Comprehensive Multi-cohort Transcriptional Meta-analysis of Muscle Diseases Identifies a Signature of Disease Severity

Muscle diseases share common pathological features suggesting common underlying mechanisms. We hypothesized there is a common set of genes dysregulated across muscle diseases compared to healthy muscle and that these genes correlate with severity of muscle disease. We performed meta-analysis of transcriptional profiles of muscle biopsies from human muscle diseases and healthy controls. Studies obtained from public microarray repositories fulfilling quality criteria were divided into six categories: i) Immobility, ii) inflammatory myopathies, iii) ICU acquired weakness (ICUAW), iv) congenital muscle diseases, v) chronic systemic diseases, vi) motor neuron disease. Patient cohorts were separated in discovery and validation cohorts retaining roughly equal proportions of samples for the disease categories. To remove bias towards a specific muscle disease category we repeated the meta-analysis five times by removing data sets corresponding to one muscle disease class at a time in a “leave-one-disease-out” analysis. We used 636 muscle tissue samples from 30 independent cohorts to identify a 52 gene signature (36 up-regulated and 16 down-regulated genes). We validated the discriminatory power of this signature in 657 muscle biopsies from 12 additional patient cohorts encompassing five categories of muscle diseases with an area under the receiver operating characteristic curve of 0.91, 83% sensitivity, and 85.3% specificity. The expression score of the gene signature inversely correlated with quadriceps muscle mass (r =-0.50, p-value = 0.011) in ICUAW and shoulder abduction strength (r=-0.77, p-value = 0.014) in amyotrophic lateral sclerosis (ALS). The signature also positively correlated with histologic assessment of muscle atrophy in ALS (r=0.88, p-value=1.62x10−3) and fibrosis in muscular dystrophy (Jonckheere trend test p-value = 4.45 x 10−9). Our results identify a conserved transcriptional signature associated with clinical and histologic muscle disease severity. Several genes in this conserved signature have not been previously associated with muscle disease severity.

Diagnostic Approaches to Various Muscle Diseases Based on Muscle Pathology

Muscle pathology can give much information to reach the diagnosis of neuromuscular disorders. Major pathological changes occurred in skeletal muscles include muscle fiber atrophy/hypertrophy, necrosis/regeneration, inflammation, myofibrillar disorganization, abnormal inclusions, and disruptions in cellular organelles. Physicians should be able to understand what each of these findings indicates. However, these are not always specific to a certain disease, and instead most of them are commonly found in many of muscle diseases. Thus, muscle pathological findings should be carefully interpreted under the given clinical settings.

Recent Trends in Biofabrication Technologies for Studying Skeletal Muscle Tissue-Related Diseases

In native skeletal muscle, densely packed myofibers exist in close contact with surrounding motor neurons and blood vessels, which are embedded in the fibrous connective tissue. In comparison to conventional two-dimensional (2D) cultures, the three-dimensional (3D) engineered skeletal muscle models allow structural and mechanical resemblance with native skeletal muscle tissue by providing geometric confinement and physiological matrix stiffness to the cells. In addition, various external stimuli applied to these models enhance muscle maturation along with cell–cell and cell–extracellular matrix interaction. Therefore, 3D in vitro muscle models can adequately recapitulate the pathophysiologic events occurring in tissue–tissue interfaces inside the native skeletal muscle such as neuromuscular junction. Moreover, 3D muscle models can induce pathological phenotype of human muscle dystrophies such as Duchenne muscular dystrophy by incorporating patient-derived induced pluripotent stem cells and human primary cells. In this review, we discuss the current biofabrication technologies for modeling various skeletal muscle tissue-related diseases (i.e., muscle diseases) including muscular dystrophies and inflammatory muscle diseases. In particular, these approaches would enable the discovery of novel phenotypic markers and the mechanism study of human muscle diseases with genetic mutations.

Alteration of STIM1/Orai1-Mediated SOCE in Skeletal Muscle: Impact in Genetic Muscle Diseases and Beyond

Intracellular Ca2+ ions represent a signaling mediator that plays a critical role in regulating different muscular cellular processes. Ca2+ homeostasis preservation is essential for maintaining skeletal muscle structure and function. Store-operated Ca2+ entry (SOCE), a Ca2+-entry process activated by depletion of intracellular stores contributing to the regulation of various function in many cell types, is pivotal to ensure a proper Ca2+ homeostasis in muscle fibers. It is coordinated by STIM1, the main Ca2+ sensor located in the sarcoplasmic reticulum, and ORAI1 protein, a Ca2+-permeable channel located on transverse tubules. It is commonly accepted that Ca2+ entry via SOCE has the crucial role in short- and long-term muscle function, regulating and adapting many cellular processes including muscle contractility, postnatal development, myofiber phenotype and plasticity. Lack or mutations of STIM1 and/or Orai1 and the consequent SOCE alteration have been associated with serious consequences for muscle function. Importantly, evidence suggests that SOCE alteration can trigger a change of intracellular Ca2+ signaling in skeletal muscle, participating in the pathogenesis of different progressive muscle diseases such as tubular aggregate myopathy, muscular dystrophy, cachexia, and sarcopenia. This review provides a brief overview of the molecular mechanisms underlying STIM1/Orai1-dependent SOCE in skeletal muscle, focusing on how SOCE alteration could contribute to skeletal muscle wasting disorders and on how SOCE components could represent pharmacological targets with high therapeutic potential.