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Current Medicinal Chemistry

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ISSN (Online): 1875-533X

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Review Article

Protein Post-Translational Modification Crosstalk in Acute Myeloid Leukemia Calls for Action

Author(s): Maria Hernandez-Valladares*, Rebecca Wangen, Frode S. Berven and Astrid Guldbrandsen*

Volume 26, Issue 28, 2019

Page: [5317 - 5337] Pages: 21

DOI: 10.2174/0929867326666190503164004

Price: $65

Abstract

Background: Post-translational modification (PTM) crosstalk is a young research field. However, there is now evidence of the extraordinary characterization of the different proteoforms and their interactions in a biological environment that PTM crosstalk studies can describe. Besides gene expression and phosphorylation profiling of acute myeloid leukemia (AML) samples, the functional combination of several PTMs that might contribute to a better understanding of the complexity of the AML proteome remains to be discovered.

Objective: By reviewing current workflows for the simultaneous enrichment of several PTMs and bioinformatics tools to analyze mass spectrometry (MS)-based data, our major objective is to introduce the PTM crosstalk field to the AML research community.

Results: After an introduction to PTMs and PTM crosstalk, this review introduces several protocols for the simultaneous enrichment of PTMs. Two of them allow a simultaneous enrichment of at least three PTMs when using 0.5-2 mg of cell lysate. We have reviewed many of the bioinformatics tools used for PTM crosstalk discovery as its complex data analysis, mainly generated from MS, becomes challenging for most AML researchers. We have presented several non-AML PTM crosstalk studies throughout the review in order to show how important the characterization of PTM crosstalk becomes for the selection of disease biomarkers and therapeutic targets.

Conclusion: Herein, we have reviewed the advances and pitfalls of the emerging PTM crosstalk field and its potential contribution to unravel the heterogeneity of AML. The complexity of sample preparation and bioinformatics workflows demands a good interaction between experts of several areas.

Keywords: Acute myeloid leukemia, post-translational modifications, crosstalk, proteome, phosphoproteome, acetylproteome, methylproteome, glycoproteome, ubiquitinome, mass spectrometry, biomarkers, proteoform.

« Previous Next »
[1]
Döhner, H.; Weisdorf, D.J.; Bloomfield, C.D. Acute Myeloid Leukemia. N. Engl. J. Med., 2015, 373(12), 1136-1152.
[http://dx.doi.org/10.1056/NEJMra1406184] [PMID: 26376137]
[2]
Almeida, A.M.; Ramos, F. Acute myeloid leukemia in the older adults. Leuk. Res. Rep., 2016, 6, 1-7.
[http://dx.doi.org/10.1016/j.lrr.2016.06.001] [PMID: 27408788]
[3]
Zhou, J.; Ng, Y.; Chng, W.J. ENL: structure, function, and roles in hematopoiesis and acute myeloid leukemia. Cell. Mol. Life Sci., 2018, 75(21), 3931-3941.
[http://dx.doi.org/10.1007/s00018-018-2895-8] [PMID: 30066088]
[4]
Irish, J.M.; Anensen, N.; Hovland, R.; Skavland, J.; Børresen-Dale, A.L.; Bruserud, O.; Nolan, G.P.; Gjertsen, B.T. Flt3 Y591 duplication and Bcl-2 overexpression are detected in acute myeloid leukemia cells with high levels of phosphorylated wild-type p53. Blood, 2007, 109(6), 2589-2596.
[http://dx.doi.org/10.1182/blood-2006-02-004234] [PMID: 17105820]
[5]
Bullinger, L.; Döhner, K.; Döhner, H. Genomics of acute myeloid leukemia diagnosis and pathways. J. Clin. Oncol., 2017, 35(9), 934-946.
[http://dx.doi.org/10.1200/JCO.2016.71.2208] [PMID: 28297624]
[6]
Pastore, F.; Levine, R.L. Epigenetic regulators and their impact on therapy in acute myeloid leukemia. Haematologica, 2016, 101(3), 269-278.
[http://dx.doi.org/10.3324/haematol.2015.140822] [PMID: 26928248]
[7]
Majhail, N.S.; Farnia, S.H.; Carpenter, P.A.; Champlin, R.E.; Crawford, S.; Marks, D.I.; Omel, J.L.; Orchard, P.J.; Palmer, J.; Saber, W.; Savani, B.N.; Veys, P.A.; Bredeson, C.N.; Giralt, S.A.; LeMaistre, C.F. Indications for autologous and allogeneic hematopoietic cell transplantation: guidelines from the american society for blood and marrow transplantation. Biol. Blood Marrow Transplant., 2015, 21(11), 1863-1869.
[http://dx.doi.org/10.1016/j.bbmt.2015.07.032] [PMID: 26256941]
[8]
Schlenk, R.F.; Kayser, S. Midostaurin: A multiple tyrosine kinases inhibitor in acute myeloid leukemia and systemic mastocytosis. Recent Results Cancer Res., 2018, 212, 199-214.
[http://dx.doi.org/10.1007/978-3-319-91439-8_10] [PMID: 30069632]
[9]
Davis, J.R.; Benjamin, D.J.; Jonas, B.A. New and emerging therapies for acute myeloid leukaemia. J. Investig. Med., 2018, 66(8), 1088-1095.
[http://dx.doi.org/10.1136/jim-2018-000807] [PMID: 30127098]
[10]
Yan, S.K.; Liu, R.H.; Jin, H.Z.; Liu, X.R.; Ye, J.; Shan, L.; Zhang, W.D. “Omics” in pharmaceutical research: overview, applications, challenges, and future perspectives. Chin. J. Nat. Med., 2015, 13(1), 3-21.
[http://dx.doi.org/10.1016/S1875-5364(15)60002-4] [PMID: 25660284]
[11]
Rylova, G.; Ozdian, T.; Varanasi, L.; Soural, M.; Hlavac, J.; Holub, D.; Dzubak, P.; Hajduch, M. Affinity-based methods in drug-target discovery. Curr. Drug Targets, 2015, 16(1), 60-76.
[http://dx.doi.org/10.2174/1389450115666141120110323] [PMID: 25410410]
[12]
Aasebø, E.; Forthun, R.B.; Berven, F.; Selheim, F.; Hernandez-Valladares, M. Global cell proteome profiling, phospho-signaling and quantitative proteomics for identification of new biomarkers in acute myeloid leukemia patients. Curr. Pharm. Biotechnol., 2016, 17(1), 52-70.
[http://dx.doi.org/10.2174/1389201016666150826115626] [PMID: 26306748]
[13]
Roboz, G.J.; Roboz, J. The application of mass spectrometry to leukemia drug discovery. Expert Opin. Drug Discov., 2016, 11(11), 1029-1032.
[http://dx.doi.org/10.1080/17460441.2016.1233175] [PMID: 27662537]
[14]
Noberini, R.; Sigismondo, G.; Bonaldi, T. The contribution of mass spectrometry-based proteomics to understanding epigenetics. Epigenomics, 2016, 8(3), 429-445.
[http://dx.doi.org/10.2217/epi.15.108] [PMID: 26606673]
[15]
Zhang, C.; Suo, J.; Katayama, H.; Wei, Y.; Garcia-Manero, G.; Hanash, S. Quantitative proteomic analysis of histone modifications in decitabine sensitive and resistant leukemia cell lines. Clin. Proteomics, 2016, 13, 14.
[http://dx.doi.org/10.1186/s12014-016-9115-z] [PMID: 27382363]
[16]
Minguez, P.; Parca, L.; Diella, F.; Mende, D.R.; Kumar, R.; Helmer-Citterich, M.; Gavin, A.C.; van Noort, V.; Bork, P. Deciphering a global network of functionally associated post-translational modifications. Mol. Syst. Biol., 2012, 8, 599.
[http://dx.doi.org/10.1038/msb.2012.31] [PMID: 22806145]
[17]
Jin, H.; Zangar, R.C. Protein modifications as potential biomarkers in breast cancer. Biomark. Insights, 2009, 4, 191-200.
[http://dx.doi.org/10.4137/BMI.S2557] [PMID: 20072669]
[18]
Nedić, O.; Rogowska-Wrzesinska, A.; Rattan, S.I.S. Standardization and quality control in quantifying non-enzymatic oxidative protein modifications in relation to ageing and disease: Why is it important and why is it hard? Redox Biol., 2015, 5, 91-100.
[http://dx.doi.org/10.1016/j.redox.2015.04.001] [PMID: 25909343]
[19]
Zhang, W.; Xiao, S.; Ahn, D.U. Protein oxidation: basic principles and implications for meat quality. Crit. Rev. Food Sci. Nutr., 2013, 53(11), 1191-1201.
[http://dx.doi.org/10.1080/10408398.2011.577540] [PMID: 24007423]
[20]
Post-translational modifications. Nat. Rev. Mol. Cell Biol., 2017.
[21]
Krueger, K.E.; Srivastava, S. Posttranslational protein modifications: current implications for cancer detection, prevention, and therapeutics. Mol. Cell. Proteomics, 2006, 5(10), 1799-1810.
[http://dx.doi.org/10.1074/mcp.R600009-MCP200] [PMID: 16844681]
[22]
Li, L.; Tibiche, C.; Fu, C.; Kaneko, T.; Moran, M.F.; Schiller, M.R.; Li, S.S.; Wang, E. The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer. Genome Res., 2012, 22(7), 1222-1230.
[http://dx.doi.org/10.1101/gr.128819.111] [PMID: 22194470]
[23]
Hitosugi, T.; Chen, J. Post-translational modifications and the Warburg effect. Oncogene, 2014, 33(34), 4279-4285.
[http://dx.doi.org/10.1038/onc.2013.406] [PMID: 24096483]
[24]
Birkenkamp, K.U.; Geugien, M.; Lemmink, H.H.; Kruijer, W.; Vellenga, E. Regulation of constitutive STAT5 phosphorylation in acute myeloid leukemia blasts. Leukemia, 2001, 15(12), 1923-1931.
[http://dx.doi.org/10.1038/sj.leu.2402317] [PMID: 11753614]
[25]
Chen, Y.; Pan, Y.; Guo, Y.; Zhao, W.; Ho, W.T.; Wang, J.; Xu, M.; Yang, F.C.; Zhao, Z.J. Tyrosine kinase inhibitors targeting FLT3 in the treatment of acute myeloid leukemia. Stem Cell Investig., 2017, 4, 48.
[http://dx.doi.org/10.21037/sci.2017.05.04] [PMID: 28607922]
[26]
Brown, F.C.; Still, E.; Koche, R.P.; Yim, C.Y.; Takao, S.; Cifani, P.; Reed, C.; Gunasekera, S.; Ficarro, S.B.; Romanienko, P.; Mark, W.; McCarthy, C.; de Stanchina, E.; Gonen, M.; Seshan, V.; Bhola, P.; O’Donnell, C.; Spitzer, B.; Stutzke, C.; Lavallée, V.P.; Hébert, J.; Krivtsov, A.V.; Melnick, A.; Paietta, E.M.; Tallman, M.S.; Letai, A.; Sauvageau, G.; Pouliot, G.; Levine, R.; Marto, J.A.; Armstrong, S.A.; Kentsis, A. MEF2C phosphorylation is required for chemotherapy resistance in acute myeloid leukemia. Cancer Discov., 2018, 8(4), 478-497.
[http://dx.doi.org/10.1158/2159-8290.CD-17-1271] [PMID: 29431698]
[27]
Aksnes, H.; Drazic, A.; Marie, M.; Arnesen, T. First things first: vital protein marks by n-terminal acetyltransferases. Trends Biochem. Sci., 2016, 41(9), 746-760.
[http://dx.doi.org/10.1016/j.tibs.2016.07.005] [PMID: 27498224]
[28]
Ali, I.; Conrad, R.J.; Verdin, E.; Ott, M. Lysine acetylation goes global: from epigenetics to metabolism and therapeutics. Chem. Rev., 2018, 118(3), 1216-1252.
[http://dx.doi.org/10.1021/acs.chemrev.7b00181] [PMID: 29405707]
[29]
Verdin, E.; Ott, M. 50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond. Nat. Rev. Mol. Cell Biol., 2015, 16(4), 258-264.
[http://dx.doi.org/10.1038/nrm3931] [PMID: 25549891]
[30]
Yang, X.; Lu, B.; Sun, X.; Han, C.; Fu, C.; Xu, K.; Wang, M.; Li, D.; Chen, Z.; Opal, P.; Wen, Q.; Crispino, J.D.; Wang, Q.F.; Huang, Z. ANP32A regulates histone H3 acetylation and promotes leukemogenesis. Leukemia, 2018, 32(7), 1587-1597.
[http://dx.doi.org/10.1038/s41375-018-0010-7] [PMID: 29467488]
[31]
Sauer, T.; Arteaga, M. F.; Isken, F.; Rohde, C.; Hebestreit, K.; Mikesch, J. H.; Stelljes, M.; Cui, C.; Zhou, F.; Gollner, S.; Baumer, N.; Kohler, G.; Krug, U.; Thiede, C.; Ehninger, G.; Edemir, B.; Schlenke, P.; Berdel, W. E.; Dugas, M.; Muller-Tidow, C. MYST2 acetyltransferase expression and Histone H4 Lysine acetylation are suppressed in AML., 2015, 43(9), 794-802.
[http://dx.doi.org/10.1016/j.exphem.2015.05.010]] [PMID: 26072331]
[32]
Fredly, H.; Gjertsen, B.T.; Bruserud, O. Histone deacetylase inhibition in the treatment of acute myeloid leukemia: the effects of valproic acid on leukemic cells, and the clinical and experimental evidence for combining valproic acid with other antileukemic agents. Clin. Epigenetics, 2013, 5(1), 12.
[http://dx.doi.org/10.1186/1868-7083-5-12] [PMID: 23898968]
[33]
Thaysen-Andersen, M.; Packer, N.H.; Schulz, B.L. Maturing glycoproteomics technologies provide unique structural insights into the n-glycoproteome and its regulation in health and disease. Mol. Cell. Proteomics, 2016, 15(6), 1773-1790.
[http://dx.doi.org/10.1074/mcp.O115.057638] [PMID: 26929216]
[34]
Kalxdorf, M.; Gade, S.; Eberl, H.C.; Bantscheff, M. Monitoring cell-surface N-Glycoproteome dynamics by quantitative proteomics reveals mechanistic insights into macrophage differentiation. Mol. Cell. Proteomics, 2017, 16(5), 770-785.
[http://dx.doi.org/10.1074/mcp.M116.063859] [PMID: 28336715]
[35]
Pickart, C.M.; Eddins, M.J. Ubiquitin: structures, functions, mechanisms. Biochim. Biophys. Acta, 2004, 1695(1-3), 55-72.
[http://dx.doi.org/10.1016/j.bbamcr.2004.09.019] [PMID: 15571809]
[36]
Sahtoe, D.D.; Sixma, T.K. Layers of DUB regulation. Trends Biochem. Sci., 2015, 40(8), 456-467.
[http://dx.doi.org/10.1016/j.tibs.2015.05.002] [PMID: 26073511]
[37]
Rape, M. Ubiquitylation at the crossroads of development and disease. Nat. Rev. Mol. Cell Biol., 2018, 19(1), 59-70.
[http://dx.doi.org/10.1038/nrm.2017.83] [PMID: 28928488]
[38]
Kane, L.A.; Lazarou, M.; Fogel, A.I.; Li, Y.; Yamano, K.; Sarraf, S.A.; Banerjee, S.; Youle, R.J. PINK1 phosphorylates ubiquitin to activate Parkin E3 ubiquitin ligase activity. J. Cell Biol., 2014, 205(2), 143-153.
[http://dx.doi.org/10.1083/jcb.201402104] [PMID: 24751536]
[39]
Ohtake, F.; Saeki, Y.; Sakamoto, K.; Ohtake, K.; Nishikawa, H.; Tsuchiya, H.; Ohta, T.; Tanaka, K.; Kanno, J. Ubiquitin acetylation inhibits polyubiquitin chain elongation. EMBO Rep., 2015, 16(2), 192-201.
[http://dx.doi.org/10.15252/embr.201439152] [PMID: 25527407]
[40]
Senft, D.; Qi, J.; Ronai, Z.A. Ubiquitin ligases in oncogenic transformation and cancer therapy. Nat. Rev. Cancer, 2018, 18(2), 69-88.
[http://dx.doi.org/10.1038/nrc.2017.105] [PMID: 29242641]
[41]
Sanarico, A.G.; Ronchini, C.; Croce, A.; Memmi, E.M.; Cammarata, U.A.; De Antoni, A.; Lavorgna, S.; Divona, M.; Giacò, L.; Melloni, G.E.M.; Brendolan, A.; Simonetti, G.; Martinelli, G.; Mancuso, P.; Bertolini, F.; Coco, F.L.; Melino, G.; Pelicci, P.G.; Bernassola, F. The E3 ubiquitin ligase WWP1 sustains the growth of acute myeloid leukaemia. Leukemia, 2018, 32(4), 911-919.
[http://dx.doi.org/10.1038/leu.2017.342] [PMID: 29209041]
[42]
McBride, A.E.; Silver, P.A. State of the arg: protein methylation at arginine comes of age. Cell, 2001, 106(1), 5-8.
[http://dx.doi.org/10.1016/S0092-8674(01)00423-8] [PMID: 11461695]
[43]
Chen, C.; Nott, T.J.; Jin, J.; Pawson, T. Deciphering arginine methylation: Tudor tells the tale. Nat. Rev. Mol. Cell Biol., 2011, 12(10), 629-642.
[http://dx.doi.org/10.1038/nrm3185] [PMID: 21915143]
[44]
Blanc, R.S.; Richard, S. Arginine methylation: the coming of age. Mol. Cell, 2017, 65(1), 8-24.
[http://dx.doi.org/10.1016/j.molcel.2016.11.003] [PMID: 28061334]
[45]
Carlson, S.M.; Gozani, O. Nonhistone lysine methylation in the regulation of cancer pathways. Cold Spring Harb. Perspect. Med., 2016, 6(11)a026435
[http://dx.doi.org/10.1101/cshperspect.a026435] [PMID: 27580749]
[46]
Hamamoto, R.; Saloura, V.; Nakamura, Y. Critical roles of non-histone protein lysine methylation in human tumorigenesis. Nat. Rev. Cancer, 2015, 15(2), 110-124.
[http://dx.doi.org/10.1038/nrc3884] [PMID: 25614009]
[47]
Cho, H.S.; Shimazu, T.; Toyokawa, G.; Daigo, Y.; Maehara, Y.; Hayami, S.; Ito, A.; Masuda, K.; Ikawa, N.; Field, H.I.; Tsuchiya, E.; Ohnuma, S.; Ponder, B.A.; Yoshida, M.; Nakamura, Y.; Hamamoto, R. Enhanced HSP70 lysine methylation promotes proliferation of cancer cells through activation of Aurora kinase B. Nat. Commun., 2012, 3, 1072.
[http://dx.doi.org/10.1038/ncomms2074] [PMID: 22990868]
[48]
Metzger, E.; Wissmann, M.; Yin, N.; Müller, J.M.; Schneider, R.; Peters, A.H.; Günther, T.; Buettner, R.; Schüle, R. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature, 2005, 437(7057), 436-439.
[http://dx.doi.org/10.1038/nature04020] [PMID: 16079795]
[49]
Hart, G.W.; Greis, K.D.; Dong, L.Y.; Blomberg, M.A.; Chou, T.Y.; Jiang, M.S.; Roquemore, E.P.; Snow, D.M.; Kreppel, L.K.; Cole, R.N. O-linked N-acetylglucosamine: the “yin-yang” of Ser/Thr phosphorylation? Nuclear and cytoplasmic glycosylation. Adv. Exp. Med. Biol., 1995, 376, 115-123.
[http://dx.doi.org/10.1007/978-1-4615-1885-3_10] [PMID: 8597237]
[50]
Strahl, B.D.; Allis, C.D. The language of covalent histone modifications. Nature, 2000, 403(6765), 41-45.
[http://dx.doi.org/10.1038/47412] [PMID: 10638745]
[51]
Venne, A.S.; Kollipara, L.; Zahedi, R.P. The next level of complexity: crosstalk of posttranslational modifications. Proteomics, 2014, 14(4-5), 513-524.
[http://dx.doi.org/10.1002/pmic.201300344] [PMID: 24339426]
[52]
Gu, B.; Zhu, W.G. Surf the post-translational modification network of p53 regulation. Int. J. Biol. Sci., 2012, 8(5), 672-684.
[http://dx.doi.org/10.7150/ijbs.4283] [PMID: 22606048]
[53]
Kontaxi, C.; Piccardo, P.; Gill, A.C. Lysine-directed post-translational modifications of Tau protein in alzheimer’s disease and related tauopathies. Front. Mol. Biosci., 2017, 4, 56.
[http://dx.doi.org/10.3389/fmolb.2017.00056] [PMID: 28848737]
[54]
Gadadhar, S.; Bodakuntla, S.; Natarajan, K.; Janke, C. The tubulin code at a glance. J. Cell Sci., 2017, 130(8), 1347-1353.
[http://dx.doi.org/10.1242/jcs.199471] [PMID: 28325758]
[55]
Csizmok, V.; Forman-Kay, J.D. Complex regulatory mechanisms mediated by the interplay of multiple post-translational modifications. Curr. Opin. Struct. Biol., 2018, 48, 58-67.
[http://dx.doi.org/10.1016/j.sbi.2017.10.013] [PMID: 29100108]
[56]
Cheung, P.; Tanner, K.G.; Cheung, W.L.; Sassone-Corsi, P.; Denu, J.M.; Allis, C.D. Synergistic coupling of histone H3 phosphorylation and acetylation in response to epidermal growth factor stimulation. Mol. Cell, 2000, 5(6), 905-915.
[http://dx.doi.org/10.1016/S1097-2765(00)80256-7] [PMID: 10911985]
[57]
Lo, W.S.; Trievel, R.C.; Rojas, J.R.; Duggan, L.; Hsu, J.Y.; Allis, C.D.; Marmorstein, R.; Berger, S.L. Phosphorylation of serine 10 in histone H3 is functionally linked in vitro and in vivo to Gcn5-mediated acetylation at lysine 14. Mol. Cell, 2000, 5(6), 917-926.
[http://dx.doi.org/10.1016/S1097-2765(00)80257-9] [PMID: 10911986]
[58]
Kim, J.; Guermah, M.; McGinty, R.K.; Lee, J.S.; Tang, Z.; Milne, T.A.; Shilatifard, A.; Muir, T.W.; Roeder, R.G. RAD6-mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. Cell, 2009, 137(3), 459-471.
[http://dx.doi.org/10.1016/j.cell.2009.02.027] [PMID: 19410543]
[59]
Su, Y.F.; Shyu, Y.C.; Shen, C.K.; Hwang, J. Phosphorylation-dependent SUMOylation of the transcription factor NF-E2. PLoS One, 2012, 7(9)e44608
[http://dx.doi.org/10.1371/journal.pone.0044608] [PMID: 22970264]
[60]
Hart, G.W.; Slawson, C.; Ramirez-Correa, G.; Lagerlof, O. Cross talk between O-GlcNAcylation and phosphorylation: roles in signaling, transcription, and chronic disease. Annu. Rev. Biochem., 2011, 80, 825-858.
[http://dx.doi.org/10.1146/annurev-biochem-060608-102511] [PMID: 21391816]
[61]
Wang, Z.; Gucek, M.; Hart, G.W. Cross-talk between GlcNAcylation and phosphorylation: site-specific phosphorylation dynamics in response to globally elevated O-GlcNAc. Proc. Natl. Acad. Sci. USA, 2008, 105(37), 13793-13798.
[http://dx.doi.org/10.1073/pnas.0806216105] [PMID: 18779572]
[62]
Jensen, O.N. Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr. Opin. Chem. Biol., 2004, 8(1), 33-41.
[http://dx.doi.org/10.1016/j.cbpa.2003.12.009] [PMID: 15036154]
[63]
Yang, X.; Qian, K. Protein O-GlcNAcylation: emerging mechanisms and functions. Nat. Rev. Mol. Cell Biol., 2017, 18(7), 452-465.
[http://dx.doi.org/10.1038/nrm.2017.22] [PMID: 28488703]
[64]
Tomonaga, T.; Matsushita, K.; Yamaguchi, S.; Oh-Ishi, M.; Kodera, Y.; Maeda, T.; Shimada, H.; Ochiai, T.; Nomura, F. Identification of altered protein expression and post-translational modifications in primary colorectal cancer by using agarose two-dimensional gel electrophoresis. Clin. Cancer Res., 2004, 10(6), 2007-2014.
[http://dx.doi.org/10.1158/1078-0432.CCR-03-0321] [PMID: 15041719]
[65]
Karihtala, P.; Soini, Y.; Auvinen, P.; Tammi, R.; Tammi, M.; Kosma, V.M. Hyaluronan in breast cancer: correlations with nitric oxide synthases and tyrosine nitrosylation. J. Histochem. Cytochem., 2007, 55(12), 1191-1198.
[http://dx.doi.org/10.1369/jhc.7A7270.2007] [PMID: 17827165]
[66]
Chang, W.W.; Lee, C.H.; Lee, P.; Lin, J.; Hsu, C.W.; Hung, J.T.; Lin, J.J.; Yu, J.C.; Shao, L.E.; Yu, J.; Wong, C.H.; Yu, A.L. Expression of Globo H and SSEA3 in breast cancer stem cells and the involvement of fucosyl transferases 1 and 2 in Globo H synthesis. Proc. Natl. Acad. Sci. USA, 2008, 105(33), 11667-11672.
[http://dx.doi.org/10.1073/pnas.0804979105] [PMID: 18685093]
[67]
Thingholm, T.E.; Jørgensen, T.J.; Jensen, O.N.; Larsen, M.R. Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat. Protoc., 2006, 1(4), 1929-1935.
[http://dx.doi.org/10.1038/nprot.2006.185] [PMID: 17487178]
[68]
Larsen, M.R.; Thingholm, T.E.; Jensen, O.N.; Roepstorff, P.; Jørgensen, T.J. Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell. Proteomics, 2005, 4(7), 873-886.
[http://dx.doi.org/10.1074/mcp.T500007-MCP200] [PMID: 15858219]
[69]
Kokubu, M.; Ishihama, Y.; Sato, T.; Nagasu, T.; Oda, Y. Specificity of immobilized metal affinity-based IMAC/C18 tip enrichment of phosphopeptides for protein phosphorylation analysis. Anal. Chem., 2005, 77(16), 5144-5154.
[http://dx.doi.org/10.1021/ac050404f] [PMID: 16097752]
[70]
Thingholm, T.E.; Jensen, O.N.; Robinson, P.J.; Larsen, M.R. SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol. Cell. Proteomics, 2008, 7(4), 661-671.
[http://dx.doi.org/10.1074/mcp.M700362-MCP200] [PMID: 18039691]
[71]
Engholm-Keller, K.; Larsen, M.R. Improving the phosphoproteome coverage for limited sample amounts using TiO2-SIMAC-HILIC (TiSH) phosphopeptide enrichment and fractionation. Methods Mol. Biol., 2016, 1355, 161-177.
[http://dx.doi.org/10.1007/978-1-4939-3049-4_11] [PMID: 26584925]
[72]
Casado, P.; Rodriguez-Prados, J.C.; Cosulich, S.C.; Guichard, S.; Vanhaesebroeck, B.; Joel, S.; Cutillas, P.R. Kinase-substrate enrichment analysis provides insights into the heterogeneity of signaling pathway activation in leukemia cells. Sci. Signal., 2013, 6(268), rs6.
[http://dx.doi.org/10.1126/scisignal.2003573] [PMID: 23532336]
[73]
Schaab, C.; Oppermann, F.S.; Klammer, M.; Pfeifer, H.; Tebbe, A.; Oellerich, T.; Krauter, J.; Levis, M.; Perl, A.E.; Daub, H.; Steffen, B.; Godl, K.; Serve, H. Global phosphoproteome analysis of human bone marrow reveals predictive phosphorylation markers for the treatment of acute myeloid leukemia with quizartinib. Leukemia, 2014, 28(3), 716-719.
[http://dx.doi.org/10.1038/leu.2013.347] [PMID: 24247654]
[74]
Casado, P.; Wilkes, E.H.; Miraki-Moud, F.; Hadi, M.M.; Rio-Machin, A.; Rajeeve, V.; Pike, R.; Iqbal, S.; Marfa, S.; Lea, N.; Best, S.; Gribben, J.; Fitzgibbon, J.; Cutillas, P.R. Proteomic and genomic integration identifies kinase and differentiation determinants of kinase inhibitor sensitivity in leukemia cells. Leukemia, 2018, 32(8), 1818-1822.
[http://dx.doi.org/10.1038/s41375-018-0032-1] [PMID: 29626197]
[75]
Aasebø, E.; Mjaavatten, O.; Vaudel, M.; Farag, Y.; Selheim, F.; Berven, F.; Bruserud, Ø.; Hernandez-Valladares, M. Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows. J. Proteomics, 2016, 145, 214-225.
[http://dx.doi.org/10.1016/j.jprot.2016.03.049] [PMID: 27107777]
[76]
Hernandez-Valladares, M.; Aasebø, E.; Mjaavatten, O.; Vaudel, M.; Bruserud, Ø.; Berven, F.; Selheim, F. Reliable FASP-based procedures for optimal quantitative proteomic and phosphoproteomic analysis on samples from acute myeloid leukemia patients. Biol. Proced. Online, 2016, 18, 13.
[http://dx.doi.org/10.1186/s12575-016-0043-0] [PMID: 27330413]
[77]
van der Mijn, J. C.; Labots, M.; Piersma, S. R.; Pham, T. V.; Knol, J. C.; Broxterman, H. J.; Verheul, H. M.; Jimenez, C. R. Evaluation of different phospho-tyrosine antibodies for label-free phosphoproteomics. J. Proteomics, , 2015, 127(Pt B), 259-263.
[78]
Labots, M.; van der Mijn, J.C.; Beekhof, R.; Piersma, S.R.; de Goeij-de Haas, R.R.; Pham, T.V.; Knol, J.C.; Dekker, H.; van Grieken, N.C.T.; Verheul, H.M.W.; Jiménez, C.R. Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection. J. Proteomics, 2017, 162, 99-107.
[http://dx.doi.org/10.1016/j.jprot.2017.04.014] [PMID: 28442448]
[79]
Tong, J.; Helmy, M.; Cavalli, F.M.; Jin, L.; St-Germain, J.; Karisch, R.; Taylor, P.; Minden, M.D.; Taylor, M.D.; Neel, B.G.; Bader, G.D.; Moran, M.F. Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome, and tyrosine-phosphatome in acute myeloid leukemia. Proteomics, 2017, 17(6)
[http://dx.doi.org/10.1002/pmic.201600361] [PMID: 28176486]
[80]
Mertins, P.; Qiao, J.W.; Patel, J.; Udeshi, N.D.; Clauser, K.R.; Mani, D.R.; Burgess, M.W.; Gillette, M.A.; Jaffe, J.D.; Carr, S.A. Integrated proteomic analysis of post-translational modifications by serial enrichment. Nat. Methods, 2013, 10(7), 634-637.
[http://dx.doi.org/10.1038/nmeth.2518] [PMID: 23749302]
[81]
Carlson, S.M.; Gozani, O. Emerging technologies to map the protein methylome. J. Mol. Biol., 2014, 426(20), 3350-3362.
[http://dx.doi.org/10.1016/j.jmb.2014.04.024] [PMID: 24805349]
[82]
Guo, A.; Gu, H.; Zhou, J.; Mulhern, D.; Wang, Y.; Lee, K.A.; Yang, V.; Aguiar, M.; Kornhauser, J.; Jia, X.; Ren, J.; Beausoleil, S.A.; Silva, J.C.; Vemulapalli, V.; Bedford, M.T.; Comb, M.J. Immunoaffinity enrichment and mass spectrometry analysis of protein methylation. Mol. Cell. Proteomics, 2014, 13(1), 372-387.
[http://dx.doi.org/10.1074/mcp.O113.027870] [PMID: 24129315]
[83]
Cao, X.J.; Arnaudo, A.M.; Garcia, B.A. Large-scale global identification of protein lysine methylation in vivo. Epigenetics, 2013, 8(5), 477-485.
[http://dx.doi.org/10.4161/epi.24547] [PMID: 23644510]
[84]
Cao, X.J.; Garcia, B.A. Global Proteomics Analysis of Protein Lysine Methylation. Curr. Protoc. Protein Sci., 2016, 86(24), 1-24.
[http://dx.doi.org/10.1002/cpps.16] [PMID: 27801517]
[85]
Carlson, S.M.; Moore, K.E.; Green, E.M.; Martín, G.M.; Gozani, O. Proteome-wide enrichment of proteins modified by lysine methylation. Nat. Protoc., 2014, 9(1), 37-50.
[http://dx.doi.org/10.1038/nprot.2013.164] [PMID: 24309976]
[86]
Chen, R.; Seebun, D.; Ye, M.; Zou, H.; Figeys, D. Site-specific characterization of cell membrane N-glycosylation with integrated hydrophilic interaction chromatography solid phase extraction and LC-MS/MS. J. Proteomics, 2014, 103, 194-203.
[http://dx.doi.org/10.1016/j.jprot.2014.03.040] [PMID: 24721674]
[87]
Mysling, S.; Palmisano, G.; Højrup, P.; Thaysen-Andersen, M. Utilizing ion-pairing hydrophilic interaction chromatography solid phase extraction for efficient glycopeptide enrichment in glycoproteomics. Anal. Chem., 2010, 82(13), 5598-5609.
[http://dx.doi.org/10.1021/ac100530w] [PMID: 20536156]
[88]
Li, X.; Jiang, J.; Zhao, X.; Zhao, Y.; Cao, Q.; Zhao, Q.; Han, H.; Wang, J.; Yu, Z.; Peng, B.; Ying, W.; Qian, X. In-depth analysis of secretome and N-glycosecretome of human hepatocellular carcinoma metastatic cell lines shed light on metastasis correlated proteins. Oncotarget, 2016, 7(16), 22031-22049.
[http://dx.doi.org/10.18632/oncotarget.8247] [PMID: 27014972]
[89]
Hoffmann, M.; Marx, K.; Reichl, U.; Wuhrer, M.; Rapp, E. Site-specific O-Glycosylation analysis of human blood plasma proteins. Mol. Cell. Proteomics, 2016, 15(2), 624-641.
[http://dx.doi.org/10.1074/mcp.M115.053546] [PMID: 26598643]
[90]
King, S.L.; Joshi, H.J.; Schjoldager, K.T.; Halim, A.; Madsen, T.D.; Dziegiel, M.H.; Woetmann, A.; Vakhrushev, S.Y.; Wandall, H.H. Characterizing the O-glycosylation landscape of human plasma, platelets, and endothelial cells. Blood Adv., 2017, 1(7), 429-442.
[http://dx.doi.org/10.1182/bloodadvances.2016002121] [PMID: 29296958]
[91]
Palmisano, G.; Lendal, S.E.; Engholm-Keller, K.; Leth-Larsen, R.; Parker, B.L.; Larsen, M.R. Selective enrichment of sialic acid-containing glycopeptides using titanium dioxide chromatography with analysis by HILIC and mass spectrometry. Nat. Protoc., 2010, 5(12), 1974-1982.
[http://dx.doi.org/10.1038/nprot.2010.167] [PMID: 21127490]
[92]
Zhu, J.; Wang, F.; Cheng, K.; Dong, J.; Sun, D.; Chen, R.; Wang, L.; Ye, M.; Zou, H. A simple integrated system for rapid analysis of sialic-acid-containing N-glycopeptides from human serum. Proteomics, 2013, 13(8), 1306-1313.
[http://dx.doi.org/10.1002/pmic.201200367] [PMID: 23335361]
[93]
Bengsch, F.; Tu, Z.; Tang, H.Y.; Zhu, H.; Speicher, D.W.; Zhang, R. Comprehensive analysis of the ubiquitinome during oncogene-induced senescence in human fibroblasts. Cell Cycle, 2015, 14(10), 1540-1547.
[http://dx.doi.org/10.1080/15384101.2015.1026492] [PMID: 25785348]
[94]
van der Wal, L.; Bezstarosti, K.; Sap, K.A.; Dekkers, D.H.W.; Rijkers, E.; Mientjes, E.; Elgersma, Y.; Demmers, J.A.A. Improvement of ubiquitylation site detection by Orbitrap mass spectrometry. J. Proteomics, 2018, 172, 49-56.
[http://dx.doi.org/10.1016/j.jprot.2017.10.014] [PMID: 29122726]
[95]
Casanovas, A.; Pinto-Llorente, R.; Carrascal, M.; Abian, J. Large-scale filter-aided sample preparation method for the analysis of the ubiquitinome. Anal. Chem., 2017, 89(7), 3840-3846.
[http://dx.doi.org/10.1021/acs.analchem.6b04804] [PMID: 28260372]
[96]
Mertins, P.; Tang, L.C.; Krug, K.; Clark, D.J.; Gritsenko, M.A.; Chen, L.; Clauser, K.R.; Clauss, T.R.; Shah, P.; Gillette, M.A.; Petyuk, V.A.; Thomas, S.N.; Mani, D.R.; Mundt, F.; Moore, R.J.; Hu, Y.; Zhao, R.; Schnaubelt, M.; Keshishian, H.; Monroe, M.E.; Zhang, Z.; Udeshi, N.D.; Mani, D.; Davies, S.R.; Townsend, R.R.; Chan, D.W.; Smith, R.D.; Zhang, H.; Liu, T.; Carr, S.A. Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry. Nat. Protoc., 2018, 13(7), 1632-1661.
[http://dx.doi.org/10.1038/s41596-018-0006-9] [PMID: 29988108]
[97]
Yu, H.; Diao, H.; Wang, C.; Lin, Y.; Yu, F.; Lu, H.; Xu, W.; Li, Z.; Shi, H.; Zhao, S.; Zhou, Y.; Zhang, Y. Acetylproteomic analysis reveals functional implications of lysine acetylation in human spermatozoa (sperm). Mol. Cell. Proteomics, 2015, 14(4), 1009-1023.
[http://dx.doi.org/10.1074/mcp.M114.041384] [PMID: 25680958]
[98]
Cheng, K.; Chen, R.; Seebun, D.; Ye, M.; Figeys, D.; Zou, H. Large-scale characterization of intact N-glycopeptides using an automated glycoproteomic method. J. Proteomics, 2014, 110, 145-154.
[http://dx.doi.org/10.1016/j.jprot.2014.08.006] [PMID: 25182382]
[99]
Larsen, S.C.; Sylvestersen, K.B.; Mund, A.; Lyon, D.; Mullari, M.; Madsen, M.V.; Daniel, J.A.; Jensen, L.J.; Nielsen, M.L. Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells. Sci. Signal., 2016, 9(443), rs9.
[http://dx.doi.org/10.1126/scisignal.aaf7329] [PMID: 27577262]
[100]
Palmisano, G.; Parker, B.L.; Engholm-Keller, K.; Lendal, S.E.; Kulej, K.; Schulz, M.; Schwämmle, V.; Graham, M.E.; Saxtorph, H.; Cordwell, S.J.; Larsen, M.R. A novel method for the simultaneous enrichment, identification, and quantification of phosphopeptides and sialylated glycopeptides applied to a temporal profile of mouse brain development. Mol. Cell. Proteomics, 2012, 11(11), 1191-1202.
[http://dx.doi.org/10.1074/mcp.M112.017509] [PMID: 22843994]
[101]
Melo-Braga, M.N.; Ibáñez-Vea, M.; Larsen, M.R.; Kulej, K. Comprehensive protocol to simultaneously study protein phosphorylation, acetylation, and N-linked sialylated glycosylation. Methods Mol. Biol., 2015, 1295, 275-292.
[http://dx.doi.org/10.1007/978-1-4939-2550-6_21] [PMID: 25820729]
[102]
Parker, B.L.; Shepherd, N.E.; Trefely, S.; Hoffman, N.J.; White, M.Y.; Engholm-Keller, K.; Hambly, B.D.; Larsen, M.R.; James, D.E.; Cordwell, S.J. Structural basis for phosphorylation and lysine acetylation cross-talk in a kinase motif associated with myocardial ischemia and cardioprotection. J. Biol. Chem., 2014, 289(37), 25890-25906.
[http://dx.doi.org/10.1074/jbc.M114.556035] [PMID: 25008320]
[103]
Grimes, M.; Hall, B.; Foltz, L.; Levy, T.; Rikova, K.; Gaiser, J.; Cook, W.; Smirnova, E.; Wheeler, T.; Clark, N.R.; Lachmann, A.; Zhang, B.; Hornbeck, P.; Ma’ayan, A.; Comb, M. Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks. Sci. Signal., 2018, 11(531)eaaq1087
[http://dx.doi.org/10.1126/scisignal.aaq1087] [PMID: 29789295]
[104]
White Iii, R.A.; Callister, S.J.; Moore, R.J.; Baker, E.S.; Jansson, J.K. The past, present and future of microbiome analyses. Nat. Protoc., 2016, 11, 2049.
[http://dx.doi.org/10.1038/nprot.2016.148]
[105]
Doll, S.; Burlingame, A.L. Mass spectrometry-based detection and assignment of protein posttranslational modifications. ACS Chem. Biol., 2015, 10(1), 63-71.
[http://dx.doi.org/10.1021/cb500904b] [PMID: 25541750]
[106]
Kolbowski, L.; Mendes, M.L.; Rappsilber, J. Optimizing the parameters governing the fragmentation of cross-linked peptides in a tribrid mass spectrometer. Anal. Chem., 2017, 89(10), 5311-5318.
[http://dx.doi.org/10.1021/acs.analchem.6b04935] [PMID: 28402676]
[107]
Cheng, L.C.; Tan, V.M.; Ganesan, S.; Drake, J.M. Integrating phosphoproteomics into the clinical management of prostate cancer. Clin. Transl. Med., 2017, 6(1), 9.
[http://dx.doi.org/10.1186/s40169-017-0138-5] [PMID: 28197968]
[108]
Hogrebe, A.; von Stechow, L.; Bekker-Jensen, D.B.; Weinert, B.T.; Kelstrup, C.D.; Olsen, J.V. Benchmarking common quantification strategies for large-scale phosphoproteomics. Nat. Commun., 2018, 9(1), 1045.
[http://dx.doi.org/10.1038/s41467-018-03309-6] [PMID: 29535314]
[109]
Yuan, Z.F.; Lin, S.; Molden, R.C.; Garcia, B.A. Evaluation of proteomic search engines for the analysis of histone modifications. J. Proteome Res., 2014, 13(10), 4470-4478.
[http://dx.doi.org/10.1021/pr5008015] [PMID: 25167464]
[110]
Bogdanow, B.; Zauber, H.; Selbach, M. Systematic errors in peptide and protein identification and quantification by modified peptides. Mol. Cell. Proteomics, 2016, 15(8), 2791-2801.
[http://dx.doi.org/10.1074/mcp.M115.055103] [PMID: 27215553]
[111]
Verheggen, K.; Raeder, H.; Berven, F.S.; Martens, L.; Barsnes, H.; Vaudel, M. Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows. Mass Spectrom. Rev., 2017. Epub ahead of print
[http://dx.doi.org/10.1002/mas.21543] [PMID: 28902424]
[112]
Knudsen, G.M.; Chalkley, R.J. The effect of using an inappropriate protein database for proteomic data analysis. PLoS One, 2011, 6(6)e20873
[http://dx.doi.org/10.1371/journal.pone.0020873] [PMID: 21695130]
[113]
Dorl, S.; Winkler, S.; Mechtler, K.; Dorfer, V. PhoStar: identifying tandem mass spectra of phosphorylated peptides before database search. J. Proteome Res., 2018, 17(1), 290-295.
[http://dx.doi.org/10.1021/acs.jproteome.7b00563] [PMID: 29057658]
[114]
Audagnotto, M.; Dal Peraro, M. Protein post-translational modifications: In silico prediction tools and molecular modeling. Comput. Struct. Biotechnol. J., 2017, 15, 307-319.
[http://dx.doi.org/10.1016/j.csbj.2017.03.004] [PMID: 28458782]
[115]
Li, F.; Li, C.; Wang, M.; Webb, G.I.; Zhang, Y.; Whisstock, J.C.; Song, J. GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome. Bioinformatics, 2015, 31(9), 1411-1419.
[http://dx.doi.org/10.1093/bioinformatics/btu852] [PMID: 25568279]
[116]
Gupta, R.; Brunak, S. Prediction of glycosylation across the human proteome and the correlation to protein function. Pac. Symp. Biocomput., 2002, •••, 310-322.
[PMID: 11928486]
[117]
Blom, N.; Gammeltoft, S.; Brunak, S. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol., 1999, 294(5), 1351-1362.
[http://dx.doi.org/10.1006/jmbi.1999.3310] [PMID: 10600390]
[118]
Pejaver, V.; Hsu, W.L.; Xin, F.; Dunker, A.K.; Uversky, V.N.; Radivojac, P. The structural and functional signatures of proteins that undergo multiple events of post-translational modification. Protein Sci., 2014, 23(8), 1077-1093.
[http://dx.doi.org/10.1002/pro.2494] [PMID: 24888500]
[119]
Huang, Y.; Xu, B.; Zhou, X.; Li, Y.; Lu, M.; Jiang, R.; Li, T. Systematic characterization and prediction of post-translational modification cross-talk. Mol. Cell. Proteomics, 2015, 14(3), 761-770.
[http://dx.doi.org/10.1074/mcp.M114.037994] [PMID: 25605461]
[120]
Dewhurst, H.M.; Choudhury, S.; Torres, M.P. Structural analysis of PTM Hotspots (SAPH-ire)--A quantitative informatics method enabling the discovery of novel regulatory elements in protein families. Mol. Cell. Proteomics, 2015, 14(8), 2285-2297.
[http://dx.doi.org/10.1074/mcp.M115.051177] [PMID: 26070665]
[121]
Torres, M.P.; Dewhurst, H.; Sundararaman, N. Proteome-wide structural analysis of PTM hotspots reveals regulatory elements predicted to impact biological function and disease. Mol. Cell. Proteomics, 2016, 15(11), 3513-3528.
[http://dx.doi.org/10.1074/mcp.M116.062331] [PMID: 27697855]
[122]
Li, G.X.H.; Vogel, C.; Choi, H. PTMscape: an open source tool to predict generic post-translational modifications and map modification crosstalk in protein domains and biological processes. Mol Omics, 2018, 14(3), 197-209.
[http://dx.doi.org/10.1039/C8MO00027A] [PMID: 29876573]
[123]
Vaudel, M.; Verheggen, K.; Csordas, A.; Raeder, H.; Berven, F.S.; Martens, L.; Vizcaíno, J.A.; Barsnes, H. Exploring the potential of public proteomics data. Proteomics, 2016, 16(2), 214-225.
[http://dx.doi.org/10.1002/pmic.201500295] [PMID: 26449181]
[124]
Lee, T.Y.; Huang, H.D.; Hung, J.H.; Huang, H.Y.; Yang, Y.S.; Wang, T.H. dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res., 2006, 34(Database issue), D622-D627.
[http://dx.doi.org/10.1093/nar/gkj083] [PMID: 16381945]
[125]
Hornbeck, P.V.; Kornhauser, J.M.; Tkachev, S.; Zhang, B.; Skrzypek, E.; Murray, B.; Latham, V.; Sullivan, M. PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res., 2012, 40(Database issue), D261-D270.
[http://dx.doi.org/10.1093/nar/gkr1122] [PMID: 22135298]
[126]
Pagel, O.; Loroch, S.; Sickmann, A.; Zahedi, R.P. Current strategies and findings in clinically relevant post-translational modification-specific proteomics. Expert Rev. Proteomics, 2015, 12(3), 235-253.
[http://dx.doi.org/10.1586/14789450.2015.1042867] [PMID: 25955281]
[127]
Beltrao, P.; Albanèse, V.; Kenner, L.R.; Swaney, D.L.; Burlingame, A.; Villén, J.; Lim, W.A.; Fraser, J.S.; Frydman, J.; Krogan, N.J. Systematic functional prioritization of protein posttranslational modifications. Cell, 2012, 150(2), 413-425.
[http://dx.doi.org/10.1016/j.cell.2012.05.036] [PMID: 22817900]
[128]
Minguez, P.; Letunic, I.; Parca, L.; Bork, P. PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. Nucleic Acids Res., 2013, 41(Database issue), D306-D311.
[PMID: 23193284]
[129]
Minguez, P.; Letunic, I.; Parca, L.; Garcia-Alonso, L.; Dopazo, J.; Huerta-Cepas, J.; Bork, P. PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. Nucleic Acids Res., 2015, 43(Database issue), D494-D502.
[http://dx.doi.org/10.1093/nar/gku1081] [PMID: 25361965]
[130]
Schwämmle, V.; Aspalter, C.M.; Sidoli, S.; Jensen, O.N. Large scale analysis of co-existing post-translational modifications in histone tails reveals global fine structure of cross-talk. Mol. Cell. Proteomics, 2014, 13(7), 1855-1865.
[http://dx.doi.org/10.1074/mcp.O113.036335] [PMID: 24741113]
[131]
Khare, S.P.; Habib, F.; Sharma, R.; Gadewal, N.; Gupta, S.; Galande, S. HIstome--a relational knowledgebase of human histone proteins and histone modifying enzymes. Nucleic Acids Res., 2012, 40(Database issue), D337-D342.
[http://dx.doi.org/10.1093/nar/gkr1125] [PMID: 22140112]
[132]
Li, H.; Xing, X.; Ding, G.; Li, Q.; Wang, C.; Xie, L.; Zeng, R.; Li, Y. SysPTM: a systematic resource for proteomic research on post-translational modifications. Mol. Cell. Proteomics, 2009, 8(8), 1839-1849.
[http://dx.doi.org/10.1074/mcp.M900030-MCP200] [PMID: 19366988]
[133]
Li, J.; Jia, J.; Li, H.; Yu, J.; Sun, H.; He, Y.; Lv, D.; Yang, X.; Glocker, M.O.; Ma, L.; Yang, J.; Li, L.; Li, W.; Zhang, G.; Liu, Q.; Li, Y.; Xie, L. SysPTM 2.0: an updated systematic resource for post-translational modification. Database (Oxford), 2014, 2014bau025
[http://dx.doi.org/10.1093/database/bau025] [PMID: 24705204]
[134]
Nahnsen, S.; Sachsenberg, T.; Kohlbacher, O. PTMeta: increasing identification rates of modified peptides using modification prescanning and meta-analysis. Proteomics, 2013, 13(6), 1042-1051.
[http://dx.doi.org/10.1002/pmic.201200315] [PMID: 23335442]
[135]
Huang, X.; Huang, L.; Peng, H.; Guru, A.; Xue, W.; Hong, S.Y.; Liu, M.; Sharma, S.; Fu, K.; Caprez, A.P.; Swanson, D.R.; Zhang, Z.; Ding, S.J. ISPTM: an iterative search algorithm for systematic identification of post-translational modifications from complex proteome mixtures. J. Proteome Res., 2013, 12(9), 3831-3842.
[http://dx.doi.org/10.1021/pr4003883] [PMID: 23919725]
[136]
Bern, M.; Kil, Y.J.; Becker, C. Byonic: advanced peptide and protein identification software. Curr. Protoc. Bioinformatics, 2012, 13.
[http://dx.doi.org/10.1002/0471250953.bi1320s40] [PMID: 23255153]
[137]
Vermeulen, M.; Eberl, H.C.; Matarese, F.; Marks, H.; Denissov, S.; Butter, F.; Lee, K.K.; Olsen, J.V.; Hyman, A.A.; Stunnenberg, H.G.; Mann, M. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell, 2010, 142(6), 967-980.
[http://dx.doi.org/10.1016/j.cell.2010.08.020] [PMID: 20850016]
[138]
Wagner, S. A.; Beli, P.; Weinert, B. T.; Nielsen, M. L.; Cox, J.; Mann, M.; Choudhary, C. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol. Cell Proteomics, 2011, 10(10), M111.013284.
[http://dx.doi.org/10.1074/mcp.M111.013284] [PMID: PMC3205876]
[139]
Levy, D.; Kuo, A.J.; Chang, Y.; Schaefer, U.; Kitson, C.; Cheung, P.; Espejo, A.; Zee, B.M.; Liu, C.L.; Tangsombatvisit, S.; Tennen, R.I.; Kuo, A.Y.; Tanjing, S.; Cheung, R.; Chua, K.F.; Utz, P.J.; Shi, X.; Prinjha, R.K.; Lee, K.; Garcia, B.A.; Bedford, M.T.; Tarakhovsky, A.; Cheng, X.; Gozani, O. Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling. Nat. Immunol., 2011, 12(1), 29-36.
[http://dx.doi.org/10.1038/ni.1968] [PMID: 21131967]
[140]
Leney, A.C.; El Atmioui, D.; Wu, W.; Ovaa, H.; Heck, A.J.R. Elucidating crosstalk mechanisms between phosphorylation and O-GlcNAcylation. Proc. Natl. Acad. Sci. USA, 2017, 114(35), E7255-E7261.
[http://dx.doi.org/10.1073/pnas.1620529114] [PMID: 28808029]
[141]
Cox, J.; Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol., 2008, 26(12), 1367-1372.
[http://dx.doi.org/10.1038/nbt.1511] [PMID: 19029910]
[142]
Wang, T.Y.; Chai, Y.R.; Jia, Y.L.; Gao, J.H.; Peng, X.J.; Han, H.F. Crosstalk among the proteome, lysine phosphorylation, and acetylation in romidepsin-treated colon cancer cells. Oncotarget, 2016, 7(33), 53471-53501.
[http://dx.doi.org/10.18632/oncotarget.10840] [PMID: 27472459]
[143]
Zhu, D.; Hou, L.; Hu, B.; Zhao, H.; Sun, J.; Wang, J.; Meng, X. Crosstalk among proteome, acetylome and succinylome in colon cancer HCT116 cell treated with sodium dichloroacetate. Sci. Rep., 2016, 6, 37478.
[http://dx.doi.org/10.1038/srep37478] [PMID: 27874079]
[144]
Schwämmle, V.; Sidoli, S.; Ruminowicz, C.; Wu, X.; Lee, C.F.; Helin, K.; Jensen, O.N. Systems level analysis of histone H3 Post-translational modifications (PTMs) reveals features of PTM crosstalk in chromatin regulation. Mol. Cell. Proteomics, 2016, 15(8), 2715-2729.
[http://dx.doi.org/10.1074/mcp.M115.054460] [PMID: 27302890]
[145]
Nguyen, L.K.; Kolch, W.; Kholodenko, B.N. When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling. Cell Commun. Signal., 2013, 11, 52.
[http://dx.doi.org/10.1186/1478-811X-11-52] [PMID: 23902637]
[146]
Simithy, J.; Sidoli, S.; Garcia, B.A. Integrating proteomics and targeted metabolomics to understand global changes in histone modifications. Proteomics, 2018, 18(18)e1700309
[http://dx.doi.org/10.1002/pmic.201700309] [PMID: 29512899]
[147]
Wouters, B.J.; Delwel, R. Epigenetics and approaches to targeted epigenetic therapy in acute myeloid leukemia. Blood, 2016, 127(1), 42-52.
[http://dx.doi.org/10.1182/blood-2015-07-604512] [PMID: 26660432]
[148]
Izutsu, K.; Kurokawa, M.; Imai, Y.; Maki, K.; Mitani, K.; Hirai, H. The corepressor CtBP interacts with Evi-1 to repress transforming growth factor beta signaling. Blood, 2001, 97(9), 2815-2822.
[http://dx.doi.org/10.1182/blood.V97.9.2815] [PMID: 11313276]
[149]
Senyuk, V.; Chakraborty, S.; Mikhail, F.M.; Zhao, R.; Chi, Y.; Nucifora, G. The leukemia-associated transcription repressor AML1/MDS1/EVI1 requires CtBP to induce abnormal growth and differentiation of murine hematopoietic cells. Oncogene, 2002, 21(20), 3232-3240.
[http://dx.doi.org/10.1038/sj.onc.1205436] [PMID: 12082639]
[150]
Tsai, C.T.; So, C.W. Epigenetic therapies by targeting aberrant histone methylome in AML: molecular mechanisms, current preclinical and clinical development. Oncogene, 2017, 36(13), 1753-1759.
[http://dx.doi.org/10.1038/onc.2016.315] [PMID: 27593928]
[151]
Gallipoli, P.; Giotopoulos, G.; Huntly, B.J. Epigenetic regulators as promising therapeutic targets in acute myeloid leukemia. Ther. Adv. Hematol., 2015, 6(3), 103-119.
[http://dx.doi.org/10.1177/2040620715577614] [PMID: 26137202]
[152]
Stein, E.M.; Tallman, M.S. Emerging therapeutic drugs for AML. Blood, 2016, 127(1), 71-78.
[http://dx.doi.org/10.1182/blood-2015-07-604538] [PMID: 26660428]
[153]
Walasek, A. The new perspectives of targeted therapy in acute myeloid leukemia. Adv. Clin. Exp. Med., 2019, 28(2), 271-276.
[http://dx.doi.org/10.17219/acem/81610] [PMID: 30141284]
[154]
Gu, H.; Ren, J.M.; Jia, X.; Levy, T.; Rikova, K.; Yang, V.; Lee, K.A.; Stokes, M.P.; Silva, J.C. Quantitative profiling of post-translational modifications by immunoaffinity enrichment and lc-ms/ms in cancer serum without immunodepletion. Mol. Cell. Proteomics, 2016, 15(2), 692-702.
[http://dx.doi.org/10.1074/mcp.O115.052266] [PMID: 26635363]
[155]
Murray-Stewart, T.; Woster, P.M.; Casero, R.A., Jr The re-expression of the epigenetically silenced e-cadherin gene by a polyamine analogue lysine-specific demethylase-1 (LSD1) inhibitor in human acute myeloid leukemia cell lines. Amino Acids, 2014, 46(3), 585-594.
[http://dx.doi.org/10.1007/s00726-013-1485-1] [PMID: 23508577]
[156]
Angelov, D.; Bondarenko, V.A.; Almagro, S.; Menoni, H.; Mongélard, F.; Hans, F.; Mietton, F.; Studitsky, V.M.; Hamiche, A.; Dimitrov, S.; Bouvet, P. Nucleolin is a histone chaperone with FACT-like activity and assists remodeling of nucleosomes. EMBO J., 2006, 25(8), 1669-1679.
[http://dx.doi.org/10.1038/sj.emboj.7601046] [PMID: 16601700]
[157]
Hein, N.; Cameron, D.P.; Hannan, K.M.; Nguyen, N.N.; Fong, C.Y.; Sornkom, J.; Wall, M.; Pavy, M.; Cullinane, C.; Diesch, J.; Devlin, J.R.; George, A.J.; Sanij, E.; Quin, J.; Poortinga, G.; Verbrugge, I.; Baker, A.; Drygin, D.; Harrison, S.J.; Rozario, J.D.; Powell, J.A.; Pitson, S.M.; Zuber, J.; Johnstone, R.W.; Dawson, M.A.; Guthridge, M.A.; Wei, A.; McArthur, G.A.; Pearson, R.B.; Hannan, R.D. Inhibition of Pol I transcription treats murine and human AML by targeting the leukemia-initiating cell population. Blood, 2017, 129(21), 2882-2895.
[http://dx.doi.org/10.1182/blood-2016-05-718171] [PMID: 28283481]

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