Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.
Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts.
Cancer Res. 2021 May 1;81(9):2495-2509. doi: 10.1158/0008-5472.CAN-20-3804. Epub 2021 Jan 28.
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 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. SIGNIFICANCE: SureQuant pTyr is a mass spectrometry-based targeted method that enables sensitive and selective targeted quantitation of several hundred low-abundance tyrosine phosphorylated peptides commonly dysregulated in cancer, including oncogenic signaling networks.
酪氨酸磷酸化（pTyr）在信号转导中起着关键作用，并且在癌症中经常失调。因此，分析肿瘤 pTyr 水平可能会揭示对抗疾病的关键治疗见解。现有的发现和基于靶向的质谱方法用于监测 pTyr 网络，涉及到 pTyr 网络的广泛覆盖、在分析中目标识别的可重复性和准确的定量之间的权衡。为了解决这些限制，我们开发了一种靶向方法，称为“SureQuant pTyr”，它将低输入 pTyr 富集与一组同位素标记的内部标准肽结合，以指导低丰度酪氨酸磷酸肽的数据采集。SureQuant pTyr 允许可靠地定量几百个常见失调的 pTyr 靶标，具有高精度的定量准确性，提高了靶向质谱分析的稳健性和可用性。我们通过使用最小样本输入在人结直肠肿瘤中对 pTyr 信号水平进行了 SureQuant pTyr 分析，描述了患者特异性的致癌驱动机制，从而确立了 SureQuant pTyr 的临床适用性。虽然在某些情况下，pTyr 谱与以前报道的蛋白质组学、基因组学和转录组学分子特征一致，但我们强调了使用 pTyr 特征获得的新见解，并强调了 pTyr 测量与传统生物标志物相结合用于改善患者分层和识别治疗靶点的互补性。这种方法的即用型特性为在研究和临床环境中快速和可重复的 pTyr 分析打开了大门，并为精准医学中的 pTyr 测量提供了应用。意义：SureQuant pTyr 是一种基于质谱的靶向方法，能够灵敏和选择性地定量分析数百种常见失调的低丰度酪氨酸磷酸化肽，包括致癌信号网络。
