Chemicals
Okadaic acid (Purity≥95% by HPLC, Zaoyan, China) was dissolved in dimethyl sulfoxide (DMSO) at the stock concentration of 1 mM. The stock concentration of OA was then diluted with phosphate-buffered saline (PBS) to concentration of 100 nM.
Chick embryos
Fertilized chicken eggs were purchased from an avian farm of South China Agricultural University in Guangzhou, China. For early stage of chick embryos, early chick (EC) culture [28] was employed, in which a filter paper carrier was used to hold the early blastoderm when vitelline membrane was under tension, and the embryo grew on a substratum of agar-albumen. The agar-albumen medium was prepared as described in our previous study [19]. The HH1 chick embryos were incubated with PBS (control) or the culture media containing different concentrations of OA in an incubator (37 ℃ and 70% humidity) (Boxun, Shanghai, China) until the embryos developed to the desired stage (HH10). For the late stage of chick embryos, the eggs that have been pre-incubated for 1.5 days were administrated with the same volume of PBS or OA through pre-windowed small hole, and then incubated in an incubator (37℃ and 70% humidity) for further 3 days. The holes were sealed with UV-irradiated transparent tape to avoid dehydration and contamination.
Immunofluorescent staining
The HH 10 chick embryos were fixed in 4% paraformaldehyde (PFA) overnight at 4℃. The primary antibodies, including (NF, 1:200, Life Technologies, USA), Tuj1 (1:200, Neuromics, USA), (1:200, DSHB, USA), Pax7 (1:400, DSHB, USA), Pax6 (1:200, DSHB, USA), pHIS3 (1:400, Santa Cruz, USA) and c-Caspase3 (1:400, Cell Signaling Technology, USA), were employed in the immunofluorescent staining of whole-mount embryos. Briefly, the fixed HH 10 chick embryos were incubated with the primary antibody at 4℃ overnight on a shaker and then washed carefully in PBST (0.1% tween-20). Next, the embryos were washed with PBT for 5 min, then blocked in blocking buffer for 6 h. Subsequently, they were incubated with a related Alexa Fluor® 488 or 555 labelled secondary antibodies (1:1000, Invitrogen, USA) at 4℃ overnight on a shaker. Finally, all the chick embryos were counterstained with DAPI (1:1000, Invitrogen, USA) at room temperature for 40 min. After photographed, the stained embryos were embedded in a solution of 7.5% gelatin-15% sucrose (w/v) and stored at -80°C. Whereafter, the embedded embryo was sectioned at a thickness of 12 μm using a freezing microtome (Leica CM1900, Germany).
In situ hybridization
In situ hybridization of whole-mount chick embryo was carried out according to the method described previously [29]. Briefly, HH 10 chick embryos were fixed in 4% paraformaldehyde overnight at 4℃, washed twice with PTW (dissolve 0.1% tween-20 in PBS) for 5 min each time, and in a graded series of methanol (25%, 50%, 75%, 100%) for 5 min, respectively. After rehydrated in methanol (75%, 50%, 25%) and PTW for 5 min, respectively, the embryos were incubated in hybridization buffer for 5 h. Subsequently, antisense probes were added to the cultures, and the embryo were incubated overnight at 65℃. Digoxigenin-labeled antisense probes were generated to specifically detect mRNA levels of bone morphogenetic protein 4 (BMP4) and Sonic hedgehog (Shh). The primer sequences used in probes are summarized in Table 1. After hybridization, the embryos were washed by using post-hybridization buffer and TBST (dissolve 0.1% tween -20 in TBS) twice for 30 min at 65℃, respectively. After blocked with a blocking reagent (Roche, Switzerland) for 5 h, the embryos were incubated with anti-DIG (digoxigenin) antibody (1:1000, Roche, Switzerland) overnight at 4℃ on a shaker. Finally, the embryos were incubated in BCIP/NBT chromogen solution (Sigma, USA) at room temperature for staining. The stained embryos were pictured and sectioned at a thickness of 16 μm using a freezing microtome (Leica CM1900, Germany). Image-Pro Plus 7.0 (IPP 7.0) was employed to calculate the area of the target region (labelled with probes).
Photography
After immunofluorescent staining or in situ hybridization staining, the stained embryos and the regions of interest were pictured using a stereo-fluorescence microscope and processed with Image-Pro Plus 7.0 (IPP 7.0). The sliced embryos were pictured by using an Olympus IX51epi-fluorescent microscope, and the obtained pictures were analyzed with a CW4000 FISH Olympus software.
RNA isolation and quantitative real-time PCR analysis
Total RNA was extracted from the HH10 chick embryos using a total RNA kit (R6834-01, Omega, USA) based on the manufacturer’s instructions. Some of the RNA isolated was subjected to high-throughput sequencing, while others were used to reverse transcription. Agarose gel electrophoresis and NanoDrop 2000 (Thermo Scientific, USA) were employed to evaluate integrity, concentration, and purity of RNA for reverse transcription, respectively. First-strand cDNA was generated from 1 μg of total RNA by using a HiScript® II Q RT SuperMix for qPCR (+gDNA wiper) (Vazyme, China). The integrity, concentration, and purity of RNA for high-throughput sequencing were determined by an Agilent 2100 Bioanalyzer and RNA Nano 6000 assay kit (Agilent Technologies, CA, USA).
Specific primers employed in this study were designed by Primer 5.0. Reference genes were screened using geVanNorm, NormFinder and BestKepper. Among the six candidate genes, including glyceraldehyde 3-phosphate dehydrogenase (GAPDH), ubiquitin A-52 (UBA52), cyclophilin-A, succinate dehydrogenase complex subunit A (SDHA), ribosomal protein S15e (RPS15) and ribosomal protein L30 (RPL30). RPS15 and RPL30 exhibited the most stable expression. Therefore, the two genes were employed as reference genes to normalize expression of target genes. The primer characters used in qRT-PCR are summarized in Table 2. The PCR reaction system and procedure were performed as described in our previous paper [30].
The comparative Cq method was employed to analyze the relative expression of target genes as described by [31], in which multiple reference genes and inter-run calibration algorithms were considered. Standard curves were generated to check the efficiency of PCR amplification [32]. Amplification efficiency for each reaction should vary from 0.900 to 1.110, while correlation coefficients range between 0.990 and 0.999.
RNA-seq assay
The sequencing was conducted in BGI-Shenzhen (Shenzhen, China). Total RNA was qualified and quantified using a NanoDrop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, USA). Oligo (dt)-attached magnetic beads were used to purified mRNA. Purified mRNA was randomly fragmented into small pieces, and sequencing libraries were established using a MGIEasy RNA-seq library prep kit (BGI-Shenzhen, China) based on the manufacturer's instructions. The library quality was assessed on the Agilent Bioanalyzer 2100 system. The final library was then sequenced on BGISEQ-500 platform (BGI-Shenzhen, China) at paired-end mode (PE150).
Trimmomatic (Version 0.36) was employed to trim adapters and low-quality bases, and Q20 was chosen for quality trimming [33]. Bowtie2 (Version 2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of genes was calculated by RSEM (v1.2.12) [34]. Differential expressed genes (DEGs) analyses were performed using the DESeq2 (v1.4.5) [35] with |Fold Change | ≥2 and Q-values ≤ 0.001. Gene Ontology (GO, http://www.geneontology.org/) and the Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.kegg.jp/) enrichment analyses of annotated different expressed genes were performed with Phyper based on hypergeometric test. The significant levels of terms and pathways were corrected by Q-values with a rigorous threshold (Q value ≤ 0.05) by [36].
Western blot
Total protein concentration was measured by using a BCA Protein Assay Kit (Beyotime, China) according to the manufacturer’s instructions. The samples containing equal amounts of proteins were separated by 12% SDS-PAGE and transferred to PVDF membranes (Millipore, Bedford, USA). The membranes were blocked with 5% Difco™ skim milk (BD, USA), and then incubated with primary and secondary antibodies. All primary and secondary anti-bodies used were diluted to 1:1000 and 1:3000 in 5% skim milk, respectively. The protein bands were visualized with an ECL substrate kit (BIO-RAD, USA). The antibody-stripped membrane was then blocked again and re-incubated with other antibodies.
Detection of MDA content and SOD activity
Thirty HH10 chick embryos were harvested from each experimental group. The ten embryos within the same treatment were pooled together as one sample, and each group contains three pooled samples. The malondialdehyde (MDA) levels and superoxide dismutase (SOD) activities were detected in tree homogenized samples isolated from control or OA-treated groups according to the manufacturer’s instructions. MDA content was measured by using a lipid peroxidation MDA assay kit (Beyotime, China). SOD activity was determined by using a total superoxide dismutase assay kit with WST-8 (Beyotime, China). A microplate reader (Tecan Sunrise, Switzerland) was available for absorbance detection in the experiments.
Flow cytometry analysis
The HH10 chick embryos were harvested in a cell culture dish on a clean bench. After being rinsed with sterilized PBS (phosphate buffer saline), the tissue was transferred to a sterile centrifuge tube. To the centrifuge tube, trypsin (0.25%) was added, and the tissue was blown to homogenate with a pipette. Cell culture medium (Gibco, USA) was introduced to terminate trypsin digestion. Finally, the mixture was filtered with a 200-mesh sterile cell filter sieve (Jing An, China), and the filtered cell suspension was centrifuged at 1600 × g for 2 min, and liquid was discarded.
For the analysis of apoptosis, we re-suspended cells in 100 µl of binding buffer (BD, USA), then added 2.5 µl of Annexin V-FITC and propidium iodide (PI) to the cell suspension. Thereafter, another 200 µl of the binding buffer were added to the mixture. After being incubated for 15 min at room temperature in the dark, the cell suspension was transferred to the upper sample tube. For the detection of reactive oxygen species (ROS) content, we re-suspended cells in 200 µl of dichlorofluorescein diacetate (DCFH-DA) reagent and incubated at room temperature for 15 min in the dark. After being washed with sterile PBS, the cell suspension was centrifuged at 1600 × g for 5 min. Finally, we re-suspended cells in 300 µl of PBS and transferred it to the upper sample tube for ROS detection. Flow cytometry analysis was performed on the FACSCanto (BD, USA) system.
Statistical analyses
Statistical analyses were carried out by using GraphPad Prism 7 software (CA, USA). All data are presented as mean ± SD. After testing for homogeneity of variance, Student’s t-test was employed to check the differences between the control and OA-treated groups.