Regents and antibodies
All the experimental reagents and antibodies are purchased from Sigma Chemical Co. (St. Louis, MO, USA) unless otherwise stated in this study. Bafilomycin A1 (Baf A1) was purchased from Sangon Biotech, China. The antibodies used in this study are anti-FOXO1 antibody (Cat# 2880, Cell signaling Technology, USA), anti-phospho-FOXO1 antibody (Cat# WL03634, Wanlaibio, China) and anti-Lamin AC antibody (Cat# 10298-1-AP, Proteintech, USA).
Cell culture
The MDA-MB-231 triple-negative breast cancer cell lines was purchased from Chinese Cells Bank. Cell line was maintained in Dulbecco’s Modified Eagle Medium (DMEM) (Cat# C11995500BT, Gibco, USA) supplemented with 10% fetal bovine serum (FBS) (Cat# 10099-141, Gibco, USA), penicillin (100 units/ml) and streptomycin (100 μg/ml) (Invitrogen, Carlsbad, CA) in a humidified atmosphere of 5 % CO2 at 37 °C.
Cell morphological observation
Exponentially growing MDA-MB-231 cells were transferred to 12-well plates and cultured at 37 °C in a 5% CO2 atmosphere. Cells were treated with different concentration of PTX for 24 h. When the cells were at 60 to 70% confluence, they were rinsed twice with PBS, and the supernatant was discarded. Then, images were taken using an OLYMPUS IX 71 microscope (OLYMPUS, Tokyo, Japan).
Annexin V-FITC/PI staining for apoptosis analysis
The cell apoptosis assay was performed according to manufacturer's instructions using Annexin V-FITC/PI test kit (Cat# FXP018-100, 4A Biotech Co., Ltd, China). The cell flow cytometry analysis was performed by using a Beckman CytoFLEX flow cytometer (Beckman, California, USA).
Immunofluorescence
The immunofluorescence analysis of LC3 and FOXO1 proteins was performed according to our previous study [13]. In brief, the treated cells were fixed in methanol for 10 min and blocked with a buffer containing 1% BSA and 0.1% Triton X-100 for 1 h. Then the fixed cells were incubated with primary antibodies against LC3B and FOXO1, respectively, at 4 °C overnight. After that, cells were incubated with secondary fluorescence-conjugated antibodies for 1 h to visualize via laser confocal microscopy (OLYMPUS FV 1000, Tokyo, Japan).
Colony formation assay
The assay was performed according to our previous study [14]. Briefly, the adherent cells were treated with or without 3-MA (5nM) and/or PTX for 72 h and then cultured for 15 days. Thereafter, the cells were fixed and stained with 10% Giemsa (Solarbio, Beijing, China). The colonies were washed, air dried, imaged and counted. Finally, colonies formation ratio was calculated according to the formula, Colony formation ratio = No. of colonies/No. of seeded cells × 100%.
Small interfering RNA (siRNA) and transient transfection
MDA-MB-231 cells was seed into 96 or 6-well plates. Then the control random small interference RNA (siRNA) or targeting FOXO1-targeted siRNA (Santa Cruz Biotechnology, California, USA, 100 pmol/well) were transfected into MDA-MB-231 cells using the siRNA transfection reagent (Santa Cruz Biotechnology, California, USA) according to the manufacturer’s protocol. After 7 h transfection, cells were treated with paclitaxel for an additional 24 h. Then, the cells were collected and cell lysates were prepared for q-PCR and western blotting. Cell were also for cell viability and apoptosis analysis.
Reverse transcription and q-PCR
Total RNA was extracted by Trizol agent (Invitrogen, California, USA). cDNA was synthesized from total RNA using a Prime-Script RT reagent kit (TaKaRa, Japan). The obtained cDNA was used as a template in SYBR green-based q-PCR (CFX-96, Bio-Rad, California, USA). The mRNA expression levels of the ATG genes were assessed with quantitative polymerase chain reaction (q-PCR). GAPDH was used for normalization. The primers are shown in supplementary Table 1.
Western blotting
At the end of the designed treated time, cells were washed twice with PBS and collected. Then, total protein concentrations of cell lysates were determined with a BCA Protein Assay kit (Beyotime, Shanghai, China). Protein samples (total protein loading of 100 mg) were separated by 12% SDS–PAGE and transferred onto PVDF membranes. These membranes were incubated for 30 min in 5% BSA buffer (Solarbio, Beijing, China) with gentle shaking to block non-specific binding before incubation with the diluted primary antibody (LC3B: 1:2000, p62: 1:2000, FOXO1: 1:1000, p-FOXO1: 1: 1000, β-actin: 1:5000) overnight at 4 °C. Subsequently, membranes were incubated with 5000-fold diluted secondary antibody (BD, California, USA) for 90 min at room temperature. The membrane was washed three times in PBS, for 10 min each time. Then, the membrane was treated for 3 min in the dark with reagent from an Easysee Western Blot Kit (Transgene, Alsace, France).
Statistical analysis
All western blotting and image data presented are representatives from at least 3 independent experiments. The numeric data are presented as means ± standard deviation (SD) from 3 independent experiments and analyzed using Student’s t-test.