Cell culture and M1 viruses
HCT 116 (RRID:CVCL_0291) and HCT-8 (RRID:CVCL_2514) cell lines were from American Type Culture Collection (ATCC). Cells were cultured in DMEM supplemented with 10% (vol/vol) FBS (Thermo Fisher Scientific) and 1% penicillin/streptomycin (Thermo Fisher Scientific). All cell lines were cultured at 37 °C in a 5% CO2 environment. All cell lines were authenticated by GENWIZ, Inc. China using the GenePrint 10 System (Promega) and were mycoplasma free according to the MycoGuard mycoplasma PCR detection kit (MPD-T-050, GeneCopoeia).
The M1 virus was grown in the Vero cell line and collected for experiments. The M1 virus was provided by Guangzhou Virotech Pharmaceutical Technology Co., Ltd. M1-GFP is a recombinant M1 engineered to express jellyfish green fluorescent protein [10].
Cell viability assay
Cells were seeded in 96-well plates at 3000 cells per well. After different treatments indicated in the figure legends were administered, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) was added (1 mg/ml) and incubated at 37 °C for 3 h. The supernatants were removed, and the MTT precipitate was dissolved in 100 μl of DMSO. The optical absorbance was determined at 570 nm by a microplate reader (synergy H1, Gene Company).
Antibodies and reagents
The following antibodies and reagents were used in this study: HK2 (#2867S, Cell Signaling Technology, RRID: AB_2232946); Ki-67 (#9449, Cell Signaling Technology, RRID: AB_2797703); MYC (#MA1-980, ThermoFisher Scientific, RRID: AB_558470); SECTM1 (#PA5-42725, ThermoFisher Scientific, RRID: AB_2606358); ADAM11 (#PA5-50593, ThermoFisher Scientific, RRID: AB_2636046); 2-DG (#S4701, Selleckchem); Lonidamine (#S2610, Selleckchem). Human IFN-α High sensitivity ELISA kit (EK199HS-01, MultiSciences). Human IFN-β ELISA kit (EK1236-01, MultiSciences).
RNA-sequencing
HCT 116 tumor cells were treated with control, M1 (MOI = 1 pfu/cell), Lonidamine (50 μM) or M1 (MOI = 1 pfu/cell) plus Lonidamine (50 μM) for 24 h. Total RNA was extracted from 1 × 106 cells with TRIzol Reagent (Thermo Fisher Scientific) and was sent to HaploX Genomics Center (HGC, China) for RNA sequencing by Illumina platform.
RNA interference
siRNAs specific to different genes and control nontargeting siRNA were synthesized by Sigma-Aldrich. The cells were transfected with the siRNAs (50 nM) using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in Opti-MEM medium (Thermo Fisher Scientific). The sequences of the siRNAs are listed below.
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si-HK2 001: 5′-CTGTGAAGTTGGCCTCATT-3’
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si-HK2 002: 5′-ACGACAGCATCATTGTTAA-3’
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si-HK2 003: 5′-CTGGCTAACTTCATGGATA-3’
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si-MYC 001: 5′-GAGGAGACATGGTGAACCA-3’
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si-MYC 002: 5′-GGGTCAAGTTGGACAGTGT-3’
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si-MYC 003: 5′-CGACGAGACCTTCATCAAA-3’
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si-ADAM11 001: 5′-GCTGTAGCATCGACGAGTA-3’
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si-ADAM11 002: 5′-TCCTCTCCTCGCAATACGT-3’
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si-ADAM11 003: 5′-GCAAAGACTGCAGTATCCA-3’
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si-SECTM1 001: 5′-GTGGGACACCAGAGAAATA-3’
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si-SECTM2 002: 5′-TGGTCATGTTCGCCTGGTA-3’
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si-SECTM3 003: 5′-GGCACAGCTGGTGATCAAA-3’.
RT-qPCR
Total RNA was extracted using TRIzol (Thermo Fisher Scientific), and 2 μg of total RNA was reverse-transcribed to cDNA with oligo (dT) (synthesized by Thermo Fisher Scientific) and RevertAid Reverse Transcriptase (Thermo Fisher Scientific). The expression levels of the specific genes were calculated by the comparative Ct method using SuperReal PreMix SYBR Green (FP204-02, TIANGEN) and an Applied Biosystem 7500 Fast Real-Time PCR system (Thermo Fisher Scientific, RRID: SCR_014596). The sequences of the primers are listed below:
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C10orf10 Forward: 5′-GTGAGGTCTATATCTCGACTGGC-3’.
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C10orf10 Reverse: 5′-ACTGAAACGTGCGGTGATGT-3’.
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UCP2 Forward: 5′-GGAGGTGGTCGGAGATACCAA-3’.
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UCP2 Reverse: 5′-ACAATGGCATTACGAGCAACAT-3’.
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PLEKHA4 Forward: 5′-TTGGCCGCTGACACCTTAG-3’.
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PLEKHA4 Reverse: 5′-GGTTGCCCATAGTCGTCCC-3’.
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SECTM1 Forward: 5′-CGCCATCTTCAATGAGGTGG-3’.
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SECTM1 Reverse: 5′-CCAGCGTGACTTGTCTGTTATT-3’.
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ETV6 Forward: 5′-GCTCAGTGTAGCATTAAGCAGG-3’.
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ETV6 Reverse: 5′-CGAGGAAGCGTAACTCGGC-3’.
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MYC Forward: 5′-GTCAAGAGGCGAACACACAAC-3’.
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MYC Reverse: 5′-TTGGACGGACAGGATGTATGC-3’.
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FKBP5 Forward: 5′-AATGGTGAGGAAACGCCGATG-3’.
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FKBP5 Reverse: 5′-TCGAGGGAATTTTAGGGAGACT-3’.
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IFIT1 Forward: 5′-GCGCTGGGTATGCGATCTC-3’.
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IFIT1 Reverse: 5′-CAGCCTGCCTTAGGGGAAG-3’.
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ADAM11 Forward: 5′-AACCCAGCCGTCTGGTTAG-3’.
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ADAM11 Reverse: 5′-TGGGATGACGAAACTCACCTG-3’.
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SAT1 Forward: 5′-ACCCGTGGATTGGCAAGTTAT-3’.
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SAT1 Reverse: 5′-TGCAACCTGGCTTAGATTCTTC-3’.
Western blot analysis
Cell samples were prepared using M-PER Mammalian Protein Extraction Reagent (Thermo Fisher Scientific) and then separated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis. The membranes were visualized with a ChemiDoc XRS + System (Bio-Rad) using Immobilon Western Chemiluminescent HRP Substrate (Millipore).
Caspase activity assay
HCT 116 and HCT-8 cell lines were treated with different drugs as the figure legend indicated, 100 μl of caspase 3/7, 8 and 9 (Promega) reaction buffer was added to the supernatant and incubated for 30 min. The liquids were transferred to a black-bottomed plate, the luminescence was detected by Synergy H1 microplate reader (Gene Company). The values were normalized to cell numbers (MTT assay).
HK2 activity assay
Hexokinase II Inhibitor Screening Kit (Colorimetric) (abcam, ab211114) was used to detect the activity of HK2. In brief, prepare the hexokinase 2 enzyme solution by adding hexokinase recombinant enzyme solution to the assay buffer and incubate for 5 min at 25 °C. Then prepare the hexokinase substrate mix according to the instruction. Mix the hexokinase 2 enzyme solution and hexokinase substrate with lonidamine or positive HK2 inhibitor (Bromopyruvic Acid) by gentle shaking. Measure absorbance (OD = 450 nm) on a microplate reader (Gene company) immediately in kinetic mode for 5–30 min at 25 °C. When detecting the activity of hexokinase in cells, cell protein lysate is used to replace the human HK2 recombinant protein as HK2 enzyme for the reaction. Four HK isoforms (HK1, HK2, HK3 and HK4) are found in human, all HK isoforms are capable of converting glucose into glucose-6-phosphate. So in the assay with cell protein lysate, we can only determine whether lonidamine can inhibit the activity of total HK, the activity of each specific HK isoform is unable to be distinguished.
Animal models
The mouse study was approved by the Animal Ethics and Welfare Committee of Sun Yat-sen University, and all experiments were conducted according to the US “Public Health Service Policy on Humane Care and Use of Laboratory Animals”. HCT 116 (1 × 106 cells/mouse) tumor cells were implanted subcutaneously into the hind flanks of 5-week-old 16 g female BALB/c-nu/nu mice (the mice were bought from Nanjing Biomedical Research Institute, China, and housed in an SPF facility with normal temperature and food). After 6 days, tumors were observed (approximately 50 mm3). The mice were randomized and grouped to 4 treatment groups: vehicle control, M1 virus (i.v., 2 × 106 pfu per mouse, daily for 5 days), Lonidamine (i.p., 10 mg/kg, daily for 5 days), combination of M1 virus and Lonidamine. The lengths and widths of the tumors were measured every 3 days, and the tumor volume was calculated according to the formula (length × width2)/2. At the termination of the experiment, all mice were euthanized by overdose anesthesia, and the tumors were removed and fixed in 4% paraformaldehyde for subsequent immunohistochemistry (IHC) assays. The study was blind.
Immunohistochemistry (IHC) assay
The expression of Ki-67 in the tumors was assessed by immunohistochemistry (IHC). Briefly, tumor sections were dewaxed in xylene, hydrated in decreasing concentrations of ethanol, immersed in 0.3% H2O2-methanol for 30 min, washed with phosphate-buffered saline, and probed with monoclonal antibodies or isotype controls at 4 °C overnight. After being washed, the sections were incubated with biotinylated goat anti-rabbit or anti-mouse IgG at room temperature for 2 h. Immunostaining was visualized with streptavidin/peroxidase complex and diaminobenzidine, and sections were counterstained with hematoxylin.
Statistics
All statistical analyses were performed using GraphPad Prism software 8.0 (RRID: SCR_002798) and SPSS 18.0 software (RRID: SCR_002865). Most of the data were analyzed by a two-tailed Student’s t test or one-way ANOVA with Dunnett’s test for pairwise comparisons. Tumor volumes were analyzed by repeated measures of ANOVA. Phase contrast and fluorescence pictures were taken with a Nikon Eclipse A1 microscope. The IHC staining intensity was analyzed by ImageScope software (ImageScope, RRID: SCR_014311). The Wilcoxon signed-rank test was used to compare non-normally distributed data. Bars show the mean ± SD of three independent repeated experiments. Significant differences were accepted if the p-value was < 0.05.