Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane-treated human breast epithelial cells reveals common expression profiles

Breast Cancer Res Treat. 2012 Feb;132(1):175-87. doi: 10.1007/s10549-011-1536-9. Epub 2011 May 20.


Sulforaphane (SFN), an isothiocyanate found in cruciferous vegetables, is a potent inhibitor of experimental mammary carcinogenesis and may be an effective, safe chemopreventive agent for use in humans. SFN acts in part on the Keap1/Nrf2 pathway to regulate a battery of cytoprotective genes. In this study, transcriptomic and proteomic changes in the estrogen receptor negative, non-tumorigenic human breast epithelial MCF10A cell line were analyzed following SFN treatment or KEAP1 knockdown with siRNA using microarray and stable isotopic labeling with amino acids in culture (SILAC), respectively. Changes in selected transcripts and proteins were confirmed by PCR and Western blot in MCF10A and MCF12A cells. There was strong correlation between the transcriptomic and proteomic responses in both the SFN treatment (R = 0.679, P < 0.05) and KEAP1 knockdown (R = 0.853, P < 0.05) experiments. Common pathways for SFN treatment and KEAP1 knockdown were xenobiotic metabolism and antioxidants, glutathione metabolism, carbohydrate metabolism, and NADH/NADPH regeneration. Moreover, these pathways were most prominent in both the transcriptomic and the proteomic analyses. The aldo-keto reductase family members, AKR1B10, AKR1C1, AKR1C2 and AKR1C3, as well as NQO1 and ALDH3A1, were highly upregulated at both the transcriptomic and the proteomic levels. Collectively, these studies served to identify potential biomarkers that can be used in clinical trials to investigate the initial pharmacodynamic action of SFN in the breast.

Publication types

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

MeSH terms

  • Alcohol Oxidoreductases / genetics
  • Alcohol Oxidoreductases / metabolism
  • Aldehyde Dehydrogenase / genetics
  • Aldehyde Dehydrogenase / metabolism
  • Anticarcinogenic Agents / pharmacology*
  • Breast / cytology*
  • Cell Line
  • Epithelial Cells / drug effects
  • Epithelial Cells / metabolism*
  • Female
  • Gene Expression Profiling
  • Gene Knockdown Techniques
  • Humans
  • Intracellular Signaling Peptides and Proteins / genetics*
  • Intracellular Signaling Peptides and Proteins / metabolism
  • Isothiocyanates
  • Kelch-Like ECH-Associated Protein 1
  • NAD(P)H Dehydrogenase (Quinone) / genetics
  • NAD(P)H Dehydrogenase (Quinone) / metabolism
  • Oligonucleotide Array Sequence Analysis
  • Proteome / metabolism*
  • RNA Interference
  • Sulfoxides
  • Thiocyanates / pharmacology*
  • Transcriptome*
  • Up-Regulation


  • Anticarcinogenic Agents
  • Intracellular Signaling Peptides and Proteins
  • Isothiocyanates
  • KEAP1 protein, human
  • Kelch-Like ECH-Associated Protein 1
  • Proteome
  • Sulfoxides
  • Thiocyanates
  • Alcohol Oxidoreductases
  • ALDH3A1 protein, human
  • Aldehyde Dehydrogenase
  • NAD(P)H Dehydrogenase (Quinone)
  • NQO1 protein, human
  • sulforaphane