ArticleCancer research2021
Quantitative Analysis of Tyrosine Phosphorylation from FFPE Tissues Reveals Patient-Specific Signaling Networks.
Article in Cancer research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 37 citations in OpenAlex.
- Tyrosine phosphoproteome profiling identifies cell-intrinsic signals limiting the efficacy of tyrosine kinase inhibitor therapies.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Multiplexed Quantitation of Post-Translationally Modified Peptides in Single Cells Using Triggered MS/MS Combined with Super Heavy Tandem Mass Tags.Journal of proteome research · 2026Article
- Critical role of cell competition in gliomagenesis.bioRxiv : the preprint server for biology · 2026Article
- Spatial omics technology potentially promotes the progress of tumor immunotherapy.British journal of cancer · 2025Review
- An Optimized SP3 Sample Processing Workflow for In-Depth and Reproducible Phosphoproteomics.Journal of proteome research · 2025Article
- Structural and systems characterization of phosphorylation on metabolic enzymes identifies sex-specific metabolic reprogramming in obesity.Molecular cell · 2025Article
- R2HaPpY: Rapid-robust phosphotyrosine peptide enrichment using HaloTag-Src SH2 pY superbinder.bioRxiv : the preprint server for biology · 2025Article
- Overlap of Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Matched Tissues for Proteomics and Phosphoproteomics.ACS omega · 2025Article
- Phosphoproteomic Analysis Identified Mutual Phosphorylation of FAK and Src as a Mechanism of Osimertinib Resistance inJTO clinical and research reports · 2024Article
- Illuminating function of the understudied druggable kinome.Drug discovery today · 2024Review
- Patient-specific signaling signatures predict optimal therapeutic combinations for triple negative breast cancer.Molecular cancer · 2024Article
- A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Phosphoproteomic Changes Induced by Cell-Derived Matrix and Their Effect on Tumor Cell Migration and Cytoskeleton Remodeling.ACS biomaterials science & engineering · 2023Article
- Actuated tissue engineered muscle grafts restore functional mobility after volumetric muscle loss.Biomaterials · 2023Article
- ASAP─Automated Sonication-Free Acid-Assisted Proteomes─from Cells and FFPE Tissues.Analytical chemistry · 2023Article
- Highly Accurate and Robust Absolute Quantification of Target Proteins in Formalin-Fixed Paraffin-Embedded (FFPE) Tissues by LC-MS.Analytical chemistry · 2023Article
- Proteomics separates adult-type diffuse high-grade gliomas in metabolic subgroups independent of 1p/19q codeletion and across IDH mutational status.Cell reports. Medicine · 2023Article
- Article
- Comparative Assessment of Quantification Methods for Tumor Tissue Phosphoproteomics.Analytical chemistry · 2022Article
- Dendritic cell-mediated cross presentation of tumor-derived peptides is biased against plasma membrane proteins.Journal for immunotherapy of cancer · 2022Article
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
Abstract
Human tissue samples commonly preserved as formalin-fixed paraffin-embedded (FFPE) tissues after diagnostic or surgical procedures in the clinic represent an invaluable source of clinical specimens for in-depth characterization of signaling networks to assess therapeutic options. Tyrosine phosphorylation (pTyr) plays a fundamental role in cellular processes and is commonly dysregulated in cancer but has not been studied to date in FFPE samples. In addition, pTyr analysis that may otherwise inform therapeutic interventions for patients has been limited by the requirement for large amounts of frozen tissue. Here we describe a method for highly sensitive, quantitative analysis of pTyr signaling networks, with hundreds of sites quantified from one to two 10-μm sections of FFPE tissue specimens. A combination of optimized magnetic bead-based sample processing, optimized pTyr enrichment strategies, and tandem mass tag multiplexing enabled in-depth coverage of pTyr signaling networks from small amounts of input material. Phosphotyrosine profiles of flash-frozen and FFPE tissues derived from the same tumors suggested that FFPE tissues preserve pTyr signaling characteristics in patient-derived xenografts and archived clinical specimens. pTyr analysis of FFPE tissue sections from breast cancer tumors as well as lung cancer tumors highlighted patient-specific oncogenic driving kinases, indicating potential targeted therapies for each patient. These data suggest the capability for direct translational insight from pTyr analysis of small amounts of FFPE tumor tissue specimens. SIGNIFICANCE: This study reports a highly sensitive method utilizing FFPE tissues to identify dysregulated signaling networks in patient tumors, opening the door for direct translational insights from FFPE tumor tissue banks in hospitals.
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