3.1. Cell Culture
Human normal liver epithelial cells THLE-2 (CL-0833), HCC cell lines HCCLM3 (CL-0278) and Huh-7 (CL-0120) were from Pricella Biotechnology (Wuhan, Hubei, China). THLE-2 cells were maintained in THLE-2-specific medium (CM-0833, Pricella Biotechnology). Hepatocellular carcinoma cells were grown in complete medium containing 10% fetal bovine serum (FBS, A5256701, Gibco, Grand Island, NY, USA), 1% penicillin/streptomycin (15140122, Gibco), and 89% DMEM (12491015, Gibco). The incubation temperature was 37°C in an environment containing 5% CO2. Fluid was changed 2-3 times per week and the passaging ratio was 1:3.
Ubiquitin-specific protease 7 overexpression plasmid (OE-USP7), USP7 short hairpin RNA (sh-USP7), and their controls (OE-NC, sh-NC) were synthesized by Sangon Biotech Co. Ltd. (Shanghai, China). Hepatocellular carcinoma cells were digested by 0.25% trypsin (T2605, Sigma-Aldrich, St. Louis, MO, USA), then inoculated in 24-well plates (2 × 104/well). On the second day, the transfection system was prepared according to the guidelines provided for Lipofectamine 3000 (L3000001, Invitrogen, Carlsbad, CA, USA). Fifty microliters of the configured transfection system was mixed well with HCC cells in a 24-well plate, and after 48 h of reaction, the cells were lysed with RIPA lysis buffer (15596026, Invitrogen). Proteins were fully extracted, and the effectiveness of the transfection was assessed by measuring USP7 protein level in the cells, and subsequent cellular experiments were performed.
For signaling pathway exploration, HCC cells were exposed to the PI3K activator 740Y-P (30 μM, HY-P0175, MedChemExpress, Monmouth Junction, NJ, USA) or the PI3K inhibitor LY294002 (25 μM, HY-10108, MedChemExpress) for 1 h, then transfected with OE-USP7, recorded as OE-USP7+LY294002 group or OE-USP7+740Y-P group (
28,
29).
3.2. Immunofluorescence
Hepatocellular carcinoma cells were seeded into 6-well plates (with built-in sterile coverslips), and when the cells grew to a density of 50%-60%, the cell crawls were treated with 4% paraformaldehyde (441244, Sigma-Aldrich) for 20 min. After that, 0.3% Triton X-100 (T824275, Macklin Inc., Shanghai, China) was added to the surface of cell crawls and incubated for 10 min to increase the permeability of the cell membrane. It was blocked with 5% bovine serum albumin (BSA, A801320, Macklin Inc.) for 30 min. Subsequently, cells were exposed to primary antibodies USP7 (PA5-34911, 1:200, Invitrogen, Carlsbad, CA, USA), E-cadherin (PA5-32178, 1:200, Invitrogen), and Vimentin (PA5-27231, 1:500, Invitrogen) at 4°C overnight. The following day, cells were exposed to secondary antibody goat anti-rabbit IgG (65-6111, 1:2000, Invitrogen) for 60 min in the dark at 37°C. After that, cells were incubated with DAPI solution (C1005, Beyotime, Shanghai, China) for 10 min, and then observed through a BX53 (LED) fluorescence microscope (Olympus, Tokyo, Japan).
3.3. Cell Counting Kit-8 Assay
Huh-7 and HCCLM3 cells transfected with OE-USP7, sh-USP7, or their control vectors in good growth status were taken and seeded into 96-well plates (1.0×104 cells/well, 100 μL). Once the cells had completely adhered, 10% cell counting kit-8 (CCK-8) reagent (96992, Sigma-Aldrich) was added at 24, 48, 72, and 96 h. After mixing well, the cells were allowed to incubate for 2 h at a temperature of 37°C, and OD450 values were measured through a microplate reader (1410101, Thermo Fisher Scientific, Waltham, MA, USA). In addition, cell morphology was observed with a CX33 light microscope (Olympus) to assess cell viability.
3.4. Transwell Assay
Matrigel (HY-K6002, MedChemExpress) was melted at ambient temperature and mixed with culture medium. One hundred microliters of diluted matrix gel was aspirated and uniformly covered on the basement membrane of the Transwell (8 μm, Corning, Tewksbury, MA, USA). After the matrix gel solidified naturally for 30 min at 37°C, the chambers were transferred to 24-well cell culture plates. Subsequently, complete medium (500 μL) was dispensed into the lower chamber, followed by the addition of 100 μL of HCCLM3 and Huh-7 cell suspensions to the upper chamber, then incubated for 24 h at 37°C. After incubation, Transwell chambers were carefully retrieved. Subsequently, the chambers were rinsed twice with PBS, and gently wiped with a sterile cotton swab to remove non-invaded cells adhering to the upper surface of the matrix gel. Subsequently, the chambers were immersed in 4% paraformaldehyde for fixation for 15 min and rinsed under running water for 2 min. The invaded cells were exposed to 0.1% crystal violet (C805211, Macklin Inc.) for 15 min, then rinsed slowly with running water for 2 min and dried naturally. A light microscope was used to capture images of five randomly chosen fields of view from each chamber, and the invaded cell count was recorded using Image J 1.54h software (Wavne Resband, National Institute of Mental Health, USA).
Transwell migration assay did not require the addition of Matrigel matrix gel to the chambers, and all other experimental procedures and analysis were aligned with those of the invasion assay.
3.5. Flow Cytometry
HCCLM3 and Huh-7 cells were collected by centrifugation in 5 mL centrifuge tubes. Cells were resuspended by adding PBS buffer containing 1% FBS to make a single-cell suspension (approximately 1.0×10
6/mL). FITC-labeled CD44 antibody (11-0441-82, Invitrogen) and PE-labeled CD133 antibody (12-1331-82, Invitrogen) were added and mixed well, then incubated at 4°C for 30 min under light protection (
30). The samples were then transferred to a BD FACSCaliburTM flow cytometer (BD Biosciences, San Jose, CA, USA) for fluorescence cell sorting analysis. Subsequently, the proportion of positive cells was quantified using FlowJo software (version 10.8, BD Biosciences).
3.6. Cancer Stem Cells Sphere Formation Assay
Tumor cell spheroid formation assay is the gold standard for measuring tumor cell stemness. DMEM medium was supplemented with insulin (4 μg/mL, P3376, Beyotime), 1 × B-27 (17504044, Gibco), human recombinant epidermal growth factor protein (EGF, 20 ng/mL, HY-P72982, MedChemExpress), and human recombinant fibroblast growth factor protein (FGF, 20 ng/mL, GF003, Sigma-Aldrich), and formulated into cell-forming medium (
31). After Huh-7 cells were digested and resuspended, they were rinsed twice with PBS and inoculated in 24-well ultra-low adhesion culture plates (1×10
4/well). After 7-10 days of culture, most spheroplasts were observed to grow to more than 100 μm for counting, and the spheroplast formation efficiency was calculated (
32).
3.7. Subcutaneous Tumor Formation in Nude Mice
Male Balb/c nude mice (15 - 19 g, 6 weeks old) were from Vitalriver (Beijing, China). The animals were maintained at 22°C, and were free to eat and drink, and the experiments were conducted after one week of acclimatization. Animals were split into 4 groups (n = 6) using a random number table method, and 200 μL of Huh-7 cell suspension transfected with OE-USP7, OE-NC, sh-USP7, or sh-NC was injected into the right axilla of nude mice in each group (5.0×10
6 cells/mice), respectively (
33). On days 7, 14, 21, and 28 after the Huh-7 cell suspension was injected, the dimensions of subcutaneous tumors were examined using vernier calipers. On the 28th day, all nude mice underwent execution via an intraperitoneal injection of sodium pentobarbital (100 mg/kg). The tumors were entirely excised using tissue shears, then weighed and photographed for record. To minimize bias, a double-blind approach was adopted. All the researchers involved in animal breeding, model construction, behavioral assessment, and pathological section staining were unaware of the grouping situation.
3.8. Immunohistochemistry
Mouse tumor tissues were immersed in 4% paraformaldehyde for 24 h to fix them, followed by a dehydration procedure with graded ethanol, embedding in paraffin, and sectioning into 4 μm-thick slices for subsequent analysis. Subsequently, sections were put into xylene (X821391, Macklin Inc.) for deparaffinization, hydrated in gradient ethanol, and then washed using distilled water. The antigens were microwave repaired by placing sections in citric acid solution (pH = 6, 0.1 mol/L). The tissue sections were incubated in 3% H2O2 solution for 30 min, and then covered evenly with 5% BSA and blocked for 30 min. Subsequently, Ki67 primary antibody (PA1-38032, 1:100, Invitrogen) was introduced and allowed to incubate at 37°C for 90 min. Subsequently, sections were incubated with horseradish peroxidase (HRP)-labeled goat anti-rabbit IgG (31460, 1:500, Invitrogen) for 20 min at 25°C. The color development reaction was carried out using DAB (P0203, Beyotime), and the color development was terminated with distilled water when the color development reached the desired effect. Hematoxylin (H9627, Sigma-Aldrich) was restained for 5 min, rinsed in distilled water, and the samples were visualized using a fluorescence microscope after blocking with Neutral Balsam (C0173, Beyotime).
3.9. Western Blot
Tumor tissues were cut with tissue shears, ground thoroughly, and mixed well with RIPA lysis buffer. Hepatocellular carcinoma cells were rinsed two times with PBS, and mixed well with RIPA lysis buffer. After completion of lysis, protein contents in tissues and cells were examined through the bicinchoninic acid (BCA) protein assay kit (P0012, Beyotime). Next, proteins were separated by SDS-PAGE electrophoresis, and the proteins were transferred to PVDF membranes (Invitrogen), then blocked with 5% BSA for 2 h. Subsequently, the membranes underwent an overnight incubation with primary antibodies SOX2 (PA1-094, 1:1000, Invitrogen), USP7 (PA5-34911, 1:2000, Invitrogen), E-cadherin (PA5-32178, 1:500, Invitrogen), Vimentin (ab16700, 1:1000, Abcam, Cambridge, MA, USA), N-cadherin (PA5-19486, 1:100, Invitrogen), Snail (PA5-23482, 1:100, Invitrogen), CD44 (PA5-21419, 1:2000, Invitrogen), C-Myc (PA5-85185, 1:500, Invitrogen), CD133 (PA5-38014, 1:100, Invitrogen), Octamer-binding transcription factor 4 (OCT4, PA1-16943, 1:500, Invitrogen), Nanog (PA1-097, 1:1000, Invitrogen), Krüppel-like factor 4 (KLF4, PA5-27441, 1:5000, Invitrogen), p-AKT (Ser473) (9271S, 1:1000, cell signaling technology, Danvers, MA, USA), glycogen synthase kinase-3β (GSK3β, ab32391, 1:5000, Abcam), AKT (ab81283, 1:5,000, Abcam), β-catenin (MA5-34961, 1:500, Invitrogen) or p-GSK3β (44-604G, 1:1000, Invitrogen) at 4°C. The following day, the membranes were rinsed 3 times, and incubated with the secondary antibody (ab205718, 1:10000, Abcam) for 2 h. Developing solution (HY-K2005, MedChemExpress) was prepared, dropped evenly on the membrane, and then analyzed using the 5200 Multi gel imaging system (Tanon, Shanghai, China). The internal reference GAPDH (ab128915, 1:10000, Abcam) was employed for normalization. Images were processed using Image J 1.54 h software to quantify the gray values of each protein band, from which relative levels were determined by normalizing to the GAPDH signal.
3.10. Statistical analysis
All experimental data were derived from at least three independent replicates and are presented as the mean ± standard deviation. Statistical analyses were performed using SPSS 26.0 software (IBM SPSS Statistics 26). The data were initially analyzed for normality using the Shapiro-Wilk test and for homogeneity of variance via Levene's test. In the two comparisons, parametric data were analyzed using a two-tailed unpaired t-test (with Bonferroni correction applied to P-values for multiple comparisons), whereas nonparametric data were assessed via Mann-Whitney U-test. A one-way analysis of variance (ANOVA) was utilized to evaluate the overall differences between multiple groups, and two-by-two comparisons were performed using Tukey's HSD post hoc test (with built-in multiple comparison correction, controlling the overall type I error rate at α = 0.05). P < 0.05 represents a statistically significant difference. Plotting was performed using Prism software (Graphpad 9.0).