Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells.
The development of in vitro molecular biomarkers to accurately predict toxicological effects has become a priority to advance testing strategies for human health risk assessment. The application of in vitro transcriptomic biomarkers promises increased throughput as well as a reduction in animal use. However, the existing protocols for predictive transcriptional signatures do not establish appropriate guidelines for dose selection or account for the fact that toxic agents may have pleiotropic effects. Therefore, comparison of transcriptome profiles across agents and studies has been difficult. Here we present a dataset of transcriptional profiles for TK6 cells exposed to a battery of well-characterized genotoxic and nongenotoxic chemicals. The experimental conditions applied a new dose optimization protocol that was based on evaluating expression changes in several well-characterized stress-response genes using quantitative real-time PCR in preliminary dose-finding studies. The subsequent microarray-based transcriptomic analyses at the optimized dose revealed responses to the test chemicals that were typically complex, often exhibiting substantial overlap in the transcriptional responses between a variety of the agents making analysis challenging. Using the nearest shrunken centroids method we identified a panel of 65 genes that could accurately classify toxicants as genotoxic or nongenotoxic. To validate the 65-gene panel as a genomic biomarker of genotoxicity, the gene expression profiles of an additional three well-characterized model agents were analyzed and a case study demonstrating the practical application of this genomic biomarker-based approach in risk assessment was performed to demonstrate its utility in genotoxicity risk assessment.
Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC.|Department of Oncology, Georgetown University Medical Center, Washington, DC.
Heng-Hong
HH
Li
Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC.|Department of Oncology, Georgetown University Medical Center, Washington, DC.|Biological Engineering Department, Utah State University, Logan, Utah.
Daniel R
DR
Hyduke
Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC.|Department of Oncology, Georgetown University Medical Center, Washington, DC.
Renxiang
R
Chen
Pfizer Global Research and Development, Drug Safety Research and Development, Groton, Connecticut, 06340.
Pamela
P
Heard
Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
Carole L
CL
Yauk
Pfizer Global Research and Development, Drug Safety Research and Development, Groton, Connecticut, 06340.
Jiri
J
Aubrecht
Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC.|Department of Oncology, Georgetown University Medical Center, Washington, DC.|Center of Excellence In Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
Albert J
AJ
Fornace
D051700:Activating Transcription Factor 3 / Q000235:genetics; D002110:Caffeine / Q000633:toxicity; D018797:Cell Cycle Proteins / Q000235:genetics; D002460:Cell Line / Q000187:drug effects; D016000:Cluster Analysis; D050759:Cyclin-Dependent Kinase Inhibitor p21 / Q000235:genetics; D030541:Databases, Genetic; D004305:Dose-Response Relationship, Drug; D020869:Gene Expression Profiling; D005819:Genetic Markers; D006801:Humans; D008698:Mesylates / Q000633:toxicity; D009152:Mutagenicity Tests / Q000379:methods*; D009574:Nitro Compounds / Q000633:toxicity; D009687:Nuclear Proteins / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D011422:Propionates / Q000633:toxicity; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D018570:Risk Assessment / Q000379:methods*; D043922:Toxicogenetics / Q000379:methods*; D000097642:GADD45 Proteins
D051700:Activating Transcription Factor 3; D002110:Caffeine; D018797:Cell Cycle Proteins; D050759:Cyclin-Dependent Kinase Inhibitor p21; D005819:Genetic Markers; D008698:Mesylates; D009574:Nitro Compounds; D009687:Nuclear Proteins; D011422:Propionates; C490449:ATF3 protein, human; C493956:CDKN1A protein, human; C439070:GADD45A protein, human; D000097642:GADD45 Proteins; C015392:3-nitropropionic acid; C002531:isopropylmethanesulfonate
DNA-damage inducible; bioinformatics; stress genes; super-paramagnetic clustering