Clinical data
The clinical data including miRNAs and LATS2 expression levels were downloaded from The Cancer Genome Atlas database (TCGA, http://xena.ucsc.edu/getting-started/). 10 pair-matched GC tissue samples used for detection of circARHGEF12 and miR-130b-5p expression levels were frozen at − 80°C in Central Laboratory of Shanghai Sixth People's Hospital. The tissue microarray (TMA, Lot No. XT18-003) containing 90 pairs of GC tissue samples was provided by Shanghai Outdo Biotech (Shanghai, China). Our study protocols were approved by the Ethics Committee of Shanghai Sixth People’s Hospital.
RNA fluorescence in situ hybridization (FISH)
FISH analysis was used to confirm the subcellular localization and expression levels of hsa_circ_0002089 (circARHGEF12) and miR-130b-5p in GC tissue samples from TMA. Biotin-labeled probe sequence for circARHGEF12 (Green fluorescence, 5’- AAGCTTTGTTATCTGGACTCTGCTTAAAA-3') and Digoxin-labeled probe sequence for Homo sapiens miR-130b-5p (Red fluorescence, 5’- GTAGTGCAACAGGGAAAGAGTAAAAAA-3’) were used for FISH analysis as previously reported 7.
Cell culture and Drug treatment
Oridonin (C20H28O6, CAS No. 28957-04-2, purity: 99.89%) was purchased from MedChemExpress (Shanghai, China). Oridonin was dissolved in dimethyl sulfoxide (DMSO) as a stock solution and stored at − 20 ℃. MKN-28 and HGC-27 cells were treated for 48h with the specified concentrations of oridonin (0, 5, 10 and 20 µM). The human GC cell lines (MKN-28, HGC-27) and the human embryonic kidney cell HEK293T were obtained from stocks at Digestive Disease Laboratory of Shanghai Sixth People’s Hospital. These cell lines were maintained in RPMI 1640 medium (Hyclone, Logan, Utah) supplemented with 10% of fetal bovine serum (Gibco, United States), 100 U/mL of penicillin and 100 µg/mL of streptomycin (PenicillinStreptomycin-Glutamine, Gibco, United States). The cells were grown at 37°C in a humidified incubator containing 5% CO2. GC cell (MKN-28) were exposed to gradually increasing doses of Cisplatin (DDP) (Selleck, USA) over a 6-month period to establish DDP-resistant cells (MKN-28/DDP) until the cells acquired resistance to 1µg/ml. Prior to each experiment, MKN-28/DDP cells were cultured in drug-free RPMI 1640 medium for 2 weeks.
Molecular docking model
The crystal structure of ALKBH5 (code: 4o7x) was obtained from the Protein Data Bank (https://www.rcsb.org/). The compound Oridonin was retrieved through the TCMSP database (https://old.tcmsp-e.com/tcmsp.php). Subsequently, AutoDock Vina1.5.6 software was employed for hydrogenation, dehydration and molecular docking analysis. PyMOL2.1.0 was utilized for 3-D structure visualization.
RNA extraction and Real-Time Quantitative PCR (RT-qPCR)
The RNA extraction was executed by Trizol method (Lot No. 15596-026, Ambion) and then was reversely transcribed into cDNA for further qPCR analysis by HiScript® II Q Select RT SuperMix (Lot No. R233, VAZYME) and SYBR Green Master Mix (Lot No. Q111-02, VAZYME) according to the manufacturer’s instructions. The primer sequences used for qPCR analysis were included in Supplementary Table S1. Relative mRNA levels of circARHGEF12, miR-130b-5p, ALKBH5, LATS2 and YAP were quantified using the 2−ΔΔCt.
Western blot
GC tissues and cells were lysed with RIPA Pyrolysis liquid (P0013B, Beyotime). The
supernatants were resolved in SDS-PAGE and transferred onto polyvinylidene fluoride (PVDF) membranes, which were probed with anti-ALKBH5 (44KD, Affinity, 1:1000, DF2585), anti-LATS2 (150KD, Affinity, 1:1000, AF7940), anti-p-LATS2 (150KD, Affinity, 1:1000, AF7440), anti-YAP (78KD, CST, 1:1000, 14074) and anti-GAPDH (37KD, 1:1000, AB-P-R001) overnight at 4°C. The protein bands were developed by enhanced chemiluminescence (ECL).
Plasmid, shRNA, miRNA mimic and inhibitor
Lentivirus-mediated ALKBH5 15 or circARHGEF12 and si-circARHGEF12 (5’-GAGTCCAGATAACAAAG CTTT-3’) as well as miR-130b-5p mimic or inhibitor was offered by GenePharma (Shanghai, China). The negative control (NC or CON) and miR-NC were considered as the control groups. MKN-28 and HGC-27 cells were planted in 6-well plates 48 h prior to ALKBH5, circARHGEF12, miR-130b-5p mimic or inhibitor transfection with 50–60% confluence, and then mixed with Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacture instructions.
mA-circRNA epi-transcriptomic microarray
Total RNA was extracted from ALKBH5 or NC stably-transfected MKN-28 cells and m6A-circRNA epi-transcriptomic microarray was utilized to screen ALKBH5-dependent m6A modification of circRNAs in GC cells as previously reported 7.
RNA immunoprecipitation (RIP) and m6A-RIP (MeRIP)
RIP assay was performed using RNA-Binding Protein Immunoprecipitation Kit (17–700, Millipore) and HiScript II qRT SuperMix II kit (R223, VAZYME). The antibodies against m6A (68055-1-Ig, Proteintech, Wuhan, China), ALKBH5 (44KD, Affinity, 1:1000, DF2585) and Ago2 (67934-1-Ig, Proteintech, Wuhan, China) were used for MeRIP or RIP analysis.
Bioinformatic analysis
The specific binding between circARHGEF12 and miRNAs (miR-103a-2-5p, miR-335-5p, miR-130b-5p, miR-339-3p and miR-605-5p) was identified using the miRbase database (http://www.mirbase.org/index.shtml). The target genes of miR-186-3p were identified byTargetScanHuman7.1 (http://www.targetscan.org/vert_71/).
Luciferase gene reporter assay
Luciferase gene reporter assay was performed by double luciferase gene reporter kit (RG027, Beyotime). HEK293T cells were seeded into 96-well plates and co-transfected with PRL-TK-pMIR-circARHGEF12 or PRL-TK-pMIR-LATS2 3’UTR, miR-130b-5p inhibitor, and miR-130b-5p mimics or miR-NC. After 48 h of incubation, the firefly and Renilla luciferase activities were examined with a dual-luciferase reporter assay.
In vivo tumorigenesis assay and caudal vein pulmonary metastasis model
Female BALB/c nude mice (6-8-week, SPF) were purchased from the Shanghai Laboratory Animal Central (SLAC, Shanghai, China). MKN-28 cells (1×107) transfected with circARHGEF12 or NC lentiviruses were resuspended in 200µL of sterile PBS and injected subcutaneously under the right forearm armpit of mice. Based on recent studies, the mice were treated with 5 ~ 6 mg/kg DDP three times per week36–38. Therefore, the mice were intraperitoneally injected with 0, 3 or 6 mg/kg DDP at days 10, 13, 16, 19, 22, and 25 after inoculation with HGC-27 cells. After 30 days, the mice were anaesthetized with isoflurane and sacrificed, then the xenografted tumors were collected. Tumor volume = (length * width2)/2.
MKN-28 cells stably transfected with circARHGEF12 or NC lentiviruses were cultured in complete medium. When the cells were 70% confluent, the medium was replaced with fresh medium to remove dead and detached cells. 1×107 MKN-28 cells were injected into the mice tail vein. The mice were sacrificed after 28 days, and the lung tissues were removed, photographed, and fixed. All animal studies were conducted in accordance with institutional ethical guidelines for animal experiments and approved by the Institutional Animal Care and Use Committee or the Ethics Committee for Animal Experiments of Shanghai Sixth People’s Hospital (No: DWLL2024-966).
Cell Counting Kit-8 (CCK8), Colony formation, Transwell assays, m 6 A dot blot, RNase R treatment and Nuclear and cytoplasmic fractionation, hematoxylin-eosin (HE) staining and Immunohistochemical (IHC) analysis
These experiments were performed as previously reported 7,32.
Statistical analysis
Statistical analysis was performed with GraphPad Prism 9 (La Jolla, CA, USA). In brief, the values are expressed as the mean ± standard deviation (SD). Student’s test and analysis of variance were used for comparisons between groups. Survival curves were generated using the Kaplan-Meier method and log-rank testing. Pearson Correlation Analysis was used to analyze the correlation of circARHGEF12 with miR-130b-5p. The half-maximal inhibitory concentration (IC50) values were determined using a curve fitting model with a four-parameter logistic equation model in GraphPad Prism software. P < 0.05 was considered statistically significant.