Patients and clinical tissue samples
The present study involved a total of 50 patients with asthma hospitalized at the Second Affiliated Hospital of Harbin Medical University between January 2018 and September 2019. The diagnosis of asthmatics met the American Thoracic Society refractory asthma definition [24]. The control group included 50 healthy volunteers. Controls had no history of lung disease, allergy, respiratory infection or exposure to tobacco smoke. The clinical characteristics of all subjects are summarized in Table 1. Each patient signed informed consent regarding the trial. The ethical committee of the Second Affiliated Hospital of Harbin Medical University approved this study.
Isolation of human basophils
Venous blood was obtained from consenting healthy volunteers and subjects with asthma. Basophils were semi-purified by means of density centrifugation using Percoll solution as previously described [25]. Briefly, Percoll solutions with two different densities (1.079 and 1.070 g/ml) were used. The blood samples were centrifugated at room temperature for 15 min at 700 × g, after which cells in the layer between the two Percoll solutions were further purified by negative selection using an EasySep Human Basophil Kit (StemCell Technologies, CAN) according to the manufacturer’s instructions. The yield was 1-3 × 104 basophils/ml of peripheral \jblood, depending on the donor. Fluorescence activating cell sorter results showed the mean basophil purity to be consistently >98%, and the viability was consistently >94%. AGEs were prepared by adding 5 g of bovine serum albumin and 9 g of D-glucose to 100 mL PBS at 37°C for 8 hours. The basophils were the treated with 400 mg/L AGEs.
Transfection
miR-3934 mimics, miR-3934 mimics negative control (NC) and a RAGE overexpression plasmid were synthesized by Shanghai GenePharma Co., Ltd (Shanghai, China). Using lipofectamine 3000 (Invitrogen) according to the manufacturer’s protocol, basophils were transfected with miR-3934 mimics or miR-3934 mimics NC with or without the RAGE overexpression plasmid. Reverse transcriptase quantitative real-time PCR (RT-qPCR) methods were used to determine transfection efficiency.
RT-qPCR
Total RNAs were extracted from cells using TRIzol reagent (Invitrogen) and reversed transcribed into cDNAs using PrimeScript RT Master Mix (Takara, Dalian, China). qPCR was then performed to detect the expression levels of miR-3934 in different samples using SYBR premix Ex Taq (Takara) on an ABI 7500 qPCR System (Applied Biosystems Life Technologies, Foster City, USA). Relative expression levels of miRNA-3934 were determined using the 2-ΔΔCt method and were normalized to U6. The PCR protocol entailed 95°C for 30 s followed by 40 cycles of 95°C for 5 s and 60°C for 30 s. The primers were synthesized by Sangon Biotech (Shanghai) Co., Ltd (Shanghai, China).
RNA-seq analysis
Total RNA extracted from the SW480 cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. The quality of the RNAs was assessed using Nanodrop 2000 spectrophotometry (Thermo Fisher Scientific, Inc), after which the samples were sent to Vazyme Biotech (Nanjing, China) for RNA-sequencing.
Bioinformatics, plasmid construction, and dual-luciferase reporter assay.
The target of miRNA-3934 was obtained from starBase (Version 3.0) prediction. GenePharma synthesized a plasmid containing the sequences of miRNA-3934 paired with the RAGE 3’-UTR (RAGE-wild type (WT)) or mutant 3’-UTR (RAGE-mutant type (MUT)) regions. The miRNA-3934 mimics and RAGE (GenePharma) were co-transfected into 293T cells. Luciferase activity was then examined 48 h after transfection using the dual-luciferase reporter assay kit (Beyotime, Shanghai, China).
Flow cytometric apoptosis assay
Human basophils were collected after various treatments and stained with Annexin-V-FITC/PI following the manufacturer’s instructions. Analysis of the apoptotic and live cells was performed using FACSCalibur (BD Biosciences, San Jose, CA) flow cytometry. The scatter diagram of the FACS results were as follows: Q4, non-apoptotic cells (FITC-/PI-); Q3, apoptotic cells at early stage (FITC+/PI-); Q2, apoptotic cells at advanced stage (FITC+/PI+); Q1, mechanically injured cells (FITC-/PI+). The apoptosis rate was calculated as the sum of the ratio of apoptotic cells in Q3 + Q2.
Western Blot
Protease inhibitor cocktail was used to isolate total proteins, after which aliquots (30 μg/μl) were separated by SDS-PAGE and transferred to PDVF membranes. The membranes were then incubated with the primary antibodies (anti-RAGE, anti-Smad2, anti-p-Smad2, anti-Smad3, anti-p-Smad3, anti-p38, anti-p-p38, anti-Smad7 and anti-GAPDH, all purchased from Abcam, Cambridge, MA, USA) overnight at 4°C. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as a loading control. The following day, the membranes were incubated with the chemiluminescent reagent BeyoECL Plus and HRP-conjugated secondary antibodies (Beyotime, Shanghai, China). The signals were detected and photographed using a Tanon 6100 Chemiluminescent Imaging System (Tanon, Shanghai, China).
Enzyme-linked immunosorbent assays
Commercially available ELISA kits (Nanjing Jiancheng Bio-Engineering Institute Co., Ltd, Nanjing, China) were used to determine the expression levels of IL-6, IL-8 and IL-33. The ELISAs were performed following the manufacturer’s protocols.
Statistical analysis
Continuous variables are expressed as the median (interquartile range), and categorical variables are described as a number and percentage (%). Student’s t-test or analysis of variance (ANOVA) were used for data comparison. The diagnostic value of miR-3934 was calculated using ROC curve analysis. Pearson coefficient analysis was performed for the correlation analysis. Values of P<0.05 were considered statistically significant. All statistical analyses were performed using GraphPad Prism v6.0.