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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.

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Related in: MedlinePlus

Schematic representation of gene expression profile comparisons made between each experimental condition and cell type.Each comparison (legend) is annotated with the most significant KEGG reference pathways and the activation status of that pathway as predicted using a Signalling Pathway Topology Analysis (SPIA), Supplementary Data, SD18,19. For each comparison and cell type the trend in expression of genes validated by qPCR is indicated, for example, in dedifferentiation a reduction in the expression of Col2a1 and Acan is found in chondrocytes. Common upstream master regulators predicted to be associated with the observed gene expression profiles, from Ingenuity® Pathway Analysis, are also provided.
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f4: Schematic representation of gene expression profile comparisons made between each experimental condition and cell type.Each comparison (legend) is annotated with the most significant KEGG reference pathways and the activation status of that pathway as predicted using a Signalling Pathway Topology Analysis (SPIA), Supplementary Data, SD18,19. For each comparison and cell type the trend in expression of genes validated by qPCR is indicated, for example, in dedifferentiation a reduction in the expression of Col2a1 and Acan is found in chondrocytes. Common upstream master regulators predicted to be associated with the observed gene expression profiles, from Ingenuity® Pathway Analysis, are also provided.

Mentions: Signalling Pathway Impact Analysis (SPIA), which uses a combination of over-expression analysis of differentially expressed gene lists, magnitude of fold-change, and the topology of KEGG canonical signalling pathways to define global pathway perturbation scores, predicted activation of ‘focal adhesion’, ‘rheumatoid arthritis’ and ‘systemic lupus erythematosus’ reference pathways in both native tissue to monolayer comparisons, Fig. 4. The HIF-1 and PI3K signalling pathways were predicted to be reciprocally inhibited or activated in de- and redifferentiation, respectively, for both cell types, see Supplementary Data (SD18–19). Inhibition of the ‘chemokine signalling pathway’ was common to both chondrocytes and tenocytes cultivated as a monolayer in comparison to those in three-dimensional culture systems. Alginate and fibrin cultures were shown to have significant activation of ‘osteoclast differentiation’ and ‘HIF1 signalling’ pathways, respectively. These perturbed pathways were consistent with the gene ontology functional annotations.


A systems biology approach to defining regulatory mechanisms for cartilage and tendon cell phenotypes
Schematic representation of gene expression profile comparisons made between each experimental condition and cell type.Each comparison (legend) is annotated with the most significant KEGG reference pathways and the activation status of that pathway as predicted using a Signalling Pathway Topology Analysis (SPIA), Supplementary Data, SD18,19. For each comparison and cell type the trend in expression of genes validated by qPCR is indicated, for example, in dedifferentiation a reduction in the expression of Col2a1 and Acan is found in chondrocytes. Common upstream master regulators predicted to be associated with the observed gene expression profiles, from Ingenuity® Pathway Analysis, are also provided.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: Schematic representation of gene expression profile comparisons made between each experimental condition and cell type.Each comparison (legend) is annotated with the most significant KEGG reference pathways and the activation status of that pathway as predicted using a Signalling Pathway Topology Analysis (SPIA), Supplementary Data, SD18,19. For each comparison and cell type the trend in expression of genes validated by qPCR is indicated, for example, in dedifferentiation a reduction in the expression of Col2a1 and Acan is found in chondrocytes. Common upstream master regulators predicted to be associated with the observed gene expression profiles, from Ingenuity® Pathway Analysis, are also provided.
Mentions: Signalling Pathway Impact Analysis (SPIA), which uses a combination of over-expression analysis of differentially expressed gene lists, magnitude of fold-change, and the topology of KEGG canonical signalling pathways to define global pathway perturbation scores, predicted activation of ‘focal adhesion’, ‘rheumatoid arthritis’ and ‘systemic lupus erythematosus’ reference pathways in both native tissue to monolayer comparisons, Fig. 4. The HIF-1 and PI3K signalling pathways were predicted to be reciprocally inhibited or activated in de- and redifferentiation, respectively, for both cell types, see Supplementary Data (SD18–19). Inhibition of the ‘chemokine signalling pathway’ was common to both chondrocytes and tenocytes cultivated as a monolayer in comparison to those in three-dimensional culture systems. Alginate and fibrin cultures were shown to have significant activation of ‘osteoclast differentiation’ and ‘HIF1 signalling’ pathways, respectively. These perturbed pathways were consistent with the gene ontology functional annotations.

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