In vivo Monitoring of Transcriptional Dynamics After Lower-Limb Muscle Injury Enables Quantitative Classification of Healing

Abstract

Traumatic lower-limb musculoskeletal injuries are pervasive amongst athletes and the military and typically an individual returns to activity prior to fully healing, increasing a predisposition for additional injuries and chronic pain. Monitoring healing progression after a musculoskeletal injury typically involves different types of imaging but these approaches suffer from several disadvantages. Isolating and profiling transcripts from the injured site would abrogate these shortcomings and provide enumerative insights into the regenerative potential of an individual’s muscle after injury. In this study, a traumatic injury was administered to a mouse model and healing progression was examined from 3 hours to 1 month using high-throughput RNA-Sequencing (RNA-Seq). Comprehensive dissection of the genome-wide datasets revealed the injured site to be a dynamic, heterogeneous environment composed of multiple cell types and thousands of genes undergoing significant expression changes in highly regulated networks. Four independent approaches were used to determine the set of genes, isoforms, and genetic pathways most characteristic of different time points post-injury and two novel approaches were developed to classify injured tissues at different time points. These results highlight the possibility to quantitatively track healing progression in situ via transcript profiling using high- throughput sequencing.

Robust inflammatory and fibrotic signaling following volumetric muscle loss: a barrier to muscle regeneration

“…Using RNA-seq on the injured tissues and several types of bioinformatics analyses, the investigators found a series of enriched gene sets associated with chemotaxis and inflammation that were followed by pathways associated with excessive extracellular matrix (ECM) deposition and remodeling. These results were in contrast to many muscle regenerative studies 8 , where inflammatory pathways subsided after several days 9 . Instead, VML injury appears to stimulate complement, Wnt and TGF-β signaling in a sustained fashion, which in turn activates fibrosis development.…”

Distinct skeletal muscle molecular responses to pulmonary rehabilitation in chronic obstructive pulmonary disease: a cluster analysis

“…Indeed, as expected upon exercise training, C1 displayed an increase in OXCAP markers upon PR, reflecting a restoration of the oxidative metabolic machinery. This is corroborated by the decreased expression of oxidative metabolism regulation markers, as a normalization of metabolism‐related mRNA has previously been shown in late‐stage muscle regeneration . Conversely, in C2, oxidative metabolism regulation and OXCAP were statistically unaltered, although oxidative metabolism regulation seemed to increase upon PR.…”

“…Furthermore, the differential regulation of myogenesis is reflected by a differential change in the expression of specific markers. Interestingly, the reduction in the myogenesis markers MYOD1 and CDH15, and induction in MYMK mRNA expression upon PR in C1, was previously shown to be reflective of late‐stage muscle regeneration . Conversely, the apparent increase in MYOD1 and CDH15 mRNA expression, together with only a tendency towards an increase in MYMK upon PR in C2, is reflective of an earlier phase of muscle regeneration .…”

Transcriptional and Chromatin Dynamics of Muscle Regeneration after Severe Trauma

“…To gain insights into the healing process after administration of trauma, we performed expression profiling by RNA sequencing (RNA-seq) and small RNA-seq (miRNA-seq) (Aguilar et al., 2015) for both the injured and contralateral tissues for multiple time points (Figure 1), and lumped the datasets into three key stages (early, 3–24 hr; middle, 48–168 hr; late, 336–672 hr). Hierarchical clustering of the RNA-seq data through time revealed clusters up- and downregulated that were associated with different stages of muscle repair and regeneration (Figure 1B).…”