Label-free quantitative proteomic analysis reveals potential biomarkers and pathways in renal cell carcinoma
Label-free quantitative proteomic analysis reveals potential biomarkers and pathways in renal cell carcinoma
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DOI：
10.1007/s13277-014-2694-2
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发表时间：
2015-02
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通讯作者：
Zuohui Zhao;Fei Wu;S. Ding;Liang Sun;Zhao Liu;K. Ding;Jiaju Lu
中科院分区：
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作者：
Zuohui Zhao;Fei Wu;S. Ding;Liang Sun;Zhao Liu;K. Ding;Jiaju Lu
肾细胞癌(RCC)是成人最常见的恶性肿瘤之一，其诊断、预后、复发监测和治疗分层尚无公认的生物标志物。此外，对肾癌中蛋白质的翻译后修饰(PTM)知之甚少。在本研究中，我们对12对配对的肾透明细胞癌(CcRCC)及其邻近肾组织进行了定量蛋白质组学分析，使用液相色谱-串联质谱仪(NanLCMS/MS)和Progensis LC-MS软件(无标记)来鉴定和定量异常的蛋白质。在肾细胞癌和癌旁肾组织中分别鉴定出1872个和1927个蛋白质。在这些蛋白质中，Progensis LC-MS定量了1037个蛋白质，213个蛋白质被鉴定为肾细胞癌与邻近组织之间的异常调节蛋白质。使用IPA、STRING和David工具进行的通路分析表明，与癌症相关的信号通路和生物学过程，如线粒体功能障碍、代谢途径、细胞死亡和乙酰化，都得到了丰富。用Western blotting和免疫组织化学方法对6对肾细胞癌及癌旁组织进行检测，筛选出乙酰辅酶A乙酰转移酶1(ACAT1)和锰超氧化物歧化酶(MnSOD)两种线粒体蛋白表达异常。进一步的质谱分析表明，ACAT1和MnSOD都具有赖氨酸残基的乙酰化特征，这是首次在ccRCC中鉴定到ACAT1和MnSOD的乙酰化。总之，这些数据通过无标记定量蛋白质组学方法揭示了肾细胞癌中一些调控异常的蛋白质和信号通路，为临床干预肾癌提供了潜在的诊断或预后生物标志物和治疗分子靶点。
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.