Transcriptomics,Genomics

Dataset Information

28

Comparative Analyses: Expression Differences for Repair Tissue, Chondrocytes, and Mesenchymal Stromal Cells


ABSTRACT: Previous studies have demonstrated relative deficiencies of repair tissue within articular lesions when compared to articular cartilage. While cells occupying the lesions might be of mesenchymal origin, they do not recapitulate differentiation to the chondrogenic phenotype of normal articular chondrocytes. Nevertheless, attributes of repair tissue appear similar to chondrocytes and their precursors at various other different states. We hypothesized that analyses of gene expression profiles for these other cell phenotypes would elucidate the identity of repair tissue cells. Total RNA was isolated from repair tissue samples, neonatal articular cartilage, primary articular chondrocytes maintained in monolayer culture and passaged weekly over 28 days, and bone marrow stromal cells expanded to 80% confluence in monolayer culture. Total RNA was linearly amplified and applied to a 9413-probe set equine-specific cDNA microarray. Four repair tissue samples were compared with a dye-swap experimental design to four samples from each of the three other cell populations for a total of twelve comparisons, or twenty-four slides. Differential expression of genes of interest was validated by real-time quantitative polymerase chain reaction. Statistical analysis revealed that a total of 934 (9.9%), 1839 (19.5%), and 940 (10.0%) probe sets were differentially expressed for the bone marrow stromal cells versus repair tissue, de-differentiated chondrocytes versus repair tissue, and neonatal articular chondrocytes versus repair tissue comparisons, respectively. Transcriptional and translational machinery gene ontological categories were over-represented in transcripts demonstrating stable expression amongst the three comparisons. Biomarkers typically associated with normal articular cartilage and fibrocartilage repair tissue comprised much of the genes with the greatest levels of differential expression amongst the three comparisons. Overall, the profiles indicated that repair cells were more chondrogenic than bone marrow stromal cells and de-differentiated chondrocytes. However, transcript levels of key biomarkers and growth factors for repair tissue cells four months post-operatively fell far short of those of neonatal articular chondrocytes destined to undergo normal cartilage maturation. Overall design: This is a direct comparison between repair tissue and three cell phenotypes: full-thickness neonatal, de-differentiated chondrocytes, and bone marrow stromal cells. Each cell type was compared to repair tissue; four replicates representing different horses were used in each comparison (e.g., 4 REP, 4 DDCs, 4 NEO, 4 BMSCs). Thus, each comparison involves one of four repair tissue samples and one of each cell type with a dye-swap.

INSTRUMENT(S): MacLeod custom equine cartilage cDNA microarray, Version 2

SUBMITTER: Michael J. Mienaltowski  

PROVIDER: GSE14252 | GEO | 2010-03-30

SECONDARY ACCESSION(S): PRJNA111323

REPOSITORIES: GEO

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Publications

Transcriptional comparisons between equine articular repair tissue, neonatal cartilage, cultured chondrocytes and mesenchymal stromal cells.

Mienaltowski Michael J MJ   Huang Liping L   Bathke Arne C AC   Stromberg Arnold J AJ   MacLeod James N JN  

Briefings in functional genomics 20100326 3


Human and equine cell transplant strategies for cartilage lesions usually result in scar tissue that is similar to what is produced naturally during the repair process. In this study, culture-expanded de-differentiated chondrocytes and primary bone marrow stromal cells at a pre-transplantation time-point were compared along with neonatal cartilage to repair tissue. Transcriptional profiling using a 9413-probeset equine-specific cDNA microarray and targeted real-time quantitative polymerase chain  ...[more]

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