1. Cell culture and tumor specimens
The BRCA cell lines, ZR-75-1, MCF-7, T47D, BT474, HCC1937, MDA-MB-231, MDA-MB-435, MDA-MB-453, MDA-MB-468, and SKBR3 were purchased from American Type Culture Collection (ATCC). The Dulbecco’s modified Eagle’s medium (DMEM) and RPMI 1640 (Gibco, CA, USA) with 10% fetal bovine serum (FBS) was applied to culture MCF-7, MDA-MB-231, MDA-MB-435, MDA-MB-453, MDA-MB-468, SKBR3 and BT474, HCC1937, T47D, ZR-75-1 cell, respectively. The serum was purchased from Procell Life Science&Technology (Wuhan, China). All cells were cultured in a humidified incubator with 5% CO2 at 37℃. The human BRCA and adjacent normal tissue used in this article were gifted from Dr Bailin Zhang (National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College), which have been approved by Institutional Review Board (IRB).
2. Construction of stable cell lines and Transfection
For the construction of MCF-7 and T47D cell lines stably overexpressing ERCC6L, control and ERCC6L lentiviruses were used to infect both cells for 72 h, followed by selection with 3 µg/mL puromycin. For stably silencing of ERCC6L, MDA-MB-231 cells were infected with control, shERCC6L#1 and shERCC6L#2 lentiviruses respectively. Subsequently, they were screened with 3 µg/mL puromycin. For transient overexpression of KIF4A, the human full-length KIF4A cDNA clone was transfected into 231 cell lines using Lipofectamine 3000 regent in accordance with manufacturer's instructions.
3. Transgenic mice model and Tumor monitoring
The construction of ERCC6Lflox/flox and MMTV-Cre/Line D mice were provided by Biocytogen Pharmaceuticals Co., Ltd. Mice were kept in the Laboratory Animal Center, Institute of Materia Medica, Chinese Academy of Medical Sciences under 12 h/d light, 22 ± 3 ° C temperature and 50 ± 5% relative humidity. All experimental conditions and experiments performed on animals were in accordance with the guidelines of Animal Ethics Committee of Institute of Materia Medica, Chinese Academy of Medical Sciences (Ethics number: 00008101).
The flox-Cre recombination system was applied to generate the mice with mammary epithelial-cell specific ERCC6L deletion. ERCC6Lflox/wt Cre+/− mice were generated by crossing ERCC6Lflox/flox mice with MMTV-Cre mice. And then, ERCC6Lflox/wt Cre+/− mice were hybridized with ERCC6Lflox/y Cre+/− mice and ERCC6Lwt/y Cre+/− mice to obtain ERCC6Lflox/flox Cre+/− mice and ERCC6Lwt/wt Cre+/− mice, respectively. At 6, 8 and 12 weeks, the fourth groin mammary glands of female mice were weighed and performed with whole mount assay.
To generate PyMT mice, we crossbred female ERCC6L mice of different genotypes with MMTV-PyMT mice. At 8 weeks, whole mount staining was performed on the fourth groin mammary gland of female mice to evaluate multifocal dysplasia. To assess palpable tumor onset, animals were palpated weekly. After the formation of palpable tumors, the body weight of mice was recorded and tumor volume was measured using vernier calipers within 42 days. At 16 weeks, the mice were dissected and their body weight, the number of tumors per mice, and the wet weight of each tumor were recorded. Tumor tissues, lungs, and spleens were soaked in 4% paraformaldehyde (PFC) for Immunohistochemistry (IHC) and Immunofluorescence (IF). The genotypes of all female mice were identified by specific PCR analysis of mouse tail genomic DNA. Primer information was listed in Supplementary Table 1.
4. Nude mice axillary xenograft tumor model
Female BALB/c-nu nude mice, purchased from Beijing Vital River Laboratory Animal Technology, were divided into three groups (n = 6) and separately injected with MDA-MB-231 shNC, MDA-MB-231 shERCC6L#1, and MDA-MB-231 shERCC6L#2 cells (1x107/0.1 mL). After the tumor has grown (less than 1000 mm3), each mouse was dissected to measure the volume of tumors. The calculation formula is: V = 0.5xLxW2 mm3 (L represents length and W represents width, Unit: mm).
5. Whole mount staining
The fourth inguinal mammary gland was removed, spread on a glass slide, and air-dried for 5–10 min. Fixation was performed with Carnoy's solution (60% ethanol, 30% chloroform, and 10% glacial acetic acid) for 2–4 h. The slides were then immersed in gradient concentrations of ethanol (75%-50%-30%) for 15 min, respectively. After immersion in ddH2O for 5 min, the slides were immersed in a container with dye liquor (0.2% carmine and 0.5% aluminum potassium sulfate) for 1–2 days. They were then decolorized with 70% ethanol containing 2% hydrochloric acid for 2 h, immersed in gradient concentrations of ethanol (70%-95%-100%) for 15 min, defatted with xylene for 20 min, and finally stored in methyl salicylate.
6. The assays of cell viability, migration and invasion
CCK-8 was carried out to check cell proliferation. The cells were first seeded in 96-well plates and then incubated in incubator for 24, 48,72 and 96 h. Finally, the plates were placed in SpectraMax M5 and the absorbance value of each well was measured at 450 nm for quantification. In terms of migration and invasion assay, the cells were counted and inoculated in 8 µm polycarbonate membranes in Costar 24-Transwell plates. Then, being cultured for 3–4 h (after cell attachment), serum-free medium and 10% FBS medium were added to the upper and bottom chambers, respectively. After 19 h (for migration) and 22 h (for invasion), cells were fixed with 4% paraformaldehyde (PFA) and stained with 1% crystal violet. Subsequently, after cells on upper chamber were wiped off, the chambers were placed under a microscope for observation. Note that in the invasion assay, the upper chambers need to be coated with Matrigel™ diluted in serum-free medium (1:7) before seeding the cells.
7. Soft agar colony formation assay and 3D Matrigel cell culture
The low melting point agarose was prepared at 3.5% mother liquor which need to be autoclaved before use. The mother liquor was diluted 1:5 (0.7% agar) and 1:10 (0.35% agar), respectively, and successively spread in 6-well plates to form the bottom and upper layers. The upper layer contains prepared cells (about 3000/well). Before being placed into the incubator, plates were first put in a 4 ° C refrigerator for 30 min. After being plated in incubator for 2–3 weeks, cells were stained with MTT solution (5 mg/mL) and then counted. For the 3D Matrigel assay, the cell suspension and Matrigel were mixed in a 1:1 ratio and inoculated in 96-well plates. After two weeks, clones can be observed and photographed.
8. Edu assay
Cells were plated in 96-well plates. Edu reagent (1:1000 dilution) was added to plates and incubated for 2 h. The cells were then fixed with 4% PFA for 30 min, washed with 2 mg/mL glycine solution and PBS for 2–3 times, respectively, and then permeabilized with PBS with 0.5% Triton X. After the permeabilization, the prepared 1 x Apollo staining solution and hochest3342 staining solution were added successively, and the cells were incubated in the dark at room temperature for 30 min. Finally, the cells were observed under a microscope.
9. Flow cytometry for cell cycle assay
The cells were seeded in 60-mm medium dishes. After 48 h, cells were collected, washed with PBS, and fixed overnight with 70% ethanol at 4 ° C. Then, the cells were washed again with PBS and incubated successively in PBS with RNase (20 µg/mL) and PBS with 50 µg/mL PI and 0.5% Triton X for 30 min at room temperature in the dark. Finally, the cell suspension was filtered through a 300-mesh screen and its fluorescence was detected using Accuri C6. FlowJo v10 was used for data processing.
10. Immunohistochemistry (IHC) and Immunofluorescence (IF)
Human BRCA tissue samples and animal tissues were prefixed and made into paraffin sections. After roasted, dewaxed, and hydrated, the sections were infiltrated with preheated blocking permeabilizing solution (PBS with 30% H2O2 and Triton X) for 30 min to reduce endogenous peroxidase activity. Subsequently, the sections were antigen repaired and blocked using sodium citrate buffer (PH 6.0) and serum, respectively. ERCC6L, KIF4A, Ki67, F4/80, and CD31 (1:200 dilution) were added to the tissue sections for incubation at 4 ° C overnight. The next day, sections were washed and incubated with secondary antibodies for 1–2 h at 37 ° C. Diaminobenzidine (DAB), Mayer's Hematoxylin Stain Solution and neutral balata were subsequently applied to stain, counterstain (negative controls were treated with rabbit serum) and seal slides. Finally, the stained sections can be photographed under a Leica TCS SP8X confocal microscope. The staining density and positive rate of protein were analyzed by Image J (V1.8.0).
The cells were pre-seeded onto the glass bottom cell culture dishes, and 24 h later, the cells were fixed with 4% PFA for 20 min, permeabilized with 0.3% Triton X for 10 min, and blocked with 5% BSA for 30 min at room temperature. At the end of blocking, diluted KIF4A (1:100) and ERCC6L (1:100) antibodies were added to the bottom of the dish and cells were incubated overnight at 4 ℃. Subsequently, the cells were stained with the corresponding fluorescent secondary antibodies for 1 h at room temperature (Alexa 488 for ERCC6L and Alexa 574 for KIF4A). In the end, cells were further stained with DAPI for 30 min. A confocal microscope was used to acquire images.
11. Protein extraction and immunoblotting analysis by Western blotting (WB)
Total proteins in human BRCA tissue samples, animal tissues and cells were extracted by RIPA lysates with protease and phosphatase inhibitors (CwBio, Beijing) and subsequently quantified by BCA method. For immunoblot, the equal amounts of proteins were electrophoresed on 8%-10% SDS-PAGE and subsequently transferred to PVDF membranes. After blocking the membranes with 5% BSA or 5% defatted milk for 1 h at room temperature, the membranes were incubated with primary antibody overnight at 4 ° C. After being washed with TBST, membranes were incubated with commensurable secondary antibodies. Finally, the membrane was cleaned again with TBST and then exposed in Tanon 5200 (Shanghai, China) by dropping ECL regents on it. Data was handled by Image J V1.8.0. The used antibodies are shown in Supplementary Table 1.
12. Co-immunoprecipitation (Co-IP)
Cells seeded into 100 mm dishes were lysed using IP lysis buffer and centrifuged to obtain the supernatant. Part of the supernatant could be directly applied for Western blotting after denaturation. For Co-IP, the supernatant was mixed with protein A/G agarose beads and anti-DDK beads, and then rotated overnight at 4 ° C. Subsequently, the beads were washed, mixed with 2 x SDS-PAGE loading buffer, and heated at 95 ° C for 5 min for Western blotting analysis.
13. Statistical analysis
Mean ± standard deviation (SD) was used for the presentation of the results. P values were used to evaluate the significance of the differences, which were calculated by unpaired two-tailed Student’s t-test or one-/two-way ANOVA. There were statistically significant differences when P values < 0.05.