Tissue samples
Paired NSCLC and adjacent noncancerous lung tissue samples were collected with the informed consent of patients from the First Affiliated Hospital of Soochow University. The patients had been diagnosed with NSCLC based on their histological and pathological characteristics according to the revised International System for Staging Lung Cancer. They had not undergone chemotherapy or radiotherapy before tissue sampling. The tissue samples were snap frozen and stored in a cryogenic freezer at −80 °C. This study was approved by the Academic Advisory Board of Soochow University.
Cell culture
The human NSCLC cell lines A549, H1299, SPC-A1, and HCC827 and HEK293T cells were purchased from the Cell Bank of the Chinese Academy of Sciences (Shanghai, China). Cells were cultured in RPMI 1640 medium and DMEM supplemented with 10% foetal bovine serum (Gibco, Carlsbad, CA, USA) and L-glutamine (Invitrogen, Carlsbad, CA, USA) under standard cell culture conditions (5 % CO2/37 °C).
Immunohistochemical (IHC) assay
Immunohistochemical assays were performed as previously described29. In brief, slides were incubated with an anti-CPNE1 antibody (diluted 1:100; Abcam, shanghai, China) and an anti-NEDD4L antibody (diluted 1:100; Abcam, shanghai, China) overnight at 4 °C and were then incubated with the corresponding biotinylated secondary antibodies. Immunoreactions were visualized using a DAB kit (BD Biosciences, San Jose, CA, USA). Briefly, the proportion score was graded as follows: staining in 0% of the cells examined was counted as 0; 0.01%–25% was counted as 1; 25.01%–50% was counted as 2; 50.01%–75% was counted as 3; and 75%-100% was counted as 4. The staining intensity was graded as follows: 0, no signal; 1, weak; 2, moderate; and 3, strong. The histological score for each section was computed using the formula: histological score = proportion score × intensity score. A total score in the range of 0–12 was calculated and graded as follows: negative (-, score: 0), weak (+, score: 1–4), moderate (++, score: 5–8) or strong (+++, score: 9–12).
Plasmid construction and mutagenesis.
The CDS region of CPNE1 was amplified using cDNA from H1299 cells as the template and was cloned into FLAG-PCDH. For mutagenesis, Flag-CPNE1 was used as the template for PCR amplification. Amplification products were mixed with 2 µl of buffer and 1µlof DpnI restriction enzyme and incubated at 37 °C for 3 h. Then, the mixture was used for bacterial transformation, and sequencing was then conducted at Suzhou GENEWIZ Biotechnology. The primer sequences used for the construction of Flag-CPNE1 and mutagenesis are shown in Supplementary Table S2.
Protein stability assays
CHX, an inhibitor of protein synthesis, was used to determine the half-life of CPNE1. Cells were treated with CHX (100μg/ml) for 2, 4, 6, 8, and 10 h separately before protein extraction. CPNE1 degradation was analysed by Western blotting.
RNA interference
Two pre-designed small interfering RNA (siRNA) sequences corresponding to the target sequences were directly synthesized (GenePharma). The siRNA constructs are described as follows: siRNA-NEDD4L-1: 5'-GAGTACCTATGAATGGATT-3'(sense) and 5'-AATCCATTC ATAGGTACTC-3'(antisense); siRNA-NEDD4L-2: 5'-CAGAAATAATGGTCACAAA-3'(sense) and 5'-TTTGTGACCATTATTTCTG-3' (antisense); siRNA-CPNE1-1: 5'-GCAGGUCUCGCAU GAAUUUTT-3'(sense) and 5'-AAAUUCAUGCGAGACCUGCTT-3'(antisense). Transfection of siRNA into cells was performed with Lipofectamine 2000 according to the instructions of the manufacturer.
Western blot analysis and co-immunoprecipitation assay
Western blotting (WB) was performed as previously described [29]. The antibodies used for the analysis were anti-CPNE1 (Abcam, Shanghai, China) and anti-NEDD4L (CST, UK). For co-immunoprecipitation experiments, 2×105 HEK293T cells were transfected with the required plasmids for 48 h. Cells were harvested with 1mlof RIPA buffer. Equal amounts of protein were incubated with 2μg of M2 anti-Flag affinity agarose at 4 °C for 4 h with end-over-end rotation. The protein-antibody complexes were collected by centrifugation and washed 3 times with RIPA buffer. Then, the precipitates were analysed by Western blotting.
Immunofluorescence
In brief, cells were fixed with 4% formaldehyde for 15 min and blocked with 5% BSA for 30 min. Then, the cell climbing slices were incubated overnight with a rat anti-NEDD4L antibody (1:100; CST, UK) and a mouse anti-CPNE1 antibody (1:100; Santa, Temecula, CA). After washing with PBS three times, the cell climbing slices were incubated with a fluorescent secondary antibody at room temperature for 1h. Nuclei were then stained with DAPI. Finally, the slices were observed and images were acquired under a confocal microscope.
Cell proliferation analysis
Cell proliferation was evaluated using CCK-8 assays. Cells were digested and plated at a concentration of 3× 103 cells per well in 96-well plates under standard cell culture conditions. A Cell Counting Kit-8 (Boster, Wuhan, China) was used to detect cell proliferation after culture for 24, 48, and 72h.
Colony Formation Assay
A colony formation assay was used to confirm malignant transformation. Three thousand cells were seeded in 3ml of RPMI 1640 medium supplemented with 10% foetal bovine serum and incubated at 37 °C with 5% CO2. The number of colonies formed after 14 days was counted using ImageJ.
Migration and invasion assays
Cell motility was assayed using 12-well transwell plates (Corning) as described before [28]. Experiments were performed in 24-well transwell plates with 8-µm pore-size chambers. The difference between the cell migration and invasion assays was whether the top surface of the filter was pre-coated with Matrigel. In brief, lung cancer cells (5× 104) were plated in the upper compartment of the transwell chamber in medium containing 1% FBS. Then, 0.8ml of complete medium was added to the lower compartment of the chamber. Cells on the upper surface of the filter were removed after 24 hours in both the migration and invasion assays. Images were acquired using a microscope (CKX41, Olympus)
Statistical analysis
We used Student’s t-test (two-tailed) and two-way ANOVA to analyse the results when required. P<0.05 indicates thatadifference between groups was significant. All data were analysed using GraphPad Prism 8.