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Gene expression profiles in the rat streptococcal cell wall-induced arthritis model identified using microarray analysis.

Rioja I, Clayton CL, Graham SJ, Life PF, Dickson MC - Arthritis Res. Ther. (2004)

Bottom Line: The genes exhibiting the highest fold increase in expression on days -13.8, -13, or 3 were involved in chemotaxis, inflammatory response, cell adhesion and extracellular matrix remodelling.The majority of the downregulated genes were associated with metabolism, transport and regulation of muscle development.These findings improve our understanding of the molecular events that underlie the pathology in this animal model, which is potentially a valuable comparator to human rheumatoid arthritis (RA).

View Article: PubMed Central - HTML - PubMed

Affiliation: Rheumatoid Arthritis Disease Biology Department, GlaxoSmithKline, Medicines Research Centre, Stevenage, UK. inma_rioja@yahoo.com

ABSTRACT
Experimental arthritis models are considered valuable tools for delineating mechanisms of inflammation and autoimmune phenomena. Use of microarray-based methods represents a new and challenging approach that allows molecular dissection of complex autoimmune diseases such as arthritis. In order to characterize the temporal gene expression profile in joints from the reactivation model of streptococcal cell wall (SCW)-induced arthritis in Lewis (LEW/N) rats, total RNA was extracted from ankle joints from naive, SCW injected, or phosphate buffered saline injected animals (time course study) and gene expression was analyzed using Affymetrix oligonucleotide microarray technology (RAE230A). After normalization and statistical analysis of data, 631 differentially expressed genes were sorted into clusters based on their levels and kinetics of expression using Spotfire profile search and K-mean cluster analysis. Microarray-based data for a subset of genes were validated using real-time PCR TaqMan analysis. Analysis of the microarray data identified 631 genes (441 upregulated and 190 downregulated) that were differentially expressed (Delta > 1.8, P < 0.01), showing specific levels and patterns of gene expression. The genes exhibiting the highest fold increase in expression on days -13.8, -13, or 3 were involved in chemotaxis, inflammatory response, cell adhesion and extracellular matrix remodelling. Transcriptome analysis identified 10 upregulated genes (Delta > 5), which have not previously been associated with arthritis pathology and are located in genomic regions associated with autoimmune disease. The majority of the downregulated genes were associated with metabolism, transport and regulation of muscle development. In conclusion, the present study describes the temporal expression of multiple disease-associated genes with potential pathophysiological roles in the reactivation model of SCW-induced arthritis in Lewis (LEW/N) rat. These findings improve our understanding of the molecular events that underlie the pathology in this animal model, which is potentially a valuable comparator to human rheumatoid arthritis (RA).

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Heat map diagram of differential gene expression in joints from the time course study in the streptococcal cell wall (SCW)-induced arthritis in Lewis (LEW/N) rat. Gene expression data were obtained using Affymetrix Rat Genome RAE230A GeneChip®. The cluster diagram represents 631 differentially expressed probes with P < 0.01 and Delta > 1.8. Each column represents a single joint tissue and each row represents a single gene. Expression levels are coloured green for low intensities and red for high intensities (see scale at the top left corner). At the top of the cluster diagram is an enlarged panel including the names and hierarchical clustering order of the individual samples analyzed. Red names are joint tissues from SCW-injected animals, indicating the corresponding time point of sample collection, and blue names are the samples from the phosphate-buffered saline (PBS) control groups. As shown, the major changes in gene expression occurred in samples corresponding to arthritic animals from days -13.8 (4 hours after intra-articular injection of SCW), -13 and 3. N, naïve animals.
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Figure 4: Heat map diagram of differential gene expression in joints from the time course study in the streptococcal cell wall (SCW)-induced arthritis in Lewis (LEW/N) rat. Gene expression data were obtained using Affymetrix Rat Genome RAE230A GeneChip®. The cluster diagram represents 631 differentially expressed probes with P < 0.01 and Delta > 1.8. Each column represents a single joint tissue and each row represents a single gene. Expression levels are coloured green for low intensities and red for high intensities (see scale at the top left corner). At the top of the cluster diagram is an enlarged panel including the names and hierarchical clustering order of the individual samples analyzed. Red names are joint tissues from SCW-injected animals, indicating the corresponding time point of sample collection, and blue names are the samples from the phosphate-buffered saline (PBS) control groups. As shown, the major changes in gene expression occurred in samples corresponding to arthritic animals from days -13.8 (4 hours after intra-articular injection of SCW), -13 and 3. N, naïve animals.

Mentions: An overview of the experimental RAE230A GeneChip® data was obtained using PCA (graphs not shown) [13] and agglomerative hierarchical clustering [14]. Both two-dimensional analyses identified day -13.8 (4 hours after intra-articular injection of SCW), day -13 and day 3 as the time points at which the greatest changes in gene expression in arthritic joints occurred in comparison with corresponding PBS control groups. The results from the hierarchical clustering are shown for visual inspection as a coloured heat map in Fig. 4. As shown on the x-axis (panel at the top of Fig. 4), the majority of the PBS samples clustered together, except the PBS samples from day -13.8, which clustered close to the SCW-injected animals from day 3. This observation indicated the presence of a mild inflammatory response in joints from rats killed 4 hours after the initial intra-articular injection of PBS, when compared with expression levels in joints from naïve animals or the PBS samples from later time points.


Gene expression profiles in the rat streptococcal cell wall-induced arthritis model identified using microarray analysis.

Rioja I, Clayton CL, Graham SJ, Life PF, Dickson MC - Arthritis Res. Ther. (2004)

Heat map diagram of differential gene expression in joints from the time course study in the streptococcal cell wall (SCW)-induced arthritis in Lewis (LEW/N) rat. Gene expression data were obtained using Affymetrix Rat Genome RAE230A GeneChip®. The cluster diagram represents 631 differentially expressed probes with P < 0.01 and Delta > 1.8. Each column represents a single joint tissue and each row represents a single gene. Expression levels are coloured green for low intensities and red for high intensities (see scale at the top left corner). At the top of the cluster diagram is an enlarged panel including the names and hierarchical clustering order of the individual samples analyzed. Red names are joint tissues from SCW-injected animals, indicating the corresponding time point of sample collection, and blue names are the samples from the phosphate-buffered saline (PBS) control groups. As shown, the major changes in gene expression occurred in samples corresponding to arthritic animals from days -13.8 (4 hours after intra-articular injection of SCW), -13 and 3. N, naïve animals.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC1064886&req=5

Figure 4: Heat map diagram of differential gene expression in joints from the time course study in the streptococcal cell wall (SCW)-induced arthritis in Lewis (LEW/N) rat. Gene expression data were obtained using Affymetrix Rat Genome RAE230A GeneChip®. The cluster diagram represents 631 differentially expressed probes with P < 0.01 and Delta > 1.8. Each column represents a single joint tissue and each row represents a single gene. Expression levels are coloured green for low intensities and red for high intensities (see scale at the top left corner). At the top of the cluster diagram is an enlarged panel including the names and hierarchical clustering order of the individual samples analyzed. Red names are joint tissues from SCW-injected animals, indicating the corresponding time point of sample collection, and blue names are the samples from the phosphate-buffered saline (PBS) control groups. As shown, the major changes in gene expression occurred in samples corresponding to arthritic animals from days -13.8 (4 hours after intra-articular injection of SCW), -13 and 3. N, naïve animals.
Mentions: An overview of the experimental RAE230A GeneChip® data was obtained using PCA (graphs not shown) [13] and agglomerative hierarchical clustering [14]. Both two-dimensional analyses identified day -13.8 (4 hours after intra-articular injection of SCW), day -13 and day 3 as the time points at which the greatest changes in gene expression in arthritic joints occurred in comparison with corresponding PBS control groups. The results from the hierarchical clustering are shown for visual inspection as a coloured heat map in Fig. 4. As shown on the x-axis (panel at the top of Fig. 4), the majority of the PBS samples clustered together, except the PBS samples from day -13.8, which clustered close to the SCW-injected animals from day 3. This observation indicated the presence of a mild inflammatory response in joints from rats killed 4 hours after the initial intra-articular injection of PBS, when compared with expression levels in joints from naïve animals or the PBS samples from later time points.

Bottom Line: The genes exhibiting the highest fold increase in expression on days -13.8, -13, or 3 were involved in chemotaxis, inflammatory response, cell adhesion and extracellular matrix remodelling.The majority of the downregulated genes were associated with metabolism, transport and regulation of muscle development.These findings improve our understanding of the molecular events that underlie the pathology in this animal model, which is potentially a valuable comparator to human rheumatoid arthritis (RA).

View Article: PubMed Central - HTML - PubMed

Affiliation: Rheumatoid Arthritis Disease Biology Department, GlaxoSmithKline, Medicines Research Centre, Stevenage, UK. inma_rioja@yahoo.com

ABSTRACT
Experimental arthritis models are considered valuable tools for delineating mechanisms of inflammation and autoimmune phenomena. Use of microarray-based methods represents a new and challenging approach that allows molecular dissection of complex autoimmune diseases such as arthritis. In order to characterize the temporal gene expression profile in joints from the reactivation model of streptococcal cell wall (SCW)-induced arthritis in Lewis (LEW/N) rats, total RNA was extracted from ankle joints from naive, SCW injected, or phosphate buffered saline injected animals (time course study) and gene expression was analyzed using Affymetrix oligonucleotide microarray technology (RAE230A). After normalization and statistical analysis of data, 631 differentially expressed genes were sorted into clusters based on their levels and kinetics of expression using Spotfire profile search and K-mean cluster analysis. Microarray-based data for a subset of genes were validated using real-time PCR TaqMan analysis. Analysis of the microarray data identified 631 genes (441 upregulated and 190 downregulated) that were differentially expressed (Delta > 1.8, P < 0.01), showing specific levels and patterns of gene expression. The genes exhibiting the highest fold increase in expression on days -13.8, -13, or 3 were involved in chemotaxis, inflammatory response, cell adhesion and extracellular matrix remodelling. Transcriptome analysis identified 10 upregulated genes (Delta > 5), which have not previously been associated with arthritis pathology and are located in genomic regions associated with autoimmune disease. The majority of the downregulated genes were associated with metabolism, transport and regulation of muscle development. In conclusion, the present study describes the temporal expression of multiple disease-associated genes with potential pathophysiological roles in the reactivation model of SCW-induced arthritis in Lewis (LEW/N) rat. These findings improve our understanding of the molecular events that underlie the pathology in this animal model, which is potentially a valuable comparator to human rheumatoid arthritis (RA).

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Related in: MedlinePlus