Systematic identification of ALK substrates by integrated phosphoproteome and interactome analysis.
Systematic identification of ALK substrates by integrated phosphoproteome and interactome analysis.
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DOI：
10.26508/lsa.202101202
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发表时间：
2022-08
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
--
作者：
间变性淋巴瘤激酶（ALK）过表达HEK 293细胞的磷酸化蛋白质组和相互作用组的综合分析显示了37种ALK底物候选物，有助于改善激酶活性预测。质谱鉴定磷酸化位点的灵敏度显著提高。然而，激酶-底物关系（KSR）数据的缺乏阻碍了激酶活性预测范围和准确性的提高。在这项研究中，我们的目的是开发一种方法，获得系统的KSR数据间变性淋巴瘤激酶（ALK）使用质谱，并将此方法应用于激酶活性的预测。通过对多西环素诱导的ALK过表达的HEK 293细胞的磷酸化蛋白质组和交联相互作用组的综合分析，确定了37种ALK候选底物，包括34个PhosphoSitePlus数据库中未注释的磷酸化位点。此外，通过体外激酶试验验证了ALK的KSR。最后，使用来自ALK突变细胞系和ALK抑制剂处理的患者源性细胞的磷酸化蛋白质组学数据，我们发现当使用本研究中鉴定的KSR而不是公共KSR数据集时，ALK活性的预测得到改善。我们的方法也适用于其他激酶，未来KSR的鉴定将有助于更准确地估计激酶活性和阐明磷酸化信号。
Integrated analysis of the phosphoproteome and interactome of anaplastic lymphoma kinase (ALK)-overexpressing HEK 293 cells revealed 37 ALK substrate candidates, contributing to the improvement of kinase activity prediction. The sensitivity of phosphorylation site identification by mass spectrometry has improved markedly. However, the lack of kinase–substrate relationship (KSR) data hinders the improvement of the range and accuracy of kinase activity prediction. In this study, we aimed to develop a method for acquiring systematic KSR data on anaplastic lymphoma kinase (ALK) using mass spectrometry and to apply this method to the prediction of kinase activity. Thirty-seven ALK substrate candidates, including 34 phosphorylation sites not annotated in the PhosphoSitePlus database, were identified by integrated analysis of the phosphoproteome and crosslinking interactome of HEK 293 cells with doxycycline-induced ALK overexpression. Furthermore, KSRs of ALK were validated by an in vitro kinase assay. Finally, using phosphoproteomic data from ALK mutant cell lines and patient-derived cells treated with ALK inhibitors, we found that the prediction of ALK activity was improved when the KSRs identified in this study were used instead of the public KSR dataset. Our approach is applicable to other kinases, and future identification of KSRs will facilitate more accurate estimations of kinase activity and elucidation of phosphorylation signals.
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影响因子：
64.5
作者：
Gillette, Michael A.;Satpathy, Shankha;Carr, Steven A.
通讯作者：
Carr, Steven A.
影响因子：
4.6
作者：
Abe Y;Nagano M;Kuga T;Tada A;Isoyama J;Adachi J;Tomonaga T
通讯作者：
Tomonaga T
影响因子：
64.8
作者：
Mosse, Yael P.;Laudenslager, Marci;Longo, Luca;Cole, Kristina A.;Wood, Andrew;Attiyeh, Edward F.;Laquaglia, Michael J.;Sennett, Rachel;Lynch, Jill E.;Perri, Patrizia;Laureys, Genevieve;Speleman, Frank;Kim, Cecilia;Hou, Cuiping;Hakonarson, Hakon;Torkamani, Ali;Schork, Nicholas J.;Brodeur, Garrett M.;Tonini, Gian P.;Rappaport, Eric;Devoto, Marcella;Maris, John M.
通讯作者：
Maris, John M.
DOI：
10.15252/embj.2020105784
发表时间：
2021-02-01
期刊：
The EMBO journal
影响因子：
--
作者：
Borenäs M;Umapathy G;Lai WY;Lind DE;Witek B;Guan J;Mendoza-Garcia P;Masudi T;Claeys A;Chuang TP;El Wakil A;Arefin B;Fransson S;Koster J;Johansson M;Gaarder J;Van den Eynden J;Hallberg B;Palmer RH
通讯作者：
Palmer RH
影响因子：
9.3
作者：
Invergo, Brandon M.;Petursson, Borgthor;Beltrao, Pedro
通讯作者：
Beltrao, Pedro