RC patients and clinical samples
All RC tissue samples involved in the study were obtained from Changhai Hospital, which had signed informed consent and been approved by the Ethics Committee of Changhai Hospital. RC specimens used in this study were biopsy tissues before neoadjuvant radiotherapy or surgically resected specimens after neoadjuvant radiotherapy in the Department of Colorectal Surgery. Tumor regression grade (TRG) was obtained to evaluate the response of neoadjuvant radiotherapy[52]. Inclusion criteria: 1. Pathological diagnosis of RC; 2. Aged between 18 and 75; 3. Neoadjuvant radiotherapy was performed in Changhai Hospital. Exclusion criteria: 1. Withdrawal during neoadjuvant radiotherapy; 2. No operation was performed after neoadjuvant radiotherapy; 3. There was no TRG score in pathology. Five pairs of radiation-sensitive (TRG0) and resistant (TRG3) RC biopsy tissues were used for Illumina Human Methylation 850K microarray (Table S1). Ten pairs of radiation-sensitive (TRG0-1) and resistant (TRG2-3) RC biopsy tissues were used for mRNA expression detection (Table S2). Another ten pairs of radiation-sensitive (TRG0-1) and resistant (TRG2-3) RC biopsy tissues were used for Agena MassARRAY Methylation verification (Table S3). Surgical specimens of 68 RC patients after neoadjuvant radiotherapy were collected to construct a tissue microarray and detect the expression of DSTN by IHC (Table S4).
Illumina Human Methylation 850K microarray
The 850K microarray can detect the methylation status of about 853,307 CpG sites in the whole human genome, including 91% of the original 450K microarray sites, and an increase of 413,745 sites. The 850K microarray not only maintains the comprehensive coverage of CpG island, gene promoter region, but also specially increases the probe coverage of the enhancer region and gene coding region. Illumina Human Methylation 850K microarray detection and data analysis were performed by Genergy (Shanghai).
Agena MassARRAY methylation
The Agena MassARRAY Methylation process includes bisulfite conversion, PCR amplification, in vitro transcription and RNase A-specific digestion, and matriX-assisted laser desorption/ionization-time of flight. Agena MassARRAY methylation detection and data analysis were performed by CapitalBio Technology Corporation (Beijing).
Proteomics
The process of proteomics includes protein or peptide fluorescence quantification, filter-aided sample preparation, tandem mass tag, peptide stage tip desalination, classification of inverted peptides, and multi-dimensional liquid chromatography with mass spectrometry analysis. Proteomics detection and data analysis were performed by Shanghai Academy of Biological Sciences, Chinese Academy of Sciences.
Cell Lines and reagents
The human CRC cell lines (HCT116, HT29, SW480, SW620, CACO2) and FHC cells were obtained from the Chinese Academy of Sciences (Shanghai, China). Cells were incubated in Dulbecco's Modified Eagle Medium (DMEM) (SH30022.01, HyClone, USA) supplemented with 10% foetal bovine serum (FBS, 10099141, Gibco, USA). Decitabine were purchased from Selleck Chemicals (China). Cycloheximide (CHX) were purchased from APExBIO (USA).
Animal studies
The animal studies were approved by the Institutional Animal Care and Use Committee of the Second Military Medical University, Shanghai, China. Male athymic BALB/c nude mice (5 weeks old) were used. A total of 5×106 lv-DSTN cells were injected subcutaneously into one side of groin (n=3). When the xenografts grew to 100 mm3, simulated radiotherapy was started (a total of 20Gy radiation and control). Xenograft volumes were evaluated by caliper measurements and calculated individually with the following formula: Volume = a×b2/2 (where a represents the longest diameter and b represents the shortest diameter). Xenograft volumes was measured every 3 days and xenograft growth curve was drawn for 30 days in total.
RNA extraction, cDNA preparation and qRT -PCR
Total RNA was extracted from cells and tissues with TRIzol reagents (Takara, Japan), and the quality of RNA was determined with a Nanodrop 2000 and agarose gel electrophoresis. First-strand cDNA was generated from total RNA with PrimeScript™ RT Master Mix (Takara, Japan). qRT-PCR was performed with TB Green Premix Ex Taq (Takara, Japan) in a Step One Plus System (Applied Biosystems, USA), and β-actin served as the endogenous control. The primer sequences used were as follows: DSTN, 5'-GCTGATGAAGTATGTCGCATTT-3' (forward) and 5'-CGACAATCTTTTTCAGGAAGCA-3'
(reverse); DSG3, 5'-TAAAGACAGCGGTTATGGGATT-3' (forward) and 5'-CTGACAAAGTCTGGCACTTAAC-3' (reverse); DCN, 5'-GACAACAACAAGCTTACCAGAG-3' (forward) and 5'-TGAAAAGACTCACACCCGAATA-3' (reverse); RECK, 5'-GCACAACAATCTCTGCACTTTA-3' (forward) and 5'-CAGTCCCCATAGTAATCGACTG-3' (reverse); β-catenin, 5'-TGGATTGATTCGAAATCTTGCC-3' (forward) and 5'-GAACAAGCAACTGAACTAGTCG-3' (reverse) and β-actin, 5'-GGGCACGAAGGCTCATCATT-3' (forward) and 5'-AGCGAGCATCCCCCAAAGTT-3' (reverse). Relative mRNA expression levels were calculated based on the corresponding relative quantitation (RQ) values and were normalized to β-actin expression.
Western blot analysis
Protein was extracted from cells and tissues with lysis buffer, protease inhibitor mixture, loading buffer according to the manufacturer’s instructions (Beyotime, China). Then the protein went through gel electrophoresis and transferred onto polyvinylidene fluoride membranes. After incubating with primary and secondary antibodies, the bands were detected through Odyssey infrared scanner (Li-Cor). The primary antibodies included against DSTN (ab186754, Abcam, USA), β-catenin (51067-2-AP, Proteintech, China), C-Myc (10828-1-AP, Proteintech, China), Cyclin D1 (60186-1-Ig, Proteintech, China) and β-actin (66009-1-Ig, Proteintech, China) for control. The secondary antibodies included goat anti-mouse IgG (A327300, Thermo Fisher Scientific, USA) and goat anti-rabbit IgG (A32734, Thermo Fisher Scientific, USA).
siRNA transfection
The CRC cells were inoculated into a six-well plate, and when the cell density reached about 50%, the transfection reagent was added according to the manufacturer’s instructions for lipofectamine 3000 (Thermo Fisher Scientific, USA). DSTN siRNA was synthesized by GenePharma (Shanghai, China), with the following sequences: 5’-GCUGAUGAAGUAUGUCGCATT-3’ (forward) and 5’-UGCGACAUACUUCAUCAGCTT-3’ (reverse); and 5’-UCAAGCAAAUGGACCAGAATT-3’ (forward) and 5’-UUCUGGUCCAUUUGCUUGATT-3’ (reverse). A non-silencing siRNA oligonucleotide that does not recognize any known mammalian gene homologue (GenePharma, Shanghai, China) was used as the negative control, with the following sequence: 5’-UUCUCCGAACGUGUCACGUTT-3’ (forward) and 5’-ACGUGACACGUUCGGAGAATT-3’ (reverse).
Lentiviral packaging and transfection
The lentivirus with stable overexpression of DSTN was constructed by GenePharma (Shanghai, China), where the overexpression sequence is ATGGCCTCAGGAGTGCAAGTAGCTGATGAAGTATGTCGCAT TTTTTATGACATGAAAGTTCGTAAATGCTCCACACCAGAAGAAATCAAGAAAAGAAAGAAGGCTGTCATTTTTTGTCTCAGTGCAGACAAAAAGTGCATCATTGTAGAAGAAGGCAAAGAGATCTTGGTTGGAGATGTTGGTGTAACCATAACTGATCCTTTCAAGCATTTTGTGGGAATGCTTCCTGAAAAAGATTGTCGCTATGCTTTGTATGATGCAAGCTTTGAAACAAAAGAATCCAGAAAAGAAGAGTTGATGTTTTTTTTGTGGGCACCAGAACTAGCACCTCTGAAAAGTAAAATGATCTATGCAAGCTCCAAGGATGCAATTAAAAAGAAATTTCAAGGCATAAAACATGAATGTCAAGCAAATGGACCAGAAGATCTCAATCGGGCTTGTATTGCTGAAAAGTTAGGTGGATCCTTAATTGTAGCCTTTGAAGGATGCCCTGTGTAG. Infection was performed following the manufacturer’s instructions and fluorescence of lentivirus was observed 72h after infection.
Cell counting kit 8 (CCK-8) assay
The cells were inoculated into 96-well plates containing 10μl of CCK-8 reagent and radiated with different doses (0Gy, 2Gy, 4Gy, 8Gy, 10Gy, 16Gy, 20Gy). The optical density (OD) value at 450nm was measured with a microplate reader. Then the dose-response curve of CRC cells to radiation was drawn and half maximal inhibitory concentration (IC50) was calculated.
Plate colony formation assay
CRC cells were inoculated in 6-well plates with 1000 cells per well the day before radiation. After 10 days, the 6-well plate was washed twice with PBS, fixed with 4% paraformaldehyde for 1h, stained with crystal violet for 1h, cleaned with PBS, dried and photographed, and the number of clones was calculated.
Flow cytometric analysis
Cell apoptosis was quantified using flow cytometric analysis (BD Biosciences, San Jose, CA). For apoptosis experiments, CRC cells after radiation were collected and washed twice with ice-cold PBS and then re-suspended in 200μl of binding buffer. Fluorescein isothiocyanate (FITC)-conjugated Annexin V was added at a final concentration of 0.5μg/ml and incubated for 20 minutes at room temperature in the dark; then, 1μg/ml propidium iodide (PI) was added. The samples were immediately analyzed by flow cytometry.
Co-immunoprecipitation
Co-immunoprecipitation (co-IP) was performed according to the manufacturer’s instructions (KIP-1, Proteintech). Antibodies against DSTN (ab186754, Abcam, 1:50) and β-catenin (51067-2-AP, Proteintech, 1:30) were used.
Immunofluorescence (IF)
The cells were inoculated in a 6-well plate containing slides the day before radiation. The medium was removed and the plate was cleaned with PBS 48h after radiation. The cells were fixed with 4% paraformaldehyde for 30min, then the paraformaldehyde was discarded and the plate was washed with PBS for 3 times. The follow-up experiment was completed by Servicebio (Shanghai, China). Representative images were acquired using the Leica Microsystem. DAPI glows blue by UV excitation wavelength 330-380 nm and emission wavelength 420 nm; FITC glows green by excitation wavelength 465-495 nm and emission wavelength 515-555 nm; CY3 glows red by excitation wavelength 510-560 nm and emission wavelength 590 nm. Nucleus is blue by labeling with DAPI, DSTN is green by labeling with FITC and β-catenin is red by labeling with CY3. After merging under the microscope, the yellow fluorescence indicates co-localization of DSTN and β-catenin.
Immunohistochemistry (IHC)
Specimens were stained with antibodies for DSTN (ab186754, 1:100) or β-catenin (51067-2-AP, 1:100). The follow-up experiment of IHC was completed by Servicebio (Shanghai, China). Staining intensities and percentages of positive tumour cells was automatically calculated using the Servicebio image analysis system.
Data analysis
All statistical analyses in this study were performed with SPSS 26.0 software (SPSS Inc, USA). The measurement data were expressed as means±sd, and a two-tailed Student's t test was used for comparison between groups. Spearman correlation analysis was performed to determine the correlation between two variables. Kaplan-meier method was used to draw disease free survival (DFS) curve and overall survival (OS) curve, and log-rank test was used for survival analysis. A p-value less than 0.05 was considered significant.