Enrichment of histones from patient samples for mass spectrometry-based analysis of post-translational modifications

R. Noberini; C. Restellini; E.O. Savoia; T. Bonaldi

doi:10.1016/j.ymeth.2019.10.001

Enrichment of histones from patient samples for mass spectrometry-based analysis of post-translational modifications

R. Noberini, C. Restellini, E.O. Savoia, T. Bonaldi

Istituto Europeo di Oncologia

Research output: Contribution to journal › Article › peer-review

Abstract

Aberrations in histone post-translational modifications (PTMs) have been implicated with the development of numerous pathologies, including cancer. Therefore, profiling histone PTMs in patient samples could provide information useful for the identification of epigenetic biomarkers, as well as for the discovery of potential novel targets. While antibody-based methods have been traditionally employed to analyze histone PTM in clinical samples, mass spectrometry (MS) can provide a more comprehensive, unbiased and quantitative view on histones and their PTMs. To combine the power of MS-based methods and the potential offered by histone PTM profiling of clinical samples, we have recently developed a series of methods for the extraction and enrichment of histones from different types of patient samples, including formalin-fixed paraffin-embedded tissues, fresh- and optimal cutting temperature-frozen tissues, and primary cells. Here, we provide a detailed description of these protocols, together with indications on the expected results and the most suitable workflow to be used downstream of each procedure. © 2019 The Authors

Original language	English
Pages (from-to)	19-28
Number of pages	10
Journal	Methods
Volume	184
DOIs	https://doi.org/10.1016/j.ymeth.2019.10.001
Publication status	Published - 2020

Keywords

Epigenetics
Formalin-fixed paraffin-embedded tissues
Frozen tissues
Histone post-translational modifications
Mass spectrometry
animal tissue
Article
controlled study
histone modification
human
human cell
human tissue
immunohistochemistry
laser microdissection
male
mass spectrometry
nonhuman
polyacrylamide gel electrophoresis
practice guideline
primary cell
priority journal
protein processing
tissue embedding
tissue section
workflow

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10.1016/j.ymeth.2019.10.001

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@article{9272581d39c74e8c9144140b6c1bb1fa,

title = "Enrichment of histones from patient samples for mass spectrometry-based analysis of post-translational modifications",

abstract = "Aberrations in histone post-translational modifications (PTMs) have been implicated with the development of numerous pathologies, including cancer. Therefore, profiling histone PTMs in patient samples could provide information useful for the identification of epigenetic biomarkers, as well as for the discovery of potential novel targets. While antibody-based methods have been traditionally employed to analyze histone PTM in clinical samples, mass spectrometry (MS) can provide a more comprehensive, unbiased and quantitative view on histones and their PTMs. To combine the power of MS-based methods and the potential offered by histone PTM profiling of clinical samples, we have recently developed a series of methods for the extraction and enrichment of histones from different types of patient samples, including formalin-fixed paraffin-embedded tissues, fresh- and optimal cutting temperature-frozen tissues, and primary cells. Here, we provide a detailed description of these protocols, together with indications on the expected results and the most suitable workflow to be used downstream of each procedure. {\textcopyright} 2019 The Authors",

keywords = "Epigenetics, Formalin-fixed paraffin-embedded tissues, Frozen tissues, Histone post-translational modifications, Mass spectrometry, animal tissue, Article, controlled study, histone modification, human, human cell, human tissue, immunohistochemistry, laser microdissection, male, mass spectrometry, nonhuman, polyacrylamide gel electrophoresis, practice guideline, primary cell, priority journal, protein processing, tissue embedding, tissue section, workflow",

author = "R. Noberini and C. Restellini and E.O. Savoia and T. Bonaldi",

note = "Cited By :4 Export Date: 4 March 2021 CODEN: MTHDE Correspondence Address: Noberini, R.; Department of Experimental Oncology, Italy; email: roberta.noberini@ieo.it Funding details: GR-2016-02361522 Funding details: Ecumenical Project for International Cooperation, EPIC, 823839 Funding details: Horizon 2020 Framework Programme, H2020 Funding details: European Commission***Delivered and deleted from Elsevier end because this record is to be no longer updated or in business with Elsevier on Date 10-03-2020***, EC Funding details: Associazione Italiana per la Ricerca sul Cancro, AIRC, IG-2018-21834 Funding text 1: Funding: This research was supported by the Italian Association for Cancer Research , grant number IG-2018-21834 (to T.B.), by EPIC -XS, project number 823839 , funded by the Horizon 2020 programme of the European Union (to T.B.), and by the Italian Ministry of Health, grant number GR-2016-02361522 (to R.N.). Appendix A Funding text 2: Funding: This research was supported by the Italian Association for Cancer Research, grant number IG-2018-21834 (to T.B.), by EPIC-XS, project number 823839, funded by the Horizon 2020 programme of the European Union (to T.B.), and by the Italian Ministry of Health, grant number GR-2016-02361522 (to R.N.). References: Zhao, Y., Garcia, B.A., Comprehensive Catalog of Currently Documented Histone Modifications (2015) Cold Spring Harb. Perspect. Biol., 7 (9); Audia, J.E., Campbell, R.M., Histone Modifications and Cancer (2016) Cold Spring Harb. Perspect. Biol., 8 (4); Portela, A., Esteller, M., Epigenetic modifications and human disease (2010) Nat. Biotechnol., 28 (10), pp. 1057-1068; Elsheikh, S.E., Green, A.R., Rakha, E.A., Powe, D.G., Ahmed, R.A., Collins, H.M., Soria, D., Ellis, I.O., Global histone modifications in breast cancer correlate with tumor phenotypes, prognostic factors, and patient outcome (2009) Cancer Res., 69 (9), pp. 3802-3809; Seligson, D.B., Horvath, S., McBrian, M.A., Mah, V., Yu, H., Tze, S., Wang, Q., Kurdistani, S.K., Global levels of histone modifications predict prognosis in different cancers (2009) Am. J. Pathol., 174 (5), pp. 1619-1628; Seligson, D.B., Horvath, S., Shi, T., Yu, H., Tze, S., Grunstein, M., Kurdistani, S.K., Global histone modification patterns predict risk of prostate cancer recurrence (2005) Nature, 435 (7046), pp. 1262-1266; Shechter, D., Dormann, H.L., Allis, C.D., Hake, S.B., Extraction, purification and analysis of histones (2007) Nat. Protoc., 2 (6), pp. 1445-1457; Cuomo, A., Soldi, M., Bonaldi, T., SILAC-based quantitative strategies for accurate histone posttranslational modification profiling across multiple biological samples (2017) Methods Mol. Biol., 1528, pp. 97-119; Sidoli, S., Bhanu, N.V., Karch, K.R., Wang, X., Garcia, B.A., Complete workflow for analysis of histone post-translational modifications using bottom-up mass spectrometry: from histone extraction to data analysis (2016) J. Vis. Exp., 111; Bauden, M., Kristl, T., Andersson, R., Marko-Varga, G., Ansari, D., Characterization of histone-related chemical modifications in formalin-fixed paraffin-embedded and fresh-frozen human pancreatic cancer xenografts using LC-MS/MS (2017) Lab. Invest., 97 (3), pp. 279-288; Farrelly, L.A., Dill, B.D., Molina, H., Birtwistle, M.R., Maze, I., Current proteomic methods to investigate the dynamics of histone turnover in the central nervous system (2016) Methods Enzymol., 574, pp. 331-354; Zhang, Q., Xue, P., Li, H.L., Bao, Y.H., Wu, L.H., Chang, S.Y., Niu, B., Zhang, T., Histone modification mapping in human brain reveals aberrant expression of histone H3 lysine 79 dimethylation in neural tube defects (2013) Neurobiol. Dis., 54, pp. 404-413; Noberini, R., Longuespee, R., Richichi, C., Pruneri, G., Kriegsmann, M., Pelicci, G., Bonaldi, T., PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples (2017) Clin. Epigenetics, 9, p. 69; Noberini, R., Osti, D., Miccolo, C., Richichi, C., Lupia, M., Corleone, G., Hong, S.P., Bonaldi, T., Extensive and systematic rewiring of histone post-translational modifications in cancer model systems (2018) Nucleic Acids Res.; Noberini, R., Uggetti, A., Pruneri, G., Minucci, S., Bonaldi, T., Pathology tissue-quantitative mass spectrometry analysis to profile histone post-translational modification patterns in patient samples (2016) Mol. Cell. Proteomics, 15 (3), pp. 866-877; Restellini, C., Cuomo, A., Lupia, M., Giordano, M., Bonaldi, T., Noberini, R., Alternative digestion approaches improve histone modification mapping by mass spectrometry in clinical samples (2019) Proteomics Clin. Appl., 13 (1); Noberini, R., Restellini, C., Savoia, E.O., Raimondi, F., Ghiani, L., Jodice, M.G., Bertalot, G., Bonaldi, T., Profiling of epigenetic features in clinical samples reveals novel widespread changes in cancer (2019) Cancers (Basel), 11 (5); Fowler, C.B., O'Leary, T.J., Mason, J.T., Protein mass spectrometry applications on FFPE tissue sections (2011) Methods Mol. Biol., 724, pp. 281-295; Rachdaoui, N., Li, L., Willard, B., Kasumov, T., Previs, S., Sarkar, D., Turnover of histones and histone variants in postnatal rat brain: effects of alcohol exposure (2017) Clin. Epigenetics, 9, p. 117; Tvardovskiy, A., Schwammle, V., Kempf, S.J., Rogowska-Wrzesinska, A., Jensen, O.N., Accumulation of histone variant H3.3 with age is associated with profound changes in the histone methylation landscape (2017) Nucleic Acids Res., 45 (16), pp. 9272-9289; Gruppuso, P.A., Boylan, J.M., Zabala, V., Neretti, N., Abshiru, N.A., Sikora, J.W., Doud, E.H., Sanders, J.A., Stability of histone post-translational modifications in samples derived from liver tissue and primary hepatic cells (2018) PLoS ONE, 13 (9); Nestor, C.E., Ottaviano, R., Reinhardt, D., Cruickshanks, H.A., Mjoseng, H.K., McPherson, R.C., Lentini, A., Meehan, R.R., Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems (2015) Genome Biol., 16, p. 11; Govaert, E., Van Steendam, K., Scheerlinck, E., Vossaert, L., Meert, P., Stella, M., Willems, S., Deforce, D., Extracting histones for the specific purpose of label-free MS (2016) Proteomics, 16 (23), pp. 2937-2944; Minshull, T.C., Cole, J., Dockrell, D.H., Read, R.C., Dickman, M.J., Analysis of histone post translational modifications in primary monocyte derived macrophages using reverse phasexreverse phase chromatography in conjunction with porous graphitic carbon stationary phase (2016) J. Chromatogr. A, 1453, pp. 43-53; Luense, L.J., Wang, X., Schon, S.B., Weller, A.H., Lin Shiao, E., Bryant, J.M., Bartolomei, M.S., Berger, S.L., Comprehensive analysis of histone post-translational modifications in mouse and human male germ cells (2016) Epigenetics Chromatin, 9, p. 24; Olszowy, P., Donnelly, M.R., Lee, C., Ciborowski, P., Profiling post-translational modifications of histones in human monocyte-derived macrophages (2015) Proteome Sci., 13, p. 24; von Holt, C., Brandt, W.F., Greyling, H.J., Lindsey, G.G., Retief, J.D., Rodrigues, J.D., Schwager, S., Sewell, B.T., Isolation and characterization of histones (1989) Methods Enzymol., 170, pp. 431-523; Simon, R.H., Felsenfeld, G., A new procedure for purifying histone pairs H2A + H2B and H3 + H4 from chromatin using hydroxylapatite (1979) Nucleic Acids Res., 6 (2), pp. 689-696; Rappsilber, J., Mann, M., Ishihama, Y., Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips (2007) Nat. Protoc., 2 (8), pp. 1896-1906; Soldi, M., Cuomo, A., Bonaldi, T., Improved bottom-up strategy to efficiently separate hypermodified histone peptides through ultra-HPLC separation on a bench top Orbitrap instrument (2014) Proteomics; Sidoli, S., Yuan, Z.F., Lin, S., Karch, K., Wang, X., Bhanu, N., Arnaudo, A.M., Garcia, B.A., Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis (2015) Proteomics, 15 (9), pp. 1459-1469; Maile, T.M., Izrael-Tomasevic, A., Cheung, T., Guler, G.D., Tindell, C., Masselot, A., Liang, J., Arnott, D., Mass spectrometric quantification of histone post-translational modifications by a hybrid chemical labeling method (2015) Mol. Cell. Proteomics, 14 (4), pp. 1148-1158; Sidoli, S., Garcia, B.A., Middle-down proteomics: a still unexploited resource for chromatin biology (2017) Expert Rev. Proteomics, 14 (7), pp. 617-626; Huang, H., Lin, S., Garcia, B.A., Zhao, Y., Quantitative proteomic analysis of histone modifications (2015) Chem. Rev., 115 (6), pp. 2376-2418; Noberini, R., Bonaldi, T., A super-SILAC strategy for the accurate and multiplexed profiling of histone posttranslational modifications (2017) Methods Enzymol., 586, pp. 311-332; Lin, S., Wein, S., Gonzales-Cope, M., Otte, G.L., Yuan, Z.F., Afjehi-Sadat, L., Maile, T., Garcia, B.A., Stable-isotope-labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry (2014) Mol. Cell. Proteomics, 13 (9), pp. 2450-2466; Noberini, R., Pruneri, G., Minucci, S., Bonaldi, T., Mass-spectrometry analysis of histone post-translational modifications in pathology tissue using the PAT-H-MS approach (2016) Data Brief, 7, pp. 188-194; Picotti, P., Aebersold, R., Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions (2012) Nat. Methods, 9 (6), pp. 555-566; Darwanto, A., Curtis, M.P., Schrag, M., Kirsch, W., Liu, P., Xu, G., Neidigh, J.W., Zhang, K., A modified “cross-talk” between histone H2B Lys-120 ubiquitination and H3 Lys-79 methylation (2010) J. Biol. Chem., 285 (28), pp. 21868-21876",

year = "2020",

doi = "10.1016/j.ymeth.2019.10.001",

language = "English",

volume = "184",

pages = "19--28",

journal = "Methods",

issn = "1046-2023",

publisher = "Academic Press Inc.",

}

TY - JOUR

T1 - Enrichment of histones from patient samples for mass spectrometry-based analysis of post-translational modifications

AU - Noberini, R.

AU - Restellini, C.

AU - Savoia, E.O.

AU - Bonaldi, T.

N1 - Cited By :4 Export Date: 4 March 2021 CODEN: MTHDE Correspondence Address: Noberini, R.; Department of Experimental Oncology, Italy; email: roberta.noberini@ieo.it Funding details: GR-2016-02361522 Funding details: Ecumenical Project for International Cooperation, EPIC, 823839 Funding details: Horizon 2020 Framework Programme, H2020 Funding details: European Commission***Delivered and deleted from Elsevier end because this record is to be no longer updated or in business with Elsevier on Date 10-03-2020***, EC Funding details: Associazione Italiana per la Ricerca sul Cancro, AIRC, IG-2018-21834 Funding text 1: Funding: This research was supported by the Italian Association for Cancer Research , grant number IG-2018-21834 (to T.B.), by EPIC -XS, project number 823839 , funded by the Horizon 2020 programme of the European Union (to T.B.), and by the Italian Ministry of Health, grant number GR-2016-02361522 (to R.N.). Appendix A Funding text 2: Funding: This research was supported by the Italian Association for Cancer Research, grant number IG-2018-21834 (to T.B.), by EPIC-XS, project number 823839, funded by the Horizon 2020 programme of the European Union (to T.B.), and by the Italian Ministry of Health, grant number GR-2016-02361522 (to R.N.). References: Zhao, Y., Garcia, B.A., Comprehensive Catalog of Currently Documented Histone Modifications (2015) Cold Spring Harb. Perspect. Biol., 7 (9); Audia, J.E., Campbell, R.M., Histone Modifications and Cancer (2016) Cold Spring Harb. Perspect. Biol., 8 (4); Portela, A., Esteller, M., Epigenetic modifications and human disease (2010) Nat. Biotechnol., 28 (10), pp. 1057-1068; Elsheikh, S.E., Green, A.R., Rakha, E.A., Powe, D.G., Ahmed, R.A., Collins, H.M., Soria, D., Ellis, I.O., Global histone modifications in breast cancer correlate with tumor phenotypes, prognostic factors, and patient outcome (2009) Cancer Res., 69 (9), pp. 3802-3809; Seligson, D.B., Horvath, S., McBrian, M.A., Mah, V., Yu, H., Tze, S., Wang, Q., Kurdistani, S.K., Global levels of histone modifications predict prognosis in different cancers (2009) Am. J. Pathol., 174 (5), pp. 1619-1628; Seligson, D.B., Horvath, S., Shi, T., Yu, H., Tze, S., Grunstein, M., Kurdistani, S.K., Global histone modification patterns predict risk of prostate cancer recurrence (2005) Nature, 435 (7046), pp. 1262-1266; Shechter, D., Dormann, H.L., Allis, C.D., Hake, S.B., Extraction, purification and analysis of histones (2007) Nat. Protoc., 2 (6), pp. 1445-1457; Cuomo, A., Soldi, M., Bonaldi, T., SILAC-based quantitative strategies for accurate histone posttranslational modification profiling across multiple biological samples (2017) Methods Mol. Biol., 1528, pp. 97-119; Sidoli, S., Bhanu, N.V., Karch, K.R., Wang, X., Garcia, B.A., Complete workflow for analysis of histone post-translational modifications using bottom-up mass spectrometry: from histone extraction to data analysis (2016) J. Vis. Exp., 111; Bauden, M., Kristl, T., Andersson, R., Marko-Varga, G., Ansari, D., Characterization of histone-related chemical modifications in formalin-fixed paraffin-embedded and fresh-frozen human pancreatic cancer xenografts using LC-MS/MS (2017) Lab. Invest., 97 (3), pp. 279-288; Farrelly, L.A., Dill, B.D., Molina, H., Birtwistle, M.R., Maze, I., Current proteomic methods to investigate the dynamics of histone turnover in the central nervous system (2016) Methods Enzymol., 574, pp. 331-354; Zhang, Q., Xue, P., Li, H.L., Bao, Y.H., Wu, L.H., Chang, S.Y., Niu, B., Zhang, T., Histone modification mapping in human brain reveals aberrant expression of histone H3 lysine 79 dimethylation in neural tube defects (2013) Neurobiol. Dis., 54, pp. 404-413; Noberini, R., Longuespee, R., Richichi, C., Pruneri, G., Kriegsmann, M., Pelicci, G., Bonaldi, T., PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples (2017) Clin. Epigenetics, 9, p. 69; Noberini, R., Osti, D., Miccolo, C., Richichi, C., Lupia, M., Corleone, G., Hong, S.P., Bonaldi, T., Extensive and systematic rewiring of histone post-translational modifications in cancer model systems (2018) Nucleic Acids Res.; Noberini, R., Uggetti, A., Pruneri, G., Minucci, S., Bonaldi, T., Pathology tissue-quantitative mass spectrometry analysis to profile histone post-translational modification patterns in patient samples (2016) Mol. Cell. Proteomics, 15 (3), pp. 866-877; Restellini, C., Cuomo, A., Lupia, M., Giordano, M., Bonaldi, T., Noberini, R., Alternative digestion approaches improve histone modification mapping by mass spectrometry in clinical samples (2019) Proteomics Clin. Appl., 13 (1); Noberini, R., Restellini, C., Savoia, E.O., Raimondi, F., Ghiani, L., Jodice, M.G., Bertalot, G., Bonaldi, T., Profiling of epigenetic features in clinical samples reveals novel widespread changes in cancer (2019) Cancers (Basel), 11 (5); Fowler, C.B., O'Leary, T.J., Mason, J.T., Protein mass spectrometry applications on FFPE tissue sections (2011) Methods Mol. Biol., 724, pp. 281-295; Rachdaoui, N., Li, L., Willard, B., Kasumov, T., Previs, S., Sarkar, D., Turnover of histones and histone variants in postnatal rat brain: effects of alcohol exposure (2017) Clin. Epigenetics, 9, p. 117; Tvardovskiy, A., Schwammle, V., Kempf, S.J., Rogowska-Wrzesinska, A., Jensen, O.N., Accumulation of histone variant H3.3 with age is associated with profound changes in the histone methylation landscape (2017) Nucleic Acids Res., 45 (16), pp. 9272-9289; Gruppuso, P.A., Boylan, J.M., Zabala, V., Neretti, N., Abshiru, N.A., Sikora, J.W., Doud, E.H., Sanders, J.A., Stability of histone post-translational modifications in samples derived from liver tissue and primary hepatic cells (2018) PLoS ONE, 13 (9); Nestor, C.E., Ottaviano, R., Reinhardt, D., Cruickshanks, H.A., Mjoseng, H.K., McPherson, R.C., Lentini, A., Meehan, R.R., Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems (2015) Genome Biol., 16, p. 11; Govaert, E., Van Steendam, K., Scheerlinck, E., Vossaert, L., Meert, P., Stella, M., Willems, S., Deforce, D., Extracting histones for the specific purpose of label-free MS (2016) Proteomics, 16 (23), pp. 2937-2944; Minshull, T.C., Cole, J., Dockrell, D.H., Read, R.C., Dickman, M.J., Analysis of histone post translational modifications in primary monocyte derived macrophages using reverse phasexreverse phase chromatography in conjunction with porous graphitic carbon stationary phase (2016) J. Chromatogr. A, 1453, pp. 43-53; Luense, L.J., Wang, X., Schon, S.B., Weller, A.H., Lin Shiao, E., Bryant, J.M., Bartolomei, M.S., Berger, S.L., Comprehensive analysis of histone post-translational modifications in mouse and human male germ cells (2016) Epigenetics Chromatin, 9, p. 24; Olszowy, P., Donnelly, M.R., Lee, C., Ciborowski, P., Profiling post-translational modifications of histones in human monocyte-derived macrophages (2015) Proteome Sci., 13, p. 24; von Holt, C., Brandt, W.F., Greyling, H.J., Lindsey, G.G., Retief, J.D., Rodrigues, J.D., Schwager, S., Sewell, B.T., Isolation and characterization of histones (1989) Methods Enzymol., 170, pp. 431-523; Simon, R.H., Felsenfeld, G., A new procedure for purifying histone pairs H2A + H2B and H3 + H4 from chromatin using hydroxylapatite (1979) Nucleic Acids Res., 6 (2), pp. 689-696; Rappsilber, J., Mann, M., Ishihama, Y., Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips (2007) Nat. Protoc., 2 (8), pp. 1896-1906; Soldi, M., Cuomo, A., Bonaldi, T., Improved bottom-up strategy to efficiently separate hypermodified histone peptides through ultra-HPLC separation on a bench top Orbitrap instrument (2014) Proteomics; Sidoli, S., Yuan, Z.F., Lin, S., Karch, K., Wang, X., Bhanu, N., Arnaudo, A.M., Garcia, B.A., Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis (2015) Proteomics, 15 (9), pp. 1459-1469; Maile, T.M., Izrael-Tomasevic, A., Cheung, T., Guler, G.D., Tindell, C., Masselot, A., Liang, J., Arnott, D., Mass spectrometric quantification of histone post-translational modifications by a hybrid chemical labeling method (2015) Mol. Cell. Proteomics, 14 (4), pp. 1148-1158; Sidoli, S., Garcia, B.A., Middle-down proteomics: a still unexploited resource for chromatin biology (2017) Expert Rev. Proteomics, 14 (7), pp. 617-626; Huang, H., Lin, S., Garcia, B.A., Zhao, Y., Quantitative proteomic analysis of histone modifications (2015) Chem. Rev., 115 (6), pp. 2376-2418; Noberini, R., Bonaldi, T., A super-SILAC strategy for the accurate and multiplexed profiling of histone posttranslational modifications (2017) Methods Enzymol., 586, pp. 311-332; Lin, S., Wein, S., Gonzales-Cope, M., Otte, G.L., Yuan, Z.F., Afjehi-Sadat, L., Maile, T., Garcia, B.A., Stable-isotope-labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry (2014) Mol. Cell. Proteomics, 13 (9), pp. 2450-2466; Noberini, R., Pruneri, G., Minucci, S., Bonaldi, T., Mass-spectrometry analysis of histone post-translational modifications in pathology tissue using the PAT-H-MS approach (2016) Data Brief, 7, pp. 188-194; Picotti, P., Aebersold, R., Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions (2012) Nat. Methods, 9 (6), pp. 555-566; Darwanto, A., Curtis, M.P., Schrag, M., Kirsch, W., Liu, P., Xu, G., Neidigh, J.W., Zhang, K., A modified “cross-talk” between histone H2B Lys-120 ubiquitination and H3 Lys-79 methylation (2010) J. Biol. Chem., 285 (28), pp. 21868-21876

PY - 2020

Y1 - 2020

N2 - Aberrations in histone post-translational modifications (PTMs) have been implicated with the development of numerous pathologies, including cancer. Therefore, profiling histone PTMs in patient samples could provide information useful for the identification of epigenetic biomarkers, as well as for the discovery of potential novel targets. While antibody-based methods have been traditionally employed to analyze histone PTM in clinical samples, mass spectrometry (MS) can provide a more comprehensive, unbiased and quantitative view on histones and their PTMs. To combine the power of MS-based methods and the potential offered by histone PTM profiling of clinical samples, we have recently developed a series of methods for the extraction and enrichment of histones from different types of patient samples, including formalin-fixed paraffin-embedded tissues, fresh- and optimal cutting temperature-frozen tissues, and primary cells. Here, we provide a detailed description of these protocols, together with indications on the expected results and the most suitable workflow to be used downstream of each procedure. © 2019 The Authors

AB - Aberrations in histone post-translational modifications (PTMs) have been implicated with the development of numerous pathologies, including cancer. Therefore, profiling histone PTMs in patient samples could provide information useful for the identification of epigenetic biomarkers, as well as for the discovery of potential novel targets. While antibody-based methods have been traditionally employed to analyze histone PTM in clinical samples, mass spectrometry (MS) can provide a more comprehensive, unbiased and quantitative view on histones and their PTMs. To combine the power of MS-based methods and the potential offered by histone PTM profiling of clinical samples, we have recently developed a series of methods for the extraction and enrichment of histones from different types of patient samples, including formalin-fixed paraffin-embedded tissues, fresh- and optimal cutting temperature-frozen tissues, and primary cells. Here, we provide a detailed description of these protocols, together with indications on the expected results and the most suitable workflow to be used downstream of each procedure. © 2019 The Authors

KW - Epigenetics

KW - Formalin-fixed paraffin-embedded tissues

KW - Frozen tissues

KW - Histone post-translational modifications

KW - Mass spectrometry

KW - animal tissue

KW - Article

KW - controlled study

KW - histone modification

KW - human

KW - human cell

KW - human tissue

KW - immunohistochemistry

KW - laser microdissection

KW - male

KW - mass spectrometry

KW - nonhuman

KW - polyacrylamide gel electrophoresis

KW - practice guideline

KW - primary cell

KW - priority journal

KW - protein processing

KW - tissue embedding

KW - tissue section

KW - workflow

U2 - 10.1016/j.ymeth.2019.10.001

DO - 10.1016/j.ymeth.2019.10.001

M3 - Article

VL - 184

SP - 19

EP - 28

JO - Methods

JF - Methods

SN - 1046-2023

ER -