Cell culture
Human umbilical vein endothelial cells (HUVECs, Cat#8000, ScienCell) were cultured at a 37 ℃ incubator in ECM (Cat#1001, ScienCell) with 5% FBS (Cat#0025, ScienCell), 1% ECGS (Cat#1052, ScienCell) and 1% P/S (Cat#0503, ScienCell). For normoxic treatment, HUEVCs were grown at atmospheric oxygen concentrations (21%) with 5% CO2. For hypoxic treatment, they were exposed to an atmosphere of 1% oxygen, 5% CO2 and 94% N2. Human embryonic kidney 293 T (HEK293T) cells were purchased from Shanghai Zhongqiaoxinzhou Biotechnology Co., Ltd. (China) and cultured in DMEM supplemented with 10% FBS and 1% P/S.
Small interfering RNAs, plasmid transfection and adenovirus infection
HUVECs or HEK293T were transfected with small interfering RNAs (siRNAs) or plasmid using jetPRIME (Cat#114, Polyplus-transfenction) and infected with adenovirus according to the manufacturer’s protocol. The sequences of siRNAs were listed in Additional file 2: Table S1. The plasmid of STAT3, ΔNTD domain (2–120 aa delated), ΔCCD domain (141–313 aa delated), ΔDBD domain (325–464 aa delated), ΔSH2 domain (584–647 aa delated) and TET2 were constructed by Shanghai Genechem Co., Ltd., as well as the adenoviruses. The plasmid of N-terminal region of TET2 (N1127) and CD domain of TET2 were obtained from Prof. Dan Ye (Fudan University).
Proliferation assay
EdU Cell Proliferation kit (Cat#C10339, Invitrogen) was used to determine the cell proliferation. After starvation, HUVECs were cultured with EdU-labeling mixture (10 mM) under hypoxia for 12 h. Then cell proliferation was detected according to the manufacturer’s instruction. In summary, 4% paraformaldehyde was used to fix HUVECs, and 0.5% TritonX‐100 was used to permeabilized them. Subsequently, HUVECs were incubated with 1 × Click-iT EdU reaction mixture and stained with Hoechst 33342 for another 15 min. The cell proliferation rate was calculated as EdU-positive cells/total cells of each field.
Scratch assay
A cross-scratch wound was made by a 200 μl pipette tip in the center of the well after starvation of transfected HUVECs under hypoxia. Pictures were taken from each well after 24 h culture. Wound areas were analyzed by ImageJ software (v1.52a, National Institutes of Health).
Tube formation assay
Tube formation was detected in a 24-well plate using Matrigel (Cat#354230, Corning), on which transfected HUVECs (2 × 105 cells/well) were seeded under hypoxia. After 8 h culture, pictures were taken from each well. The tube length and tube number were measured by ImageJ software (v1.52a, National Institutes of Health).
Apoptosis assay
After being transfected with siRNA or infected with adenovirus for 24 h, HUVECs were incubated under hypoxia. After 48 h hypoxia, HUVECs were digested by trypsin and resuspended in binding buffer. 5 μl PI was added into HUVECs and flow cytometry was analyzed with 1 h.
RNA extraction and RT-qPCR
Total RNAs were isolated using TRIzol Reagent (Cat#15596026, Invitrogen). 1 µg of total RNAs was used for reverse transcription by HiScript III RT SuperMix (Cat#R323, Vazyme) and qPCR was performed using ChamQ Universal SYBR qPCR Master Mix (Cat#711, Vazyme). Quantitative analysis was performed with the 2−△△CT method. The sequence of primers was listed in Additional file 2: Table S2.
Western blot
Proteins were extracted from cells by Cell Lysis Buffer (Cat#9803 s, Cell Signaling Technologies) and determined using the BCA Protein Quantification Kit (Cat#20201ES76, Yeasen). 30 μg protein for each group was separated on the SDS‐PAGE and transferred to PVDF membranes. After being blocked with 5% BSA at room temperature for 1 h, membranes were incubated with primary antibodies at 4 °C overnight. The next day, they were incubated with the HRP‐linked secondary antibodies at room temperature for 1 h and exposed to ECL substrate (Cat#180–5001, Tanon). The Amersham Imager 600 system (GE Healthcare, USA) was used to develop the membrane and ImageJ software (v1.52a, National Institutes of Health) was used for quantification. The primary and secondary antibodies were listed in Additional file 2: Table S3.
Co-immunoprecipitation
Cell lysis buffer (Cat#9803, Cell Signaling Technologies) with protease inhibitors (Cat#04693159001, Roche) was used to harvest HUVECs or HEK293T. After determination by the BCA Protein Quantification Kit (Cat#20201ES76, Yeasen), 500 µg of cell lysate was incubated with the primary antibodies at 4 °C overnight. The next day, 20 µl of protein A/G agarose (Cat#sc-2003, Santa Cruz) was used to purify the cell lysate at 4 °C for 4 h. The immunoprecipitated proteins were then used for western blot. The antibodies were listed in Additional file 2: Table S3.
Extraction of cytoplasmic and nuclear proteins
The cytoplasmic and nuclear proteins were extracted from HUVECs using the kit of NE-PER Nuclear and Cytoplasmic Extraction Reagent (Cat#78,833, Invitrogen). Briefly, HUVECs were transfected with siRNAs for 48 h and then treated with IL-6 (20 ng/mL, Cat#200–06, PeproTech) for 0, 15, 30, 60 min. After digestion by trypsin, HUVECs were suspended in completed medium. The portions of cytoplasm and nucleus were isolated extracted according to the instruction of manufacturer.
DNA extraction
TIANamp Genomic DNA Kit (Cat#DP304, Tiangen) was used to isolate genomic DNAs from cultured cells. Briefly, cultured cells were treated with lysis buffer and released genomic DNAs. Next, RNaseA and proteinase K were used to remove RNAs and histone. Then the spin column bound with DNAs and centrifugation processing removed contaminants and enzyme inhibitors. Purified DNAs were eluted in low-salt buffer and ready for use in downstream applications.
Dot blot
Total DNAs were extracted as previously mentioned and diluted to 100 ng/μl. 2 μl of total DNAs were dropped onto a Hybond‐N+ membranes and cross‐linked by UV for 30 s. Then, the membranes were blocked with 5% BSA at room temperature for 1 h and incubated with anti-5-hmC antibody at 4 °C overnight. After being washed three times, they were incubated with HRP‐linked secondary antibody at room temperature for 1 h and exposed to ECL substrate (Cat#180–5001, Tanon). The Amersham Imager 600 system (GE Healthcare, USA) was used to develop the membrane and ImageJ software (v1.52a, National Institutes of Health) was used for quantification. The antibodies were listed in Additional file 2: Table S3.
ELISA
Genomic DNA methylation was measured by the Global DNA Methylation-LINE-1 Kit (Cat#55017, Active Motif). Briefly, the genomic DNAs were enzymatically digested using MseI enzyme to generate the appropriate fragments to hybridize to a biotinylated consensus sequence corresponding to human LINE-1 transposon. Hybridized samples were immobilized to a streptavidin-coated 96-well plate while unbound DNA fragments were washed away. Methylated cytosines were identified using a 5-methylcytosine antibody, HRP-conjugated secondary antibody and colorimetric detection reagents. The colorimetric readout was quantified by microplate reader at 450 nm. Generating a standard curve using the included DNA standards with known LINE-1 methylation levels provides the relative level of 5-methylcytosine in each DNA sample.
ChIP-qPCR
Chromatin immunoprecipitation (ChIP) assays were performed using a SimpleChIP Enzymatic Chromatin IP kit (Cat#9003, Cell Signaling Technologies). HUVECs were crosslinked with 1% paraformaldehyde and the chromatin was fragmented with nuclease and sonication. Then the fragmented chromatin was incubated with anti-TET2 antibody or negative control IgG overnight. The next day, protein G magnetic beads were used to incubate with chromatin. After being washed and purified, precipitated DNAs were analyzed by qPCR. Primers used for ChIP-qPCR are listed in Additional file 2: Table S2.
GluMS-qPCR
The 5-hmC and 5-mC levels in TET2-binding regions were detected by EpiMark 5-hmC and 5-mC Analysis Kit (Cat# E3317S, New England Biolabs). In short, genomic DNAs were extracted as previously mentioned and treated with T4 β- glucosyltransferase, by which all 5-hmC would be glucosylated to 5-ghmC. Then the modified DNAs were cleaved by restriction endonucleases, including MspI and HpaII. MspI would cleave 5-mC and 5-hmC, but not 5-ghmC, while HpaII would cleave only a completely unmodified site: any modification (5-mC, 5-hmC or 5-ghmC) at either cytosine blocked cleavage. The MspI- and HpaII-resistant fractions were quantified by qPCR and normalized to the mock digestion. Primers used for GluMS-qPCR were listed in Additional file 2: Table S2.
RNA sequencing
HUVECs were transfected with control siRNA (Ctrl siRNA) or TET2 siRNA (50 nM) for 24 h, followed by 48 h of hypoxia. RNA sequencing was conducted by Berry Genomics (China). In brief, Trizol reagent was used to harvest total RNAs and 1 µg of total RNAs was used for constructing RNA libraries by Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122–1001, Illumina). RNA libraries for sequencing were prepared using the standard Illumina protocols, and RNA sequencing was performed by the Illumina NovaSeq6000 platform. DESeq (version 1.22.1) was used to screen the differentially expressed genes. The raw data of RNA sequencing were deposited in the Gene Expression Omnibus (Accession Number: GSE200080).
GVSA
To explore the underlying changes in pathway activity between two groups with significant differences, we performed gene set variation analysis (GSVA) to calculate the scores for each group based on HALLMARK gene sets. Enriched gene sets were assigned based on control P-value < 0.05 as significantly altered.
GSEA
Gene set enrichment analysis (GSEA, version 4.1.0) was used to determine whether a genetically defined genome is statistically significant between HUVECs transfected with control siRNA and TET2 siRNA under hypoxia. We constructed RNK file based on genes’ log2FoldChange and − log10P.value. GSEA was performed with default algorithm as 1000 permutations, minimum term size of 15, and maximum term size of 500. We served HALLMARK as our annotated gene sets, which were collected from the Molecular Signature Database 3.0. Enriched gene sets were assigned based on normalized P-value < 0.05 and FDR q-value < 0.25.
Animals
The wild-type mice (WT, C57BL/6) were purchased from Vital River Laboratory. CDH5Cre mice (B6-Cdh5tm1(iCre/ERT2)/Bcgen) were purchased from Biocytogen Co., Ltd. TET2-floxed mice (B6;129S-Tet2tm1.1Iaai/J) and mTmG mice (B6.129(Cg)-Gt (ROSA)26Sortm4(ACTB−tdTomato,−EGFP)Luo/J) were purchased from The Jackson Laboratory. The primers used for genotyping were listed in Additional file 2: Table S2. After continuous cross breeding, TET2flox/flox mice, CDH5Cre; TET2flox/flox mice, CDH5Cre; mTmG mice and CDH5Cre; TET2flox/flox; mTmG mice were generated. To obtain TET2EC−KO mice and TET2EC−KO; mTmG mice, 8-week-old male CDH5Cre; TET2flox/flox mice and CDH5Cre; TET2flox/flox; mTmG mice were injected with tamoxifen (75 mg/kg body weight, Cat#T5648, Sigma) for 5 consecutive days. The control mice received the same treatment. Animal studies were conducted in compliance with the Guide for the Care and Use of Laboratory Animals published by the NIH and approved by the Animal Care and Use Committees of Shanghai Tenth People’s Hospital.
Hindlimb ischemia model
The hindlimb ischemia (HLI) model was performed as previously described [26]. After anesthetization with 2% isoflurane, the hair of hindlimb was removed. The left femoral artery was ligated and excised, while sham operations were performed on the contralateral hindlimb. Perfusion recovery was detected by PeriCam PSI System (PeriMed, Sweden) on day 0, 3, 7, 14 and 21 post-HLI. The ischemic limb perfusion was normalized to the sham limb for each mouse.
Tumor transplant
8 week-old male TET2flox/flox and TET2EC−KO mice underwent xenograft experiments. The B16F10 mouse melanoma cells were provided by Prof. Ping Wang of Tongji University. Cells were cultured in DMEM complete medium (high glucose, 5% FBS, 0.5% PS) and suspended in PBS (1 × 107 cells/mL), then injected subcutaneously in the murine flank (100 µl/mouse). The volume of tumors was calculated as 4π/3 × (width/2)2 × (length/2) by measuring the length and width every 2 days. Then mice were euthanized and tumors were dissected 12 days after injection.
Immunofluorescence and histology
Tissues of mice were harvested and sliced into 5 µm-thick Sect. 4% formaldehyde-fixed sections were incubated in 10% normal goat serum and 0.5% Triton-X 100 for half an hour. DAPI (1:5000, Vector Laboratories) was used to stain the nuclei for 30 min. All steps should be operated in the dark. Olympus IX83 fluorescence microscope (Olympus Corporation, Japan) was used to obtain images. H&E staining was used to quantify tissue necrosis and regenerating muscle fibers, and Masson staining was used to quantify tissue fibrosis. Necrotic tissues were identified by morphological alterations of myofibers or loss of sarcolemmal integrity, the presence of cellular debris and many mononuclear cell infiltrates in the surrounding interstitial space. Regenerating tissues were identified by the predominant presence of fibers with centrally positioned nuclei and/or some lingering mononuclear cell infiltrates. The quantification was performed by ImageJ software (v1.52a, National Institutes of Health), and expressed as the ratio of positive area to the total surface area of the tissue section.
Flow cytometry analysis
The flow cytometry analysis was performed as Liu et al. [27] described. Briefly, the muscles of anesthetized mice were cut into small pieces and digested in a mixture of 5 mL HBSS containing 1 mL collagenase II (100 U/mL, Cat#1148089, Sigma-Aldrich) and 2 mL (1 U/mL) dispase (Cat#354235, Corning) at 37 °C for 1 h. Next, the tissues were digested in 1 U/mL dispase for 30 min. After digestion, the cells were filtered with 70 μm filters and red blood cells were lysed in FACS Lysing Solution (Cat#349202, BD Pharmingen) for 5 min at room temperature. Finally, cells were resuspended in 0.1% BSA solution.
Statistical analysis
Each study was performed with at least 3 independent experiments and run-in triplicate. Data were calculated and presented as the mean ± SEM. For two groups, statistical significance was determined by Student’s t-test if data had equal variance and by Mann–Whitney test if data had unequal variance. For more than two groups, statistical significance was determined by one-way or two-way ANOVA with Bonferroni post hoc test. P-value < 0.05 was defined as statistical significance. The statistical analysis was performed using GraphPad Prism (v6.01, GraphPad Software).