Protocol for proteogenomic dissection of intronic splicing enhancer interactome for prediction of individualized cancer prognosis.
Protocol for proteogenomic dissection of intronic splicing enhancer interactome for prediction of individualized cancer prognosis.
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DOI：
10.1016/j.xpro.2021.100338
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发表时间：
2021-03-19
期刊：
影响因子：
--
通讯作者：
Chen X
中科院分区：
文献类型：
--
作者：
Wang L;Wrobel JA;Xie L;Chen X
患者间或患者内的肿瘤异质性阻碍了用于预测个体化预后的生物标志物的发现。在这里，我们提出了一个协议的选择性剪接活性为基础的蛋白基因组学方法，用于识别候选预后标志物的癌细胞系和人乳腺癌标本。用内含子剪接增强子（伊势）探针下拉蛋白质复合物，然后进行串联质谱（MS/MS）肽测序。来自这些ISE-MS/MS测定的数据的蛋白基因组学分析鉴定了可用于对具有不良预后的患者进行分层的新的预后标志物。有关本方案使用和执行的完整详细信息，请参阅。用于对来自癌细胞系或组织的伊势相互作用物进行LC-MS/MS分析的方案用于对具有预后意义的伊势相互作用物进行蛋白质组学鉴定的方案用于蛋白质提取、伊势下拉、MS/MS和蛋白质组学分析的方案适用于癌细胞系和临床标本的方案患者间或患者内肿瘤异质性阻碍了用于预测个体化预后的生物标志物的发现。在这里，我们提出了一个协议的选择性剪接活性为基础的蛋白基因组学方法，用于识别候选预后标志物的癌细胞系和人乳腺癌标本。用内含子剪接增强子（伊势）探针下拉蛋白质复合物，然后进行串联质谱（MS/MS）肽测序。来自这些ISE-MS/MS测定的数据的蛋白基因组学分析鉴定了可用于对具有不良预后的患者进行分层的新的预后标志物。
Inter- or intra-patient tumor heterogeneity hinders the discovery of biomarkers for predicting individualized prognosis. Here, we present a protocol for an alternative splicing activity-based proteogenomic approach for identification of candidate prognostic markers in cancer cell lines and human breast cancer specimens. The pull-down of protein complexes with intronic splicing enhancer (ISE) probes is followed by tandem mass spectrometry (MS/MS) peptide sequencing. The proteogenomic analysis of data from these ISE-MS/MS assays identifies new prognostic markers that can be utilized to stratify patients with poor prognosis. For complete details on the use and execution of this protocol, please refer to. Protocol for LC-MS/MS analysis of ISE interactomes from cancer cell lines or tissues Protocol for proteogenomic identification of ISE interactors of prognostic significance Protocol for protein extraction, ISE pull-downs, MS/MS, and proteogenomic analysis Protocols applicable to cancer cell lines and clinical specimens Inter- or intra-patient tumor heterogeneity hinders the discovery of biomarkers for predicting individualized prognosis. Here, we present a protocol for an alternative splicing activity-based proteogenomic approach for identification of candidate prognostic markers in cancer cell lines and human breast cancer specimens. The pull-down of protein complexes with intronic splicing enhancer (ISE) probes is followed by tandem mass spectrometry (MS/MS) peptide sequencing. The proteogenomic analysis of data from these ISE-MS/MS assays identifies new prognostic markers that can be utilized to stratify patients with poor prognosis.
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影响因子：
7.3
作者：
Gao J;Aksoy BA;Dogrusoz U;Dresdner G;Gross B;Sumer SO;Sun Y;Jacobsen A;Sinha R;Larsson E;Cerami E;Sander C;Schultz N
通讯作者：
Schultz N
影响因子：
5.8
作者：
Wrobel, John A.;Xie, Ling;Chen, Xian
通讯作者：
Chen, Xian
影响因子：
14.8
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Rappsilber, Juri;Mann, Matthias;Ishihama, Yasushi
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通讯作者：
Aparicio, Samuel
影响因子：
64.5
作者：
Ciriello G;Gatza ML;Beck AH;Wilkerson MD;Rhie SK;Pastore A;Zhang H;McLellan M;Yau C;Kandoth C;Bowlby R;Shen H;Hayat S;Fieldhouse R;Lester SC;Tse GM;Factor RE;Collins LC;Allison KH;Chen YY;Jensen K;Johnson NB;Oesterreich S;Mills GB;Cherniack AD;Robertson G;Benz C;Sander C;Laird PW;Hoadley KA;King TA;TCGA Research Network;Perou CM
通讯作者：
Perou CM