ArticleJournal of proteome research2016
Quantitative Proteomic and Phosphoproteomic Comparison of 2D and 3D Colon Cancer Cell Culture Models.
Article in Journal of proteome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
40 citing papers in PubMed, 71 citations in OpenAlex.
- Systematic standardization of organ-on-a-chip under controlled flow conditions: Use case with Caki-1 and A549 cell lines.MethodsX · 2026Article
- Proteomic analysis of malignant ascites and its impact on ovarian cancer spheroids.Clinical proteomics · 2026Article
- Targeting Phosphoinositide 3-Kinase to Reduce the Progression of Ovarian Cancer Cells in a 3D Collagen Model.Biomolecules · 2026Article
- Heart Scar-In-A-Dish: Tissue Culture Platform to Study Myocardial Injury and Mechanics In Vitro.Journal of biomechanical engineering · 2026Article
- Proteomic Landscapes of 3D and 2D Models of High-Grade Serous Ovarian Carcinoma: Implications for Carboplatin Response.Journal of proteome research · 2025Article
- A comparison of human skeletal muscle cell maturation in 2D versus 3D culture: A quantitative proteomic study.Physiological reports · 2025Article
- Mass Spectrometry-Based Applications of Spheroids in Cancer Biology.Annual review of analytical chemistry (Palo Alto, Calif.) · 2025Review
- Multi-Omic Evaluation of PLK1 Inhibitor-Onvansertib-In Colorectal Cancer Spheroids.Journal of mass spectrometry : JMS · 2025Article
- Genes and proteins expression profile of 2D vs 3D cancer models: a comparative analysis for better tumor insights.Cytotechnology · 2025Review
- Article
- Lipidomics Profiling Reveals Differential Alterations after FAS Inhibition in 3D Colon Cancer Cell Culture Models.Journal of proteome research · 2024Article
- 3D hUC-MSC spheroids exhibit superior resistance to autophagy and apoptosis of granulosa cells in POF rat model.Reproduction (Cambridge, England) · 2024Article
- Hydrophobic surface induced pro-metastatic cancer cells forBioactive materials · 2024Article
- Integration of pan-omics technologies and three-dimensional in vitro tumor models: an approach toward drug discovery and precision medicine.Molecular cancer · 2024Review
- Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids.Nature communications · 2023Article
- Multi-glycomic analysis of spheroid glycocalyx differentiates 2- and 3-dimensional cell models.Glycobiology · 2023Article
- Lipidomic comparison of 2D and 3D colon cancer cell culture models.Journal of mass spectrometry : JMS · 2022Article
- Proteomic Changes in the Monolayer and Spheroid Melanoma Cell Models of Acquired Resistance to BRAF and MEK1/2 Inhibitors.ACS omega · 2022Article
- Neutrophils Culture in Collagen Gel System.Frontiers in immunology · 2022Article
- Spatial Stable Isotopic Labeling by Amino Acids in Cell Culture: Pulse-Chase Labeling of Three-Dimensional Multicellular Spheroids for Global Proteome Analysis.Analytical chemistry · 2021Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Cell cultures are widely used model systems. Some immortalized cell lines can be grown in either two-dimensional (2D) adherent monolayers or in three-dimensional (3D) multicellular aggregates, or spheroids. Here, the quantitative proteome and phosphoproteome of colon carcinoma HT29 cells cultures in 2D monolayers and 3D spheroids were compared with a stable isotope labeling of amino acids (SILAC) labeling strategy. Two biological replicates from each sample were examined, and notable differences in both the proteome and the phosphoproteome were determined by nanoliquid chromatography tandem mass spectrometry (LC-MS/MS) to assess how growth configuration affects molecular expression. A total of 5867 protein groups, including 2523 phosphoprotein groups and 8733 phosphopeptides were identified in the samples. The Gene Ontology analysis revealed enriched GO terms in the 3D samples for RNA binding, nucleic acid binding, enzyme binding, cytoskeletal protein binding, and histone binding for their molecular functions (MF) and in the process of cell cycle, cytoskeleton organization, and DNA metabolic process for the biological process (BP). The KEGG pathway analysis indicated that 3D cultures are enriched for oxidative phosphorylation pathways, metabolic pathways, peroxisome pathways, and biosynthesis of amino acids. In contrast, analysis of the phosphoproteomes indicated that 3D cultures have decreased phosphorylation correlating with slower growth rates and lower cell-to-extracellular matrix interactions. In sum, these results provide quantitative assessments of the effects on the proteome and phosphoproteome of culturing cells in 2D versus 3D cell culture configurations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.