A large scale mass spectrometry-based histone screening for assessing epigenetic developmental toxicity

Abstract

Toxicoepigenetics is an emerging field that studies the toxicological impact of compounds on protein expression through heritable, non-genetic mechanisms, such as histone post-translational modifications (hPTMs). Due to substantial progress in the large-scale study of hPTMs, integration into the field of toxicology is promising and offers the opportunity to gain novel insights into toxicological phenomena. Moreover, there is a growing demand for high-throughput human-based in vitro assays for toxicity testing, especially for developmental toxicity. Consequently, we developed a mass spectrometry-based proof-of-concept to assess a histone code screening assay capable of simultaneously detecting multiple hPTM-changes in human embryonic stem cells. We first validated the untargeted workflow with valproic acid (VPA), a histone deacetylase inhibitor. These results demonstrate the capability of mapping the hPTM-dynamics, with a general increase in acetylations as an internal control. To illustrate the scalability, a dose–response study was performed on a proof-of-concept library of ten compounds (1) with a known effect on the hPTMs (BIX-01294, 3-Deazaneplanocin A, Trichostatin A, and VPA), (2) classified as highly embryotoxic by the European Centre for the Validation of Alternative Methods (ECVAM) (Methotrexate, and All-trans retinoic acid), (3) classified as non-embryotoxic by ECVAM (Penicillin G), and (4) compounds of abuse with a presumed developmental toxicity (ethanol, caffeine, and nicotine).

Change of histone H3 lysine 14 acetylation stoichiometry in human monocyte derived macrophages as determined by MS-based absolute targeted quantitative proteomic approach: HIV infection and methamphetamine exposure

“…Based on the absolute abundances of the native modified K9[Poy]K14[Ac] and unmodified K9[Poy]K14[Poy] peptides, we calculated stoichiometry of the K14Ac in the donors’ samples as a percentage of total amount—a sum of K14 modified (acetylated, Ac) and unmodified (propionylated, Poy) fractions—of the investigated H3 peptide [ 17 ]. Although PTMs stoichiometry can be was determined using label free, relative MS approaches (eg [ 35 ]. ), we chose to calculate it based on the absolute amounts of modified and unmodified peptides determined in LC–MS/MS analysis in MRM mode using SIL standards.…”

An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia

“…These potential biomarkers will be validated both in vitro and in vivo . Further optimization of MS analysis time could facilitate the analysis of patient samples in a clinical setting in the future 23 . Here we describe the functionalities available in the atlas, as an illustration of data reuse potential.…”

An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia

“…These potential biomarkers will be validated both in vitro and in vivo . Further optimization of MS analysis time could facilitate the analysis of patient samples in a clinical setting in the future 25 . Here we describe the functionalities available in the atlas, as an illustration of data reuse potential.…”