HNPCs culture
HNPCs (Sciencell Research Laboratories; Carlsbad, CA, USA) maintained in NPC Medium (NPCM, Cat. #4801, ScienCell) under normoxic (Nx) culture conditions (37°C, 20% oxygen, 5% carbon dioxide, 75% nitrogen) or hypoxic (Hx) culture conditions (37°C, 1% oxygen, 5% carbon dioxide, 94% nitrogen). Hx cell culture conditions were generated in a hypoxia incubator .
qRT-PCR assay
Total RNA of HNPCs was extracted with TRIzol (Invitrogen) reagent and diluted with DEPC water (Invitrogen) and reverse transcribed into cDNA using the PrimeScript RT reagent kit (Invitrogen) according to the manufacturer's instructions. RT-qPCR was then performed using the SYBR Premix Extaq II kit (Thermo Fisher Scientific, Inc., Waltham, MA, USA) on Real-Time PCR system (7500; Applied Biosystems; Thermo Fisher Scientific, Inc.). Cycling conditions were as follows: 50°C (2min), 95 °C (10min), 72 °C (2min), followed by 40 cycles of 95 °C (15 s) and 60 °C (32s). The sequences of primers for miR-338-3p and U6 were as follows: miR-338-3p-F, 5′-ACACTCCAGCTGGGACATCAGTGATTTTGTTG-3′, miR-338-3p-R, 5′-CTCAACTGGTGTCGTGGA-3′; U6-F, 5′-CTCGCTTCGGCAGCACA-3′, U6-R, 5′-AACGCTTCACGAATTTGCGT-3′. Relative miR-338-3p expression levels were calculated using the 2−ΔΔCt method.
Differentially expressed miRNA analysis via GEO2R
Using GEO2R (ncbi.nlm.nih.gov/geo/geo2r) for identifying the set of two or more samples differential expression of miRNAs, and with P <0.05 and log2 |fold change| >2 for differentiation standard.
Prediction of miRNA target genes
The TargetScan7.2 database (targetscan.org/vert_72/) and the miRDB database (mirdb.org) were used to predict the miR-338-3p binding sites on the downstream target genes. Putative target genes were predicted by the two programs. Using DAVID tool (https://david.ncifcrf.gov/) to perform the functional classification analysis of miR-338-3p predicted target genes.
Dual luciferase assay
Use of Lipofectamine® 2000 (Invitrogen) transfection HNPCs with luciferase reporter vector (psi-CHECK-2) containing a 3'-UTR fragment of HIF-1α, according to the manufacturer's instructions. co-transfected with 50 nM miR-338-3p mimics or control (mimic NC) with psi-CHECK-2 (0.5 µg) luciferase reporter vector or empty vector containing the wild-type (WT) or mutant (mut) HIF-1α 3'-UTR sequence. Then, a dual luciferase reporting detection system (Glomax; Promega Corporation, Madison, WI, USA) after 48 h of transfection. The results are normalized using Renilla/Firefly method.
Western blotting
Transfected NPCs were cleaved using RIPA lysis buffer (Beyotime, Shanghai, China) on ice using BCA protein assay kit (Boster Biological Technology co.ltd; California, USA) pyrolysis lysate protein concentration calculation. Equivalent of denatured proteins were resolved using 10% SDS-polyacrylamide gel electrophoresis (Solarbio), and protein bands were transferred to a polyvinylidene fluoride membrane (Solarbio). Using TBST (Beyotime) wash membranes twice and blocked(Solarbio), incubated overnight with the primary antibodies at 4 °C, rinsed, and then incubated with secondary antibody (goat anti-rabbit; 2 mg/ml; ab205718; Abcam, Cambridge, UK) for 2 h at 23 ± 2 °C. Protein bands were visualized by the addition of ELC-enhanced chemiluminescence reagent (Thermo Fisher Scientific) in conjunction with an imaging system (FluorChem R; ProteinSimple co., Ltd., Silicon Valley, California, USA). An anti-GAPDH antibody (1:10,000) was used as the loading control. Anti-HIF-1α antibody (1:1,000; ab179483; Abcam), Anti-PCNA antibody (1:1,000; ab92552; Abcam), Anti-Ki-67 antibody (1:5,000; ab92742; Abcam), Anti-Caspase-3 antibody (1:2,000; ab184787; Abcam), Anti-caspase-9 antibody (1:2,000; ab202068; Abcam), Anti-YAP antibody (1:1,000; ab205270; Abcam), Anti-p-YAP antibody (2.5 µg/ml; ab76252; Abcam) and Anti-CTGF antibody (1:1,000; ab209780; Abcam) were used.
Cell proliferation assay
According to the manufacturer's manual, HNPCs (2.5×103) was incubated for the indicated time periods (12, 24, 48, and 72 h) in an incubator, and 10 μL of CCK8 solution (Beyotime) was added and incubate for 1 hour. The absorbance at 490 nm was measured with the enzyme-labeled instrument (Thermo Fisher Scientific, Inc.).
Cell apoptosis assay
Annexin V-FITC (5 μL; BD Biosciences, CA, USA) and propidium iodide (10 μL; BD Biosciences) were incubated with HNPCs (1×106 cells/ml) in the dark (15 min, 23±2°C), and rinsed twice with phosphate-buffered saline (Gibco). Apoptosis was assessed by flow cytometry (FCM; BD Biosciences).
Statistical analysis
All experiments were triplicate and the data are expressed as the mean ± standard deviation (SD). Using SPSS version 19.0 statistical analysis package (SPSS Inc., Chicago, IL, USA) for more than two groups of data. Student’s t-test was used to analyses independent two-group (unpaired).