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12 protocols using sfemii media

1

Evaluating Cytotoxic Effects on BCP-ALL Primografts

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For testing drug cytotoxic/cytostatic effects, BCP‐ALL primografts were cocultured with BM‐MSC (Pal et al., 2016). To this end, BM‐MSC were seeded onto 48‐well plate at a density of 2.5–5.0 × 104 cells per well, in DMEM (low glucose) supplemented with 20% FBS (Gibco), 2 mm of l‐glutamine (Sigma‐Aldrich), and 1% penicillin/streptomycin solution (Sigma‐Aldrich). The next day, BCP‐ALL primograft cells were added at a density of 0.5 × 106 cells·mL−1 in SFEM II media (STEMCELL Technologies) supplemented with 20% FBS (Gibco), 20 ng·mL−1 of recombinant IL‐3 (R&D Systems, Minneapolis, MN, USA), 10 ng·mL−1 of recombinant IL‐7 (R&D Systems), and penicillin/streptomycin solution (Sigma‐Aldrich). After 24 h of coculture, cells were treated with auranofin (AUR) or adenanthin (ADE) at indicated concentration ranges, in a final volume of 700 μL. For each drug concentration, samples were run in duplicate. After 5 days, cells in suspension (BCP‐ALL cells) and adherent cells (BCP‐ALL+MSC) were collected and the number of viable cells was assessed in a hemocytometer. The numbers of viable BCP‐ALL cells in control groups after 5‐day‐long coculture exceeded the number of seeded cells, confirming the growth‐supporting role of BM‐MSC. Primograft samples used in drug‐testing experiments are listed in Table S7.
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2

Multi-Lineage Differentiation of Frozen CD34+ Cells

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A custom optimized cytokine cocktail was developed using commercially available cytokines (Peprotech, New Jersey) to facilitate simultaneous multi-lineage differentiation and self-renewal of freeze-thawed primary human bone marrow-derived CD34+ cells in SFEM II media (cells and media from StemCell Technologies, Vancouver). Cultures were carried out in ultra-low attachment 96-well plates (Corning, New York) with test article added on day 0 and cultured at 37°C, 85% relative humidity, and 5% CO2 for six days before interrogating drug impact via 17-parameter flow cytometry.
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3

Transcriptional Profiling of U2AF1 Mutant CD34+ Cells

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Human hematopoietic mononuclear cells (MNCs) were separated from cord blood using density gradient centrifugation (Ficoll Paque, GE Healthcare). CD34+ cells were isolated from MNCs using the CD34 MicroBead kit (Miltenyi Biotec) on an autoMACs magnetic separator. These cells were cultured in SFEMII media (Stemcell Technologies) supplemented with IL-3, SCF, FLT-3 and TPO cytokines. WT and S34F U2AF1 cDNAs were generated, as previously described,1 (link) and then cloned into pcDNA3.1-Ires-GFP (PIG) to create PIG-U2AF1 (WT or S34F). CD34+ cells then were transfected with PIG-U2AF1 (WT or S34F) using the Nucleofector Kit for Human CD34+ Cells (Lonza). GFP+CD34+ cells were sorted 24 hours later, followed by RNA extraction using the RNeasy kit (Qiagen). Ribosomal RNA was depleted (Ribozero, Epicenter), followed by cDNA preparation and Illumina library production. Sequencing was performed on the HiSeq2000 platform (Illumina). Bioinformatics analysis of RNA-seq data is described in the supplementary material.
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4

Genome Editing of CD34+ Hematopoietic Cells

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CD34+ cells were cultured overnight in SFEMII media (Stemcell Technologies #09605) supplemented with Pen-Strep (50 Units/mL), human stem cell factor (SCF; 100 ng/mL), human thrombopoietin (TPO; 100 ng/mL), and human Flt3L (100 ng/mL). 12–24h post-culture, CD34+ cells were nucleofected with Cas9/ribonucleoprotein (IDT #1074181) complexed with gRNAs as previously described (36 (link)). Synthetic gRNAs sequences were purchased from Synthego as follows: gPIM1.1: GUGGCGUGCAGGUCGUUGCA, gPIM1.2: CUGGAGUCGCAGUACCAGGU, gEZH2.1: CTTCTGTGAGCTCATTGCGC, gEZH2.2: TTATGATGGGAAAGTACACG. A gRNA targeting the AAVS1 locus was used as a negative control: GGGGCCACUAGGGACAGGAU. 48 hrs post-nucleofection, approximately 100,000 cells were set aside to measure CRISPR/Cas9 targeting efficiency using PCR amplicon-based deep sequencing. The remaining cells were transplanted into sublethally irradiated (200 rads) NSGS mice via X-ray guided intra-tibial injection.
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5

Isolation and Characterization of HSPC Subsets

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Mobilized blood or fetal liver–derived CD34+ HSPCs were treated with AAV6 vectors and ZFN mRNA as described above. One or two days post-mRNA electroporation, cells were washed, blocked in FCS (Denville), and stained with the following fluorophore conjugated antibodies: CD34 (581) (BD Biosciences), CD90 (5E10) (BD Biosciences), and CD133/2 (293C3) (Miltenyi Biotec). Cell sorting into subsets based on expression of these markers was performed using a BD FACS Aria II (BD Biosciences), with all compensations performed using Diva software (BD Biosciences). Subsets were defined as primitive (P; CD34+CD133+CD90+), early (E; CD34+CD133+CD90), and committed (C; CD34+CD133CD90) progenitors23 (link). The subsets derived from fetal liver HSPCs were cultured in fetal liver maintenance media, and the subsets derived from mobilized blood HSPCs were maintained in SFEM-II media (Stemcell Technologies, Vancouver, Canada) supplemented with SCF, Flt3L, TPO, and IL-6, for a further 6–7 days. GFP expression was determined in each population by flow cytometry, and site-specific insertion of GFP at either the CCR5 or AAVS1 loci was analyzed by In-Out PCR, as described above.
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6

Conditional Rab27b Knockout Mouse Model for MPN and AML

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Rab27bfl/fl and Rab27bfl/fl; crevav mice on the C57/BL6 background were generated as previously described (39 (link)). C57/B6.SJL mice were originally purchased from the Jackson Laboratories. Both male and female mice (8–12 weeks old) were used.
Primary BM– or PB– derived mononuclear cells from patients with MPN or AML were obtained from the Stem Cell and Xenograft Core Facility at the University of Pennsylvania. Patients’ primary cells were cultured in SFEM II media (STEMCELL) supplemented with 10% FBS, 10 ng/mL human IL-3, 50 ng/mL human stem cell factor (SCF) and 10ng/mL human GM-CSF at 37°C and 95% humidity in an atmosphere of 5% CO2. All cytokines were purchased from PeproTech.
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7

Expansion of Hematopoietic Stem Cells

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Sorted primary murine cKit+ and LSK cells were cultured in SFEMII media (Stemcell technology) supplemented with; rhFlt3/Flk-2 ligand (Stemcell technology), rhTPO (Stemcell technology), rhIL-6 (R&D system), rmIL-3 (R&D systems) and rmSCF (R&D systems) at a concentration of 20 ng/mL. UCB samples were provided by the Karolinska Hospital (Stockholm, Sweden) with informed consent from the parents and all investigation has been performed according ethical standards and to the declaration of Helsinki and to national and international guidelines. The experiments on the UCB samples were approved by The Regional Ethical Review Board in Stockholm (Dnr: 2012/480-31/1).
Lymphoprep solution (Invitrogen) was used to isolate mononuclear cell fraction and CD34+ cells were enriched by using CD34 microbead kit (Miltenyi Biotec). The CD34+ and sorted HSC UBC cells were expanded in SFEMII media supplemented with; rhIL-6, rhIL-3 (R&D systems), rhFl3/Flk-2 ligand, rhTPO and rhSCF (R&D systems) all in final concentrations of 20 ng/mL.
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8

Isolation and Culture of CD34+ Cells

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De-identified cord blood specimens were obtained from the St. Louis Cord Blood Bank. Peripheral blood samples were obtained from MPN patients after obtaining written informed consent in accordance with Declaration of Helsinki ethical guidelines. Human studies were approved by an institutional review board, the Washington University Human Studies Committee (protocol WU #01-1014). De-identified peripheral blood mononuclear cells (PBMCs) from MPN patients and cord blood samples were isolated by Ficoll gradient extraction according to standard procedures. CD34+ cells were isolated using magnetic enrichment (Miltenyi Biotec #130-100-453) and cultured overnight in SFEMII media (StemCell Technologies #09605) supplemented with Pen-Strep (50 Units/mL), human stem cell factor (SCF; 100 ng/mL), human thrombopoietin (TPO; 100 ng/mL), and human FLT3L (100 ng/mL).
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9

Isolation and Characterization of HSPC Subsets

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Mobilized blood or fetal liver–derived CD34+ HSPCs were treated with AAV6 vectors and ZFN mRNA as described above. One or two days post-mRNA electroporation, cells were washed, blocked in FCS (Denville), and stained with the following fluorophore conjugated antibodies: CD34 (581) (BD Biosciences), CD90 (5E10) (BD Biosciences), and CD133/2 (293C3) (Miltenyi Biotec). Cell sorting into subsets based on expression of these markers was performed using a BD FACS Aria II (BD Biosciences), with all compensations performed using Diva software (BD Biosciences). Subsets were defined as primitive (P; CD34+CD133+CD90+), early (E; CD34+CD133+CD90), and committed (C; CD34+CD133CD90) progenitors23 (link). The subsets derived from fetal liver HSPCs were cultured in fetal liver maintenance media, and the subsets derived from mobilized blood HSPCs were maintained in SFEM-II media (Stemcell Technologies, Vancouver, Canada) supplemented with SCF, Flt3L, TPO, and IL-6, for a further 6–7 days. GFP expression was determined in each population by flow cytometry, and site-specific insertion of GFP at either the CCR5 or AAVS1 loci was analyzed by In-Out PCR, as described above.
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10

Coculture of Leukemia Cells and iMSC/iANG

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Patient derived leukaemia samples and non malignant CD45+ hematopoietic cells derived from human bone marrow were seeded on iMSC or iANG cultures at a seeding density of 0.5-1 million cells/mL in SFEMII media (Stemcell Technologies) using protocols adapted from existing studies.15 (link),69 (link) I-niche cells were seeded onto Vitronectin XF™(Stemcell Technologies) coated plates. 24 hours later, the i-niche cells were seeded onto the coated plastic in their respective media at a seeding density of 10,000 cells/cm2. Following another 24 hours leukaemia cells were seeded onto the i-niche cells with drug treatment starting on the following day and lasting for 7 days. Leukaemia cells were harvested from the co-cultures at end of experiment by trypsinization. Following this leukaemia cells were separated from the feeder cells using a 10μM cell strainer. Consequently tagged leukaemia cells (eg: with CTV) were further purified using fluorescence-activated cell sorting (FACSAria, BD Biosciences).
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