KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-TAZ (F-7) | Santa Cruz Biotechnology | Cat# Sc-365810 RRID: AB_10842049 |
| Rabbit polyclonal anti-PISD | Proteintech Group | Cat# 16401-1-AP, RRID:AB_2186673 |
| Rabbit monoclonal PTDSS1 antibody | Abcam | Cat# ab157222 |
| Rabbit monoclonal PSS2 antibody | Abcam | Cat# ab183504 |
| Rabbit monoclonal anti-citrate synthase | Abcam | Cat# ab129095 |
| Mouse monoclonal anti-beta-Actin (AC-15) | Santa Cruz Biotechnology | Cat# sc-69879, RRID:AB_1119529 |
| Rabbit polyclonal anti-beta Tubulin (H-235) | Santa Cruz Biotechnology | Cat# sc-9104, RRID:AB_2241191 |
| Sheep Anti-Mouse IgG, Whole Ab ECL Antibody, HRP Conjugated | GE Healthcare | Cat# NA931, RRID:AB_772210 |
| Donkey Anti-Rabbit IgG, Whole Ab ECL Antibody, HRP Conjugated | GE Healthcare | Cat# NA934, RRID:AB_772206 |
| BB515 Rat Anti-Mouse Ly-6A/E | BD Biosciences | Cat# 565397 |
| Pe/Cy7 Rat anti-mouse CD117 (c-Kit) | BioLegend | Cat# 105814 RRID: AB_2131136 |
| PE Rat anti-mouse CD150 (SLAM) | BioLegend | Cat# 115904 RRID: AB_313683 |
| APC Hamster anti-mouse CD48 | ThermorFisher Scientific | Cat# 17-0481-82 RRID: AB_469408 |
| APC/Cy7 Rat anti-mouse CD16/32 | BioLegend | Cat# 101328 RRID: AB_2104158 |
| eFluor 450 Rat anti-mouse CD34 | ThermoreFisher Scientific | Cat# 48-0341-82 RRID: AB_2043837 |
| APC Mouse anti-human CD11b | BD Biosciences | Cat# 340937 |
| APC Mouse anti-human CD14 | BD Biosciences | Cat# 555399 |
| CD34 | BD Biosciences | Cat# 348053, RRID:AB_2228982 |
| CD38 | BD Biosciences | Cat# 342371, RRID:AB_400453 |
| CD122 | Lab Stock | N/A |
| Biological Samples | ||
| Human AML Patient Samples | Leukemia Biobank, Princess Margaret Hospital | N/A |
| Normal Peripheral Blood Stem Cells (PBSC’s) | Leukemia Biobank, Princess Margaret Hospital | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Iscove’s Modification Dulbecco’s Modification Eagle’s Medium (IMDMEM) | Wisent | Cat# 319-701-CL |
| RPMI 1640 | Wisent | Cat# 350-700-CL |
| Alpha MEM | Lab Stock | N/A |
| MyeloCult H5100 | STEMCELL Technologies | Cat# 05150 |
| X-VIVO 10 Chemically Defined, Serum-free Hematopoietic Cell Medium | Lonza | Cat# 04-380Q |
| Dulbecco’s Modification Eagle’s Medium (DMEM) | Wisent | Cat# 319-005-CL |
| Fetal Bovine Serum | Sigma-Aldrich | Cat# F1051 |
| Recombinant Human SCF Protein (TEX) | R&D Systems | 255-sc/cf., R&D, |
| Recombinant Human IL-3 Protein (TEX) | R&D Systems | 203-IL |
| L-Glutamine 200mM (TEX) | ThermoFisher Scientific | Cat# 25030081 |
| Recombinant Human IL-3 (8227, and Primary Sample Transductions) | PeproTech | Cat# 200-03 |
| Recombinant Human SCF (78227, and Primary Sample Transductions) | PeproTech | Cat# 300-07 |
| Recombinant Human Flt3-Ligand (8227, and Primary Sample Transductions) | PeproTech | Cat# 300-19 |
| Recombinant Human TPO (8227, and Primary Sample Transductions) | PeproTech | Cat# 300-18 |
| Recombinant Human IL-6 (8227, and Primary Sample Transductions) | PeproTech | Cat# 200-06 |
| BIT 9500 Serum Substitute (8227, and Primary Sample Transductions) | STEMCELL Technologies | Cat# 09500 |
| Human GM-CSF, premium grade (primary samples) | Miltenyi Biotec | Cat# 130-093-866 |
| Human IL-6 (primary samples) | Miltenyi Biotec | Cat# 130-095-365 |
| Human Flt3-Ligand (primary samples) | Miltenyi Biotec | Cat# 130-096-479 |
| Human IL-7 (primary samples) | Miltenyi Biotec | Cat# 130-095-363 |
| Granulocyte colony stimulating factor (G-CSF), [Filgrastim] | Amgen Canada | CAS#121181-53-1 |
| Puromycin HCL | Sigma-Aldrich | Cat# P8833 |
| Protamine Sulfate | MP Biomedicals | Cat#194729 |
| Laemmli buffer | Lab Stock | N/A |
| RIPA buffer | Lab Stock | N/A |
| TBS (10X) | Wisent | Cat# 311-030-LL |
| Thermo Scientific Pierce ECL western blotting substrate | ThermorFisher Scientific | Cat# PI32106 |
| Annexin V-FITC Reagent | CEDARLANE, BioVision | Cat# 1001-1000 |
| Propidium Iodide | CEDARLANE, BioVision | Cat# 1056-1 |
| Annexin V Binding Buffer | Lab Stock | N/A |
| Sodium Fluoride | Sigma-Aldrich | Cat# 919 |
| Rodent Chow with 625mg doxycycline/kg chow | Ren’s Pets Depot | Cat# 58MY-1811541 |
| Red Blood Cell Lysing Buffer Hybri-Max | Sigma-Aldrich | Cat# R7757 |
| Lineage Cell Depletion Kit mouse | MACS Miltenyi Biotec | Cat# 130-090-858 |
| autoMACs Rinsing Solution | MACS Miltenyi Biotec | Cat# 130-091-222 |
| MACs BSA Stock Solution | MACS Miltenyi Biotec | Cat# 130-091-376 |
| 7AAD | BD Biosciences | Cat# 559925 |
| UltraComp eBeads | affymetrix eBioscience | Cat# 01-2222-42 |
| mSCF | Miltenyi Biotec | Cat# 130-101-697 |
| mIL-6 | Miltenyi Biotec | Cat# 130-096-683 |
| mIL-3 Conditioned Media | Karasuyama and Melchers, 1998 | N/A |
| 5-Fluorouracil | Sigma-Aldrich | Cat# F6627-10G |
| Chloroform (UHPLC/MS) | Fisher Scientific | Cat# C6074 |
| Methanol CHROMASOLV, Riedel-de Haen (UHPLC/MS) | Fisher Scientific | Cat# 60046513 |
| Sodium-Phosphate Monobasic Anhydrous (UHPLC/MS) | Fisher Scientific | Cat# BP329-500 |
| Alfa Aesar Acetonitrile (UHPLC/MS) | Fisher Scientific | Cat# AA47138K7 |
| Isopopanol, Optima (UHPLC/MS) | Fisher Scientific | Cat# A4614 |
| Formic Acid, Optima (UHPLC/MS) | Fisher Scientific | Cat# A11750 |
| Amonium Formate (UHPLC/MS) | Sigma-Aldrich | Cat# 70221-100G-F |
| Standard (UHPLC/MS): 14:0 Cardiolipin | Avanti, Polar Lipids | Cat# 710332C |
| Human Recombinant KillerTRAIL | Alexis Biochemicals | Cat# 201-123-C500 |
| Cyclohexamide | Sigma-Aldrich | Cat# C7698 |
| Oligomycin | Sigma-Aldrich | Cat# 75351 |
| FCCP | Cayman Chemical | Cat# 15218 |
| Corning Cell-Tak | FisherScientific | Cat# C354240 |
| Seahorse XF assay medium | Agilent | Cat# 102365-100 |
| Paraformaldehyde | Electron Microscopy Sciences | Cat# RT19200 |
| 70% Glutaraldehyde | Electron Microscopy Sciences | Cat# 16360 |
| Sodium Phosphate Monobasic monohydrate (NaH2P04. H2O Buffer) | Sigma-Aldrich | Cat# S9638 |
| Sodium Phosphate Dibasic (Na2H2P04, Buffer) | Lab Stock | Cas# 7558-79-4 |
| 1N Sodium Hydroxide [NaOH] | Lab stock | Cas# 1310-73-2 |
| Osmium tetraoxide [OsO4] | Electron Microscopy Sciences | Cat# RT19100 |
| Embed-812 kit | Electron Microscopy Sciences | Cat# 14120 |
| 300 Mesh Copper grids | Electron Microscopy Sciences | Cat# G300H-Cu |
| Uranyl Acetate | Electron Microscopy Sciences | Cat# 22400 |
| Lead Nitrate [Pb(NO3)2] for staining for electron microscopy | Electron Microscopy Sciences | Cat# RT17900 |
| Sodium Citrate [Na3C6H5O7·2H2O] for staining | Electron Microscopy Sciences | Cat# RT21140 |
| MitoTracker Red CMXRos | ThermoFisher Scientific | Cat# M7512 |
| Poly-L-lysine | Sigma-Aldrich | Cat#P4707 |
| Chloroform (CHCL3, Spot Densitometry) | Sigma-Aldrich | Cat# 34854 |
| Methanol (CH3OH, Spot Densitometry) | Sigma-Aldrich | Cat# 34860 |
| Acetic Acid (C3H6O, Spot Densitometry) | Canadawide Scientific | Cat# CWA0302-4 |
| Standard (Spot Densitometry): Sphingomyelin | Sigma-Aldrich | Cat# S0756 |
| Standard (Spot Densitometry): L-α-Phosphatidylcholine | Sigma-Aldrich | Cat# P3556 |
| Standard (Spot Densitometry): L-α-Phosphatidyl-L-serine | Sigma-Aldrich | Cat# P0474 |
| Standard (Spot Densitometry): L-α-Phosphatidylinositol | Sigma-Aldrich | Cat# P6636 |
| Standard (Spot Densitometry): L-α-Phosphatidylethanolamine | Sigma-Aldrich | Cat# P7943 |
| Standard (Spot Densitometry): Cardiolipin Sodium Salt from Bovine Heart | Sigma-Aldrich | Cat# C0563 |
| Copper (II) sulfate pentahydrate (Spot Densitometry) | Sigma-Aldrich | Cat# C-6283 |
| O-Phosphoric Acid (Spot Densitometry) | Fisher Scientific | Cat# A242-212 |
| PBS (Spot Densitometry) | Sigma-Aldrich | Cat# P3813 |
| H20 (Spot Densitometry) | Fisher Scientific | Cat# 2745 |
| HPTLC plates (Spot Densitometry) | Sigma-Aldrich | Cat# 1.05633.0001 |
| Chloroform | Lab Stock | Cas# 67-66-3 |
| HPLC methanol | Sigma-Aldrich | Cat# 646377 |
| Dimethyl sulfoxide (DMSO) | Sigma-Aldrich | Cat# D8418 |
| Tween 80 | Sigma-Aldrich | Cat# P4780 |
| Propylene Glycol (PEG) | Sigma-Aldrich | Cat# P4347 |
| Methanol | BioShop Canada | Cat# MET302 |
| Soy PS | Avanti Polar Lipids | Cat# 870336P |
| Soy PE | Avanti Polar Lipids | Cat# 840024P |
| Egg Lyso PE | Avanti Polar Lipids | Cat# 860081P |
| Saponin | Sigma-Aldrich | 47036-50G-F |
| Bovine Serum Albumin | Sigma-Aldrich | Cat# A9647 |
| 16% paraformaldehyde (CAT#15710) | Electron Microscopy Sciences | Cat# 15710 |
| AnnexinV Alexa-647 | ThermoFisher Scientific | Cat# A23204 |
| ProLong Gold Antifade Mountant | ThermoFisher Scientific | Cat# P36934 |
| SuperScript IV Reverse Transcriptase | ThermoFisher Scientific | Cat# 18090050 |
| 7-chloro-N-(4-ethoxyphenyl)-4-quinolinamine (MMV007285) | This paper | Jae-Yeon Choi et. al, 2016 |
| CL075 | TOCRIS | Cat# 6142 |
| Formic acid (Pharmacokinetic Studies) | Sigma-Aldrich | Cat# 33015 |
| CellTiter 96 Aqueous MTS Reagent Powder | Promega | Cat# G1111 |
| RetroNectin Recombinant Human Fibronectin Fragment | Takara | Cat# T100A |
| Acetonitrile, Optima, Fisher Chemical (Pharmacokinetic Studies) | ThermoFisher Scientific | Cat# A996-4 |
| Critical Commercial Assays | ||
| E.N.Z.A Plasmid Midi Kit | Omega BIO-TEK | Cat# D6904-04 |
| Cytochrome c Releasing Apoptosis Assay Kit | abcam | Cat# ab65311 |
| α-Naphthyl Acetate (Non-Specific Esterase) | Sigma-Aldrich® | Cat# 91A-1KT |
| Protein Assay Dye | Bio-Rad | Cat# 5000006 |
| DC Protein Assay kit II | Bio-Rad | Cat#5000112 |
| MethoCult H4100 | STEMCELL Technologies | Cat# 04100 |
| MethoCult H4434 | STEMCELL Technologies | Cat# 04434 |
| MethoCult GF M3534 | STEMCELL Technologies | Cat# 03534 |
| Bioanalyzer RNA Analysis Kit | Agilent Technologies | Cat# 5067-1511 |
| KAPA Library Complete Quantification Kit for ABI Prism genetic analyzer and Illumina | KAPABiosystems | Cat# KK4835 |
| Agilent High Sensitivity DNA Kit | Agilent Technologies | Cat# 5067-4626 |
| NEBNext Ultra Directional RNA Library Prep Kit for Illumia | New England BioLabs | Cat# E7420S |
| HiSeq SBS kit V4 250 cycle kit | Illumina | Cat# FC-401-4003 |
| Carboxy-H2DCFDA | ThermoFisher Scientific | Cat# C400 |
| RNeasy Plus Mini Kit | QIAGEN | Cat# 74134 |
| Power SYBR Green PCR Master Mix | ThermoFisher Scientific | Cat# 4367659 |
| Lenti-X Concentrator | Takara | Cat# 631231 |
| Lipid strips | Echelon Biosciences | Cat# P-6002 |
| Fatty acid-free Bovine Serum Albumin | Sigma-Aldrich® | Cat# A7030 |
| PISD recombinant protein | OriGene | Cat# TP761730 |
| Deposited Data | ||
| AML2 gene expression after TAZ-KD | This paper | GEO: GSE107045 |
| Experimental Models: Cell Lines | ||
| Human: OCI-AML2 | Wang C et al., 1989 | N/A |
| Human: TEX | Warner et al., 2005 | N/A |
| Human: K562 | ATCC | Cat# CCL-243 |
| Human: U937 | ATCC | Cat# CRL-1593 |
| 8227 cells | Lechman et al., 2016 | N/A |
| 293T/17 | ATCC | Cat# CRL-11268 |
| Experimental Models: Organisms/Strains | ||
| Mouse: NOD.Cg-Prkdcscid II2rgtm1WjI Tg(CMV-IL3,CSF2,KITLG)1Eav/MloySzJ (NOD-SCID-GF) | Nicolini et al., 2004 | N/A |
| Mouse: B6.Cg-Gt(ROSA)26Sortm37(H1/tetO-RNAi:Taz)Arte/ZkhuJ doxycycline-Inducible-TAZ-Knockdown (iDOX-Taz-KD) | Acehan et al., 2011 | N/A |
| Mouse: C57BL/6J | Jackson Laboratory | Cat# 000664; RRID: IMSR_JAX:000664 |
| Mouse: NOD.CB17-Prkdcscid/J (NOD-SCID) | Jackson Laboratory | Cat# 001303 |
| Mouse: Prkdcscid (SCID) | In house | RRID: IMSR_ARC: SCID |
| Oligonucleotides | ||
| Primers for TAZ, PISD, 18srRNA, LYZ, iDOX-Taz-shRNA, ND1, HGB, TLR4, TLR8, IL6, and IFNβ | See Table | Table S4 |
| sgRNAs targeting TAZ, PISD, and control sequences | See Table | Table S6 |
| shRNAs targeting TAZ, and control sequences | See Table | Table S6 |
| Recombinant DNA | ||
| pCMV-R8.74psPAX2 Packaging Plasmid | Moffat et al., 2006 | N/A |
| VSV-G/pMD2.G Envelope Plasmid | Moffat et al., 2006 | N/A |
| pLKO.1-Puro-shRNA lentiviral plasmid | Moffat et al., 2006 | N/A |
| Cas9-2A-Blast lentivrial plasmid | Hart et al., 2015 | N/A |
| pLCKO-Puro-sgRNA lentiviral plasmid | Hart et al., 2015 | Addgene #73311 |
| pRS19-Puro-GFP-shRNA lentiviral plasmid | Chan et al., 2015 | N/A |
| TKO CRISPR library V1 | Hart et al., 2015 | N/A |
| pLenti-EF1a-C-Myc-DDK-IRES-Bsd plasmid | OriGene | Cat# PS100085 |
| Software and Algorithms | ||
| MAGeCk | Lietal., 2014,_S1_Reference34 | https://sourceforge.net/projects/mageck/ |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| GraphPad Prism | GraphPad Software version 6.03 for Windows, GraphPad Software, La Jolla California USA | https://www.graphpad.com/ |
| FLOWJO | FlowJo v 7.7.1, TreeStar, Ashland Oregon USA | https://www.flowjo.com/ |
| Xcalibur v.2.1 | Thermo-Fisher Scientific | Part# XCALI-97213 |
| Chromeleon Xpress v.7.2 | Thermo-Fisher Scientific | Cat# CHROMELEON7 |
| NIST MS Search v.2.0 | NIST | https://chemdata.nist.gov/mass-spc/ms-search/ |
| FastQC v.0.11.2 | Babraham Institute | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| Trim Galore v. 0.4.0. | Babraham Institute | http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| FastQ-Screen v.0.4.3 | Babraham Institute | http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/ |
| RSeQC v. 2.3.7 | http://rseqc.sourceforge.net/ | |
| Tophat v. 2.0.11 | John’s Hopkins University | https://ccb.jhu.edu/software/tophat/index.shtml |
| htseq-v.0.6.1p2 | Simon Anders | https://ccb.jhu.edu/software/tophat/index.shtml |
| DESeq v.1.18.0 | Bioconductor | http://bioconductor.org/packages/release/bioc/html/DESeq.html |
| edgeR, R package, v.3.16.5 (Differential Gene Expression Analysis, Control shRNA Vs. TAZ-KD) | Bioconductor | http://www.bioconductor.org/packages/release/bioc/html/edgeR.html |
| edgeR, R package, v.3.28.21 (Differential Gene Expression Analysis, LSC-versus LSC+, TCGA clusters) | Bioconductor | http://bioconductor.org/packages/release/bioc/html/edgeR.html |
| Gene Set Enrichment Analysis Software | Broad Institute | http://software.broadinstitute.org/gsea/msigdb/ |
| Cytoscape 3.6.1 | The Cytoscape Consortium | http://www.cytoscape.org/?gclid=CjwKCAjw_tTXBRBsEiwArqXyMp1y9jXNftKoksBpO7Q2BCKzWsvEGPteq7VRCpoVHH22tEsWgCnb7BoCnL4QAvD_BwE |
| EnrichmentMap 3.1 | The Cytoscape Consortium | https://enrichmentmap.readthedocs.io/en/docs-3.1/ |
| AutoAnnotate 1.2. | The Cytoscape Consortium | http://apps.cytoscape.org/apps/autoannotate |
| affy, R package, affy_1.38.1 | Bioconductor | https://www.bioconductor.org/packages/release/bioc/html/affy.html |
| sva, R package, sva_3.6.0 | Bioconductor | http://bioconductor.org/packages/release/bioc/html/sva.html |
| Other | ||
| LSC+ and LSC− Geneset | Ng et al., 2016 | GEO: GSE76008 |
| TCGA Repository | National Cancer Institute | https://portal.gdc.cancer.gov/ |
| DMAP | Novershtern et al., 2011 | GEO: GSE24759 |
| Bader Lab Database | This paper | http://baderlab.org/GeneSets, version from September 2017 |