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Yeast As a Chassis for Developing Functional Assays to Study Human P53
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Identification of p53 Activators in a Human Microarray Compendium.

J Christopher Corton1, Kristine L Witt2, Carole L Yauk3

  • 1Integrated Systems Toxicology Division, NHEERL , United States Environmental Protection Agency , Research Triangle Park, Durham , North Carolina 27711 , United States.

Chemical Research in Toxicology
|August 10, 2019
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Summary
This summary is machine-generated.

The TGx-DDI biomarker accurately predicts DNA damage and identifies chemicals activating the p53 pathway. This study confirms its p53-dependent mechanism, aiding toxicological assessments.

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Area of Science:

  • Toxicogenomics
  • Molecular Toxicology
  • Biomarker Discovery

Background:

  • High-throughput transcriptomics requires reliable biomarkers for molecular and toxicological effect interpretation.
  • The 63-gene TGx-DDI biomarker, including 20 p53-regulated genes, predicts DNA damage in chemically treated cells.
  • The molecular basis of TGx-DDI predictions, specifically its p53-dependency, required comprehensive evaluation.

Purpose of the Study:

  • To comprehensively evaluate whether the TGx-DDI biomarker's predictions of DNA damage response (DDI) are p53-dependent.
  • To validate the TGx-DDI biomarker's utility in identifying chemicals that activate the p53 signaling pathway.
  • To screen a large chemical library for p53-activating compounds using the TGx-DDI biomarker.

Main Methods:

  • Comparison of the TGx-DDI biomarker with microarray data using the nonparametric Running Fisher test.
  • Assessment of gene expression dependency on p53 status via TP53 overexpression and knockdown experiments.
  • Screening of approximately 1950 chemicals across 9800 human cell line comparisons to identify p53 activators.

Main Results:

  • 75% of the TGx-DDI biomarker genes showed dependency on p53 activation status.
  • The biomarker identified DDI chemicals that strongly induced p53 in wild-type cells, with diminished responses in p53-knockdown cells.
  • Approximately 100 chemicals were identified as p53 activators, including known DNA-damaging agents.

Conclusions:

  • The TGx-DDI biomarker's predictions are largely dependent on p53 activation.
  • The biomarker effectively identifies chemicals that cause DNA damage and activate the p53 pathway.
  • These findings support the TGx-DDI biomarker's utility in toxicological screening and mechanistic studies.