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Updated: Nov 11, 2025
Assays for Validating Histone Acetyltransferase Inhibitors
Published on: August 6, 2020
Development and validation of the TGx-HDACi transcriptomic biomarker to detect histone deacetylase inhibitors in
Eunnara Cho1,2, Andrea Rowan-Carroll1, Andrew Williams1
1Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
Abstract:
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.
Insights
Researchers developed a new transcriptomic biomarker, TGx-HDACi, to identify histone deacetylase inhibitors (HDACi). This biomarker accurately classifies compounds, improving the detection of epigenotoxicants and aiding toxicant mode of action analysis.
Area of Science:
- Toxicogenomics
- Epigenetics
- Molecular Toxicology
Background:
- Transcriptomic biomarkers offer insights into toxicant mechanisms.
- Limited methods exist for identifying epigenotoxicants, particularly histone deacetylase inhibitors (HDACi).
Purpose of the Study:
- To develop and validate a transcriptomic biomarker for identifying HDACi.
- To enhance the analysis of toxicant modes of action using gene expression profiling.
Main Methods:
- Reference compounds (10 HDACi, 10 non-HDACi) were used for concentration-response experiments in TK6 cells.
- Whole transcriptome profiling via Templated Oligo-Sequencing (TempO-Seq) was performed after 4-hour exposures.
- The nearest shrunken centroid (NSC) method was applied to derive an 81-gene signature (TGx-HDACi).
Main Results:
- The TGx-HDACi signature accurately classified all 20 reference compounds.
- Validation with an additional 11 compounds (4 HDACi, 7 non-HDACi) showed correct classification for all.
- The biomarker demonstrated promising specificity towards HDACi, correctly identifying 3 non-HDACi epigenotoxicants.
Conclusions:
- The developed TGx-HDACi biomarker effectively identifies HDACi.
- This tool expands capabilities for toxicant mode of action analysis through gene expression.
- TGx-HDACi contributes to improved identification of epigenotoxicants.
