2.1 Data and resources
We obtained the RNA-seq data shown in Fig. 1A, B and E from the TCGA database, which contains 415 GC tissues and 34 normal tissues from the UALCAN website (https://ualcan.path.uab.edu/). The RNA-seq data are listed in Supplementary Table 1. The RNA-seq data shown in Fig. 1C were obtained from the TCGA and GETx databases, which contain 211 GC tissues and 408 normal tissues from the GEPIA website (http://gepia.cancer-pku.cn/). Supplementary Fig. 1A data were obtained from the CCLE database (https://depmap.org/portal/gene/APOC1). Kaplan–Meier survival curves for 875 patients with GC were obtained from the Kaplan–Meier Plotter website (https://kmplot.com/analysis/index.php?p=service). The prediction of protein interaction was performed by AlphaFold 3 (https://alphafoldserver.com/).
2.2 Cell lines and cell culture
A human normal gastric epithelial cell line (GES-1) and gastric cancer cell lines (AGS, MKN-28, MKN-45, HGC-27 and MFC) were obtained from the Cell Type Bank of the Chinese Academy of Sciences and Shanghai Institute of Biochemistry and Cell Biology. The cell lines were cultured in RPMI-1640, DMEM or DF12 supplemented with 10% FBS. All the cell culture experiments were performed in an incubator at 37°C under 5% CO2.
2.3 Cell line transfection
The overexpression and shRNA plasmids were designed by Youbio Biotech (China). Plasmid transfection was performed using Lipofectamine 2000 Reagent (Invitrogen, California, USA) and 1 µg of plasmid according to the manufacturer’s instructions. The shRNA sequences used are listed in Supplementary Table 2.
2.4 Viral transduction
The constructed overexpression and silencing plasmids were transfected into 293T cells together with the packaging plasmids psPAX and PMD2.G at a ratio of 4:3:1 using the transfection reagent Lipofectamine 2000 (Invitrogen). The supernatants were collected and filtered through a 0.45 µm filter membrane after 72 h. The cells were plated in 6-well plates at 1 × 106 cells per well and transfected with the collected lentivirus particles. The transfected cells were then selected with puromycin for 2 weeks. The establishment of stable cell lines was verified by western blotting.
2.5 Real-time quantitative polymerase chain reaction (real-time qPCR) and PCR array
Real-time qPCR was performed with SYBR Green using a previously described protocol[23]. Human GAPDH was used as the internal control, and the relative expression of mRNA was calculated using the 2−△△Ct method. The primer sequences are listed in Supplementary Table 2. A human oxidative stress PCR array (Wcgene® Biotech, China) was used according to the manufacturer’s instructions. The genes differentially expressed are listed in Supplementary Table 3.
2.6 Western blot analysis
Protein was extracted from cells using RIPA buffer, and western blotting was performed as described previously[23]. The following primary antibodies were used: APOC1 (ab198288, Abcam, UK); CPT1A (15184-1-AP, Proteintech, Chicago, USA); AP-2 (13019-3-AP, Proteintech); EGFR (A11351, ABclonal, China); and phospho-EGFR-Y1068 (AP0301, ABclonal).
2.7 Coimmunoprecipitation (Co-IP) and mass spectrometry (MS)
For co-IP, lysates of 1×107 MKN-28 cells were immunoprecipitated with IP buffer containing IP antibody-coupled agarose beads, and protein-protein complexes were subsequently subjected to western blot and MS assays. MS was performed with a Shanghai bioprofile (China) to detect potential interacting proteins. Here, IgG was used as a negative control. The following primary antibodies were used: APOC1 (ab198288, Abcam) and CPT1A (15184-1-AP, Proteintech).
2.8 Immunohistochemical (IHC) staining
A total of 20 formalin-fixed, paraffin-embedded GC tissues and corresponding adjacent nontumor tissues were purchased from Shanghai Outdo Biotechnology (China). IHC and IHC scoring were performed essentially as described previously[23]. The following primary antibodies were used: APOC1 (ab198288, Abcam), APOC1 (ab189866, Abcam), and Ki-67 (28074-1-AP, Proteintech).
2.9 Cell Counting Kit-8 (CCK-8)
A 1000-well cell suspension was seeded in a 96-well plate and incubated for 8 h, after which the CCK-8 (Beyotime Biotechnology, China) reagent (1:10) was added, and the mixture was further incubated for 2 h at 37°C. The absorbance at 450 nm was measured using a microplate reader.
2.10 Colony formation assays
A total of 1000 cells were plated in 6-well plates and incubated for 2 weeks at 37°C, with media replenishment every 3–7 days. The cells were then washed with PBS, fixed with 4% paraformaldehyde and stained with 1% crystal violet for 30 minutes. Colonies were counted manually.
2.11 Proliferation assay
The cells were plated in 24-well plates at 2×104 cells/well. After 24 h, cell proliferation was assessed using an EdU Apollo In Vitro Kit (C10310, RiboBio, China) per the manufacturer’s instructions. In brief, the cells were incubated with EdU reagent for 3 h, after which the supernatant was discarded and the cells were fixed in 4% paraformaldehyde for 20 min and washed. The cell membranes were then permeabilized in 0.2% Triton X-100 for 20 min, after which a fluorescent probe was added. A fluorescence microscope (Leica, Germany) was used for detection.
2.12 Transwell migration assay
The cells were digested with trypsin, washed twice and resuspended in serum-free basal medium. The cells in the lower chamber were suspended in RPMI-1640 (0.6 ml) supplemented with 10% FBS, whereas a 2×104 cell suspension with serum-free basal medium was added to the upper chamber. The cells were then incubated at 37°C for 24 h, after which the cells were fixed with 4% paraformaldehyde and stained with 1% crystal violet for 30 minutes. Excess dye and water were removed from the cells, and then different fields were randomly selected and counted under a microscope.
2.13 Wound healing assay
The cells were seeded at a density of 5×105 cells/well in 6-well plates. A wound was created in each well using a P200 tip. Images were taken at 0 h and 48 h using a bright-field microscope at 4× magnification.
2.14 Mitochondrial reactive oxygen species (ROS) measurement
For determination of ROS levels in mitochondria, MKN-28 cells were seeded into 6-well plates with 3 ml of culture medium. 24 h later, the cells were stained with MitoSOX™ Red (5 µM in PBS; S0061S, Beyotime, China) for 20 min. Finally, the nuclei were counterstained with DAPI. The data were collected using a fluorescence microscope (Leica).
2.15 Evaluation of the mitochondrial membrane potential
To evaluate the mitochondrial membrane potential, MKN-28 cells were washed with PBS and stained with JC-1 (5 µg/mL, C2006, Beyotime) at 37°C for 30 min to detect changes in the mitochondrial membrane potential. Then, the cells were washed with PBS three times and observed under a fluorescence microscope (excitation wavelength: 475 nm; green emission: 530 nm; red emission: 590 nm).
2.16 Fatty acid oxidation assay
A fatty acid oxidation kit (ab217602, Abcam) and an extracellular O2 consumption kit (ab197243, Abcam) were used for FAO analysis according to the manufacturer’s protocol. Briefly, cells were seeded in 96-well plates at a density of 1×105 cells/well. After incubation overnight, the medium was replaced. Every group was divided into two subgroups, and etomoxir (40 µM) was added to block FAO or was not added. After 20 min of incubation, 10 µL of extracellular O2 consumption reagent and 2 drops of high-sensitivity mineral oil (preheated at 37°C) were added to each well. The fluorescence was measured with a plate reader at 4 min intervals for 60 min at excitation/emission = 380/650 nm. The relative FAO rate was calculated as the (fluorescence intensity (total) − fluorescence intensity (etomoxir)) / time. At least three replicates were included for each measurement.
2.17 Immunofluorescence
For immunofluorescence colocalization, MKN-28 cells were cultured on confocal dishes for 24 h. MKN-28 cells were incubated with APOC1 antibody (ab198288, Abcam) and CPT1A antibody (66039-1-Ig, Proteintech) at 4°C overnight after fixation with 4% paraformaldehyde and permeabilization with 0.2% Triton X-100. Then, the cells were incubated with goat anti-rabbit-conjugated antibodies (A0408, Beyotime) and anti-mouse-conjugated antibodies (A0473, Beyotime) at room temperature for 30 min in the dark. Finally, the nuclei were counterstained with DAPI. Images were taken using a confocal laser scanning microscope (Olympus, Japan).
2.18 Dual-luciferase reporter assay
Primers were designed from the genomic DNA to clone the required promoter fragments and mutant sequences, and then the sequences were inserted into the luciferase reporter plasmid (pGL3-basic). The target and control plasmids were prepared and purified for later use. The reporter gene plasmid and transcription factor expression plasmid were transfected into MKN-28 cells. All experimental groups of cells were transfected with pRL-TK plasmids as an internal control. Luciferase activities were detected with a Dual-Luciferase Reporter Assay System (Promega, E1910, Massachusetts, USA). The relative luciferase intensity is shown as the numerical value of the firefly luciferase activity divided by the Renilla luciferase activity. The sequences of the primers used for the luciferase reporter assay are listed in Supplementary Table 2.
2.19 Animal experiments
All animal procedures were approved by the Experimental Animal Center, Capital Medical University (approval number M-2019–037) and carried out in accordance with the guidelines of the Capital Medical University Animal Care Committee. Four-week-old female nude mice were divided into 4 groups and subcutaneously inoculated with 1×106 stable APOC1-knockdown, APOC1-overexpressing or control MFC cells in the lateral flank. The mice were sacrificed 2 weeks later, and the tumors were harvested.
For the drug validation experiments, four-week-old female nude mice were divided into 5 groups and subcutaneously inoculated with 1×106 stable APOC1-overexpressing or control MFC cells in the lateral flank. Three days after inoculation, gefitinib (10 mg/kg) alone, etomoxir (40 mg/kg) alone or both were injected intraperitoneally every day for one week. The control mice received vehicle. The mice were monitored every two days, tumor growth was measured using a Vernier caliper over time, and the tumors were removed after one week of treatment. The tumor volume was calculated as (L×W2)/2, where length (L) is the longest dimension and width (W) is the shortest dimension. Tumor weight was also measured. The mice were sacrificed 10 days later, and the tumors were harvested.
For the tumor metastasis model, 1×106 stable APOC1-knockdown or APOC1-overexpressing MFC cells were injected into the tail veins of nude mice, the mice were sacrificed 2 weeks later, and the lungs were harvested.
2.20 Statistical analysis
All the experiments were performed at least three times. Statistical analysis was performed using GraphPad Prism 7.02 software. The experimental data are expressed as the mean ± standard deviation (x ± SD).