1
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Pino JC, Posso C, Joshi SK, Nestor M, Moon J, Hansen JR, Hutchinson-Bunch C, Gritsenko MA, Weitz KK, Watanabe-Smith K, Long N, McDermott JE, Druker BJ, Liu T, Tyner JW, Agarwal A, Traer E, Piehowski PD, Tognon CE, Rodland KD, Gosline SJC. Mapping the proteogenomic landscape enables prediction of drug response in acute myeloid leukemia. Cell Rep Med 2024; 5:101359. [PMID: 38232702 PMCID: PMC10829797 DOI: 10.1016/j.xcrm.2023.101359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/20/2023] [Accepted: 12/10/2023] [Indexed: 01/19/2024]
Abstract
Acute myeloid leukemia is a poor-prognosis cancer commonly stratified by genetic aberrations, but these mutations are often heterogeneous and fail to consistently predict therapeutic response. Here, we combine transcriptomic, proteomic, and phosphoproteomic datasets with ex vivo drug sensitivity data to help understand the underlying pathophysiology of AML beyond mutations. We measure the proteome and phosphoproteome of 210 patients and combine them with genomic and transcriptomic measurements to identify four proteogenomic subtypes that complement existing genetic subtypes. We build a predictor to classify samples into subtypes and map them to a "landscape" that identifies specific drug response patterns. We then build a drug response prediction model to identify drugs that target distinct subtypes and validate our findings on cell lines representing various stages of quizartinib resistance. Our results show how multiomics data together with drug sensitivity data can inform therapy stratification and drug combinations in AML.
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Affiliation(s)
- James C Pino
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Camilo Posso
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Michael Nestor
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jamie Moon
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Joshua R Hansen
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chelsea Hutchinson-Bunch
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marina A Gritsenko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karl K Weitz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kevin Watanabe-Smith
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Nicola Long
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Jason E McDermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA; Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Tao Liu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Paul D Piehowski
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Karin D Rodland
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
| | - Sara J C Gosline
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
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2
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Gosline SJC, Tognon C, Nestor M, Joshi S, Modak R, Damnernsawad A, Posso C, Moon J, Hansen JR, Hutchinson-Bunch C, Pino JC, Gritsenko MA, Weitz KK, Traer E, Tyner J, Druker B, Agarwal A, Piehowski P, McDermott JE, Rodland K. Proteomic and phosphoproteomic measurements enhance ability to predict ex vivo drug response in AML. Clin Proteomics 2022; 19:30. [PMID: 35896960 PMCID: PMC9327422 DOI: 10.1186/s12014-022-09367-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/22/2022] [Indexed: 11/23/2022] Open
Abstract
Acute Myeloid Leukemia (AML) affects 20,000 patients in the US annually with a five-year survival rate of approximately 25%. One reason for the low survival rate is the high prevalence of clonal evolution that gives rise to heterogeneous sub-populations of leukemic cells with diverse mutation spectra, which eventually leads to disease relapse. This genetic heterogeneity drives the activation of complex signaling pathways that is reflected at the protein level. This diversity makes it difficult to treat AML with targeted therapy, requiring custom patient treatment protocols tailored to each individual's leukemia. Toward this end, the Beat AML research program prospectively collected genomic and transcriptomic data from over 1000 AML patients and carried out ex vivo drug sensitivity assays to identify genomic signatures that could predict patient-specific drug responses. However, there are inherent weaknesses in using only genetic and transcriptomic measurements as surrogates of drug response, particularly the absence of direct information about phosphorylation-mediated signal transduction. As a member of the Clinical Proteomic Tumor Analysis Consortium, we have extended the molecular characterization of this cohort by collecting proteomic and phosphoproteomic measurements from a subset of these patient samples (38 in total) to evaluate the hypothesis that proteomic signatures can improve the ability to predict response to 26 drugs in AML ex vivo samples. In this work we describe our systematic, multi-omic approach to evaluate proteomic signatures of drug response and compare protein levels to other markers of drug response such as mutational patterns. We explore the nuances of this approach using two drugs that target key pathways activated in AML: quizartinib (FLT3) and trametinib (Ras/MEK), and show how patient-derived signatures can be interpreted biologically and validated in cell lines. In conclusion, this pilot study demonstrates strong promise for proteomics-based patient stratification to assess drug sensitivity in AML.
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Affiliation(s)
| | - Cristina Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | | | - Sunil Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Rucha Modak
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Alisa Damnernsawad
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Camilo Posso
- Pacific Northwest National Laboratory, Seattle, WA, USA
| | - Jamie Moon
- Pacific Northwest National Laboratory, Seattle, WA, USA
| | | | | | - James C Pino
- Pacific Northwest National Laboratory, Seattle, WA, USA
| | | | - Karl K Weitz
- Pacific Northwest National Laboratory, Seattle, WA, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jeffrey Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Brian Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | | | - Jason E McDermott
- Pacific Northwest National Laboratory, Seattle, WA, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Karin Rodland
- Pacific Northwest National Laboratory, Seattle, WA, USA.
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
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3
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Heilig CE, Laßmann A, Mughal SS, Mock A, Pirmann S, Teleanu V, Renner M, Andresen C, Köhler BC, Aybey B, Bauer S, Siveke JT, Hamacher R, Folprecht G, Richter S, Schröck E, Brandts CH, Ahrens M, Hohenberger P, Egerer G, Kindler T, Boerries M, Illert AL, von Bubnoff N, Apostolidis L, Jost PJ, Westphalen CB, Weichert W, Keilholz U, Klauschen F, Beck K, Winter U, Richter D, Möhrmann L, Bitzer M, Schulze-Osthoff K, Brors B, Mechtersheimer G, Kreutzfeldt S, Heining C, Lipka DB, Stenzinger A, Schlenk RF, Horak P, Glimm H, Hübschmann D, Fröhling S. Gene expression-based prediction of pazopanib efficacy in sarcoma. Eur J Cancer 2022; 172:107-118. [PMID: 35763870 DOI: 10.1016/j.ejca.2022.05.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/28/2022] [Accepted: 05/12/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND The multi-receptor tyrosine kinase inhibitor pazopanib is approved for the treatment of advanced soft-tissue sarcoma and has also shown activity in other sarcoma subtypes. However, its clinical efficacy is highly variable, and no reliable predictors exist to select patients who are likely to benefit from this drug. PATIENTS AND METHODS We analysed the molecular profiles and clinical outcomes of patients with pazopanib-treated sarcoma enrolled in a prospective observational study by the German Cancer Consortium, DKTK MASTER, that employs whole-genome/exome sequencing and transcriptome sequencing to inform the care of young adults with advanced cancer across histology and patients with rare cancers. RESULTS Among 109 patients with available whole-genome/exome sequencing data, there was no correlation between clinical parameters, specific genetic alterations or mutational signatures and clinical outcome. In contrast, the analysis of a subcohort of 62 patients who underwent molecular analysis before pazopanib treatment and had transcriptome sequencing data available showed that mRNA levels of NTRK3 (hazard ratio [HR] = 0.53, p = 0.021), IGF1R (HR = 1.82, p = 0.027) and KDR (HR = 0.50, p = 0.011) were independently associated with progression-free survival (PFS). Based on the expression of these multi-receptor tyrosine kinase genes, i.e. the features NTRK3-high, IGF1R-low and KDR-high, we developed a pazopanib efficacy predictor that stratified patients into three groups with significantly different PFS (p < 0.0001). Application of the pazopanib efficacy predictor to an independent cohort of patients with pazopanib-treated sarcoma from DKTK MASTER (n = 43) confirmed its potential to separate patient groups with significantly different PFS (p = 0.02), whereas no such association was observed in patients with sarcoma from DKTK MASTER (n = 97) or The Cancer Genome Atlas sarcoma cohort (n = 256) who were not treated with pazopanib. CONCLUSION A score based on the combined expression of NTRK3, IGF1R and KDR allows the identification of patients with sarcoma and with good, intermediate and poor outcome following pazopanib therapy and warrants prospective investigation as a predictive tool to optimise the use of this drug in the clinic.
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Affiliation(s)
- Christoph E Heilig
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany. https://twitter.com/ChrisHeiligMD
| | - Andreas Laßmann
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sadaf S Mughal
- Division of Applied Bioinformatics, DKFZ, Heidelberg, Germany
| | - Andreas Mock
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany. https://twitter.com/am0ck
| | - Sebastian Pirmann
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Veronica Teleanu
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcus Renner
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Carolin Andresen
- Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
| | - Bruno C Köhler
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany. https://twitter.com/koehlerlab
| | - Bogac Aybey
- Division of Applied Bioinformatics, DKFZ, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sebastian Bauer
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany; DKTK, Essen, Germany. https://twitter.com/seppobauer
| | - Jens T Siveke
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany; DKTK, Essen, Germany; Division of Solid Tumor Translational Oncology, DKTK, Essen, and DKFZ, Heidelberg, Germany; Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Rainer Hamacher
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany; DKTK, Essen, Germany
| | - Gunnar Folprecht
- Department of Medicine I, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Stephan Richter
- Department of Medicine I, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Evelin Schröck
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, Dresden, Germany; Center for Personalized Oncology, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany; DKTK, Dresden, Germany
| | - Christian H Brandts
- University Cancer Center (UCT) Frankfurt, University Hospital Frankfurt, Goethe University, Frankfurt, Germany; Department of Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany; Frankfurt Cancer Institute, Frankfurt, Germany; DKTK, Frankfurt, Germany
| | - Marit Ahrens
- Department of Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Peter Hohenberger
- Department of Surgery, Mannheim University Medical Center, Heidelberg University, Mannheim, Germany; Sarcoma Unit, Interdisciplinary Tumor Center Mannheim, Mannheim University Medical Center, Heidelberg University, Mannheim, Germany
| | - Gerlinde Egerer
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Kindler
- UCT Mainz, Johannes Gutenberg University Mainz, Mainz, Germany; Department of Hematology, Medical Oncology and Pneumology, University Medical Center, Mainz, Germany; DKTK, Mainz, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Comprehensive Cancer Center Freiburg, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; DKTK, Freiburg, Germany
| | - Anna L Illert
- Comprehensive Cancer Center Freiburg, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; DKTK, Freiburg, Germany; Department of Internal Medicine I, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nikolas von Bubnoff
- Department of Internal Medicine I, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Lübeck, Germany
| | - Leonidas Apostolidis
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - Philipp J Jost
- Department of Hematology and Oncology, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany; Division of Clinical Oncology, Department of Medicine, Medical University of Graz, Graz, Austria; DKTK, Munich, Germany
| | - C Benedikt Westphalen
- DKTK, Munich, Germany; Comprehensive Cancer Center, University Hospital, Ludwig Maximilians University Munich, Munich, Germany; Department of Medicine III, University Hospital, Ludwig Maximilians University Munich, Munich, Germany
| | - Wilko Weichert
- DKTK, Munich, Germany; Institute of Pathology, Technical University Munich, Munich, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany; DKTK, Berlin, Germany
| | - Frederick Klauschen
- DKTK, Berlin, Germany; Institute of Pathology, Charité - Universitätsmedizin Berlin, And Berlin Institute of Health, Berlin, Germany; Institute of Pathology, Ludwig Maximilians University Munich, Munich, Germany
| | - Katja Beck
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ulrike Winter
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniela Richter
- Center for Personalized Oncology, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany; DKTK, Dresden, Germany; Department of Translational Medical Oncology, NCT Dresden and DKFZ, Dresden, Germany
| | - Lino Möhrmann
- Center for Personalized Oncology, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany; DKTK, Dresden, Germany; Department of Translational Medical Oncology, NCT Dresden and DKFZ, Dresden, Germany
| | - Michael Bitzer
- Department of Internal Medicine I, University Hospital, Eberhard-Karls University, Tübingen, Germany; DKTK, Tübingen, Germany
| | - Klaus Schulze-Osthoff
- DKTK, Tübingen, Germany; Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, Tübingen, Germany
| | - Benedikt Brors
- German Cancer Consortium (DKTK), Heidelberg, Germany; Division of Applied Bioinformatics, DKFZ, Heidelberg, Germany
| | | | - Simon Kreutzfeldt
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christoph Heining
- Center for Personalized Oncology, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany; DKTK, Dresden, Germany; Department of Translational Medical Oncology, NCT Dresden and DKFZ, Dresden, Germany. https://twitter.com/ChrisHeining
| | - Daniel B Lipka
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany. https://twitter.com/dblipka1
| | - Albrecht Stenzinger
- German Cancer Consortium (DKTK), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Richard F Schlenk
- German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany; Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany; NCT Trial Center, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Peter Horak
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany. https://twitter.com/PeterHorak_MD
| | - Hanno Glimm
- Center for Personalized Oncology, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany; DKTK, Dresden, Germany; Department of Translational Medical Oncology, NCT Dresden and DKFZ, Dresden, Germany
| | - Daniel Hübschmann
- German Cancer Consortium (DKTK), Heidelberg, Germany; Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany; Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
| | - Stefan Fröhling
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany.
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4
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Myers PJ, Lee SH, Lazzara MJ. MECHANISTIC AND DATA-DRIVEN MODELS OF CELL SIGNALING: TOOLS FOR FUNDAMENTAL DISCOVERY AND RATIONAL DESIGN OF THERAPY. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:100349. [PMID: 35935921 PMCID: PMC9348571 DOI: 10.1016/j.coisb.2021.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A full understanding of cell signaling processes requires knowledge of protein structure/function relationships, protein-protein interactions, and the abilities of pathways to control phenotypes. Computational models offer a valuable framework for integrating that knowledge to predict the effects of system perturbations and interventions in health and disease. Whereas mechanistic models are well suited for understanding the biophysical basis for signal transduction and principles of therapeutic design, data-driven models are particularly suited to distill complex signaling relationships among samples and between multivariate signaling changes and phenotypes. Both approaches have limitations and provide incomplete representations of signaling biology, but their careful implementation and integration can provide new understanding for how manipulating system variables impacts cellular decisions.
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Affiliation(s)
- Paul J. Myers
- Department of Chemical Engineering, Charlottesville, VA 22904
| | - Sung Hyun Lee
- Department of Chemical Engineering, Charlottesville, VA 22904
| | - Matthew J. Lazzara
- Department of Chemical Engineering, Charlottesville, VA 22904
- Department of Biomedical Engineering University of Virginia, Charlottesville, VA 22904
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5
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Bakouny Z, Braun DA, Shukla SA, Pan W, Gao X, Hou Y, Flaifel A, Tang S, Bosma-Moody A, He MX, Vokes N, Nyman J, Xie W, Nassar AH, Abou Alaiwi S, Flippot R, Bouchard G, Steinharter JA, Nuzzo PV, Ficial M, Sant'Angelo M, Forman J, Berchuck JE, Dudani S, Bi K, Park J, Camp S, Sticco-Ivins M, Hirsch L, Baca SC, Wind-Rotolo M, Ross-Macdonald P, Sun M, Lee GSM, Chang SL, Wei XX, McGregor BA, Harshman LC, Genovese G, Ellis L, Pomerantz M, Hirsch MS, Freedman ML, Atkins MB, Wu CJ, Ho TH, Linehan WM, McDermott DF, Heng DYC, Viswanathan SR, Signoretti S, Van Allen EM, Choueiri TK. Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma. Nat Commun 2021; 12:808. [PMID: 33547292 PMCID: PMC7865061 DOI: 10.1038/s41467-021-21068-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Sarcomatoid and rhabdoid (S/R) renal cell carcinoma (RCC) are highly aggressive tumors with limited molecular and clinical characterization. Emerging evidence suggests immune checkpoint inhibitors (ICI) are particularly effective for these tumors, although the biological basis for this property is largely unknown. Here, we evaluate multiple clinical trial and real-world cohorts of S/R RCC to characterize their molecular features, clinical outcomes, and immunologic characteristics. We find that S/R RCC tumors harbor distinctive molecular features that may account for their aggressive behavior, including BAP1 mutations, CDKN2A deletions, and increased expression of MYC transcriptional programs. We show that these tumors are highly responsive to ICI and that they exhibit an immune-inflamed phenotype characterized by immune activation, increased cytotoxic immune infiltration, upregulation of antigen presentation machinery genes, and PD-L1 expression. Our findings build on prior work and shed light on the molecular drivers of aggressivity and responsiveness to ICI of S/R RCC. Sarcomatoid and rhabdoid tumours are highly aggressive forms of renal cell carcinoma that are also responsive to immunotherapy. In this study, the authors perform a comprehensive molecular characterization of these tumours discovering an enrichment of specific alterations and an inflamed phenotype.
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Affiliation(s)
- Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David A Braun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sachet A Shukla
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wenting Pan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xin Gao
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Yue Hou
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Abdallah Flaifel
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Stephen Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alice Bosma-Moody
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Meng Xiao He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Natalie Vokes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jackson Nyman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wanling Xie
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amin H Nassar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Abou Alaiwi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ronan Flippot
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gabrielle Bouchard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John A Steinharter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Miriam Ficial
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Juliet Forman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shaan Dudani
- Tom Baker Cancer Centre, University of Calgary, Calgary, AB, Canada
| | - Kevin Bi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jihye Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sabrina Camp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Laure Hirsch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Maxine Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven L Chang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xiao X Wei
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bradley A McGregor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lauren C Harshman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Giannicola Genovese
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Leigh Ellis
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael B Atkins
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thai H Ho
- Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Daniel Y C Heng
- Tom Baker Cancer Centre, University of Calgary, Calgary, AB, Canada
| | | | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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6
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Paull EO, Aytes A, Jones SJ, Subramaniam PS, Giorgi FM, Douglass EF, Tagore S, Chu B, Vasciaveo A, Zheng S, Verhaak R, Abate-Shen C, Alvarez MJ, Califano A. A modular master regulator landscape controls cancer transcriptional identity. Cell 2021; 184:334-351.e20. [PMID: 33434495 PMCID: PMC8103356 DOI: 10.1016/j.cell.2020.11.045] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 08/06/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023]
Abstract
Despite considerable efforts, the mechanisms linking genomic alterations to the transcriptional identity of cancer cells remain elusive. Integrative genomic analysis, using a network-based approach, identified 407 master regulator (MR) proteins responsible for canalizing the genetics of individual samples from 20 cohorts in The Cancer Genome Atlas (TCGA) into 112 transcriptionally distinct tumor subtypes. MR proteins could be further organized into 24 pan-cancer, master regulator block modules (MRBs), each regulating key cancer hallmarks and predictive of patient outcome in multiple cohorts. Of all somatic alterations detected in each individual sample, >50% were predicted to induce aberrant MR activity, yielding insight into mechanisms linking tumor genetics and transcriptional identity and establishing non-oncogene dependencies. Genetic and pharmacological validation assays confirmed the predicted effect of upstream mutations and MR activity on downstream cellular identity and phenotype. Thus, co-analysis of mutational and gene expression profiles identified elusive subtypes and provided testable hypothesis for mechanisms mediating the effect of genetic alterations.
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Affiliation(s)
- Evan O Paull
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alvaro Aytes
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Molecular Mechanisms and Experimental Therapeutics in Oncology (ONCOBell), Bellvitge Institute for Biomedical Research, L'Hospitalet de Llobregat, Barcelona 08908, Spain; Program Against Cancer Therapeutics Resistance (ProCURE), Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Sunny J Jones
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Prem S Subramaniam
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Eugene F Douglass
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Somnath Tagore
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Brennan Chu
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alessandro Vasciaveo
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Siyuan Zheng
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Roel Verhaak
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Cory Abate-Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Mariano J Alvarez
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; DarwinHealth, Inc. New York, NY 10018, USA.
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; DarwinHealth, Inc. New York, NY 10018, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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7
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Corsello SM, Nagari RT, Spangler RD, Rossen J, Kocak M, Bryan JG, Humeidi R, Peck D, Wu X, Tang AA, Wang VM, Bender SA, Lemire E, Narayan R, Montgomery P, Ben-David U, Garvie CW, Chen Y, Rees MG, Lyons NJ, McFarland JM, Wong BT, Wang L, Dumont N, O'Hearn PJ, Stefan E, Doench JG, Harrington CN, Greulich H, Meyerson M, Vazquez F, Subramanian A, Roth JA, Bittker JA, Boehm JS, Mader CC, Tsherniak A, Golub TR. Discovering the anti-cancer potential of non-oncology drugs by systematic viability profiling. NATURE CANCER 2020; 1:235-248. [PMID: 32613204 PMCID: PMC7328899 DOI: 10.1038/s43018-019-0018-6] [Citation(s) in RCA: 384] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/06/2019] [Indexed: 12/26/2022]
Abstract
Anti-cancer uses of non-oncology drugs have occasionally been found, but such discoveries have been serendipitous. We sought to create a public resource containing the growth inhibitory activity of 4,518 drugs tested across 578 human cancer cell lines. We used PRISM, a molecular barcoding method, to screen drugs against cell lines in pools. An unexpectedly large number of non-oncology drugs selectively inhibited subsets of cancer cell lines in a manner predictable from the cell lines' molecular features. Our findings include compounds that killed by inducing PDE3A-SLFN12 complex formation; vanadium-containing compounds whose killing depended on the sulfate transporter SLC26A2; the alcohol dependence drug disulfiram, which killed cells with low expression of metallothioneins; and the anti-inflammatory drug tepoxalin, which killed via the multi-drug resistance protein ABCB1. The PRISM drug repurposing resource (https://depmap.org/repurposing) is a starting point to develop new oncology therapeutics, and more rarely, for potential direct clinical translation.
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Affiliation(s)
- Steven M Corsello
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Jordan Rossen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mustafa Kocak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jordan G Bryan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Duke University, Durham, NC, USA
| | - Ranad Humeidi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Peck
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaoyun Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew A Tang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vickie M Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Evan Lemire
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rajiv Narayan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Uri Ben-David
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel
| | | | - Yejia Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Bang T Wong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- 10x Genomics, Pleasanton, CA, USA
| | - Nancy Dumont
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick J O'Hearn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Relay Therapeutics, Cambridge, MA, USA
| | - Eric Stefan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biogen, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Matthew Meyerson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | | | - Joshua A Bittker
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Vertex Pharmaceuticals, Boston, MA, USA
| | - Jesse S Boehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher C Mader
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Flatiron Health, New York, NY, USA
| | | | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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8
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Corsello SM, Nagari RT, Spangler RD, Rossen J, Kocak M, Bryan JG, Humeidi R, Peck D, Wu X, Tang AA, Wang VM, Bender SA, Lemire E, Narayan R, Montgomery P, Ben-David U, Garvie CW, Chen Y, Rees MG, Lyons NJ, McFarland JM, Wong BT, Wang L, Dumont N, O'Hearn PJ, Stefan E, Doench JG, Harrington CN, Greulich H, Meyerson M, Vazquez F, Subramanian A, Roth JA, Bittker JA, Boehm JS, Mader CC, Tsherniak A, Golub TR. Discovering the anti-cancer potential of non-oncology drugs by systematic viability profiling. NATURE CANCER 2020. [PMID: 32613204 DOI: 10.6084/m9.figshare.20564034.v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Anti-cancer uses of non-oncology drugs have occasionally been found, but such discoveries have been serendipitous. We sought to create a public resource containing the growth inhibitory activity of 4,518 drugs tested across 578 human cancer cell lines. We used PRISM, a molecular barcoding method, to screen drugs against cell lines in pools. An unexpectedly large number of non-oncology drugs selectively inhibited subsets of cancer cell lines in a manner predictable from the cell lines' molecular features. Our findings include compounds that killed by inducing PDE3A-SLFN12 complex formation; vanadium-containing compounds whose killing depended on the sulfate transporter SLC26A2; the alcohol dependence drug disulfiram, which killed cells with low expression of metallothioneins; and the anti-inflammatory drug tepoxalin, which killed via the multi-drug resistance protein ABCB1. The PRISM drug repurposing resource (https://depmap.org/repurposing) is a starting point to develop new oncology therapeutics, and more rarely, for potential direct clinical translation.
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Affiliation(s)
- Steven M Corsello
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Jordan Rossen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mustafa Kocak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jordan G Bryan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Duke University, Durham, NC, USA
| | - Ranad Humeidi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Peck
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaoyun Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew A Tang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vickie M Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Evan Lemire
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rajiv Narayan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Uri Ben-David
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel
| | | | - Yejia Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Bang T Wong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- 10x Genomics, Pleasanton, CA, USA
| | - Nancy Dumont
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick J O'Hearn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Relay Therapeutics, Cambridge, MA, USA
| | - Eric Stefan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biogen, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Matthew Meyerson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | | | - Joshua A Bittker
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Vertex Pharmaceuticals, Boston, MA, USA
| | - Jesse S Boehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher C Mader
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Flatiron Health, New York, NY, USA
| | | | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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