Identification of Potential Biomarkers for Ryanodine Receptor 1 (RYR1) Mutation-Associated Myopathies Using Bioinformatics Approach

Abstract

Background. Myopathies related to Ryanodine receptor 1 (RYR1) mutation are the most common nondystrophy muscle disorder in humans. Early detection and diagnosis of RYR1 mutation-associated myopathies may lead to more timely treatment of patients, which contributes to the management and preparation for malignant hyperthermia. However, diagnosis of RYR1 mutation-associated myopathies is delayed and challenging. The absence of diagnostic morphological features in muscle biopsy does not rule out the possibility of pathogenic variations in RYR1. Accordingly, it is helpful to seek biomarkers to diagnose RYR1 mutation-associated myopathies. Methods. Skeletal muscle tissue microarray datasets of RYR1 mutation-associated myopathies or healthy persons were built in accordance with the gene expression synthesis (GEO) database. Differentially expressed genes (DEGs) were identified on the basis of R software. Genes specific to tissue/organ were identified through BioGPS. An enrichment analysis of DEGs was conducted in accordance with the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). We also built protein-protein interaction (PPI) networks to explore the function and enrichment pathway of DEGs and the identification of hub genes. Lastly, the ROC curve was drawn for hub genes achieving specific expressions within skeletal muscle. Moreover, the area under the curve (AUC) was obtained to calculate the predictive value of key genes. The transcription factors of hub genes achieving specific expressions within skeletal muscle were predicted with the use of the iRegulon plugin. Results. We identified 170 DEGs among 11 healthy subject samples and 18 RYR1 mutation-associated myopathy samples in the dataset. Among the above DEGs, 31 genes achieving specific expressions within tissues/organs were found. GO and KEGG enrichment analysis of DEGs mainly focused on muscle contraction, actin-mediated cell contraction, actin filament-based movement, and muscular sliding. 12 hub genes were identified with the use of Cytoscape. Four hub genes were specifically expressed in skeletal muscle tissue, including MYH1 (AUC: 0.856), TNNT3 (AUC: 0.840), MYLPF (AUC: 0.786), and ATP2A1 (AUC: 0.765). The iRegulon predicted results suggested that the transcription factor MYF6 was found with the highest reliability. Conclusions. Four skeletal muscle tissue-specific genes were identified, including MYH1, TNNT3, MYLPF, and ATP2A1, as the potential biomarkers for diagnosing and treating RYR1 mutation-associated myopathies, which provided insights into the transcriptome-level development mechanism. The transcription factor MYF6 may be a vital upstream regulator of the above biomarkers.

An Association between OXPHOS-Related Gene Expression and Malignant Hyperthermia Susceptibility in Human Skeletal Muscle Biopsies

“…Age, sex, fitness, and fibre type will all influence transcriptomic profiles in addition to the underlying genetic defects. Nevertheless, the integration of genome sequencing, transcriptomics, and bioinformatics data should prove fruitful to further our understanding of complex phenotypes [ 55 ], and predicting potential biomarkers in relation to RYR1-associated disease [ 56 ]. Whilst protein studies are needed to follow up observed transcriptional differences, and their full implications with respect to pathological processes remain to be explored, this study has confirmed the importance of mitochondrial metabolism in MH.…”

CCDC78: unveiling the function of a novel gene associated to hereditary myopathy

“…Although MYH1 has not been clearly associated to date with RYR1 -related myopathies, MYH1 mutations were associated with non-exertional rhabdomyolysis phenotype in horses 40 and MYH1 was recently considered a candidate gene for recurrent rhabdomyolysis also in humans 41 . Interestingly, the proteomic study of Eckhardt et al 42 showed a quantitative reduction of MYH1 in a mouse model with biallelic RYR1 mutations; accordingly, Wang et al 43 showed a significant reduction of MYH1 expression in muscle tissue from RYR1 mutated patients and suggested MYH1 as potential biomarkers for RYR1- myopathies. These data, together with the found interaction with CCDC78, reinforce the hypothesis of an intimate role of MYH1 with other SR proteins.…”