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A systems biology approach to defining regulatory mechanisms for cartilage and tendon cell phenotypes

View Article: PubMed Central - PubMed

ABSTRACT

Phenotypic plasticity of adult somatic cells has provided emerging avenues for the development of regenerative therapeutics. In musculoskeletal biology the mechanistic regulatory networks of genes governing the phenotypic plasticity of cartilage and tendon cells has not been considered systematically. Additionally, a lack of strategies to effectively reproduce in vitro functional models of cartilage and tendon is retarding progress in this field. De- and redifferentiation represent phenotypic transitions that may contribute to loss of function in ageing musculoskeletal tissues. Applying a systems biology network analysis approach to global gene expression profiles derived from common in vitro culture systems (monolayer and three-dimensional cultures) this study demonstrates common regulatory mechanisms governing de- and redifferentiation transitions in cartilage and tendon cells. Furthermore, evidence of convergence of gene expression profiles during monolayer expansion of cartilage and tendon cells, and the expression of key developmental markers, challenges the physiological relevance of this culture system. The study also suggests that oxidative stress and PI3K signalling pathways are key modulators of in vitro phenotypes for cells of musculoskeletal origin.

No MeSH data available.


Related in: MedlinePlus

(a) Principal component analysis of gene expression data from 36 Illumina arrays profiling three cell types (cell type) and isolated from three environmental conditions (condition) – native (cartilage or tendon tissue), monolayer (passage 5, dedifferentiated), or 3D (alginate or fibrin cultures). The figure demononstrates the clustering of samples using the first two principal components (PC1, PC2), which together explain >70% of the variation in the data for the top 500 most covariant genes, Supplementary Data, SD1. Covariance is used to measure how random genes change with respect to one another. The figure demonstrates that the genes showing the greatest covariance explain the majority of the differences observed between the experimental groups. Cells in monolayer, derived from cartilage, tendon, or dermal fibroblasts, group when only the most covariant genes are considered. Chondrocytes and tenocytes in three-dimensional cultures also group together, but not with their tissues of origin. Overall, there were fewer genes differentially expressed between native tendon and 3D fibrin cultures than between native cartilage and 3D alginate cultures. This greater complexity in the synthetic profile of cartilage is indicated by the clustering of cartilage samples distant from all other samples. (b) Matrix of up- and down-regulated genes for selected pairwise comparisons involving different environmental conditions for chondrocytes and tenocytes. Values indicate the number of up- or down- regulated genes with a log2 fold change >+/−0.5, FDR <0.01 and a log-odds ratio of expression >0 (~50%). Duplicate Entrez gene identifiers are removed. The fewest differentially expressed genes were found between cultured cells, for example only 154 genes were more highly expressed in chondrocytes relative to monolayer tenocytes; 135 genes had lower expression in chondrocytes than tenocytes (289 differentially expressed in total). Number of genes showing higher expression (positive log2 fold-change, upward hatch) and lower expression (negative log2 fold-change, downward hatch) in each comparison are indicated.
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f1: (a) Principal component analysis of gene expression data from 36 Illumina arrays profiling three cell types (cell type) and isolated from three environmental conditions (condition) – native (cartilage or tendon tissue), monolayer (passage 5, dedifferentiated), or 3D (alginate or fibrin cultures). The figure demononstrates the clustering of samples using the first two principal components (PC1, PC2), which together explain >70% of the variation in the data for the top 500 most covariant genes, Supplementary Data, SD1. Covariance is used to measure how random genes change with respect to one another. The figure demonstrates that the genes showing the greatest covariance explain the majority of the differences observed between the experimental groups. Cells in monolayer, derived from cartilage, tendon, or dermal fibroblasts, group when only the most covariant genes are considered. Chondrocytes and tenocytes in three-dimensional cultures also group together, but not with their tissues of origin. Overall, there were fewer genes differentially expressed between native tendon and 3D fibrin cultures than between native cartilage and 3D alginate cultures. This greater complexity in the synthetic profile of cartilage is indicated by the clustering of cartilage samples distant from all other samples. (b) Matrix of up- and down-regulated genes for selected pairwise comparisons involving different environmental conditions for chondrocytes and tenocytes. Values indicate the number of up- or down- regulated genes with a log2 fold change >+/−0.5, FDR <0.01 and a log-odds ratio of expression >0 (~50%). Duplicate Entrez gene identifiers are removed. The fewest differentially expressed genes were found between cultured cells, for example only 154 genes were more highly expressed in chondrocytes relative to monolayer tenocytes; 135 genes had lower expression in chondrocytes than tenocytes (289 differentially expressed in total). Number of genes showing higher expression (positive log2 fold-change, upward hatch) and lower expression (negative log2 fold-change, downward hatch) in each comparison are indicated.

Mentions: Using the top 500 genes showing the greatest covariance in expression (Supplementary Data, SD1) 36 samples could be clustered into four distinct groups by principal component analysis (PCA), Fig. 1a. The first two principal components described 70.2% of the variation in the data. These groups consisted of: (i) native cartilage; (ii) native tendon; (iii) all monolayer cultured chondrocytes, tenocytes, and fibroblasts; (iv) or three-dimensional culture systems (alginate or fibrin cultures). Overall, few genes were differentially expressed between cell types in monolayer at passage five or between three-dimensional culture conditions, Fig. 1b. The variation in the gene expression was suggestive of a convergence of expression profiles for cells in monolayer and a failure of chondrocytes or tenocytes in three-dimensional culture to recapitulate differentiation status to parity with native tissue.


A systems biology approach to defining regulatory mechanisms for cartilage and tendon cell phenotypes
(a) Principal component analysis of gene expression data from 36 Illumina arrays profiling three cell types (cell type) and isolated from three environmental conditions (condition) – native (cartilage or tendon tissue), monolayer (passage 5, dedifferentiated), or 3D (alginate or fibrin cultures). The figure demononstrates the clustering of samples using the first two principal components (PC1, PC2), which together explain >70% of the variation in the data for the top 500 most covariant genes, Supplementary Data, SD1. Covariance is used to measure how random genes change with respect to one another. The figure demonstrates that the genes showing the greatest covariance explain the majority of the differences observed between the experimental groups. Cells in monolayer, derived from cartilage, tendon, or dermal fibroblasts, group when only the most covariant genes are considered. Chondrocytes and tenocytes in three-dimensional cultures also group together, but not with their tissues of origin. Overall, there were fewer genes differentially expressed between native tendon and 3D fibrin cultures than between native cartilage and 3D alginate cultures. This greater complexity in the synthetic profile of cartilage is indicated by the clustering of cartilage samples distant from all other samples. (b) Matrix of up- and down-regulated genes for selected pairwise comparisons involving different environmental conditions for chondrocytes and tenocytes. Values indicate the number of up- or down- regulated genes with a log2 fold change >+/−0.5, FDR <0.01 and a log-odds ratio of expression >0 (~50%). Duplicate Entrez gene identifiers are removed. The fewest differentially expressed genes were found between cultured cells, for example only 154 genes were more highly expressed in chondrocytes relative to monolayer tenocytes; 135 genes had lower expression in chondrocytes than tenocytes (289 differentially expressed in total). Number of genes showing higher expression (positive log2 fold-change, upward hatch) and lower expression (negative log2 fold-change, downward hatch) in each comparison are indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC5037390&req=5

f1: (a) Principal component analysis of gene expression data from 36 Illumina arrays profiling three cell types (cell type) and isolated from three environmental conditions (condition) – native (cartilage or tendon tissue), monolayer (passage 5, dedifferentiated), or 3D (alginate or fibrin cultures). The figure demononstrates the clustering of samples using the first two principal components (PC1, PC2), which together explain >70% of the variation in the data for the top 500 most covariant genes, Supplementary Data, SD1. Covariance is used to measure how random genes change with respect to one another. The figure demonstrates that the genes showing the greatest covariance explain the majority of the differences observed between the experimental groups. Cells in monolayer, derived from cartilage, tendon, or dermal fibroblasts, group when only the most covariant genes are considered. Chondrocytes and tenocytes in three-dimensional cultures also group together, but not with their tissues of origin. Overall, there were fewer genes differentially expressed between native tendon and 3D fibrin cultures than between native cartilage and 3D alginate cultures. This greater complexity in the synthetic profile of cartilage is indicated by the clustering of cartilage samples distant from all other samples. (b) Matrix of up- and down-regulated genes for selected pairwise comparisons involving different environmental conditions for chondrocytes and tenocytes. Values indicate the number of up- or down- regulated genes with a log2 fold change >+/−0.5, FDR <0.01 and a log-odds ratio of expression >0 (~50%). Duplicate Entrez gene identifiers are removed. The fewest differentially expressed genes were found between cultured cells, for example only 154 genes were more highly expressed in chondrocytes relative to monolayer tenocytes; 135 genes had lower expression in chondrocytes than tenocytes (289 differentially expressed in total). Number of genes showing higher expression (positive log2 fold-change, upward hatch) and lower expression (negative log2 fold-change, downward hatch) in each comparison are indicated.
Mentions: Using the top 500 genes showing the greatest covariance in expression (Supplementary Data, SD1) 36 samples could be clustered into four distinct groups by principal component analysis (PCA), Fig. 1a. The first two principal components described 70.2% of the variation in the data. These groups consisted of: (i) native cartilage; (ii) native tendon; (iii) all monolayer cultured chondrocytes, tenocytes, and fibroblasts; (iv) or three-dimensional culture systems (alginate or fibrin cultures). Overall, few genes were differentially expressed between cell types in monolayer at passage five or between three-dimensional culture conditions, Fig. 1b. The variation in the gene expression was suggestive of a convergence of expression profiles for cells in monolayer and a failure of chondrocytes or tenocytes in three-dimensional culture to recapitulate differentiation status to parity with native tissue.

View Article: PubMed Central - PubMed

ABSTRACT

Phenotypic plasticity of adult somatic cells has provided emerging avenues for the development of regenerative therapeutics. In musculoskeletal biology the mechanistic regulatory networks of genes governing the phenotypic plasticity of cartilage and tendon cells has not been considered systematically. Additionally, a lack of strategies to effectively reproduce in vitro functional models of cartilage and tendon is retarding progress in this field. De- and redifferentiation represent phenotypic transitions that may contribute to loss of function in ageing musculoskeletal tissues. Applying a systems biology network analysis approach to global gene expression profiles derived from common in vitro culture systems (monolayer and three-dimensional cultures) this study demonstrates common regulatory mechanisms governing de- and redifferentiation transitions in cartilage and tendon cells. Furthermore, evidence of convergence of gene expression profiles during monolayer expansion of cartilage and tendon cells, and the expression of key developmental markers, challenges the physiological relevance of this culture system. The study also suggests that oxidative stress and PI3K signalling pathways are key modulators of in vitro phenotypes for cells of musculoskeletal origin.

No MeSH data available.


Related in: MedlinePlus