Preparation of samples
Samples of WJT powder were provided by Jilin Wantong Pharmacy Group Company (Tonghua, China). The traditional Chinese medicine containing in WJT was indicated in Supplymentary Table S1.
Acute toxicity in rats
One hundred and twenty female specific pathogen free (SPF) Sprague-Dawley (SD) rats weighing 160 to 180g were obtained from Changchun Yisi Experimental Animal Technology Company. The rats were randomly assigned to six groups (G1, G2, G3, G4, G5, and G6), fasted for 12 h, but with free access to drinking water, before a single administration of 1 g (G1), 2 g (G2), 3.98 g (G3), 7.94 g (G4), 15.85 g (G5), 31.62 g (G6) of WJT power per kg of body weight. Signs of toxicity were evaluated based on mortality. On day 14, survival rates were measured and the LD50 value was calculated based on the Improved Koch’s method.
The rats were anaesthetised with an intraperitoneal injection of 10% pentobarbital sodium (4 ml/kg) and subsequently sacrificed by rapid decapitation. All animal experiments were approved by the Animal Research Committee of Jilin University. The principles in the ARRIVE guidelines and the Basel declaration (http://www.basel.declaration.org) have been considered when planning the experiments.
Induction of collagen-induced arthritis (CIA) in rats
Fifty female SPF SD rats were randomly divided into five groups after acclimatization for 1 week: control (no CIA), model (CIA alone), CIA + 150 mg/kg WJT, CIA + 300 mg/kg WJT, and CIA + 600 mg/kg WJT, with 10 rats per group. CIA in rats was conducted according to previously described by Jian Zuo et al. [14]. Then, rats in three WJT groups were given oral WJT solution (150, 300, or 600 mg/kg) each day starting on day-1; rats in control and model groups were given the same volume of normal saline. All rats were sacrificed on day-28 for further study.
Assessment of arthritis severity
On day 28, paw swelling and paw thickness were measured using a plethysmometer and an electronic vernier caliper, respectively. The severity of arthritis was evaluated using an arthritis index (AI) with a CIA semi-quantitative scoring system, as previously described by Nagaraja Haleagrahara et al. [15].
Measurement of inflammatory factors
On day 28, paw and ankle tissues were collected and broken apart using a homogenizer (JinXin, Shanghai, China) at 4 °C for collection of tissue fluid. The tissue fluid and blood were then centrifuged, and the supernatant was analyzed for the levels of pro-inflammatory factors (TNF-α, IL-1β, and IL-6) using enzyme linked immunosorbent assay (ELISA) kits (Abcom, Cambridge, UK), following the manufacturer’s protocols.
Histopathological evaluation of ankle joints
After fixation, the tissue samples were processed, embedded in paraffin, and then cut into 4 mm slices using a microtome (Leica, Shanghai, China). Microscopic changes of the ankle joints were visualized using a light microscope (Olympus, Japan) after hematoxylin and eosin (H&E) staining. The severity of pathological changes in the ankle joints was measured according to previously described by Acharya Balkrishna et al. [16].
Immunohistochemical analyses
The paraffin-embedded samples of the ankle joints were blocked by 5% bovine serum albumin (BSA; Solarbio, Beijing, China) for 30 min, incubated with an appropriate primary antibody from Abcom (Cambridge, UK) overnight at 4°C, and then with a secondary antibody (Bioss, Beijing, China) at room temperature for 30 min. Enhancement was performed using a DAB dye solution and counter staining with hematoxylin. Finally, the ankle samples were observed under a light microscope (Olympus) at 400×, and typical images are presented. Image analysis software (Image Pro Picture) was used for quantitative analysis.
Western blot analysis
After quantification of total protein extracted from knee and ankle synovia, equal amounts of protein lysates (20 μg per lane) were separated by 8-12% SDS-PAGE gels, and then transferred to 0.45 µm polyvinylidene fluoride (PVDF) membranes (ThermoFisher, Waltham, MA, USA). The membranes were blocked using 5% BSA, and then incubated with antibodies against Bax, Bcl-2, caspase-3, cleaved-caspase-3, MEK, pMEK, ERK1/2, pERK1/2, and β-actin (all from Abcom) at 4 °C overnight. Then, the PVDF membranes were treated with a horseradish peroxidase-conjugated secondary antibody (Bioss) at room temperature for 2 h. Protein bands were visualized on a Tanon 5200 Chemiluminescent Imaging System (Tanon, Shanghai, China).
Sequencing and data analysis
Sequencing and data analysis were performed following the manufacturer’s guidelines by Novogene bio-information technology Co., Ltd, as previously described by Jing Wang et al. [17].
Metabolism and data analysis
On day-28, blood samples from sacrificed CIA rats were centrifuged at 4000 rpm (4°C for 5 min), and the supernatant was diluted with methanol so the final methanol concentration was 60% by use of liquid chromatograph-mass spectrometer (LC-MS) grade water. Then, the samples were transferred to fresh Eppendorf tubes with 0.22 μm filters, and centrifuged at 15,000 g (4°C for 10 min). Finally, the filtrate was subjected to LC-MS/MS analysis using a Vanquish UHPLC system (Thermo Fisher, Waltham, USA) coupled with an Orbitrap Q Exactive series mass spectrometer (Thermo Fisher).
The raw data files generated by UHPLC-MS/MS were processed and normalized using Compound Discoverer version 3.1 (Thermo Fisher). Statistical analyses were performed using the R software package (version 3.4.3), Python (version 2.7.6), and CentOS (release 6.6). Then the normalized data were matched with the mzCloud (https://www.mzcloud.org) and ChemSpider (http://www.chemspider.com/) databases to obtain the accurate qualitative and relative quantitative metabolism results. Principal co-ordinates analysis (PCoA) was performed using metaX (http://metax.genomics.cn). Univariate analysis was used with the t-test to calculate statistical significance (P-value). All metabolites with a variable importance in projection (VIP) greater than 1, a P-value below 0.05, and a fold change (FC) of 2 or more or 0.5 or less or were considered to be differentially regulated metabolites. The screened out metabolites were finally visualized as volcano plots, heatmaps, and mapped onto KEGG pathways.
Statistical analysis
Except the 16S rDNA high-throughput sequencing and metabolomics, data are presented as means ± standard deviations (SDs). Student's t-test was used to compare groups, and all statistical analyses were conducted using SPSS version 20.0. All experiments were performed at least three independent times. Differences were considered to be statistically significant at p < 0.05 and highly significant at p < 0.01.