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Oncogene-Induced Senescence pp 127–137Cite as

Detection of the Ubiquitinome in Cells Undergoing Oncogene-Induced Senescence

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1534))

Abstract

Senescent cells exhibit dramatic changes in protein post-translational modifications. Here, we describe a method, stable isotope labeling with amino acids in cell culture (SILAC) coupled to liquid chromatography tandem mass spectrometry (LC-MS/MS), to identify changes in the ubiquitinome in cells that have undergone oncogene-induced senescence.

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References

  1. Munoz-Espin D, Canamero M, Maraver A, Gomez-Lopez G, Contreras J, Murillo-Cuesta S et al (2013) Programmed cell senescence during mammalian embryonic development. Cell 155:1104–1118

    Article  CAS  PubMed  Google Scholar 

  2. Rodier F, Campisi J (2011) Four faces of cellular senescence. J Cell Biol 192:547–556

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Collado M, Serrano M (2010) Senescence in tumours: evidence from mice and humans. Nat Rev Cancer 10:51–57

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Hayflick L, Moorhead PS (1961) The serial cultivation of human diploid cell strains. Exp Cell Res 585–621

    Google Scholar 

  5. Harley CB, Futcher AB, Greider CW (1990) Telomeres shorten during ageing of human fibroblasts. Nature 345:458–460

    Article  CAS  PubMed  Google Scholar 

  6. Yang J, Chang E, Cherry AM, Bangs CD, Oei Y, Bodnar A et al (1999) Human endothelial cell life extension by telomerase expression. J Biol Chem 274:26141–26148

    Article  CAS  PubMed  Google Scholar 

  7. Chen Z, Trotman LC, Shaffer D, Lin HK, Dotan ZA, Niki M (2005) Crucial role of p53-dependent cellular senescence in suppression of Pten-deficient tumorigenesis. Nature 436:725–730

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Yaswen P, Campisi J (2007) Oncogene-induced senescence pathways weave an intricate tapestry. Cell 128:233–234

    Article  CAS  PubMed  Google Scholar 

  9. Serrano M, Lin AW, McCurrach ME, Beach D, Lowe S (1997) Oncogenic ras provokes premature cell senescence associated with accumulation of p53 and p16INK4a. Cell 88:593–602

    Article  CAS  PubMed  Google Scholar 

  10. Li M, Durbin KR, Sweet SM, Tipton JD, Zheng Y, Kelleher NL (2013) Oncogene-induced cellular senescence elicits an anti-Warburg effect. Proteomics 13:2585–2596

    Article  CAS  PubMed  Google Scholar 

  11. Nalepa G, Rolfe M, Harper JW (2006) Drug discovery in the ubiquitin-proteasome system. Nat Rev Drug Discov 5:596–613

    Article  CAS  PubMed  Google Scholar 

  12. Chau V, Tobias JW, Bachmair A, Marriott D, Ecker DJ, Gonda DK, Varshavsky A (1989) A multiubiquitin chain is confined to a specific lysine in a targeted short-lived protein. Science 243:1576–1583

    Article  CAS  PubMed  Google Scholar 

  13. Neutzner M, Neutzner A (2012) Enzymes of ubiquitination and deubiquitination. Essays Biochem 52:37–50

    Article  CAS  PubMed  Google Scholar 

  14. Hershko A, Ciechanover A, Varshavsky A (2000) Basic medical research award. The ubiquitin system. Nat Med 6:1073–1081

    Article  CAS  PubMed  Google Scholar 

  15. Pickart CM (2001) Mechanisms underlying ubiquitination. Annu Rev Biochem 70:503–533

    Article  CAS  PubMed  Google Scholar 

  16. Johmura Y, Sun J, Kitagawa K, Nakanishi K, Kuno T, Naiki-Ito A et al (2016) SCF(Fbxo22)-KDM4A targets methylated p53 for degradation and regulates senescence. Nat Commun 7:10574

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Zhu H, Ren S, Bitler BG, Aird KM, Tu Z, Skordalakes E et al (2015) SPOP E3 ubiquitin ligase adaptor promotes cellular senescence by degrading the SENP7 deSUMOylase. Cell Rep 13:1183–1193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26:1367–1372

    Article  CAS  PubMed  Google Scholar 

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Acknowledgment

This work was supported in part by NIH/NCI grants R01CA160331 to R.Z., R01CA131582 to D.W.S., and an institutional grant to The Wistar Institute (NCI Cancer Core Grant CA010815).

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Authors and Affiliations

  1. Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, 19104, USA

    Hengrui Zhu & Linh Le

  2. Cell and Molecular Biology Graduate Group, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, 19104, USA

    Linh Le

  3. Molecular and Cellular Oncology Program and Proteomics Core, The Wistar Institute, Philadelphia, PA, 19104, USA

    Hsin-Yao Tang & David W. Speicher

  4. Gene Expression and Regulation Program, The Wistar Institute, Room 312, 3601 Spruce Street, Philadelphia, PA, 19104, USA

    Rugang Zhang Ph.D.

Authors
  1. Hengrui Zhu
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  2. Linh Le
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  3. Hsin-Yao Tang
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  4. David W. Speicher
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  5. Rugang Zhang Ph.D.
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Corresponding author

Correspondence to Rugang Zhang Ph.D. .

Editor information

Editors and Affiliations

  1. Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York, USA

    Mikhail A. Nikiforov

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Zhu, H., Le, L., Tang, HY., Speicher, D.W., Zhang, R. (2017). Detection of the Ubiquitinome in Cells Undergoing Oncogene-Induced Senescence. In: Nikiforov, M. (eds) Oncogene-Induced Senescence. Methods in Molecular Biology, vol 1534. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6670-7_12

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  • DOI: https://doi.org/10.1007/978-1-4939-6670-7_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6668-4

  • Online ISBN: 978-1-4939-6670-7

  • eBook Packages: Springer Protocols

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