Quantitative Analysis of Global Proteome and Lysine Acetylome Reveal the Differential Impacts of VPA and SAHA on HL60 Cells

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Zhu, Xiaoyu ^a   Liu, Xin ^a   Cheng, Zhongyi ^b   Zhu, Jun ^c   Xu, Lei ^a   Wang, Fengsong ^a   Qi, Wulin ^c   Yan, Jiawei ^a   Liu, Ning ^a   Sun, Zimin ^a   Liu, Huilan ^a   Peng, Xiaojun ^c   Hao, Yingchan ^a   Zheng, Nan ^a   Wu, Quan ^a  

^a ANHUI MEDICAL UNIVERSITY   (China)

^b TONGJI UNIVERSITY   (China)

^c Jingjie PTM BioLab (Hangzhou) Co Ltd   (China)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROXAMIC ACID; LYSINE; PROTEOME; VALPROIC ACID; VORINOSTAT;

ACETYLATION; ACUTE MYELOID LEUKEMIA; AMINO ACID SEQUENCE; BIOLOGY; CLUSTER ANALYSIS; HL-60 CELL LINE; HUMAN; METABOLISM; POSITION WEIGHT MATRIX; PROCEDURES; PROTEIN ANALYSIS; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEOMICS;

ACETYLATION; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; HL-60 CELLS; HUMANS; HYDROXAMIC ACIDS; LEUKEMIA, MYELOID, ACUTE; LYSINE; POSITION-SPECIFIC SCORING MATRICES; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; PROTEOME; PROTEOMICS; VALPROIC ACID;

EID: 84956617004     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep19926     Document Type: Article

References (54)

1. Lowenberg, B., Downing, J. R., Burnett, A. Acute myeloid leukemia. N. Engl. J. Med. 341, 1051-1062 (1999).
2. Estey, E., Döhner, H. Acute myeloid leukaemia. The Lancet 368, 1894-1907 (2006).
3. Minderman, H., Zhou, Y., O'Loughlin, K. L., Baer, M. R. Bortezomib activity and in vitro interactions with anthracyclines and cytarabine in acute myeloid leukemia cells are independent of multidrug resistance mechanisms and p53 status. Cancer Chemother. Pharmacol. 60, 245-255 (2007).
4. Kantarjian, H. et al. Intensive chemotherapy does not benefit most older patients (age 70 years or older) with acute myeloid leukemia. Blood 116, 4422-4429 (2010).
5. Kantarjian, H. et al. Results of intensive chemotherapy in 998 patients age 65 years or older with acute myeloid leukemia or high-risk myelodysplastic syndrome: predictive prognostic models for outcome. Cancer 106, 1090-1098 (2006).
6. De Ruijter, A., Van Gennip, A., Caron, H., Kemp, S., van Kuilenburg, A. Histone deacetylases (HDACs): characterization of the classical HDAC family. Biochem. J 370, 737-749 (2003).
7. Marks, P. et al. Histone deacetylases and cancer: causes and therapies. Nat. Rev. Cancer 1, 194-202 (2001).
8. Minucci, S., Pelicci, P. G. Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. Nat. Rev. Cancer 6, 38-51 (2006).
9. Arrowsmith, C. H., Bountra, C., Fish, P. V., Lee, K., Schapira, M. Epigenetic protein families: a new frontier for drug discovery. Nat. Rev. Drug Discov. 11, 384-400 (2012).
10. Falkenberg, K. J., Johnstone, R. W. Histone deacetylases and their inhibitors in cancer, neurological diseases and immune disorders. Nat. Rev. Drug Discov. 13, 673-691 (2014).
11. Marks, P. A. et al. Histone deacetylases and cancer: Causes and therapies. Nat. Rev. Cancer 1, 194-202 (2001).
12. Komatsu, N. et al. SAHA, a HDAC inhibitor, has profound anti-growth activity against non-small cell lung cancer cells. Oncol. Rep. 15, 187-191 (2006).
13. Wu, Q. et al. Suberoylanilide hydroxamic acid treatment reveals crosstalks among proteome, ubiquitylome and acetylome in nonsmall cell lung cancer A549 cell line. Sci. Rep. 5, 9520 (2015).
14. Munster, P. N. et al. The histone deacetylase inhibitor suberoylanilide hydroxamic acid induces differentiation of human breast cancer cells. Cancer Res. 61, 8492-8497 (2001).
15. Konstantinopoulos, P. A., Wilson, A. J., Saskowski, J., Wass, E., Khabele, D. Suberoylanilide hydroxamic acid (SAHA) enhances olaparib activity by targeting homologous recombination DNA repair in ovarian cancer. Gynecol. Oncol. 133, 599-606 (2014).
16. Olsen, E. A. et al. Phase IIB multicenter trial of vorinostat in patients with persistent, progressive, or treatment refractory cutaneous T-cell lymphoma. J. Clin. Oncol. 25, 3109-3115 (2007).
17. Nimmanapalli, R., Fuino, L., Stobaugh, C., Richon, V., Bhalla, K. Cotreatment with the histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA) enhances imatinib-induced apoptosis of Bcr-Abl-positive human acute leukemia cells. Blood 101, 3236-3239 (2003).
18. Sakajiri, S. et al. Histone deacetylase inhibitors profoundly decrease proliferation of human lymphoid cancer cell lines. Exp. Hematol. 33, 53-61 (2005).
19. Gottlicher, M. et al. Valproic acid defines a novel class of HDAC inhibitors inducing differentiation of transformed cells. Embo J. 20, 6969-6978 (2001).
20. Garcia-Manero, G. et al. Phase 1/2 study of the combination of 5-aza-2 '-deoxycytidine with valproic acid in patients with leukemia. Blood 108, 3271-3279 (2006).
21. Kuendgen, A. et al. Treatment of myelodysplastic syndromes with valproic acid alone or in combination with all-trans retinoic acid. Blood 104, 1266-1269 (2004).
22. Blum, W. et al. Phase I study of decitabine alone or in combination with valproic acid in acute myeloid leukemia. J. Clin. Oncol. 25, 3884-3891 (2007).
23. Choudhary, C. et al. Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions. Science 325, 834-840 (2009).
24. Chi, T. H. et al. Reciprocal regulation of CD4/CD8 expression by SWI/SNF-like BAF complexes. Nature 418, 195-199 (2002).
25. Martens, J. A., Winston, F. Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Curr. Opin. Genet. Dev. 13, 136-142 (2003).
26. Roberts, C. W. M., Orkin, S. H. The SWI/SNF complex-Chromatin and cancer. Nat. Rev. Cancer 4, 133-142 (2004).
27. Reisman, D., Glaros, S., Thompson, E. A. The SWI/SNF complex and cancer. Oncogene 28, 1653-1668 (2009).
28. Borner, C., Monney, L. Apoptosis without caspases: an inefficient molecular guillotine Cell Death Differ. 6, 497-507 (1999).
29. Kawagoe, R., Kawagoe, H., Sano, K. Valproic acid induces apoptosis in human leukemia cells by stimulating both caspasedependent and-independent apoptotic signaling pathways. Leukemia Res. 26, 495-502 (2002).
30. Insinga, A. et al. Inhibitors of histone deacetylases induce tumor-selective apoptosis through activation of the death receptor pathway. Nat. Med. 11, 71-76 (2005).
31. West, A. C. et al. An Intact Immune System Is Required for the Anticancer Activities of Histone Deacetylase Inhibitors. Cancer Res. 73, 7265-7276 (2013).
32. Bolden, J. E., Peart, M. J., Johnstone, R. W. Anticancer activities of histone deacetylase inhibitors. Nat. Rev. Drug Discov. 5, 769-784 (2006).
33. Lozano, A. C., Abe, N., Liu, Y., Rosset, S. Grouped graphical Granger modeling for gene expression regulatory networks discovery. Bioinformatics 25, i110-i118 (2009).
34. Chen, M. Y. et al. Decitabine and suberoylanilide hydroxamic acid (SAHA) inhibit growth of ovarian cancer cell lines and xenografts while inducing expression of imprinted tumor suppressor genes, apoptosis, G2/M arrest, and autophagy. Cancer 117, 4424-4438 (2011).
35. Yamamoto, S. et al. Suberoylanilide hydroxamic acid (SAHA) induces apoptosis or autophagy-associated cell death in chondrosarcoma cell lines. Anticancer Res. 28, 1585-1591 (2008).
36. Kumagai, T. et al. Histone deacetylase inhibitor, suberoylanilide hydroxamic acid (Vorinostat, SAHA) profoundly inhibits the growth of human pancreatic cancer cells. Int. J. Cancer 121, 656-665 (2007).
37. Walmod, P. S., Skladchikova, G., Kawa, A., Berezin, V., Bock, E. Antiepileptic teratogen valproic acid (VPA) modulates organisation and dynamics of the actin cytoskeleton. Cell Motil. Cytoskel. 42, 241-255 (1999).
38. Guan, K. L., Xiong, Y. Regulation of intermediary metabolism by protein acetylation. Trends Biochem. Sci. 36, 108-116 (2011).
39. Armeanu, S. et al. Natural killer cell-mediated lysis of hepatoma cells via specific induction of NKG2D Ligands by the histone deacetylase inhibitor sodium valproate. Cancer Res. 65, 6321-6329 (2005).
40. Skov, S. et al. Cancer cells become susceptible to natural killer cell killing after exposure to histone deacetylase inhibitors due to glycogen synthase kinase-3-dependent expression of MHC class I-related chain A and B. Cancer Res. 65, 11136-11145 (2005).
41. Reddy, P. et al. Histone deacetylase inhibitor suberoylanilide hydroxamic acid reduces acute graft-versus-host disease and preserves graft-versus-leukemia effect. P. Natl. Acad. Sci. USA. 101, 3921-3926 (2004).
42. Schölz, C. et al. Acetylation site specificities of lysine deacetylase inhibitors in human cells. Nat. Biotechnol. 33, 415-423 (2015).
43. Ong, S. E. et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386 (2002).
44. Li, X. L. et al. Systematic Identification of the Lysine Succinylation in the Protozoan Parasite Toxoplasma gondii. J. Proteome Res. 13, 6087-6095 (2014).
45. Pan, J. Y. et al. Systematic Analysis of the Lysine Acetylome in Vibrio parahemolyticus. J. Proteome Res. 13, 3294-3302 (2014).
46. Krokhin, O. V. et al. An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: its application to protein peptide mapping by off-line HPLC-MALDI MS. Mol. Cell. Proteomics 3, 908-919 (2004).
47. Chen, Y. et al. Quantitative Acetylome Analysis Reveals the Roles of SIRT1 in Regulating Diverse Substrates and Cellular Pathways. Mol. Cell. Proteomics 11, 1048-1062 (2012).
48. Xiong, L., Wang, Y. S. Quantitative Proteomic Analysis Reveals the Perturbation of Multiple Cellular Pathways in HL-60 Cells Induced by Arsenite Treatment. J. Proteome Res. 9, 1129-1137 (2010).
49. Hulsegge, I., Kommadath, A., Smits, M. A. Globaltest and GOEAST: two different approaches for Gene Ontology analysis. BMC Proc. 3 Suppl 4, S10 (2009).
50. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C., Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182-185 (2007).
51. Horton, P. et al. WoLF PSORT: protein localization predictor. Nucleic Acids Res. 35, W585-587 (2007).
52. Chou, M. F., Schwartz, D. Biological sequence motif discovery using motif-x. Curr. Protoc. Bioinformatics Chapter 13, Unit 13 15-24 (2011).
53. Huang, D. W. et al. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 35, W169-W175 (2007).
54. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (2003).