Open AccessDevelopment and validation of the TGx-HDACi transcriptomic biomarker to detect histone deacetylase inhibitors in human TK6 cells
Author(s) -
Eunnara Cho,
Andrea RowanCarroll,
Andrew Williams,
J. Christopher Corton,
HengHong Li,
Albert J. Fornace,
Cheryl A. Hobbs,
Carole L. Yauk
Publication year - 2021
Publication title -
archives of toxicology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.264
H-Index - 111
eISSN - 1432-0738
pISSN - 0340-5761
DOI - 10.1007/s00204-021-03014-2
Subject(s) - transcriptome , biology , histone deacetylase , histone deacetylase inhibitor , toxicant , gene expression profiling , biomarker , computational biology , histone , gene , gene expression , genetics , chemistry , toxicity , organic chemistry
Transcriptomic biomarkers can be used to inform molecular initiating and key events involved in a toxicant's mode of action. To address the limited approaches available for identifying epigenotoxicants, we developed and assessed a transcriptomic biomarker of histone deacetylase inhibition (HDACi). First, we assembled a set of ten prototypical HDACi and ten non-HDACi reference compounds. Concentration-response experiments were performed for each chemical to collect TK6 human lymphoblastoid cell samples after 4 h of exposure and to assess cell viability following a 20-h recovery period in fresh media. One concentration was selected for each chemical for whole transcriptome profiling and transcriptomic signature derivation, based on cell viability at the 24-h time point and on maximal induction of HDACi-response genes (RGL1, NEU1, GPR183) or cellular stress-response genes (ATF3, CDKN1A, GADD45A) analyzed by TaqMan qPCR assays after 4 h of exposure. Whole transcriptomes were profiled after 4 h exposures by Templated Oligo-Sequencing (TempO-Seq). By applying the nearest shrunken centroid (NSC) method to the whole transcriptome profiles of the reference compounds, we derived an 81-gene toxicogenomic (TGx) signature, referred to as TGx-HDACi, that classified all 20 reference compounds correctly using NSC classification and the Running Fisher test. An additional 4 HDACi and 7 non-HDACi were profiled and analyzed using TGx-HDACi to further assess classification performance; the biomarker accurately classified all 11 compounds, including 3 non-HDACi epigenotoxicants, suggesting a promising specificity toward HDACi. The availability of TGx-HDACi increases the diversity of tools that can facilitate mode of action analysis of toxicants using gene expression profiling.