KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit Anti-PDXK antibody | Sigma | Cat# HPA030196; RRID:AB_10599735 |
| Anti-GFP | Hypromatrix | HM2020 |
| Mouse Anti-Actin, beta Monoclonal Antibody, Horseradish Peroxidase Conjugated, Clone AC-15 | Sigma | Cat# A3854; RRID:AB_262011 |
| Anti c-Kit | BioLegend | Cat# 105811, RRID:AB_313220 |
| Anti Mac-1 | BioLegend | Cat# 101211, RRID:AB_312794 |
| Bacterial and Virus Strains | ||
| pLKO5.sgRNA.EFS.GFP vector | (Heckl et al., 2014) | Addgene plasmid # 57822 |
| RT3GEN (pQCXIX) vector | (Fellmann et al., 2013) | N/A |
| miR-E based MLS retroviral vector | (Fellmann et al., 2013) | N/A |
| LentiCas9-Blast | (Sanjana et al., 2014) | Addgene Plasmid #52962 |
| LentiCRISPR v2 vector | (Sanjana et al., 2014) | Addgene plasmid # 52961 |
| Biological Samples | ||
| PBSCs from healthy donor | Fred Hutchinson Cancer Research Center | https://www.fredhutch.org/en.html |
| Primary samples from AML patients | Memorial Sloan Kettering Cancer Center | https://www.mskcc.org |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Isoniazid | Sigma | I3377 |
| 4’-O-methoxypyridoxine | BOC Sciences | B17LM09262 |
| ABT-199 | LC Laboratory | V-3579 |
| Murine recombinant SCF | PEPROTECH | 250-03 |
| Murine recombinant IL-3 | PEPROTECH | 213-13 |
| Murine recombinant IL-6 | PEPROTECH | 216-16 |
| Doxycycline hyclate | Sigma | D9891 |
| Polybrene | Millipore | TR-1003-G |
| Putrescine dihydrochloride | Sigma | P7505 |
| Uridine | Sigma | U6381 |
| Pyridoxal-5-phosphate | Sigma | P3657-1G |
| Pyridoxine | Sigma | P2680-10G |
| Pyridoxamine | Sigma | P9380-1G |
| Pyridoxal | Sigma | 271748-5G |
| [3D]-pyridoxal phosphate | IsoSciences | 7017 |
| [3D]-pyridoxal | IsoSciences | 7098 |
| [3D]-pyridoxine | IsoSciences | P200798 |
| [3D]-pyridoxamine | IsoSciences | 7099 |
| Ammonium chloride | STEMCELL | 07850 |
| Annexin-APC | BioLegend | 640930 |
| Puromycin dihydrochloride from Streptomyces alboniger,>=98% (TLC), powder | Sigma-Aldrich | P7255-25MG |
| Blasticidin S HCl (10 mg/mL) | Life Technologies | a11139-03 |
| 2-Mercaptoethanol | Sigma-Aldrich | M3148 |
| Luciferin | GOLDBIO | LUCK-1G |
| Critical Commercial Assays | ||
| Biotin mouse lineage panel | BD Biosciences | 559971 |
| CD117 MicroBeads, mouse | Miltenyi Biotec | 130-091-224 |
| StemSpan™ SFEM | STEMCELL | 09600 |
| 4–15% Mini-PROTEAN® TGX™ Precast Protein Gels | Bio-rad | 4561084 |
| QuikChange Lightning Multi Site-Directed Mutagenesis Kit | Agilent Technologies | 210515 |
| RNeasy Mini Kit (RNA extraction) | Qiagen | 74106 |
| QIAquick Gel Extraction Kit (cloning) | Qiagen | 28704 |
| QIAquick PCR purification Kit ( cloning) | Qiagen | 28106 |
| Flow cytometry absolute count standard | Bangs Laboratories | 580 |
| EdU Alexa Fluor 647 Flow Cytometry Assay Kit | Invitrogen | C10634 |
| A/C Enzymatic Vitamin B6 Assay | A/C Diagnostics | 510k #0111260 |
| Deposited Data | ||
| All deep sequencing data | This paper | GSE139908, GSE139892, GSE139905 |
| Experimental Models: Cell Lines | ||
| Mouse: Nras(G12D)/MLL–AF9 | (Chen et al., 2013) | N/A |
| Mouse: Nras(G12D)/IDH | (Chen et al., 2013) | N/A |
| Mouse: Nras(G12D)/NPM1 | (Dovey et al., 2017) | N/A |
| Mouse: IDH/Flt3 | (Chen et al., 2013) | N/A |
| Mouse: AML1/ETO | (Zuber et al., 2009) | N/A |
| Mouse: MLL-AF9-cas9 | (Shi et al., 2015) | N/A |
| Human: MOLM13 cell line | DSMZ | Cat# ACC-554, RRID:CVCL_2119 |
| Human: MOLM13 -cas9-blast -empty-hygro | This paper | N/A |
| Human: MOLM13 -cas9-blast -mPdxk cDNA- hygro | This paper | N/A |
| Human: MOLM13 -cas9-blast -hPDXK cDNA- hygro | This paper | N/A |
| Human: MOLM13 -cas9-blast -hPDXK del 232-235 cDNA- hygro | This paper | N/A |
| Human: MOLM13 -cas9-blast -hPDXK D235A cDNA- hygro | This paper | N/A |
| Human: ML-2 cell line | DSMZ | Cat# ACC-15, RRID:CVCL_1418 |
| Human: SEMK2 cell line | (Pocock et al., 1995) | N/A |
| Human: THP-1 cell line | ATCC | Cat# TIB-202, RRID:CVCL_0006 |
| Human: K-562 cell line | ATCC | Cat# CCL-243, RRID:CVCL_0004 |
| Mouse: iMEF | (Huang et al., 2014) | N/A |
| Mouse: NIH 3T3 cell line | ATCC | Cat# CRL-1658, RRID:CVCL_0594 |
| Human: sarcoma cell (HSSC) | (Banito et al., 2018) | N/A |
| Human: HEK293T cell line | ATCC | Cat# CRL-3216, RRID:CVCL_0063 |
| Human: pluripotent stem cell | (Doulatov et al., 2013) | N/A |
| Experimental Models: Organisms/Strains | ||
| Mouse: NCI B6-Ly5.1/Cr | Charles River | B6/SJL(CD45.1) |
| Mouse: C57BL/6J | Jackson | 000664 |
| Oligonucleotides | ||
| sgRNA for CRISPR/Cas9 functional genomics screen, see Table S5 | This paper | N/A |
| shRNA or sgRNA sequence for PLP dependent enzyme screening, see Table S5 | This paper | N/A |
| Recombinant DNA | ||
| MSCV Hygro-PGK-Hygro vector | Clontech | 634401 |
| MSCV-PGK-Puro vector | (Shi et al., 2015) | N/A |
| MSCV empty-PGK-Hygro | This paper | N/A |
| MSCV mPDXK-PGK-Hygro | This paper | N/A |
| MSCV hPDXK-PGK-Hygro | This paper | N/A |
| MSCV hPDXK D235A-PGK-Hygro | This paper | N/A |
| MSCV hPDXK Del 232-235-PGK-Hygro | This paper | N/A |
| MSCV-miRE-SV40-GFP/mCherry (LMS) | (Zhao et al., 2015) | N/A |
| Human PDXK cDNA | Dharmacon | OHS6085-213574600 |
| Mouse Pdxk cDNA | Dharmacon | MMM1013-202768267 |
| Software and Algorithms | ||
| Guavasoft software 3.3 | Millipore | https://www.luminexcorp.com/guava-easycyte-software/ |
| Living Image software 4.5 | PerkinElmer | https://www.perkinelmer.com/lab-products-and-services/resources/in-vivo-imaging-software-downloads.html |
| Image J 1.49v | NIH | https://imagej.nih.gov/ij/download.html |
| MassHunter software | Agilent | https://www.agilent.com/en/products/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-instruments/triple-quadrupole-lc-ms/ultivo-triple-quadrupole-lc-ms |
| GraphPad PRISM 7 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| DAVID | NIH | https://david.ncifcrf.gov/ |
| GSEA | Broad Institute | http://www.broadinstitute.org/gsea |
| STAR | (Dobin et al., 2013) | https://github.com/alexdobin/STAR |
| Subread | (Liao et al., 2014) | http://subread.sourceforge.net/ |
| DESeq2 | (Love et al., 2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Trimmomatic | (Bolger et al., 2014) | http://www.usadellab.org/cms/?page=trimmomatic |
| CompuSyn Software | ComboSyn, Inc. | http://www.combosyn.com/index.html |