Tumor Biology

, Volume 36, Issue 2, pp 939–951 | Cite as

Label-free quantitative proteomic analysis reveals potential biomarkers and pathways in renal cell carcinoma

  • Zuohui Zhao
  • Fei Wu
  • Sentai Ding
  • Liang Sun
  • Zhao Liu
  • Kejia Ding
  • Jiaju Lu
Research Article

Abstract

Renal cell carcinoma (RCC) is one of the most common malignancies in adults, and there is still no acknowledged biomarker for its diagnosis, prognosis, recurrence monitoring, and treatment stratification. Besides, little is known about the post-translational modification (PTM) of proteins in RCC. Here, we performed quantitative proteomic analysis on 12 matched pairs of clear cell RCC (ccRCC) and adjacent kidney tissues using liquid chromatography-tandem mass spectrometry (nanoLCMS/MS) and Progenesis LC-MS software (label-free) to identify and quantify the dysregulated proteins. A total of 1872 and 1927 proteins were identified in ccRCC and adjacent kidney tissues, respectively. Among these proteins, 1037 proteins were quantified by Progenesis LC-MS, and 213 proteins were identified as dysregulated proteins between ccRCC and adjacent tissues. Pathway analysis using IPA, STRING, and David tools was performed, which demonstrated the enrichment of cancer-related signaling pathways and biological processes such as mitochondrial dysfunction, metabolic pathway, cell death, and acetylation. Dysregulation of two mitochondrial proteins, acetyl-CoA acetyltransferase 1 (ACAT1) and manganese superoxide dismutase (MnSOD) were selected and confirmed by Western blotting and immunohistochemistry assays using another 6 pairs of ccRCC and adjacent tissues. Further mass spectrometry analysis indicated that both ACAT1 and MnSOD had characterized acetylation at lysine residues, which is the first time to identify acetylation of ACAT1 and MnSOD in ccRCC. Collectively, these data revealed a number of dysregulated proteins and signaling pathways by label-free quantitative proteomic approach in RCC, which shed light on potential diagnostic or prognostic biomarkers and therapeutic molecular targets for clinical intervention of RCC.

Keywords

Renal cell carcinoma Acetylation Label-free quantitative proteomics Progenesis LC-MS 

Notes

Acknowledgments

This study was supported in part by the grants from the National Natural Science Foundation of China (No. 81202017) and the Natural Science Foundation Shandong Province (No. ZR2011HQ027).

Conflicts of interest

None.

Ethics statement

All procedures were consistent with the National Institutes of Health Guide and approved by the institutional board with patients’ written consent. This study was evaluated and approved by the Ethics Committee of Shandong Provincial Hospital Affiliated to Shandong University.

Supplementary material

13277_2014_2694_MOESM1_ESM.xls (3.5 mb)
Online resource 1 (XLS 3573 kb)
13277_2014_2694_MOESM2_ESM.xls (546 kb)
Online resource 2 (XLS 545 kb)
13277_2014_2694_MOESM3_ESM.xls (128 kb)
Online resource 3 (XLS 127 kb)

References

  1. 1.
    Rini BI, Campbell SC, Escudier B. Renal cell carcinoma. Lancet. 2009;373(9669):1119–32. doi: 10.1016/S0140-6736(09)60229-4.CrossRefPubMedGoogle Scholar
  2. 2.
    Craven RA, Stanley AJ, Hanrahan S, Dods J, Unwin R, Totty N, et al. Proteomic analysis of primary cell lines identifies protein changes present in renal cell carcinoma. Proteomics. 2006;6(9):2853–64. doi: 10.1002/pmic.200500549.CrossRefPubMedGoogle Scholar
  3. 3.
    Siegel R, Ma J, Zou Z, Jemal A. Cancer statistics, 2014. CA Cancer J Clin. 2014;64(1):9–29. doi: 10.3322/caac.21208.CrossRefPubMedGoogle Scholar
  4. 4.
    Atrih A, Mudaliar MA, Zakikhani P, Lamont DJ, Huang JT, Bray SE, et al. Quantitative proteomics in resected renal cancer tissue for biomarker discovery and profiling. Br J Cancer. 2014;110(6):1622–33. doi: 10.1038/bjc.2014.24.CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Gupta K, Miller JD, Li JZ, Russell MW, Charbonneau C. Epidemiologic and socioeconomic burden of metastatic renal cell carcinoma (mRCC): a literature review. Cancer Treat Rev. 2008;34(3):193–205. doi: 10.1016/j.ctrv.2007.12.001.CrossRefPubMedGoogle Scholar
  6. 6.
    Janech MG, Raymond JR, Arthur JM. Proteomics in renal research. Am J Physiol Ren Physiol. 2007;292(2):F501–12. doi: 10.1152/ajprenal.00298.2006.CrossRefGoogle Scholar
  7. 7.
    Ding S, Zhao Z, Sun D, Wu F, Bi D, Lu J, et al. Eg5 inhibitor, a novel potent targeted therapy, induces cell apoptosis in renal cell carcinoma. Tumour Biol J Int Soc Oncodev Biol Med. 2014;35(8):7659–68. doi: 10.1007/s13277-014-2022-x.CrossRefGoogle Scholar
  8. 8.
    Motzer RJ, Hutson TE, Cella D, Reeves J, Hawkins R, Guo J, et al. Pazopanib versus sunitinib in metastatic renal-cell carcinoma. N Engl J Med. 2013;369(8):722–31. doi: 10.1056/NEJMoa1303989.CrossRefPubMedGoogle Scholar
  9. 9.
    Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003;422(6928):198–207. doi: 10.1038/nature01511.CrossRefPubMedGoogle Scholar
  10. 10.
    White NM, Masui O, Desouza LV, Krakovska O, Metias S, Romaschin AD, et al. Quantitative proteomic analysis reveals potential diagnostic markers and pathways involved in pathogenesis of renal cell carcinoma. Oncotarget. 2014;5(2):506–18.CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Sangawa A, Shintani M, Yamao N, Kamoshida S. Phosphorylation status of Akt and caspase-9 in gastric and colorectal carcinomas. Int J Clin Exp Pathol. 2014;7(6):3312–7.PubMedPubMedCentralGoogle Scholar
  12. 12.
    Wu YM, Liu CH, Huang MJ, Lai HS, Lee PH, Hu RH, et al. C1GALT1 enhances proliferation of hepatocellular carcinoma cells via modulating MET glycosylation and dimerization. Cancer Res. 2013;73(17):5580–90. doi: 10.1158/0008-5472.CAN-13-0869.CrossRefPubMedGoogle Scholar
  13. 13.
    Noh SJ, Kang MJ, Kim KM, Bae JS, Park HS, Moon WS, et al. Acetylation status of P53 and the expression of DBC1, SIRT1, and androgen receptor are associated with survival in clear cell renal cell carcinoma patients. Pathology. 2013;45(6):574–80. doi: 10.1097/PAT.0b013e3283652c7a.CrossRefPubMedGoogle Scholar
  14. 14.
    Chen Y, Zhang J, Lin Y, Lei Q, Guan KL, Zhao S, et al. Tumour suppressor SIRT3 deacetylates and activates manganese superoxide dismutase to scavenge ROS. EMBO Rep. 2011;12(6):534–41. doi: 10.1038/embor.2011.65.CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Wang Q, Zhang Y, Yang C, Xiong H, Lin Y, Yao J, et al. Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science. 2010;327(5968):1004–7. doi: 10.1126/science.1179687.CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, et al. Regulation of cellular metabolism by protein lysine acetylation. Science. 2010;327(5968):1000–4. doi: 10.1126/science.1179689.CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Yi C, Ma M, Ran L, Zheng J, Tong J, Zhu J, et al. Function and molecular mechanism of acetylation in autophagy regulation. Science. 2012;336(6080):474–7. doi: 10.1126/science.1216990.CrossRefPubMedGoogle Scholar
  18. 18.
    Nagaprashantha LD, Talamantes T, Singhal J, Guo J, Vatsyayan R, Rauniyar N, et al. Proteomic analysis of signaling network regulation in renal cell carcinomas with differential hypoxia-inducible factor-2alpha expression. PLoS One. 2013;8(8):e71654. doi: 10.1371/journal.pone.0071654.CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Ramakrishnan S, Ellis L, Pili R. Histone modifications: implications in renal cell carcinoma. Epigenomics. 2013;5(4):453–62. doi: 10.2217/epi.13.40.CrossRefPubMedGoogle Scholar
  20. 20.
    Perroud B, Lee J, Valkova N, Dhirapong A, Lin PY, Fiehn O, et al. Pathway analysis of kidney cancer using proteomics and metabolic profiling. Mol Cancer. 2006;5:64. doi: 10.1186/1476-4598-5-64.CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Parviainen VI, Joenvaara S, Tohmola N, Renkonen R. Label-free mass spectrometry proteome quantification of human embryonic kidney cells following 24 h of sialic acid overproduction. Proteome Sci. 2013;11(1):38. doi: 10.1186/1477-5956-11-38.CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Edge SB, Compton CC. The American Joint Committee on Cancer: the 7th edition of the AJCC cancer staging manual and the future of TNM. Ann Surg Oncol. 2010;17(6):1471–4. doi: 10.1245/s10434-010-0985-4.CrossRefPubMedGoogle Scholar
  23. 23.
    Wu F, Zhao ZH, Ding ST, Wu HH, Lu JJ. High mobility group box 1 protein is methylated and transported to cytoplasm in clear cell renal cell carcinoma. Asian J Cancer Prev APJCP. 2013;14(10):5789–95.CrossRefGoogle Scholar
  24. 24.
    Theron L, Gueugneau M, Coudy C, Viala D, Bijlsma A, Butler-Browne G, et al. Label-free quantitative protein profiling of vastus lateralis muscle during human aging. Mol Cell Proteomics MCP. 2014;13(1):283–94. doi: 10.1074/mcp.M113.032698.CrossRefPubMedGoogle Scholar
  25. 25.
    Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011;39(Database issue):D561–8. doi: 10.1093/nar/gkq973.CrossRefPubMedGoogle Scholar
  26. 26.
    Saraon P, Cretu D, Musrap N, Karagiannis GS, Batruch I, Drabovich AP, et al. Quantitative proteomics reveals that enzymes of the ketogenic pathway are associated with prostate cancer progression. Molecular & cellular proteomics : MCP. 2013;12(6):1589–601. doi: 10.1074/mcp.M112.023887.CrossRefPubMedCentralGoogle Scholar
  27. 27.
    Chu SH, Liu YW, Zhang L, Liu B, Li L, Shi JZ, et al. Regulation of survival and chemoresistance by HSP90AA1 in ovarian cancer SKOV3 cells. Mol Biol Rep. 2013;40(1):1–6. doi: 10.1007/s11033-012-1930-3.CrossRefPubMedGoogle Scholar
  28. 28.
    Lebdai S, Verhoest G, Parikh H, Jacquet SF, Bensalah K, Chautard D, et al. Identification and validation of TGFBI as a promising prognosis marker of clear cell renal cell carcinoma. Urol Oncol. 2014. doi: 10.1016/j.urolonc.2014.06.005.PubMedGoogle Scholar
  29. 29.
    Arner E, Forrest AR, Ehrlund A, Mejhert N, Itoh M, Kawaji H, et al. Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells. PLoS One. 2014;9(3):e80274. doi: 10.1371/journal.pone.0080274.CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Saraon P, Trudel D, Kron K, Dmitromanolakis A, Trachtenberg J, Bapat B, et al. Evaluation and prognostic significance of ACAT1 as a marker of prostate cancer progression. Prostate. 2014;74(4):372–80. doi: 10.1002/pros.22758.CrossRefPubMedGoogle Scholar
  31. 31.
    Dhar SK, St Clair DK. Manganese superoxide dismutase regulation and cancer. Free Radic Biol Med. 2012;52(11–12):2209–22. doi: 10.1016/j.freeradbiomed.2012.03.009.CrossRefPubMedGoogle Scholar
  32. 32.
    Kim HS, Patel K, Muldoon-Jacobs K, Bisht KS, Aykin-Burns N, Pennington JD, et al. SIRT3 is a mitochondria-localized tumor suppressor required for maintenance of mitochondrial integrity and metabolism during stress. Cancer Cell. 2010;17(1):41–52. doi: 10.1016/j.ccr.2009.11.023.CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Haapalainen AM, Merilainen G, Pirila PL, Kondo N, Fukao T, Wierenga RK. Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase: the importance of potassium and chloride ions for its structure and function. Biochemistry. 2007;46(14):4305–21. doi: 10.1021/bi6026192.CrossRefPubMedGoogle Scholar
  34. 34.
    Fan J, Shan C, Kang HB, Elf S, Xie J, Tucker M, et al. Tyr phosphorylation of PDP1 toggles recruitment between ACAT1 and SIRT3 to regulate the pyruvate dehydrogenase complex. Mol Cell. 2014;53(4):534–48. doi: 10.1016/j.molcel.2013.12.026.CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Weydert CJ, Waugh TA, Ritchie JM, Iyer KS, Smith JL, Li L, et al. Overexpression of manganese or copper-zinc superoxide dismutase inhibits breast cancer growth. Free Radic Biol Med. 2006;41(2):226–37. doi: 10.1016/j.freeradbiomed.2006.03.015.CrossRefPubMedGoogle Scholar
  36. 36.
    Dhar SK, Tangpong J, Chaiswing L, Oberley TD, St Clair DK. Manganese superoxide dismutase is a p53-regulated gene that switches cancers between early and advanced stages. Cancer Res. 2011;71(21):6684–95. doi: 10.1158/0008-5472.CAN-11-1233.CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Quiros I, Sainz RM, Hevia D, Garcia-Suarez O, Astudillo A, Rivas M, et al. Upregulation of manganese superoxide dismutase (SOD2) is a common pathway for neuroendocrine differentiation in prostate cancer cells. International Journal of Cancer Journal International du Cancer. 2009;125(7):1497–504. doi: 10.1002/ijc.24501.CrossRefPubMedGoogle Scholar
  38. 38.
    Perry JJ, Hearn AS, Cabelli DE, Nick HS, Tainer JA, Silverman DN. Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis. Biochemistry. 2009;48(15):3417–24. doi: 10.1021/bi8023288.CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Qiu X, Brown K, Hirschey MD, Verdin E, Chen D. Calorie restriction reduces oxidative stress by SIRT3-mediated SOD2 activation. Cell Metab. 2010;12(6):662–7. doi: 10.1016/j.cmet.2010.11.015.CrossRefPubMedGoogle Scholar
  40. 40.
    Huang P, Feng L, Oldham EA, Keating MJ, Plunkett W. Superoxide dismutase as a target for the selective killing of cancer cells. Nature. 2000;407(6802):390–5. doi: 10.1038/35030140.CrossRefPubMedGoogle Scholar
  41. 41.
    Carew JS, Huang P. Mitochondrial defects in cancer. Mol Cancer. 2002;1:9.CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Mitrakas AG, Kalamida D, Koukourakis MI. Effect of mitochondrial metabolism-interfering agents on cancer cell mitochondrial function and radio/chemosensitivity. Anti-Cancer Drugs. 2014. doi: 10.1097/CAD.0000000000000152.PubMedGoogle Scholar
  43. 43.
    Wang Y, Zhang R, Wu D, Lu Z, Sun W, Cai Y, et al. Epigenetic change in kidney tumor: downregulation of histone acetyltransferase MYST1 in human renal cell carcinoma. Journal of experimental & clinical cancer research : CR. 2013;32:8. doi: 10.1186/1756-9966-32-8.CrossRefPubMedCentralGoogle Scholar
  44. 44.
    Juengel E, Dauselt A, Makarevic J, Wiesner C, Tsaur I, Bartsch G, et al. Acetylation of histone H3 prevents resistance development caused by chronic mTOR inhibition in renal cell carcinoma cells. Cancer Lett. 2012;324(1):83–90. doi: 10.1016/j.canlet.2012.05.003.CrossRefPubMedGoogle Scholar
  45. 45.
    Kanao K, Mikami S, Mizuno R, Shinojima T, Murai M, Oya M. Decreased acetylation of histone H3 in renal cell carcinoma: a potential target of histone deacetylase inhibitors. J Urol. 2008;180(3):1131–6. doi: 10.1016/j.juro.2008.04.136.CrossRefPubMedGoogle Scholar

Copyright information

© International Society of Oncology and BioMarkers (ISOBM) 2014

Authors and Affiliations

  • Zuohui Zhao
    • 1
  • Fei Wu
    • 2
  • Sentai Ding
    • 1
  • Liang Sun
    • 1
  • Zhao Liu
    • 1
  • Kejia Ding
    • 1
  • Jiaju Lu
    • 1
  1. 1.Department of UrologyShandong Provincial Hospital Affiliated to Shandong UniversityJinanChina
  2. 2.Department of Urology, Huashan HospitalFudan UniversityShanghaiChina

Personalised recommendations