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Verhelst S, De Clerck L, Willems S, Van Puyvelde B, Daled S, Deforce D, Dhaenens M. Comprehensive histone epigenetics: A mass spectrometry based screening assay to measure epigenetic toxicity. MethodsX 2020; 7:101055. [PMID: 32995308 PMCID: PMC7508989 DOI: 10.1016/j.mex.2020.101055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 01/23/2023] Open
Abstract
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.
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Key Words
- 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
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Affiliation(s)
- Sigrid Verhelst
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Laura De Clerck
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Sander Willems
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Simon Daled
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Dieter Deforce
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
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Bennike TB, Kastaniegaard K, Padurariu S, Gaihede M, Birkelund S, Andersen V, Stensballe A. Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples. EuPA Open Proteom 2016; 10:9-18. [PMID: 29900094 PMCID: PMC5988570 DOI: 10.1016/j.euprot.2015.10.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/19/2015] [Accepted: 10/25/2015] [Indexed: 01/14/2023]
Abstract
Large biobanks exist worldwide containing formalin-fixed, paraffin-embedded samples and samples stored in RNAlater. However, the impact of tissue preservation on the result of a quantative proteome analysis remains poorly described. Human colon mucosal biopsies were extracted from the sigmoideum and either immediately frozen, stabilized in RNAlater, or stabilized by formalin-fixation. In one set of biopsies, formalin stabilization was delayed for 30 min. The protein content of the samples was characterized by high throughput quantitative proteomics. We were able to identify a similar high number of proteins in the samples regardless of preservation method, with only minor differences in protein quantitation.
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Key Words
- CAN, acetonitrile
- DF, directly-frozen
- FA, formic acid
- FASP, filter-aided sample preparation
- FDR, false discovery rate
- FFPE, formalin-fixed
- Formalin-fixed
- HLA-A class I, histocompatibility antigen A-23 alpha chain
- HLA-DRB1 class II, histocompatibility antigen DRB1-4 beta chain
- Human colon mucosa
- LFQ, label-free quantification
- Mass spectrometry
- PCA, principle component analysis
- PSM, peptide spectral match
- PTM, post-translational modification
- Paraffin-embedded
- Preservation
- Proteomics
- RNAlater
- SDC, sodium deoxycholate
- SDS, sodium dodecyl sulfate
- TEAB, triethylammonium bicarbonate
- iFFPE, immediately formalin-fixed
- s, standard deviation
- sFFPE, stored for 30 min prior to formalin-fixed
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Affiliation(s)
- Tue Bjerg Bennike
- Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | | | - Simona Padurariu
- Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark
| | - Michael Gaihede
- Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Svend Birkelund
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Vibeke Andersen
- Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark
- Institute of Regional Health Research-Center Soenderjylland, University of Southern Denmark, Odense, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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