Identification of proteins related to epigenetic regulation in the malignant transformation of aberrant karyotypic human embryonic stem cells by quantitative proteomics

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Sun, Yi ^a,b,c   Yang, Yixuan ^d   Zeng, Sicong ^a   Tan, Yueqiu ^a,b,c   Lu, Guangxiu ^a,b   Lin, Ge ^a,b,c  

^a CENTRAL SOUTH UNIVERSITY   (China)

^b National Engineering and Research Center of Human Stem Cells   (China)

^c BEIJING HOSPITAL   (China)

^d CHONGQING MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BETA ACTIN; CELL PROTEIN; DNA METHYLTRANSFERASE 1; DNA METHYLTRANSFERASE 3B; HIGH MOBILITY GROUP B1 PROTEIN; HISTONE DEACETYLASE 2; HISTONE H3; HISTONE H4; INITIATION FACTOR 3; MYC PROTEIN; OCTAMER TRANSCRIPTION FACTOR 4; PEROXIREDOXIN 1; PROTEIN ADSS; PROTEIN ARPC3; PROTEIN BGN; PROTEIN CCND1; PROTEIN CTNNB1; PROTEIN H3F3B; PROTEIN KPNB1; PROTEIN LMNA; PROTEIN NES; PROTEIN RAB1A; PROTEIN RAP2B; PROTEIN SUB1; PROTEIN THY1; PROTEIN VIN; PROTEIN YWHAE; SMAD2 PROTEIN; UNCLASSIFIED DRUG; VOLTAGE DEPENDENT ANION CHANNEL 2;

ARTICLE; CHROMOSOME ABERRATION; CONTROLLED STUDY; EMBRYONIC STEM CELL; EPIGENETICS; GENETIC REGULATION; HUMAN; HUMAN CELL; KARYOTYPE; MALIGNANT TRANSFORMATION; MOLECULAR BIOLOGY; PROTEIN DETERMINATION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEOMICS; QUANTITATIVE ANALYSIS; TANDEM MASS SPECTROMETRY; TUMOR GROWTH;

ANIMALS; BLOTTING, WESTERN; CELL LINE; CELL TRANSFORMATION, NEOPLASTIC; CLUSTER ANALYSIS; DNA COPY NUMBER VARIATIONS; EMBRYONIC STEM CELLS; EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; HUMANS; ISOTOPE LABELING; KARYOTYPING; MASS SPECTROMETRY; MICE; MOLECULAR SEQUENCE ANNOTATION; NEOPLASM PROTEINS; PROTEOME; PROTEOMICS; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; TRANSCRIPTOME;

EID: 84898443294     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0085823     Document Type: Article

References (60)

1. Draper JS, Smith K, Gokhale P, Moore HD, Maltby E, et al. (2004) Recurrent gain of chromosomes 17q and 12 in cultured human embryonic stem cells. Nat Biotechnol 22: 53-54. (Pubitemid 38057956)
2. Maitra A, Arking DE, Shivapurkar N, Ikeda M, Stastny V, et al. (2005) Genomic alterations in cultured human embryonic stem cells. Nat Genet 37: 1099-1103. (Pubitemid 41486662)
3. Baker DE, Harrison NJ, Maltby E, Smith K, Moore HD, et al. (2007) Adaptation to culture of human embryonic stem cells and oncogenesis in vivo. Nat Biotechnol 25: 207-215. (Pubitemid 46227120)
4. Lefort N, Feyeux M, Bas C, Feraud O, Bennaceur-Griscelli A, et al. (2008) Human embryonic stem cells reveal recurrent genomic instability at 20q11.21. Nat Biotechnol 26: 1364-1366.
5. Narva E, Autio R, Rahkonen N, Kong L, Harrison N, et al. (2010) High-resolution DNA analysis of human embryonic stem cell lines reveals cultureinduced copy number changes and loss of heterozygosity. Nat Biotechnol 28: 371-377.
6. Amps K, Andrews PW, Anyfantis G, Armstrong L, Avery S, et al. (2011) Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol 29: 1132-1144.
7. Laurent LC, Ulitsky I, Slavin I, Tran H, Schork A, et al. (2011) Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture. Cell Stem Cell 8: 106-118.
8. Yang S, Lin G, Tan YQ, Zhou D, Deng LY, et al. (2008) Tumor progression of culture-adapted human embryonic stem cells during long-term culture. Genes Chromosomes Cancer 47: 665-679. (Pubitemid 351847580)
9. Yang S, Lin G, Tan YQ, Deng LY, Yuan D, et al. (2010) Differences between karyotypically normal and abnormal human embryonic stem cells. Cell Prolif 43: 195-206.
10. Mantel C, Guo Y, Lee MR, Kim MK, Han MK, et al. (2007) Checkpoint-apoptosis uncoupling in human and mouse embryonic stem cells: a source of karyotpic instability. Blood 109: 4518-4527. (Pubitemid 46743423)
11. Rodriguez-Jimenez FJ, Moreno-Manzano V, Lucas-Dominguez R, Sanchez- Puelles JM (2008) Hypoxia causes downregulation of mismatch repair system and genomic instability in stem cells. Stem Cells 26: 2052-2062.
12. Macia A, Munoz-Lopez M, Cortes JL, Hastings RK, Morell S, et al. (2011) Epigenetic control of retrotransposon expression in human embryonic stem cells. Mol Cell Biol 31: 300-316.
13. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al. (2007) Genomewide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560. (Pubitemid 47206934)
14. Vastenhouw NL, Zhang Y, Woods IG, Imam F, Regev A, et al. (2010) Chromatin signature of embryonic pluripotency is established during genome activation. Nature 464: 922-926.
15. Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, et al. (2010) Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6: 479-491.
16. Van Hoof D, Passier R, Ward-Van Oostwaard D, Pinkse MW, Heck AJ, et al. (2006) A quest for human and mouse embryonic stem cell-specific proteins. Mol Cell Proteomics 5: 1261-1273. (Pubitemid 44103397)
17. Dormeyer W, van Hoof D, Braam SR, Heck AJ, Mummery CL, et al. (2008) Plasma membrane proteomics of human embryonic stem cells and human embryonal carcinoma cells. J Proteome Res 7: 2936-2951.
18. Chaerkady R, Kerr CL, Kandasamy K, Marimuthu A, Gearhart JD, et al. (2010) Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics 10: 1359-1373.
19. Gerwe BA, Angel PM, West FD, Hasneen K, Young A, et al. (2011) Membrane proteomic signatures of karyotypically normal and abnormal human embryonic stem cell lines and derivatives. Proteomics 11: 2515-2527.
20. Xie CQ, Lin G, Luo KL, Luo SW, Lu GX (2004) Newly expressed proteins of mouse embryonic fibroblasts irradiated to be inactive. Biochem Biophys Res Commun 315: 581-588. (Pubitemid 38229383)
21. O'Brien RN, Shen Z, Tachikawa K, Lee PA, Briggs SP (2010) Quantitative proteome analysis of pluripotent cells by iTRAQ mass tagging reveals post-transcriptional regulation of proteins required for ES cell self-renewal. Mol Cell Proteomics 9: 2238-2251.
22. Yang Y, Lim SK, Choong LY, Lee H, Chen Y, et al. (2010) Cathepsin S mediates gastric cancer cell migration and invasion via a putative network of metastasis-associated proteins. J Proteome Res 9: 4767-4778.
23. Yang Y, Toy W, Choong LY, Hou P, Ashktorab H, et al. (2012) Discovery of SLC3A2 cell membrane protein as a potential gastric cancer biomarker: implications in molecular imaging. J Proteome Res 11: 5736-5747.
24. Papachristou EK, Roumeliotis TI, Chrysagi A, Trigoni C, Charvalos E, et al. (2013) The shotgun proteomic study of the human ThinPrep cervical smear using iTRAQ Mass-Tagging and 2D LC-FT-Orbitrap-MS: The detection of the human papillomavirus at the protein level. J Proteome Res 12: 2078-89.
25. Andrews PW, Damjanov I, Simon D, Banting GS, Carlin C, et al. (1984) Pluripotent embryonal carcinoma clones derived from the human teratocarcinoma cell line Tera-2. Differentiation in vivo and in vitro. Lab Invest 50: 147-162. (Pubitemid 14199076)
26. Lin G, Xie Y, Ouyang Q, Qian X, Xie P, et al. (2009) HLA-matching potential of an established human embryonic stem cell bank in China. Cell Stem Cell 5: 461-465.
27. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(2Delta Delta C(T)) Method. Methods 25: 402-408. (Pubitemid 34164012)
28. Sun Y, Yi H, Zhang PF, Li MY, Li C, et al. (2007) Identification of differential proteins in nasopharyngeal carcinoma cells with p53 silence by proteome analysis. FEBS Lett 581: 131-139. (Pubitemid 44960291)
29. Miller FJ, Rosenfeldt FL, Zhang C, Linnane AW, Nagley P (2003) Precise determination of mitochondrial DNA copy number in human skeletal and cardiac muscle by a PCR-based assay: Lack of change of copy number with age. Nucleic Acid Res 31: e61.
30. Shaffer LG, McGowan-Jordan J, Schmid M (2013) ISCN(2013): An International System for Human Cytogenetic Nomenclature(2013). S Karger Ag.
31. Hack CJ (2004) Integrated transcriptome and proteome data: the challenges ahead. Brief Funct Genomic Proteomic 3: 212-219.
32. Fathi A, Pakzad M, Taei A, Brink TC, Pirhaji L, et al. (2009) Comparative proteome and transcriptome analyses of embryonic stem cells during embryoid body-based differentiation. Proteomics 9: 4859-4870.
33. Wang D, Jensen R, Gendeh G, Williams K, Pallavicini MG (2004) Proteome and transcriptome analysis of retinoic acid-induced differentiation of human acute promyelocytic leukemia cells, NB4. J Proteome Res 3: 627-635. (Pubitemid 39207369)
34. Zheng PZ, Wang KK, Zhang QY, Huang QH, Du YZ, et al. (2005) Systems analysis of transcriptome and proteome in retinoic acid/arsenic trioxide-induced cell differentiation/apoptosis of promyelocytic leukemia. Proc Natl Acad Sci U S A 102: 7653-7658.
35. Lorenz P, Ruschpler P, Koczan D, Stiehl P, Thiesen HJ (2003) From transcriptome to proteome: differentially expressed proteins identified in synovial tissue of patients suffering from rheumatoid arthritis and osteoarthritis by an initial screen with a panel of 791 antibodies. Proteomics 3: 991-1002. (Pubitemid 36801687)
36. Asplund A, Edqvist PH, Schwenk JM, Ponten F (2012) Antibodies for profiling the human proteome-The Human Protein Atlas as a resource for cancer research. Proteomics 12: 2067-2077.
37. Gu Y, Yang P, Shao Q, Liu X, Xia S, et al. (2013) Investigation of the expression patterns and correlation of DNA methyltransferases and class I histone deacetylases in ovarian cancer tissues. Oncol Lett 5: 452-458.
38. Martens-de Kemp SR, Nagel R, Stigter-van Walsum M, van der Meulen IH, van Beusechem VW, et al. (2013) Functional Genetic Screens Identify Genes Essential for Tumor Cell Survival in Head-and-Neck and Lung Cancer. Clin Cancer Res 19: 1994-2003.
39. Zhang X, He Y, Lee KH, Dubois W, Li Z, et al. (2013) Rap2b, a novel p53 target, regulates p53-mediated pro-survival function. Cell Cycle 12: 1279-1291.
40. Turner-Ivey B, Manevich Y, Schulte J, Kistner-Griffin E, Jezierska-Drutel A, et al. (2013) Role for Prdx1 as a specific sensor in redox-regulated senescence in breast cancer. Oncogene doi: 10.1038/onc.2012.624.
41. Nishimura Y, Komatsu S, Ichikawa D, Nagata H, Hirajima S, et al. (2013) Overexpression of YWHAZ relates to tumor cell proliferation and malignant outcome of gastric carcinoma. Br J Cancer 108: 1324-1331.
42. Lee KK, Workman JL (2007) Histone acetyltransferase complexes: one size doesn't fit all. Nat Rev Mol Cell Biol 8: 284-295. (Pubitemid 46474661)
43. LeBoeuf M, Terrell A, Trivedi S, Sinha S, Epstein JA, et al. (2010) Hdac1 and Hdac2 act redundantly to control p63 and p53 functions in epidermal progenitor cells. Dev Cell 19: 807-818.
44. Zhou D, Liu T, Zhou X, Lu G (2009) Three key variables involved in feeder preparation for the maintenance of human embryonic stem cells. Cell Biol Int 33: 796-800.
45. Aranda P, Agirre X, Ballestar E, Andreu EJ, Román-Gómez J, et al. (2009) Epigenetic signatures associated with different levels of differentiation potential in human stem cells. PLoS One 4: e7809.
46. Hoffman LM, Carpenter MK (2005) Characterization and culture of human embryonic stem cells. Nat Biotechnol 23: 699-708. (Pubitemid 41716360)
47. Guo T, Gan CS, Zhang H, Zhu Y, Kon OL, et al. (2008) Hybridization of pulsed-Q dissociation and collision-activated dissociation in linear ion trap mass spectrometer for iTRAQ quantitation. J Proteome Res 7: 4831-4840.
48. Pierce A, Unwin RD, Evans CA, Griffiths S, Carney L, et al. (2008) Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases. Mol Cell Proteomics 7: 853-863. (Pubitemid 351737087)
49. Cress WD, Seto E (2000) Histone deacetylases, transcriptional control, and cancer. J Cell Physiol 184: 1-16. (Pubitemid 30349623)
50. Noh JH, Chang YG, Kim MG, Jung KH, Kim JK, et al. (2013) MiR-145 functions as a tumor suppressor by directly targeting histone deacetylase 2 in liver cancer. Cancer Lett 335: 455-462.
51. Kim JK, Noh JH, Eun JW, Jung KH, Bae HJ, et al. (2013) Targeted inactivation of HDAC2 restores p16INK4a activity and exerts antitumor effects on human gastric cancer. Mol Cancer Res 11: 62-73.
52. Giudice FS, Pinto DS Jr, Nor JE, Squarize CH, Castilho RM (2013) Inhibition of histone deacetylase impacts cancer stem cells and induces epithelial-mesenchyme transition of head and neck cancer. PLoS One 8: e58672.
53. Hatzimichael E, Crook T (2013) Cancer epigenetics: new therapies and new challenges. J Drug Deliv 2013: 529312.
54. Myant K, Stancheva I (2008) LSH cooperates with DNA methyltransferases to repress transcription. Mol Cell Biol 28: 215-226.
55. Geiman TM, Sankpal UT, Robertson AK, Zhao Y, Robertson KD (2004) DNMT3B interacts with hSNF2H chromatin remodeling enzyme, HDACs 1 and 2, and components of the histone methylation system. Biochem Biophys Res Commun 318: 544-555. (Pubitemid 38553814)
56. Enver T, Soneji S, Joshi C, Brown J, Iborra F, et al. (2005) Cellular differentiation hierarchies in normal and culture-adapted human embryonic stem cells. Hum Mol Genet 14: 3129-3140. (Pubitemid 41631288)
57. Thakur R, Mishra DP (2013) Pharmacological modulation of beta-catenin and its applications in cancer therapy. J Cell Mol Med 17: 449-456.
58. Sato N, Meijer L, Skaltsounis L, Greengard P, Brivanlou AH (2004) Maintenance of pluripotency in human and mouse embryonic stem cells through activation of Wnt signaling by a pharmacological GSK-3-specific inhibitor. Nat Med 10: 55-63. (Pubitemid 38524699)
59. Lyashenko N, Winter M, Migliorini D, Biechele T, Moon RT, et al. (2011) Differential requirement for the dual functions of beta-catenin in embryonic stem cell self-renewal and germ layer formation. Nat Cell Biol 13: 753-761.
60. Hoffmeyer K, Raggioli A, Rudloff S, Anton R, Hierholzer A, et al. (2012) Wnt/ beta-catenin signaling regulates telomerase in stem cells and cancer cells. Science 336: 1549-1554.