Limits...
Expression profiling of FSHD-1 and FSHD-2 cells during myogenic differentiation evidences common and distinctive gene dysregulation patterns.

Cheli S, François S, Bodega B, Ferrari F, Tenedini E, Roncaglia E, Ferrari S, Ginelli E, Meneveri R - PLoS ONE (2011)

Bottom Line: Interestingly, our results also suggest that miRNAs might be implied in both FSHD-1 and FSHD-2 gene dysregulation.Finally, in both cell differentiation systems, we did not observe a gradient of altered gene expression throughout the 4q35 chromosome.Taken together our results recapitulate previously reported defects of FSHD-1, and add new insights into the gene deregulation characterizing both FSHD-1 and FSHD-2, in which miRNAs may play a role.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Genetics for Medical Sciences, University of Milan, Milan, Italy.

ABSTRACT

Background: Determine global gene dysregulation affecting 4q-linked (FSHD-1) and non 4q-linked (FSHD-2) cells during early stages of myogenic differentiation. This approach has been never applied to FSHD pathogenesis.

Methodology/principal findings: By in vitro differentiation of FSHD-1 and FSHD-2 myoblasts and gene chip analysis we derived that gene expression profile is altered only in FSHD-1 myoblasts and FSHD-2 myotubes. The changes seen in FSHD-1 regarded a general defect in cell cycle progression, probably due to the upregulation of myogenic markers PAX3 and MYOD1, and a deficit of factors (SUV39H1 and HMGB2) involved in D4Z4 chromatin conformation. On the other hand, FSHD-2 mytubes were characterized by a general defect in RNA metabolism, protein synthesis and degradation and, to a lesser extent, in cell cycle. Common dysregulations regarded genes involved in response to oxidative stress and in sterol biosynthetic process. Interestingly, our results also suggest that miRNAs might be implied in both FSHD-1 and FSHD-2 gene dysregulation. Finally, in both cell differentiation systems, we did not observe a gradient of altered gene expression throughout the 4q35 chromosome.

Conclusions/significance: FSHD-1 and FSHD-2 cells showed, in different steps of myogenic differentiation, a global deregulation of gene expression rather than an alteration of expression of 4q35 specific genes. In general, FSHD-1 and FSHD-2 global gene deregulation interested common and distinctive biological processes. In this regard, defects of cell cycle progression (FSHD-1 and to a lesser extent FSHD-2), protein synthesis and degradation (FSHD-2), response to oxidative stress (FSHD-1 and FSHD-2), and cholesterol homeostasis (FSHD-1 and FSHD-2) may in general impair a correct myogenesis. Taken together our results recapitulate previously reported defects of FSHD-1, and add new insights into the gene deregulation characterizing both FSHD-1 and FSHD-2, in which miRNAs may play a role.

Show MeSH

Related in: MedlinePlus

Selected gene classifications according to biological processes.Biological processes significantly enriched in the set of genes identified by microarray as up- or down-regulated in A) FSHD-1 myoblasts, and B) in FSHD-2 myotubes, and categorized in the DAVID program. Numbers in the bars indicate the number of genes assigned to each gene ontology term. p-value <0.05.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3113851&req=5

pone-0020966-g002: Selected gene classifications according to biological processes.Biological processes significantly enriched in the set of genes identified by microarray as up- or down-regulated in A) FSHD-1 myoblasts, and B) in FSHD-2 myotubes, and categorized in the DAVID program. Numbers in the bars indicate the number of genes assigned to each gene ontology term. p-value <0.05.

Mentions: The probes identified by microarray as up- or down-regulated in FHSD-1 and FSHD-2 cells were categorized in the DAVID program (see criteria in Materials and Methods). As shown in Fig. 2A, the most severely affected biological processes in FSHD-1 myoblasts in respect to control cells were mainly linked to cell cycle (94 genes, 35% of total deregulated probes), particularly M-phase (65 genes out of 94), and to DNA metabolic process (65 genes) and replication (44 genes). More precisely, these classes that represent the most significant ones (p-value <10−30) are essentially composed by down-regulated genes. In these biological categories we found, all down-regulated, seven cell division cycle genes (CDC, involved in G1/S and G2/M transitions), eight minichromosome maintenance complex components (MCM, required for the entry in S phase and cell division), two cyclins (CCNA2 and CCNF), two cyclin-dependent kinases (CDK1 and CDK2), several factors involved in DNA replication (four DNA-dependent DNA polymerases, one primase and one helicase) and repair (MSH2, DCLRE1B, BRCA1 and BRCA2), eight kinesins (KIF, involved in spindle formation and the movements of chromosomes during mitosis), and five centromere proteins (CEMP). Among the up-regulated genes, of particular interest was GAS1, involved in growth arrest. Furthermore, the careful inspection of the deregulated gene list of FSHD-1 myoblasts allowed the identification of several entries previously reported to be involved in FSHD-1 and in the myogenic program. We found the down-regulation of two genes (SUV39H1 and HMGB2) involved in chromatin conformation mechanism, and the up-regulation of two myogenic markers (PAX3 and MYOD1) and of SOD2 involved in oxidative stress response (Table S1A). All together the above results suggest the occurrence in FSHD-1 myoblasts of a damage in cell cycle progression, and in myogenic differentiation.


Expression profiling of FSHD-1 and FSHD-2 cells during myogenic differentiation evidences common and distinctive gene dysregulation patterns.

Cheli S, François S, Bodega B, Ferrari F, Tenedini E, Roncaglia E, Ferrari S, Ginelli E, Meneveri R - PLoS ONE (2011)

Selected gene classifications according to biological processes.Biological processes significantly enriched in the set of genes identified by microarray as up- or down-regulated in A) FSHD-1 myoblasts, and B) in FSHD-2 myotubes, and categorized in the DAVID program. Numbers in the bars indicate the number of genes assigned to each gene ontology term. p-value <0.05.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3113851&req=5

pone-0020966-g002: Selected gene classifications according to biological processes.Biological processes significantly enriched in the set of genes identified by microarray as up- or down-regulated in A) FSHD-1 myoblasts, and B) in FSHD-2 myotubes, and categorized in the DAVID program. Numbers in the bars indicate the number of genes assigned to each gene ontology term. p-value <0.05.
Mentions: The probes identified by microarray as up- or down-regulated in FHSD-1 and FSHD-2 cells were categorized in the DAVID program (see criteria in Materials and Methods). As shown in Fig. 2A, the most severely affected biological processes in FSHD-1 myoblasts in respect to control cells were mainly linked to cell cycle (94 genes, 35% of total deregulated probes), particularly M-phase (65 genes out of 94), and to DNA metabolic process (65 genes) and replication (44 genes). More precisely, these classes that represent the most significant ones (p-value <10−30) are essentially composed by down-regulated genes. In these biological categories we found, all down-regulated, seven cell division cycle genes (CDC, involved in G1/S and G2/M transitions), eight minichromosome maintenance complex components (MCM, required for the entry in S phase and cell division), two cyclins (CCNA2 and CCNF), two cyclin-dependent kinases (CDK1 and CDK2), several factors involved in DNA replication (four DNA-dependent DNA polymerases, one primase and one helicase) and repair (MSH2, DCLRE1B, BRCA1 and BRCA2), eight kinesins (KIF, involved in spindle formation and the movements of chromosomes during mitosis), and five centromere proteins (CEMP). Among the up-regulated genes, of particular interest was GAS1, involved in growth arrest. Furthermore, the careful inspection of the deregulated gene list of FSHD-1 myoblasts allowed the identification of several entries previously reported to be involved in FSHD-1 and in the myogenic program. We found the down-regulation of two genes (SUV39H1 and HMGB2) involved in chromatin conformation mechanism, and the up-regulation of two myogenic markers (PAX3 and MYOD1) and of SOD2 involved in oxidative stress response (Table S1A). All together the above results suggest the occurrence in FSHD-1 myoblasts of a damage in cell cycle progression, and in myogenic differentiation.

Bottom Line: Interestingly, our results also suggest that miRNAs might be implied in both FSHD-1 and FSHD-2 gene dysregulation.Finally, in both cell differentiation systems, we did not observe a gradient of altered gene expression throughout the 4q35 chromosome.Taken together our results recapitulate previously reported defects of FSHD-1, and add new insights into the gene deregulation characterizing both FSHD-1 and FSHD-2, in which miRNAs may play a role.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Genetics for Medical Sciences, University of Milan, Milan, Italy.

ABSTRACT

Background: Determine global gene dysregulation affecting 4q-linked (FSHD-1) and non 4q-linked (FSHD-2) cells during early stages of myogenic differentiation. This approach has been never applied to FSHD pathogenesis.

Methodology/principal findings: By in vitro differentiation of FSHD-1 and FSHD-2 myoblasts and gene chip analysis we derived that gene expression profile is altered only in FSHD-1 myoblasts and FSHD-2 myotubes. The changes seen in FSHD-1 regarded a general defect in cell cycle progression, probably due to the upregulation of myogenic markers PAX3 and MYOD1, and a deficit of factors (SUV39H1 and HMGB2) involved in D4Z4 chromatin conformation. On the other hand, FSHD-2 mytubes were characterized by a general defect in RNA metabolism, protein synthesis and degradation and, to a lesser extent, in cell cycle. Common dysregulations regarded genes involved in response to oxidative stress and in sterol biosynthetic process. Interestingly, our results also suggest that miRNAs might be implied in both FSHD-1 and FSHD-2 gene dysregulation. Finally, in both cell differentiation systems, we did not observe a gradient of altered gene expression throughout the 4q35 chromosome.

Conclusions/significance: FSHD-1 and FSHD-2 cells showed, in different steps of myogenic differentiation, a global deregulation of gene expression rather than an alteration of expression of 4q35 specific genes. In general, FSHD-1 and FSHD-2 global gene deregulation interested common and distinctive biological processes. In this regard, defects of cell cycle progression (FSHD-1 and to a lesser extent FSHD-2), protein synthesis and degradation (FSHD-2), response to oxidative stress (FSHD-1 and FSHD-2), and cholesterol homeostasis (FSHD-1 and FSHD-2) may in general impair a correct myogenesis. Taken together our results recapitulate previously reported defects of FSHD-1, and add new insights into the gene deregulation characterizing both FSHD-1 and FSHD-2, in which miRNAs may play a role.

Show MeSH
Related in: MedlinePlus