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1

Cell Culture Protocol for AML Research

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THP-1 and U937 cell lines were purchased from the American Type Culture Collection (Manassas, VA, USA). MOLM-13 cells were purchased from AddexBio (San Diego, CA, USA). The cell lines have not been authenticated since receiving them in our laboratory. The cell lines were cultured in RPMI 1640 media with 10% fetal bovine serum (Life Technologies, Carlsbad, CA, USA) and 2 mM L-glutamine, plus 100 U ml−l penicillin and 100 μg ml−1 streptomycin, in a 37 °C humidified atmosphere containing 5% CO2/95% air. Cell lines were tested for the presence of mycoplasma. Diagnostic AML blast samples derived from patients were purified by standard Ficoll-Hypaque density centrifugation, then cultured in RPMI 1640 with 20% fetal bovine serum, ITS Solution (Sigma-Aldrich, St Louis, MO, USA) and 20% supernatant of the 5637 bladder cancer cell line (as a source of granulocyte–macrophage colony-stimulating factor, granulocyte colony-stimulating factor, interleukin-1 beta, macrophage colony-stimulating factor and stem cell factor).18–20
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2

Hepatocyte Differentiation of Mouse SSCs

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GPSCs (129Sv/C57B (H2b)), derived from mouse SSCs, were cultured and induced to differentiate into hepatocytes in IMDM complete media containing IMDM-Glutamax (Invitrogen), 9% FCS, 300 μmol/L mercaptoethanol, 100 U/ml penicillin, 100 μg/ml Streptomycin, 1mM sodium pyruvate, and 1x non-essential amino acids (NEAA) (Invitrogen). Feeder-free GPSCs were cultured in hanging drops (300 cells/drop) in the absence of LIF, and at Day 2, embryoid bodies (EBs) were plated on gelatin for further differentiation. The following factors were added: 20ng/ml acidic fibroblast growth factor (FGF) and 10ng/ml basic FGF from Day 6; 10ng/ml rat recombinant hepatocyte growth factor (HGF, Peprotech) from Day 10; 10ng/ml recombinant mouse oncostatin M (R&D systems), 10−7 M dexamethasone and 1x ITS solution (Sigma) from Day 16 (Fig 1A)[16 (link)]. At Day 13, EBs were trypsinised for cell sorting as described below.
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3

Culturing Diverse Myeloid Leukemia Cell Lines

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U937, THP-1, MV4-11, and HL60 cell lines were purchased from the American Type Culture Collection (Manassas, VA). The CMY, CMS, and CTS cell lines were gifts from Dr. A Fuse from the National Institute of Infectious Diseases, Tokyo, Japan. The CMK, NB4, and OCI-AML3 cell lines were purchased from the German Collection of Microorganisms and Cell Cultures (DSMZ, Braunschweig, Germany). MOLM-13 cells were purchased from AddexBio (San Diego, CA). The cell lines were cultured in RPMI 1640 (except OCI-AML3, which was cultured in alpha-MEM) with 10–15% fetal bovine serum (Life Technologies, Grand Island, NY), 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin. All cells were cultured in a 37°C humidified atmosphere containing 5% CO2/95% air.
Diagnostic AML blast samples derived from patients either at initial diagnosis or at relapse were purified by standard Ficoll-Hypaque density centrifugation, then cultured in RPMI 1640 with 20% fetal bovine serum supplemented with ITS solution (Sigma-Aldrich, St. Louis, MO, USA) and 20% supernatant of the 5637 bladder cancer cell line (as a source of granulocyte-macrophage colony-stimulating factor [12 (link), 38 (link), 39 (link)]).
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4

Multilineage Differentiation of ADSCs

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To induce adipogenic differentiation, ADSCs at passage 3 were cultured in DMEM-LG supplemented with 10% FBS. After cells reached 70% confluence, the medium was replaced with adipogenic differentiation medium [DMEM-LG supplemented with 10% FBS, 1 μM dexamethasone (Sigma, Bloomington, MN), 10 μM insulin (Sigma), 200 μM indomethacin (Sigma) and 1% penicillin/streptomycin] for an additional 14 days. Adipogenic differentiation was assessed by oil red O staining.
For osteogenic differentiation, the cells were cultured in osteogenic induction medium [DMEM-LG supplemented with 10% FBS, 10 mM β-glycerophosphate (Sigma,), 100 nM dexamethasone, 50 µM ascorbicacid-2-phosphatea (Sigma), and 1% penicillin/streptomycin] for 14 days. Osteogenic differentiation was detected by alizarin red S staining.
To induce chondrogenic differentiation, cells were pellet-cultured in chondrogenic medium [DMEM-LG containing 1% penicillin/streptomycin, 40 μM L-proline (Sigma), 1% ITS solution (Sigma), 5.35 μM linoleic acid (Sigma), 50 μM ascorbate-2-phosphate, 100 nM dexamethasone, 1.25 μM bovine serum albumin (Sigma), and 10 ng/mL recombinant human TGF-ß3 (R&D Systems, Minneapolis, MN, USA)] for 21 days. Chondrogenesis was detected by immunohistochemistry staining of frozen sections of the pellets using a 1:200 dilution of anti-collagen type II antibody (Santa Cruz Biotechnology, Santa Cruz, CA).
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5

Culturing Leukemia Cell Lines and Primary AML Blasts

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MV4–11, THP-1, and U937 cell lines were purchased from the American Type Culture Collection (2006, 2014, and 2002, respectively; Manassas, VA). OCI-AML3 cell line was purchased from the German Collection of Microorganisms and Cell Cultures (2011; DSMZ, Braunschweig, Germany). The CMS cell line was a gift from Dr. A Fuse from the National Institute of Infectious Diseases, Tokyo, Japan (2004). The cell lines have not been authenticated since receiving them in our laboratory. The cell lines were cultured in RPMI 1640 (or αMEM for OCI-AML3 cells) media with 10–20% fetal bovine serum (Life Technologies, Carlsbad, CA) and 2 mM L-glutamine, plus 100 U/ml penicillin and 100 µg/ml streptomycin, in a 37 °C humidified atmosphere containing 5% CO2/95% air. Cell lines were tested for the presence of mycoplasma.
Diagnostic AML blast samples derived from patients were purified by standard Ficoll-Hypaque density centrifugation, then cultured in RPMI 1640 with 20% fetal bovine serum, ITS solution (Sigma-Aldrich, St. Louis, MO) and 20% supernatant of the 5637 bladder cancer cell line (as a source of granulocyte-macrophage colony-stimulating factor, granulocyte colony-stimulating factor, interleukin-1 beta, macrophage colony-stimulating factor, and stem cell factor (12 (link), 16 (link), 17 (link))).
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6

Isolation of Retinal Pigment Epithelium

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Eyecups with intact RPE monolayers were prepared as previously described [1 (link),3 (link),4 (link)]. In brief, eyes from euthanized healthy C57BL/6J mice were enucleated, placed in ice cold DMEM (Lonza, Walkersvile, PA), where external muscles, and connective tissue were cut from the eyes. A circumferential incision was performed below the level of the ciliary body, and the anterior segment and lens was discarded. The neural retina was gently lifted off the RPE by microsurgical forceps. Each RPE eyecup were placed into individual wells of a 96-well round-bottom culture plate submerged in 200 μL of serum-free media consisting of RPMI 1640, 0.1 M HEPES, NEAA, L- glutamine, sodium pyruvate, 0.1% bovine serum albumin, 1% gentamicin, and supplemented with 0.1 x ITS+ solution (Sigma Chemical, St. Louis, MO). The conditioned media (CM) from the eyecup cultures were removed 48 hours after incubation, and used in the assays.
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7

Isolation and Culture of Diagnostic Blast Cells

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Diagnostic blast samples were obtained from the First Hospital of Jilin University, Changchun, China. Written informed consent was provided according to the Declaration of Helsinki. This study was approved by the Human Ethics Committee of The First Hospital of Jilin University. The samples were purified by standard Ficoll-Hypaque density centrifugation, then cultured in RPMI 1640 with 20% fetal bovine serum, ITS solution (Sigma-Aldrich) and 20% supernatant of the 5637 bladder cancer cell line (as a source of granulocyte-macrophage colony-stimulating factor).48 (link)
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8

Characterization of AML Patient Samples

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Primary AML patient samples and human umbilical cord blood samples were obtained from the First Hospital of Jilin University. Normal peripheral blood mononuclear cells (PBMCs) were donated by healthy individuals. Informed consent was obtained in all cases as per the Declaration of Helsinki. Both the study and patient sample collection were approved by the Human Ethics Committee of The First Hospital of Jilin University. All AML patient samples were screened for the following gene mutations via PCR amplification and automated DNA sequencing: FLT3-ITD, NPM1, C-kit, CEBPA, IDH1, IDH2, SF3B1, TP53, ZRSR2, GATA2, KMT2A, SH2B3, TCF, TET2, RUNX1, and DNMT3A. Cytogenetics and detection of fusion genes via real-time PCR were also performed, as previously described16 (link),17 (link). Characteristics of the individual AML patients are listed in Supplementary Table S1. Primary patient samples were purified with Ficoll-Hypaque density centrifugation, and then cultured in RPMI 1640 media plus 20% fetal bovine serum, ITS Solution (Sigma-Aldrich, St Louis, MO, USA), and 20% supernatant of the 5637 bladder cancer cell line (to provide sources of granulocyte–macrophage colony-stimulating factor, granulocyte colony-stimulating factor, interleukin-1 beta, macrophage colony-stimulating factor, and stem cell factor)16 (link),18 (link),19 (link).
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9

Culturing Leukemia and HEK293 Cell Lines

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Human HEK293 cells transiently expressing proteins (ABCC4, ABCC4ΔC, and/or MPP1) were maintained in Dulbecco’s DMEM supplemented with 10% FBS, 4500 mg/l glucose, 2 mM l-glutamine, 100 U/ml penicillin, and 100 µg/ml streptomycin in a humidified incubator with 5% CO2 at 37 °C. The AML cell lines derived from a pediatric patient20 (link),21 (link), MO7e and the Meg0128 (link) were maintained in RPMI-1640 supplemented with 10% FBS, 4500 mg/l glucose, 2 mM l-glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin in a humidified incubator with 5% CO2 at 37 °C with the MO7e supplemented with human IL3 at 10 ng/ml. These cell lines were obtained from Dr. Brian Sorrentino (MO7e) and Dr. Sharyn Baker (Meg01) at St. Jude Children’s Research Hospital and Ohio State University, respectively. These cell lines were verified as mycoplasma free.
Diagnostic AML blast samples derived from patients either at initial diagnosis or at relapse were purified by standard Ficoll-Hypaque density centrifugation, then cultured in RPMI 1640 with 20% fetal bovine serum supplemented with ITS solution (Sigma-Aldrich, St. Louis, MO, USA) and 20% supernatant of the 5637 bladder cancer cell line (as a source of granulocyte-macrophage colony-stimulating factor)29 (link)–31 (link).
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10

Culturing Acute Myeloid Leukemia Cell Lines

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MV4‐11 and THP‐1 cell lines were purchased from the American Type Culture Collection (Manassas, VA, USA). CTS was a gift from Dr. A Fuse from the National Institute of Infectious Diseases (Tokyo, Japan). OCI‐AML3 was purchased from the German Collection of Microorganisms and Cell Cultures (DSMZ). MOLM‐13 was purchased from AddexBio (San Diego, CA, USA). The cell lines were cultured as previously described,36 and were authenticated in August 2017 at the Genomics Core at Karmanos Cancer Institute using the PowerPlex® 16 System from Promega (Madison, WI, USA). The cell lines were tested for the presence of mycoplasma by PCR on a monthly basis.37Diagnostic AML patient samples and peripheral blood mononuclear cells (PMNCs) from healthy donors were purified by standard Ficoll‐Hypaque density centrifugation, then cultured in RPMI 1640 (ThermoFisher, Waltham, MA, USA) with 20% foetal bovine serum (ThermoFisher), ITS Solution (Sigma‐Aldrich), and 20% supernatant of the 5637 bladder cancer cell line (as a source of granulocyte‐macrophage colony‐stimulating factor, granulocyte colony stimulating factor, interleukin‐1 beta, macrophage colony‐stimulating factor, and stem cell factor14, 38, 39).
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