Cell culture and lentivirus infection
CRC cell lines HCT116, SW480, and DLD1 were obtained from Procell Life Science & Technology Company (Wuhan, China) and verified through STR profiling analysis. HCT116 cells were cultured in McCoy’s 5A medium (HyClone, Utah, USA), SW480 cells in Leibovitz’s L15 medium (HyClone, Utah, USA), and DLD1 cells in RPMI-1640 medium (HyClone, Utah, USA), each supplemented with 10% fetal bovine serum (Gibco, South America, SA, USA). HEK 293T cells were maintained in complete DMEM (HyClone, Utah, USA).
For cell treatments, 20 µg/mL cycloheximide (CHX, Glpbio) was added for 8, 24, and 48 hours. Cells were incubated with 5 µM MG132 (Selleckchem) for 4 hours and treated with 20 µM chloroquine (CQ, MCE) for 8 hours. In vitro treatments with Santacruzamate A (Sellechem) were conducted at 50 µM for 6 hours.
Lentivirus packaging involved co-transfection of HEK 293T cells (6×10^6 cells/10 cm plate) with psPAX2 (9 µg), pMD2G (3 µg), and target gene plasmid (12 µg) using 76.8 µL HiGene (Applygen, Beijing, China) for 24 hours. Lentivirus supernatant was collected after 48 hours and used to infect cancer cells for 12 hours, followed by selection of positive cells with puromycin (Yeasen, Shanghai, China). The shRNA sequences are detailed in Table 1.
Table 1
The sequences of different shRNAs used in the study.
shRNA | Sequence |
shNUCKS1#1 | CCGGGTTGTTGATTACTCACAGTTTCTCGAGAAACTGTGAGTAATCAACAACTTTTTG |
shNUCKS1#2 | CCGGCACTCAGCAGAGGATAGTGAACTCGAGTTCACTATCCTCTGCTGAGTGTTTTTG |
shHDAC2 | CAGTCTCACCAATTTCAGAAA |
The transwell migration and invasion assays
The experiment utilized 8 µm pore transwell chambers (BD Biosciences). For cell migration assays, cells were seeded into the chamber with 200 µL of serum-free medium, while culture medium containing 10% FBS was added to the lower chamber. For invasion assays, matrigel (BD Biosciences) diluted 1:20 with serum-free medium was added to the chamber, followed by incubation for 4 hours to allow solidification before adding cells. After 24 hours, cells were fixed with 95% ethanol for 15 minutes and stained with 1% crystal violet for 30 minutes. The chambers were rinsed with tap water, and the cells on the upper surface were removed using a cotton swab. Then, an inverted microscope was used for observation, and ImageJ was used to count the number of migrated or invaded cells in five randomly selected fields of view.
Wound healing assay
Cells were seeded in 6-well plates and allowed to adhere for 24 hours. A pipette tip was used to create a scratch in the cell monolayer. Cells were then incubated with cell tracker green CMFDA (Invitrogen) for 15 minutes in the incubator. After washing with PBS (HyClone, Utah, USA), the cells were observed and photographed under a fluorescence microscope. The medium was replaced with 1% FBS culture medium, and the cells were observed and photographed again after 24 hours.
Immunofluorescence staining and confocal microscopy
Cells were seeded in a confocal dish and fixed with 4% paraformaldehyde (Biosharp, Shanghai, China) for 15 minutes after washing with PBS. Permeabilization was performed with 0.5% Triton X-100 at room temperature for 20 minutes, followed by blocking for 30 minutes. Cells were then incubated with primary antibodies overnight at 4°C. After washing three times with PBS, secondary antibodies were added and incubated for 1 hour at room temperature in the dark. After a final wash with PBS, an anti-fade reagent was added, and cells were observed under a confocal microscope, selecting three fields of view for statistical analysis. Mean fluorescence intensity (MFI) was calculated using ImageJ software. Primary antibodies used included NUCKS1 (catalog# 12023-2-AP, Proteintech) at 1:400 dilution; HDAC2 (catalog# 67165-1-Ig, Proteintech) at 1:800 dilution; HDAC2 (catalog# ET1607-78, HUABIO) at 1:100 dilution; LC3B (catalog# 81004-1-RR, Proteintech) at 1:1000 dilution; LAMP2 (catalog# M1603-5, HUABIO) at 1:100 dilution. Secondary antibodies used: anti-rabbit IgG (H + L) Alexa FluorTM 594 (catalog# A-21207, Thermo Fisher) at 1:500 dilution; anti-rabbit IgG (H + L) Alexa FluorTM 488 (catalog# A-21206, Thermo Fisher) at 1:500 dilution; anti-mouse IgG (H + L) Alexa FluorTM 594 (catalog# A-21203, Thermo Fisher) at 1:500 dilution; and anti-mouse IgG (H + L) Alexa FluorTM 488 (catalog# A-21202, Thermo Fisher) at 1:500 dilution.
For FITC-phalloidin staining of F-actin, the TraKind™ F-actin staining kit (Abbkine, Wuhan, China) was used, and cells were observed under a confocal microscope.
Coimmunoprecipitation (Co-IP) and Western blotting
Cells were lysed using IP lysis buffer (Applygen, Beijing, China) supplemented with phosphatase and protease inhibitor cocktails (Roche, USA). After 30 minutes on ice, lysates were centrifuged at 4°C and 12,000 rpm for 20 minutes. A 100 µL aliquot of the supernatant was mixed with a loading buffer as input. The remaining supernatant was divided into two parts, with IgG and HDAC2 antibodies added to each. Following overnight incubation at 4°C, protein A/G magnetic beads (Bimake, Texas, USA) were added and incubated at 4°C for 4 hours. Magnetic beads were collected using a magnetic rack, washed five times with cold PBS, and mixed with loading buffer. Samples were boiled at 100°C for 10 minutes, and magnetic beads were removed to obtain protein samples. For HEK 293T cells overexpressing NUCKS1-flag, anti-flag magnetic beads (Bimake, Texas, USA) were directly added to the protein supernatant, followed by magnetic bead collection and sample preparation.
Western blotting analysis was conducted as previously described (14). ImageJ software was used to perform grayscale analysis on protein bands, and the experiment was repeated at least three times. Primary antibodies used: NUCKS1 (catalog# 12023-2-AP, Proteintech) at 1:500 dilution; HDAC2 (catalog# ET1607-78, HUABIO) at 1:1000 dilution; AKT (catalog# 4691, Cell Signaling Technology) at 1:1000 dilution; p-AKT (Ser-473) (catalog# 4060, Cell Signaling Technology) at 1:1000 dilution; GAPDH (catalog# 60004-1-Ig, Proteintech) at 1:10000 dilution. Secondary antibodies used: anti-rabbit-HRP (catalog# AS014, ABclonal) at 1:4000 dilution; anti-mouse-HRP (catalog# AS003, ABclonal) at 1:4000 dilution.
Quantitative real-time PCR (q-PCR)
Cells were collected and washed twice with PBS, followed by the removal of the supernatant. RNA was extracted from cell pellet using the M5 Universal RNA Mini Kit (Mei5Bio, Beijing, China). Complementary DNA (cDNA) was synthesized using the Evo M-MLV RT Mix Kit (Accurate Biotechnology, Changsha, China). Real-time PCR was performed with the SYBR Green Premix Pro Taq HS qPCR Kit (Accurate Biotechnology, Changsha, China). All experimental procedures were conducted according to the manufacturer's instructions. Primer sequences are listed in Table 2.
Table 2
The primers used in the study.
Primer | Forward/ reverse | Sequence (5’-3’) |
HDAC2 | Forward | ATGGCGTACAGTCAAGGAGG |
Reverse | TGCGGATTCTATGAGGCTTCA |
GAPDH | Forward | GGAGTCCACTGGCGTCTTCA |
Reverse | GTCATGAGTCCTTCCACGATACC |
Animal experiments
Female nude mice (6–8 weeks old, 18–22 g) were supplied by the Air Force Medical University Animal Center and randomly divided into four groups (n = 6 per group). Each mouse was injected with 1×106 CRC cells via the tail vein. Four weeks later, the mice were euthanized, and lung and liver tissues were collected, embedded in paraffin, and sliced for hematoxylin–eosin (HE) staining using the Hematoxylin and Eosin Staining Kit (Beyotime, Shanghai, China). HDAC2 inhibitor Santacruzamate A (Sellechem) was administered by intraperitoneal injection at a dose of 25 mg/kg once daily for three weeks, with a one-day break each week. All experimental procedures were approved by the Institutional Animal Care and Use Committee of Tangdu Hospital (Number: 20230743).
Statistical analysis
Quantitative data are presented as mean ± SD and analyzed using GraphPad Prism 8.0 and SPSS Statistics 25.0. Statistical analyses utilized two-tailed Student's t-test or one-way ANOVA. Significance levels were defined as *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001.