Animal surgery
A total of 41 wildtype male Lewis rats (Sankyo Labo Service Corporation, Tokyo, Japan) at 10–12 weeks old were used for the experiments. All animal care and experiments were conducted in accordance with the institutional guidelines of the Animal Committee of Tokyo Medical and Dental University (permission number: A2021-267A). Partial medial meniscectomy (pMx) was performed on either the right or left knee under 2% isoflurane anesthesia [16]. The contralateral knee received sham surgery (joint capsule incision). At 2, 4, and 6 weeks after the surgery, the knee joints and SF were collected. Intact rats that received no surgery were also prepared. All rats were allowed to walk freely in a cage.
Culture Of Colony-forming Cells In Sf
SF was collected from rat knee joints by pumping the joints twice with 50 µL of phosphate-buffered saline (PBS) [17]. The collected fluid was plated in a 145 cm2 dish (Thermo Fisher Scientific, Waltham, MA, USA) and cultured in growth medium consisting of α-modified essential medium (α-MEM; Thermo Fisher Scientific), 10% fetal bovine serum (FBS; Thermo Fisher Scientific), and 1% antibiotic-antimycotic (Thermo Fisher Scientific) at 37°C in 5% humidified CO2. Seven days after the initial plating, the cells were stained with 0.5% crystal violet (Wako, Osaka, Japan). The numbers and sizes of the colonies were assessed using Fiji/Image J (National Institute of Health, Bethesda, MD, USA) and the “Analyze Particles” command [18]. Colonies less than 1 mm2 in area were ignored. The MSC properties were evaluated by detaching colony-forming cells from intact knees and from knees 4 weeks after the sham and pMx surgeries with 0.25% trypsin (Thermo Fisher Scientific) and expanding the detached MSCs in growth medium to passage 2.
Histology
Rat knee joints were fixed with 10% formalin neutral buffer solution (Wako), decalcified in 20% ethylenediaminetetraacetic acid (EDTA) for 21 days, and then embedded in paraffin wax. The specimens were cut into 5 µm sagittal sections and stained with hematoxylin/eosin (HE) and safranin O/fast green. Synovitis, cartilage degeneration, meniscus regeneration, and bone marrow lesions (BMLs) were evaluated using Krenn's score [5] (Supplementary Table 1), the OARSI score [2](Supplementary Table 2), the modified Pauli’s score [3, 19] (Supplementary Table 3), and the osteoarthritis bone score (OABS) [4] (Supplementary Table 4), respectively. Infrapatellar fat pad (IFP) fibrosis was assessed as the percentage of the fibrotic area determined using Fiji/ImageJ.
Immunohistochemistry
Immunostaining of CD68, CD73, and ZO-1 was conducted by immersing the sections in 10 mM Tris containing 1 mM EDTA (pH 9.0) at 60°C for 16 h to retrieve antigens. The slides were then immersed in methanol containing 0.3% H2O2 for 30 min and washed with Tris-buffered saline containing 0.1% Tween-20 (TBS-T). After blocking with Blocking One Histo (NACALAI TESQUE, Kyoto, Japan), the sections were incubated overnight at 4°C with antibody against CD68 (1:200; Novus), CD73 (1:200; R&D), or ZO-1 (1:50; Thermo Fisher Scientific). After three washes with TBS-T, the sections were incubated with secondary antibodies conjugated with horseradish peroxidase (1:200; Abcam) for 1 h at room temperature. DAB solution (Dako) was then applied for 5 min, and the cells were counterstained with hematoxylin. DAB-positive areas were quantified using the color deconvolution for Fiji/Image J in two fields of view of the synovium (465 × 620 µm) for CD68 and CD73, and four fields of view at the surface of the synovium (100 × 500 µm) for ZO-1.
Surface Epitopes
Colony-forming cells from SF were detached at passage 2 with TrypLE (Thermo Fisher Scientific) and suspended in FACS buffer (2% FBS and 5 mM EDTA in PBS). The cells were stained with the CD34-PerCP (Novus Biologicals, Littleton, CO, USA), CD44-PE (R&D Systems, Minneapolis, MN, USA), CD45-FITC (BD Biosciences, San Jose, CA, USA), CD90-PE-Cy7 (BD), CD105-APC (Novus), and Ghost Dye Violet 510 for dead cells (Tonbo Biosciences, CA, USA). For CD73, a mouse anti-CD73 antibody (BD) was used, followed by the secondary antibody conjugated with Alexa Fluor 488 (abcam). The proportion of antigen-positive cells was evaluated using a FACSVerse instrument (BD).
Colony-forming Unit (Cfu) Assays
Colony-forming cells at passage 2 were plated at 100 cells/dish in 60 cm2 dishes (Thermo Fisher Scientific) and cultured in growth medium for 2 weeks. The cells were then fixed with 10% neutral buffered formalin and stained with 0.5% crystal violet. Colonies were counted manually, and colonies less than 1 mm2 in area were ignored.
Differentiation Assays
Adipogenesis was evaluated by plating 100 cells in a 60 cm2 dish and culturing them in growth medium for 14 days to allow colony formation. The medium was then switched to an adipogenic induction medium consisting of growth medium supplemented with 100 nM dexamethasone, 0.5 mM isobutyl methylxanthine (Sigma-Aldrich, St Louis, MO, USA), 4.5 mg/mL D-(+)-glucose (Wako), and 100 µM indomethacin (Sigma-Aldrich). After 2 weeks of adipogenic induction, the cells were stained with oil red O (Sigma-Aldrich).
Calcification was examined by plating 100 cells in a 60 cm2 dish and culturing them in growth medium for 14 days to allow colony formation. Adherent cells were subsequently cultured in an osteogenic induction medium consisting of growth medium supplemented with 50 µg/mL ascorbic acid 2-phosphate (Wako), 100 nM dexamethasone (Wako), and 10 mM β-glycerophosphate (Sigma-Aldrich) After 3 weeks of osteogenic induction, the cells were stained with alizarin red (Sigma-Aldrich).
For chondrogenesis, 2.5 × 105 cells were transferred into a 15 mL tube (Thermo Fisher Scientific) and centrifuged for 10 min at 580 × g. The cell pellets were cultured in chondrogenic induction medium consisting of high glucose Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific), 1% insulin–transferrin–selenium (ITS; BD), 50 µg/mL ascorbate-2-phosphate, 40 µg/mL L-proline (Sigma-Aldrich), 100 nM dexamethasone, 100 µg/mL pyruvate (Sigma-Aldrich), 1% antibiotic–antimycotic, 10 ng/mL human transforming growth factor-β3 (Miltenyi Biotec Japan, Tokyo, Japan), and 1000 ng/mL human bone morphogenetic protein 2 (Medtronic, Minneapolis, MN). After 3 weeks, the cell pellets were fixed, embedded in paraffin, and sectioned. The slides were stained with safranin O/fast green (Wako).
Rna Sequencing
SF from intact knees and knees 4 weeks after sham and pMx surgery was plated in 145 cm2 dishes and cultured in growth medium. After 1 week of cultivation, total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Hilden, Germany). RNA sequencing was performed by the Beijing Genomics Institute (BGI; Shenzhen, Guangdong, China). Briefly, mRNA was isolated using oligo-dT beads and fragmented. Single-strand cDNA was generated using random N6-primed reverse transcription, followed by a second-strand cDNA with dUTP. After PCR amplification, the products were sequenced on the DNBSEQ platform. The sequence reads were aligned to a rat reference genome (GCF_000001895.5_Rnor_6.0).
Analysis Of Sequencing Data
All data were analyzed using Dr. Tom, a BGI data mining system. The gene expression levels were calculated as transcripts per million (TPM) values. Differentially expressed genes (DEGs) were determined between each group (FDR < 0.05). Gene ontology (GO) enrichment analysis was performed on DEGs that were upregulated in the pMx group compared with the intact and sham groups.
Statistical Analysis
All data were expressed as mean ± standard deviation. All statistical analyses, except for RNA sequencing statistics, were performed using EZR (Saitama Medical Center, Jichi Medical University, Japan), a graphical user interface of R (The R Foundation for Statistical Computing, Vienna, Austria, version 2.7.1) [20]. Statistical significance was accepted at p < 0.05. The Steel-Dwass test was used for comparisons of time-course changes, and the Mann-Whitney U test was used for comparisons between 2 groups. Spearman's rank correlation coefficient was used for evaluating correlations. Bonferroni correction was used to adjust the p values of multiple Spearman's rank correlation coefficients.