2.1 Cell Cultures
Highly metastatic MDA-MB-231 cells provided by S.J. Lee (FNCT Biotech, Korea) laboratory. MDA-MB-231 and H460 cells obtained from the Korea Cell Line Bank (KCLB). H460 and MDA-MB-231 cells were cultured in RPMI 1640 media (Mediatech, Inc., Manassas, VA) and DMEM (Mediatech, Inc., Manassas, VA) with 10% FBS (Tissue Culture Biologicals, CA, USA) and penicillin-streptomycin antibiotics (PAA Laboratories GmbH, Austria), respectively. All cells were cultured in a 5% CO2 incubator at 37℃.
2.2 RNA Extraction and qRT-PCR
Plasma was isolated from normal and breast cancer patients and metastasis mouse model by 13,000 rpm, 15 min centrifugation. Total RNA was extracted with TRIzol reagent (Molecular Research Center Inc., OH, USA) from plasma obtained from patients and mice. The miRNA was synthesized using the Mir-X miRNA First-Stand cDNA Synthesis Kit (Takara, Japan) and the mRNA using the Tetro cDNA Synthesis Kit (BIOLINE, London, UK). Real time PCR was quantified with U6 (Takara, Japan) and GAPDH. All data were analyzed by the 2−△△Cr method. The sequences of primers were as follows : primary-miR-5088-5p: (forward) 5’-CCTCTGCATGTTTGCTGCCA − 3’ and (reverse) 5’-TGAGGGCCCAGGAAGAAGGGA-3’, precursor-miR-5088-5p: (forward) 5’-CAGGGCT CAGGGATTGGATGGAGG-3’ and (reverse) 5’-TGAGGGCCCAGGAAGAAGGGA-3’, mature-miR-5088-5p: 5’-CAGGGCTCAGGGATTGGATGGAGG-3’, MMP-2: (forward) 5′-CATCAAGGGCATTCAGGAGC-3′ and (reverse) 5′-A GAACACAGCCTTCTCCTCC-3′, MMP-9: (forward) 5′-AGGACGACGTGAATGGCAT G-3′ and (reverse) 5′-ATCGTCCACCGGACTCAAAG-3′, Oct4: (forward) 5’-GAGCAAAACCCGGAGGAGT-3’ (reverse) 5’-TTCTCTTTCGGGCCTGCAC-3’, Nanog: (forward) 5’-GCTTGCCTTGCTTTGAAGCA-3’ (reverse) 5’-GTTCTTGCATCTGCTGGAGG-3’, Sox2: (forward) 5’-ATGCACCGCTACGACGTGA-3’ and (reverse) 5’-CTTTTGCACCCCTCCCATT-3’, CD133: (forward) 5’-GCCACCGCTCTAGATACTGC-3’ and (reverse) 5’-GCTTTTCCTATGCCAAACCA-3’, CD44: (forward) 5’-AAGGTGGAGCAAACACAACC-3’ and (reverse) 5’-ACTGCAATGCAAACTGCAAG-3’, DBC2: (forward) 5’-CAGAGCAGTAGACAGTGACC-3’ and (reverse) 5’-TGTAGTTGGTGCAGATGTGG-3’ and GAPDH: (forward) 5′-CATCTCTGCCCCCTCTGCT GA-3′ and (reverse) 5′-GGATGACCTTGCCCACAGCCT-3′.
2.3 Western blot analysis
Cells were lysed with RIPA buffer containing protease and phosphatase inhibitor cocktails (Roche, Indianapolis, USA). The extracted protein concentration was measured using Bradford assay (Bio-Rad Laboratories Inc, CA, USA). Proteins were separated using SDS-PAGE and then transferred to PVDF (Millipore Corporation, MA, USA). The membrane was blocked with 5% BSA (bovine serum albumin) in Tris-buffered saline-Tween 20 (TBST) (10 mM TrisHCl, pH 8.0, 150 mM NaCl and 0.05% Tween 20) and the primary antibody was treated. The secondary antibody was treated by dilution in 5% skim milk. After washing with TBST, it was detected with ECL solution (Thermo Scientific, Pierce, USA) using AmershamTM Imager 600 system equipment (GE Healthcare Bio-Sciences, PA, USA).
Antibodies against Slug and ß-actin were obtained from Santa Cruz Biotechnology (CA, USA). Zeb1 were purchased from Sigma (Sigma-Aldrich Company, MO, USA). Twist and N-cadherin were purchased from Abcam Inc. (Cambridge, MA, USA). Snail, Vimentin, DNMT1, DNMT3a, and DNMT3b were purchased from Cell Signaling technology (Beverly, MA, USA).
2.4 Irradiation
Ionizing radiation (IR) was performed H460 and MDA-MB-231 cells in 60 mm dishes as 5Gy and cells were harvested after 48 hours. We irradiated with a 3.81Gy/min dose rate using a 137Cs γ-rays source (Atomic Energy of Canada, Ltd, Canada). The mouse model is irradiated at 2Gy/min dose rate using X-RAD 320 irradiator (PXi, North Branford, CT) equipment.
2.5 Plasmid DNA, RNA oligoribonucleotides, and transfection
To make Slug-overexpressing vector, the Slug gene was inserted to the pCMV-taq2 vector. Each sequence of primers for plasmid constructs was as follows: Slug (forward) 5’-CGCGGATCCATGCCGCGCTCCTTCCTG-3’ and (reverse) 5’-CGGAATTCTCAGTGTGCTACACAGCAGCCA-3’. The inhibitor of miR-5088-5p was a 2’-O-methyl-modified oligoribonucleotide single strand with the sequence as 5’-CCUCCAUCCAAUCCCUGAGC CCU-3’ and was synthesized by IDT (Integrated DNA Technologies, Coralville, IA, USA). All siRNAs (Slug, Zeb1, and Snail) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). siRNAs (20 mM), miRNAs (10 mM), and plasmids (4 ug) were introduced into cells using G-fectin (Genolution, Seoul, Korea) or Lipofectamine 2000 reagent (Thermo Fisher Scientific, Invitrogen, USA) according to the manufacturer’s instructions, respectively.
2.6 Wound healing assay
Cells were seeded on 6-well culture plates and a plastic tip was scraped to mimic wound damage. Cells were washed with PBS to remove cell debris and moved for 16–24 hours. The recovery of wound damage was quantified by counting cells after observation with a light microscope (CKX53, OLYMPUS, Tokyo, Japan) [33].
2.7 Transwell invasion assay
After coating matrigel (BD Biosciences, CA, USA) in a transwell chamber (8µm pore) (Corning, Corning, NY), transfected cells were placed in the upper transwell chamber with opti-MEM (Gibco, USA) medium. After culture media was added to the lower chamber and cultured for 16 hours, the invaded cells in the lower transwell chamber were fixed and stained with Hemacolor solution (Merck, MA, USA). Stained cells were counted under a light microscope (CKX53, OLYMPUS, Tokyo, Japan).
2.8 Tube formation assay
The supernatant of MDA-MB-231 cells transfected with negative control (NC) or miR-5088-5p inhibitor using G-fectin (Genolution, Seoul, Korea) was harvested after 72 hours. After coating a 96-well plate with matrigel, 1x104 cells/well of HUVECs and supernatant obtained from MDA-MB-231 cells were simultaneously added to the plate. After 16 hours, tube forming ability was observed under a microscope (Miotic AE31 series, Motic, Hong Kong).
2.9 Sphere formation assay
After transfection of MDA-MB-231 cells (1 × 105/dish) with negative control (NC) or miR-5088-5p inhibitor, cells seeded in Dulbecco's Modified Eagle Medium-F12 (Gibco, USA) containing B27(1:50) (Gibco, USA) Cellgro, Manassas, VA) and grown for 7–10 days. Spheres (> 20 µm in diameter) were counted in an inverted microscope (Miotic AE31 series, Motic, Hong Kong).
2.10 In vivo promoter methylation analysis
H460 cells were 1x107 cells were injected into subcutaneously injected of a six-week-old mouse. After 14 days, 2.5Gy of radiation was fractionated to the mouse's chest every day for 3 days. After 56 days, the mouse was sacrificed, and tumors generated from the subcutaneous tissue were isolated and ground to extract genomic DNA and mRNA. Methylation of miR-5088-5p promoter was confirmed using genomic DNA by phenol-chloroform extraction method, and the level of miR-5088-5p was confirmed using mRNA by TRIzol method. This experiment was reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) of Korea Institute of Radiological & Medical Science.
2.11 Pyrosequencing analysis
To confirm the methylation of miR-5088-5p at 10 sites on the CpG islands of the miR-5088-5p promoter, pyrosequencing analysis was performed. PCR was performed with taq polymerase (TaKaRa, Kyoto, Japan) using the primers of miR-5088-5p (methy-miR-5088-5p: 5’-ATTTTTGTTTTAGGAGATGTTGAAG-3’ (forward) and 5’-CCTAACCACCCTAAAAACTCAC-3’ (reverse)) [32]. Pyrosequencing was conducted on a PyroMark ID system (Qiagen, Hilden, Germany) using streptavidin Sepharose HP beads (Amersham Biosciences, Piscataway, NJ) and a Pyro Gold Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
2.12 Methylation specific PCR (MSP) and quantitative methylation-specific PCR (qMSP) analysis
After genomic DNA was extracted according to a standard phenol-chloroform extraction method, bisulfite modification of genomic DNA was performed using an EZ DNA methylation kit (Zymo Research, USA). The methylation analysis of the miR-5088-5p promoters was performed using MSP primer pairs covering the putative transcriptional start site in the 5′ CpG islands with 1 µℓ of bisulfite-treated DNA as template and JumpStart Red Taq DNA Polymerase (Sigma-Aldrich Company, MO, USA) for amplification as previously described [34]. DKO (DNMT1(-/-), DNMT3B(-/-) double knockout in HCT116 cells) as unmethylation control, IVD (in vitro methylated DNA) as methylation control, and ddH2O as PCR negative control were used. Primers of the miR-5088-5p promoter region across the upstream from − 225 to 34 from mature form sites (Fig. E2A). The unmethylation forward primer of the miR-5088-5p; 5’-GTTTTAGGAGATGTTGAAGGATGA-3’ and unmethylation reverse primer; 5’-CATACAAAAAATACCAATACCCAAA-3’. The methylation forward primer of the miR-5088-5p; 5’-TTTGTTTTAGGAGATGTTGAAGGAC-3’ and the methylation reverse primer; 5’-ATACAAAAAATACCGATACCCGAA-3’. MSP amplification was performed on bisulfite treated samples and normalized using the Alu element. Real-time PCR was performed by a CFX96TM real-time system (Bio-Rad, Hercules, CA, USA). Alu primer sequence information is previously described [35].
2.13 In vivo metastasis assay
Human lung cancer cells, H460 cells were transfected with negative control (NC) and anti-miR-5088-5p. 2x106 cells were injected into tail vein of a six-week-old mouse. After 14 days, 2.5Gy of radiation was fractionated to the mouse's chest every day for 3 days. After 56 days, the mouse was sacrificed, and blood and lungs were collected. The lungs were fixed with 4% paraformaldehyde, metastatic nodules were counted, and a block was made to perform hematoxylin and eosin (H&E) staining (shandon™, Thermo Scientific, Pierce, USA). This experiment was reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) of Korea Institute of Radiological & Medical Science.
2.14 Colony formation assay
Cells (5x102) were seeded in 60mm dishes cultured for 3 weeks. When visible colonies appeared, the cells were washed twice with PBS, fixed in methanol for 15 minutes, stained with crystal violet for 20 minutes, washed with water, and air dried. The number of dishes repeated 3 times was counted. The number of visible colonies is the rate of colony formation = (number of colonies / number of seeding cells) × 100%.
2.15 MTT assay
H460 and MDA-MB-231 cells (5x103 cells per well) were seeding on 96-well plates in triplicate wells. The next day, the cells were treated with 50µM of cisplatin (Sigma-Aldrich Company, MO, USA) or 5Gy radiation. MTT reagent (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, Sigma-Aldrich Company, MO, USA) was added at 24h, 48h, and 72h, and proliferation was measured at 450nm after 4h.
2.16 Clinical specimens
Biospecimens and data used in this study were provided by the Korea Institute of Radiological and Medical Sciences (KIRAMS) Radiation Biobank (KRB) of Korea Cancer Center Hospital in Republic of Korea. Breast cancer patient plasma was provided in samples from normal (n = 26) and breast cancer patients with (n = 15) and without (n = 21) radiotherapy, respectively (KRB-2016-I005). Lung cancer patient plasma was provided in samples from cancer patients with (n = 26) and without (n = 26) radiotherapy (KRB-2021-I002). All samples used in this experiment have Institutional Review Board (IRB) approval (K-1907-002-002, KIRAMS 2021-04-002-001) in KIRAMS.
2.17 Statistical Analysis
All experiments were performed in triplicate. Data are presented as mean standard deviations and, where appropriate, Student's t tests were analyzed using GraphPad Prism software. P values of P < 0.05 were considered by Student t test to be statistically significant.