Sampling and EV71 isolation
EV71 was isolated from clinical specimens including throat and anal swabs and stools of a patient with HFMD due to EV71 infection, provided by the Center for Disease Control and Prevention of Guangdong Province (Guangzhou, China). The patient was diagnosed at Zhongshan School of Medicine, Sun Yat-sen University (Guangzhou, China). The study was approved by the ethics committee of the Guangzhou Medical University, Guangzhou Women and Children’s Medical Center, IRB, Wuhan Institute of Virology, CAS (no. 2017122501, 2017 − 396 and WIVA07201904). All procedures performed involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. Written informed consent was obtained from the legal guardians of the patient from whom EV71 was isolated for research purposes.
Cell line and culture
Mouse Schwann cells(ScienCell Research Laboratories, Inc., Cat. #M1700)were cultured in Schwann Cell Medium༈ ScienCell Research Laboratories, Inc., Cat. #1701༉. Cell culture reagents: Penicillin-streptomycin solution (Hyclone Laboratories, Inc., Cat. #SH30010), PBS Potassium phosphate buffer (Hyclone Laboratories, Inc., Cat. #SH30256.01B). Cell resuscitation and cell subculture were carried out according to the experimental procedure, and the cell concentration was adjusted to 5×107/ml for the experiment. Schwann cell medium containing penicillin (100 U/ml) and streptomycin (100 µg/ml) in poly-L-lysine-coated (2 µg/cm2) flasks at 37˚C in a humidified atmosphere of 5% CO2. DMEM medium was replaced every other day. The third-generation chondrocytes were counted and used to prepare cell suspension. Trypan blue staining to detect cell viability was 90%, and the cell concentration was adjusted to 5×107/ml for experiments.
Plasmid preparation and transfection for overexpression
Total RNA (EV71) was extracted using TRIzol (Thermo Fisher Scientific, Inc., Cat. #15596026) and reverse transcribed to obtain cDNA (Promega corporation, Cat. #A3800). The 894-bp VP1 cDNA was synthesized by reverse transcription-polymerase chain reaction (RT-PCR; Takara Bio, Inc., Cat. #2011A) using the primers: Forward 5'-ccGcTcGAGGccAccATGGGTGATGGAATTGcAGAcATGA-3' and reverse 5'-cGcGGATccTAG TGTTGTTATTTT GTcccTAcT TGT Gc-3' (Genewiz, Inc.). The PCR products were subcloned into the pEGFP-c3 expression vector (Clontech Laboratories, Inc.) following manufacturer’s protocol. To determine if the VP1 cDNA was successfully cloned into the pEGFP-c3 vector, plasmids from transformed bacteria were prepared and digested with BamHI and XhoI. Sequencing was performed by Sangon Biotech for confirmation of successful cloning. The results were compared with the VP1 cDNA sequence reported in the GenBank database (GenBank accession number: U55763). The EV71-VP1 overexpression plasmid is annotated as pEGFP-c3 + EV71-VP1. Cells were transiently transfected with 2 mg plasmid using Lipofectamine 2000 (Invitrogen; Thermo Fisher Scientific, Inc.) for 24 h, according to the manufacturer's instructions.
Gene silencing by siRNA
Genes of interest are targeted and silenced by siRNA. METTL14 and YTHDF1 siRNA (minic) are ordered from Santa Cruz Biotechnology., Inc. (Cat. #sc-42037, Santa Cruz, CA, USA) (Table 1, Fig. 3A). siRNA was transfected into mouse Schwann cells by Lipofectamine 2000 ( Invitrogen,Cat. #11668019) and Opti-MEM (Invitrogen༌Cat. #31985070). Non-targeting siRNA sequences were transfected into the cells as negative controls.
Table 1
Target sequence for siRNA-METTL14 and siRNA-YTHDF1
| Ranking | siRNA ID | Sequence Start | Target sequence |
siRNA-METTL14 | 1 | SASI_Mm01_00071493 | 555 | agaatttcatcagggatgtag |
2 | SASI_Mm01_00071495 | 761 | agagagactggcatcactgcg |
3 | SASI_Mm02_00351698 | 1399 | tcccagaggtggaggaagggg |
siRNA-YTHDF1 | 1 | SASI_Mm01_00078555 | 407 | ccaccatccattggatttcct |
2 | SASI_Mm01_00078556 | 1726 | acctgtcacaaactcccgtga |
3 | SASI_Mm01_00078557 | 1264 | tgacagtaactctgttggaaa |
Note: METTL14 methyltransferase like 14 [ Mus musculus (house mouse)]. |
Gene ID: 210529, updated on 8-Nov-2020. |
Mus musculus methyltransferase like 14 (Mettl14), mRNA. |
NCBI Reference Sequence: NM_201638.2 |
Ythdf1 YTH N6-methyladenosine RNA binding protein 1 [ Mus musculus (house mouse)]. |
Gene ID: 228994, updated on 20-Oct-2020. |
Mus musculus YTH N6-methyladenosine RNA binding protein 1 (Ythdf1), mRNA. |
NCBI Reference Sequence: NM_173761.3. |
Experimental grouping and operation
m6A-related gene detection experiment
Mouse Schwann cells were divided into three groups: cell (normal control group), NC (negative control group), SC + EV71-VP1 (experimental group). Gene expression was quantified by qPCR at 24-hour time point and protein expression was confirmed by immunoblotting at 48-hour respectively (Please see methods below).
DAA treatment of mouse Schwann cells
Selective mRNA methylation inhibitor 3-deazaadenosine (DAA) (Selleck Chemicals, Cat. # S0787, Huston, TX, USA) was employed to determine which elements involved in the m6A pathway are targeted by VP1. Mouse Schwann cells were treated with DAA [3.9 µM (Ki), 60mg/ml].
mRNA methylation
Mouse Schwann cells were divided into four groups: cell (normal control group), NC (negative control group), EV71-VP1 (experimental control group) and EV71-VP1-siRNA-METTL14 or -YTHDF1 (siRNA experimental group).
Quantitative real-time PCR (qPCR)
The total RNA of the sample was extracted using TRE-Trizol (Invitrogen,Cat. #15596-026). The design of fluorescence quantitative PCR primers is shown in Table 2. Complementary DNA (cDNA) was obtained by the reverse transcription of mRNA, which was performed in strict accordance with the instructions of TaKaRa PrimeScript II 1st Strand cDNA Synthesis Kit (TaKaRa Bio Inc., Cat. # D6210A). The preparation and reaction parameters of the fluorescent quantitative PCR reaction System were performed according to the instructions of the TaKaRa SYBR® Premix Ex Taq™ II (Perfect Real Time) kit (TaKaRa Bio Inc., Cat. # RR039B). Amplification and fusion curves of Real Time PCR were performed using ABI PRISM® 7500 Sequence Detection System (REAL-TIME PCR System). Fluorescence quantitative RT-PCR data was analysis using the SDSShell Software1.6 software, and the 2 − Δ Δ Ct method to calculate.
Table 2
Primers used for fluorescence quantitative PCR
Gene | ID | Forward primer | Reverse primer | Product length (bp) |
ALKBH5 | 268420 | ATTGCCACCCAGCTATGCTT | CTCATCTTCACCTTGCGGGT | 273 |
EV71-VP1 | 1461111 | TCGTGCGCTGACATCCTTAC | ATGGTTCAACACACACCGGG | 166 |
FTO | 26383 | TGAAAGTGAGGACGAGTCCAG | TGAGTGGAACTAAACCGAGGC | 201 |
METTL14 | 210529 | CTGGCATCACTGCGAATGAG | CGCAAGCATACTCTCCCAAG | 142 |
METTL3 | 56335 | ATCTTGGCTCTATCCGGCTG | CCTTAAATCCAAGTGCCCAGAG | 231 |
YTHDC1 | 231386 | GGAAGAGAACCAGAGCACGG | CCATCTTTCTCCTCCCGGC | 219 |
YTHDF1 | 228994 | CGTGATACACAGGAGGTGCC | CGATTCTGTCTTTCCTTACGCAC | 152 |
YTHDF2 | 213541 | CAGGCAAGGCCGAATAATGC | TCTCCGTTGCTCAGTTGTCC | 167 |
YTHDF3 | 229096 | TCAGAGACCTAAAGGGCAAGG | TGGCATAGGCTGATCTCCAG | 235 |
Rn18s | 19791 | CCTGGATACCGCAGCTAGGA | GCGGCGCAATACGAATGCCCC | 112 |
PMP22* | | cTGccAGcTcTTcAcTcTcA | GTTGAcATGccAcTcAcTGT | |
GAPdH | | GGccTccAAGGAGTAAGAAA | GccccTccTGTTATTATGG | |
Note: * PMP22, peripheral myelin protein 22. |
Western blot
Mouse Schwann cells were lysed with RIPA lysis and extraction buffer (Thermo Fisher Scientific, Inc, Cat. #89900). Protein concentration was determined by the bicinchoninic acid protein assay kit (Beyotime Institute of Biotechnology, Cat. # P0012). Then, 50 ng of each protein sample was separated by 10% SDS-PAGE and transferred to polyvinylidene fluoride membranes. The membranes were blocked with 5% nonfat milk powder in Tris-buffered saline/Tween 20 (TBST) at room temperature and then incubated with anti-GAPdH (1:1 000, Abcam, Cat. # ab181602) for 1–2 h at room temperature, and then with peroxidase-conjugated secondary antibody (1:4 000, Thermo Fisher Scientific, Inc., Cat. # 31460) for 1 h at room temperature. Membranes were visualized with an enhanced chemiluminescent development reagent (BeyoECL Plus, GE Healthcare, Cat. # 28935599) and densitometry analysis was performed using Quantity One (Bio-Rad Laboratories, Inc.).
Primary antibodies used in the study were: Enterovirus 71 VP1 Monoclonal Antibody (3656), Thermo Fisher, Cat. # MA5-33257; Rabbit Anti-METTL14 antibody & Rabbit Anti-FTO antibody & Rabbit Anti-ALKBH5 antibody, Bioss, Cat. # bs-17608R, bs-7056R, bs-20540R; Recombinant Anti-METTL3 antibody [EPR18810] & Recombinant Anti-YTHDF1 antibody [EPR22349-16] & Recombinant Anti-YTHDF2 antibody [EPR20318] & Recombinant Anti-YTHDF3 antibody [EPR21912-3] & Recombinant Anti-YTHDC1 antibody [EPR21821], abcam, Cat. #ab195352 & ab252346 & ab220163 & ab220161& ab220159. Secondary antibodies are Rabbit Anti-Mouse IgG (H + L), 1:4 000, Southern Biotech, Cat. # 6170-05; Goat Anti-Rabbit IgG (H + L chain specific), 1:5 000, Southern Biotech, Cat. #4050-05).
Statistical analysis
All experiments were repeated at least three times. data are expressed as mean ± standard error (SE). Statistical significance was assessed by the Student's t test or one-way ANOVA with the Least Significance Difference (LSD) post hoc test, using the SPSS 16.0 statistical software (SPSS, IBM). P < 0.05 indicates statistical significance.