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Bottomly D, Long N, Schultz AR, Kurtz SE, Tognon CE, Johnson K, Abel M, Agarwal A, Avaylon S, Benton E, Blucher A, Borate U, Braun TP, Brown J, Bryant J, Burke R, Carlos A, Chang BH, Cho HJ, Christy S, Coblentz C, Cohen AM, d'Almeida A, Cook R, Danilov A, Dao KHT, Degnin M, Dibb J, Eide CA, English I, Hagler S, Harrelson H, Henson R, Ho H, Joshi SK, Junio B, Kaempf A, Kosaka Y, Laderas T, Lawhead M, Lee H, Leonard JT, Lin C, Lind EF, Liu SQ, Lo P, Loriaux MM, Luty S, Maxson JE, Macey T, Martinez J, Minnier J, Monteblanco A, Mori M, Morrow Q, Nelson D, Ramsdill J, Rofelty A, Rogers A, Romine KA, Ryabinin P, Saultz JN, Sampson DA, Savage SL, Schuff R, Searles R, Smith RL, Spurgeon SE, Sweeney T, Swords RT, Thapa A, Thiel-Klare K, Traer E, Wagner J, Wilmot B, Wolf J, Wu G, Yates A, Zhang H, Cogle CR, Collins RH, Deininger MW, Hourigan CS, Jordan CT, Lin TL, Martinez ME, Pallapati RR, Pollyea DA, Pomicter AD, Watts JM, Weir SJ, Druker BJ, McWeeney SK, Tyner JW. Integrative analysis of drug response and clinical outcome in acute myeloid leukemia. Cancer Cell 2022; 40:850-864.e9. [PMID: 35868306 PMCID: PMC9378589 DOI: 10.1016/j.ccell.2022.07.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/30/2022] [Accepted: 06/30/2022] [Indexed: 12/17/2022]
Abstract
Acute myeloid leukemia (AML) is a cancer of myeloid-lineage cells with limited therapeutic options. We previously combined ex vivo drug sensitivity with genomic, transcriptomic, and clinical annotations for a large cohort of AML patients, which facilitated discovery of functional genomic correlates. Here, we present a dataset that has been harmonized with our initial report to yield a cumulative cohort of 805 patients (942 specimens). We show strong cross-cohort concordance and identify features of drug response. Further, deconvoluting transcriptomic data shows that drug sensitivity is governed broadly by AML cell differentiation state, sometimes conditionally affecting other correlates of response. Finally, modeling of clinical outcome reveals a single gene, PEAR1, to be among the strongest predictors of patient survival, especially for young patients. Collectively, this report expands a large functional genomic resource, offers avenues for mechanistic exploration and drug development, and reveals tools for predicting outcome in AML.
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Affiliation(s)
- Daniel Bottomly
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Nicola Long
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Anna Reister Schultz
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Stephen E Kurtz
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kara Johnson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Melissa Abel
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA; Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Sammantha Avaylon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Erik Benton
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Aurora Blucher
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Uma Borate
- Division of Hematology, Department of Internal Medicine, James Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Theodore P Braun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jordana Brown
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jade Bryant
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Russell Burke
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Amy Carlos
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA
| | - Bill H Chang
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology and Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hyun Jun Cho
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Stephen Christy
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Cody Coblentz
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Aaron M Cohen
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Amanda d'Almeida
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rachel Cook
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alexey Danilov
- Department of Hematology and Hematopoietic Stem Cell Transplant, City of Hope National Medical Center, Duarte, CA 91010, USA
| | | | - Michie Degnin
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - James Dibb
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christopher A Eide
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Isabel English
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Stuart Hagler
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Heath Harrelson
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rachel Henson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hibery Ho
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Brian Junio
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Andy Kaempf
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Biostatistics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Yoko Kosaka
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | | | - Matt Lawhead
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hyunjung Lee
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jessica T Leonard
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Chenwei Lin
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA
| | - Evan F Lind
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Selina Qiuying Liu
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Pierrette Lo
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Marc M Loriaux
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Pathology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Samuel Luty
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julia E Maxson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Tara Macey
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jacqueline Martinez
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jessica Minnier
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Biostatistics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA; OHSU-PSU School of Public Health, VA Portland Health Care System, Oregon Health & Science University, Portland, OR 97239, USA
| | - Andrea Monteblanco
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Motomi Mori
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Quinlan Morrow
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Dylan Nelson
- High-Throughput Screening Services Laboratory, Oregon State University, Corvallis, OR 97331, USA
| | - Justin Ramsdill
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Angela Rofelty
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alexandra Rogers
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kyle A Romine
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Peter Ryabinin
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jennifer N Saultz
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - David A Sampson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Samantha L Savage
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | | | - Robert Searles
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rebecca L Smith
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Stephen E Spurgeon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Tyler Sweeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ronan T Swords
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Aashis Thapa
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Karina Thiel-Klare
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jake Wagner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Beth Wilmot
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joelle Wolf
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Guanming Wu
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Amy Yates
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Haijiao Zhang
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christopher R Cogle
- Department of Medicine, Division of Hematology and Oncology, University of Florida, Gainesville, FL 32610, USA
| | - Robert H Collins
- Department of Internal Medicine/ Hematology Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390-8565, USA
| | - Michael W Deininger
- Division of Hematology & Hematologic Malignancies, Department of Internal Medicine, University of Utah, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Christopher S Hourigan
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20814-1476, USA
| | - Craig T Jordan
- Division of Hematology, University of Colorado, Denver, CO 80045, USA
| | - Tara L Lin
- Division of Hematologic Malignancies & Cellular Therapeutics, University of Kansas, Kansas City, KS 66205, USA
| | - Micaela E Martinez
- Clinical Research Services, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Rachel R Pallapati
- Clinical Research Services, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Daniel A Pollyea
- Division of Hematology, University of Colorado, Denver, CO 80045, USA
| | - Anthony D Pomicter
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Justin M Watts
- Division of Hematology, Department of Medicine, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Scott J Weir
- Department of Cancer Biology, Division of Medical Oncology, Department of Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA.
| | - Shannon K McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA.
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA.
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