Bioinformatics analysis
PARPBP expression levels in various types of cancers and normal tissues were identified in the Oncomine database (www.oncomine.org)10.The threshold was set at a 1.5-fold difference in expression between cancers and normal tissues with a P-value < 0.0001. The Cancer Genome Atlas (TCGA)11 and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC)12 datasets were analyzed and the figures were generated using Gene Expression Profiling Interactive Analysis (GEPIA) (http://gepia.cancerpku.cn/index.html)13 and the cBio Cancer Genomics Portal (http://cbioportal.org)14,15. All TCGA data included in this manuscript are following the TCGA publication guidelines. The KM Plotter Online Tool (http://www.kmplot.com) is a public database that combined survival analysis across multiple microarray datasets2,16.
Patients and tissue specimens
In total, 162 breast cancer tissues (cohorts 1, 2) were obtained from the Sun Yat-Sen University Cancer Centre and prepared as paraffin blocks. The Ethics Committee of Sun Yat-Sen University Cancer Centre Health Authority approved this study. All samples were collected in accordance with Health Insurance Portability and Accountability Act guidelines and the Declaration of Helsinki. Cohorts 1: a total of 137 breast cancer tissues used for survival analysis were collected between March 2005 and September 2011. Using the formalin-fixed paraffin-embedded (FFPE), a tissue microarray was built for immunohistochemistry (IHC) studies. Cohorts 2: a total of 25 patients received anthracycline-based neoadjuvant chemotherapy. Tissue specimens were collected between March 2017 and September 2018 before patients received neoadjuvant chemotherapy. Progressive disease or stable disease defined as chemo resistant. Complete response or complete response defined as chemo sensitive.
Cell lines and culture conditions
Human breast cancer cell lines (MDA-MB-231, BT549, HCC38, T47D, MDA-MB-468, BT474, Skbr-3 and MCF-7) and normal mammary epithelial cell lines (MCF-10A) were obtained from the American Type Culture Collection (Manassas, VA, USA). The drug resistance cell subline of MCF-7 (MCF-7/ EPI) was derived from the parental cells by using low concentration epirubicin stepwise incremental method17. All cells were passaged in our laboratory for fewer than 6 months on receipt and were tested mycoplasma free.
Quantitative reverse transcription polymerase chain reaction (qRT-PCR)
Total RNA was isolated using TRIzol reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions. The Nano Drop ND-1000 Spectrophotometer (Nano Drop, Waltham, MA, USA) was used to evaluate RNA quality. Complementary DNA was synthesized using the PrimeScript RT reagent kit (Takara Bio Inc., Dalian, China). RT-PCR were performed using SYBR Premix Ex Taq (Takara Bio Inc., Dalian, China). Each reaction was performed in triplicate. The primer sequences are given in Supplementary Table S1. The values were normalized to internal controls and fold changes were calculated through relative quantification (2-ΔΔCt).
CCK8 assay
Cell viability was assessed by cell counting kit-8 assay (CCK-8; Dojindo Laboratories, Kumamoto, Japan). The cells (1×103) were seeded into 96-well plates. After 2 h of CCK-8 solution (10 μL) incubation at 37 °C, the absorbance at 450 nM was measured using a microtiter plate reader (Bio-Tek EPOCH2, BioTek Instrument, Inc., USA)18.
Colony formation assay
At 48 h after transfection, cells were cultured with or without EPI at the indicated concentrations for 3h. Then, the cells were harvested, seeded 500 cells per well into six-well plates and cultured for an additional 2 weeks. For scoring the colony-forming units, plates were stained with crystal violet (crystal violet 0.5%, ethanol 2%) and photographed.
Western blot analysis
Western blot analysis was performed as previously described19. The following antibodies were used in western blot analysis: anti-PARPBP (1:500, Abcam, USA), anti- FOXM1 (1:1000, Cell Signaling Technology, MA, USA) and β-actin (1:5000, Cell Signaling Technology, MA, USA). The membranes were further incubated in a secondary antibody (1:5000 dilution) and ECL reagents (New England Biolabs, Ipswich, MA, USA) were used to detect the protein.
Apoptosis assay
Cell apoptosis was detected using an Andy Fluor 488 Annexin V and PI Apoptosis Kit (GeneCopoeia, Rockville, MD, USA). After breast cancer cells were treated with or without EPI at the indicated concentrations for 48 h, they were harvested and resuspended in 400 ml of binding buffer. Next, 5 μl of Annexin V-FITC and 2 μl of PI were added to the suspensions, and the cells were incubated in the dark at 4 °C for 15 min. Ten thousand events were considered for the analysis.
Immunohistochemistry (IHC) analysis
Immunohistochemistry staining was performed as described previously20. Staining intensity scored as (0, negative staining; 1, weak staining; 2, moderate staining; 3, strong staining) and the extent of staining scored as the percentage of positive cells (1,0∼25%; 2, 26∼50%; 3, 51∼75%; 4, 76∼100%). The final quantitation of each staining was obtained by multiplying the two scores. PARPBP expression was classified into two groups: high expression group (score was higher than 2.0) and low expression group (score was 2.0 or less).
RNA interference and plasmid
Sequences of siRNAs were listed in Supplementary Table S2. Expression construct pcDNA3.1-PARPBP-HA, pcDNA3.1-FOXM1 and shFOXM1 were obtained from GeneCopoeia, USA. The lentivirus knocking down PARPBP (shPARPBP) were packaged and purchased from GenePharma, Shanghai using siPARPBP1 corresponding sequences. The cell transfection was performed using Lipofectamine 2000 (Invitrogen, USA).
Promoter Reporters and Dual-luciferase Assay
The PARPBP promoter region (–1500, +76) was amplified and the fragment was cloned into the luciferase reporter plasmids pGL3-basic vector (Promega, USA), designated as pGL3-PARPBP. Mutant construct pGL3-PARPBP-MU was generated by site-directed mutagenesis. Luciferase assay was performed as described previously19. Each experiment analysis was repeated three times.
Chromatin immunoprecipitation assay
The chromatin immunoprecipitation (ChIP) assay was performed using a Zymo-Spin ChIP kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instructions. Chromatin was mechanically sheared using sonication after cells were collected and cross-linked by formaldehyde. Protein-DNA complexes were precipitated by control immunoglobulin G and anti-FOXM1 antibody respectively, followed by eluting the complex from the antibody. The amount of DNA was further assessed by quantitative real-time PCR, using the primers specific for PARPBP promoter and SYBR Select Master Mix (Applied Biosystems, Grand Island, NY, USA).
Tumor xenograft experiments
Cells were collected and suspended in 200 μl of PBS at a concentration of 5 × 106 cells per ml, then injected into the mammary fat pads of six-week-old female BALB/c nude mice. Ten days after injection, the mice were then intraperitoneally injected with 5 mg/kg EPI (once per 2 days) for another 2 weeks. The xenograft tumors were harvested after 4 weeks. Tumor tissues were also processed and sectioned for histological evaluation. Animal experimentation was conducted in accordance with the guidelines of the local institutional animal care and use committee.
Statistical analysis
Statistical analyses were performed using SPSS 22.0 software (SPSS, Chicago, IL, USA). Student’s t-test was used to make a statistical comparison between groups. The Chi-squared test and Fisher’s exact test were used to investigate the significance of the correlation of PARPBP expression with clinicopathological features in breast cancer patients. Survival curves were calculated by the Kaplan-Meier method and compared with the log-rank test. A P value <0.05 was considered significant.