Rotator cuff (RC) tears present a treatment challenge due to muscle atrophy and degeneration, fatty infiltration, and fibrosis. The purpose of this study was to generate a high time-resolution model of RC tear in rabbits and to characterize the progression of architectural and histological changes. Thirty-five female New Zealand White rabbits (age: 6 months) underwent left supraspinatus tenotomy. Five rabbits were used to evaluate immediate muscle architectural changes. The remaining 30 rabbits underwent right shoulder sham surgery and sacrifice at 1, 2, 4, 8, or 16 weeks. Histology was used to quantify muscle fiber cross-sectional area (CSA), muscle degeneration and regeneration, and fat localized to inter- versus intrafascicular regions. Muscle fiber CSA decreased by 26.5% compared to sham at 16 weeks (effect of treatment, p < 0.0001). Muscle degeneration increased after tenotomy (effect of treatment, p = 0.0006) without any change in regeneration. Collagen and fat content increased by 4 weeks and persisted through 16 weeks. Interfascicular fat was increased at all time points, but intrafascicular fat was increased only at 1, 4, and 16 weeks posttenotomy. Intrafascicular fat adjacent to degenerating muscle fibers increased as well (effect of treatment, p < 0.0001; effect of time, p = 0.0102). Statement of clinical relevance: Rabbit supraspinatus tenotomy recapitulates key features of the pathophysiology of human RC tears, including muscle atrophy and degeneration, lack of regeneration, fat accumulation, and fibrosis.

Introduction: Rotator cuff tears are prevalent in the population above the age of 60. The disease progression leads to muscle atrophy, fibrosis, and fatty infiltration, which is not improved upon with surgical repair, highlighting the need to better understand the underlying biology impairing more favorable outcomes. Methods: In this study, we collected supraspinatus muscle tissue from 6 month old female rabbits who had undergone unilateral tenotomy for 8 weeks at 1, 2, 4, or 8 weeks post-repair (n = 4/group). RNA sequencing and enrichment analyses were performed to identify a transcriptional timeline of rotator cuff muscle adaptations and related morphological sequelae. Results: There were differentially expressed (DE) genes at 1 (819 up/210 down), 2 (776/120), and 4 (63/27) weeks post-repair, with none at 8 week post-repair. Of the time points with DE genes, there were 1092 unique DE genes and 442 shared genes, highlighting that there are changing processes in the muscle at each time point. Broadly, 1-week post-repair differentially expressed genes were significantly enriched in pathways of metabolism and energetic activity, binding, and regulation. Many were also significantly enriched at 2 weeks, with the addition of NIF/NF-kappaB signaling, transcription in response to hypoxia, and mRNA stability alongside many additional pathways. There was also a shift in transcriptional activity at 4 weeks post-repair with significantly enriched pathways for lipids, hormones, apoptosis, and cytokine activity, despite an overall decrease in the number of differentially expressed genes. At 8 weeks post-repair there were no DE genes when compared to control. These transcriptional profiles were correlated with the histological findings of increased fat, degeneration, and fibrosis. Specifically, correlated gene sets were enriched for fatty acid metabolism, TGF-B-related, and other pathways. Discussion: This study identifies the timeline of transcriptional changes in muscle after RC repair, which by itself, does not induce a growth/regenerative response as desired. Instead, it is predominately related to metabolism/energetics changes at 1 week post-repair, unclear or asynchronous transcriptional diversity at 2 weeks post-repair, increased adipogenesis at 4 weeks post-repair, and a low transcriptional steady state or a dysregulated stress response at 8 weeks post-repair.