Bioinformatics analysis of differentially expressed genes in rotator cuff tear patients using microarray data

Transcriptional time course after rotator cuff repair in 6 month old female rabbits

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.

Transcriptional Time Course After Rotator Cuff Tear

Rotator cuff (RC) tears are prevalent in the population above the age of 60. The disease progression leads to muscle atrophy, fibrosis, and fatty infiltration in the chronic state, which is not improved with intervention or surgical repair. This highlights the need to better understand the underlying dysfunction in muscle after RC tendon tear. Contemporary studies aimed at understanding muscle pathobiology after RC tear have considered transcriptional data in mice, rats and sheep models at 2–3 time points (1 to 16 weeks post injury). However, none of these studies observed a transition or resurgence of gene expression after the initial acute time points. In this study, we collected rabbit supraspinatus muscle tissue with high temporal resolution (1, 2, 4, 8, and 16 weeks) post-tenotomy (n = 6/group), to determine if unique, time-dependent transcriptional changes occur. RNA sequencing and analyses were performed to identify a transcriptional timeline of RC muscle changes and related morphological sequelae. At 1-week post-tenotomy, the greatest number of differentially expressed genes was observed (1,069 up/873 down) which decreases through 2 (170/133), 4 (86/41), and 8 weeks (16/18), followed by a resurgence and transition of expression at 16 weeks (1,421/293), a behavior which previously has not been captured or reported. Broadly, 1-week post-tenotomy is an acute time point with expected immune system responses, catabolism, and changes in energy metabolism, which continues into 2 weeks with less intensity and greater contribution from mitochondrial effects. Expression shifts at 4 weeks post-tenotomy to fatty acid oxidation, lipolysis, and general upregulation of adipogenesis related genes. The effects of previous weeks’ transcriptional dysfunction present themselves at 8 weeks post-tenotomy with enriched DNA damage binding, aggresome activity, extracellular matrix-receptor changes, and significant expression of genes known to induce apoptosis. At 16 weeks post-tenotomy, there is a range of enriched pathways including extracellular matrix constituent binding, mitophagy, neuronal activity, immune response, and more, highlighting the chaotic nature of this time point and possibility of a chronic classification. Transcriptional activity correlated significantly with histological changes and were enriched for biologically relevant pathways such as lipid metabolism. These data provide platform for understanding the biological mechanisms of chronic muscle degeneration after RC tears.

Surgical rotator cuff muscle biopsies: are they representative of overall muscle quality?

BACKGROUND

Current research on human rotator cuff pathology relies on superficial biopsy specimens. It is unclear whether these biopsies are representative of overall muscle quality. The purpose of this study is to use magnetic resonance imaging with iterative decomposition of echoes of asymmetric length sequencing to investigate variability of fatty infiltration within the supraspinatus and infraspinatus muscle.

METHODS

We retrospectively identified 45 patients who underwent arthroscopic rotator cuff repair with preoperative iterative decomposition of echoes of asymmetric length imaging completed. The supraspinatus and infraspinatus were segmented on 4 consecutive slices, including the scapular Y, 2 slices medial, and 1 slice lateral. Intramuscular fat was measured in multiple regions for both supraspinatus (whole muscle, anterior, posterior, superficial band, anterior band, and posterior band) and infraspinatus (whole muscle, superior, inferior, superficial band, superior band, and inferior band). Comparisons of intramuscular fat were determined with Wilcoxon sign-rank tests. Analysis of variance was used to compare between the 4 consecutive slices. Significance was defined as P < .05.

RESULTS

Magnetic resonance imaging showed 31 full-thickness supraspinatus tears, 10 partial-thickness supraspinatus tears, and 4 intact supraspinatus tendons and 3 full-thickness infraspinatus tears, 2 partial-thickness infraspinatus tears, and 40 intact infraspinatus tendons. The anterior supraspinatus contained significantly higher fat content than the posterior supraspinatus (7.4% ± 7.4% vs. 5.4% ± 5.7%, P = .003). The superior and inferior halves of the infraspinatus were not different from each other (P = .11). The superficial band did not differ from the whole muscle in both supraspinatus (P = .14) and infraspinatus (P = .20). However, the anterior band of the supraspinatus had significantly more fat than the posterior band (8.2% ± 9.3% vs. 5.0% ± 5.7%, respectively, P < .0001), and the superior band of the infraspinatus had significantly more fat than the inferior band (5.2% ± 4.8% vs. 4.2% ± 5.3%, respectively, P = .03). There was no difference between all 4 medial and lateral slices in the supraspinatus (P = .92) and infraspinatus (P = .90).

CONCLUSION

Fat fractions within the supraspinatus and infraspinatus demonstrate significant spatial variability that may influence interpretation of local biopsy samples. Future biopsy studies may benefit from multiple samples between different specific locations.

Extended adverse effects of cyclophosphamide on mouse ovarian function

PURPOSE

Most patients with cancer undergo multiple administrations of anticancer drugs during treatment, resulting in chronic impairment of their reproductive health. As improved treatment options increase cancer survival, it has become increasingly important to address fertility issues in cancer survivors. In this study, we examined the pathophysiological effects of multiple exposures to cyclophosphamide (Cy) on the ovaries of mice and their underlying molecular mechanism.

METHODS

Female C57BL/6 mice were intraperitoneally injected with 100 mg/kg Cy six times over 2 weeks; 4 weeks later, the mice were sacrificed and their ovaries, sera, and oocytes were collected for histological observation, measurement of anti-Müllerian hormone levels, and assessment of oocyte quantity and quality in response to hormonal stimulation. Gene expression changes in Cy-treated ovaries were examined by microarray and bioinformatics analyses.

RESULTS

After repeated Cy exposure, the anti-Müllerian hormone level was decreased, and follicle loss and impairments in the quality of oocyte were irreversible. The expression levels of genes involved in folliculogenesis, oogenesis, and zona pellucida glycoprotein transcription displayed sustained alterations in Cy-exposed ovaries even after 4 weeks.

CONCLUSION

The adverse effects of Cy on ovarian function and oocytes remained even after chemotherapy was complete. Therefore, strategies to prevent ovarian damage or restore ovarian function after treatment are required to safeguard the fertility of young cancer survivors.

Acromial morphology is not associated with rotator cuff tearing or repair healing

BACKGROUND

The purposes of this study were to determine whether acromial morphology (1) could be measured accurately on magnetic resonance images (MRIs) as compared to computed tomographs (CTs) as a gold standard, (2) could be measured reliably on MRIs, (3) differed between patients with rotator cuff tears (RCTs) and those without evidence of RCTs or glenohumeral osteoarthritis, and (4) differed between patients with rotator cuff repairs (RCRs) that healed and those that did not.

METHODS

This is a retrospective comparative study. We measured coronal, axial, and sagittal acromial tilt; acromial width, acromial anterior and posterior coverage, and glenoid version and inclination on MRI corrected into the plane of the glenoid. We determined accuracy by comparison with CT via intraclass correlation coefficients (ICCs). To determine reliability, these same measurements were made on MRI by 2 observers and ICCs calculated. We compared these measurements between patients with a full-thickness RCT and patients aged >50 years without evidence of an RCT or glenohumeral osteoarthritis. We then compared these measurements between those patients with healed RCRs and those with a retorn rotator cuff on MRI. In this portion, we only included patients with both a preoperative MRI and a postoperative MRI at least 1 year from RCR. Only those patients without tendon defects on postoperative MRIs were considered to be healed. In these patients, we also radiographically measured the critical shoulder angle.

RESULTS

In a validation cohort of 30 patients with MRI and CT, all ICCs were greater than 0.86. In these patients, the inter-rater ICCs of the MRI measurements were >0.53. In our RCT group of 110 patients, there was greater acromial width [mean difference (95% confidence interval) = 0.1 (0, 0.2) mm, P = .012] and significantly less sagittal acromial tilt [9° (5°-12°), P < .001] than in our comparison group of 107 patients. A total of 110 RCRs were included. Postoperative MRI scans were obtained at a mean follow-up of 24.2 ± 15.8 months, showing 84 patients (76%) had healed RCRs. Aside from acromial width, which was 0.2 mm different and thus did not have clinical significance, there was no association between healing and any of the measured morphologic characteristics. Patients with healed repairs had significantly smaller tears in terms of both width (P < .001) and retraction (P < .001).

CONCLUSION

Although the acromion is wider in RCTs, the difference of 0.1 mm likely has no clinical significance. The acromion is more steeply sloped from posteroinferior to anterosuperior in those with RCTs. These findings call into question subacromial impingement due to native acromial morphology as a cause of rotator cuff tearing. Acromial morphology, critical shoulder angle, and glenoid inclination were not associated with healing after RCR. This study does not support lateral acromioplasty.

Genetic Aspects in Shoulder Disorders

The influence of genetic inheritance has been increasingly investigated in shoulder disorders, such as rotator cuff injury, instability and frozen shoulder. Although the initial findings are enlightening, it is necessary to progressively build a database of genetic markers to catalog genomic profiles that, later, may contribute for predicting the risk of the disease, as well as to the development of better diagnostic and treatment tools. The present article seeks to update what is evidence of genetic studies in the literature for these diseases, from polymorphism analyses, expression of candidate genes in tissues and broad genomic association studies (GWAS). However, it is necessary to point out that there is great difficulty in replicating and using the findings, mainly due to the lack of statistical power, the high rate of false-positive results and the large number of variables involved.

Identify differential gene expressions in fatty infiltration process in rotator cuff

Background

Rotator cuff tears are one of the most frequent upper extremity injuries and lead to pain and disability. Recent studies have implicated fatty infiltration in rotator cuff is a key failure element with the higher re-tear rates and poorer functional prognosis. Therefore, we investigated the differential expression of key genes in each stage of rotator cuff tear.

Methods

A published expression profile was downloaded from the Gene Expression Omnibus database and analyzed using the Linear Models for Microarray Data (LIMMA) package in R language to identify differentially expressed genes (DEGs) in different stages of injured rotator cuff muscles. Gene ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to annotate the function of the DEGs. Finally, PPI network and module analysis were used to identify hub genes.

Results

A total of 1089 fatty infiltration-related DEGs were identified, including 733 upregulated and 356 downregulated genes, and GO analyses confirmed that fatty infiltration was strongly associated with inflammatory response, aging, response to lipopolysaccharide, and immune response. Significantly enriched KEGG pathways associated with these DEGs included the phagosome, cell adhesion molecules, tuberculosis, and osteoclast differentiation. Further analyses via a PPI network and module analysis identified a total of 259 hub genes. Among these, Tmprss11d, Ptprc, Itgam, Mmp9, Tlr2, Il1b, Il18, Ccl5, Cxcl10, and Ccr7 were the top ten hub genes.

Conclusions

Our findings indicated the potential key genes and pathways involved in fatty degeneration in the development of fatty infiltration and supplied underlying therapeutic targets in the future.

Electronic supplementary material

The online version of this article (10.1186/s13018-019-1182-1) contains supplementary material, which is available to authorized users.