1. Mouse and patient samples
Male C57Bl/6 mice (6–8 weeks old) were purchased from Shanghai Slac Laboratory Animal Co., Ltd,and housed under specific-pathogen-free conditions. Animal experiments were approved by the Ethics Committee. The model of partial liver ischemia reperfusion injury was established as described previously[15]. The animals were randomly divided into four groups: Sham group (Sham), miR-216a-5p agomir group (agomir), miR-216a-5p antagomir group (antagomir), and miR-216a-5p negative control group (NC). miR-216a-5p agomir (20 nmol) or antagomir (200 nmol) was administrated by intravenous injection 1 h before the induction of liver IRI. The mice were sacrificed 24 h after reperfusion, and serum and liver tissues were collected for subsequent analyses.
Human serum samples were obtained from patients undergoing liver transplantation within the 6 h prior to transplantation and at 2 6, 24, and 48 h postoperatively with their written informed consent. This approach was approved by the ethics committees.
2. Exosome extraction and identification
Serum samples collected from liver transplant patients and mice were used to purify exosomes thought ultracentrifugation[16]. Serum was centrifuged at 2,000 g and 13,500 g for 20 minutes to eliminate cell debris and large vesicles. Pellets were then washed once with phosphate-buffered saline (PBS) and purified by centrifugation at 200,000 g for 2 h. Exosome samples were diluted 5-fold with PBS, stained with 2% phosphotungstic acid at room temperature, and examined by transmission electron microscopy (Hitachi, HT7700, Japan). The size and concentration of exosomes were measured by a nanoparticle tracking analysis (NTA) at 80 kV using a ZetaView PMX 110 (Particle Metrix, Meerbusch, Germany).
3. Cell isolation, extraction, and culture
Bone marrow macrophages (BMMs) isolated from femurs and tibias of C57BL/6 mice (8–9 weeks old) were cultured for 6 days in a medium containing 10% FBS, penicillin (100 U/ml), streptomycin (100 µg/ml), and 10 ng/mL mouse M-CSF (Peprotech-In, Suzhou, China). All cells were cultured in a humidified incubator at 37°C with 5% CO2, and the medium was changed every 2 days. The human promyelocytic leukemia cell line HL-60 was cultured in RPMI medium (Invitrogen, Carlsbad, CA, USA) containing 10% FBS, 2 mM L-glutamine, and 1% penicillin and streptomycin. Dimethyl sulfoxide at 12.7 µL/ml/million cells was added for 5 days to induce HL-60 cells to differentiate into neutrophils (dHL-60).
4. Western blotting
Pretreated liver tissue and cells were added to ice-cold RIPA lysis buffer (Beyotime, Shanghai, China) with 1 mM PMSF. Protein concentrations were then determined with a BCA assay kit. Approximately 20 µg of protein samples was loaded onto 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gels and transferred to PVDF membranes (Millipore, Massachusetts, USA). After blocking with 5% skimmed milk for 2 h, the membranes were incubated at 4°C with INOS (1:1000; Abcam, Waltham, USA), GAPDH (1:5000; Bioss, Suzhou, China), CD206 (1:1000; Proteintech, Wuhan, China), p-Akt (1:1000; Proteintech), p-PI3K (1:1000; Servicebio, Wuhan, China), P-p65 (1:1000; Cell Signaling, Massachusetts, USA), and TLR-4 (1:1000; Proteintech), followed by 3 washes in tris buffered saline with tween20 (TBST) and incubation with the corresponding secondary antibodies for 2 h at 4°C. Specific proteins were visualized by applying the ECL kit to specific protein bands.
5. Polymerase chain reaction (PCR)
Total RNA was extracted from cells or liver tissue using the RNAiso plus reagent (Takara, Kyoto, Japan). miRNA was extracted from serum and exosomes using the miRNeasy Mini Kit (TIANGEN, Beijing, China). cDNA was then synthesized using the PrimeScript RT kit. Quantitative real-time PCR was performed using a 7300plus (Applied Biosystems, California, USA) real-time PCR instrument. GAPDH (mRNA) and miRNA external reference (TIANGEN) (miRNA in serum and exosomes), U6 (miRNA in tissues) were used to normalize the expression of target genes calculated relative to normal controls. All primer sequences are listed in Supplementary Table S1.
6. Sequencing and enrichment analyses
Serum exosomes were isolated from sham control (n = 3) and IRI (n = 3) mice, and total RNA was extracted using the miRNeasy Micro Kit (217084; Qiagen, North Rhine-Westphalia, Germany). The miRNA sequencing analysis was performed on an Illumina HiSeq 2500 system (Ribo Bio, Guangzhou, China). Differentially expressed miRNAs between the two groups were identified by the fold change and P-value. Hierarchies were clustered to show samples with distinguishable miRNA expression profiles between samples. Metascape was used to identify the functional and interaction networks of the miR-216a-5p target genes (Table S2).
7. Immunofluorescence staining of liver tissue sections
Frozen sections of liver were incubated overnight at 4°C with primary antibodies (F4/80, LY6G, MPO; Abcam). The next day, the nuclei were stained with DAPI after incubation with the corresponding secondary antibodies conjugated with Cy3 or FITC (Servicebio, Wuhan, China). They were then observed with a confocal laser microscope.
8. Histology
Liver tissue was fixed in 4% paraformaldehyde and then embedded in paraffin wax, and paraffin sections were soaked in 100% xylene and a mixture of xylene and alcohol (1:1) for 15 minutes and dewaxed. After soaking in 100%, 95%, and 75% alcohol solutions for 1 minute, the sections were washed with 0.1 saline. Hematoxylin/eosin (HE) staining was used to assess pathological liver damage according to Suzuki's criteria[18].
9. Flow cytometry
Macrophage polarization was detected by flow cytometry. Macrophages were centrifuged and resuspended cells in cold PBS and then incubated with antibodies against anti-CD86-PE (#105106, BioLegend, California, USA), anti-CD206-APC (#141706, BioLegend, california, USA) and anti-F4/80-PerCP (#123116, BioLegend, alifornia, USA) for fluorescent staining for 30 minutes at 4°C. A FACS analysis was performed after washing, and data were obtained using a BD Accuri™ C6 flow cytometer (BD Biosciences, San Jose, CA, USA).
10. The dual luciferase assay
The potential binding sites for miR-216a-5p and TLR-4 were predicted by TargetScan. To verify the direct binding of miR-216a-5p to TLR-4, miR-216a-5p and wild-type TLR-4 3'UTR or mutant TLR-4 3'UTR were reconstructed with pmirGLO plasmid in 293T cells, using Lipofectamine 3000 (Invitrogen; Thermo Fisher Scientific, Inc. Massachusetts, USA) according to the manufacturer's protocol. After 48 h, the luciferase activity was measured using a dual luciferase reporter assay system (Promega, Wisconsin, USA) according to the manufacturer's protocol.
11. Statistical analyses
Group sizes are indicated in the figure legends. Data are presented as the mean ± standard deviation unless otherwise noted. Statistical analyses were performed by either an analysis of variance or t-test. A difference of p < 0.05 was considered statistically significant.