Human Tissue samples
Ovarian cancer tissues and normal ovarian tissues were collected from the Women’s Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital). All samples were confirmed by another pathologist, rapidly frozen with liquid nitrogen and stored at -80°C. All of the patients signed informed consent forms. This study of patient specimens was approved by the Ethical Committee of Women’s Hospital of Nanjing Medical University. Clinical and pathological information for ovarian cancer patients is shown in the Supplementary table 1.
Cell culture
Human ovarian epithelial cancer cell line A2780 and OVCAR3 were purchased from Shanghai Mingjin Biology Co., Ltd.; human ovarian epithelial cancer cell line SKOV3 and human ovarian clear cell cancer cell line ES-2 were purchased from National Collection of Authenticated Cell Cultures; and human normal ovarian epithelial cell line IOSE80 was donated by Ms. Li Jing of the General Hospital of the Eastern Theater Command. SKOV3 was cultured in McCoy’s 5A medium (KeyGEN, China) supplemented with 10% FBS (Gibco, USA). OVCAR3 was cultured in RPMI-1640 medium (KeyGEN, China) supplemented with 20% FBS (Gibco, USA). A2780, ES-2, and IOSE80 were cultured in DMEM medium (KeyGEN, China) supplemented with 10% FBS (Gibco, USA). All the cells were supplemented with 1% Pen/Strep (Gibco, USA) and maintained in 5% CO2 cell culture incubator at 37℃.
Plasmids and siRNA
The CDS of IGF2BP2 was linked to the CMV promoter in pEZ-M98 vector to construct the IGF2BP2-overexpressing plasmid. IGF2BP2 KH3-4 mutant plasmid was constructed by mutating GxxG to GDDG in the IGF2BP2 KH3-4 domains. The CDS and 3’UTR of CKAP2L was linked to the CMV promoter in pVAX1 vector to construct the CKAP2L m6A wild type plasmid. CKAP2L m6A mutant plasmid was constructed by mutating A to G at positions 1260, 2369, 3332 and 3473 on CKAP2L mRNA. All plasmids were purchased from Nanjing Genebay Biotech Co., Ltd.
Small interfering RNAs (siRNAs) targeting IGF2BP2 and CKAP2L were synthesized by Guangzhou RiboBio Co., Ltd. The related sequences of siRNAs were as follows: si-IGF2BP2-1: 5’-CATGCCGCATGATTCTTGA-3’, si-IGF2BP2-2: 5’-GAACGAACTGCAGAACTTA-3’, si-CKAP2L: 5’-GGTGTACCTTCTAATGAAA-3’. The plasmids and siRNAs were transfected using Lipofectamine 3000 transfection reagent (Thermo Fisher Scientific, USA) according to the manufacturer’s instructions.
Stable cell line establishment
The IGF2BP2-overexpressing and control lentiviral were constructed and packaged by Nanjing Genebay Biotech Co., Ltd. Briefly, the IGF2BP2-overexpressing and control vector were constructed in the PLVX vector, and the vector as well as the assistant plasmid pSPAX2 and pMD2G were transfected into HEK293T cells to package the lentiviral particles. The lentiviral particles were then harvest and purified. The titer of IGF2BP2-overexpressing lentivirus and control lentivirus were 1.85 × 108 TU/ml and 2.99 × 108 TU/ml, respectively. SKOV3 and A2780 cells at 30% density were infected with IGF2BP2-overexpressing lentivirus and control lentivirus. About 72 hours after infection, puromycin (P8833, Sigma) was added to the culture medium to select the infected cells.
RNA extraction and quantitative real-time PCR (qRT-PCR)
Total RNA was extracted from cells and tissues using GeneJET RNA Purification Kit (Thermo Fisher Scientific, USA) according to the manufacturer’s instruction. For qRT-PCR, RNA was reverse transcribed to cDNA by using HiScript III RT SuperMix for qPCR Kit (Vazyme, China). qRT-PCR was subsequently conducted using an Applied Biosystems ViiA™ 7 DX machine (Thermo Fisher Scientific, USA). The primers used were shown in Supplementary table 2.
Methylated RNA immunoprecipitation sequencing
Total RNAs were extracted from the OC tissues or cells. An m6A-specific antibody (Sigma-Aldrich, no ABE572) was used to immunoprecipitate RNA. m6A RNA-seq service was provided by Shanghai Biotechnology Corporation (Shanghai, China). Briefly, m6A RNA immunoprecipitation was performed with the GenSeqTM m6A-MeRIP Kit (GenSeq Inc, Malaysia) following the manufacturer’s instructions. Both the input samples without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation. The library quality was evaluated with Bioptic Qsep100 Analyzer (Bioptic lnc, China). Library sequencing was performed on illumina NovaSeq instrument with 150bp paired-end reads.
RNA immunoprecipitation sequencing and RIP-qPCR
RIP assays were performed using the Magna RIP RNA-binding Protein Immunoprecipitation Kit (17-700, Millipore) according to the manufacturer’s instructions. Briefly, cells were washed twice with PBS, collected and then the pellet was resuspended in complete RIP lysis buffer. Magnetic beads coated with 5 μg of antibody of IGF2BP2 (11601-1-AP, Proteintech) or negative control antibody (17–700, Millipore) were incubated with prepared cell lysates overnight at 4 °C, respectively. Then, the RNA-protein complexes were washed 6 times with wash buffer and incubated with proteinase K digestion buffer. RNA was finally extracted by phenol-chloroform RNA extraction methods. For qRT-PCR, RNA was reverse transcribed to cDNA by using RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, USA). For sequencing, cDNA libraries were produced by VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina® (Vazyme, NR603) and sequenced on Illumina HiSeq X Ten platform.
High-throughput RNA sequencing (RNA-seq)
Total RNA was isolated from IGF2BP2-overexpressing SKOV3 cells and control cells using TRIzol Reagent (Life technologies, USA). The sequencing libraries were generated using the TruSeq Stranded Total RNA Library Prep Kit from Illumina according to the manufacturer’s instructions. The samples were paired-end sequenced with a read length of 100 bp on an Illumina HiSeq 2500 sequencer. The process of sequencing was controlled by Illumina Data collection software. The library construction and sequencing were performed at Shanghai Biotechnology Corporation (Shanghai, China).
Western blotting
Cells were washed twice with PBS and lysed with RIPA (Servicebio, China) and 1% PMSF (Beyotime, China) on ice for 30 minutes. The lyses was collected in a centrifuge tube and centrifuged at 12000 rpm, 4℃ for 30min. Proteins were fractionated by SDS-PAGE, transferred onto PVDF membranes, blocked in 5% nonfat milk and then blotted with specific antibodies. Antibodies used were as follows: anti-β-actin (1:500, Santa Cruz), anti-IGF2BP2 (1:1500, Cell Signaling Technology), anti-CKAP2L (1:1000, Proteintech), anti-ERCC6L (1:1000, Proteintech), anti-ZNF20 (1:1000, Signalway Antibody), anti-MET (1:1000, Proteintech), anti-c-Myc (1:1000, Proteintech) , Goat anti-Mouse IgG-HRP (1:5000, Biosharp), Goat anti-Rabbit IgG-HRP (1:5000, Biosharp).
Hematoxylin and eosin staining and Immunohistochemistry
Human OC, fallopian tube and nude mice xenograft tumor tissues paraffin embedded sections were deparaffinized and rehydrated in succession. Sections were stained with hematoxylin and eosin. Immunohistochemistry was performed by using Anti-mouse/rabbit Immunohistochemistry Detection Kit (Proteintech, PK10006). Antibodies used were as follows: anti-IGF2BP2 (1:200, Proteintech), anti-CKAP2L (1:200, Proteintech), anti-Ki-67 (1:4000, Proteintech). Cells were viewed and photographed with a microscope. The score for staining was assessed on the staining intensity and the percentage of positive cells identified by Image J Immunohistochemistry Profiler. The intensity of the staining cell was graded as 0 (negative), 1 (low positive), 2 (postive), 3 (high positive). The final score was determined by multiplying the score for staining intensity with the percentage of positive cells.
Cell proliferation assay
For colony formation assay, about 2 × 103 cells were seeded into each well of six well plates and the medium were refreshed every 3 days. After 7 days, colonies were fixed with 4% paraformaldehyde (Biosharp, China) for 15min, stained with 0.1% crystal violet (Biosharp, China) for 15min and washed with ddH2O.
Transwell migration and invasion assays
The migration and invasion assays were conducted using the transwell (Corning, USA) according to the protocol described before. 5 × 104 cells were seeded in the upper chambers with 200μL serum-free medium. 0.6 ml culture media with 20% FBS were added to the lower chamber. For invasion assay, 60μl Matrigel (1:7, Corning, USA) was prepared in the upper chamber. After 24~72h incubation, cells were fixed with 4% paraformaldehyde, stained with 0.1% crystal violet and washed with ddH2O. Gently wipe off the remaining Matrigel and cells on the upper chamber of the Transwell, migrated or invaded cells were imaged and counted under a microscope.
Subcutaneous and orthotopic ovarian xenograft tumor studies
All mice used in this study were purchased from GemPharmatech (Nanjing, China). Female nude mice, aged 6 weeks (weighing approximately 20 g), were housed and cared for at the animal center of Nanjing Agricultural University.
To establish subcutaneous xenograft tumor model, 14 healthy female Balb/c nude mice were chosen and assigned to two groups: control group (injected with control SKOV3 cells) and ov-IGF2BP2 group (injected with IGF2BP2-overexpressing SKOV3 cells). 9×106 cells suspended in 100ul PBS were subcutaneous injected into the right armpit of each mouse. Tumor volume was measured every 3 days. 3 weeks later, all mice were sacrificed and tumor weight was measured.
To establish orthotopic xenograft tumor model, 12 healthy female Balb/c nude mice were chosen and assigned to two groups. Nude mice were anesthetized by isoflurane inhalation, and after disinfecting the skin with iodophor, a 5 mm incision was made in the skin and abdominal wall, parallel and ventral to the spine, midway and between the last rib and the iliac crest. After pulling out the ovary, the cell suspensions (10 mL) containing 1 ´ 106 IGF2BP2-overexpressing or control SKOV3 cells, were inoculated inserting the needle at the junction between the bursa and the fat pad. Ovary was put back in place, and if no bleeding was noted, the incision on the muscle layer and body wall was closed separately.
Fluorescence in situ hybridization (FISH) and Immunofluorescence
The location of CKAP2L mRNA was detected by FISH according to the instruction of Fluorescent In Situ Hybridization Kit (C10910, RiboBio). First, cells were fixed with 4% paraformaldehyde and permeabilized with 0.1% Triton X-100. Then, cells were incubated with prehybridization solution followed by hybridization solution containing 0.5 μM probe and washed with washing solution. Finally, nucleus was stained with DAPI.
The location of IGF2BP2 protein was detected by Immunofluorescence. Cells were fixed with 4% paraformaldehyde, permeabilized with 0.1% TritonX-100, blocked in 5% goat serum and incubated with IGF2BP2 antibody (ab128175, Abcam) at 4℃ overnight. Then, cells were washed with PBS, incubated with Alexa Fluor Plus 647 goat anti-mouse IgG and stained with DAPI.
RNA and Protein stability assays
To evaluate RNA stability, medium of IGF2BP2-overexpressing SKOV3 cells and control cells were added with 5 ug/ml Actinomycin D (A9415, Sigma). Cells were collected at 0 min, 30 min, 60 min and 90 min to detect c-Myc mRNA expression, and collected at 0 h, 2 h, 4 h and 8 h to detect CKAP2L mRNA expression. RT-qPCR assay was used to detect mRNA expression in both groups.
To evaluate protein stability, medium of IGF2BP2-overexpressing SKOV3 cells and control cells were added with 20 ug/ml Cycloheximide (M4879, AbMole). The control group received constant volume of DMSO (Sigma-Aldrich, USA). Cells were collected at the specified time (0h, 4h, 8h, 12h). Western blotting assay was used to detect the level of CKAP2L protein in both groups.
Nascent protein synthesis assay
Nascent protein synthesis was detected by using Click-iT L-homopropargylglycine Alexa Fluor Protein Synthesis Assay Kits (C10428, Invitrogen) according to the manufacturer’s recommendations. Briefly, cells were cultured in L-methionine-free medium with L-homopropargylglycine at 37℃ for 30 min. Then, cells were washed once with PBS, fixed by 3.7% formaldehyde in PBS followed by a permeabilization step using 0.5% Triton X-100 for 20 min. Subsequently, Click-iT reaction cocktail mix was added with incubation for 30 min protected from light and washed with Click-iT reaction rinse buffer. Finally, nucleus was stained with high-content screening Nuclear Mask Blue Stain working solution for another 30 min and proceeded to imaging and analysis.
Data and software availability
Gene Expression Profiling Interactive Analysis (GEPIA) was used to analyze the gene expression in TCGA and GTEx databases. The University of Alabama at Birmingham CANcer data analysis Portal (UALCAN) was used to analyze the protein level in Clinical Proteomic Tumor Analysis Consortium (CPTAC) database. The m6A sites of CKAP2L mRNA were predicted online using the SRAMP website.
Statistical Analysis
All the analyses were performed by SPSS (Statistical Package for the Social Sciences) version 26.0 (Chicago, USA). Unless otherwise noted, the data are expressed as mean ± SD. The significance of difference was evaluated using Student’s t test. The Kaplan–Meier method and the Gehan-Breslow-Wilcoxon test were applied to estimate overall survival. The correlation between IGF2BP2 levels and clinical characteristics of OC tissues was analyzed by chi-square test. Two-way ANOVA was used to analyze the difference in the growth curves of subcutaneous xenografts in nude mice. P values < 0.05 were considered significant. β-Actin was used as the loading control. The relative expression level was normalized to β-Actin.