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 LuEmail author
Research Article


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.


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



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


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

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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
    Email author
  1. 1.Department of UrologyShandong Provincial Hospital Affiliated to Shandong UniversityJinanChina
  2. 2.Department of Urology, Huashan HospitalFudan UniversityShanghaiChina

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