RNA‐Seq analysis reveals sex‐dependent transcriptomic profiles of human subacromial bursa stratified by tear etiology

Abstract

Rotator cuff tendinopathy, a major cause of shoulder disability, occurs due to trauma or degeneration. Our molecular understanding of traumatic and degenerative tears remains elusive. Here, we probed transcript level differences between traumatic and degenerative tears. Subacromial bursa tissues were collected from patients with traumatic or degenerative tears during arthroscopy (N = 32). Transcripts differentially expressed by tear etiology were detected by RNA‐seq. RNA‐seq results were validated by real‐time quantitative polymerase chain reaction. We identified 334 protein‐coding transcripts differentially expressed between traumatic and degenerative tears in females and 167 in males at a fold‐change greater than 2. In females, XIRP2, MYL1, MYBPC1, TNNT1, and LMOD2, were highly expressed in traumatic tears whereas TPSD1, CDSN, RCVRN, LTBP4, and PTGS1 were elevated in degen tears. Transcripts elevated in traumatic tears represented muscle cell differentiation and development, and muscle contraction whereas those elevated in degenerative tears represented cell activation and immune response. In males, AZGP1, CNTFR, COL9A1, ZNF98, and EREG were highly elevated in traumatic tears whereas MYL2, HOXD11, SLC6A7, CADM1, and MMP17 were highly expressed in degenerative tears. Transcripts elevated in traumatic tears represented metabolic/catabolic processes, and transmembrane protein transport while processes related to cell cycle were mainly enriched in degenerative tears. Numerous long noncoding RNAs were differentially expressed between traumatic and degenerative tears in both sexes. In summary, this study provides insights into molecular biology of bursa in patients with rotator cuff tendon disease based on tear acuity and novel sex‐based transcript differences that could inform clinical decision making in treating patients with traumatic or degenerative shoulder injuries.

Are there sex‐dependent transcriptional differences in human subacromial bursa from traumatic versus degenerative rotator cuff tears?

“…In the original data, it appeared that Patient 6 would largely drive the reported differences between traumatic versus degenerative tears in females (fig. 1A in Rai et al 1 ), but this was not discussed by the authors. 1 Therefore, we ran a principal component analysis (PCA) including all samples to visualize sex-and diagnosis-related differences at the macrolevel (Figure 1A).…”

“…1A in Rai et al 1 ), but this was not discussed by the authors. 1 Therefore, we ran a principal component analysis (PCA) including all samples to visualize sex-and diagnosis-related differences at the macrolevel (Figure 1A). Principal components one and two, which accounted for 26% and 16% of the variance in the data, respectively, separated Sample 6 from the rest of the samples (Figure 1A).…”

“…Using RNA sequencing, the recent study by Rai et al 1 compared the transcriptomes of subacromial bursa collected from male and female patients suffering from traumatic or degenerative rotator cuff tears.…”

“…Interestingly, the authors found transcriptional differences in bursae between traumatic and degenerative rotator cuff tears in female but not male patients. We read and discussed this publication with great interest as we believe that the bursa is an understudied tissue in rotator cuff pathologies; thus, the work by Rai et al 1 is a much needed contribution to the field. However, we found some of the methodological details to be unclear and therefore decided to reanalyze their publicly available dataset to gain a better understanding of their very interesting results.…”

“…1D and tables S1-3 in Rai et al), but this was not addressed. 1 Third, to generate the key heatmaps and Venn diagrams, and to calculate differentially expressed genes in the original publication, the authors used raw instead of adjusted p values for multiple comparisons testing. 1 In RNA sequencing data it is standard to use adjusted p values to correct for multiple comparisons to decrease the risk of false positives.…”