Epigenetic and transcriptomic signatures of human slow‐ and fast‐twitch muscle fibers across the lifespan

Abstract

The clinical condition of sarcopenia, a hallmark of aging, is characterized by a loss of muscle mass and function, which is more pronounced in fast‐twitch muscle fibers. Exercise can partially mitigate these effects, but little is known about how aging and exercise may impact the control of muscle gene expression through DNA methylation. Therefore, we examined epigenetic and transcriptome signatures of human slow‐twitch (MHC I) and fast‐twitch (MHC IIa) muscle cells (i.e. fibers) in lifelong endurance exercisers (LLE; n=8, 74±1 y, 180±3 cm, 77±2 kg, VO2 max 2.9±0.1 l/min, Quadriceps CSA 68.1±7 cm2), age‐matched healthy non‐exercisers (OH; n=9, 75±1 y, 177±2 cm, 88±3 kg, VO2 max 2.0±0.2 l/min, Quadriceps CSA 55.5±9 cm2), and a young exercising cohort (YE; n=8, 25±1 y, 182±2 cm, 75±3 kg, VO2max 4.1±0.2 l/min, Quadriceps CSA 79.3±9 cm2). For each subject, 96 individual vastus lateralis muscle fibers were separated from a muscle bundle (~5–6 mm length) under a light microscope using fine tweezers. The fiber type (MHC) was determined using SDS‐PAGE before fiber‐type specific DNA and RNA extractions of pooled single muscle fibers (~30 fibers). DNA methylation was assessed using Reduced Representation Bisulfite Sequencing on 32 ng of DNA. Gene expression was examined with RNA‐Sequencing using 9 ng of RNA. Differentially methylated regions (DMRs, methylation difference ≥35%, p<0.05) and differentially expressed transcripts (fold‐change ≥1.5, p<0.01) between fiber types were identified in each subject cohort and overlaid to identify common genes between YE, OH, and LLE. Ingenuity Pathway Analysis software and the gene ontology database were utilized to interpret the biology of the common genes. We identified 183 differentially methylated genes and 141 differentially expressed genes between fiber types, which were common in all three groups (YE, OH, and LLE). The molecular and biological processes of these genes, such as ATP‐dependent microfilament and microtubule motor activities or glycolysis, were consistent with the fiber‐type functional and structural phenotypic differences. We interrogated the 183 differentially methylated genes with the 141 differentially expressed genes, and identified 12 genes with both gene methylation and expression differences between fiber types across all three groups. Seven of them were myosin and troponin genes. These data provide the first fiber‐type specific gene methylation and expression signatures of healthy human skeletal muscle across the lifespan. Future analysis of the epigenetic and transcriptomic signatures specific to YE, LLE, and OH could add knowledge and further our understanding on slow‐ and fast‐twitch fiber biology with aging and exercise. Furthermore, fiber‐type specific epigenetic and transcriptomic characterization of healthy human skeletal muscles will contribute to a better understanding of age‐ and disease‐related muscle dysfunctions.Support or Funding InformationNIH grant R01 AG‐038576 and Ball State University Academic Excellence AwardThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.