1. A gene expression biomarker for predictive toxicology to identify chemical modulators of NF-κB.
- Author
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Korunes KL, Liu J, Huang R, Xia M, Houck KA, and Corton JC
- Subjects
- Cell Line, Databases, Chemical, Gene Expression Regulation drug effects, High-Throughput Screening Assays, Humans, I-kappa B Proteins genetics, I-kappa B Proteins metabolism, NF-kappa B agonists, NF-kappa B antagonists & inhibitors, NF-kappa B p50 Subunit deficiency, NF-kappa B p50 Subunit genetics, Small Molecule Libraries chemistry, Small Molecule Libraries pharmacology, Tumor Necrosis Factor-alpha pharmacology, Biomarkers metabolism, Gene Expression Regulation genetics, NF-kappa B metabolism
- Abstract
The nuclear factor-kappa B (NF-κB) is a transcription factor with important roles in inflammation, immune response, and oncogenesis. Dysregulation of NF-κB signaling is associated with inflammation and certain cancers. We developed a gene expression biomarker predictive of NF-κB modulation and used the biomarker to screen a large compendia of gene expression data. The biomarker consists of 108 genes responsive to tumor necrosis factor α in the absence but not the presence of IκB, an inhibitor of NF-κB. Using a set of 450 profiles from cells treated with immunomodulatory factors with known NF-κB activity, the balanced accuracy for prediction of NF-κB activation was > 90%. The biomarker was used to screen a microarray compendium consisting of 12,061 microarray comparisons from human cells exposed to 2,672 individual chemicals to identify chemicals that could cause toxic effects through NF-κB. There were 215 and 49 chemicals that were identified as putative or known NF-κB activators or suppressors, respectively. NF-κB activators were also identified using two high-throughput screening assays; 165 out of the ~3,800 chemicals (ToxCast assay) and 55 out of ~7,500 unique compounds (Tox21 assay) were identified as potential activators. A set of 32 chemicals not previously associated with NF-κB activation and which partially overlapped between the different screens were selected for validation in wild-type and NFKB1-null HeLa cells. Using RT-qPCR and targeted RNA-Seq, 31 of the 32 chemicals were confirmed to be NF-κB activators. These results comprehensively identify a set of chemicals that could cause toxic effects through NF-κB., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2022
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