Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

This article is part of the supplement: Ninth International Conference on Bioinformatics (InCoB2010): Bioinformatics

Open Access Highly Accessed Proceedings

Analysis and verification of the HMGB1 signaling pathway

Haijun Gong1*, Paolo Zuliani1*, Anvesh Komuravelli1, James R Faeder2 and Edmund M Clarke1

Author Affiliations

1 Computer Science Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA

2 Department of Computational Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA

For all author emails, please log on.

BMC Bioinformatics 2010, 11(Suppl 7):S10  doi:10.1186/1471-2105-11-S7-S10

Published: 15 October 2010

Abstract

Background

Recent studies have found that overexpression of the High-mobility group box-1 (HMGB1) protein, in conjunction with its receptors for advanced glycation end products (RAGEs) and toll-like receptors (TLRs), is associated with proliferation of various cancer types, including that of the breast and pancreatic.

Results

We have developed a rule-based model of crosstalk between the HMGB1 signaling pathway and other key cancer signaling pathways. The model has been simulated using both ordinary differential equations (ODEs) and discrete stochastic simulation. We have applied an automated verification technique, Statistical Model Checking, to validate interesting temporal properties of our model.

Conclusions

Our simulations show that, if HMGB1 is overexpressed, then the oncoproteins CyclinD/E, which regulate cell proliferation, are overexpressed, while tumor suppressor proteins that regulate cell apoptosis (programmed cell death), such as p53, are repressed. Discrete, stochastic simulations show that p53 and MDM2 oscillations continue even after 10 hours, as observed by experiments. This property is not exhibited by the deterministic ODE simulation, for the chosen parameters. Moreover, the models also predict that mutations of RAS, ARF and P21 in the context of HMGB1 signaling can influence the cancer cell's fate - apoptosis or survival - through the crosstalk of different pathways.