Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| BV650 Mouse Anti-Human PEAR1, clone 492621 | BD Biosciences | Catalog # 748063 |
| Human TruStain FcX (Fc Receptor Blocking Solution) | Biolegend | Catalog # 422301 |
| Bacterial and virus strains | ||
| n/a | ||
| Biological samples | ||
| AML Patient Samples | Oregon Health & Science University (OHSU), University of Utah, University of Texas Medical Center (UT Southwestern), Stanford University, University of Miami, University of Colorado, University of Florida, National Institutes of Health (NIH), Fox Chase Cancer Center and University of Kansas (KUMC) | OHSU; IRB#9570; #4422; NCT01728402 |
| Healthy Bone Marrow CD34+ Cells | AllCells | Custom Order |
| Chemicals, peptides, and recombinant proteins | ||
| Drug | Source | Catalog # | CAS # |
| 17-AAG (Tanespimycin) | LC Labs | A-6880 | 75747–14-7 |
| A-674563 | Selleck | S2670 | 552325–73-2 |
| ABT-737 | Selleck | S1002 | 852808–04-9 |
| Afatinib (BIBW-2992) | LC Labs | A-8644 | 850140–72-6 |
| AGI-5198 | Selleck | S7185 | 1355326–35-0 |
| AGI-6780 | Selleck | S7241 | 1432660–47-3 |
| AKT Inhibitor IV | Millipore Sigma (EMD Biosciences; Calbiochem) | 124011 | 681281–88-9 |
| AKT Inhibitor X | Millipore Sigma (EMD Biosciences; Calbiochem) | 124020 | 925681–41-0 |
| Alisertib (MLN8237) | Selleck | S1133 | 1028486–01-2 |
| AMPK Inhibitor | Millipore Sigma (EMD Biosciences; Calbiochem) | 171260 | 866405–64-3 |
| Arsenic trioxide | Fisher | NC0244675 | 1327–53-3 |
| Artemisinin | Selleck | S1282 | 63968–64-9 |
| AST487 | Selleck | S6662 | 630124–46-8 |
| AT-101 | Selleck | S2812 | 866541–93-7 |
| AT7519 | Selleck | S1524 | 844442–38-2 |
| Axitinib (AG-013736) | LC Labs | A-1107 | 319460–85-0 |
| Azacytidine | Selleck | S1782 | 320–67-2 |
| AZD1480 | Selleck | S2162 | 935666–88-9 |
| Baicalein | Selleck | S2268 | 491–67-8 |
| Barasertib (AZD1152-HQPA) | Selleck | S1147 | 722544–51-6 |
| Bay 11–7085 | Selleck | S7352 | 196309–76-9 |
| BEZ235 | LC Labs | N-4288 | 915019–65-7 |
| BI-2536 | Selleck | S1109 | 755038–02-9 |
| Birinapant | Selleck | S7015 | 1260251–31-7 |
| BLZ945 | Selleck | S7725 | 953769–46-5 |
| BMS-345541 | Selleck | S8044 | 445430–58-0 |
| BMS-754807 | Selleck | S1124 | 1001350–96-4 |
| Bortezomib (Velcade) | LC Labs | B-1408 | 179324–69-7 |
| Bosutinib (SKI-606) | LC Labs | B-1788 | 380843–75-4 |
| Cabozantinib (XL184) | Selleck | S1119 | 849217–68-1 |
| Canertinib (CI-1033) | LC Labs | C-1201 | 289499–45-2 |
| Cediranib (AZD2171) | LC Labs | C-4300 | 288383–20-0 |
| CHIR-99021 | LC Labs | C-6556 | 252917–06-9 |
| CI-1040 (PD184352) | LC Labs | P-8499 | 212631–79-3 |
| Crenolanib | Selleck | S2730 | 670220–88-9 |
| Crizotinib (PF-2341066) | LC Labs | C-7900 | 877399–52-5 |
| CYT387 | Selleck | S2219 | 1056634–68-4 |
| Cytarabine | Selleck | S1648 | 147–94-4 |
| Dasatinib | LC Labs | D-3307 | 302962–49-8 |
| DBZ | Tocris | 4489 | 209984–56-5 |
| Doramapimod (BIRB 796) | LC Labs | D-2744 | 285983–48-4 |
| Dovitinib (CHIR-258) | LC Labs | D-3608 | 405169–16-6 |
| Elesclomol | Selleck | S1052 | 488832–69-5 |
| Entospletinib (GS-9973) | Selleck | S7523 | 1229208–44-9 |
| Entrectinib | Selleck | S7998 | 1108743–60-7 |
| Erlotinib | LC Labs | E-4007 | 183319–69-9 |
| Etomoxir | Selleck | S8244 | 828934–41-4 |
| Everolimus | Selleck | S1120 | 159351–69-6 |
| Flavopiridol | Selleck | S1230 | 131740–09-5 |
| Foretinib (XL880) | LC Labs | F-4185 | 849217–64-7 |
| GDC-0879 | Selleck | S1104 | 905281–76-7 |
| GDC-0941 | LC Labs | G-9252 | 957054–30-7 |
| Gefitinib | LC Labs | G-4408 | 84475–35-2 |
| Gilteritinib | Selleck | S7754 | 1254053–43-4 |
| Go6976 | LC Labs | G-6203 | 136194–77-9 |
| GSK-2879552 | Selleck | S7796 | 1902123–72-1 |
| GSK690693 | Selleck | S1113 | 937174–76-0 |
| GW-2580 | LC Labs | G-5903 | 870483–87-7 |
| H-89 | LC Labs | H5239 | 127243–85-0 |
| Ibrutinib (PCI-32765) | LC Labs | I-3311 | 936563–96-1] |
| Idelalisib (GS-1101) | Selleck | S2226 | 870281–82-6 |
| Imatinib | LC Labs | I5577 | 152459–95-5 |
| Indisulam | Selleck | S9742 | 165668–41-7 |
| INK-128 | Selleck | S2811 | 1224844–38-5 |
| JAK Inhibitor I | Millipore Sigma (EMD Biosciences; Calbiochem) | 420099 | 457081–03-7 |
| JNJ-28312141 | SYN Kinase | SYN-1154 | 885692–52-4 |
| JNJ-38877605 | Selleck | S1114 | 943540–75-8 |
| JNJ-7706621 | Selleck | S1249 | 443797–96-4 |
| JNK Inhibitor II (SP600126) | LC Labs | S-7979 | 129–56-6 |
| JQ1 | Selleck | S7110 | 1268524–70-4 |
| KI20227 | Tocris | 4481 | 623142–96-1 |
| KN92 | Tocris | 4130 | 1135280–28-2 |
| KN93 | Tocris | 1278 | 139298–40-1 |
| KU-55933 | Selleck | S1092 | 587871–26-9 |
| KW-2449 | Selleck | S2158 | 1000669–72-6 |
| Lapatinib | Selleck | S2111 | 231277–92-2 |
| Lenalidomide | Selleck | S1029 | 191732–72-6 |
| Lenvatinib | Selleck | S1164 | 857890–39-2 |
| Lestaurtinib (CEP-701) | LC Labs | L-6307 | 111358–88-4 |
| Linifanib (ABT-869) | Selleck | S1003 | 796967–16-3 |
| Lovastatin | Selleck | S2061 | 75330–75-5 |
| LY-333531 | Tocris | 4738 | 169939–93-9 |
| LY294002 | LC Labs | L-7962 | 154447–36-6 |
| Masitinib (AB-1010) | LC Labs | M-7007 | 790299–79-5 |
| MEK Inhibitor VII | Millipore Sigma (EMD Biosciences; Calbiochem) | 444939 | 305350–87-2 |
| Metformin | Selleck | S5958 | 657–24-9 |
| MGCD-265 | Selleck | S1361 | 875337–44-3 |
| Midostaurin | LC Labs | P-7600 | 120685–11-2 |
| MK-2206 | Selleck | S1078 | 1032350–13-2 |
| MLN120B | MedChem Express | HY-15473 | 783348–36-7 |
| MLN8054 | Selleck | S1100 | 869363–13-3 |
| Motesanib (AMG-706) | LC Labs | M-2900 | 857876–30-3 |
| Neratinib (HKI-272) | Selleck | S2150 | 698387–09-6 |
| NF-kB Activation Inhibitor | Selleck | S4902 | 545380–34-5 |
| Nilotinib | Selleck | S1033 | 641571–10-0 |
| Nutlin 3a | Selleck | S8059 | 675576–98-4 |
| NVP-ADW742 | Selleck | S1088 | 475488–23-4 |
| NVP-AEW541 | Selleck | S1034 | 475489–16-8 |
| NVP-TAE684 | Selleck | S1108 | 761439–42-3 |
| Olaparib | Selleck | S1060 | 763113–22-0 |
| OTX-015 | Selleck | S7360 | 202590–98-5 |
| p38 MAP Kinase Inhibitor | Millipore Sigma (EMD Biosciences; Calbiochem) | 506126 | 219138–24-6 |
| Palbociclib | Selleck | S4482 | 571190–30-2 |
| Panobinostat | Selleck | S1030 | 404950–80-7 |
| Pazopanib (GW786034) | LC Labs | P6706 | 444731–52-6 |
| PD153035 | Millipore Sigma (EMD Biosciences; Calbiochem) | SML0564 | 183322–45-4 |
| PD173955 | Symansis | SY-PD173955 | 260415–63-2 |
| PD98059 | LC Labs | P-4313 | 167869–21-8 |
| Pelitinib (EKB-569) | Selleck | S1392 | 257933–82-7 |
| Perhexiline maleate | Selleck | S6959 | 6724–53-4 |
| PH-797804 | Selleck | S2726 | 586379–66-0 |
| PHA-665752 | Selleck | S1070 | 477575–56-7 |
| PHT-427 | Selleck | S1556 | 1191951–57-1 |
| PI-103 | Selleck | S1038 | 371935–74-9 |
| PLX-4720 | Selleck | S1152 | 918505–84-7 |
| Ponatinib (AP24534) | LC Labs | P-7022 | 943319–70-8 |
| PP2 | Millipore Sigma (EMD Biosciences; Calbiochem) | 529573 | 172889–27-9 |
| PP242 | LC Labs | P-6666 | 1092351–67-1 |
| PRT062070 HCL | Selleck | S7634 | 1369761–01-2 |
| PRT062607 | Selleck | S8032 | 1370261–97-4 |
| Quizartinib (AC220) | LC Labs | Q-4747 | 950769–58-1 |
| R406 | Selleck | S2194 | 841290–81-1 |
| R547 | Selleck | S2688 | 741713–40-6 |
| RAF265 (CHIR-265) | Selleck | S2161 | 927880–90-8 |
| Ralimetinib (LY2228820) | Selleck | S1494 | 862507–23-1 |
| Ranolazine (free base) | Selleck | S1799 | 95635–55-5 |
| Rapamycin | LC Labs | R-5000 | 53123–88-9 |
| Regorafenib (BAY 73–4506) | Selleck | S1178 | 755037–03-7 |
| Roscovitine (CYC-202) | LC Labs | R-1234 | 186692–46-6 |
| Ruxolitinib, free base | LC Labs | R-6600 | 120685–11-2 |
| S31–201 | Santa Cruz Biotech | sc-204304 | 501919–59-1 |
| Saracatinib (AZD0530) | LC Labs | S-8906 | 379231–04-6 |
| SB-202190 | LC Labs | S-1700 | 152121–30-7 |
| SB-203580 | LC Labs | S-3400 | 152121–47-6 |
| SB-431542 | Selleck | S1067 | 301836–41-9 |
| Selinexor | Selleck | S7252 | 1393477–72-9 |
| Selumetinib (AZD6244) | LC Labs | S-4490 | 606143–52-6 |
| SGX-523 | Selleck | S1112 | 1022150–57-7 |
| SNS-032 (BMS-387032) | Selleck | S1145 | 345627–80-7 |
| Sorafenib tosylate | LC Labs | S-8502 | 475207–59-1 |
| SR9011-HCL | MedChem Express | HY-16988A | 2070014–94-5 |
| Staurosporine, free base | LC Labs | S-9300 | 62996–74-1] |
| STO609 | Millipore Sigma (EMD Biosciences; Calbiochem) | 570250 | 52029–86-4 |
| SU11274 | Selleck | S1080 | 658084–23-2 |
| SU14813 | Selleck | S0504 | 627908–92-3 |
| Sunitinib malate | LC Labs | S-8803 | 341031–54-7 |
| SYK Inhibitor | Millipore Sigma (EMD Biosciences; Calbiochem) | 574711 | 622387–85-3 |
| Tandutinib (MLN518) | LC Labs | T-7802 | 387867–13-2 |
| TG100–115 | Selleck | S1358 | 677297–51-7 |
| TG101348 | Active Biochem | A-1140 | 936091–26-8 |
| Tivozanib (AV-951) | LC Labs | T-6466 | 475108–18-0 |
| Tofacitinib (CP-690550) | LC Labs | T-1377 | 477600–75-2 |
| Tozasertib (VX-680) | LC Labs | T-2304 | 639089–54-6 |
| Trametinib (GSK1120212) | LC Labs | T-8132 | 871700–17-3 |
| Vandetanib (ZD6474) | LC Labs | V-9402 | 443913–73-3 |
| Vargetef (Nintedanib) | LC Labs | N-9077 | 656247–17-5 |
| Vatalanib (PTK787) | LC Labs | V-8303 | 212141–51-0 |
| Vemurafenib (PLX4032) | LC Labs | V-2800 | 918504–65-1 |
| Venetoclax | LC Labs | V-3579 | 1257044–40-8 |
| Vismodegib (GDC-0449) | LC Labs | V-4050 | 879085–55-9 |
| Volasertib (BI-6727) | Selleck | S2235 | 755038–65-4 |
| VX-745 | Tocris | 3915 | 209410–46-8 |
| XAV-939 | Selleck | S1180 | 284028–89-3 |
| XMD 8–87 | Selleck | S8272 | 1234480–46-6 |
| YM-155 | Selleck | S1130 | 781661–94-7 |
| Other Chemical | Source | Catalog # |
| Zombie Aqua Fixable Viability Dye | Biolegend | Catalog # 423101 |
| Critical commercial assays | ||
| Nextera RapidCapture Exome | Illumina | |
| SureSelect Strand-Specific RNA Library Preparation Kit | Agilent | |
| DNeasy Blood & Tissue Kit | Qiagen | |
| RNeasy Mini Kit | Qiagen | |
| Deposited data | ||
| DNA Sequencing Data | This paper | http://vizome.org/aml2/, dbGaP study ID is 30641 and accession ID is phs001657.v2.p1 |
| RNA Sequencing Data | This paper | http://vizome.org/aml2/, dbGaP study ID is 30641 and accession ID is phs001657.v2.p1 |
| Experimental models: Cell lines | ||
| n/a | ||
| Experimental models: Organisms/strains | ||
| n/a | ||
| Oligonucleotides | ||
| Custom capture probes for DNA sequencing (11.9 MB) | Roche-Nimblegen | Sequencing coordinates listed Table S14 of (Tyner et al., 2018) |
| Forward Primer FLT3: 5′- AGCA ATT TAG GTA TGA AAG CCA GCTA - 3′ | Eurofins | (Kottaridis et al., 2001) |
| Reverse Primer FLT3: 5′ - CTT TCA GCA TTT TGA CGG CAA CC - 3′ | Eurofins | (Kottaridis et al., 2001) |
| Forward Primer NPM1: 5′ - GTT TCT TTT TTT TTT TTT CCA GGC TAT TCA AG - 3′ | Eurofins | (Falini et al., 2007) |
| Reverse Primer NPM1: 5′ - CAC GGT AGG GAA AGT TCT CAC TCT GC - 3′ | Eurofins | (Falini et al., 2007) |
| Recombinant DNA | ||
| n/a | ||
| Software and algorithms | ||
| R version 4.03 | R Core Team | https://www.r-project.org |
| R package GSVA v1.38 | Bioconductor | DOI: 10.18129/B9.bioc.GSVA |
| R package cqn v1.36 | Bioconductor | DOI: 10.18129/B9.bioc.cqn |
| R package qvalue v2.22.0 | Bioconductor | DOI: 10.18129/B9.bioc.qvalue |
| R package partykit v1.2–15 | CRAN | https://CRAN.R-project.org/package=partykit |
| R package survival v3.2–7 | CRAN | https://CRAN.R-project.org/package=survival |
| R package WGCNA v1.69 | CRAN | https://CRAN.R-project.org/package=WGCNA |
| R package data.table v1.13.6 | CRAN | https://CRAN.R-project.org/package=data.table |
| Manuscript analysis workflow |
This paper | DOI: 10.5281/zenodo.6773715 |
| Other | ||
| Ex Vivo Drug Sensitivity Data | This paper | http://vizome.org/aml2/ and https://biodev.github.io/BeatAML2/ |
| Clinical Annotations | This paper | Table S1 |