Krull, Mathias;Choi, Claudia;Pistor, Susanne;Voss, Nico;Wingender, Edgar - Analysis of the lipopolysaccharide (LPS)-stimulated innate immune response with TRANSPATH®

ECCB 2002 Poster sorted by: Author | Number

Next | Previous poster (in order of the view you have selected)

Title: Analysis of the lipopolysaccharide (LPS)-stimulated innate immune response with TRANSPATH®	P86
Krull, Mathias; Choi, Claudia; Pistor, Susanne; Voss, Nico; Wingender, Edgar mkl@biobase.de BIOBASE GmbH, Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany

New technologies and methods such as microarray chips, proteomic analysis with 2D-PAGE, or yeast two-hybrid screens have generated an enormous amount of data about the abundance of gene transcripts and proteins in different cell types at varying states and protein-protein interactions. The vast amount of information and the complex connectivity of the underlying network make it difficult to establish the significance of data and to derive biological context. Bioinformatics has to provide a solution for this dilemma.

TRANSPATH® is an integrated database system on regulatory networks that combines encyclopedic information about signal transduction with tools for visualization and analysis [1]. The integration with TRANSFAC®, a database about transcription factors and their DNA binding sites, makes it possible to obtain complete signaling pathways from ligand to target genes and their products, which may be involved themselves in regulatory action.

The ArrayAnalyzer(TM) in TRANSPATH® is a new approach for efficiently finding regulatory key molecules as potential new drug targets for a given set of genes or proteins (e.g. microarray data). It runs a proximity search for the set's most common nodes in the network. The search method is based on a priori calculated and compressed shortest-distance data. Once the key molecules are identified, it is possible to display the results with the PathwayBuilder(TM) in a compact way by cutting off all parts of the picture that are not absolutely necessary to precisely represent the sub network that comprises those molecular components which the array data have shown to be up or down-regulated.

We applied TRANSPATH® and its tools for retrieving information about LPS signalling. LPS (also known as endotoxin) is the major structural component of the outer membrane of Gram-negative bacteria such as Salmonella, Pseudomonas, or Legionella. It is recognized by monocytes, macrophages and neutrophils [2] of the innate immune system and can also stimulate B and T lymphocytes [3]. As a first consequence of host defense, a variety of chemokines and inflammatory cytokines including TNFalpha, IL-1, IL-6 and IL-8 are expressed and secreted, resulting, among other things, in the recruitment of phagocytic neutrophils to sites of infection and in elevation of body temperature. Over-reaction to LPS can result in sepsis, septic shock, systemic inflammatory response syndrome [4], or contribute to allergy [3].

The signalling pathways and regulatory mechanisms that lead to the expression or repression of a repertoire of LPS-induced genes can be obtained from TRANSPATH® either by viewing a hand-drawn clickable pathway map with a focus on TLR4-mediated LPS signalling, or by using the PathwayBuilder(TM) to create views on the network with selectable parameters such as size, direction, and complexity.

Fessler et al. carried out a genomic and proteomic analysis of the LPS response in human neutrophils using microarray chips and 2D-PAGE gels. We made a query with the set of up or down-regulated genes (n = 177) and retrieved a list of 50 matched database entries. Matching is possible via EMBL/GenBank or SwissProt accession numbers or via Affymetrix probe set identifiers. The relatively low number of matches is mainly due to a high number of metabolic and structural genes in the set, which were not yet in the focus of TRANSPATH®.
Applying the ArrayAnalyzer(TM) on the search result list retrieved primarily a set of prominent transcription factors such as c-Jun, c-Fos, NF-kappaB (p50, RelA), CREB, c-Myc, ATF-2, p300, C/EBPalpha and beta as the most significant molecules. They are known as downstream effectors of LPS-triggered MAPK or IKK/IkappaBalpha pathways [4]. Here, significance is a value that describes the number of entries from the molecule/gene set that can be reached from this entry with respect to the selected parameter settings.
The dominance of transcriptional regulators in the result list of the most significant molecules (with few exceptions such as the kinases JNK1 and ASK1) may be explained with the importance of these factors in the regulation of genes involved in the early secretory response to infection: C/EBPbeta regulates at least four genes (IL-1beta, IL-6, TNFalpha, and complement factor C3) that are essential for the innate immune system.
For details of the gene regulatory events and the involved components at the end of this pathway, see the poster of Shelest et al. ("Composing a promoter model for antibacterial response of epithelial cells").

Summary and perspectives:
We analysed gene expression data from human neutrophils that were stimulated with LPS [2] using TRANSPATH® and the ArrayAnalyzer(TM). A set of transcription factors was identified as key regulators for the up and down-regulated genes.
Increasing the database content by manual curation and with additional in silico data (e.g. from domain-matching promoter-analysis) to augment the number of matches and the network connectivity and establishing TRANSPATH® as a tool for drug target discovery are the objectives for future work.

Acknowledgement:
This work is partially funded by the German Ministry for Education and Research (BMBF; grant no. 031U210B).

[1] Schacherer F., Choi C., Götze U., Krull M., Pistor S., Wingender E. (2001), "The TRANSPATH signal transduction database: a knowledge base on signal transduction networks", Bioinformatics 17, 1053-1057.
[2] Fessler M. B., Malcolm K. C., Duncan M. W., Worthen G. S. (2002) "A genomic and proteomic analysis of activation of the human neutrophil by lipopolysaccharide and its mediation by p38 mitogen-activated protein kinase", J. Biol. Chem., in press.
[3] Ulmer A. J., Flad H.-D., Rietschel Th., Mattern T. (2000) "Induction of proliferation and cytokine production in human T lymphocytes by lipopolysaccharide (LPS)", Toxicology 152, 37-45.
[4] Guha M., Mackman N. (2001) "LPS induction of gene expression in human monocytes", Cell. Signal. 13, 85-94.