# Single cell atlas decodes the molecular dynamics of scar repair after human rotator cuff tear

**Authors:** Yiming Qin, Guang Yang, Tao Zhang, Yuying Yang, Liyang Wan, Tao Zhang, Linfeng Wang, Zhiyu Hu, Zhu Dai, Hongkang Zhou, Chengjun Li, Jianzhong Hu, Hongbin Lu

PMC · DOI: 10.1038/s41413-025-00501-5 · Bone Research · 2026-02-05

## TL;DR

This study uses single-cell RNA sequencing to understand the cellular and molecular changes in scar formation after human rotator cuff tears, identifying potential therapeutic targets.

## Contribution

The study provides a detailed single-cell atlas of the fibrotic scarring microenvironment after human RCT, identifying novel pro-fibrotic cell types and signaling pathways.

## Key findings

- Heterogeneous pro-fibrotic subclusters, including tendon stem cells and SOX9-driven macrophages, contribute to scar formation.
- Osteopontin and TGF-β signaling are key drivers of extracellular matrix deposition in fibrotic scarring.
- Blocking osteopontin and TGF-β signaling ameliorates fibrotic scarring after RCT.

## Abstract

Irreversible fibrotic scarring after rotator cuff tear (RCT) compromises the mechanical properties of the healing tendon, yet the underlying mechanisms remain poorly understood. Here, we analyzed the histological features of human RCT scars, characterized by disruption of tendon architecture, disorganized collagen fibrils, and imbalance in type I/III collagen ratios and fibril diameters. Using single-cell RNA sequencing of tendon stumps from patients with RCT, we deconvolved the cellular and molecular landscape of the fibrotic scarring microenvironment. Heterogenous pro-fibrotic subclusters were identified and validated to participate into scar formation, including tendon stem cell, senescent tenocyte, SOX9-driven pro-fibrotic macrophage, and pro-fibrotic endothelial cells undergoing endothelial-mesenchymal transition (EndoMT). Furthermore, we found that osteopontin and TGF-β signaling were key drivers of extracellular matrix deposition, and their blockade ameliorated fibrotic scarring after RCT. Collectively, our study dissected the dynamic scarring microenvironment in human RCT and highlights potential therapeutic targets for preventing pathological scar formation.

## Linked entities

- **Genes:** SOX9 (SRY-box transcription factor 9) [NCBI Gene 6662]
- **Proteins:** TGFB1 (transforming growth factor beta 1)

## Full-text entities

- **Genes:** FOLR3 (folate receptor gamma) [NCBI Gene 2352] {aka FR-G, FR-gamma, FRgamma, gamma-hFR}, HLF (HLF transcription factor, PAR bZIP family member) [NCBI Gene 3131], POSTN (periostin) [NCBI Gene 10631] {aka OSF-2, OSF2, PDLPOSTN, PN}, HLA-C (major histocompatibility complex, class I, C) [NCBI Gene 3107] {aka D6S204, HLA-JY3, HLAC, HLC-C, MHC, PSORS1}, CXCL12 (C-X-C motif chemokine ligand 12) [NCBI Gene 6387] {aka IRH, PBSF, SCYB12, SDF1, TLSF, TPAR1}, ITGA5 (integrin subunit alpha 5) [NCBI Gene 3678] {aka CD49e, FNRA, VLA-5, VLA5A}, PROX1 (prospero homeobox 1) [NCBI Gene 5629], ITGB1 (integrin subunit beta 1) [NCBI Gene 3688] {aka CD29, FNRB, GPIIA, MDF2, MSK12, VLA-BETA}, COL5A2 (collagen type V alpha 2 chain) [NCBI Gene 1290] {aka EDSC, EDSCL2}, LYVE1 (lymphatic vessel endothelial hyaluronan receptor 1) [NCBI Gene 10894] {aka CRSBP-1, HAR, LYVE-1, XLKD1}, PDPN (podoplanin) [NCBI Gene 10630] {aka AGGRUS, D2-40, GP36, GP40, Gp38, HT1A-1}, CD44 (CD44 molecule (IN blood group)) [NCBI Gene 960] {aka CDW44, CSPG8, ECM-III, ECMR-III, H-CAM, HCELL}, SMAD3 (SMAD family member 3) [NCBI Gene 4088] {aka HSPC193, HsT17436, JV15-2, LDS1C, LDS3, MADH3}, Lef1 (lymphoid enhancer binding factor 1) [NCBI Gene 161452], COL3A1 (collagen type III alpha 1 chain) [NCBI Gene 1281] {aka EDS4A, EDSVASC, PMGEDSV}, TSC1 (TSC complex subunit 1) [NCBI Gene 7248] {aka LAM, TSC}, Atf3 (activating transcription factor 3) [NCBI Gene 25389] {aka LRF-1, LRFI}, TREM2 (triggering receptor expressed on myeloid cells 2) [NCBI Gene 54209] {aka AD17, PLOSL2, TREM-2, Trem2a, Trem2b, Trem2c}, COL1A1 (collagen type I alpha 1 chain) [NCBI Gene 1277] {aka CAFYD, EDSARTH1, EDSC, OI1, OI2, OI3}, IL1A (interleukin 1 alpha) [NCBI Gene 3552] {aka IL-1 alpha, IL-1A, IL1, IL1-ALPHA, IL1F1}, Sox9 (SRY-box transcription factor 9) [NCBI Gene 140586] {aka SRY}, CD68 (CD68 molecule) [NCBI Gene 968] {aka GP110, LAMP4, SCARD1}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, Tgfbi (transforming growth factor, beta induced) [NCBI Gene 116487] {aka BIGH3, Big-h3}, LUM (lumican) [NCBI Gene 4060] {aka LDC, SLRR2D}, CD9 (CD9 molecule) [NCBI Gene 928] {aka BTCC-1, DRAP-27, MIC3, MRP-1, TSPAN-29, TSPAN29}, Cebpd (CCAAT/enhancer binding protein delta) [NCBI Gene 25695] {aka C/EBPd, CELF}, CCL2 (C-C motif chemokine ligand 2) [NCBI Gene 6347] {aka GDCF-2, HC11, HSMCR30, MCAF, MCP-1, MCP1}, SMAD5 (SMAD family member 5) [NCBI Gene 4090] {aka DWFC, JV5-1, MADH5}, DCN (decorin) [NCBI Gene 1634] {aka CSCD, DSPG2, PG40, PGII, PGS2, SLRR1B}, VEGFA (vascular endothelial growth factor A) [NCBI Gene 7422] {aka L-VEGF, MVCD1, VEGF, VPF}, FOXO1 (forkhead box O1) [NCBI Gene 2308] {aka FKH1, FKHR, FOXO1A}, Itgav (integrin subunit alpha V) [NCBI Gene 296456] {aka Cd51}, MANEA (mannosidase endo-alpha) [NCBI Gene 79694] {aka ENDO, hEndo}, IFNA1 (interferon alpha 1) [NCBI Gene 3439] {aka IFL, IFN, IFN-ALPHA, IFN-alphaD, IFNA13, IFNA@}, CCL21 (C-C motif chemokine ligand 21) [NCBI Gene 6366] {aka 6Ckine, CKb9, ECL, SCYA21, SLC, TCA4}, CCN2 (cellular communication network factor 2) [NCBI Gene 1490] {aka CTGF, HCS24, IBP-8, IGFBP8, KMD, NOV2}, Fos (Fos proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 314322] {aka c-fos}, THBS2 (thrombospondin 2) [NCBI Gene 7058] {aka EDSCLL3, TSP2}, SPP1 (secreted phosphoprotein 1) [NCBI Gene 6696] {aka BNSP, BSPI, ETA-1, OPN}, SMAD2 (SMAD family member 2) [NCBI Gene 4087] {aka CHTD8, JV18, JV18-1, LDS6, MADH2, MADR2}, ITGB5 (integrin subunit beta 5) [NCBI Gene 3693], ACTA1 (actin alpha 1, skeletal muscle) [NCBI Gene 58] {aka ACTA, ASMA, CFTD, CFTD1, CFTDM, CMYO2A}, Spp1 (secreted phosphoprotein 1) [NCBI Gene 25353] {aka OSP}, DBP (D-box binding PAR bZIP transcription factor) [NCBI Gene 1628] {aka DABP, taxREB302}, BMP1 (bone morphogenetic protein 1) [NCBI Gene 649] {aka OI13, PCOLC, PCP, TLD}, EGF (epidermal growth factor) [NCBI Gene 1950] {aka HOMG4, URG}, PECAM1 (platelet and endothelial cell adhesion molecule 1) [NCBI Gene 5175] {aka CD31, CD31/EndoCAM, GPIIA', PECA1, PECAM-1, endoCAM}, MMP1 (matrix metallopeptidase 1) [NCBI Gene 4312] {aka CLG}, MMP2 (matrix metallopeptidase 2) [NCBI Gene 4313] {aka CLG4, CLG4A, MMP-2, MMP-II, MONA, TBE-1}, MAF (MAF bZIP transcription factor) [NCBI Gene 4094] {aka AYGRP, CCA4, CTRCT21, c-MAF}, THBS4 (thrombospondin 4) [NCBI Gene 7060] {aka TSP-4, TSP4}, SOX9 (SRY-box transcription factor 9) [NCBI Gene 6662] {aka CMD1, CMPD1, ENH13, SRA1, SRXX2, SRXY10}, KLF3 (KLF transcription factor 3) [NCBI Gene 51274] {aka BKLF}, CD248 (CD248 molecule) [NCBI Gene 57124] {aka CD164L1, TEM1}, Junb (JunB proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 24517], Barx1 (BARX homeobox 1) [NCBI Gene 364680], Postn (periostin) [NCBI Gene 361945] {aka Plf}, COL1A2 (collagen type I alpha 2 chain) [NCBI Gene 1278] {aka EDSARTH2, EDSCV, OI4}, PDGFA (platelet derived growth factor subunit A) [NCBI Gene 5154] {aka PDGF-A, PDGF1}
- **Diseases:** re-tear (MESH:D000084063), hypoxia (MESH:D000860), fibrotic disease (MESH:D004194), necrotic (MESH:D009336), supraspinatus tendon rupture (MESH:D012421), BMDMs (MESH:D001855), Inflammation (MESH:D007249), tendon injury (MESH:D013708), EndoMT (MESH:D008579), supraspinatus tear (MESH:D012167), RCT (MESH:D000070636), ACL tear (MESH:D000070598), Fibrosis (MESH:D005355), Fibro-Macro (MESH:D009810), UMAP (MESH:C567162)
- **Chemicals:** SB-431542 (MESH:C459179), H&amp;E (MESH:D006371), Picrosirius red (MESH:C009798), LPS (MESH:D008070), isoflurane (MESH:D007530), lipid (MESH:D008055), HY-10431 (-)
- **Species:** Rattus norvegicus (brown rat, species) [taxon 10116], Homo sapiens (human, species) [taxon 9606]

## Full text

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## Figures

9 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12877062/full.md

## References

7 references — full list in the complete paper: https://tomesphere.com/paper/PMC12877062/full.md

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Source: https://tomesphere.com/paper/PMC12877062