Tissue specimens and serum samples
Six SCLC tissues and five normal lung tissues were obtained from Beijing Shi Ji Tan hospital. All samples were confirmed as SCLC by pathologic examination. A paraffin-embedded tissue specimen was available for each included patient. Forty-six serum samples from SCLC patients and 18 normal controls were collected from Beijing Chest Hospital. All patients were informed consent prior to the collection of specimens according to the institutional guidelines. Under the protocol approved by the Institutional Review Board, informed consents were obtained from the patients or their guardians.
Cell culture
The lung cancer cell lines NCI-H446 were obtained from Chinese National Infrastructure of Cell Line Resource. Cell lines were maintained in RPMI1640 supplemented with 10% FBS (PAN). Other cell lines, including 293T, were cultured in DMEM and supplemented with 10% FBS. All cell lines were cultured at 37℃ with 5% CO2.
Lentivirus package and stably transfected cell lines construction
The overexpression lentivirus vector of HuD (HuD-OE), the knockdown (HuD-KD), overexpression of LYPLAL1-DT and their negative controls (HuD-OC, HuD-KC, LYPLAL1-DT) were constructed. For constructing stable expressing cells, SCLC cell lines H446 were respectively infected with lentivirus vectors for 48h. Then, cells were selected with 2 μg/ml puromycin (Invivogen, Cat#ant-pr-1) for 3 weeks. Further, realtime RT-PCR was used to examine the overexpression and knockdown efficiency of these cells.
Transient transfection
The PFN2 expression vector pLV-PFN2 and control vector were purchased from Abcam company. For the knockdown of PFN2, siRNAs or negative control siRNA (Abcam) were transfected into the cells by using Lipofectamine 3000 (Invitrogen, CA, USA, Cat# L3000015). The miR-204-5p mimic and negative controls were purchased from HANBIO Ltd (HANBIO, Shanghai, China). They were transfected at a final concentration of 50nM via an RNAfit reagent (HANBIO, Shanghai, China), following the manufacturer’s instruction.
Cell proliferation assay
The cell proliferation rate was assessed using a real-time cell analyzer (RTCA). Cells were suspended in the culture medium, 8000 cells per well of the E-plate with 4 replicates. After incubation at room temperature for 15 min, the E-plate was placed onto the RTCA Station in the incubator for continuous recording. Cell index values were recorded every 15 min for 72 h.
Western blot analysis
The protein samples were separated using sodium dodecylsulphate polyacrylamide gel electrophoresis and transferred onto poly(vinylidene fluoride) membranes (Millipore, Cat#IPVH00010). The membranes were blocked with 5% skimmed milk (BD, Cat#232100) for 1h at room temperature and incubated with primary antibody overnight at 4 °C. The membranes were subsequently incubated with secondary antibody for 1h at room temperature. Protein signals were detected using enhanced chemiluminescence. The antibodies used in this study are listed in Table 1.
Table 1. Antibodies used in the study
Protein names
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Manufacturer
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ELAVL4(HuD)
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Proteintech, Cat#24992-1-AP
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PFN2
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Abcam, Cat#ab191054
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GAPDH
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CST, Cat#5174
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PFN1
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Abcam, Cat#ab50667
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Mouse IgG
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Proteintech, Cat#B900620
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Monoclonal ANTI-FLAG
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SIGMA, Cat#F1804-50UG
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Quantitative PCR analysis
Total RNA was extracted using TRIzol (Vazyme, Cat#R401-01) and reverse transcribed using PrimeScriptTM RT Kit (Abcam, Cat#G490). qRT-PCR was performed using EvaGreen 5×qPCR MasterMix (Abcam, Cat# MasterMix-5S). mRNA level was quantified by the 2-ΔΔCt algorithm with β-actin as the normalizer gene. All the primers used are found in Table 2.
Table 2. Primer sequences for qPCR
Gene names
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Forward primers
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Reverse primers
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PFN2
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5’-AGCAAGGTGCCGGTGTACA-3’
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5’-AACCATGCGCTACAAAAGGAA-3’
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HuD
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5’-CGGGATCCGAGCCTCAGGTGTCAAATG-3’
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5’-CCGCTCGAGGTCAGGACTTGTGGGCTTT
GTGTG-3’
|
LYPLAL1-DT
|
5’-CAGCCTCGTGTGGACTTCTG-3’
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5’-CTGCAAACATCCTGTGCGAG-3’
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miR-204-5p
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5’-CGCGTTCCCTTTGTCATCCT-3’
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5’-AGTGCAGGGTCCGAGGTATT-3’
|
Migration and invasion assay
Migration assays were performed using a transwell plate (Corning, Cat#3422),invasion assay were performed using a transwell plate with matrigel (Corning, Cat#354480). Cells at the density of 2×104/200 μL of serum-free RPMI 1640 were added into the upper chamber, and 500 μL of the complete medium was placed into the lower chamber. The cells were incubated at 37 °C for 24h. Migrated cells on the bottom surface of the filter were fixed, stained with 0.1% crystal violet, and the average number of random five fields under a microscope was calculated. All assays were repeated three times.
Confocal immunofluorescence
Cells were seeded in glass bottom cell culture dishes (NEST, Cat#801001) at 2×105 cells/well, fixed with 4% paraformaldehyde and permeabilized in 0.1% Triton X-100/PBS. Coverslips were blocked for 1h by 1% BSA, washed and exposed to a 1:100 dilution of HuD antibody (Proteintech, Cat#24992-1-AP) overnight at 4 °C. Then the cells were incubated with 1 mg/ml diluted Hochest for 5 min at room temperature. The cells were photographed using scanning confocal microscope.
Actin cytoskeleton staining
Actin cytoskeleton staining was performed after scratching using DyLight™ 594 Phalloidin (CST, Cat#12877) according to the manufacturer's instructions. The cells were stained with phalloidin and the nuclei were stained with Hoechst 33358. The cells were then photographed with fluorescent microscope with at least 5 random fields along the scratch lines in each culture dish were taken. The number of cells with lamellopodia was counted and the percent of cell with lamellopodia was calculated via analyzing 40× micrographs.
Subcellular Isolation
The cell fractionation assay was performed according to the manufacturer's instructions (CST, Cat#9038). In brief, H446 cells were suspended in 0.5 ml of cold 1×PBS, aliquoted 100 µl of cell suspension for the whole cell lysate (WCL), sonicated and centrifuge for 5 min at 500 g. The pellet was resuspended in 500 μl of Membrane Isolation Buffer and centrifuged for 5 min at 8,000 g. The pellet was resuspended in 250 μl of Cytoskeleton/Nucleus Isolation Buffer.
RNA immunoprecipitation (RIP) analysis
RIP analysis was performed using Anti-Flag antibodies and Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore, Billerica, MA, USA, Cat#17-700) following the manufacturer’s protocol. Cell lysate was incubated with anti-HuD or Ago2 antibody (CST, USA) and IgG antibody at 4°C for 6h. A protein-RNA complex was captured and digested with 0.5 mg/ml proteinase K containing 0.1% sodium dodecyl sulphate (SDS) to extract RNA. The magnetic beads were repeatedly washed with RIP washing buffer to remove non-specific adsorption as much as possible. Finally, the extracted RNA was subjected to mRNA level determination using qRT-PCR.
mRNA stability assay
ActD (5 μg/ml, MCE, Cat#HY-17559), inhibiting the de novo RNA synthesis, was added to HuD-OE cells or its control cells. Total RNA was extracted at the indicated time points and PFN2 or expression was evaluated by qRT-PCR assay. The mRNA decay rate was calculated by comparing to the initial mRNA level before ActD addition.
Dual-luciferase reporter gene assay
The 3’-UTR of PFN2 mRNA and the mutant were cloned and inserted into pGL3 plasmid. Dual-luciferase reporter assay was performed following the manufacturer’s instruction. The full length of the 3’-UTR of mRNA, the first section of 3’-UTR (S1), the middle section of 3’-UTR (S2) and the last section of the 3’-UTR (S3) were cloned and inserted into the Xbal-Fsel restriction site downstream to firefly luciferase (pGL3 promoter plasmid). 239T cells were seeded on 6-well plate and co-transfected with the constructed recombinant (2μg/well) or control plasmids and Renilla luciferase reporter (0.1μg/well) or HuD overexpression plasmids. After 48h, luciferase and Renilla luciferase activities were separately measured using the Dual-Luciferase Reporter Assay Kit following the manufacturer’s instruction (Vazyme, Cat# DL101-01).
CCK-8 and colony formation assay
For CCK-8 assays, cells were seeded into 96-well plates at a density of 1,000 cells/well, and 10μL of CCK-8 (Vazyme, Nanjing, CHINA) was added per well in days 0 to 5. The cells were subsequently incubated at 37℃ for 2 hours, and the optical density was measured at 450nm. For the colony formation assays, 600 cells were inoculated into 6-well plates and cultured at 37℃ for 10 days. The colonies were the fixed with methanol and stained with crystal violet.
Tumor xenograft model
Four-week-old NOD-SCID mice (Weitonglihua Biotechnology) were raised under specific pathogen-free conditions. HuD-OC and HuD-OE–transfected cells or LYPLAL1-DT-OC and LYPLAL1-DT-OE were, respectively, injected subcutaneously into the flank region of the mice (5×106 cells/150 μL per flank, n = 5). The tumor volumes were measured every 7 days after inoculation. Eight weeks after injection, the mice were sacrificed, and the tumor nodules were harvested. The tumors, lungs, liver, and kidneys were isolated from the mice for further analysis. The protocol was approved by the Committee on the Ethics of Animal Experiments of Capital Medical University.
IHC
Small cell lung cancer tissue sections were cut into 5-μm sections and then analyzed by IHC using antibodies against HuD (1:50; CST). Brown signals in the nuclei and cytoplasm indicated positive immunostaining. Tumor tissues from xenograft mice were fixed and incubated with anti-HuD, anti-Ki-67 or anti-PFN2 antibodies overnight at 4 ℃, and normal goat serum was used as a negative control. IHC staining was visualized using the DAKO REAL EnVision Inspection System (DAKO). The fluorescence intensity and positive staining cell number were calculated.
Statistical analysis
Statistical analyses were performed using Graphpad Prism. Data were presented as mean ±SEM, and the statistical significance was determined by Student’s t-test (t-test) or two-way ANOVA as indicated in the figure legend. Sample size (n) is also reported in the figure legend for each experiment, with n as the number of identically treated replicates. All tests were two-tailed, and P values < 0.05 were considered statistically significant.