Functional classification of skeletal muscle networks. I. Normal physiology

Abstract

Extensive measurements of the parts list of human skeletal muscle through transcriptomics and other phenotypic assays offer the opportunity to reconstruct detailed functional models. Through integration of vast amounts of data present in databases and extant knowledge of muscle function combined with robust analyses that include a clustering approach, we present both a protein parts list and network models for skeletal muscle function. The model comprises the four key functional family networks that coexist within a functional space; namely, excitation-activation family (forward pathways that transmit a motoneuronal command signal into the spatial volume of the cell and then use Ca(2+) fluxes to bind Ca(2+) to troponin C sites on F-actin filaments, plus transmembrane pumps that maintain transmission capacity); mechanical transmission family (a sophisticated three-dimensional mechanical apparatus that bidirectionally couples the millions of actin-myosin nanomotors with external axial tensile forces at insertion sites); metabolic and bioenergetics family (pathways that supply energy for the skeletal muscle function under widely varying demands and provide for other cellular processes); and signaling-production family (which represents various sensing, signal transduction, and nuclear infrastructure that controls the turn over and structural integrity and regulates the maintenance, regeneration, and remodeling of the muscle). Within each family, we identify subfamilies that function as a unit through analysis of large-scale transcription profiles of muscle and other tissues. This comprehensive network model provides a framework for exploring functional mechanisms of the skeletal muscle in normal and pathophysiology, as well as for quantitative modeling.

Fig. 1.

The flow chart of the procedures used to construct the parts list and functional family. GEO, Gene Expression Omnibus; EA, excitation-activation; MECH, mechanical transmission; METB, metabolic and bioenergetics; SIGP, signaling and production.

Fig. 2.

The results of K-means classification of normal skeletal muscle microarrays (MAs). The same dominant cluster of 120 MAs, representing the gene expression pattern of normal skeletal muscle, were identified whether K = 2, 3, or 4; it was not until K = 5 or 6 that this cluster could be split into two (quite similar) clusters.

Fig. 3.

Z-score histogram of the 120 main normal MAs, with the y-axis (number of probes) being rescaled as the z-score increases and the number decreases. The blue line is the mean of the number of probes, and the red lines are the means ± SD. As expected, most of the probes (69%) have negative z-scores, indicating that many of these are essentially “off” or of very low expression for muscle tissue. Only 5.9% had a z-score value above 1.0, only 2.4% above 2.0, and only 0.6% above 5.0.

Fig. 4.

The functional protein families of skeletal muscle. EA model family addresses the challenge of near-synchronous temporal coactivation of spatially distributed nano-actuators. MECH model family manages transmission of forces between these nano-actuators and gross skeletal structures that can also generate forces (including force transmission across the mechanically vulnerable plasmalemma bilayer). METB model family manages production of energy to meet ongoing demands, including transport of energy fuels and materials such as oxygen. SIGP family “senses” key states and functional demands of the aforementioned families and up/downregulates transcriptional and proteomic levels so as to adapt materials and structure over timeframes of days to weeks. In the middle part (skeletal muscle), the blue (solid) lines are the output to input of a key highly regulated state variable operating between certain protein families, the gray (dashed) lines represent sensory signals to the SIGP family, and the yellow (solid) lines represent the slower remodeling signals continually sent back to the other three families.

Fig. 5.

A: primary set of transcripts in EA model family, organized into four subfamilies. Transcripts with bold and italic font have higher z-scores in skeletal muscle than in other tissues (P < 0.05). For skeletal muscle, the color corresponds to the absolute z-score values, but with positive scaling from z = 0 to 10 (black to bright red), and negative only from 0 to −0.1 (black to bright green); for other tissues, the color corresponds to the difference between other respective tissue and skeletal muscle [i.e., z(other tissue) − z(skeletal muscle), with black indicating no saturation (z = 0), and color saturation at z = −3 (bright green) or z = 3 (bright red)]. B: key structural connectivity, as unicausal signals, of the four subfamilies of EA model. Forward membrane path subfamily includes proteins responsible for signal transmission, starting from the neuromuscular junction to the release of calcium from sarcoplasmic reticulum through ryanodine receptor (RYR1). Ion pumps/exchangers subfamily includes proteins within complexes that pump ions across key membranes against a concentration gradient. Calcium-handling subfamily includes proteins involved in the regulation of calcium homeostasis within cytoplasm. ExAct size-handling subfamily includes proteins that are regulators of the structural size and location of sarcoplasmic reticulum (SR). See text and supplemental tables for definitions of acronyms.

Fig. 6.

A: key transcripts in MECH model family. Transcripts with bold and italic font have higher z-scores in skeletal muscle than in other tissues (P < 0.05). See Fig. 5A legend for color-coding scheme. B: structural protein connectivity of the five subgroups composing the MECH model family. Connections ending with solid circle represent mechanical bonding. The “*” at the end of some proteins' names indicates that the protein has different isoforms in different types of fibers. Actin subfamily includes proteins associated mainly with the thin filament. Myosin subfamily includes proteins associated mainly with the thick filament. Z-disk subfamily includes proteins localized at the Z-disk and some intermediate filament proteins also associated with costameres. TransMem subfamily includes transmembrane “scaffolding” proteins just internal to or crossing the sarcolemma. ECM subfamily includes proteins composing the extracellular matrix for muscle tissue. See text and supplemental tables for definitions of acronyms.

Fig. 7.

A: key transcripts in METB family. Transcripts with bold and italic font have higher z-scores in skeletal muscle than in other tissues (P < 0.05). See Fig. 5A legend for description of color-coded scheme. B: the protein network of METB model family. This model is partitioned into four subfamilies: oxidative, including members helping transfer lipid into mitochondria, enzymes involved in β-oxidation and TCA cycle; glycolytic, including members involved in supporting immediate energy, glycolysis, and glycogenesis; electron transport, including members generating the mitochondrial membrane potential and producing ATP; and transport, involved in transporting materials such as glucose and oxygen. See text and supplemental tables for definitions of acronyms. See text and supplemental tables for definitions of acronyms.

Fig. 8.

Signaling proteins involved in skeletal muscle remodeling processes. The green nodes are proteins in SIGP family, the red nodes are other protein families, and the blue nodes are key dynamic states in the final muscle model framework. Along the bottom are functional consequences related to phenotypic remodeling of skeletal muscle, including changes in the mass/size (atrophy and hypertrophy), fiber composition (percentage of slow type I and fast type II fibers), and fatigue resistance (proportion of oxidative vs. glycolytic fibers, and volume of mitochondria). See text and supplemental tables for definitions of acronyms.