High-Density, Targeted Monitoring of Tyrosine Phosphorylation Reveals Activated Signaling Networks in Human Tumors.
High-Density, Targeted Monitoring of Tyrosine Phosphorylation Reveals Activated Signaling Networks in Human Tumors.
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DOI：
10.1158/0008-5472.can-20-3804
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发表时间：
2021-05-01
期刊：
影响因子：
11.2
通讯作者：
White FM
中科院分区：
文献类型：
--
作者：
Stopfer LE;Flower CT;Gajadhar AS;Patel B;Gallien S;Lopez-Ferrer D;White FM
酪氨酸磷酸化（pTyr）在信号转导中起关键作用，并且通常在癌症中失调。因此，分析肿瘤pTyr水平可能揭示对对抗疾病至关重要的治疗见解。用于监测pTyr网络的现有发现和基于靶向质谱的方法涉及pTyr网络的广泛覆盖范围、分析中目标识别的可重复性和准确量化之间的权衡。为了解决这些限制，我们开发了一种靶向方法，称为“SureQuant pTyr”，将低输入pTyr富集与一组同位素标记的内标（IS）肽偶联，以指导低丰度酪氨酸磷酸肽的数据采集。SureQuant pTyr允许以高定量准确度可靠地定量数百种常见失调的pTyr靶标，从而提高靶向质谱分析的稳健性和可用性。我们通过使用最少的样本输入分析人结直肠肿瘤中的pTyr信号传导水平，确定了SureQuant pTyr的临床适用性，表征了患者特异性致癌驱动机制。虽然在某些情况下，pTyr图谱与先前报道的蛋白质组学、基因组学和转录组学分子表征一致，但我们强调了使用pTyr表征获得的新见解的实例，并强调了pTyr测量与传统生物标志物的互补性，以改善患者分层和识别治疗靶点。这种方法的交钥匙性质为研究和临床环境中快速和可重现的pTyr分析打开了大门，并使基于pTyr的测量能够应用于精密医学。
Tyrosine phosphorylation (pTyr) plays a pivotal role in signal transduction and is commonly dysregulated in cancer. As a result, profiling tumor pTyr levels may reveal therapeutic insights critical to combating disease. Existing discovery and targeted mass spectrometry-based methods used to monitor pTyr networks involve a tradeoff between broad coverage of the pTyr network, reproducibility in target identification across analyses, and accurate quantification. To address these limitations, we developed a targeted approach, termed “SureQuant pTyr,” coupling low input pTyr enrichment with a panel of isotopically labeled internal standard (IS) peptides to guide data acquisition of low-abundance tyrosine phosphopeptides. SureQuant pTyr allowed for reliable quantification of several hundred commonly dysregulated pTyr targets with high quantitative accuracy, improving the robustness and usability of targeted mass spectrometry assays. We established the clinical applicability of SureQuant pTyr by profiling pTyr signaling levels in human colorectal tumors using minimal sample input, characterizing patient specific oncogenic driving mechanisms. While in some cases pTyr profiles aligned with previously reported proteomic, genomic, and transcriptomic molecular characterizations, we highlighted instances of new insights gained using pTyr characterization and emphasized the complementary nature of pTyr measurements with traditional biomarkers for improving patient stratification and identifying therapeutic targets. The turn-key nature of this approach opens the door to rapid and reproducible pTyr profiling in research and clinical settings alike and enables pTyr-based measurements for applications in precision medicine.