Date source
Three AML LSCs sequencing chips and one AML minimal disease residue (MDR) sequencing chip were sourced from the publicly available database. Microarray 1: (GSE24006) https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24006/?query=GSE24006; Microarray2:(GSE24395)https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24395/?query=GSE24395; Microarray 3: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005290/; MRD: A group of Minimal Residual Disease was from https://insight.jci.org/articles/view/98561/sd/3.
Cell lines and leukemic cells from patients
The THP-1 and HL-60 AML cells line were obtained from our lab and cell lines were authenticated by short tandem repeat analysis. THP-1 was cultured in RPMI 1640 (Gibco) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin. HL-60 was cultured in IMDM (Gibco) supplemented with 20% FBS and penicillin/streptomycin.
Primary AML cells were obtained from bone marrows of patients with AML with informed consent from all patients according to protocols approved by the Institutional Review Board of the Southwest Hospital, Army Medical University. All the patients’ information was in supplement table 1.
The primary AML cells were cultured in RPMI 1640 (Gibco) supplemented with 20% FBS, penicillin/streptomycin, and cytokines including IL-3, Flt-3 ligand, TPO and SCF, all of which were bought from Peprotech. The normal bone marrow samples were obtained from volunteers.
Antibodies, Cell Staining, and Sorting
All the antibodies for flow cytometry were purchased from BioLegend and BD Biosciences. For analyses of CD9 expression in THP-1 and HL-60, cells were stained with PE anti-human CD9 Antibody. For primary AML cells, cells were stained with FITC anti-human CD3/CD19 antibody, PerCP anti-human CD45 antibody, APC/Cyanine7 anti-human CD34 antibody, APC anti-human CD38 antibody and PE anti-human CD9 antibody. Briefly, THP-1 and primary AML cells were harvested and suspended with 50ul staining/washing buffer (PBS including 1% FBS), then stained with antibodies and incubated for 30 minutes at 4℃. Cells were washed with staining/washing buffer and suspended in buffer for flow cytometry or cell sorting.
Migration assay
The migration of THP-1 and primary AML cells was tested by using Falcon® Permeable Support for 24-well Plate with 8.0 µm Transparent PET Membrane (Corning). 2x105 CD9+ and CD9- cells were suspended in 200μl RPMI 1640 medium (without FBS) and seeded in the upper chambers, respectively. 900μl medium with 20% FBS was added to bottom chamber of each well. After incubation for 6 hours, migrated cells were calculated [23].
Drug resistance assay
The drug resistances of THP-1 and primary AML cells were assessed using MTS assay. 5x103 CD9+ and CD9- THP-1 and primary AML cells were sorted and seeded in 96-well microtiter plates (NEST) with different concentrations of cytarabine (10, 100μg/ml) in 100μl medium [24]. After 24 hour incubation, 10μl MTS (Promega) was added to each well. After 2 hours’ incubation, the plate was measured at wavelength of 490nm with microplate reader (Thermo Fisher Scientific).
Cell proliferation assay
Sorted CD9+ and CD9- THP-1 and primary AML cells were seeded in 96 well plates with 5x103 cells/well. At the indicated time, 10μl MTS (Promega) was added to cells and then detected the absorbance at 490 nm after 2 hours using the microplate reader (Thermo Fisher Scientific). The medium without cells was used as a negative control [25].
Transplantation of AML cells into immunodeficient mice
The animal study was performed in accordance with the protocol approved by the Institutional Animal Care and Use Committee of Southwest Hospital, Third Military Medical University (TMMU). NOG mice at age of 6 to 8 weeks were used for xenogeneic transplantation assays. THP-1 cells were infected with lentivirus expressing luciferase according to the previous method[26]. Sorted CD9+ and CD9- THP-1 cells were transplanted into NOG mice via tail vein injection. Tumor growth was monitored by bioluminescence imaging using In Vivo Imaging System (IVIS) Spectrum (Perkin Elmer, USA) and Living Image Software for IVIS (Perkin Elmer).
Microarray analysis
Three pairs of sorted CD9+ and CD9- primary AML cells (patient 6, patient 7, and patient 8) were investigated with the BGISEU-500 platform for gene expression. In brief, total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer’s instructions from sorted CD9+ and CD9- primary AML cells, respectively. Then all samples are submitted to the BGISEQ-500 platform.
Real time PCR
Total RNA was extracted from CD9+ and CD9- THP-1 cells using RNAiso Plus (Takara), and then Single-stranded cDNA was synthesized with the PrimeScript RT Reagent Kit (Takara) according to the manufacturer’s instruction. Quantitative-PCR analysis was performed using SYBR premix Ex Taq (Takara). The sequence of the primers and the housekeeping gene GAPDH were all from Primer Bank (https://pga.mgh.harvard.edu/primerbank/).
Western blotting
Cells were washed by ice PBS and lysed with RIPA buffer added with protease and phosphatase inhibitor cocktail (Roche). Primary antibody for GAPDH (2118), A2M (4929), CD9 (9750) were purchased from Abcam and EGR1 (100899-T32) from Sino Biological.
Plasmids, Lentivirus construction, and Cell infection
The interference sequence targeting A2M is CCGGCCTAACATCTATGTACTGGATTAGTACTATCCAGTACATAGATGTTAGGTTTTTT and synthesized by Thermo Fisher Scientific. The annealing step was performed with the Annealing Buffer for DNA Oligos (BiYunTian) according to the manufacturer’s instruction after the primers were dissolved. The annealed A2M interference sequence was cloned into the PLKO.1 interference plasmid and detected by gene sequencing. The lentiviruses construction was completed by Chongqing Precision Biotech Co., Ltd. Cell infection was performed as previously described [26]. 10 MOI of lentiviruses supplemented with polybrene (8 ng/ml) was used to infect target cells.
A2M network with CD9 utilizing the GeneMANIA database
Datasets, including physical interactions, pathway, and genetic interactions, were collected from the public domain GeneMANIA database. The dataset relevant to A2M and CD9 network was produced from the GeneMANIA database (http://www.genemania.org).
Statistical analysis
All experiments were repeated at least in triplicate. Collected data were analyzed using GraphPad Prism 8.0 software (GraphPad Software, Inc., San Diego, CA) and estimated variation was taken into account for each group of data and is indicated as SEM or SD in each figure legend. Comparison between two groups was analyzed with unpaired Student’s t test (two tailed), and differences among more than two groups were determined by a one-way ANOVA followed by Newman-Keuls test. Difference with p < 0.05 was considered statistically significant.