High-Density, Targeted Monitoring of Tyrosine Phosphorylation Reveals Activated Signaling Networks in Human Tumors
Autor: | Lauren E. Stopfer, Daniel Lopez-Ferrer, Aaron S. Gajadhar, Sebastien Gallien, Bhavin Patel, Cameron T. Flower, Forest M. White |
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Rok vydání: | 2020 |
Předmět: |
0301 basic medicine
Phosphopeptides Proteomics Cancer Research Proteome Computer science High density Computational biology CD8-Positive T-Lymphocytes Quantitative accuracy Mass Spectrometry Article Transcriptome 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine Oncogenic signaling Humans Protein Interaction Maps Tyrosine Phosphorylation Chemistry Low input Tyrosine phosphorylation Precision medicine ErbB Receptors 030104 developmental biology Targeted mass spectrometry Oncology A549 Cells 030220 oncology & carcinogenesis Signal transduction Colorectal Neoplasms Protein Processing Post-Translational Chromatography Liquid Signal Transduction |
Zdroj: | Cancer Res bioRxiv |
ISSN: | 1538-7445 |
Popis: | 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, tyrosine phosphorylated internal standard (IS) peptides. Using internal standard guided acquisition, the real-time detection of IS peptides during the analysis initiates the sensitive and selective quantitation of endogenous pTyr targets. This framework allows for reliable quantification of several hundred commonly dysregulated pTyr targets with high quantitative accuracy, enhances target detection success rates, and improves the robustness and usability of targeted acquisition. We establish 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 align with previously reported proteomic, genomic, and transcriptomic molecular characterizations, we highlight instances of new insights gained using pTyr characterization and emphasize 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 enable pTyr-based measurements for applications in precision medicine.SummaryA targeted, mass spectrometry-based method, termed “SureQuant pTyr,” enables highly sensitive and reproducible profiling of tyrosine phosphorylation levels in human colorectal tumors and reveals dysregulated signaling networks for enhanced tumor characterization and biomarker identification. |
Databáze: | OpenAIRE |
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