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Updated: Dec 27, 2025
Glycomics-Guided Glycoproteomics Facilitates Comprehensive Profiling of the Glycoproteome in Complex Tumor Microenvironments
Published on: February 7, 2025
Comprehensive characterization of the phosphoproteome of gastric cancer from endoscopic biopsy specimens
Yuichi Abe1,2, Hidekazu Hirano3, Hirokazu Shoji3
1Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan.
Abstract:
Rationale: Cancer phosphoproteomics can provide insights regarding kinases that can be targeted for therapeutic applications. Monitoring the phosphoproteomics in cancer is expected to play a key role in optimizing treatments with kinase inhibitors. Clinical phosphoproteomics in surgical tissues and patient-derived models has been studied intensively. However, the reported data may not accurately reflect the phosphosignaling status in patients due to the effect of ischemia occurring during surgery or changes in the characteristics of cancer cells when establishing the models. In contrast, endoscopic biopsies have an advantage for clinical phosphoproteomics because they can be rapidly cryo-preserved. We aimed to develop a highly sensitive method for phosphoproteomics in endoscopic biopsies of gastric cancer. Methods: Three tumor biopsies and three normal gastric biopsies were obtained by endoscopy at one time, and subjected to our optimized phosphoproteomics. Phosphopeptides were enriched with an immobilized metal affinity chromatography, and labeled with Tandem Mass Tag reagent. Quantified phosphosites were compared between the pairs of tumor/normal biopsies within same patient. Cancer-specific activated pathways and kinases were identified by pathway enrichment analysis and kinase-substrate enrichment analysis. Results: Our protocol enabled the identification of more than 10,000 class 1 phosphosites from endoscopic biopsies. A comparison between samples from cancer tissue and normal mucosa demonstrated differences in the phosphosignaling, including biomarkers of response to DNA damage. Finally, cancer-specific activation of DNA damage response signaling was validated by additional phosphoproteomics of other patients and western blotting of gastric cancer/normal cells. Conclusion: In summary, our pioneering approach will facilitate more accurate clinical phosphoproteomics in endoscopic biopsies, which can be applied to monitor the activities of therapeutic kinases and, ultimately, can be a useful tool to precision medicine.
Insights
This study presents a new phosphoproteomics method for endoscopic gastric cancer biopsies, enabling precise monitoring of kinase activity for targeted cancer therapies and advancing precision medicine.
Area of Science:
- Oncology
- Proteomics
- Biochemistry
Background:
- Cancer phosphoproteomics identifies therapeutic kinase targets.
- Clinical phosphoproteomics is limited by tissue ischemia and model changes.
- Endoscopic biopsies offer rapid cryopreservation for accurate phosphoproteomics.
Purpose of the Study:
- Develop a sensitive phosphoproteomics method for gastric cancer endoscopic biopsies.
- Identify cancer-specific activated pathways and kinases.
- Establish a tool for monitoring therapeutic kinase activity in precision medicine.
Main Methods:
- Optimized phosphoproteomics protocol applied to paired tumor and normal gastric biopsies.
- Phosphopeptide enrichment using immobilized metal affinity chromatography and Tandem Mass Tag labeling.
- Pathway and kinase-substrate enrichment analysis to identify cancer-specific signaling.
Main Results:
- Identification of over 10,000 class 1 phosphosites from endoscopic biopsies.
- Detected significant differences in phosphosignaling between tumor and normal tissues.
- Validated cancer-specific activation of DNA damage response signaling.
Conclusions:
- Pioneering approach enables accurate clinical phosphoproteomics in endoscopic biopsies.
- Facilitates monitoring of therapeutic kinase activities.
- Provides a valuable tool for precision medicine in gastric cancer treatment.
