Collection of human RA synovial fluids and synovial tissues
RA was diagnosed according to the American College of Rheumatology/European League Against Rheumatism (ACR/EULAR) classification criteria [14, 15]. RA synovial membrane tissues (n = 10) were collected from the patients during knee joint arthroscopic synovectomy. The clinical information of the patients who provided synovial tissues and synovial fluids is shown in Supplementary Table 1. Human blood (n=36) and synovial fluids (n = 36) were collected from patients with RA. The use of samples for research was approved by The Ethics Committee of The Affiliated Hospital of Qingdao University (Approval number: 20190302). The clinical information of the patients who provided synovial fluids is shown in Supplementary Table 2. We also obtained 36 peripheral blood samples from healthy volunteers from the physical examination center of the hospital. The physical information of these healthy volunteers is also shown in Supplementary Table 2. All patients and healthy volunteers who joined this study provided informed consent.
Metabolomic profiling of synovial fluids
Synovial fluids from patients with RA (10 patients; Patient No. R41 to No. R50) and OA (10 patients; Patient No. O41 to No. O50) were injected into an ACQUITY UPLC I-Class system (Waters Corporation, Milford, USA) through a BEH amide column (100 mm × 2.1 mm i.d., 1.7 m; Waters, Milford, USA) and analyzed in a VION IMS QT mass spectrometer (Waters Corporation, Milford, USA). The LC flow rate was 0.4 mL/min with solvents A (a mixture of acetonitrile and 10 mmol ammonium acetate (pH = 9) (90/10%, volume/volume)) and B (10 mmol ammonium acetate (pH = 9)). The sample volume was 3 μL, the column temperature was held at 45°C, and the elution gradient of solvent B was as follows: 0 min, 5%; 1.5 min, 25%; 10 min, 90%; 13 min, 90%; 13.5 min, 5% and 14.5 min, 5%. Data acquisition was performed in full scan mode (over a m/z range of 50 to 1000), and the scan time was 0.1 seconds. The capillary voltage was 1.0 kV, and the sampling cone voltage was 40 V. The source temperature was 120°C. The desolvation temperature was 550°C, and the flow rate of the desolvation gas was 900 L/hour. To assess the stability of the system, quality control (QC) samples were injected at regular intervals throughout the analysis operation.
Volcano plots were generated by analyzing the fold change (FC) and p values from the t-test results and the variable importance in projection (VIP) scores from orthogonal partial least squares discriminant analysis (OPLS-DA). Metabolites meeting the criteria of VIP>1, FC > 2 or < 0.5 and p < 0.05 were defined as differentially expressed metabolites (DEMs).
Weighted gene coexpression network analysis (WGCNA)
WGCNA was performed with R software (v3.6.1). The correlation coefficients of all metabolites were calculated according to their expression values, and a soft thresholding power (β=8) was selected. The coexpression similarity was mapped into a weighted undirected network and topological overlap matrix (TOM). The dynamic tree cut algorithm was used to cluster metabolites into modules. The following parameters were used: MaxBlockSize, 6000; TOMType, unsigned; and minModuleSize, 30.
Establishment of collagen-induced arthritis in rats
Six-week-old male Sprague-Dawley (SD) rats were purchased from JNPY Laboratory Animal Co., Ltd. (Jinan, China). The animal study protocols complied with the Guide for the Care and Use of Laboratory Animals [16] and were approved by the Experimental Animal Care and Ethics Committee of The Affiliated Hospital of Qingdao University (approval number: 20190302). These rats were randomly divided into a normal control (NC) group and a CIA control group. Bovine type II collagen (Chondrex, USA) was mixed with complete Freund’s adjuvant (Sigma-Aldrich, Germany) at a proportion of 1:1 and fully emulsified. The initial immunization was performed by intracutaneous injection at the tail root. Three weeks later, a booster immunization was administered using a mixture of bovine type II collagen and incomplete Freund’s adjuvant (Sigma-Aldrich, Germany) by the same route as the initial immunization at a proportion of 1:1. The next week, rats with successful establishment of CIA were randomly divided into a PBS treatment group (n = 9), a UDP treatment group (n = 9), an MRS2578 treatment group (n = 9), and a UDP (Sigma-Aldrich, Germany) and MRS2578 (MedChemExpress, USA) treatment group (n=9). UDP and MRS2578 were dissolved in PBS (containing 1% DMSO). Rats in the UDP treatment group were injected intraperitoneally with UDP (10 mg/kg). Rats in the MRS2578 treatment group were injected intraperitoneally with MRS2578 solution (3 mg/kg). Rats in the UDP and MRS2578 treatment groups were injected with the same volume of a solution containing UDP (10 mg/kg) and MRS2578 (3 mg/kg). Rats in the PBS treatment group were injected with the same volume of PBS vehicle (containing 1% DMSO). The injections were for a total of 6 consecutive administrations (twice weekly). Rats were sacrificed 20 days after the first UDP injection (3 days after the last UDP injection). The inflammation curve showing the degree of joint swelling with time was constructed. We decided to use doses of UDP and MRS2578 based on previously published literature [4, 17]. The animals were housed in specific pathogen-free (SPF) conditions. The rats were fed a commercial pelleted diet (JNPY Laboratory Animals, Jinan, China). The animals were kept in a room with a controlled 12-h light-dark cycle under controlled temperature at 22±2°C, humidity of 50-70% and controlled bacterial conditions.
Rats were anesthetized by intraperitoneal injection of 3% sodium pentobarbital, and blood samples were collected from the inferior vena cava. In addition, the articular cavity of the rats was collected and washed 3 times with PBS (1 mL) to obtain synovial fluids. These rats were euthanized with lethal doses of ketamine and xylazine, and the joint tissues within 0.5 cm of the knee joints were collected.
Evaluation of joint inflammation
The inflammation curve of the joint swelling degree was constructed according to the size of the hind paws, which was measured every other day using Vernier calipers according to the method we mentioned before [18]. Bone erosion and cartilage destruction in the ankle joint and knee joint were assessed by X-ray imaging (75 kV, 195.3 mA) before sacrifice. The joint tissue within 0.5 cm of the knee joint of rats was collected, fixed with 4% paraformaldehyde and embedded in paraffin. Hematoxylin-eosin staining was used to examine the pathological changes in joint tissues. According to clinical and histological evidence, the disease score was calculated as follows: 0 = normal joint; 1 = local swelling and/or erythema without histological damage; 2 = swelling and/or rigidity of the whole paw without histological damage; 3 = limb deformity with reversible histological damage; and 4 = limb deformity accompanied by permanent histological damage such as bone or cartilage erosion. The above protocol was designed based on other studies. We mentioned this method in our previous work [18].
Isolation and culture of human synovial fibroblast cells
Synovial tissues from patients with RA (Patient No. R41 to No. R50, n = 10) or OA (Patient No. 41 to No. O50, n = 10) were minced into small pieces and digested for 4 h at 37°C and 5% CO2 in 3 mL of DMEM containing 4% type II collagenase (Solarbio, China) until the tissue pieces were dispersed into a cell suspension. The cell suspension was filtered through a 70 μm cell strainer and resuspended in DMEM containing 10% FBS. Synovial fibroblast cells were incubated at 37°C in a humidified incubator containing 5% CO2. Cells that passed for 3-8 generations were used in subsequent experiments.
Measurement of UDP content
Peripheral blood samples from healthy donors (No. H1 to No. H36, n=36) and RA patients (Patient No. R1 to No. R36, n=36) were collected into pyrogen-free and endotoxin-free test tubes with anticoagulants. Synovial fluids from OA (Patient No. O1 to No. O36, n=36) or RA patients (Patient No. R1 to No. R36, n=36) were added to an equal volume of PBS. Rat synovial fluids and peripheral blood were collected as described above. These samples were centrifuged at 1000 ×g for 20 min at 4°C, and the supernatant was carefully collected. The UDP content in the samples was measured using a Transcreener UDP Assay (BellBrook Labs, USA) via a fluorescence polarization readout according to the manufacturer’s protocol. A 15 μL mixture of reagents, including 8 nm UDP2 antibody-Tb, 1× Stop & Detect Buffer C and UDP HiLyte647 Tracer, was mixed with 5 μL of each sample in a 96-well plate. The plate was incubated for 1.5 h at room temperature and analyzed in a FlexStation® 3 Multimode Plate Reader (Molecular Devices, USA). The concentration of UDP was calculated by the standard curve prepared with standard UDP solution before analysis.
Measurement of cytokine concentrations in blood and culture medium
RA synovial fibroblast cells (Patient No. R41 to No. R45, n = 5) were isolated and seeded in 96-well plates at a density of 3 × 104 cells per well and incubated overnight. UDP was dissolved in PBS (containing 0.1% DMSO). Cells were incubated with UDP at a final concentration of 100 μM for 24 h. The supernatants were collected after centrifugation at 1000 × g for 20 min. The IL-2, IL-4, IL-6, IL-10, TNF-α and IFN-g concentrations in the supernatants were quantified using a Human Th1/Th2 Subgroup Detection Kit (CellGene, China). In brief, antibodies specific for IL-2, IL-4, IL-6, IL-10, TNF-α and IFN-g were conjugated to fluorescence-encoded beads, and beads with biotinylated detection antibodies were mixed with the samples. Streptavidin-PE was added, and the mixture was incubated with shaking for 2 h at room temperature. The beads were washed and then analyzed in a NovoCyte D2040R flow cytometer (ACEA Biosciences, USA). The data were analyzed using FlowJo software (Tree Star, USA).
Measurement of IL-6 levels using enzyme-linked immunosorbent assay (ELISA)
Synovial fibroblast cells from RA patients (Patient No. R41 to No. R45, n = 5) were cultured and treated with different concentrations (0 μM, 10 μM, 50 μM and 100 μM) of UDP (Sigma-Aldrich, Germany), and the supernatants were collected at 24 h. The rat joint cavity lavage fluid was collected as a synovial fluid sample by flushing with 0.5 mL of PBS. The concentration of human or rat IL-6 was measured with an ELISA kit (eBioscience, USA) according to the protocol. In brief, a 100 μL volume of the standard, control or samples was added to each well and incubated for 2 h at room temperature. After three washes, 200 μL of human IL-6 conjugate antibody was added to each well, incubated for 2 h at room temperature and washed three times. A 200 μL aliquot of substrate solution was then added to each well and incubated for 20 min at room temperature. Then, 50 μL of Stop Solution was added to each well, and the optical density of each well was measured at 450 nm in a microplate reader (BioTek, USA).
Measurement of IL-6 levels using flow assay
RA synovial fibroblast cells (Patient No. R41 to No. R45, n = 5) were isolated and seeded in 96-well plates at a density of 3 × 104 cells per well and incubated overnight. UDP and MRS2578 were dissolved in PBS vehicle containing 0.1% DMSO. The cells were incubated with or without MRS2578 (Med Chem Express, USA) at a final concentration of 10 μM for 1 h. UDP (Sigma-Aldrich, Germany) was then added at a final concentration of 100 μM, and incubation was continued for 24 h. The supernatants were collected after centrifugation at 1000 × g for 20 min. The IL-6 concentrations in the supernatants were quantified using a human IL-6 flow assay kit (Cell Gene, China). In brief, anti-IL-6 antibodies were conjugated to fluorescence-encoded beads, and the beads and biotinylated anti-IL-6 detection antibodies were mixed with the samples. Streptavidin-PE was added, and the mixture was incubated with shaking for 2 h at room temperature. The beads were washed and then analyzed in a NovoCyte D2040R flow cytometer (ACEA Biosciences, USA). The data were analyzed using FlowJo software (Tree Star, USA).
Rat peripheral blood was collected from rat inferior vena cava, and the IL-6 level was measured using a similar protocol as the rat IL-6 capture bead B6 product commercially obtained from BioLegend. The data were analyzed using LEGENDplex v8.0 software (BioLegend).
Evaluation of synovial fibroblast cell proliferation using a CCK-8 assay
RA synovial fibroblast cells (Patient No. R41 to No. R45, n = 5) were treated with different concentrations (0 μM, 10 μM, 50 μM or 100 μM) of UDP for 0, 6, 12 and 24 h. A 10 μL volume of CCK-8 solution (Dojindo, Japan) was added to each well and incubated for an additional 4 h. The absorbance was measured at 450 nm in a spectrophotometer (BioTek, USA).
Evaluation of synovial fibroblast cell proliferation using real-time cell analysis (RTCA)
A dual-plate RTCA instrument (ACEA Biosciences, USA) was placed in a humidified incubator maintained at 37°C and 5% CO2. RA synovial fibroblast cells (Patient No. R41 to No. R45, n = 5) were isolated and seeded in cell culture E-plates (1×104 cells per well) (ACEA Biosciences, USA) and treated with 100 μM UDP with or without MRS2578 (MedChemExpress, USA) at a final concentration of 10 μM for 3 days. The 96-well E-plate was monitored every 30 min for 48 h, and cell proliferation was monitored in real time by measuring the electrical impedance using the xCELLigence RTCA TP System (ACEA Biosciences, USA). The cell growth curves were automatically recorded based on continuous quantitative monitoring of cell proliferation. The data were analyzed with Real-Time Cell Analyzer software (version 1.2).
Detection of synovial fibroblast cell apoptosis using flow cytometry
RA synovial fibroblast cells (Patient No. R41 to No. R45, n = 5) were cultured and treated with or without MRS2578 at a final concentration of 10 μM for 1 h. Then, UDP at a final concentration of 100 μM was added, and incubation was continued for 24 h. Cells (6×104) were collected and resuspended in binding buffer. An Annexin V-FITC-conjugated antibody and a PI-conjugated antibody (BioLegend) were added to the suspended cells. Apoptosis was detected by flow cytometry.
Cell migration assay
RA synovial fibroblast cells (Patient No. R41 to No. R45, n = 5) were isolated and seeded in 6-well plates. When the cells were 80-90% confluent, the wound healing assay was conducted by scratching the cell layer in each well with a sterile P200 pipette tip. The cells were preincubated with or without MRS2578 at a final concentration of 10 μM for 1 h. UDP at a final concentration of 100 μM was then added, and incubation was continued for 24 h. The cells were photographed at 0 h and 24 h (Olympus IX51, Japan), and the wound area was calculated with ImageJ software (NIH, Bethesda, MD, USA).
Transwell assay
RA synovial fibroblast cells (Patient No. R41 to No. R45, n = 5) (1×104 cells/mL) in serum-free medium were seeded in the upper compartments of Matrigel invasion chambers (Corning, USA). Medium containing 10% FBS was added to the lower compartments of the chambers. The cells were incubated with or without MRS2578 at a final concentration of 10 μM for 1 h. UDP (Sigma-Aldrich, Germany) at a final concentration of 100 μM was then added, and incubation was continued for 24 h. The cells on the top surface of the membrane were removed with cotton swabs, and the cells that penetrated to the bottom surface of the membrane were stained with crystal violet. Images were acquired by fluorescence microscopy (Olympus IX51, Japan), and the cells were quantified with ImageJ software (NIH, Bethesda, MD, USA).
Sources of microarray data
The expression level of P2Y6 in RA or OA synovial tissues was analyzed in four published gene expression profile datasets (dataset type: expression profiling by array) in the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geoprofiles) database. The expression data of 10 patients with RA and 6 OA controls from dataset GDS5402/208373_s_at, 5 patients with RA and 5 OA controls from dataset GDS2126/38222_at, 10 patients with RA and 10 OA controls from dataset GDS5401/208373_s_at, and 13 patients with RA and 10 OA controls from dataset GDS5403/208373_s_at were analyzed in SPSS software v. 21.0 (IBM, USA) using an unpaired Student’s t-test.
RNA isolation and quantitative real-time PCR
Human (Patient No. R41 to No. R50, n = 10) and rat synovial tissues were collected as described above. Total RNA was isolated using TRIzol reagent (Invitrogen) and reverse transcribed to cDNA (Vazyme, China). Reak-time PCR was performed in a StepOnePlusTM Real-Time PCR System (Thermo Fisher Scientific, USA) using iQ SYBR Green Supermix (Bio-Rad) according to the manufacturer’s guidelines. The PCR primers were designed as follows: human P2Y6 sense: 5ʹ-GTGTCTACCGCGAGAACTTCA-3ʹ, human P2Y6 antisense: 5ʹ-CCAGAGCAAGGTTTAGGGTGTA-3ʹ; human β-actin sense: 5ʹ-CATGTACGTTGCTATCCAGGC-3ʹ, human β-actin antisense: 5ʹ-CTCCTTAATGTCACGCACGAT-3ʹ; rat P2Y6 sense: 5ʹ-GTGGTATGTGGAGTCGTTTGA-3ʹ, rat P2Y6 antisense: 5ʹ-CTGTAGGAGATCGTGGTT-3ʹ; rat GAPDH sense: 5ʹ-TCCCTCAAGATTGTCAGCAA-3ʹ, rat GAPDH antisense: 5ʹ-AGATCCACAACGGATACATT-3ʹ. The PCR primers were designed based on a study by Kim [19].
Evaluation of P2Y6 expression using Western blotting
Human synovial tissues (Patient No. R46 to No. R50, n = 5) were collected as described above. Samples were homogenized on ice in radioimmunoprecipitation assay (RIPA) lysis buffer (Beyotime), separated by 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to polyvinylidene fluoride (PVDF) membranes (Millipore, USA). Membranes were incubated with a rabbit anti-P2Y6 antibody (Abcam, Catalog number: ab198805) and horseradish peroxidase (HRP)-conjugated goat anti-rabbit IgG (Abcam, Catalog number: ab205718). β-Actin (Abcam, Catalog number: ab115777) was used as the internal reference for normalization of the P2Y6 expression level. Immunoreactive bands were visualized using Western Chemiluminescent Horseradish Peroxidase Substrate (ECL, Millipore), and band densities were quantified using ImageJ software (NIH, Bethesda, MD, USA).
Evaluation of P2Y6 expression using immunofluorescence
Paraffin sections of human synovial tissues (Patient No. R46 to No. R50, n = 5) were permeabilized with 0.05% Triton X-100 for 10 min, blocked with 5% goat serum for 1 h, and incubated with a rabbit anti-P2Y6 antibody (1:200, Abcam, Catalog number: ab198805) at 4°C overnight. The tissue sections were incubated with goat anti-rabbit IgG H&L (Alexa Fluor® 555) (1:200, Abcam, ab150078) for 1 hour in the dark. Nuclei were stained with 4ʹ,6-diamidino-2-phenylindole (DAPI) (Abcam, ab228549). Images were acquired under a fluorescence microscope, and quantification of the signal density was conducted in Image-Pro Plus 6.0 (Media Cybernetics, Inc., Rockville, MD, USA).
Examination of P2Y6 expression using immunohistochemical staining
Paraffin sections of human synovial tissues (Patient No. R46 to No. R50, n = 5) were incubated first with a rabbit anti-P2Y6 antibody (1:200, Abcam, Catalog number: ab198805) at 4°C overnight and then with HRP-conjugated goat anti-rabbit IgG (Abcam, Catalog number: ab205718). Sections were treated with diaminobenzidine (DAB) and counterstained with hematoxylin. The results were analyzed, and the expression level was quantified in ImageJ software (NIH, Bethesda, MD, USA).
Statistical analysis
Statistical analyses were performed using GraphPad Prism 7.0 (GraphPad, USA) and SPSS software v.21.0 (IBM, USA). The significance of differences between groups was evaluated using Student’s unpaired t-test. Differences with p values of <0.05 were considered significant.