ArticlePloS one2012
Genome-wide gene expression analysis in cancer cells reveals 3D growth to affect ECM and processes associated with cell adhesion but not DNA repair.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
66 citing papers in PubMed, 128 citations in OpenAlex.
- α7 integrin co-regulates chromatin accessibility and gene expression in HPV-negative head and neck cancer.Signal transduction and targeted therapy · 2026Article
- Beyond DNA damage: 3D tumor models and the integrin mechanobiology of radioresistance.Journal of experimental & clinical cancer research : CR · 2026Review
- Tissue-Cultured Chondrocytes Survive After Irradiation in 1300 Gy Dose.Biomedicines · 2025Article
- A multi-stage weakly supervised design for spheroid segmentation to explore mesenchymal stem cell differentiation dynamics.BMC bioinformatics · 2025Article
- Are 3D Tumor Cell Spheroids a Utile System for the In Vitro Evaluation of Diagnostic Radiotracers?ACS omega · 2024Article
- Challenges of Spatially Resolved Metabolism in Cancer Research.Metabolites · 2024Review
- Biomaterial-basedCancer pathogenesis and therapy · 2023Review
- Technical report: liquid overlay technique allows the generation of homogeneous osteosarcoma, glioblastoma, lung and prostate adenocarcinoma spheroids that can be used for drug cytotoxicity measurements.Frontiers in bioengineering and biotechnology · 2023Article
- Changes of protein expression during tumorosphere formation of small cell lung cancer circulating tumor cells.Oncology research · 2023Article
- Three-dimensional in vitro culture models in oncology research.Cell & bioscience · 2022Review
- Optical tissue clearing associated with 3D imaging: application in preclinical and clinical studies.Histochemistry and cell biology · 2022Review
- RNA-seq of nine canine prostate cancer cell lines reveals diverse therapeutic target signatures.Cancer cell international · 2022Article
- Analysis of Cell Proliferation by Three-Dimensional Culture.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Growth environment influences B16.F10 mouse melanoma cell response to gene electrotransfer.Bioelectrochemistry (Amsterdam, Netherlands) · 2021Article
- Validation of a multicellular tumor microenvironment system for modeling patient tumor biology and drug response.Scientific reports · 2021Article
- Distinct Murine Pancreatic Transcriptomic Signatures during Chronic Pancreatitis Recovery.Mediators of inflammation · 2021Article
- Application of an open-chamber multi-channel microfluidic device to test chemotherapy drugs.Scientific reports · 2020Article
- Development of a 3D functional assay and identification of biomarkers, predictive for response of high-grade serous ovarian cancer (HGSOC) patients to poly-ADP ribose polymerase inhibitors (PARPis): targeted therapy.Journal of translational medicine · 2020Article
- High-Throughput Tumor-on-a-Chip Platform to Study Tumor-Stroma Interactions and Drug Pharmacokinetics.Advanced healthcare materials · 2020Article
- Review
6 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell morphology determines cell behavior, signal transduction, protein-protein interaction, and responsiveness to external stimuli. In cancer, these functions profoundly contribute to resistance mechanisms to radio- and chemotherapy. With regard to this aspect, this study compared the genome wide gene expression in exponentially growing cell lines from different tumor entities, lung carcinoma and squamous cell carcinoma, under more physiological three-dimensional (3D) versus monolayer cell culture conditions. Whole genome cDNA microarray analysis was accomplished using the Affymetrix HG U133 Plus 2.0 gene chip. Significance analysis of microarray (SAM) and t-test analysis revealed significant changes in gene expression profiles of 3D relative to 2D cell culture conditions. These changes affected the extracellular matrix and were mainly associated with biological processes like tissue development, cell adhesion, immune system and defense response in contrast to terms related to DNA repair, which lacked significant alterations. Selected genes were verified by semi-quantitative RT-PCR and Western blotting. Additionally, we show that 3D growth mediates a significant increase in tumor cell radio- and chemoresistance relative to 2D. Our findings show significant gene expression differences between 3D and 2D cell culture systems and indicate that cellular responsiveness to external stress such as ionizing radiation and chemotherapeutics is essentially influenced by differential expression of genes involved in the regulation of integrin signaling, cell shape and cell-cell contact.
Indexed as
Identifiers
What OpenQuestion holds
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.