Comprehensive histone epigenetics: A mass spectrometry based screening assay to measure epigenetic toxicity.
AUC, area under the curve
DDA, data-dependent acquisition
DIA, data-independent acquisition
DTT, dithiothreitol
Drug safety
FA, formic acid
FDR, false discovery rate
GABA, gamma-aminobutyric acid
GRX, gingisrex
HAT, histone acetyltransferase
HDACi, histone deacetylase inhibitor
HLB, hypotonic lysis buffer
HPLC, high-performance liquid chromatography
Histone post-translational modifications
K, Lysine
LC-MS/MS
M, Methionine
MS, Mass spectrometry
MS/MS, tandem mass spectrometry
N, asparagine
PBS, phosphate buffered saline
Pharmacoepigenetics
Proteomics
Q, glutamine
R, arginine
RA, relative abundance
RP, reversed phase
RT, room temperature
S, serine
SWATH, sequential window acquisition of all theoretical fragment ion spectra
T, threonine
TEAB, triethylammonium bicarbonate
Toxicoepigenetics
VPA, valproic acid
Y, tyrosine
hESC, human embryonic stem cell
hPTM, histone post-translational modification
Journal
MethodsX
ISSN: 2215-0161
Titre abrégé: MethodsX
Pays: Netherlands
ID NLM: 101639829
Informations de publication
Date de publication:
2020
2020
Historique:
received:
09
06
2020
accepted:
02
09
2020
entrez:
30
9
2020
pubmed:
1
10
2020
medline:
1
10
2020
Statut:
epublish
Résumé
Evidence of the involvement of epigenetics in pathologies such as cancer, diabetes, and neurodegeneration has increased global interest in epigenetic modifications. For nearly thirty years, it has been known that cancer cells exhibit abnormal DNA methylation patterns. In contrast, the large-scale analysis of histone post-translational modifications (hPTMs) has lagged behind because classically, histone modification analysis has relied on site specific antibody-based techniques. Mass spectrometry (MS) is a technique that holds the promise to picture the histone code comprehensively in a single experiment. Therefore, we developed an MS-based method that is capable of tracking all possible hPTMs in an untargeted approach. In this way, trends in single and combinatorial hPTMs can be reported and enable prediction of the epigenetic toxicity of compounds. Moreover, this method is based on the use of human cells to provide preliminary data, thereby omitting the need to sacrifice laboratory animals. Improving the workflow and the user-friendliness in order to become a high throughput, easily applicable, toxicological screening assay is an ongoing effort. Still, this novel toxicoepigenetic assay and the data it generates holds great potential for, among others, pharmaceutical industry, food science, clinical diagnostics and, environmental toxicity screening. •There is a growing interest in epigenetic modifications, and more specifically in histone post-translational modifications (hPTMs).•We describe an MS-based workflow that is capable of tracking all possible hPTMs in an untargeted approach that makes use of human cells.•Improving the workflow and the user-friendliness in order to become a high throughput, easily applicable, toxicological screening assay is an ongoing effort.
Identifiants
pubmed: 32995308
doi: 10.1016/j.mex.2020.101055
pii: S2215-0161(20)30275-2
pmc: PMC7508989
doi:
Types de publication
Journal Article
Langues
eng
Pagination
101055Informations de copyright
© 2020 The Authors.
Déclaration de conflit d'intérêts
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Références
Proteomics. 2016 Oct;16(20):2605-2614
pubmed: 27392809
Open Biol. 2018 Mar;8(3):
pubmed: 29593118
Proteomics. 2015 Sep;15(17):2966-71
pubmed: 26010583
Anal Chem. 2020 May 5;92(9):6278-6287
pubmed: 32227882
Chem Rev. 2015 Mar 25;115(6):2376-418
pubmed: 25688442
Trends Neurosci. 2018 Sep;41(9):587-598
pubmed: 29885742
J Proteome Res. 2017 Feb 3;16(2):655-664
pubmed: 28152592
J Proteome Res. 2019 Nov 1;18(11):3840-3849
pubmed: 31429292
Stem Cell Res. 2014 Jul;13(1):123-34
pubmed: 24874291
Nat Methods. 2014 Jul;11(7):703-4
pubmed: 24972168
Clin Epigenetics. 2019 Jan 15;11(1):7
pubmed: 30646939
Cold Spring Harb Perspect Biol. 2015 Sep 01;7(9):a025064
pubmed: 26330523
Anal Chem. 2014 Jun 3;86(11):5526-34
pubmed: 24823915
Nat Chem Biol. 2016 Aug 18;12(9):662-8
pubmed: 27538025
F1000Res. 2016 Mar 31;5:
pubmed: 27092249
Anal Chem. 2020 Mar 17;92(6):4217-4225
pubmed: 32058701
Anal Chem. 2015 Oct 6;87(19):10006-14
pubmed: 26356480
Cell Stem Cell. 2019 Jan 3;24(1):123-137.e8
pubmed: 30472157
Annu Rev Pharmacol Toxicol. 2018 Jan 6;58:161-185
pubmed: 29029592
Sci Rep. 2019 Nov 21;9(1):17240
pubmed: 31754138
J Proteomics. 2012 Jun 27;75(12):3419-33
pubmed: 22234360
Anal Chem. 2009 Aug 1;81(15):6481-8
pubmed: 19572557
Pharmacogenet Genomics. 2013 Apr;23(4):236-41
pubmed: 23407051
Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450
pubmed: 30395289
Proteomics. 2016 Jul;16(14):1970-4
pubmed: 27139031
Proteomes. 2018 Jun 21;6(3):
pubmed: 29933573
Nature. 2007 May 24;447(7143):396-8
pubmed: 17522671
Bone Rep. 2017 Aug 16;7:33-40
pubmed: 28856178
Proteomics. 2016 Dec;16(23):2937-2944
pubmed: 27718312
Nature. 2019 Oct;574(7779):575-580
pubmed: 31645732
Epigenetics Chromatin. 2013 Jul 05;6(1):20
pubmed: 23826629
Nat Rev Mol Cell Biol. 2014 Nov;15(11):703-8
pubmed: 25315270
Nat Methods. 2013 Mar;10(3):186-7
pubmed: 23443629
Nat Biotechnol. 2017 Aug;35(8):781-788
pubmed: 28604659
Mol Cell Proteomics. 2015 Sep;14(9):2420-8
pubmed: 25636311