Bioinformatics analysis
We used the following bioinformatics analysis strategies and tools at each experimental stage. We measured CENPF expression in TNBC and adjacent peritumoral tissues from the The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression Program (GTEx) databases using the Gene Expression Profiling Interactive Analysis (GEPIA). And GSE86374 and GSE58135 from the Gene Expression Omnibus (GEO) databases also used for that. We also performed survival analysis of CENPF in breast cancer, especially in the patient with neoadjuvant chemotherapy, using the Kaplan Meier Plotter with the best-performing threshold as a cutoff. We downloaded data of TNBC from GSE25066 and used Sangerbox to analyze the relationship between the expression level of CENPF and patient survival prognosis with the best-performing threshold as a cutoff.
Patient Samples And Ihc
TNBC tissue blocks were collected from 32 patients operated at Qilu Hospital and The Second Hospital of Shandong University between 2013 and 2020. All the 32-patient received at least four cycles of neoadjuvant chemotherapy before surgical resection. Tumor grade and MP grade as previously described [16]. According to MP grading system, grade 3 to grade 5 tumors were classified into chemotherapy-sensitive group; and grade 1 and grade 2 tumors were regarded as chemotherapy-resistant. IHC and evaluation of immunohistochemical (IHC) staining were performed as previously described [16].
Cell Lines And Cell Culture
We purchased the human breast cancer cell line MDA-MB-231 from the American Type Culture Collection (ATCC; Manassas, VA, USA). Cell authentication was verified by short tandem repeat profiling. The cell line of MDA-MB-231 with adriamycin-resistant (MDA-MB-231/ADR) was induced by long-term adriamycin treatment at the laboratory in the early stage, and was tested for adriamycin resistance[17]. We cultured these cell lines in Leibovitz’s L15 medium (MDA-MB-231 and MDA-MB-231/ADR) supplemented with 10% fetal bovine serum at 37°C with 5% CO2. All cell lines were tested as free from mycoplasma contamination by the mycoplasma PCR testing and no more than 20 generations of growth for any experiment.
Antibodies And Reagents
Anti-Phospho-Chk1-Ser317 antibody (1:1000,12302), anti-Phospho-Chk1-Ser345 antibody (1:10002348), anti-Rb antibody (1:500,9309) were purchased from Cell Signaling Technology (CST, Danvers, Massachusetts, US). Anti-CENPF antibody (1:1000, DF2310), anti-Chk1 antibody (1:1000, AF6007), anti-E2F1 antibody (1:500, DF6797) and anti-GAPDH antibody (1:3000, AF7021) were purchased from Affinity Biotech (Cincinnati, Ohio, US). Anti-CENPF antibody (1:1000, ab5) was purchased from Abcam, (Cambridge, UK).
Cell Transfection And Sirnas
Both si-CENPF and si-Control were synthesized by GenePharma (Shanghai, China) according to the sequence verified by SigmaAldrich. We used Lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA) and transfected MDA-MB-231, MDA-MB-231/ADR with siRNA (50 nM) according to the manufacturer's protocol. We confirmed the knockdown efficiency of CENPF by RT-qPCR and western blotting 48 hours after cell transfection. All siRNA sequences are shown in Supplementary Table S1
Quantitative Real-time Pcr (Qrt-pcr)
Total RNA and RT-qPCR were performed as previously described[18]. All primer sequences are presented in Supplementary Table S2
Western Blotting
Cells were lysed on ice for 20 min in RIPA lysis buffer (Beyotime, Beijing, China) supplemented with 1% phenylmethanesulfonyl fluoride (Beyotime, Beijing, China) and 1% ProtLytic Phosphatase Inhibitor Cocktail (New Cell and Molecular Biotech, Suzhou, China). The solution was then centrifuged at 12 000 G for 10 min and the supernatants were collected. Next, total protein concentration was measured using the BCA kit (Invitrogen, Carlsbad, CA, USA). After denaturation at 100°C for 8 minutes, 20 µg protein samples were separated on 7.5% SDS/PAGE gels and then transferred to PVDF membranes (Merck Millipore, Billerica, MA, USA).
Drug Sensitivity Assay
5,000 cells were seeded in 96-well plates. After 24 h, changed medium containing adriamycin (MB1087, Dalian Meilun Bio, Dalian, China), and the culture was continued for 72 h at drug concentrations of 0, 0.1, 0.5, 1, 2, 5, 10 and 20 µM. Cell viability was assessed using the Cell Counting Kit-8 (CCK-8; K1018A, PExBIO, Houston, TX, USA) following the manufacturer's instructions. After 2 h incubation at 37°C, absorbance was read at 450 nm.
Cell Proliferation Assay
3,000 cells were seeded in 96-well plates. Cell viability was assessed using the Cell Counting Kit-8 kit (CCK-8; K1018A, PExBIO, Houston, TX, USA) following the manufacturer's instructions at 24, 48, 72, and 96 h. After 2 h incubation at 37°C, absorbance was read at 450 nm. Furthermore, EdU cell proliferation assays were further confirmed as previously described[19].
Cell Apoptosis Assay
We collected MDA-MB-231 and MDA-MB-231/ ADR cells transfected with si-CENPF-1, si-CENPF-2 or si-control after 48 h’ exposure to ADR at a concentration of 1 or 5 µM, which was consistent with the process for the ADR-free group. Annexin staining V-fluorescein isothiocyanate (FITC) and propidium iodide (PI) staining were performed using the Annexin V-FITC/PI Apoptosis Assay Kit (BestBio, Shanghai, China) according to the manufacturer's instructions. Apoptosis was then detected immediately by flow cytometry (Cytoflex S, Beckman Coulter, California, US).
Cell Cycle Analysis
We collected MDA-MB-231 cells transfected with si-CENPF-1, si-CENPF-2 or si-control after 48 h’ exposure to ADR at a concentration of 1 µM, which was consistent with the process for the ADR-free group. Staining was performed using a Cell Cycle Detection Kit (BestBio, Shanghai, China) according to the manufacturer's instructions, and flow cytometry (Cytoflex S, Beckman Coulter, CA, USA) was performed to determine the effects of CENPF inhibition on cell cycle distribution with or without 48 hours action of 1µM adriamycin in MDA-MB-231 and using Histograms to statistical analysis the cell cycle distribution.
Immunofluorescence
Cells were cultured on glass slides and washed twice with PBS before fixation. Cells were fixed with 4% paraformaldehyde for 15 min and permeabilized with 0.1% Triton X-100 in PBS for 10 min at room temperature. To reduce nonspecific binding of antibodies, cells were incubated in PBS containing 1% BSA for 1 hour at room temperature. Primary antibodies (anti-CENPF and anti-Rb) were diluted in PBS containing 1% BSA, dropped on cells and incubated overnight at 4°C. Next, the samples were incubated with secondary antibodies Dylight488 and Dylight594 (Beyotime, Beijing, China) which diluted in PBS containing 1% BSA for 1 hour at room temperature. Then dropwise added Antifade Mounting Medium with DAPI (Beyotime, Beijing, China), and the images were observed and collected under a fluorescence microscope.
Co-immunoprecipitation
Cell lysis and protein concentration determination were as described above. For immunoprecipitation, equal amounts of lysate were incubated with protein A/G magnetic beads (Beyotime, Beijing, China) and anti-CENPF antibody overnight at 4°C. Thereafter, the beads were washed 3 times with cell lysis buffer and immunoprecipitated proteins were analyzed by western blotting.
Statistical analysis
Statistical analysis was performed using GraphPad Prism software version 5 ( GraphPad Software, Inc., San Diego, California, US) and SPSS 16.0 (SPSS Inc, IL, USA), and t-test was used to detect the difference between two independent samples. One-way ANOVA was used to analyze the statistical differences between three or more independent samples. Analysis of the relationship between CENPF expression and neoadjuvant chemotherapy grade and clinicopathological parameters using chi-square test and Fisher's exact test. We used The Kaplan-Meier method and log-rank t test to determine the significance of the survival curve. Analysis of correlations between co-expressed genes in the TCGA dataset in breast cancer using Pearson's correlation coefficient; immunofluorescence co-localization of CENPF and Rb proteins analyzed using Pearson's correlation coefficient, R values > 0.3 or < -0.3 were considered statistically significant. Each experiment was repeated at least 3times, P < 0.05 was considered statistically significant.