Mining a human transcriptome database for chemical modulators of NRF2

PLoS ONE, vol. 15, pp. e0239367

Abstract

Nuclear factor erythroid-2 related factor 2 (NRF2) encoded by the NFE2L2 gene is a transcription factor critical for protecting cells from chemically-induced oxidative stress. We developed computational procedures to identify chemical modulators of NRF2 in a large database of human microarray data. A gene expression biomarker was built from statistically-filtered gene lists derived from microarray experiments in primary human hepatocytes and cancer cell lines exposed to NRF2-activating chemicals (oltipraz, sulforaphane, CDDO-Im) or in which the NRF2 suppressor Keap1 was knocked down by siRNA. Directionally consistent biomarker genes were further filtered for those dependent on NRF2 using a microarray dataset from cells after NFE2L2 siRNA knockdown. The resulting 143-gene biomarker was evaluated as a predictive tool using the correlation-based Running Fisher algorithm. Using 59 gene expression comparisons from chemically-treated cells with known NRF2 activating potential, the biomarker gave a balanced accuracy of 93%. The biomarker was comprised of many well-known NRF2 target genes (AKR1B10, AKR1C1, NQO1, TXNRD1, SRXN1, GCLC, GCLM), 69% of which were found to be bound directly by NRF2 using ChIP-Seq. NRF2 activity was assessed across ~9840 microarray comparisons from ~1460 studies examining the effects of ~2260 chemicals in human cell lines. A total of 260 and 43 chemicals were found to activate or suppress NRF2, respectively, most of which have not been previously reported to modulate NRF2 activity. Using a NRF2-responsive reporter gene in HepG2 cells, we confirmed the activity of a set of chemicals predicted using the biomarker. The biomarker will be useful for future gene expression screening studies of environmentally-relevant chemicals.

Authors 8

1. John P. Rooney

   Environmental Protection Agency

   Affiliation as printed

   Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC, United States of America

   ORISE, US-EPA, Research Triangle Park, NC, United States of America

2. Brian N. Chorley

   Environmental Protection Agency

   Affiliation as printed

   Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC, United States of America

3. Steven W. Hiemstra Aachen Division of Toxicology, Leiden Academic Center for Drug Research

   Leiden University

   Affiliation as printed

   Division of Toxicology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands

4. Steven Wink Aachen Division of Toxicology, Leiden Academic Center for Drug Research

   Leiden University

   Affiliation as printed

   Division of Toxicology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands

5. Xuting Wang

   National Institutes of Health · National Institute of Environmental Health Sciences

   Affiliation as printed

   Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States of America

6. Douglas A. Bell

   National Institutes of Health · National Institute of Environmental Health Sciences

   Affiliation as printed

   Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States of America

7. Bob van de Water Aachen Division of Toxicology, Leiden Academic Center for Drug Research

   Leiden University

   Affiliation as printed

   Division of Toxicology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands

8. J. Christopher Corton corresponding

   Environmental Protection Agency

   Affiliation as printed

   Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC, United States of America