2.1 Antibodies and reagents
C2F, chemical structure shown as Fig. 1A, was synthesized by Shenzhen Small Molecule New Drug Innovation Center Co., Ltd. Antibodies of β-actin, PCNA, Bax, Bcl-2, Cleaved Caspase-9, Cleaved Caspase-3, E-Cadherin, Vimentin, N-Cadherin, PI3K were obtained from Cell Signaling Technology (Danvers, MA, USA). Antibodies of cyclin B1, CDK1, STAT3, Phosphorylated STAT3 (Tyr705), Phosphorylated STAT3 (Ser727) were purchased from Zen bioscience (Chengdu, China). BeyoClick™ EdU-594 and methylthiazolyldiphenyl-tetrazolium bromide (MTT) were supplied by Beyotime Biotechnology. The recombinant human IL-6 was purchased from Peprotech (London, UK). The STAT inhibitor Stattic was purchased from MedChem Express (NJ, USA). Matrigel was purchased from ABW (CAT: 082704). Exkine™ Nuclear and Cytoplasmic Protein Extraction Kit was supplied by Abbkine (Wuhan, China). Alanine aminotransferase (ALT) test kit and aspartate aminotransferase (AST) test kit was purchased from Nanjing Jiancheng Bioengineering Institute (Nanjing, China).
2.2 Cell cultures
The CRC cell lines DLD-1, SW620 and human normal colon cells HCoEpiC used in this study were developed and provided by Shenzhen Ruike Biotechnology Co., Ltd. Cell culture has been described in detail in our previous research(Xuehong et al., 2022).
2.3 MTT cytotoxicity assay
After overnight attachment, the DLD-1, SW620 and HCoEpiC cells were processed with a multi-Concentrationn of C2F (0, 1, 5, 10, 15, and 20 µM) and 5-FU (5, 10 and 15 µM). We followed the MTT experimental steps for subsequent operations(Priti et al., 2018).
2.4 Colony formation assay
DLD-1 and SW620 cells (500 per well) were seeded in 6-well plates overnight and then the medium was replaced with different concentrations of C2F. Two weeks later, 4% paraformaldehyde was added for 15 min for cell fixation and then aspirated, washed twice with PBS and finally stained with 0.1% crystal violet for 15 min.
2.5 EdU cell proliferation detection
The proliferative capacity of DLD-1 and SW620 cells were treated by EdU method according to the protocol provided by the manufacturer. Briefly, seeded of cells into 24-well plates and after adhesion, cells were stimulated with different concentrations of C2F for 24 hours. Then the reaction system was prepared according to BeyoClick™ EdU-594, and the reaction system was incubated at room temperature for 30 min, protected from light. Finally, the nuclei were stained with Hoechst33342 reaction solution. The results were observed by an inverted fluorescence microscope (200 × magnification, Olympus, Tokyo, Japan).
2.6 Cell cycle and apoptosis analysis
The methods for analyzing cell cycle and apoptosis have been specifically described in our previous research(Xuehong et al., 2022).
2.7 Hoechst 33342 staining
DLD-1 and SW620 cells were seeded in 12-well plates at a density of 1 × 104 cells per well. After 24 hours, we followed the Hoechst 33342 staining experimental steps for subsequent operations(Yao et al., 2020). Fluorescence microscopy was used for analysis.
2.8 Wound-healing assay
The wound healing assay was conducted with reference to our previous study(Xuehong et al., 2022).
2.9 Transwell migration/invasion assay
To rule out the effects of cell proliferation inhibition and induction of cell apoptosis on migration and invasion assay, we first set 4 × 104 DLD-1 cells and SW620 cells were suspended in 200 µl serum-free medium and then inoculated into the upper chamber, while the lower chamber was filled with 600 µl of medium containing 20% FBS. After 48 hours, fixed the cells on the pore membrane at the bottom of the chamber, and then soaked the cells in crystal violet staining solution for staining. Finally, the chamber was observed and photographed under an optical microscope, and the inhibitory effect of C2F on the migration and invasion of DLD-1 cells and SW620 cells was statistically analyzed using Image J.
2.10 Western blot analysis
After overnight attachment, the cells were processed with a gradient concentration of C2F (0, 1, 5, 10, 15, and 20 µM). The cells were then washed gently with PBS 2 times. The CRC cells were lysed using cell lysates for 30 min on ice, which were transferred to new tubes and then centrifuged. Protein concentration was determined by Coomassie Brilliant Blue staining to configure the reaction system. Protein was separated by sodium dodecyl sulfate- polyacryl- amide gel electrophoresis gel and transferred onto polyvinylidene difluoride membranes. The membranes were then blocked with 5% skim milk for 1.5 h and then washed with Tris Buffered Saline with Tween 20. The blots were ultimately incubated with specific primary antibodies and incubated with secondary antibodies on the following day. The membranes were imaged using the BIO-RAD high sensitivity chemiluminescence imaging system ChemiDoc touch and the software Image J was used to analyze the reactive bands.
2.11 Predicting the therapeutic targets of C2F for CRC by bioinformatic analysis
We downloaded the structure of C2F (PubChem CID: 132961735) from the PubChem(Kim et al., 2019) database (https://pubchem.ncbi.nlm.nih.gov/),and input it into the SwissTarget-Prediction(David et al., 2014) (http://www.swisstargetprediction.ch/) and Pharmmapper(Xiaofeng et al., 2010) (http://www.swisstargetprediction.ch/) platforms to predict the potential targets of C2F. The Uniprot(2020) database (https://www.uniprot.org/) was used to convert the protein target name into the corresponding gene symbol. We merged targets from two databases and removed duplicates to obtain targets related to C2F.
2.12 Determination of potential CRC-related targets
Four databases were then searched using Genes related to CRC: Genecards(Gil et al., 2016) database (https://www.genecards.org/), OMIM(S et al., 2019) database (https://omim.org/), TTD(Yunxia et al., 2020) database (https://db.idrblab.net/ttd/) and DrugBank(S et al., 2018) database (https://www.drugbank.com/). After the removal of repeated targets, Venny2.1.0 (http://www.liuxiaoyuyuan.cn/) was used to study the intersection of C2F with pathologic targets to identify potential targets for C2F in the treatment of colorectal cancer.
2.13 Network construction and enrichment analysis
To identify the possible interactions between all target genes in the pharmacological network, we constructed the PPI network using the STRING(Damian et al., 2019) database. When we used the database, we selected "Homo sapiens" for the species, chose 0.4 as the cutoff value for the confidence score, and left all other settings unchanged. Cytoscape(Paul et al., 2003) software version 3.8.2 was used to analyze and visualize the network topology of the results obtained by STRING. Nodes in the network diagram were intersection targets, and edges represent the relationship between targets and targets. We used the built-in Network Analyzer program to analyze network topology parameters such as degree, betweenness centrality, closeness centrality, etc.(Ziyu et al., 2022). Next, we used CytoHubba, a Cytoscape plugin that can be used for network centrality analysis, to identify the centroids in the network. The 10 genes with the highest degree centrality values were identified as central genes. Analysis of GO functional enrichment and KEGG pathway enrichment for target genes was performed using metascape(Yingyao et al., 2019) (https://metascape.org/gp/index.html#/main/step1) database. Bioinformatics (http://www.bioinformatics.com.cn/) platform was used to draw a bar graph and a bubble graph.
2.14 Targets-pathways network construction
Cytoscape software version 3.8.2 was used to build a targets-pathways network. The nodes in the network were targets and pathways, respectively, and the edges represented the interaction relationship between targets and pathways.
2.15 Molecular docking validation of C2F and core targets
The most important genes were selected for subsequent molecular docking analysis. The 3D structure of the ligand molecule (C2F) was first downloaded from the PubChem database. The Uniprot database was searched for receptor protein encoded by the input genes. The 3D structure of the protein was obtained from RCSB PDB database (https://www.rcsb.org/) and modified using PyMol software version 2.4.0, including ligand and water removal. Autodocktools was used to calculate protein loads. Finally, receptor proteins were docked to C2F using Autodock Vina and visualized using PyMol.
2.16 Immunofluorescence staining
We first inoculated DLD-1 and SW620 cells onto the glass slides, then fixed the cells with 4% paraformaldehyde, penetrated the cells with 0.5% Triton X-100 (in PBS), rinsed several times with PBS, and finally blocked the cells with 1% bovine serum albumin for 1 h. The cells were incubated with the primary antibody in an appropriate proportion, and the second day with the secondary antibody. We stained the cells with DAPI in the dark, then washed the cell slides with PBS again, and sealed them with anti-fluorescence quenching sealing sheets to prevent fluorescence quenching until they were captured by confocal microscopy.
2.17 Cytoplasmic and nuclear protein extraction
DLD-1 and SW620 cells were cultured at 80%-90% concentration in 10 cm dishes and treated with C2F (0, 5 and 10 µM). Immediately after IL-6 stimulation for 1 hour, cells were placed on ice. Nuclear and cytoplasmic proteins were extracted using the NE-PER Nuclear and Cytoplasmic Extraction Kit. The expression of related proteins was detected by western blot.
2.18 Animal experiments
Animal experiments are conducted in strict compliance with international standards and the 3R's of animal protection, and through the Shenzhen People's Hospital Laboratory Animal Ethics Committee approval. Approximately 5 weeks old female balb/c nude mice (18–20 g) were acqired from the Laboratory Animal Center of Guangdong Medical University (Dongguan, China) and were housed at the Laboratory Animal Center of Shenzhen People's Hospital. Approximately 1 × 107 SW620 cells suspended in 0.1 ml of serum-free culture medium and Matrigel (medium:Matrigel = 1:1) were subcutaneously injected into the right flank of each mouse. Tumor volume was calculated using recognized calculation methods(Yao et al., 2020). In our previous research, we found that C2F has an inhibitory effect on the growth of non-small cell lung cancer cell xenograft tumors. Accordingly, the mice were randomly divided into five groups in this study (control group, mice were intraperitoneally injected with olive oil five times per week. C2F group A were intraperitoneally injected with 10 mg/kg C2F five times per week, C2F group B were intraperitoneally injected with 20 mg/kg C2F five times per week, C2F group C were intraperitoneally injected with 30 mg/kg C2F five times per week, fluorouracil group, mice were intraperitoneally injected with 20 mg/kg fluorouracil three times per week. After 21 days of treatment, blood was collected from the posterior orbital sinus of nude mice for further analysis. Next, the nude mice were sacrificed by spinal dislocation and the tumors were obtained and weighed. The tumors were fixed in formalin and used for histological studies.
2.19 Statistical analysis
Each experiment was repeated at least three times independently to ensure reproducibility and reliability and statistically analyzed using Prism (version 8.0, GraphPad Software, San Diego California, U.S.A.). All results are shown as mean ± SD. One -way analysis of variance (ANOVA) was used for comparisons among multiple groups. P < 0.05 was considered to denote statistical significance.