2.1 BMSC isolation and culture
BMSCs from rats were isolated and cultured according to previously described protocols 15. Briefly, the femurs and tibias were bluntly dissected aseptically after the rats were sacrificed by cervical dislocation. The bone marrow was then flushed quickly with DMEM containing 10% fetal bovine serum (FBS, HyClone, Logan UT, USA), 100 U/mL penicillin, 100 U/mL streptomycin and 200 U/mL heparin (Sigma, St Louis, MO, USA). The primary cells were resuspended in DMEM after centrifugation at 2000 rpm for 10 min and then cultured at 37°C in a humidified atmosphere of 5% CO2. Twenty-four hours later, the nonadherent cells were removed. The DMEM was refreshed every 3 days, and the cells at passage 2 or 3 were used for future experiments. Each experiment was repeated 3 times using 3 different BMSCs strains isolated from 3 rats. This study was conducted under the approval of the Animal Research Ethical Committee of the Ninth People's Hospital Affiliated with Shanghai Jiao Tong University School of Medicine.
2.2 Lentiviral packaging and BMSC transduction
Human embryonic kidney 293T cells (HEK293T) were used for lentiviral packing. The cells were cultured in 10 cm dishes for 2-3 days until they reached 90-95% confluency. The recombinant virus plasmid pLV-nol3-EGFP, which encodes the full-length nol3, and the control vector pLV-EGFP, together with packaging plasmids (pLP1, pLP2 and pLP/VSVG), were cotransfected into HEK293T cells using Lipofectamine™ 2000 (all from GeneChem Co., Ltd., Shanghai, China). After 48 h of transduction, the lentiviral particles contained in the supernatant of 293T cells were harvested and then concentrated by passing through a 0.45 μm filter. The concentrated solutions were then added to cultured BMSCs at a variety of multiplicities of infections ranging from 0 to 100. After 72 h, the transduction efficiency was assessed via fluorescence microscopy and qRT-PCR.
2.3 Analysis of cell proliferation
Cell Counting Kit-8 (CCK-8, Dojindo, Kumamoto, Japan) was used to detect cell proliferation. Cells were seeded on 96-well plates at a density of 1.5 × 103 cells/well, and the proliferation was detected for 72 consecutive hours. Ten microliters of CCK-8 reagent with 100 μl of DMEM was added to each well and then incubated at 37°C for 2 h. The absorbance was then measured with a microplate reader (Bio-Tek, Winooski, VT, USA) at a wavelength of 490 nm according to the manufacturer’s instructions.
2.4 Analysis of cell apoptosis
Cells were seeded on 6-well plates at a density of 1x105 cells/well and then cultured for 72 h. The supernatant and adherent cells were collected and then centrifuged at 1500 rpm for 10 min at 4°C. For detection of cell apoptosis, the BD Pharmingen™ APC Annexin V Apoptosis Detection kit (BD Biosciences, Franklin Lakes, NJ, USA) was used according to the manufacturer’s protocol. Briefly, the cells were washed with cold PBS twice and resuspended in 500 μL of binding buffer. Then, 5 μL of Annexin V-APC solution was added to the solution and incubated in the dark for 15 min at 37°C. Finally, 1 μL of energy-coupled dye (ECD-A) solution was added for the subsequent flow cytometry for cell apoptosis analysis.
2.5 Immunofluorescence staining
Cells were seeded at a density of 2.5×104 cells/well in 24‑well plates. After the corresponding treatment, the cells were washed with PBS, fixed with 4% paraformaldehyde for 15 min at 4°C and then permeabilized with 0.5% PBST (PBS containing 0.5% Triton X-100). Next, the cells were blocked with 5% bovine serum albumin for 1 h at room temperature and then incubated with anti-OCN antibodies for 1 h at 37°C. The cells were washed twice with PBST and incubated with secondary antibody for 1 h at room temperature. After two washes with PBST, the nuclei were stained with DAPI (Invitrogen) for 5 min. Photographs were visualized under a light microscope (Olympus Corporation, Tokyo, Japan).
2.6 Alkaline phosphatase activity (ALP) detection and Alizarin red staining (ARS)
Cells were seeded at a density of 2.5×104 cells/well in 24‑well plates and cultured for 7 days. For ALP staining, the cells were washed twice with PBS and fixed with paraformaldehyde for 15 min at 4°C. Then, paraformaldehyde was removed, and the cells were washed again twice with PBS. Then, BCIP/NBT solution was added to each well and incubated in the dark for 30 min. All procedures were performed according to the protocols of the ALP staining kit (Beyotime Institute of Biotechnology, Shanghai, China). For ALP activity detection, a BCA protein assay kit (Beyotime Institute of Biotechnology, Shanghai, China) was used, and the ALP levels were normalized to the total protein content and are described as the percentage of total protein.
For ARS measurements, the cells were cultured in DMEM for 21 days, washed twice with PBS, and then fixed with paraformaldehyde for 15 min at 4°C. The paraformaldehyde was removed, and the cells were washed twice again with PBS. Then, the cells were stained with 40 mM ARS for 20 min at room temperature. The stain was desorbed with 10% cetylpyridinium chloride (Sigma) for 1 h, and the solution was collected and equally distributed on a 96-well plate. Finally, a spectrophotometer (Bio-Tek) was used to determine the concentration of Alizarin red at 590 nm wavelength.
2.7 Real-time PCR analysis of gene expression
TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.) was used to extract total cellular RNA. Reverse transcription was performed using the PrimeScript RT reagent kit (TaKaRa Bio, Inc., Otsu, Japan). Gene-specific primers were synthesized commercially (Shengong Co., Ltd., Shanghai, China), and their sequences are listed in Table 1. In one reaction, 10 μl of SYBR Premix Ex Taq kit (TaKaRa Bio, Inc.) was used to amplify 1 μl of cDNA (mixed with 8 μl of distilled water and 0.5 μl of each primer). The Bio-Rad iQ5 real-time PCR system (Bio-Rad Laboratories, Inc., Hercules, CA, USA) was then used to detect gene expression. All relative gene expression values were normalized to β‑actin based on the 2‑ΔΔCq method.
2.8 Western blot analysis
For Western blot analysis, cells were lysed with RIPA buffer supplemented with a protease inhibitor cocktail after culture for 7 days. The obtained protein concentrations were measured by a BCA protein assay kit (Beyotime, Shanghai) according to the manufacturer’s instructions, and then, equal amounts of protein from different samples were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred to polyvinylidene difluoride membranes. Membranes were incubated overnight at 4°C with the following primary antibodies: rabbit anti-rat Akt, rabbit anti-rat pi-Akt and rabbit anti-rat pi-PI3K (1:1000, Cell Signaling Technology, Inc.). Finally, the membranes were visualized with horseradish peroxidase-conjugated goat anti-rabbit using ECL Plus reagents and an UVItec Alliance 4.7 gel imaging system.
2.9 Ectopic new bone formation and cell apoptosis analysis in nude mice
Cells were seeded in calcium phosphate cement (CPC) scaffolds after being cultured for seven days under normoxic conditions. A total of 14 constructs were divided into two groups: Group A, CPC/BMSC-CON n=7; Group B, CPC/BMSC-NOL3 n=7. Then, they were inserted into the subcutaneous space of nude mice. Ten weeks later, the mice were sacrificed by an overdose injection of ketamine, and the implanted specimens were harvested. After 4% paraformaldehyde fixation, the specimens were decalcified in 20% EDTA (pH=7.4) for 10 days followed by paraffin‑embedding, sectioning and staining with HE (hematoxylin and eosin). Immunohistochemical staining was carried out with a primary antibody against OCN (Cell Signaling Technology, Inc.). Cell apoptosis was detected by using a TUNEL kit (Cell Signaling Technology, Inc.). Tissue slides were visualized under a light microscope (Olympus Corporation, Tokyo, Japan), and Image-Pro 6.0 software (Media Cybernetics, Inc., Rockville, MD, USA) was used to perform histomorphological analysis. New bone formation was defined as the percentage of observed new bone area in the entire implant.
2.10 Surgical procedures
Cells were loaded in the CPC scaffold at a density of 2.0x105 cells/ml before being implanted into the defect area of the rat calvarium. The scaffold was shaped into a cylinder (5 mm×2 mm3) and had an average pore size of 400 mm±50 mm and 75% porosity. A rat calvarial defect model was created to evaluate the in vivo new bone formation of BMSCs. The surgical procedures were performed according to previously described protocols.16 Briefly, the rats were placed in a prone position after anaesthetization by intraperitoneal injection of ketamine. A 1.5 cm long sagittal incision was made on the scalp, and then, the calvarium was exposed by blunt dissection. Then, defects 5 mm in diameter were created bilaterally by using a trephine bur (Fine Science Tools, Foster City, CA, USA). The BMSC/CPC constructs were inserted into the defective area, and the wound was tightly closed. The rats were housed in ventilated rooms with access to sterilized water and food after the surgery. Nine 12-week-old male Sprague Dawley rats (SD rats) were randomly divided into three groups: (1) CPC with BMSC-CON (n=3); (2) CPC with BMSC-NOL3 (n=3); (3) CPC alone (n=3).
2.11 Sequential fluorescence labeling
Polychrome sequential fluorescence labeling was used to characterize the mineralizing tissues. At 2, 4 and 6 weeks after the operation, different fluorochromes were injected intraperitoneally in the following sequence: tetracycline hydrochloride (25 mg/kg, Sigma Aldrich), Alizarin red S (30 mg/kg, Sigma Aldrich, USA), and calcein (20 mg/kg, Sigma Aldrich).
2.12 Sample preparation
The rats were sacrificed by an overdose injection of ketamine 8 weeks after surgery. The calvarium with the implants was harvested and fixed in 10% paraformaldehyde for the following histological evaluation.
2.13 Histological evaluation
Three specimens from each group were dehydrated in ascending concentrations of ethanol and then embedded in polymethylmethacrylate (PMMA). The specimens were cut into 150 mm thick sections by using a saw microtome (Leica, Hamburg, Germany) and polished to a final thickness of approximately 40 mm. A confocal laser scanning microscope (Leica TCS, Sp2 AOBS) was used for fluorescence labeling detection. The excitation/emission wavelengths used to observe fluorochromes were 405/580 nm, 543/617 nm and 488/580 nm for tetracycline (yellow), Alizarin (red) and calcein (green), respectively. Then, the sections were stained with Van Gieson’s picro fuchsin for mineralized bone tissue visualization. The images were acquired by using a fluorescence microscope (Olympus, Japan). Histomorphometric analysis was conducted by Image-Pro Plus 6.0 software. New bone formation was defined as the percentage of observed new bone area in the entire implant.
2.14 RNA-seq and Bioinformatics
Three paired samples were used for RNA-sequencing and bioinformatic analysis. Total RNA was extracted from BMSCs transfected with lenti-virus and then was converted into cDNA. The tophat software (v2.1.0) was used to locate clean reads on the rat reference genome (RNO_6, Ensembl), allowing up to four base mismatches, and using default parameters for the rest of the parameters. The HTSeq tool (V0.6.1p2) was used to quantify gene expression based on rat genome annotation information (RNO_6) provided by Ensembl database. We analyzed the differential expression of genes by MARS (MA-plot-based method with Random Sampling model) using R's DEGSEq software package, and then screened the significant differential expression genes between these two groups. The threshold was log2FC (normalized) > 0.585, and the Q value corrected by BH method was less than 0.001. The GO function enrichment and KEGG pathway analysis of differentially expressed genes were performed using DAVID (v6.8) online tools. The parameters were set as the number of enriched genes count >=2, and the hypergeometric test significance threshold P value < 0.05 (considered as the result of significant enrichment).
2.15 Statistical analysis
Statistical analysis was performed with the GraphPad Prism 6 statistical software package. Data are expressed as the mean ± standard deviation (SD). Differences between two groups were analyzed by independent sample t-tests. Statistically significant differences were defined at *p < 0.05 and **p < 0.01.