111:924-931.
40. Silvestri L., Pagani A., Nai A., De Domenico I., Kaplan J., Camaschella D. The serine protease matriptase-2 (TMPRSS6) inhibits hepcidin activation by cleaving membrane hemojuvelin. Cell Metab 2008, 8:502-511.
41. Souchelnytskyi S., Rönnstrand L., Heldin C.H., ten Dijke P. Phosphorylation of Smad signaling proteins by receptor serine/threonine kinases. Methods Mol Biol 2001, 124:107-120.
42. Szallasi Z., Stelling J., Perival V. System modeling in cellural biology: from concepts to nuts and bolts 2006, The MIT Press, Cambridge, Massachusetts.
43. Truksa J., Lee P., Beutler E. Two BMP responsive elements, STAT, and bZIP/HNF4/COUP motifs of the hepcidin promoter are critical form BMP, SMAD1, and HJV responsiveness. Blood 2009, 113:688-695.
44. Wang J., Pantopoulos K. Regulation of cellular iron metabolism. Biochem J 2011, 434:365-381.
45. Wegener JT, Schwarick M, Heiner M. A plugin system for charlie. In: Proceedings of international workshop CSP; 2011. p. 531-54.
46. Wessling-Resnick M. Iron homeostasis and the inflammatory response. Annu Rev Nutr 2010, 30:105-122.
47. Westergaard M., Kristensen L.M. The access/cpn framework: a tool for interacting with the cpn tools simulator. Lect Notes Comput Sci 2009, 5606:313-322.
48. Zhang A-S., Enns C.A. Molecular mechanisms of normal iron homeostasis. Hematology 2009, 1:207-214.
49. Zhu H., Kavsak P., Abdollah S., Wrana J.L., Thomsen G.H. A SMAD ubiquitin ligase targets the BMP pathway and affects embryonic pattern formation. Nature 1999, 400:687-693.