Gene expression microarrays and respiratory muscles

Systems biology of skeletal muscle: fiber type as an organizing principle

Skeletal muscle force generation and contraction are fundamental to countless aspects of human life. The complexity of skeletal muscle physiology is simplified by fiber type classification where differences are observed from neuromuscular transmission to release of intracellular Ca(2+) from the sarcoplasmic reticulum and the resulting recruitment and cycling of cross-bridges. This review uses fiber type classification as an organizing and simplifying principle to explore the complex interactions between the major proteins involved in muscle force generation and contraction.

Gene expression profiling in the type 1 diabetes rat diaphragm

BACKGROUND

Respiratory muscle contractile performance is impaired by diabetes, mechanisms of which included altered carbohydrate and lipid metabolism, oxidative stress and changes in membrane electrophysiology. The present study examined to what extent these cellular perturbations involve changes in gene expression.

METHODOLOGY/PRINCIPAL FINDINGS

Diaphragm muscle from streptozotocin-diabetic rats was analyzed with Affymetrix gene expression arrays. Diaphragm from diabetic rats had 105 genes with at least +/-2-fold significantly changed expression (55 increased, 50 decreased), and these were assigned to gene ontology groups based on over-representation analysis using DAVID software. There was increased expression of genes involved in palmitoyl-CoA hydrolase activity (a component of lipid metabolism) (P = 0.037, n = 2 genes, fold change 4.2 to 27.5) and reduced expression of genes related to carbohydrate metabolism (P = 0.000061, n = 8 genes, fold change -2.0 to -8.5). Other gene ontology groups among upregulated genes were protein ubiquitination (P = 0.0053, n = 4, fold change 2.2 to 3.4), oxidoreductase activity (P = 0.024, n = 8, fold change 2.1 to 6.0), and morphogenesis (P = 0.012, n = 10, fold change 2.1 to 4.3). Other downregulated gene groups were extracellular region (including extracellular matrix and collagen) (P = 0.00032, n = 13, fold change -2.2 to -3.7) and organogenesis (P = 0.032, n = 7, fold change -2.1 to -3.7). Real-time PCR confirmed the directionality of changes in gene expression for 30 of 31 genes tested.

CONCLUSIONS/SIGNIFICANCE

These data indicate that in diaphragm muscle type 1 diabetes increases expression of genes involved in lipid energetics, oxidative stress and protein ubiquitination, decreases expression of genes involved in carbohydrate metabolism, and has little effect on expression of ion channel genes. Reciprocal changes in expression of genes involved in carbohydrate and lipid metabolism may change the availability of energetic substrates and thereby directly modulate fatigue resistance, an important issue for a muscle like the diaphragm which needs to contract without rest for the entire lifetime of the organism.

An adult tissue-specific stem cell in its niche: a gene profiling analysis of in vivo quiescent and activated muscle satellite cells

The satellite cell of skeletal muscle provides a paradigm for quiescent and activated tissue stem cell states. We have carried out transcriptome analyses on satellite cells purified by flow cytometry from Pax3(GFP/+) mice. We compared samples from adult skeletal muscles where satellite cells are mainly quiescent, with samples from growing muscles or regenerating (mdx) muscles, where they are activated. Analysis of regulation that is shared by both activated states avoids other effects due to immature or pathological conditions. This in vivo profile differs from that of previously analyzed satellite cells activated after cell culture. It reveals how the satellite cell protects itself from damage and maintains quiescence, while being primed for activation on receipt of the appropriate signal. This is illustrated by manipulation of the corepressor Dach1, and by the demonstration that quiescent satellite cells are better protected from oxidative stress than those from mdx or 1-week-old muscles. The quiescent versus in vivo activated comparison also gives new insights into how the satellite cell controls its niche on the muscle fiber through cell adhesion and matrix remodeling. The latter also potentiates growth factor activity through proteoglycan modification. Dismantling the extracellular matrix is important for satellite cell activation when the expression of proteinases is up-regulated, whereas transcripts for their inhibitors are high in quiescent cells. In keeping with this, we demonstrate that metalloproteinase function is required for efficient regeneration in vivo.

Isotonic fatigue in laminin alpha2-deficient dy/dy dystrophic mouse diaphragm

Laminin alpha2 deficiency causes approximately 50% of human congenital muscular dystrophies. Muscle in the corresponding dy/dy mouse model has reduced force but increased fatigue resistance during isometric contractions. To determine whether a similar pattern of alterations is present during isotonic contractions, dy/dy diaphragm was studied in vitro. During 20% load, dystrophic diaphragm had significantly reduced shortening, shortening velocity, work and power deficits, which persisted during the fatigue-inducing stimulation. In contrast, during 40% load, isotonic contractile performance of diseased muscle was impaired only mildly and only for some contractile parameters. At both loads, rate of isotonic fatigue when expressed relative to initial contractile values was similar for dystrophic and normal muscle, or in some instances slightly higher for dystrophic muscle. Therefore, fatigue resistance is considerably impaired during isotonic contractions relative to that reported previously for isometric contractions. This has important implications for increased susceptibility to respiratory failure in laminin alpha2-deficient muscular dystrophy.

Contrast between cardiac left ventricle and diaphragm muscle in expression of genes involved in carbohydrate and lipid metabolism

The heart and diaphragm both need appropriate metabolic machinery to ensure long-term energy supplies, as they must contract rhythmically without cessation for the entire lifetime of the organism to ensure homeostasis of oxygen and carbon dioxide exchange. However, their energy requirements differ due to disparities in mechanical loads. Understanding how these two muscles converge and diverge in their approaches to meeting their metabolic demands may suggest novel strategies for improving cardiac and skeletal muscle long-term performance in health and disease. To assess this at a transcriptional level, expression of genes involved in carbohydrate and lipid metabolism was assessed using microarrays in rats. There were 594 genes with >2-fold differential expression between left ventricle of the heart and diaphragm; 307 were expressed heart>diaphragm and 287 diaphragm>heart. Assignment to gene ontology groups revealed over-representation for "carbohydrate metabolism" (P=0.005, n=32 genes or 5.4% of all genes with differential expression) and "lipid metabolism" (P=0.0012, n=48 genes or 8.1% of all genes with differential expression). For carbohydrate there were 14 genes with heart>diaphragm and 18 genes with diaphragm>heart, and for lipid there were 30 genes with heart>diaphragm and 18 genes with diaphragm>heart. The magnitude of differential expression between heart and diaphragm ranged up to 30-fold for carbohydrate and up to 59-fold for lipid. Carbohydrate-related genes were almost all involved in energy metabolism (e.g. Pfkm, Pgm1, Pgam1, Pfkfb1, Pfkfb2), whereas lipid-related genes were involved in energetics as well as other cellular processes; for both groups this included genes involved in rate-limiting metabolic steps. Data thus indicate that diaphragm and heart have both shared and differential transcriptional strategies for ensuring long-term energy supplies, with a relative favoring of lipid metabolism in the heart and carbohydrate metabolism in the diaphragm.