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cDNA microarray gene expression profiling of hedgehog signaling pathway inhibition in human colon cancer cells

Ting Shi1, Tapati Mazumdar, Jennifer Devecchio

  • 1Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America.

Plos One
|October 20, 2010
PubMed
Abstract

Insights

Hedgehog (HH) signaling inhibition in colon cancer cells reveals key genes regulating cell cycle progression. This study identifies novel targets involved in cell cycle control and DNA repair pathways.

Area of Science:

  • Oncology
  • Molecular Biology
  • Genetics

Background:

  • Hedgehog (HH) signaling is crucial for normal development and implicated in cancer, including colon cancer.
  • Limited genomic data exists on HH signaling's role in colon cancer oncogenesis and metastasis.
  • Understanding HH signaling in colon cancer is vital for targeted therapies.

Purpose of the Study:

  • To identify downstream targets of GLI genes, the transcriptional regulators of HH signaling, in colon cancer.
  • To investigate the effects of GLI inhibition on colon cancer cell cycle progression.
  • To elucidate novel genes regulated by HH signaling in colon carcinoma.

Main Methods:

  • Utilized GANT61, a small molecule inhibitor of GLI1 and GLI2, in HT29 and GC3/c1 human colon cancer cell lines.
  • Performed cell cycle analysis and cDNA microarray gene expression profiling of over 18,000 genes.
  • Employed bioinformatics tools (GenomeStudio, Matlab, Ingenuity) and qRT-PCR for data analysis.

Main Results:

  • GANT61 treatment caused cell cycle arrest at the G1/S boundary.
  • Identified differentially expressed genes (DEGs) common and unique to both cell lines.
  • Observed up-regulation of cell cycle inhibitors p21(Cip1) and p15(Ink4b), and down-regulation of cell cycle progression genes (e.g., E2F2, CCNE2, CDK2, CCNA2, CDK1).
  • Discovered novel genes involved in stress response, DNA damage, replication, and repair pathways.

Conclusions:

  • This study identifies critical genes regulated by HH signaling in colon cancer cell proliferation.
  • HH signaling inhibition impacts genes controlling cell cycle progression, particularly at the G1/S boundary.
  • Revealed novel downstream targets of HH signaling relevant to colon cancer therapy.

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