Identification of NF-kappa B-regulated genes induced by TNFalpha utilizing expression profiling and RNA interference

Oncogene. 2003 Apr 3;22(13):2054-64. doi: 10.1038/sj.onc.1206262.


Tumor necrosis factor alpha (TNF alpha) is a proinflammatory cytokine with important roles in regulating inflammatory responses as well as cell cycle proliferation and apoptosis. Although TNFalpha stimulates apoptosis, it also activates the transcription factor NF-kappa B, and studies have shown that inhibition of NF-kappa B potentiates the cytotoxicity of TNFalpha. Since several chemotherapy agents act like TNFalpha to both promote apoptosis and activate NF-kappa B, understanding the role of NF-kappa B in suppressing apoptosis may have significant clinical applications. To understand the effects of stimulation with TNFalpha and the role of NF-kappa B in regulating this response, a 23k human cDNA microarray was used to screen TNFalpha-inducible genes in HeLa cells. Real-time PCR verified expression changes in 16 of these genes and revealed three distinct temporal patterns of expression after TNFalpha stimulation. Using RNA interference to disrupt expression of the p65 subunit of NF-kappa B, all but two of the genes were shown to depend on this transcription factor for their expression, which correlated well with the existence of NF-kappa B binding sites in most of their promoters. Inflammatory, proapoptotic, and antiapoptotic genes were all shown to be regulated by NF-kappa B, demonstrating the wide variety of targets activated by NF-kappa B signaling and the necessity of differentiating among these genes for therapeutic purposes.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Computer Systems
  • Gene Expression Profiling*
  • Gene Expression Regulation* / drug effects
  • HeLa Cells / drug effects
  • HeLa Cells / metabolism
  • Humans
  • NF-kappa B / genetics
  • NF-kappa B / physiology*
  • Neoplasm Proteins / biosynthesis
  • Neoplasm Proteins / genetics
  • Oligonucleotide Array Sequence Analysis
  • Polymerase Chain Reaction
  • Promoter Regions, Genetic / genetics
  • RNA Interference*
  • Transcription Factor RelA
  • Tumor Necrosis Factor-alpha / pharmacology


  • NF-kappa B
  • Neoplasm Proteins
  • Transcription Factor RelA
  • Tumor Necrosis Factor-alpha