2.1 Cell culture
Human CRC cell lines (DLD1, HCT116, HCT15, SW480, SW620, LoVo and HT29) were obtained and authenticated by short tandem repeat profiling from the Chinese Academy of Sciences Cell Bank (Shanghai, China). All cells were cultured in Dulbecco’s modified Eagle’s medium (Gibco) with 10% fetal bovine serum (Gibco) and 100 μg/ml penicillin/streptomycin at 37°C in a 5% CO2 incubator.
2.2 Human clinical samples and immunohistochemical analysis
Clinical specimens in this study (cohort I), including CRC tissues (n = 133) and adjacent normal tissues (n = 69), from CRC patients who underwent surgical resection from 2008 to 2013 were obtained from West China Hospital. Cohort 2 contained 17 paired CRC liver metastasis and matched primary CRC tissues. All patients were of Han nationality and provided signed informed consent. This study was approved by the Ethics Committee on Biomedical Research, West China Hospital of Sichuan University (2021(594)) and performed in accordance with the Helsinki Declaration of 1975. All animal experiments were performed in accordance with relevant guidelines and regulations, and approved by the Institutional Animal Care and Use Committee of West China Hospital (2021087A). The clinical pathological information of HCC patients is summarized in Table 1. The expression of DDX17 in CRC tissues was determined by immunohistochemical analysis as described previously 21. Each staining was independently evaluated by two pathologists.
2.3 Lentivirus infection and transfection
The DDX17 cDNA (NM_006386.4) fragment was inserted into the lentiviral GV248 vector (Genechem Company). Two short hairpin RNAs (shRNAs) targeting DDX17 (DDX17 shRNA#1: 5’-CAAGGGUACCGCCUAUACC-3’; and DDX17 shRNA#2: 5’-GAGAGACUCUGCAAGCUAU-3’) and negative control (shNC: 5’-UUCUCCGAACGUGUCAGGU-3) were cloned into the lentiviral GV358 vector (Genechem Company), respectively. The packaging and purification of lentivirus were performed by Genechem Company (Shanghai, China). CRC cells with stable DDX17 deficiency or overexpression were selected with puromycin for 1-2 weeks. Human miR-149-3p mimic: 5’-AGGGAGGGACGGGGGCUGUGC-3’ and miR-149-3p antisense: 5’-GCACAGCCCCCGTCCCTCCCT-3’ were synthetized by Genepharma Company (Shanghai, China). Small interfering RNAs (siRNAs) targeting CYBRD1 and DDX5 were purchased from Thermo Fisher Scientific. MiRNA and siRNA were transfected into CRC cells using Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to the manufacturer’s instructions.
2.4 RNA extraction and RT‒qPCR
Total RNA was extracted from the cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. Reverse transcription was performed with PrimeScript RT Reagent Kit (Takara Biomedical Technology) for mRNA or All-in-One™ miRNA First-Strand cDNA Synthesis Kit (Genecopoeia) for miRNA according to the manufacturer’s instructions. Quantitative PCR was performed with TB Green® Premix Ex Taq™ II (Takara Biomedical Technology) for mRNA or All-in-One™ miRNA qRT‒PCR Detection Kits (Genecopoeia) for miRNA using a CFX Connect real-time PCR system (Bio-Rad). The relative expression levels of miRNA and mRNA were calculated by the 2‑∆∆Cq method and normalized to the internal controls U6 and 18S, respectively. The primers for pri-miR-149, pre-miR-149, miR-149-5p and miR-149-3p were purchased from Genecopoeia, and the primers for mRNA were used as follows: DDX17 forward: 5’-GATGAAGAAGGAGGCGGAGAAGAG-3’ and reverse: 5’-GGGGTCAGTATCAGCCGCTTTCAG-3’; DDX5 forward: 5’-CGGGACCGAGGGTTTGGTG-3’ and reverse: 5’-GCAGCTCATCAAGATTCCACTTC-3’; CYBRD1 forward: 5’-GCAACAGCACTTATGGGATTG-3’ and reverse: 5’-CATTGCGGTCTGGTGACTATC-3’; 18S forward: 5’-TTGACGGAAGGGCACCACCAG-3’ and reverse: 5’-GCACCACCACCCACGGAATCG-3’.
2.5 Cell migration and invasion assays
Cell migration and invasion assays were carried out in Transwell chambers (8 μm pore size, Corning). For the invasion assay, the chambers were precoated with growth-factor reduced Matrigel (Sigma). CRC cells resuspended in 200 μL serum-free DMEM medium were added to the upper chambers, while the bottom chambers were filled with DMEM medium supplemented with 10% fetal bovine serum. After 48 h of incubation, the cells in the chamber were fixed with 4% paraformaldehyde for 20 min and stained with 0.1% crystal violet for 15 min. The cells were observed and counted in five randomly selected fields under a microscope. The numbers of migratory and invasive cells were photographed by a microscope and counted using ImageJ software.
2.6 Cell adhesion assays
Cell adhesion assays were performed as described previously 22. Briefly, the 96-well plate was precoated with extracellular matrix for 2 h. Then, 100 μl CRC cell suspensions were plated into the covered wells and incubated for 30, 60, 90, 120 minutes. The unadhered cells were washed away with PBS, and the number of adhered cells was measured in five random fields under a microscope.
2.7 Luciferase reporter assay
The luciferase reporter assay was carried out as described previously 23. Briefly, dual-luciferase reporter plasmids PEZx-FR02 (Genecopoeia) inserted with a fragment of the CYBRD1 3’-UTR containing putative or mutated binding sites of miR-149-3p were cotransfected into HEK293T cells along with miR-149-3p mimic or mimic control by Lipofectamine 3000 (Thermo Fisher Scientific). After 36 hours posttransfection, the relative luciferase activity was analyzed by the Dual-Luciferase Reporter Assay System (Promega Corporation) using a MultiMode Microplate Reader (Synergy 2, BioTek) following the manufacturer’s protocols.
2.8 Western blot and immunoprecipitation
CRC cells were lysed in RIPA buffer (50 mM Tris-HCl pH 7.5, 1% NP-40, 0.25% sodium deoxycholate and 150 mM NaCl) supplemented with protease inhibitors (TargetMol, C0001). Lysates were loaded and separated by SDS–PAGE, transferred to a PVDF membrane (Millipore), and then incubated with the following antibodies: anti-DDX17 (Santa Cruz Biotechnology), anti-DDX5 (Cell Signaling Technology), anti-CYBRD1 (Abcam), anti-E-cadherin (Cell Signaling Technology), anti-Claudin-1 (Cell Signaling Technology), anti-Vimentin (Cell Signaling Technology), anti-N-cadherin (Cell Signaling Technology), and anti-β-actin (Sangon). On the next day, the membrane was probed with secondary antibodies at room temperature for 1 h, and protein bands were visualized using Immobilon™ Western Chemiluminescent HRP Substrate (Millipore). For RNA immunoprecipitation, pri-miR-149 and pri-miR-21 were in vitro transcribed and biotinylated by using T7 RNA polymerase and RNA 3’ End Desthiobiotinylation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions, respectively. The biotinylated pri-miRNA was incubated with protein lysates from SW620 cells, immunoprecipitated with streptavidin beads and then subjected to western blot analysis by using anti-DDX17 antibody. Pri-miR-21 has been demonstrated to bind with DDX17 24 and thus was used as a positive control.
2.9 Intracellular iron assay
CRC cells were collected and washed twice with ice-cold PBS, and then rapidly homogenized in 4–10 volumes of Iron Assay buffer. The intracellular iron content was quantified by using an Iron Assay Kit (Sigma–Aldrich, MAK025) following the manufacturer’s protocols.
2.10 In vivo assays for tumor metastasis
Female BALB/c nude mice (6 weeks old) were obtained from Gempharmatech Company (Jiangsu, China) and raised in specific pathogen-free conditions. The indicated CRC cells were infected with lentivirus stably expressing luciferase (pLV-Neo-CMV-luciferase, Yunzhou Biosciences, China). The mouse liver metastatic model was established as described previously 25. Briefly, 1×106 CRC cells were injected into the spleen of anesthetized mice. For luciferase intensity detection, mice were intraperitoneally injected with D-luciferin (150 mg/kg). Ten minutes later, the mice were euthanized, and the liver tissues were removed to detect light emission by an IVIS Spectrum in vivo imaging system. All animal experiments were approved by the Institutional Animal Care and Use Committee (IACUC) of West China Hospital Sichuan University.
2.11 Statistical analysis
All experiments were performed independently with at least three biological replicates, and all data are displayed as the mean ± SD. Student’s t test was applied to compare two groups, and one-way ANOVA was used for the comparison of more than two groups. Pearson’s χ2 test was used for the correlation analysis. Survival analysis was evaluated by the Kaplan–Meier method. A multivariate Cox proportional hazards model was used to assess the independent prognostic factors for overall survival. Statistical analysis was performed using SPSS 22.0 (IBM Corp) and Prism 6 (GraphPad Software). P < 0.05 was considered statistically significant.