Genome-Wide Gene Expression Analysis in Cancer Cells Reveals 3D Growth to Affect ECM and Processes Associated with Cell Adhesion but Not DNA Repair

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.

• Publication year

  2012

• Venue

  PLoS ONE

• Publication date

  2012-04-11

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1371/journal.pone.0034279PMID 22509286PMCID 3324525
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• β₁Integrin/FAK/cortactin signaling is essential for human head and neck cancer resistance to radiotherapy.

  2012influential reference
• p65-Dependent production of interleukin-1β by osteolytic prostate cancer cells causes an induction of chemokine expression in osteoblasts.

  2012cited by this paper
• Targeting FAK radiosensitizes 3-dimensional grown human HNSCC cells through reduced Akt1 and MEK1/2 signaling.

  2012cited by this paper
• Radiobiology goes 3D: how ECM and cell morphology impact on cell survival after irradiation.

  2011influential reference
• Three-dimensional cell growth confers radioresistance by chromatin density modification.

  2010influential reference
• Cancer Statistics, 2009

  2010cited by this paper
• PINCH1 regulates Akt1 activation and enhances radioresistance by inhibiting PP1alpha.

  2010cited by this paper
• The Small Molecule Inhibitor QLT0267 Radiosensitizes Squamous Cell Carcinoma Cells of the Head and Neck

  2009influential reference
• Comparison of gene expression profiles of conjunctival cell lines with primary cultured conjunctival epithelial cells and human conjunctival tissue.

  2009cited by this paper
• Cancer Statistics, 2009

  2009cited by this paper
• Caveolin-1 mediated radioresistance of 3D grown pancreatic cancer cells.

  2009influential reference
• 3D cell cultures of human head and neck squamous cell carcinoma cells are radiosensitized by the focal adhesion kinase inhibitor TAE226.

  2009influential reference
• ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

  2009cited by this paper
• Cross-Talk between Integrins and Oncogenes Modulates Chemosensitivity

  2009cited by this paper
• Three-dimensional polymer scaffolds for high throughput cell-based assay systems.

  2008cited by this paper
• Prognostic Breast Cancer Signature Identified from 3D Culture Model Accurately Predicts Clinical Outcome across Independent Datasets

  2008cited by this paper
• Three-Dimensional Cell Culture Matrices: State of the Art

  2008cited by this paper
• Monolayer and Spheroid Culture of Human Liver Hepatocellular Carcinoma Cell Line Cells Demonstrate Distinct Global Gene Expression Patterns and Functional Phenotypes

  2008cited by this paper
• Beta1 integrin inhibition dramatically enhances radiotherapy efficacy in human breast cancer xenografts.

  2008cited by this paper
• Three-dimensional lithographically defined organotypic tissue arrays for quantitative analysis of morphogenesis and neoplastic progression

  2008cited by this paper
• Integrin-linked kinase: dispensable for radiation survival of three-dimensionally cultured fibroblasts.

  2008influential reference
• Cell shape regulates global histone acetylation in human mammary epithelial cells.

  2007cited by this paper
• Genomic and Morphological Changes of Neuroblastoma Cells in Response to Three-Dimensional Matrices

  2007cited by this paper
• The third dimension bridges the gap between cell culture and live tissue

  2007cited by this paper
• Targeting the tumor microenvironment.

  2007cited by this paper
• Extracellular matrix, nuclear and chromatin structure, and gene expression in normal tissues and malignant tumors: a work in progress.

  2006influential reference
• Beta1 integrin inhibitory antibody induces apoptosis of breast cancer cells, inhibits growth, and distinguishes malignant from normal phenotype in three dimensional cultures and in vivo.

  2006cited by this paper
• Gene expression signature in organized and growth-arrested mammary acini predicts good outcome in breast cancer.

  2006cited by this paper
• Life ins't flat: Taking cancer biology to the next dimension

  2006cited by this paper
• The molecular portrait of in vitro growth by meta-analysis of gene-expression profiles

  2005cited by this paper
• Three‐dimensional culture of melanoma cells profoundly affects gene expression profile: A high density oligonucleotide array study

  2005cited by this paper
• Gene expression perturbation in vitro--a growing case for three-dimensional (3D) culture systems.

  2005cited by this paper
• Modeling tissue-specific signaling and organ function in three dimensions

  2003cited by this paper
• MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data

  2003cited by this paper
• In silico prediction of protein-protein interactions in human macrophages

  2001cited by this paper
• Taking Cell-Matrix Adhesions to the Third Dimension

  2001cited by this paper
• Monitoring cell growth.

  2001cited by this paper
• Systematic variation in gene expression patterns in human cancer cell lines

  2000cited by this paper
• Extracellular matrix proteins protect small cell lung cancer cells against apoptosis: A mechanism for small cell lung cancer growth and drug resistance in vivo

  1999cited by this paper
• Structural Cues from the Tissue Microenvironment Are Essential Determinants of the Human Mammary Epithelial Cell Phenotype

  1998cited by this paper
• New IR dualities in supersymmetric gauge theory in three dimensions

  1998cited by this paper
• Reversion of the Malignant Phenotype of Human Breast Cells in Three-Dimensional Culture and In Vivo by Integrin Blocking Antibodies

  1997cited by this paper
• Perturbation of epidermal barrier function correlates with initiation of cytokine cascade in human skin.

  1994cited by this paper
• Interaction with basement membrane serves to rapidly distinguish growth and differentiation pattern of normal and malignant human breast epithelial cells.

  1992cited by this paper
• Cancer statistics

  1989cited by this paper
• Functional differentiation and alveolar morphogenesis of primary mammary cultures on reconstituted basement membrane.

  1989cited by this paper
• The Influence of Extracellular Matrix on Gene Expression: Is Structure the Message?

  1987cited by this paper

• Human glioblastoma (U87) cells grown in 3D culture showed a radio-resistance to X-ray and proton radiation

  2025cites this paper
• Establishment of Three-Dimensional Polyurethane Model of Lung Cancer and Curcumin Susceptibility Test

  2025cites this paper
• A multi-stage weakly supervised design for spheroid segmentation to explore mesenchymal stem cell differentiation dynamics

  2025cites this paper
• Tissue-Cultured Chondrocytes Survive After Irradiation in 1300 Gy Dose

  2025cites this paper
• Investigation of the anticancer, antimigration and antiangiogenesis effects of an oxadiazole derivative in two- and three-dimensional cultured Ishikawa and Huvec cells; in vitro and in silico studies

  2024cites this paper
• Induction of stearoyl‐CoA desaturase confers cell density‐dependent ferroptosis resistance in melanoma

  2024cites this paper
• In-vitro assays for immuno-oncology drug efficacy assessment and screening for personalized cancer therapy: scopes and challenges

  2024cites this paper
• Are 3D Tumor Cell Spheroids a Utile System for the In Vitro Evaluation of Diagnostic Radiotracers?

  2024cites this paper
• Challenges of Spatially Resolved Metabolism in Cancer Research

  2024cites this paper
• A comparative analysis of stem cell differentiation on 2D and 3D substrates using Raman microspectroscopy.

  2024cites this paper
• Changes of protein expression during tumorosphere formation of small cell lung cancer circulating tumor cells

  2023cites this paper
• Thermoreversible gels for the encapsulation of macrophages: evaluation of polymer type on rheology and cytocompatibility

  2023cites this paper
• UNIVERSIDADE DE SÃO PAULO FACULDADE DE ZOOTECNIA E ENGENHARIA DE ALIMENTOS GIULIANA DE AVILA FERRONATO Produção in vitro de embriões bovinos

  2023cites this paper
• Biomaterial-based in vitro 3D modeling of glioblastoma multiforme

  2023cites this paper
• RNA-seq of nine canine prostate cancer cell lines reveals diverse therapeutic target signatures

  2022cites this paper
• Three-dimensional in vitro culture models in oncology research

  2022cites this paper
• Analysis of Cell Proliferation by Three-Dimensional Culture.

  2022cites this paper
• Models of Head and Neck Squamous Cell Carcinoma Using Bioengineering Approaches.

  2022cites this paper
• Optical tissue clearing associated with 3D imaging: application in preclinical and clinical studies

  2022cites this paper
• Overcoming the barriers of two-dimensional cell culture systems with three-dimensional cell culture systems: techniques, drug discovery, and biomedical applications

  2022cites this paper
• Three-dimensional bioactive hydrogel-based scaffolds for bone regeneration in implant dentistry.

  2021cites this paper
• Key Characteristics of Circulating Tumor Cell Clusters and Implications for Cancer Metastases

  2021cites this paper
• Characterization of in vitro 3D cultures

  2021cites this paper
• Distinct Murine Pancreatic Transcriptomic Signatures during Chronic Pancreatitis Recovery

  2021cites this paper
• Growth environment influences B16.F10 mouse melanoma cell response to gene electrotransfer.

  2021cites this paper
• Drug resistance evaluation in novel 3D in vitro model.

  2021cites this paper
• Screening of differentially expressed genes and identification of AMACR as a prognostic marker in prostate cancer

  2021cites this paper
• miR-29a-3p-dependent COL3A1 and COL5A1 expression reduction assists sulforaphane to inhibit gastric cancer progression.

  2021cites this paper
• Validation of a multicellular tumor microenvironment system for modeling patient tumor biology and drug response

  2021cites this paper
• A Brief Review of Current 3D Genomics Research

  2021cites this paper
• Camphorquinone alters the expression of extracellular proteases in a 3D co-culture model of the oral mucosa.

  2020cites this paper
• Application of an open-chamber multi-channel microfluidic device to test chemotherapy drugs

  2020cites this paper
• 3D In Vitro Model (R)evolution: Unveiling Tumor-Stroma Interactions.

  2020cites this paper
• 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

  2020cites this paper
• 3 Dimensional Cell Culture Techniques in Cancer Research

  2020cites this paper
• 3D Radiation Biology for Identifying Radiosensitizers

  2020cites this paper
• Three-Dimensional Cell Culture Systems in Radiopharmaceutical Cancer Research

  2020cites this paper
• High‐Throughput Tumor‐on‐a‐Chip Platform to Study Tumor–Stroma Interactions and Drug Pharmacokinetics

  2020cites this paper
• H-Ras activation and fibroblast-induced TGF-β signaling promote laminin-332 accumulation and invasion in cutaneous squamous cell carcinoma.

  2020cites this paper
• Pharmacotherapeutic Botanicals for Cancer Chemoprevention

  2020cites this paper
• Routine Optical Clearing of 3D-Cell Cultures: Simplicity Forward

  2020cites this paper
• Temozolomide in Combination With NF-κB Inhibitor Significantly Disrupts the Glioblastoma Multiforme Spheroid Formation

  2020cites this paper
• Application of three dimensional (3D) tumor cell culture systems and mechanism of drug resistance.

  2019cites this paper
• A Synthetic DNA, Multi-Neoantigen Vaccine Drives Predominately MHC Class I CD8+ T-cell Responses, Impacting Tumor Challenge

  2019cites this paper
• Radiation Responses of 2D and 3D Glioblastoma Cells: A Novel, 3D-specific Radioprotective Role of VEGF/Akt Signaling through Functional Activation of NHEJ

  2019cites this paper
• Cellular Spheroids of Mesenchymal Stem Cells and Their Perspectives in Future Healthcare

  2019cites this paper
• Effects of HEMA on Nrf2-related gene expression using a newly developed 3D co-culture model of the oral mucosa.

  2019cites this paper
• Prediction of tumor response of rectal cancer cells via 3D cell culture and in vitro cytotoxicity assay before initiating preoperative chemoradiotherapy.

  2019cites this paper
• Tissue-engineered bone tumor as a reproducible human in vitro model for studies of anti-cancer drugs.

  2019cites this paper
• Connecting Cancer Pathways to Tumor Engines: A Stratification Tool for Colorectal Cancer Combining Human In Vitro Tissue Models with Boolean In Silico Models

  2019cites this paper
• Microenvironment dependent gene expression signatures in reprogrammed human colon normal and cancer cell lines

  2018cites this paper
• Imatinib mesylate elicits extracellular signal-related kinase (ERK) activation and enhances the survival of γ-irradiated epithelial cells.

  2018cites this paper
• Advances in tumor-endothelial cells co-culture and interaction on microfluidics

  2018cites this paper
• Differential effects of α-catenin on the invasion and radiochemosensitivity of human colorectal cancer cells

  2018cites this paper
• In Vitro Models for Studying Invasive Transitions of Ductal Carcinoma In Situ

  2018cites this paper
• Glioblastoma’s Next Top Model: Novel Culture Systems for Brain Cancer Radiotherapy Research

  2018cites this paper
• Evaluating Interaction of Cord Blood Hematopoietic Stem/Progenitor Cells with Functionally Integrated Three‐Dimensional Microenvironments

  2018cites this paper
• Regulation of ATP utilization during metastatic cell migration by collagen architecture

  2018cites this paper
• Optimized delivery of siRNA into 3D tumor spheroid cultures in situ

  2018cites this paper
• Nanotoxicity in cancer research: technical protocols and tips considerations for the use of 3D tumour spheroids

  2017cites this paper
• Exploring Drug Dosing Regimens In Vitro Using Real-Time 3D Spheroid Tumor Growth Assays

  2017cites this paper
• Direct evidence for cell adhesion-mediated radioresistance (CAM-RR) on the level of individual integrin β1 clusters

  2017cites this paper
• Dynamics of nanoparticle diffusion and uptake in three-dimensional cell cultures.

  2017cites this paper
• Microenvironment and Dose-Delivery-Dependent Response after Exposure to Ionizing Radiation in Human Colorectal Cancer Cell Lines

  2017cites this paper
• Inherent aggressive character of invasive and non-invasive cells dictates the in vitro migration pattern of multicellular spheroid

  2017cites this paper
• Enhancement of death receptor-mediated apoptosis in multiple myeloma cells

  2017cites this paper
• Parametrizing the exposure of superparamagnetic iron oxide nanoparticles in cell cultures at different in vitro environments

  2017cites this paper
• Cancer-immune system interplay in the tumor microenvironment

  2017cites this paper
• Small cell lung cancer: model of circulating tumor cell tumorospheres in chemoresistance

  2017cites this paper
• Organotypic three-dimensional cancer cell cultures mirror drug responses in vivo: lessons learned from the inhibition of EGFR signaling

  2017cites this paper
• Preclinical models of pancreatic ductal adenocarcinoma.

  2017cites this paper
• 3D-cultivation of NSCLC cell lines induce gene expression alterations of key cancer-associated pathways and mimic in-vivo conditions

  2017cites this paper
• A secretome analysis reveals that PPARα is upregulated by fractionated-dose γ-irradiation in three-dimensional keratinocyte cultures.

  2017cites this paper
• Distinctive genomic signature of neural and intestinal organoids from familial Parkinson's disease patient‐derived induced pluripotent stem cells

  2017cites this paper
• Improving your four-dimensional image: traveling through a decade of light-sheet-based fluorescence microscopy research

  2017cites this paper
• Antiproliferative activity of amino substituted benzo[b]thieno[2,3-b]pyrido[1,2-a]benzimidazoles explored by 2D and 3D cell culture system.

  2017cites this paper
• High-throughput imaging: Focusing in on drug discovery in 3D.

  2016cites this paper
• Living Cell Microarrays: An Overview of Concepts

  2016cites this paper
• Time-lapse 3-D measurements of a glucose biosensor in multicellular spheroids by light sheet fluorescence microscopy in commercial 96-well plates

  2016cites this paper
• The Cohesive Metastasis Phenotype in Human Prostate Cancer.

  2016cites this paper
• 3D scaffolds in breast cancer research.

  2016cites this paper
• Transcriptomic and metabolic analyses reveal salvage pathways in creatine-deficient AGAT−/− mice

  2016cites this paper
• A novel 3D human glioblastoma cell culture system for modeling drug and radiation responses

  2016cites this paper
• Dose delivery and microenvironment dependent transcriptomic profiles of tumour cells exposed to ionizing radiation

  2016cites this paper
• Methylation of promoter of RBL1 enhances the radioresistance of three dimensional cultured carcinoma cells

  2016cites this paper
• Three-dimensional cell cultures as a new tool in drug discovery

  2016cites this paper
• Microengineered cancer-on-a-chip platforms to study the metastatic microenvironment.

  2016cites this paper
• 3D Cell Culture in a Self-Assembled Nanofiber Environment

  2016cites this paper
• Culture phases, cytotoxicity and protein expressions of agarose hydrogel induced Sp2/0, A549, MCF-7 cell line 3D cultures

  2016cites this paper
• Penetration and intracellular uptake of poly(glycerol-adipate) nanoparticles into three-dimensional brain tumour cell culture models

  2016cites this paper
• Extracellular Matrix-dependent Pathways in Colorectal Cancer Cell Lines Reveal Potential Targets for Anticancer Therapies.

  2016cites this paper
• Evaluation of surrogate tissues as indicators of drug activity in a melanoma skin model

  2016cites this paper
• Gene and miRNA expression signature of Lewis lung carcinoma LLC1 cells in extracellular matrix enriched microenvironment

  2016cites this paper
• Preclinical models of pancreatic ductal adenocarcinoma

  2015cites this paper
• 3D Cell Culture Systems: Advantages and Applications

  2015cites this paper
• Reprogramming mediated radio-resistance of 3D-grown cancer cells

  2015cites this paper
• A transfection method of PS-asODNs targeting ANGPTL4 in multicellular structures of hepatocarcinoma cell line

  2015cites this paper
• A two-scale map of global gene expression for characterising in vitro engineered cells

  2015cites this paper
• Patient-Derived Xenografts as a Model System for Radiation Research.

  2015cites this paper
• Integrative Utilization of Microenvironments, Biomaterials and Computational Techniques for Advanced Tissue Engineering.

  2015cites this paper