ArticleScientific reports2018
Improved phosphoproteomic analysis for phosphosignaling and active-kinome profiling in Matrigel-embedded spheroids and patient-derived organoids.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 26 citations in OpenAlex.
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- Contribution of the ELRs to the development of advancedFrontiers in bioengineering and biotechnology · 2024Review
- Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids.Nature communications · 2023Article
- Three-dimensional in vitro culture models in oncology research.Cell & bioscience · 2022Review
- In Vitro Cancer Models: A Closer Look at Limitations on Translation.Bioengineering (Basel, Switzerland) · 2022Review
- The promise of organoids for unraveling the proteomic landscape of the developing human brain.Molecular psychiatry · 2022Review
- The ECM: To Scaffold, or Not to Scaffold, That Is the Question.International journal of molecular sciences · 2021Review
- PlateFlo - A software-controllable plate-scale perfusion system for culture of adherent cells.HardwareX · 2021Article
- Proteomics, Personalized Medicine and Cancer.Cancers · 2021Review
- Three-Dimensional Spheroids as In Vitro Preclinical Models for Cancer Research.Pharmaceutics · 2020Review
- Article
- Comprehensive characterization of the phosphoproteome of gastric cancer from endoscopic biopsy specimens.Theranostics · 2020Article
- An Overview ofBioMed research international · 2020Review
- Proteomics of Colorectal Cancer: Tumors, Organoids, and Cell Cultures-A Minireview.Frontiers in molecular biosciences · 2020Review
- Review
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Many attempts have been made to reproduce the three-dimensional (3D) cancer behavior. For that purpose, Matrigel, an extracellular matrix from Engelbreth-Holm-Swarm mouse sarcoma cell, is widely used in 3D cancer models such as scaffold-based spheroids and patient-derived organoids. However, severe ion suppression caused by contaminants from Matrigel hampers large-scale phosphoproteomics. In the present study, we successfully performed global phosphoproteomics from Matrigel-embedded spheroids and organoids. Using acetone precipitations of tryptic peptides, we identified more than 20,000 class 1 phosphosites from HCT116 spheroids. Bioinformatic analysis revealed that phosphoproteomic status are significantly affected by the method used for the recovery from the Matrigel, i.e., Dispase or Cell Recovery Solution. Furthermore, we observed the activation of several phosphosignalings only in spheroids and not in adherent cells which are coincident with previous study using 3D culture. Finally, we demonstrated that our protocol enabled us to identify more than 20,000 and nearly 3,000 class 1 phosphosites from 1.4 mg and 150 μg of patient-derived organoid, respectively. Additionally, we were able to quantify phosphosites with high reproducibility (r = 0.93 to 0.95). Our phosphoproteomics protocol is useful for analyzing the phosphosignalings of 3D cancer behavior and would be applied for precision medicine with patient-derived organoids.
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