Patients and Samples Collection
The study was approved by the Ethical Committee of Guangzhou University of Chinese Medicine, and written informed consents were obtained from all patients (No. ZYYECK [2017] 033). As shown in Table 1, among the 50 people, 30 patients were diagnosed as SONFH, 10 patients were related to hip osteoarthritis (HOA), while others were defined as the healthy group. The average age of 30 patients in SONFH group was 45.37 years (range, 30–60 years), 46.70 years (range, 38–60 years) in HOA group and 44.40 years (range, 32–59 years) in healthy control. The diagnoses of SONFH and HOA were confirmed in all the patients [13, 14]. All urine samples were obtained from our orthopedic department from June 2017 to June 2019. The midstream urine of all the patients was collected in the 50 mL tube, then removed cell debris and other impurities using the centrifuge. Finally, the supernatant was extracted to a new tube and frozen at -80 ℃ for the following analysis.
Table 1
Patient demographics and clinical profiles.
Factors | SONFH(n = 30) | HOA(n = 10) | Healthy control (n = 10) |
Gender, n (%) | | | |
Female | 20 (66.67%) | 7 (70%) | 6 (60%) |
Male | 10 (33.33%) | 3 (30%) | 4 (40%) |
Age(years) | 45.37 ± 1.62 | 46.70 ± 2.43 | 44.40 ± 3.02 |
ARCO stages, n (%) | | | |
II | 3 (10%) | 0 (0%) | 0 (0%) |
III | 16 (53.33%) | 0 (0%) | 0 (0%) |
IV | 11 (36.67%) | 0 (0%) | 0 (0%) |
Notes: SONFH: steroid-induced osteonecrosis of femoral head; HOA: hip osteoarthritis; ARCO: Association Research Circulation Osseous |
Table 2
The miRNAs were selected to qRT-PCR validation.
miRNA ID | Forward 5’-3’ | Reverse 5’-3’ |
hsa-miR-200b-3p | GCTGCTGAATTCCATCTAATTTCCAAAAG | TATTATGGATCCGCCCCCAGGGCAATGGG |
hsa-miR-206 | CGTCAGAAGGAATGATGCACAG | ACCTGCGTAGGTAGTTTCATGT |
U6 | AGAGAAGATTAGCATGGCCCCTG | ATCCAGTGCAGGGTCCGAGG |
Urinary exosomes extraction
According to the instruction of manufacuture, the urine samples were added 1/3 volume of RiboTM Exosome Isolation Reagent and upside down until completely mixed at 4 °C overnight. Next, 2 mL mixture was transferred to a new 2 mL tube and centrifuged at 1500 RCF for 30 s at 4 °C. After the supernatant discarded, a small portion of exosome was collected. Repeating the above step, the exosome pellet remained at the bottom of the tube until all the mixture was transferred.
Transmission electron microscopy (TEM)
Morphological examination was typically carried out using TEM which allowed investigators to appreciate the vesicular shape of exosome in addition to obtain an estimated measure of their diameter. The sample of exosome was dissolved in 0.01 mol/L phosphate-buffered saline (PBS). Subsequently, 10 µl of the suspension was spotted onto a glow-discharged copper grid for 2 s and then drained by the filter paper. Finally, exosome was stained with a drop of 3% aqueous solution of phosphotungstic acid for 2 s then was dried for several minutes. Exosome was observed using a TEM at 80 K electron volts.
Nanoparticle-tracking analysis (NTA)
We analyzed the size distribution of the exosome particles by a NanoSight NS300 Instrument (Malvern Instruments, UK) under the following conditions: cell temperature: 22 °C; Syringe speed: 40 µl/s. Exosomes were diluted with particle-free PBS, then injected into the NanoSight sample pool through the syringe. The particle concentrations and size distribution profiles were recorded and analyzed by NTA 3.2 software with the camera level of 15 and detection threshold of 4.
Flow cytometry analysis of exosomes
Exosomal surface proteins extracted from urine were identified by flow cytometry following a standard protocol. Specific primary antibodies were as follows: Anti-CD63(BD 557288) and Anti-CD81 (BD 551108). Briefly, urinary exosomes were coupled with Latex Beads (Invitrogen) and then blocked with 0.1% bovine serum albumin (BSA) (Sigma Aldrich). The samples were washed by PBS, stained with antibodies and tested according to the operation procedures of the instruments (BD AccuriTM C6 flow cytometer) equipped with a 488 nm, 50 mW solid-state laser.
MiRNA-sequencing
The urine exosomal miRNA-sequencing experiment was performed by RiboBio company (Guangzhou, China). Briefly, total RNA samples were fractionated on a 15% Tris-borate-EDTA polyacrylamide gel (Invitrogen) and only small RNAs ranging from 18 to 30 nucleotides were used for library preparation. After amplification by PCR, products were sequenced using the Illumina HiSeq 2500 platform. Sequencing data with P < 0.05 were considered as differentially expressed miRNAs.
Analysis of miRNAs-mRNAs regulatory network
The two groups selected the miRNAs according to the standard of area under the receiver operator characteristic (ROC) curve > 0.8. Dysregulated miRNA target genes were predicted by ENCORI (http://starbase.sysu.edu.cn/),miRDB (http://mirdb.org/), miRwalk (http://mirwalk.umm.uni-heidelberg.de/) and TargetScan7.2 (http://www.targetscan.org/vert_72/) databases. Using three or four databases jointly predicted results as candidate target genes of miRNAs. At last, the miRNAs-mRNAs regulatory network was constructed by the open-source software Cytoscape 3.7.1.
Go annotation and KEGG pathway analysis
DAVID (Database for Annotation, Visualization and Integrated Discovery) (http://david.abcc.ncifcrf.gov/) is a bioinformatics database that integrates biological data and analysis tools to provide systematic comprehensive annotation of biological function for large-scale gene or protein list. GO function and KEGG pathway were utilized to analyze based on DAVID. GO analysis includes three aspects: biological process (BP), cellular component (CC) and molecular function (MF).
PPI network construction and modules selection
The predicted mRNAs regulated by the candidate nine miRNAs were mapped to the STRING (http://string.embl.de/) database to establish the PPI network with the highest confidence > 0.9. Subsequently, the PPI network was evaluated by gene networking tool (Cytoscape 3.7.1). Then, Hub genes, the vital nodes in the PPI network, were selected by the degree algorithm of cytoHubba. Finally, the Molecular Complex Detection (MCODE) was carried out to identify crucial modules of PPI network with degree cutoff = 2, node score cutoff = 0.2, κ-core = 2, and max. depth = 100.
qRT-PCR analysis of miRNAs
Exosomal miRNA expression was examined using qRT-PCR in bone and urine samples (10 from healthy controls, 30 from SONFH patients, and 10 from HOA patients). Total RNA was extracted by an RNeasy Mini Kit (Introgen, Australia) according to the manufacturer's protocol. The cDNA was reverse transcribed and quantified by total RNA template using RIBOBIO miRNA primers specific for hsa-miR-200b-3p and hsa-miR-206 (Table. 2) and the Bulge-Loop™ miRNA qRT-PCR Starter Kit (RIBOBIO, Guangzhou, China) following the manufacturer's instructions. qRT-PCR was performed using SYBR Green PCR Master Mix (Applied Biosystems) on the QuantStudio 6 Flex Real-Time PCR System (Applied Biosystems). PCR amplification was performed using the following parameters: 95 °C for 20 s, followed by 95 °C (10 s), 60 °C (20 s), and 70 °C (10 s) for 40 cycles, and a final extension step of 70 °C for 10 s. Relative level of miRNA expression was normalized to the housekeeping gene U6.
Statistical analysis
All data presented are acquired from at least three independent experiments. Data are displayed as means ± standard error of mean (SEM). Student’s t test was performed to measure the significant difference between two groups. Comparisons of multiple groups were calculated using one-way ANOVA. P < 0.05 was considered to be statistically significant.