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Temporal gene expression profiling of the rat knee joint capsule during immobilization-induced joint contractures.

Wong K, Sun F, Trudel G, Sebastiani P, Laneuville O - BMC Musculoskelet Disord (2015)

Bottom Line: Recovering range of motion is recognized by arthritic patients as their preference for improved health outcome secondary only to pain management.Clusters of genes with similar profiles of expression included a total of 162 genes displaying at least a 2 fold change compared to week 1.The identification of altered expression of genes and biochemical pathways in the joint capsule provides potential targets for the therapy of knee flexion contractures.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, ON, K1H 8M5, Canada. wong.kayleigh@gmail.com.

ABSTRACT

Background: Contractures of the knee joint cause disability and handicap. Recovering range of motion is recognized by arthritic patients as their preference for improved health outcome secondary only to pain management. Clinical and experimental studies provide evidence that the posterior knee capsule prevents the knee from achieving full extension. This study was undertaken to investigate the dynamic changes of the joint capsule transcriptome during the progression of knee joint contractures induced by immobilization. We performed a microarray analysis of genes expressed in the posterior knee joint capsule following induction of a flexion contracture by rigidly immobilizing the rat knee joint over a time-course of 16 weeks. Fold changes of expression values were measured and co-expressed genes were identified by clustering based on time-series analysis. Genes associated with immobilization were further analyzed to reveal pathways and biological significance and validated by immunohistochemistry on sagittal sections of knee joints.

Results: Changes in expression with a minimum of 1.5 fold changes were dominated by a decrease in expression for 7732 probe sets occurring at week 8 while the expression of 2251 probe sets increased. Clusters of genes with similar profiles of expression included a total of 162 genes displaying at least a 2 fold change compared to week 1. Functional analysis revealed ontology categories corresponding to triglyceride metabolism, extracellular matrix and muscle contraction. The altered expression of selected genes involved in the triglyceride biosynthesis pathway; AGPAT-9, and of the genes P4HB and HSP47, both involved in collagen synthesis, was confirmed by immunohistochemistry.

Conclusions: Gene expression in the knee joint capsule was sensitive to joint immobility and provided insights into molecular mechanisms relevant to the pathophysiology of knee flexion contractures. Capsule responses to immobilization was dynamic and characterized by modulation of at least three reaction pathways; down regulation of triglyceride biosynthesis, alteration of extracellular matrix degradation and muscle contraction gene expression. The posterior knee capsule may deploy tissue-specific patterns of mRNA regulatory responses to immobilization. The identification of altered expression of genes and biochemical pathways in the joint capsule provides potential targets for the therapy of knee flexion contractures.

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Time-series analysis to identify clusters of expression associated with immobilization. Posterior knee capsule samples from sham-operated and immobilized rats joints were harvested at time points of 1, 2, 4, 8, and 16 weeks and were subjected to genome-wide microarray analysis. Expression values from the sham and immobilized samples were analyzed separately to quantify fold changes and to cluster genes with similar profiles of expression. The two lists of genes included in clusters generated from temporal expression analysis were compared to identify similarities. Genes unique to immobilization were analyzed in depth to gain insight on the biological significance by integration of CAGED, GO, KEGG, Reactome, and literature biocuration results. Immunohistochemistry was used to validate the microarray results for selected genes
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Fig3: Time-series analysis to identify clusters of expression associated with immobilization. Posterior knee capsule samples from sham-operated and immobilized rats joints were harvested at time points of 1, 2, 4, 8, and 16 weeks and were subjected to genome-wide microarray analysis. Expression values from the sham and immobilized samples were analyzed separately to quantify fold changes and to cluster genes with similar profiles of expression. The two lists of genes included in clusters generated from temporal expression analysis were compared to identify similarities. Genes unique to immobilization were analyzed in depth to gain insight on the biological significance by integration of CAGED, GO, KEGG, Reactome, and literature biocuration results. Immunohistochemistry was used to validate the microarray results for selected genes

Mentions: To capture gene expression dynamics, CAGED algorithm was applied to log 2 transformed data included in the complete data sets. Probe sets with at least one time point observation above or below 2 fold change compared to week 1, were considered in the clustering analysis and summed to a total of 2322 for the sham operated group and to 3516 for the immobilization group (Fig. 1). Clustering of sham-operated data identified 13 clusters each including genes with a similar profile of expression. Eight clusters with center values, in log 2 base, higher than 1 or lower than −1, were selected for in depth analysis. The total number of probe sets included in the eight sham-operated clusters was equal to 493 corresponding to 335 different genes. Cluster analysis of the immobilization gene-expression time series identified 8 distinct clusters. Cluster center values were used to select clusters for in depth analysis and additional grouping. Six clusters were assigned to one of the three major temporal groups according to increased (clusters 1 and 7), variable (clusters 5 and 6), or decreased expression (clusters 4 and 8) (Fig. 3). The total number of probe sets included the 6 clusters of the immobility group was 396 corresponding to 288 genes.Fig. 2


Temporal gene expression profiling of the rat knee joint capsule during immobilization-induced joint contractures.

Wong K, Sun F, Trudel G, Sebastiani P, Laneuville O - BMC Musculoskelet Disord (2015)

Time-series analysis to identify clusters of expression associated with immobilization. Posterior knee capsule samples from sham-operated and immobilized rats joints were harvested at time points of 1, 2, 4, 8, and 16 weeks and were subjected to genome-wide microarray analysis. Expression values from the sham and immobilized samples were analyzed separately to quantify fold changes and to cluster genes with similar profiles of expression. The two lists of genes included in clusters generated from temporal expression analysis were compared to identify similarities. Genes unique to immobilization were analyzed in depth to gain insight on the biological significance by integration of CAGED, GO, KEGG, Reactome, and literature biocuration results. Immunohistochemistry was used to validate the microarray results for selected genes
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4443538&req=5

Fig3: Time-series analysis to identify clusters of expression associated with immobilization. Posterior knee capsule samples from sham-operated and immobilized rats joints were harvested at time points of 1, 2, 4, 8, and 16 weeks and were subjected to genome-wide microarray analysis. Expression values from the sham and immobilized samples were analyzed separately to quantify fold changes and to cluster genes with similar profiles of expression. The two lists of genes included in clusters generated from temporal expression analysis were compared to identify similarities. Genes unique to immobilization were analyzed in depth to gain insight on the biological significance by integration of CAGED, GO, KEGG, Reactome, and literature biocuration results. Immunohistochemistry was used to validate the microarray results for selected genes
Mentions: To capture gene expression dynamics, CAGED algorithm was applied to log 2 transformed data included in the complete data sets. Probe sets with at least one time point observation above or below 2 fold change compared to week 1, were considered in the clustering analysis and summed to a total of 2322 for the sham operated group and to 3516 for the immobilization group (Fig. 1). Clustering of sham-operated data identified 13 clusters each including genes with a similar profile of expression. Eight clusters with center values, in log 2 base, higher than 1 or lower than −1, were selected for in depth analysis. The total number of probe sets included in the eight sham-operated clusters was equal to 493 corresponding to 335 different genes. Cluster analysis of the immobilization gene-expression time series identified 8 distinct clusters. Cluster center values were used to select clusters for in depth analysis and additional grouping. Six clusters were assigned to one of the three major temporal groups according to increased (clusters 1 and 7), variable (clusters 5 and 6), or decreased expression (clusters 4 and 8) (Fig. 3). The total number of probe sets included the 6 clusters of the immobility group was 396 corresponding to 288 genes.Fig. 2

Bottom Line: Recovering range of motion is recognized by arthritic patients as their preference for improved health outcome secondary only to pain management.Clusters of genes with similar profiles of expression included a total of 162 genes displaying at least a 2 fold change compared to week 1.The identification of altered expression of genes and biochemical pathways in the joint capsule provides potential targets for the therapy of knee flexion contractures.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, ON, K1H 8M5, Canada. wong.kayleigh@gmail.com.

ABSTRACT

Background: Contractures of the knee joint cause disability and handicap. Recovering range of motion is recognized by arthritic patients as their preference for improved health outcome secondary only to pain management. Clinical and experimental studies provide evidence that the posterior knee capsule prevents the knee from achieving full extension. This study was undertaken to investigate the dynamic changes of the joint capsule transcriptome during the progression of knee joint contractures induced by immobilization. We performed a microarray analysis of genes expressed in the posterior knee joint capsule following induction of a flexion contracture by rigidly immobilizing the rat knee joint over a time-course of 16 weeks. Fold changes of expression values were measured and co-expressed genes were identified by clustering based on time-series analysis. Genes associated with immobilization were further analyzed to reveal pathways and biological significance and validated by immunohistochemistry on sagittal sections of knee joints.

Results: Changes in expression with a minimum of 1.5 fold changes were dominated by a decrease in expression for 7732 probe sets occurring at week 8 while the expression of 2251 probe sets increased. Clusters of genes with similar profiles of expression included a total of 162 genes displaying at least a 2 fold change compared to week 1. Functional analysis revealed ontology categories corresponding to triglyceride metabolism, extracellular matrix and muscle contraction. The altered expression of selected genes involved in the triglyceride biosynthesis pathway; AGPAT-9, and of the genes P4HB and HSP47, both involved in collagen synthesis, was confirmed by immunohistochemistry.

Conclusions: Gene expression in the knee joint capsule was sensitive to joint immobility and provided insights into molecular mechanisms relevant to the pathophysiology of knee flexion contractures. Capsule responses to immobilization was dynamic and characterized by modulation of at least three reaction pathways; down regulation of triglyceride biosynthesis, alteration of extracellular matrix degradation and muscle contraction gene expression. The posterior knee capsule may deploy tissue-specific patterns of mRNA regulatory responses to immobilization. The identification of altered expression of genes and biochemical pathways in the joint capsule provides potential targets for the therapy of knee flexion contractures.

Show MeSH
Related in: MedlinePlus