Ethics statement
All animal experiments and procedures were approved by the Institutional Animal Care and Use Committee of the Second Hospital of Jilin University. The animal experiments were conducted based on minimized animal numbers and discomfort of experimental animals.
Microarray-based analysis
The lung cancer related miRNA dataset GSE63805 was downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/gds). There were 62 tissue samples in GSE63805, including 30 normal lung samples and 32 lung cancer samples. Differential analysis of the expression datasets was performed by the limma package (http://www.bioconductor.org/packages/release/bioc/html/limma.html) in R language, with the threshold (|logFC|>1, p < 0.01). The miRNA with the lowest p value was selected for following analysis. The downstream target genes of the miRNA were predicted by mirDIP (Integrated Score > 0.2) (http://ophid.utoronto.ca/mirDIP/) and starbase (clipExpNum ≥ 3) (http://starbase.sysu.edu.cn), and differential expression analysis of the lung cancer dataset GSE74706 also was performed in R language (|logFC|>1, p < 0.01). There were 36 samples in the GSE74706 dataset, including 18 normal and 18 lung cancer samples. Then, the human transcription factors were obtained from the Cistrome database (http://cistrome.org), and these results were intersected to determine the downstream target gene of miR-21 based on the existing studies. Next, the related genes of the target gene were identified according to the GeneMANIA database (http://genemania.org), and Cistrome was used to obtain genes with a correlation greater than 0.35 or less than − 0.35 with the expression of downstream genes of target transcription factors in lung adenocarcinoma. The intersection of GeneMANIA and Cistrome results was adopted to obtain the downstream genes of key target transcription factors. The comprehensive data of lung adenocarcinoma and squamous cell carcinoma in the Cancer Genome Atlas (TCGA) database (http://gepia.cancer-pku.cn) were analyzed by the Gene Expression Profiling Interactive Analysis (GEPIA) database (http://gepia.cancer-pku.cn) to confirm the correlation of expressions between the target transcription factors and their downstream genes, and starBase was used to determine the binding site of miRNA and target transcription factors.
Cell culture and treatment
Lewis lung cancer cells were purchased from Cancer Research Institute of Chinese Academy of Medical Sciences (Beijing, China). Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum, 100 U/mL penicillin and 100 U/mL streptomycin at 37℃ in a humidified atmosphere with 5% CO2. The cells were observed daily as they grew into a monolayer adhering to the chamber walls. When the cells were in a logarithmic growth phase, they were trypsinized and passaged with 0.25% trypsin solution once every 2–3 days. The ratio of living cells was assessed by trypan blue staining. The cell concentration was diluted to 1 × 107 cells/mL in phosphate buffer saline (PBS), and the cell suspension was prepared for the following experiments.
Animal model establishment
A total of 72 C57BL/6 mice with half males and half females (aged 5–6 weeks, purchased from Beijing Vital River Laboratory Animal Technology Co., Ltd., Beijing, China) were selected. The mice of the average weight of (20 ± 0.5) g were numbered after acclimation for 1 week, and 8 of them (half male and half female) were randomly selected as the blank control, and subcutaneously injected with 0.4 mL normal saline into the armpit of the right forelimb. Then the remaining 64 mice were inoculated with 0.2 mL Lewis lung cancer cell suspension (about 2 × 106 tumor cells). The tumor growth was observed and measured three days later.
When the tumor diameter had reached about 5 mm (around the 5th day), every 8 mice (half male and half female) were infected with lentiviral particles containing miR-21 antagomir negative control (NC), miR-21 antagomir, miR-21 antagomir NC combined with sh-NC, miR-21 antagomir combined with sh-NC, miR-21 antagomir combined with sh-RUNX1, miR-21 antagomir NC combined with oe-NC, miR-21 antagomir combined with oe-NC, or miR-21 antagomir combined with oe-YAP, respectively. In brief, mice were intraperitoneally injected with 4 mg/kg normal saline (antagomir NC) or the same amount of miR-21 antagomir, and other mice were also intraperitoneally injected with the same amount of lentiviral particles or normal saline for 5 times, respectively. Then, on the 7th, 14th and 21st day after injection, the blood sample was collected from each mouse, and the tumor diameter was measured and recorded.
Preparation of mouse tumor and peripheral blood cell suspension
After about 3 weeks of subcutaneous injection of Lewis lung cancer cells, mice were anesthetized with intraperitoneal injection of 3% pentobarbital sodium at a dose of 50 mg/kg. Peripheral blood samples taken from orbit were put in 15 mL centrifuge tube (containing 1 mL anticoagulant). The mice were euthanized with cervical dislocation and displaced in 75% alcohol for 5 minutes. Then, the mice were fixed on a foam board, and the tumors were removed by scissors and forceps, before the tumors were placed into the 24-well plate with l mL PBS.
The tumor suspension was prepared as follows. In brief, the resected tumor was photograph and its length and width were measured with a vernier caliper, and the tumor volume was calculated as (length × width × width)/2. The tumor was cut with scissors into small portions in a 24 hole plate, transferred into a 15 mL centrifuge tube, added with 2 mL 1640 culture solution and 60 µL collagenase, and incubated in a shaker at 37℃ for 3 hours. After that, the centrifuge tube was mixed by vortexing, and added with PBS to a constant volume of 10 mL. After centrifugation, the supernatant was discarded and 2 mL PBS was added into the tube. Next, the solution was passed through a sieve into a 15 mL centrifuge tube, re-centrifuged and the supernatant was discarded. Finally, PBS was added to make the tumor cell suspension.
The peripheral blood cell suspension was prepared. In brief, 1 mL PBS was added into the 15 mL centrifuge tube containing anticoagulant, centrifuged and the supernatant was discarded. Upon addition of 3 mL of hemolytic solution, the tube was put aside for 4–5 minutes, and added with PBS to obtain the peripheral blood cell suspension.
Flow cytometry for cell characterization
MDSCs were characterized as follows. A total of 50 µL of peripheral blood or tumor local cell suspension was transferred respectively into 2 mL centrifuge tubes, and 0.5 µL of CD45.2, CD11b and Gr-1 (BD Biosciences, Franklin Lakes, NJ, USA) was added to each tube. Then the tubes were then added with 48 µL of PBS, and stained in a refrigerator at 4℃ for 20 minutes. Then, the tubes were added with 1 mL of PBS and centrifuged at 300 rpm for 5 minutes, added with 100 µL PBS for resuspension, and finally analyzed with a flow cytometer.
T cell phenotype was detected. Briefly, 50 µL of peripheral blood and tumor local cell suspension was placed into 2 mL centrifuge tubes, and then mixed with 0.5 µL of CD45.2, CD4 and CD8a (BD Biosciences, Franklin Lakes, NJ, USA). Then, 48 µL of PBS was added to the tubes for staining in the refrigerator at 4℃ for 20 minutes. Then, the tubes were added with another 1 mL of PBS and centrifuged at 300 rpm. After removing the supernatant, 100 µL PBS was added for resuspension and analysis with a flow cytometer.
Flow cytometry for cell proliferation
Lymphocyte isolating medium was adopted to separate cells in tumor tissues and peripheral blood samples. Then, the CD4+ or CD8+ T cells in the samples were separated using a CD4+ or CD8+ T cell separation kit (Miltenyi Biotec, Bergisch Gladbach, Germany). According to the manufacturer's instructions (Invitrogen Inc., Carlsbad, CA, USA), CD4+ or CD8+ T cells were labeled with 5-(and 6)-carboxyfluorescein diacetate, succinimidylester (CFSE), and stimulated with Con A (Sigma-Aldrich Chemical Company, St Louis MO, USA). MDSCs and T cells were derived from mice infected with lentiviral particles or control mice in the co-culture experiments. For a single co-culture, the T cells and the MDSCs were derived from the same mice. Then, the T cells were co-cultured with MDSCs at the proportions of 2:1, 4:1, 10:1 or 100:1 in 96 well plates for 96 hours. On the fourth day, the cells were analyzed by a flow cytometer. The proliferation data from MDSCs were obtained through the gradient experiments on average.
MDSC sorting of peripheral blood
The mice were euthanized, and the peripheral blood was collected, followed by removal of red blood cells with red blood cell lysis buffer. Then, the lysed blood was incubated at 4℃ for 15 minutes with the addition of biotion-conjugated anti-Gr-1 (BD Biosciences, Franklin Lakes, NJ, USA), and then added with anti-biotion beads and incubated in the dark at 4℃ for 15 minutes. After washing, the blood was resuspended with PBS and MDSC sorting was performed using a LS column from Miltenyi Biotec (Bergisch Gladbach, Germany), following the manufacturer’s instructions.
Flow cytometry for cell cycle analysis
MDSCs were collected and the cell concentration was adjusted to 1 × 106 cells/mL. Then, the cells were seeded into 24 well plates, and treated with antagomir NC + sh-NC, miR-21 antagomir + sh-NC, miR-21 antagomir + sh-RUNX1, antagomir NC + oe-NC, miR-21 antagomir + oe-NC, or miR-21 antagomir + oe-YAP. After 24 hours, the cells were collected, centrifuged at 2000 rpm for 5 minutes, fixed with 70% ethanol precooled at 4℃, and stored at 4℃. Before staining, the fixed solution was washed off with PBS, and cells were resuspended with the addition of 200 µL PBS. A total of 100 µL RNase A was added into the cells in water bath at 37℃ for 30 minutes, whereupon 400 µL propidium iodide (PI) was added. The mixture was then dyed at 4℃for 30 minutes in the dark. Before analysis, the cells were screened through a 200-mesh cell sieve, and added with 300 µL PBS to adjust the cell density. Then the cell cycle was analyzed by a flow cytometer, with the red fluorescence recorded at 488 nm, and 10000 cells were counted.
Annexin V-FITC/PI analysis
MDSCs were collected and the cell density was adjusted to 1 × 106 cells/mL. Then, the cells were seeded into 24 well plates, and infected with antagomir NC + sh-NC, miR-21 antagomir + sh-NC, miR-21 antagomir + sh-RUNX1, antagomir NC + oe-NC, miR-21 antagomir + oe-NC, or miR-21 antagomir + oe-YAP. After 24 hours, the cells were centrifuged at 2000 rpm for 5 minutes, washed twice with PBS, and suspended with the addition of 100 µL of binding buffer. The Annexin V-FITC kit was used for staining. A total of 5 µL Annexin V-FITC was added to the cell suspension, and then 5 µL PI was added and reacted for 15 minutes in the dark. Next, the cells were passed through a 200 mesh cell sieve. Finally, the cells were analyzed by a flow cytometer with the excitation wavelength at 488 nm and the emission wavelength at 530 nm, and 10000 cells were counted.
Enzyme linked immunosorbent assay (ELISA)
The eyeballs of mice were removed to collect blood samples, which were stored overnight at 4℃, and then centrifuged at 3500 × g. The clear serum from the upper layer was stored at -80℃. The serum levels of interleukin 10 (IL-10), transforming growth factor-beta (TGF-β) and granulocyte-macrophage colony stimulating factor (GM-CSF) were measured by ELISA kit. The serum was cultured for 24 hours, whereupon the culture medium was collected, centrifuged at room temperature for 10 minutes at 1000 × g, and the supernatant was taken. The standard curve was drawn and the contents of IL-10, TGF-β and GM-CSF in the cell culture medium were measured in strict accordance with the instructions of the kit. The above kits were all purchased from Wuhan Xinqidi Biological Technology Co. Ltd. (Wuhan, China).
RNA immunoprecipitation (RIP) assay
Lewis lung cancer cells were lysed with radio-immunoprecipitation assay (RIPA) cell lysis buffer (P0013B, Beyotime Biotechnology Co., Shanghai, China) on ice bath for 5 minutes, and centrifuged at 12000 × g and 4℃ for 10 minutes. One portion of the cell extract was removed to serve as input, and the other part was incubated with antibody for co-precipitation. Each co-precipitation reaction system was washed with 50 µL magnetic beads and resuspended in 100 µL RIP wash buffer, and then incubated with 5 µg antibody for binding. After washing, the magnetic beads-antibody complex was resuspended in 900 µL RIP wash buffer and incubated overnight with 100 µL cell supernatant at 4℃. Samples were then placed on magnetic pedestals to collect beads-protein complexes, whereupon the samples and input were detached by treatment with protease K to extract RNA for subsequent polymerase chain reaction (PCR) analysis. The antibodies used here were anti-RUNX1 (ab92336, Abcam Inc., Cambridge, UK) and immunoglobulin G (IgG, ab150077, Abcam Inc., Cambridge, UK), which served as NC.
Chromatin immunoprecipitation (ChIP) assay
The Lewis lung cancer cells were fixed with formaldehyde for 10 minutes to induce DNA-protein cross-linking. The, an ultrasonicator was used to break the chromatin into fragments for 15 cycles of ten seconds each, with intervals of ten seconds. After that, the supernatant was collected, divided into two equal portions, and centrifuged at 12,000 × g for 10 minutes at 4℃. The IgG (ab150077, Abcam Inc., Cambridge, UK) and protein specific antibody anti-RUNX1 (ab92336, Abcam Inc., Cambridge, UK) were added into the two tubes, respectively, which were incubated at 4℃ overnight. The DNA-protein complex was precipitated by Protein Agarose/Sepharose, and centrifuged at 12,000 × g for 5 minutes. The supernatant was discarded and the nonspecific complex was washed to remove the cross-linking with incubation at 65℃ overnight. The DNA fragments were extracted and purified with phenol/chloroform, and the binding of RUNX1 and YAP promoter was measured by RT-qPCR with YAP promoter region specific primers.
Dual luciferase reporter gene assay
The wild type and mutant reporter plasmids of RUNX1-3’utr (pGL3-wt-RUNX1-3’utr, pGL3 -mut-RUNX1-3’utr) were designed and provided by Shanghai GenePharma Co. Ltd. (Shanghai, China). The Lewis lung cancer cells were co-transfected with antagomir NC and miR-21 antagomir with wt-RUNX1-3’utr and mut-RUNX1-3’utr respectively. After 48 hours, the cells were collected and lysed. The dual luciferase reporter gene assay system (Promega Corporation, Madison, WI, USA) was used for the detection of luciferase activity.
Immunohistochemistry
The paraffin-embedded tumor tissues slices were dewaxed with xylene I and II (Shanghai Sangon Biotechnology Co. Ltd., Shanghai, China) for 10 minutes, rehydrated with 100%, 95% and 70% gradient ethanol (Shanghai Sangon Biotechnology Co. Ltd., Shanghai, China) for 2 minutes each. Then, the tissues were immersed in 3% H2O2 for 10 minutes and antigen retrieval was performed by high pressure in a pressure cooker for 90 seconds. The tissues were cooled at room temperature and cut into slices, which were blocked with 5% bovine serum albumin (BSA), incubated at 37℃ for 30 minutes, added with 50 µL RUNX1 rabbit polyclonal antibody (ab92336, Abcam Inc., Cambridge, UK) and YAP rabbit monoclonal antibody (ab52771, Abcam Inc., Cambridge, UK) for incubation at 4℃ overnight. The next day, after washing with PBS for 2 minutes, the slices were added with 50 µL HRP labeled goat anti-rabbit antibody (ab6721, Abcam Inc., Cambridge, UK), incubated at 37℃ for 30 minutes and added with single antigen beads (SAB). Then, the slices were added with diaminobenzidine (DAB) solution (Fuzhou Maixin Biotechnology Development Co. Ltd. Fuzhou, China) for color development, re-stained with hematoxylin (Sigma-Aldrich, SF, CA, USA) for 5 minutes, and finally observed and photographed under an optical microscope (XSP-36, Bostar Optical Instruments Co., Ltd, Shenzhen, China). A total of 100 cells in each field were counted in 5 randomly selected high power visual fields, and the mean proportion of positive cells was calculated.
RT-qPCR
Total RNA was extracted using the RNeasy Mini Kit (Qiagen company, Hilden, Germany). The cDNA was synthesized using the reverse transcription kit (RR047A, Takara Bio Inc., Otsu, Shiga, Japan) and the miRNA first strand cDNA synthesis first (tailing reaction) kit (B532451-0020, Shanghai Sangon Biotechnology Co. Ltd., Shanghai, China). RNA loading was performed using the SYBR® Premix Ex Taq™ II (Perfect Real Time) kit (DRR081, Takara Bio Inc., Otsu, Shiga, Japan). RT-qPCR was carried out in a real-time PCR instrument (ABI 7500, ABI Company, Oyster Bay, NY). The general negative primer for miRNA and the upstream primer for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were provided by miRNA First Strand cDNA Synthesis (Tailing Reaction) kit, and other primers were synthesized by Shanghai Sangon Biotechnology Co. Ltd. (Shanghai, China) (Table 1). The Ct value of each well was recorded. GAPDH or U6 were taken as internal references, and the relative expression of each gene was calculated by the 2−ΔΔCt method.
Table 1
The primer sequences of RT-qPCR
Gene | Primer sequences |
miR-21 (hsa) | F: GGACTAGCTTATCAGACTG |
R: CATCAGATG CGTTGCGTA |
miR-21 (mus) | F: GACATCGCATGGCTGTACCA |
R: CCATGAGATTCAACAGTCAACATC |
RUNX1 | F: TGATGGCTGGCAATGATGAA |
R: TGCGGTGGGTTTGTGAAGAC |
YAP | F: CGCTCTTCAACGCCGTCA |
R: AGTACTGGCCTGTCGGGAGT |
ARG-1 | F: CTCCAAGCCAAAGTCCTTAGAG |
R: AGGAGCTGTCATTAGGGACATC |
iNOS | F: CCAAGCCCTCACCTACTTCC |
R: CTCTGAGGGCTGACACAAGG |
GAPDH | F: TGAAGCAGGCATCTGAGGG |
R: CGAAGGTGGAAGAGTGGGAG |
U6 | F: CTCGCTTCGGCAGCACA |
R: AACGCTTCACGAATTTGCGT |
Notes: RT-qPCR, reverse transcription quantitative polymerase chain reaction; RUNX1, runt-related transcription factor 1; YAP, yes-associated protein; ARG-1, Arginase-1; iNOS, inducible nitricoxide synthase; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; F, forward ,R, reverse. |
Western blot analysis
The total protein in tissues or cells was extracted by radioimmunoprecipitation assay (RIPA) containing phenylmethylsulfonyl fluoride (PMSF). Bicinchoninic acid (BCA) kit was used to measure the total protein concentration. A total of 50 µg protein was dissolved in 2 × sodium dodecyl sulfate (SDS) sample buffer and boiled at 100℃ for 5 minutes. The protein was separated by a sodium dodecyl sulfate–polyacrylamide electrophoresis (SDS-PAGE) and transferred onto a polyvinylidene fluoride (PVDF) membrane, and sealed with 5% skim milk solution at room temperature for 1 hour. The membrane was incubated overnight at 4℃ with primary antibodies purchased from Abcam (Cambridge, UK): rabbit anti-RUNX1 (ab92336), rabbit anti-YAP (ab52771), rabbit anti-ARG-1 (ab133543), iNOS (ab3523), and GAPDH (ab181602) as internal reference. Then, the membrane was washed three times with tris-buffered saline with Tween 20 (TBST) for 10 minutes each time. The membrane was then incubated with horseradish peroxidase (HRP) labeled goat anti-rabbit IgG H&L (ab6721, Abcam, Cambridge, UK) for 1 hour, developed with an enhanced chemiluminescence (ECL) fluorescence test kit (BB-3501, Amersham, Chicago, Illinois, USA), and exposed in a gel imager. The membrane was digitally photographed using the Bio-Rad image analysis system (Bio-Rad Laboratories, Hercules, CA, USA) and analyzed with Quantity One v4.6.2 software. The relative expression of the proteins was expressed by the ratio of gray value of each protein to that of internal reference GAPDH.
Statistical analysis
Statistical analysis was conducted using SPSS 21.0 statistical software (IBM, Armonk, NY, USA). Measurement data were summarized by mean ± standard deviation. When data were in normal distribution and homogeneity, data between two unpaired groups were compared by unpaired t-test. Measurement data among multiple groups were compared by one-way analysis of variance (ANOVA) with Tukey's post hoc test. Data comparison among multiple groups at different time points was conducted using repeated measurement ANOVA with Bonferroni's post hoc test. Pearson’s correlation analysis was used to analyze the relationship between indicators. Measurement data were represented by examples, and verified by a chi-square test. A p < 0.05 demonstrated statistical significance.