Identification of interleukin-1 and interleukin-6-responsive genes in human monocyte-derived macrophages using microarrays

Biochim Biophys Acta. Jun-Jul 2008;1779(6-7):383-9. doi: 10.1016/j.bbagrm.2008.04.006. Epub 2008 May 2.

Abstract

The transcriptome profile of human monocyte-derived macrophages stimulated in vitro by low doses of IL-1 or IL-6 was analyzed by microarrays (Affymetrix, HG-U133A) in 5 independent experiments. Out of 4886 probe sets consistently detected in all 5 array replicates we found approximately 300 genes (FDR<5%) modulated by IL-1 and/or IL-6, among which 34 may be regarded as novel cytokine-responsive macrophage genes of various function. Detailed analysis indicates that cytokine-responsive genes include 125 transcripts significantly up-regulated by IL-1 and only 39 transcripts up-regulated by IL-6, whereas the number of down-regulated transcripts is lower and almost equal for both cytokines. These data indicate that, in comparison to liver cells, IL-1 is more potent than IL-6 in modulating gene expression of human macrophages. Hierarchical clustering analysis of these transcripts yielded 7 separate gene clusters. The most abundant group contains genes strongly activated by IL-1 alone and coding for chemokines, cytokines and their receptors, the components of intracellular signaling as well as transcription factors from NF-kB family. In order to validate the results obtained by microarray analysis the expression of 5 genes from various clusters was determined by quantitative RT-PCR. Moreover, the putative promoter regions of all cytokine-responsive genes were subjected to the in silico identification of transcription factor binding sites (TFBS). We found that TFBS corresponding to RelA/NF-kB is the most strongly over-represented group and we demonstrated involvement of NF-kB in the expression of selected genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites / genetics
  • Cells, Cultured
  • Gene Expression Profiling
  • Gene Expression Regulation / drug effects
  • Humans
  • Interleukin-1 / pharmacology*
  • Interleukin-6 / pharmacology*
  • Macrophages / cytology
  • Macrophages / drug effects*
  • Macrophages / metabolism*
  • Monocytes / cytology
  • Monocytes / metabolism
  • Multigene Family
  • Oligonucleotide Array Sequence Analysis
  • Promoter Regions, Genetic
  • Reverse Transcriptase Polymerase Chain Reaction
  • Transcription Factor RelA / metabolism
  • Transcription Factors / metabolism

Substances

  • IL6 protein, human
  • Interleukin-1
  • Interleukin-6
  • RELA protein, human
  • Transcription Factor RelA
  • Transcription Factors