Study design
172 subjects including100 RA patients (RA) and 72 healthy controls (HC) were recruited from General Hospital of Ningxia Medical University. Clinical features of the participants were shown in table 1. RA group were diagnosed according to the criteria of the American College of Rheumatology, and HC group were through the same period health examination and without a history of knee surgery, or keen degeneration disease a, or inflammatory diseases. The selected subjects were excluded from other autoimmune diseases and major organ system disease. Both plasma and PBMCs were obtained from the two groups patients. This study was approved by the General Hospital of Ningxia Medical University Ethics Committee and is in compliance with the Helsinki Declaration. Informed consent was obtained from the patients.
Preparation of plasma and PBMC
Blood samples (5 ml) were collected with ethylene diamine tetraacetic acid (EDTA-2K) containing tube, and plasma was separated by centrifugation at 1600 g for 10 min at room temperature,followed by centrifugation at 16,000 g for 10 min at 4°C to remove all cell debris. The plasma supernatant was collected and stored at -80°C until further analysis. PBMC were isolated from peripheral blood using Ficoll-HyPaque(Solarbio life science, Beijing, China), as previously described(Pham et al. 2008). Briefly, blood was collected into 10 mL tubes containing heparin as anticoagulant. Immediately after collection, the cells were separated from whole blood by centrifugation on a Ficoll-Hypaque density gradient. The PBMC were recovered and washed three times with 1mL RPMI culture medium, and adjusted to a final concentration of 1 × 107 cells/mL. The PBMC pellet was stored at -80ºC until further analysis.
RNA isolation, reverse transcription and quantitative PCR
RNA was isolated using RNAiso Plus isolation kit (TaKaRa, Dalian, China) according to manufacturer`s protocol. Nanodrop 2000(Thermo Fisher Scientific, CA, USA) was used to assess the concentration and purification of RNA. Reverse transcription was performed using Revert aid first strand cDNA sythesis kit (Thermo Scientific, CA, USA) with the corresponding primers (42℃ for 15 min, 70℃ for 5 min). For constructing cDNA standard curves of miRNAs and U6, the target sequences were amplified using 2×Ecotap PCR SuperMix (TransGen Biotech Co., Ltd., Beijing, China) with specific primers under the following conditions:and cloned into pEASY-T1 Cloning vector (TransGen Biotech Co., Ltd., Beijing, China), the concentrations of plasmid were detected using Nanodrop 2000(Thermo Fisher Scientific, CA, USA), then the plasmids were diluted in series by ten times to 10-8 and finally the standard curve was obtained by determining the corresponding threshold cycle (Ct), respectively. For detecting the expression of miRNAs, qRT-PCR was performed using SYBR select master mix (ABI, Carlsbad, CA, USA) on ABI StepOnePlus qPCR system (ABI, Carlsbad, CA, USA) under the following conditions: 95℃ for 5 min followed by 40 cycles consisting of 95℃ for 5 sec, 62℃ for 30 sec and 72 ℃ for 30 sec. The experiment was repeated three times. The copy numbers of experimental RNAs were calculated after real-time amplification from the linear regression of that standard curve. The relative expression of miRNAs was calculated using 2 ‑∆∆Ct method and U6 snRNA was used for normalization. The primers specific for the target genes were designed using bioinformatics tools, synthesized in Sangon Biotech Inc. (Shanghai, China).
Primer sequences were as follows: for miR-16, 5`-TAGCAGCACGTAAATATT-3`; for miR-17, 5`-CAAAGTGCTTACAGTGCA-3`; for miR-132, 5`-TAACAGTCTACAGCCATG-3`; for miR-140, 5`-AGTGGTTTTACCCTATG-3`; for miR-150, 5`-TCTCCCAACCCTTGTACC-3`; for miR-181a, 5`-AACATTCAACGCTGTCGG-3`; for miR-200c, 5`-TAATACTGCCGGGTAATG-3`; for miR-203, 5`-TGAAATGTTTAGGACCA-3`; for miR-223, 5`- TGTCAGTTTGTCAAATAC-3`; for miR-485-5p, 5`-AGAGGCTGGCCGTGAT-3`; the universal antisense primer, 5`-CTCAACTGGTGTCGTGGA-3`; for U6, sense 5`-CTCGCTTCGGCAGCACA-3`, antisense 5`-CGCTTCACGAATTTGCGT-3`.
Cells and cell culture
Murine macrophage cell line (RAW264.7) and human embryonic cell line (HEK-293T) were purchased from the Institute of Biochemistry and Cell Biology (Chinese Academy of Sciences, Shanghai, China). Cells were collected and cultivated at 37℃ with 5% CO2 in DMEM high glucose medium supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin and 100 μg/mL streptomycin (GIBCO, Invitrogen, USA).
Cell transfection
RAW264.7 cells were transiently transfected with 50 nM miR-485-5p control or miR-485-5p mimic (GenePharma, Shanghai, China); 50 nM control or miR-485-5p inhibitor (GenePharma, Shanghai, China), using Lipofectamine 2000 (Invitrogen, USA) according to the manufacturer`s instructions.
Plasmid construction and dual luciferase reporter assay
To validate the targeting role of miR-485-5p to TLR4 and IRAK4, the wild-type of TLR4 and IRAK-4 3`UTRs, which contain the binding elements of miR-485-5p, were obtained by PCR. Then the mutant 3`UTRs of TLR-4 and IRAK-4 were obtained by site-directed mutagenesis. The primers used during the study were as follows: wild-type TLR-4 3`UTR (Forward, 5`-CCCAAGCTTCACTGCCAGGAGAACTA-3`; Reverse, 5`-CGGACTAGTTCATAACGGCTACACCA-3`), mutant TLR-4 3`UTR (Forward, 5`-CCCAAGCTTCACTGCCAGGAGAACTA-3`; Reverse, 5`-CGGACTAGTGCGACCAGATGAACATT-3`), wild-type IRAK-4 3`UTR (Forward, 5`-CCCAAGCTTTTACTTATTGCCTGTACC-3`; Reverse, 5`-CGGACTAGTATAGTTAGCCCGTTTTG-3`), mutant IRAK-4 3`UTR (Forward, 5`-CCCAAGCTTCACTGCCAGGAGAACTA-3`; Reverse, 5`-CGGACTAGTGCGACGTGGTAATTTAT-3`). These above-mentioned wild-type or mutated 3`UTR fragments were then subcloned into pMIR-Report vector (Promega, Madison, WI, USA).
HEK-293T cells were plated into 96-well plates and co-transfected with 120ng of either pMIR-TLR4-WT/ TLR4-Mut/ IRAK4-WT / IRAK4-Mut, 3 pmol miR-485-5p mimic, inhibitor, nc(the control comparing with mimic or inhibitor) and 80ng PRL-TK internal-plasmid using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA). The relative luciferase activity at 48 h post-transfection was determined by the Dual-Luciferase Reporter Assay System (Promega, Madison, WI, USA) following the manufacturer`s protocol. Transfections were done in triplicate and repeated at least thrice in independent experiments.
Western-Blot Analysis
After extensively washing, cells were lysed using Whole Cell Lysis Assay and proteins were harvested according to the protocol (KeyGen Biotech Inc., Nanjing, China). Protein concentrations was determined by the BCA Assay kit ((KeyGen Biotech Inc., Nanjing, China). Total protein of each lysate was then separated by SDS-PAGE and subsequently transferred onto PVDF membranes (Millipore, MA, USA). Afterwards, the membranes were blocked with 5% non-fat milk in TBST at room temperature for 1 h, followed by incubated with antibodies against TLR4 (1:2,000, cat. no. 14358, Cell
Signaling Technology, Inc), or IRAK4 (1:2000, cat. no. 4363, cell Signaling Technoloy, Inc), or GAPDH (1:2,000, ab8245, Abcam) overnight at 4 ℃. After washing with TBST, membranes were striped with appropriate HRP-conjugated secondary antibodies for 1h at room temperature, followed by visualized using the Luminol reagent (Thermo Fisher Scientific, Carlsbad, CA, USA). Eventually, bands were imaged and densitometric analyzed by a chemiluminescence detection system (Bio-Rad, USA).
Enzyme linked immunosorbent assay (ELISA)
The levels of IL-17, IL-18, DAS-28, MMP3, TLR-4, IRAK-4 in the peripheral blood and PBMC cells of patients and were detected using ELISA kits (Bangyi Biotech, Shanghai, China) according to the manufacturer`s protocol.
Bioinformatics analysis
MiRWalk (http://mirwalk.umm.uni-heidelberg.de/),miRanda (http://www.microRNA.org), TargetScan (http://www.targetscan.org) and DIANA LAB (http://83.212.96.7/DianaToolsNew/index.php?r=mirpath) were used to predict and select miRNAs associated with inflammation, and the predicted relationship were analyzed by Cytoscape.
Statistical analysis
Data were presented as the mean ± standard deviation. Statistical analyses were performed using SPSS 17.0 (IBM, CA, USA). Differences between two groups were analyzed with Student`s t-test. Differences among three groups were analyzed with Analysis of One-way ANOVA. Correlations with miRNA concentrations and other clinical factors were analyzed with Pearson product-moment correlation coefficient. A P- value less than 0.05 was considered statistically significant.