Systems biology-defined NF-κB regulons, interacting signal pathways and networks are implicated in the malignant phenotype of head and neck cancer cell lines differing in p53 status

Bin Yan^*¹ , Guang Chen^*²^,3 , Kunal Saigal¹^,4 , Xinping Yang¹ , Shane T Jensen⁵ , Carter Van Waes¹ , Christian J Stoeckert³^,6 and Zhong Chen¹

¹Head and Neck Surgery Branch, NIDCD, National Institutes of Health, Bethesda, MD 20892, USA

²Department of Bioengineering, Smith Walk; University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA

³Center for Bioinformatics, Guardian Drive; University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA

⁴NIH-Pfizer Clinical Research Training Program Award; University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA

⁵Department of Statistics, The Wharton School, Walnut Street; University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA

⁶Department of Genetics, School of Medicine, Curie Boulevard; University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA

author email corresponding author email* Contributed equally

Genome Biology 2008, 9:R53doi:10.1186/gb-2008-9-3-r53


Published:	11 March 2008

Subject areas: Cancer, Cell biology

Abstract

Background

Aberrant activation of the nuclear factor kappaB (NF-κB) pathway has been previously implicated as a crucial signal promoting tumorigenesis. However, how NF-κB acts as a key regulatory node to modulate global gene expression, and contributes to the malignant heterogeneity of head and neck cancer, is not well understood.

Results

To address this question, we used a newly developed computational strategy, COGRIM (Clustering Of Gene Regulons using Integrated Modeling), to identify NF-κB regulons (a set of genes under regulation of the same transcription factor) for 1,265 genes differentially expressed by head and neck cancer cell lines differing in p53 status. There were 748 NF-κB targets predicted and individually annotated for RELA, NFκB1 or cREL regulation, and a prevalence of RELA related genes was observed in over-expressed clusters in a tumor subset. Using Ingenuity Pathway Analysis, the NF-κB targets were reverse-engineered into annotated signature networks and pathways, revealing relationships broadly altered in cancer lines (activated proinflammatory and down-regulated Wnt/β-catenin and transforming growth factor-β pathways), or specifically defective in cancer subsets (growth factors, cytokines, integrins, receptors and intermediate kinases). Representatives of predicted NF-κB target genes were experimentally validated through modulation by tumor necrosis factor-α or small interfering RNA for RELA or NFκB1.

Conclusion

NF-κB globally regulates diverse gene programs that are organized in signal networks and pathways differing in cancer subsets with distinct p53 status. The concerted alterations in gene expression patterns reflect cross-talk among NF-κB and other pathways, which may provide a basis for molecular classifications and targeted therapeutics for heterogeneous subsets of head and neck or other cancers.