Cell lines and cell culture
Myeloid leukemia cell line KG1a, and BM-derived stromal cell lines HS5 and HS27a, were kindly donated by Prof. H. Joachim Deeg (Fred Hutchinson Cancer Research Center; Seattle, WA, USA). SKM-1, a cell line established from MDS progressing to AML, was donated by Prof. Xiao Li (Sixth People's Hospital, Shanghai Jiao Tong University). These cell lines were all cultured in RPMI 1640 medium (Biological Industries; Beit Haemek, Israel) added with 10% FBS (Biological Industries) and 1% penicillin/ streptomycin (Beyotime Biotechnology; Haimen, Jiangsu, China) at 37°C in 5% CO2 atmosphere.
Generation of conditional MGAT3loxP/loxP mice
MGAT3fl/fl transgenic mice were generated using a homologous combination knockout strategy, in which exon 2 of MAGT3 gene was flanked with two loxP sites. The targeting construct was microinjected into embryonic stem cells of C57BL/6 background mice. Heterozygous mice were generated by standard procedures with in vivo Cre-mediated excision of loxP-neo-loxP cassette. MGAT3 and/or loxP insert were amplified by PCR using primers 5’-AAGTTGGATACAGTGGAGGGCTAG-3’ and 5’-CACTGACCTTAATGTTCTTTCTTGGAC-3’. Conditional deletion of MGAT3 gene was accomplished by crossbreeding leptin receptor (LepR)-Cre transgenic mice (donated by Prof. Caiwen Duan, Dept. of Pharmacology and Chemical Biology, Shanghai Jiao Tong University) with MGAT3fl/fl mice. Animal experiments were approved by the Animal Care and Use Committee of Northwest University, and performed in accordance with its guidelines.
Isolation and culture of mouse BM stromal cells
Mouse BM stromal cells were isolated from tibia and femoral marrow, and cultured for 24 h in minimal essential medium alpha (MEMα; Biological Industries) added with 10% FBS and 1% penicillin/ streptomycin (Beyotime) at 37°C in 5% CO2 atmosphere. Culture medium was changed every 3 days. Cells with hematopoietic markers were removed, and CD54, CD73, and CD90 expression was evaluated in adherent cells.
Human BM stromal cells
Human BM stromal cells were isolated from marrow aspirates from healthy subjects or MDS/AML patients (People’s Hospital of Shaanxi Province) (Table S1). Briefly, mononuclear cells were separated by Ficoll-Hypaque gradient centrifugation. Primary BM stroma cells were isolated from Ficoll-Hypaque–separated bone marrow mononuclear cells by culturing 2.5 to 3 × 107 cells per T75 flask in DMEM F12 (Biological Industries) cultured at 37°C with 5% CO2. After 3 days, non-adherent cells were removed. When cultures reached 80–90% confluence, cells were detached, and plated for following experiments. Written informed consent was obtained from all marrow donors in accordance with Declaration of Helsinki guidelines. All experimental designs using human tissues were reviewed and approved by the Research Ethics Committee of Northwest University.
Stable transfection of MGAT3
MGAT3 was amplified via PCR and linked to lentiviral vector pLVX-AcGFP-N1 (Takara; Shiga, Japan). Lentiviral vectors encoding short hairpin RNAs (shRNAs) targeting MGAT3 were generated using piLenti-siRNA. Scrambled piLenti-siRNA was used as negative control. Constructed lentiviral vectors, together with pMD2.G and psPAX2 (Addgene; Cambridge, MA, USA), were packed into HEK293T cells. HS27a and HS5 cells were infected with lentivirus particles. Stable transfectants were selected using puromycin and confirmed by western blotting.
Immunofluorescence staining
Cells cultured on confocal small dishes were washed with PBS, fixed with 4% paraformaldehyde (Sigma-Aldrich; St. Louis, MO, USA) in PBS for 15 min, permeabilized with 0.2% Triton X-100 in PBS for 10 min, incubated with 3% BSA in PBS at 37°C for 1 h, probed with primary antibody against MGAT3 (cat # ab75769, Abcam; Cambridge, MA, USA) or MCAM (cat # ab135514, Abcam) at 4°C overnight, incubated 1 h with FITC-conjugated anti-rabbit IgG antibody (Abcam), washed 3x with PBS, and incubated with DAPI for 15 min at room temperature (RT). For lectin staining, cells were fixed, blocked as described above, and probed with FITC-conjugated lectin PHA-E (Vector Laboratories; Burlingame, CA, USA). Fluorescence images were obtained by confocal microscopy (model TCS SP8, Leica Microsystems; Solms, Germany).
Quantitative real-time PCR (qRT-PCR)
Total RNA was isolated using RNA Pure Tissue & Cell Kit (CW Biotech; Beijing). Primers were designed using Primer-BLAST software program (ncbi.nlm.nih.gov/tools/primer-blast). First-strand cDNA was synthesized from total RNA using HiScript II Q RT SuperMix (Vazyme; Nanjing, China). qRT-PCR was performed by SYBR Green I dye detection with AceQ qPCR SYBR Green Master Mix (Vazyme), Primers are listed in Online Supplementary Table 2. and gene expression was quantified by 2−ΔΔCt method 18, 19.
In vitro co-culture model
HS5 and HS27a cells (1×105) were seeded in 6-well plates and cultured overnight in RPMI 1640 supplemented with 10% FBS. Clonal cells (3×105) were added for co-culture, incubation continued for 48 h, and stromal and clonal cells were collected.
Flow cytometry (FACS) analysis
Cells were co-cultured with stromal cells for 48 h, harvested, washed, fixed, permeabilized, and incubated with FITC-conjugated PHA-E for 2 h at 37°C. MDS/AML malignant clonal cells were distinguished from co-cultured cells using FITC-conjugated anti-human CD45 Ab (BD Biosciences; Franklin Lakes, NJ, USA). For proliferation analysis, cells were stained with EdU Alexa Fluor 647 kit (Keygen; Jiangsu, China) as per manufacturer’s protocol, and analyzed by FACS (ACEA Biosciences; San Diego, CA, USA).
Western blotting
Cells were harvested and lysed with radioimmunoprecipitation assay (RIPA) buffer (50 mM Tris, pH 7.2, 1% Triton X-100, 0.5% sodium deoxycholate, 0.1% SDS, 150 mM NaCl, 10 mM MgCl2, 5% glycerol) containing 1% protease inhibitor (Sigma-Aldrich). Lysate was centrifuged (14,000 × g, 15 min, 4°C), supernatant was collected, and protein concentration was determined by bicinchoninic acid (BCA) assay (Beyotime). Proteins (25 µg) were separated by SDS-PAGE, and transferred onto polyvinylidene difluoride (PVDF) membranes (Bio-Rad; Hercules, CA, USA). Membranes were blocked with 3% BSA (Beyotime) in TBST for 1 h at 37°C, probed overnight with primary antibody at 4°C, and incubated with appropriate HRP-conjugated secondary antibody. Bands were visualized by enhanced chemiluminescence (ECL; Vazyme), and photographed using a bioluminescence imaging system (Tanon; Shanghai).
Lectin blotting
Proteins from each sample were separated by 8% SDS-PAGE and transferred onto PVDF membranes. Membranes were soaked in 3% (w/v) BSA in TBST for 2 h at 37°C, probed with biotin-conjugated PHA-E (Vector Labs) overnight at 4°C, and incubated with appropriate HRP-conjugated streptavidin. Bands were visualized and photographed as described above.
Purification and characterization of exosomes
Exosomes were purified from plasma or cells and characterized as described previously 20. For cells, KG1a cells were cultured with RPMI 1640 containing 10% exosome-free FBS for 48 h, and supernatant was collected. For patient or healthy control, 5 mL bone marrow aspirate was collected in EDTA-anticoagulant tube, and centrifuged at 2000 x g for 20 min at 4°C, using bone marrow sample separation kit (TBD; Tianjin, China). 1 mL upper plasma was collected. Cell supernatant or plasma was centrifuged sequentially at 500 × g for 10 min, 2000 × g for 20 min, 10,000 × g for 30 min at 4°C, and ultracentrifuged twice at 100,000 × g (model Optima XE-100, Beckman Coulter Life Sciences; Indianapolis, IN, USA) for 70 min. Morphology of exosomes was evaluated by transmission electron microscopy (model H-7650; Hitachi; Tokyo) at 80 kV, and size distribution evaluated by nanoparticle tracking analyzer (NanoSight LM10, (Malvern Instruments; Malvern, UK).
Exosome uptake
Purified exosomes were labeled with ExoTracker probes as described previously21. In brief, exosomes were incubated with ExoTracker for 30 min at 37°C, unbound ExoTracker removed using 10-kD centrifugal ultrafiltration filters, and cells incubated with labeled exosomes for 2 h at 37°C and analyzed by FACS.
Exosomal miRNA-seq analysis
Total RNA from exosomes was extracted using exoRNeasy Serum/ Plasma Maxi Kit (Qiagen; Valencia, CA, USA) as per manufacturer’s instructions. miRNA libraries were constructed using QIAseq miRNA Library Kit (Qiagen) and analyzed using automated DNA analyzer (model Qsep100, BiOptic Inc.; Taiwan). miRNA-seq analysis was performed using NextSeq CN500 system (Illumina; San Diego, CA, USA).
Luciferase reporter assay
Sequences of predicted miR-188-5p binding sites of MGAT3 3’-untranslated regions (3’-UTRs), and corresponding mutants, were synthesized and inserted into luciferase reporter vector psiCHECK-2 (Promega; Madison, WI, USA). Constructed plasmids were co-transfected together with miR-188-5p mimic into HEK293T cells. Relative luciferase activity was determined using Dual Luciferase Assay Kit (Promega) as per manufacturer's instructions.
Immunoprecipitation (IP) assay
Cells from each sample were cultured and lysed as described above. Lysates (1 mg) were incubated with 2 µg primary antibody for 1 h at 4°C, and added with 20 µl protein A/G Plus-Agarose. The mixture was incubated on a shaker overnight at 4°C, rinsed with 1X PBS, denatured with SDS sample loading buffer, and analyzed by western blotting.
Proteomic analysis
Proteins (100 µg) were denatured with 8 M urea, reduced by 5 mM dithiothreitol (DTT) for 1 h at RT, alkylated with 20 mM iodoacetamide (IAM) for 30 min in the dark at RT, diluted with deionized water to lower urea concentration below 2 M, digested with lysyl endopeptidase (Wako Puro Chemical; Osaka, Japan) for 4 h at 37°C, and digested with trypsin (Promega) overnight at 37°C. The mixture was acidified with 10% trifluoroacetic acid (TFA) to pH < 3 and purified using C18 cartridges (Waters Corp.; Taunton, MA, USA). Two-dimensional liquid chromatography/ mass spectrometry (LC-MS) and data analysis were performed using LTQ Orbitrap MS (Thermo Fisher; San Jose, CA, USA) and Proteome Discoverer software tool (Thermo Fisher), with quantification by MaxQuant software program V. 1.5.2.8 (maxquant.org).
Immunoprecipitation MS (IP-MS)
Protein extraction, IP, and SDS-PAGE were performed as described previously22. Protein bands were stained with Coomassie Brilliant Blue R-250 (Thermo Fisher) and then decolorized. Target bands were diced into small pieces, destained with 25 mM NH4HCO3 in 50% acetonitrile (ACN), reduced by 10 mM DTT/ 50 mM NH4HCO3 for 1 h at RT, alkylated with 20 mM IAM/ 50 mM NH4HCO3 in the dark for 45 min, and digested with trypsin overnight at 37°C. Digested peptides were dissolved with 60% ACN/ 0.1% TFA and subjected to 2-D LC-MS analysis (Thermo Fisher).
NHS-LC-biotin labeling of membrane proteins
Cells were washed with cold PBS to remove amine-containing medium, resuspended in 2 mM EZ-Link Sulfo-NHS-LC-Biotin (Thermo Fisher), and incubated for 30 min at RT. Excess biotinylation reagent was neutralized by 100 mM glycine in PBS for 15 min at RT. For each sample, total protein was extracted, and biotin-labeled membrane protein was pulled down by streptavidin-coupled agarose beads and assayed by western blotting.
In vivo mouse experiment
Nod.cg-Prkdcscid Il2rgtm1wjll (NSG) mice (age 6–8 wk) were i.p. injected with the chemotherapy drug busulfan (30 mg/kg) to suppress BM activity. HS5, HS5-MCAM, or HS5-MCAM-Mu cells together with KG1a cells (ratio 1:3) were co-transplanted into mice via tail vein on day 1. Peripheral blood was collected and assayed on days 10, 17, and 24, and mononuclear cells were stained with anti-CD45 Ab for FACS analysis. Mice were then euthanized, and spleen and BM were collected. All animal experiments were performed in accordance with guidelines of the Animal Care and Use Committee of Northwest University.
Statistical analysis
Data are presented as mean ± SEM. Statistical significance of differences between means of two groups was evaluated by Student’s t-test. Comparisons of multiple groups were evaluated by ANOVA with Bonferroni’s post hoc test.