Animals. C57BL/6 mice were obtained from Joint Ventures Sipper BK Experimental Animal (Shanghai, China). Irg1f/f mouse was constructed by Shanghai Biomodel Organism Science & Technology Development Cooperation (Shanghai, China). Alb-Cre transgenic mouse (003574) were obtained from The Jackson Laboratory. of Genomic DNA extraction and genotyping were described previously [25]. All animal experiments were conducted in accordance with National Institute of Health Guide for the Care and Use of Laboratory Animals, with the approval of the Scientific Investigation Board of Second Military Medical University, Shanghai, China.
Reagents. Antibodies specific to human IRG1 (77510), mouse IRG1 (17805, 19857), caspase-3 (9662), cleaved caspase-3 (9661), caspase-8 (4790), human cleaved caspase-8 (9496), mouse cleaved caspase-8 (9429), cytochrome c (11940), SDHA (11998), Bax (2772), Mcl-1 (94296), Bim (2933), Flag-tag (14793), V5-tag (13202) and horseradish peroxidase-coupled secondary antibodies (7074 and 7076) were from Cell Signaling Technology (Danvers, MA). Antibody specific to β-actin (A5441), DEN (N0258), CHX (239764), LPS (L3024), MEM NAA (M7145) and anti-Flag M2 magnetic beads (M8823) were from Sigma-Aldrich (St. Louis, MO). Recombinant human TNF-α (300-01A) and mouse TNF-α (315-01A) were from Pepro Tech (Rocky Hill, NJ). TUNEL assay kit (11684817910) was from Roche (Shanghai, China). Olive oil (CAS: 8001-25-0, A502795-0100) and APAP (CAS: 103-90-2, A506808) were from Sangon Biotech (Shanghai, China). Cell (C3601) and tissue (C3606) mitochondria isolation kits were from Beyotime (Shanghai, China). Percoll solution (17-0891-01) was from GE Healthcare Life Science (Little Chalfont, UK). Type IV collagenase (LS004140) was from Worthington Biochemical Corporation (Lakewood, NJ). Protease inhibitor cocktail (539134-1SML) and apoptosis assay kit (PF032) were from Calbiochem (Darmstadt, Germany). Fetal Bovine Serum (FBS, 10099141C), DMEM (11965092), and RPMI 1640 (11875093) were from Gibco (Shanghai, China). 4-OI (HY-112675) was from MedChemExpress (Monmouth Junction, NJ).
Mouse Models. For DEN-induced hepatocarcinogenesis model, 15-day-old male mice were given a single injection of DEN (25 mg/kg) intraperitoneally and livers were harvested eight months later. For STAM HCC model, postnatal two-day-old male mice were injected with STZ (200 ug per mouse), and these mice were fed with HFD (D12492, Research Diets, New Brunswick, NJ) at one-month-old for five months. For acute liver injury model, eight-week-old male mice were treated with high-dose DEN (100 mg/kg) or APAP (400 mg/kg) intraperitoneally and sacrificed at the indicated time points. For DEN-induced compensatory proliferation model, male mice at 15 days old were stimulated with low-dose DEN (25 mg/kg) via intraperitoneal injection, and livers were examined at the indicated time periods. 4-OI (25 mg/Kg, dissolved in olive oil) was injected intraperitoneally, and livers were examined as indicated.
Cell lines and transfection. The human hepatocyte cell line HHL-5 and mouse hepatocyte cell line BNL CL.2 were both from the Type Culture Collection of the Chinese Academy of Sciences (Shanghai, China). HHL-5 was cultured in RPMI 1640 with 10% FBS, and BNL CL.2 was cultured in DMEM with 10% FBS and 1% non-essential amino acid. Cells were seeded in culture dishes, and jetPRIME transfection reagent (114 − 15, Polyplus-transfection, France) was applied for plasmid transfection according to manufacturer’s protocols described previously [26].
Primary hepatocyte isolation and treatment. Primary hepatocytes were isolated from eight-week-old mouse liver by the two-step liver perfusion and digestion methods described previously [27, 28]. After digestion, the liver capsule was peeled, minced and filtered with 70-micron membrane, then, primary hepatocytes were separated by density gradient centrifugation in 50% Percoll solution (P4937, Sigma-Aldrich) at 50 g for five minutes. The primary hepatocytes were resuspended in DMEM with 10% FBS and 1×107 cells were seeded into six-well plates for attaching overnight.
MS Analysis. The IRG1-associated proteins were immunoprecipitated from cell lysates, and the precipitates were washed, boiled and loaded to SDS-PAGE. With Coomassie Blue staining, the specific bands in IRG1 lane were cut and analyzed in reverse-phase nanospray liquid chromatography-tandem mass spectrometry. The MS and spectra analysis were performed by PTM BIO (Hangzhou, China) as described previously [29].
RNA extraction and real-time PCR. The total RNA were extracted by RNAiso Plus reagent (Takara, Dalian, China). Real-time quantitative RT-PCR (qRT-PCR) assay was performed by using LightCycler (Roche, Switzerland) and SYBR RT-PCR kit (RR430B, Takara, Dalian, China) as previously described.26 The qPCR primers for detecting mRNA expression were mouse IRG-1 (forward: 5’-ACT TCT CCA AGG AAG CCA AAG A-3’, reverse: 5’-ACT TTG TCA AGC TGA GCC CC-3’); internal control mouse β-actin (forward: 5’-AGT GTG ACG TTG ACA TCC GT-3’, reverse: 5’-GCA GCT CAG TAA CAG TCC GC-3’). The relative expression of each gene was normalized to the internal control using 2ΔΔCt cycle threshold method in each sample [30].
Primer sequences for mice genotyping. Irg1f/f forward: 5’-CTG AAA CTG TTA CCC TTA CAG-3’, reverse: 5’-AAG CTA GAT TGG CTT TAC AAT C-3’;Alb-cre forward: 5’-AAT GCT TCT GTC CGT TTG-3’, reverse: 5’-GGA TTA ACA TTC TCC CAC C-3’.
Liver function assessment. Serum ALT and AST were assessed by using an automatic biochemical analyzer FDC-7000i (Shanghai, China) according to recommended instructions.
Histological analysis. Tissues were fixed with paraformaldehyde and embedded in paraffin. Serial sections were sliced, and TUNEL, cleaved caspase-3, Ly6G, F4/80 and Ki67 staining were performed as previously described.26–28
Immunoprecipitation and western blot. All samples were lysed in cell lysis buffer (9803, Cell Signaling Technology) with additional protease inhibitor cocktail (539134, Millipore) at a ratio of 1:200. Protein lysates concentration was measured by bicinchoninic acid (BCA) assay kit (ab102536, Abcam) and equalized with lysis buffer. Equivalent amount of protein extracts was used for immunoprecipitation or loaded and subjected to SDS-PASGE, transferred onto nitrocellulose membranes, and then blotted as previously described [26, 27].
Flow cytometry. Cells were collected and labeled with Annexin Ⅴ-FITC/PI by using the apoptosis assay kit, and then subjected to flow cytometry analysis on BD Fortessa Cytometer and analyzed using FACSDiva software (Becton Dickinson).
Statistical analysis. Data are shown as mean ± s.d. from one representative of three independent experiments. Statistical comparisons between groups were computed by unpaired Student’s t-test, chi-square test, or one-way ANOVA in SPSS 17.0 (Chicago, IL), and a two-tailed P < 0.05 indicates statistical significance.