Identification of N-glycan serum markers associated with hepatocellular carcinoma from mass spectrometry data.
Identification of N-glycan serum markers associated with hepatocellular carcinoma from mass spectrometry data.
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DOI：
10.1021/pr900397n
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发表时间：
2010-01
影响因子：
4.4
通讯作者：
Ressom, Habtom W.
中科院分区：
文献类型：
--
作者：
Tang, Zhiqun;Varghese, Rency S.;Bekesova, Slavka;Loffredo, Christopher A.;Hamid, Mohamed Abdul;Kyselova, Zuzana;Mechref, Yehia;Novotny, Milos V.;Goldman, Radoslav;Ressom, Habtom W.
关键词：
糖基化代表人类蛋白质中最复杂和最广泛的翻译后修饰。糖基化的变化与致癌转化密切相关。因此，对从蛋白质上分离的聚糖进行分析是识别癌症检测生物标志物的一种有前景的策略。这项研究通过质谱法鉴定了与肝细胞癌相关的候选聚糖生物标志物。具体来说，使用峰选择程序对质谱数据进行分析，该程序结合了多种随机采样策略和基于支持向量机的递归特征选择。从不同的样品组合中获得了十个峰组。 10 个峰组各共享 7 个峰，其中选择了 7-12 个峰，表明 10 个峰组共享 58-100% 的峰。使用支持向量机和层次聚类方法来评估峰值集的性能。使用 19 个新生成的 MALDI-TOF 谱图进一步评估了七个峰的预测性能。确定了七个峰中四个聚糖的聚糖结构。文献检索表明，这四种聚糖的结构可以在一些与癌症相关的糖蛋白中找到。本研究的方法对于获得一致、准确且具有生物学意义的肝细胞癌诊断候选聚糖标记物具有重要意义。
Glycocylation represents the most complex and widespread post-translational modifications in human proteins. The variation of glycosylation is closely related to oncogenic transformation. Therefore, profiling of glycans detached from proteins is a promising strategy to identify biomarkers for cancer detection. This study identified candidate glycan biomarkers associated with hepatocellular carcinoma by mass spectrometry. Specifically, mass spectrometry data were analyzed with a peak selection procedure which incorporates multiple random sampling strategies with recursive feature selection based on support vector machines. Ten peak sets were obtained from different combinations of samples. Seven peaks were shared by each of the 10 peaksets, in which 7–12 peaks were selected, indicating 58–100% of peaks were shared by the 10 peaksets. Support vector machines and hierarchical clustering method were used to evaluate the performance of the peaksets. The predictive performance of the seven peaks was further evaluated by using 19 newly generated MALDI-TOF spectra. Glycan structures for four glycans of the seven peaks were determined. Literature search indicated that the structures of the four glycans could be found in some cancer-related glycoproteins. The method of this study is significant in deriving consistent, accurate, and biological significant glycan marker candidates for hepatocellular carcinoma diagnosis.
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DOI：
10.1158/1078-0432.ccr-07-5261
发表时间：
2009-03-01
期刊：
Clinical cancer research : an official journal of the American Association for Cancer Research
影响因子：
--
作者：
Goldman R;Ressom HW;Varghese RS;Goldman L;Bascug G;Loffredo CA;Abdel-Hamid M;Gouda I;Ezzat S;Kyselova Z;Mechref Y;Novotny MV
通讯作者：
Novotny MV
影响因子：
2.9
作者：
Keerthi, SS;Lin, CJ
通讯作者：
Lin, CJ
影响因子：
4
作者：
Kobata, A;Amano, J
通讯作者：
Amano, J
影响因子：
5.8
作者：
Cui, Juan;Liu, Qi;Xu, Ying
通讯作者：
Xu, Ying
影响因子：
7.4
作者：
Mahadevan, Sankar;Shah, Sirish L.;Slupsky, Carolyn M.
通讯作者：
Slupsky, Carolyn M.