Cell culture and treatment
Neonatal cardiomyocytes were isolated from 2-day-old Sprague Dawley rats purchased from Vital River Laboratory Animal Technology Co., Ltd. (Beijing, China). Our study was approved by Tianjin Medical University Cancer Institute and Hospital (No.NSFC-AE-2020047) and all experiments were conducted according to the Declaration of Helsinki and conformed to the US National Institutes of Health Guide for the Care and Use of Laboratory Animals. Hearts were cut into 1-mm3 pieces, placed in 1.5 mL Eppendorf tubes and digested at 37°C with 0.125% trypsin (Amersco, USA) and 0.1% collagenase II (Sigma, St Louis, MO, USA) until there was no obvious tissue structure. The digested cells were resuspended in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, USA) supplemented with 10% fetal bovine serum, 100 U/mL penicillin G, and 100 μg/mL streptomycin, at 37°C and 5% CO2. Fibroblasts were removed using a differential attachment technique. The dissociated cells were cultured for 48 h in a medium containing 0.1 mmol/L bromodeoxyuridine to prevent proliferation of non-myocytes. After 4 days in culture, the various treatments described below were performed.
H9c2, HEK293A cells purchased from the Shanghai Institute of Cell Biology (Shanghai, China). Cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin G, and 100 μg/mL streptomycin, at 37°C and 5% CO2.
To induce hypoxia-reoxygenation (H/R) injury, the medium was changed to Hanks’ balanced salt solution (Gibco) and cells were cultured at 37°C in a hypoxic incubator (Billups-Rothenberg, USA) filled with pre-mixed gas (5% CO2 and 95% N2) for 6 h. H/Post was performed after 6 h of hypoxia by exposing cells to three cycles of 30 min of hypoxia and 30 min of reoxygenation. After hypoxia or H/Post, the cells were transferred to normal culture medium and kept in an incubator for 12 h of reoxygenation.
D-galactose (Sigma) was dissolved in DMEM at 0, 5, 10, or 20 g/L to induce senescence of primary cardiomyocytes and was added to the primary cardiomyocyte cultures for different incubation periods.
Senescence-associated β-galactosidase (SA-β-gal) assay
SA-β-gal staining was performed using an SA-β-gal staining kit (Beyotime, Shanghai, China) according to the manufacturer’s instructions. Briefly, cells were washed in phosphate-buffered saline (PBS, Gibco), fixed with fixative solution for 15 min at room temperature, and rinsed three times with PBS. Subsequently, the cells were incubated overnight at 37°C with the staining solution mix. The percentage of senescent cells (blue staining) was calculated in five randomly chosen fields of view for each sample. The assay was performed in triplicate.
Cell transfection
The siRNAs against rat ALKBH5 and STAT3 as well as rno-miR-124-3p mimics, rno-miR-124-3p inhibitor, and their negative controls (NC) were purchased from Genepharma (Shanghai, China). The previously confirmed siRNA sequences used in the study are shown in the Supplemental Materials (Table 1). Two of siRNAs and their mix were transfected into cells. ALKBH5 siRNA, STAT3 siRNA, their mix, rno-miR-124-3p mimics, rno-miR-124-3p inhibitor, or their negative controls (100 nM) were combined with Lipofectamine RNAimax (Invitrogen, Carlsbad, CA, USA) and transfected according to the manufacturer’s instructions. After 48 h, samples were used in the described experiments.
The full-length sequence of H19 was cloned into pCDNA3.0 to generate the H19 expression vector, pCDNA3.0-H19. The vectors were transfected using Lipofectamine 2000 reagent (Invitrogen). After 48 h, samples were used in the further experiments.
The coding sequence region of the ALKBH5 sequence used for constructing Ad-ALKBH5 was extracted from rat heart and inserted into adenoviral vectors. The empty vector, Ad-Null, was used as a control for Ad-ALKBH5. The vectors were transfected into HEK293A cells and the virus was collected. After transfect the virous in the primary cells 24 h, samples were used in the following experiments.
Cell viability assessment
The cell counting kit 8 (CCK-8) assay (Dojindo, Kumamoto, Japan) was used to detect cell viability according to the manufacturer’s protocol. Cells were seeded in 96-well tissue culture plates at a density of 2 × 104 cells/mL and treated or transfected. After treatment, cells were cultured in DMEM with 10% CCK-8 for 1 h, and then cell viability was determined by measuring the optical absorbance at 450 nm. The assay was performed in triplicate.
Quantitative real-time PCR (qRT-PCR)
Total RNA was extracted with Trizol and chloroform, precipitated with isopropyl alcohol, washed with 75% ethanol, dissolved in diethyl pyrocarbonate (DEPC)-treated water, dried, and dissolved in RNase-free water. RNA was reverse transcribed with a reverse transcriptase kit (Takara, Kusatsu, Japan) and subjected to qRT-PCR using SYBR Green (Takara) according to the manufacturer’s instructions. The primers used for the qRT-PCR are listed in the Supplementary Materials (Table 1). qRT-PCR was carried out on a CFX96 TM Real-time System instrument (Bio-Rad, Hercules, CA, USA). GAPDH was used as an endogenous control.
miRNA was converted into cDNA using a miRcute Plus miRNA First-Strand cDNA Synthesis Kit (TIANGEN, Beijing, China) and was quantified with a miRcute miRNA qPCR Detection Kit (TIANGEN). U6 was used as a reference gene.
Each sample was run in triplicate. Comparative quantification was performed using the 2−ΔΔCt method.
Dual-Luciferase Reporter Assay
The reporter assay was performed using the Dual Luciferase Reporter Assay kit (Promega, Madison, WI, USA). Briefly, co-transfection of wild type (wt) or mutant (mut) pGL3 vectors in H9c2 cells revealed H19 and STAT3 3¢-UTR with miR-124-3p mimics or mimic NC, respectively. At 48 h post transfection, the luciferase activity was measured.
Immunoblotting
Cells were rinsed twice with PBS, and then lysed for 30 min on ice in lysis buffer containing phenylmethylsulfonyl fluoride (PMSF). Proteins were quantified using a BCA Protein Assay Kit (Beyotime). After separation using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, proteins were transferred onto polyvinylidene difluoride (PVDF) membranes, which were then blocked with non-fat milk for 1 h at room temperature. The PVDF membranes were incubated with the primary antibody at 4°C overnight, washed with PBS, and incubated with the horseradish peroxidase-conjugated secondary antibody at 37°C for 1 h. Signals were detected using a chemiluminescence imaging system (Bio-Rad). Blots were probed with antibodies against Bcl-2, Bax, ALKBH5 (Proteintech, Wuhan, China), p53 (Cell Signaling Technology, Danvers, MA, USA), STAT3, and phospho-STAT3-Y705 (Affinity, Changzhou, China), and with GAPDH (Santa Cruz Biotechnology, Dallas, TX, USA) as a loading control.
m6A Quantification
Total RNA was extracted from cells. Changes in total m6A levels of mRNA were measured using an m6A RNA Methylation Quantification Kit (Colorimetric; Abcam, Cambridge, UK) according to the manufacturer’s protocol. For analysis of each sample, 200 ng of RNA was coated on an assay well, and then the capture antibody solution and detection antibody solution were added individually at the required dilutions. m6A levels were quantified colorimetrically by reading the absorbance at a wavelength of 450 nm; calculations were performed based on a standard curve.
RNA immunoprecipitation
RNA immunoprecipitation (RIP) experiments were performed using the Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore Corporation, Burlington, MA, USA) according to the manufacturer’s protocol. Briefly, antibodies against m6A (SYSY, Goettingen, Germany) or IgG bound to magnetic beads were diluted to 1:50. H9c2 cells transfected with NC or siALKBH5 for 48 h were lysed in RIP lysis buffer. Samples of each lysate were aliquoted to serve as input controls, while the remaining lysates were immunoprecipitated with the precipitation magnetic beads. Beads and input were then treated with proteinase K buffer solution for 30 min at 55°C. Then, RNA was isolated and purified by phenol:chloroform:isoamyl alcohol extraction from inputs and precipitation magnetic beads. The immunoprecipitated RNA was subsequently analyzed using RT-qPCR.
Statistical Analysis
Data are expressed as the mean ± standard deviation (SD) of at least three independent replicates. Comparisons between two groups or multiple groups were performed using Student’s t-test or one-way analysis of variance followed by Tukey’s multiple comparisons test, respectively. All the analyses were performed using GraphPad Prism version 8.0 software (GraphPad Software, USA). Differences were considered statistically significant if P < 0.05.