Protein Ubiquitination Research in Oncology

Czech version

Authors: J. Faktor; M. Pjechová; L. Hernychová; B. Vojtěšek
Authors‘ workplace: Regionální centrum aplikované molekulární onkologie, Masarykův onkologický ústav, Brno
Published in: Klin Onkol 2019; 32(Supplementum 3): 56-64
Category: Review
doi: https://doi.org/10.14735/amko20193S

Overview

Background: Ubiquitination is a vital posttranslational protein modification involved in the regulation of many eukaryotic signalling pathways. Aberrant ubiquitin signalling is known to be a molecular causality of certain cancer, neurodegenerative, immune system or cardiovascular diseases. The recent development of mass spectrometry methods enables qualitative and quantitative ubiquitination analysis in biological material from cancer patients. Research of ubiquitination may clarify the molecular cause of aberrant changes in the protein level of tumour suppressors or oncogenes.

Purpose: We aim to explain the meaning and importance of ubiquitination in certain molecular processes taking place in the human body. We hereby emphasise the connection between ubiquitination and malignant processes. A literature search is followed by introducing our mass spectrometry platform intended for ubiquitin identification via diglycyl remnants in the CHIP protein sequence. The aim is to introduce tandem mass spectrometry identification of ubiquitin modification, ubiquitination tandem mass spectra validation and the time-dependent manner of CHIP ubiquitination to the reader.

Conclusion: A literature search familiarises the reader with known mechanisms of aberrant ubiquitination in malignant diseases. A successfully optimised mass spectrometry platform could serve as a potent tool for determining ubiquitin position in proteins that are a part of real tumour samples.

Keywords:

ubiquitin – Mass spectrometry – neoplasms – proteins – proteomics

Sources

1. Goldstein G, Scheid M, Hammerling U et al. Isolation of a polypeptide that has lymphocyte-differentiating properties and is probably represented universally in living cells. Proc Natl Acad Sci USA 1975; 72: 11– 15. doi: 10.1073/ pnas.72.1.11.

2. Ciechanover A, Elias S, Heller H et al. “Covalent affinity” purification of ubiquitin-activating enzyme. J Biol Chem 1982; 257(5): 2537– 2542.

3. Ciechanover A. The 2008 Lindau Nobel laureate meeting: Aaron Ciechanover, Chemistry 2004. J Vis Exp 2009; (29): 1559. doi: 10.3791/ 1559.

4. Pickart CM. Mechanisms underlying ubiquitination. Annu Rev Biochem 2001; 70: 503– 533. doi: 10.1146/ annurev.biochem.70.1.503.

5. Hershko A, Ciechanover A. The ubiquitin system. Annu Rev Biochem 1998; 67: 425– 479. doi: 10.1146/ annurev.biochem.67.1.425.

6. Cheng Q, Cross B, Li B et al. Regulation of MDM2 E3 ligase activity by phosphorylation after DNA damage. Mol Cell Biol 2011; 31(24): 4951– 4963. doi: 10.1128/ MCB.05553-11.

7. Herhaus L, Dikic I. Expanding the ubiquitin code through post-translational modification. EMBO Rep 2015; 16(9): 1071– 1083. doi: 10.15252/ embr.201540891.

8. Komander D, Rape M. The ubiquitin code. Annu Rev Biochem 2012; 81: 203– 229. doi: 10.1146/ annurev-biochem-060310-170328.

9. Nguyen LK, Dobrzyński M, Fey D et al. Polyubiquitin chain assembly and organization determine the dynamics of protein activation and degradation. Front Physiol 2014; 5: 4. doi: 10.3389/ fphys.2014.00004.

10. Thrower JS, Hoffman L, Rechsteiner M et al. Recognition of the polyubiquitin proteolytic signal. EMBO J 2000; 19(1): 94– 102. doi: 10.1093/ emboj/ 19.1.94.

11. Sehat B, Andersson S, Girnita L et al. Identification of c-Cbl as a new ligase for insulin-like growth factor-Ireceptor with distinct roles from Mdm2 in receptor ubiquitination and endocytosis. Cancer Res 2008; 68(14): 5669– 5677. doi: 10.1158/ 0008-5472.CAN-07-6364.

12. Yang WL, Zhang X, Lin HK. Emerging role of Lys-63 ubiquitination in protein kinase and phosphatase activation and cancer development. Oncogene 2010; 29(32): 4493– 4503. doi: 10.1038/ onc.2010.190.

13. Rahighi S, Ikeda F, Kawasaki M et al. Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation. Cell 2009; 136(6): 1098– 1109. doi: 10.1016/ j.cell.2009.03.007.

14. Fiil BK, Gyrd-Hansen M. Met1-linked ubiquitination in immune signalling. FEBS J 2014; 281: 4337– 4350. doi: 10.1111/ febs.12944.

15. Shi D, Grossman SR. Ubiquitin becomes ubiquitous in cancer: emerging roles of ubiquitin ligases and deubiquitinases in tumorigenesis and as therapeutic targets. Cancer Biol Ther 2010; 10(8): 737– 747. doi: 10.4161/ cbt.10.8.13417.

16. Gallo LH, Ko J, Donoghue DJ. The importance of regulatory ubiquitination in cancer and metastasis. Cell Cycle 2017; 16(7): 634– 648. doi: 10.1080/ 153841 01.2017.1288326.

17. Wu Z, Shen S, Zhang Z et al. Ubiquitin-conjugating enzyme complex Uev1A-Ubc13 promotes breast cancer metastasis through nuclear factor-кB mediated matrix metalloproteinase-1 gene regulation. Breast Cancer Res 2014; 16(4): 75. doi: 10.1186/ bcr3692.

18. Jung CR, Hwang KS, Yoo J et al. E2-EPF UCP targets pVHL for degradation and associates with tumor growth and metastasis. Nat Med 2006; 12(7): 809– 816. doi: 10.1038/ nm1440.

19. Tanimoto K, Makino Y, Pereira T et al. Mechanism of regulation of the hypoxia-inducible factor-1 alpha by the von Hippel-Lindau tumor suppressor protein. EMBO J 2000; 19(16): 4298– 4309. doi: 10.1093/ emboj/ 19.16.4298.

20. Tsai YC, Mendoza A, Mariano JM et al. The ubiquitin ligase gp78 promotes sarcoma metastasis by targeting KAI1 for degradation. Nat Med 2007; 13(12): 1504– 1509. doi: 10.1038/ nm1686.

21. Vaughan L, Tan CT, Chapman A et al. HUWE1 ubiquitylates and degrades the RAC activator TIAM1 promoting cell-cell adhesion disassembly, migration, and invasion. Cell Rep 2015; 10(1): 88– 102. doi: 10.1016/ j.celrep.2014.12.012.

22. Rosser MF, Washburn E, Muchowski PJ et al. Chaperone functions of the E3 ubiquitin ligase CHIP. J Biol Chem 2007; 282(31): 22267– 22277. doi: 10.1074/ jbc.M700513200.

23. Paul I, Ahmed SF, Bhowmik A et al. The ubiquitin ligase CHIP regulates c-Myc stability and transcriptional activity. Oncogene 2013; 32(10): 1284– 1295. doi: 10.1038/ onc.2012.144.

24. Kajiro M, Hirota R, Nakajima Y et al. The ubiquitin ligase CHIP acts as an upstream regulator of oncogenic pathways. Nat Cell Biol 2009; 11(3): 312– 319. doi: 10.1038/ ncb1839.

25. Ferreira JV, Fôfo H, Bejarano E et al. STUB1/ CHIP is required for HIF1A degradation by chaperone-mediated autophagy. Autophagy 2013; 9(9): 1349– 1366. doi: 10.4161/ auto.25190.

26. Xu W, Marcu M, Yuan X et al. Chaperone-dependent E3 ubiquitin ligase CHIP mediates a degradative pathway for c-ErbB2/ Neu. Proc Natl Acad Sci USA 2002; 99(20): 12847– 12852. doi: 10.1073/ pnas.202365899.

27. Wang T, Yang J, Xu J et al. CHIP is a novel tumor suppressor in pancreatic cancer through targeting EGFR. Oncotarget 2014; 5(7): 1969– 1986. doi: 10.18632/ oncotarget.1890.

28. Wang Y, Ren F, Wang Y et al. CHIP/ Stub1 functions as a tumor suppressor and represses NF-κB-mediated signaling in colorectal cancer. Carcinogenesis 2014; 35(5): 983– 991. doi: 10.1093/ carcin/ bgt393.

29. Wang S, Wu X, Zhang J et al. CHIP functions as a novel suppressor of tumour angiogenesis with prognostic significance in human gastric cancer. Gut 2013; 62(4): 496– 508. doi: 10.1136/ gutjnl-2011-301522.

30. Li F, Xie P, Fan Y et al. C terminus of Hsc70-interacting protein promotes smooth muscle cell proliferation and survival through ubiquitin-mediated degradation of FoxO1. J Biol Chem 2009; 284(30): 20090– 20098. doi: 10.1074/ jbc.M109.017046.

31. Esser C, Scheffner M, Höhfeld J. The chaperone-associated ubiquitin ligase CHIP is able to target p53 for proteasomal degradation. J Biol Chem 2005; 280(29): 27443– 27448. doi: 10.1074/ jbc.M501574200.

32. Oh KH, Yang SW, Park JM et al. Control of AIF-mediated cell death by antagonistic functions of CHIP ubiquitin E3 ligase and USP2 deubiquitinating enzyme. Cell Death Differ 2011; 18(8): 1326– 1336. doi: 10.1038/ cdd.2011.3.

33. Narayan V, Pion E, Landré V et al. Docking-dependent ubiquitination of the interferon regulatory factor-1 tumor suppressor protein by the ubiquitin ligase CHIP. J Biol Chem 2011; 286(1): 607– 619. doi: 10.1074/ jbc.M110.153122.

34. Udeshi ND, Mertins P, Svinkina T et al. Large-scale identification of ubiquitination sites by mass spectrometry. Nat Protoc 2013; 8(10): 1950– 1960. doi: 10.1038/ nprot.2013.120.

35. van der Wal L, Bezstarosti K, Sap KA et al. Improvement of ubiquitylation site detection by Orbitrap mass spectrometry. J Proteomics 2018; 172: 49– 56. doi: 10.1016/ j.jprot.2017.10.014.

36. Xu G, Paige JS, Jaffrey SR. Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling. Nat Biotechnol 2010; 28(8): 868– 873. doi: 10.1038/ nbt.1654.

37. Udeshi ND, Mani DR, Eisenhaure T et al. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Mol Cell Proteomics 2012; 11(5): 148– 159. doi: 10.1074/ mcp.M111.016857.

38. Udeshi ND, Svinkina T, Mertins P et al. Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments. Mol Cell Proteomics 2013; 12(3): 825– 831. doi: 10.1074/ mcp.O112.027094.

39. Vasilescu J, Smith JC, Ethier M et al. Proteomic analysis of ubiquitinated proteins from human MCF-7 breast cancer cells by immunoaffinity purification and mass spectrometry. J Proteome Res 2005; 4(6): 2192– 2200. doi: 10.1021/ pr050265i.

40. Ogawa Y, Ono T, Wakata Y et al. Histone variant macroH2A1.2 is mono-ubiquitinated at its histone domain. Biochem Biophys Res Commun 2005; 336(1): 204– 209. doi: 10.1016/ j.bbrc.2005.08.046.

41. Maine GN, Gluck N, Zaidi IW et al. Bimolecular affinity purification (BAP): tandem affinity purification using two protein baits. Cold Spring Harb Protoc 2009; 2009(11): 1– 7. doi: 10.1101/ pdb.prot5318.

42. Kirkpatrick DS, Weldon SF, Tsaprailis G et al. Proteomic identification of ubiquitinated proteins from human cells expressing His-tagged ubiquitin. Proteomics 2005; 5(8): 2104– 2111. doi: 10.1002/ pmic.200401089.

43. Bouchal P, Roumeliotis T, Hrstka R et al. Biomarker discovery in low-grade breast cancer using isobaric stable isotope tags and two-dimensional liquid chromatography-tandem mass spectrometry (iTRAQ-2DLC-MS/ MS) based quantitative proteomic analysis. J Proteome Res 2009; 8(1): 362– 373. doi: 10.1021/ pr800622b.

44. Faktor J, Bouchal P. Building mass spectrometry spectral libraries of human cancer cell lines. Klin Onkol 2016; 29 (Suppl 4): 54– 58. doi: 10.14735/ amko20164S54.

45. Liu J, Shaik S, Dai X et al. Targeting the ubiquitin pathway for cancer treatment. Biochim Biophys Acta 2015; 1855(1): 50– 60. doi: 10.1016/ j.bbcan.2014.11.005.

46. Wilkinson KD, Tashayev VL, O’Connor LB et al. Metabolism of the polyubiquitin degradation signal: structure, mechanism, and role of isopeptidase T. Biochemistry 1995; 34(44): 14535– 14546. doi: 10.1021/ bi00044a032.

47. Deng L, Wang C, Spencer E et al. Activation of the IkappaB kinase complex by TRAF6 requires a dimeric ubiquitin-conjugating enzyme complex and a unique polyubiquitin chain. Cell 2000; 103(2): 351– 361. doi: 10.1016/ s0092-8674(00)00126-4.

48. Sun L, Chen ZJ. The novel functions of ubiquitination in signaling. Curr Opin Cell Biol 2004; 16(2): 119– 126. doi: 10.1016/ j.ceb.2004.02.005.

49. Graf C, Stankiewicz M, Nikolay R et al. Insights into the conformational dynamics of the E3 ubiquitin ligase CHIP in complex with chaperones and E2 enzymes. Biochemistry 2010; 49(10): 2121– 2129. doi: 10.1021/ bi901829f.

50. Lumpkin RJ, Gu H, Zhu Y et al. Site-specific identification and quantitation of endogenous SUMO modifications under native conditions. Nat Commun 2017; 8(1): 1171– 1182. doi: 10.1038/ s41467-017-01271-3.

51. Akimov V, Barrio-Hernandez I, Hansen SVF et al. UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites. Nat Struct Mol Biol 2018; 25(7): 631– 640. doi: 10.1038/ s41594-018-0084-y.