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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.

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Related in: MedlinePlus

Selected gene classifications according to biological processes of genes regulated in the three differentiation programs.Diagram showing the biological processes significantly enriched in the set of genes differentially expressed in the differentiation processes of FSHD-1 (yellow bars) and FSHD-2 (grey bars) cells in respect to control. Bar on the left indicated the biological process modulated in control but not in FSHD-1 (yellow bar), and FSHD-2 (grey bars) cells, whereas bars on the right indicated the biological processes modulated in FSHD-1 (yellow bar) and FSHD-2 (grey bars) but not in control cells. All bars group many related GO categories. p-value <10−4.
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pone-0020966-g003: Selected gene classifications according to biological processes of genes regulated in the three differentiation programs.Diagram showing the biological processes significantly enriched in the set of genes differentially expressed in the differentiation processes of FSHD-1 (yellow bars) and FSHD-2 (grey bars) cells in respect to control. Bar on the left indicated the biological process modulated in control but not in FSHD-1 (yellow bar), and FSHD-2 (grey bars) cells, whereas bars on the right indicated the biological processes modulated in FSHD-1 (yellow bar) and FSHD-2 (grey bars) but not in control cells. All bars group many related GO categories. p-value <10−4.

Mentions: Another approach to investigate the gene deregulation in FSHD cells is to analyze the gene chip results in the context of the differentiation process. This could be obtained by categorizing in the DAVID program the variation in gene expression profile obtained analyzing the FSHD-1 and FSHD-2 differentiation processes subtracted with the variation showed by the control cells differentiation. The result of these analyses is schematized in Fig.3, where on the left is reported the biological process not modulated in FSHD-1 (yellow bar) and in FSHD-2 (grey bar) cells, in respect to control, whereas on the right the biological processes modulated in FSHD-1 (yellow bar) and in FSHD-2 (grey bars), but not in control cells. Both pathological differentiation processes showed as mainly deregulated categories those already derived in FSHD-1 myoblasts (cell cycle and proliferation) and FSHD-2 myotubes (RNA processing) (Figs. 2 and 3). In addition, this analysis evidenced a slight damage of cell cycle also in FSHD-2 and of the proteasomal ubiquitin-dependent processes. Interestingly, FSHD-1 and FSHD-2 cells showed the common deregulation of five genes involved in cholesterol metabolic process; four genes (HMGCR, DHCR7, DHCR24 and IDI1) implied in cholesterol biosynthesis, were up-regulated in FSHD-1 and down-regulated in FSHD-2, and one gene (ABCA1) involved in the efflux of cholesterol from the cell, was down-regulated in FSHD-1 and upregulated in FSHD-2. The complete lists of all the significant deregulated biological categories of the three differentiation processes are reported in Table S3.


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 of genes regulated in the three differentiation programs.Diagram showing the biological processes significantly enriched in the set of genes differentially expressed in the differentiation processes of FSHD-1 (yellow bars) and FSHD-2 (grey bars) cells in respect to control. Bar on the left indicated the biological process modulated in control but not in FSHD-1 (yellow bar), and FSHD-2 (grey bars) cells, whereas bars on the right indicated the biological processes modulated in FSHD-1 (yellow bar) and FSHD-2 (grey bars) but not in control cells. All bars group many related GO categories. p-value <10−4.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020966-g003: Selected gene classifications according to biological processes of genes regulated in the three differentiation programs.Diagram showing the biological processes significantly enriched in the set of genes differentially expressed in the differentiation processes of FSHD-1 (yellow bars) and FSHD-2 (grey bars) cells in respect to control. Bar on the left indicated the biological process modulated in control but not in FSHD-1 (yellow bar), and FSHD-2 (grey bars) cells, whereas bars on the right indicated the biological processes modulated in FSHD-1 (yellow bar) and FSHD-2 (grey bars) but not in control cells. All bars group many related GO categories. p-value <10−4.
Mentions: Another approach to investigate the gene deregulation in FSHD cells is to analyze the gene chip results in the context of the differentiation process. This could be obtained by categorizing in the DAVID program the variation in gene expression profile obtained analyzing the FSHD-1 and FSHD-2 differentiation processes subtracted with the variation showed by the control cells differentiation. The result of these analyses is schematized in Fig.3, where on the left is reported the biological process not modulated in FSHD-1 (yellow bar) and in FSHD-2 (grey bar) cells, in respect to control, whereas on the right the biological processes modulated in FSHD-1 (yellow bar) and in FSHD-2 (grey bars), but not in control cells. Both pathological differentiation processes showed as mainly deregulated categories those already derived in FSHD-1 myoblasts (cell cycle and proliferation) and FSHD-2 myotubes (RNA processing) (Figs. 2 and 3). In addition, this analysis evidenced a slight damage of cell cycle also in FSHD-2 and of the proteasomal ubiquitin-dependent processes. Interestingly, FSHD-1 and FSHD-2 cells showed the common deregulation of five genes involved in cholesterol metabolic process; four genes (HMGCR, DHCR7, DHCR24 and IDI1) implied in cholesterol biosynthesis, were up-regulated in FSHD-1 and down-regulated in FSHD-2, and one gene (ABCA1) involved in the efflux of cholesterol from the cell, was down-regulated in FSHD-1 and upregulated in FSHD-2. The complete lists of all the significant deregulated biological categories of the three differentiation processes are reported in Table S3.

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