title: Phenotyping of chondrocytes in vivo and in vitro using cDNA array technology.
abstract: The cDNA array technology is a powerful tool to analyze a high number of genes in parallel. We investigated whether large-scale gene expression analysis allows clustering and identification of cellular phenotypes of chondrocytes in different in vivo and in vitro conditions. In 100% of cases, clustering analysis distinguished between in vivo and in vitro samples, suggesting fundamental differences in chondrocytes in situ and in vitro regardless of the culture conditions or disease status. It also allowed us to differentiate between healthy and osteoarthritic cartilage. The clustering also revealed the relative importance of the investigated culturing conditions (stimulation agent, stimulation time, bead/monolayer). We augmented the cluster analysis with a statistical search for genes showing differential expression. The identified genes provided hints to the molecular basis of the differences between the sample classes. Our approach shows the power of modern bioinformatic algorithms for understanding and classifying chondrocytic phenotypes in vivo and in vitro. Although it does not generate new experimental data per se, it provides valuable information regarding the biology of chondrocytes and may provide tools for diagnosing and staging the osteoarthritic disease process.
authors.affiliation: Max Planck Institute for Biological Cybernetics, Tübingen, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Zien
authors.forename: Pia Margarethe
authors.initials: PM
authors.lastname: Gebhard
authors.forename: Katrin
authors.initials: K
authors.lastname: Fundel
authors.forename: Thomas
authors.initials: T
authors.lastname: Aigner
mesh_terms: D019902:Chondrocytes / Q000502:physiology*; D016000:Cluster Analysis; D019295:Computational Biology; D018076:DNA, Complementary / Q000032:analysis*; D015870:Gene Expression; D015894:Genome, Human; D006801:Humans; D066298:In Vitro Techniques; D007375:Interleukin-1 / Q000235:genetics; D008233:Lymphotoxin-alpha / Q000235:genetics; D046228:Microarray Analysis / Q000379:methods; D010003:Osteoarthritis / Q000235:genetics; D010641:Phenotype; D018709:Statistics, Nonparametric
chemical_list: D018076:DNA, Complementary; D007375:Interleukin-1; D008233:Lymphotoxin-alpha