1
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Emdal KB, Palacio-Escat N, Wigerup C, Eguchi A, Nilsson H, Bekker-Jensen DB, Rönnstrand L, Kazi JU, Puissant A, Itzykson R, Saez-Rodriguez J, Masson K, Blume-Jensen P, Olsen JV. Phosphoproteomics of primary AML patient samples reveals rationale for AKT combination therapy and p53 context to overcome selinexor resistance. Cell Rep 2022; 40:111177. [PMID: 35947955 PMCID: PMC9380259 DOI: 10.1016/j.celrep.2022.111177] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 05/18/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease with variable patient responses to therapy. Selinexor, an inhibitor of nuclear export, has shown promising clinical activity for AML. To identify the molecular context for monotherapy sensitivity as well as rational drug combinations, we profile selinexor signaling responses using phosphoproteomics in primary AML patient samples and cell lines. Functional phosphosite scoring reveals that p53 function is required for selinexor sensitivity consistent with enhanced efficacy of selinexor in combination with the MDM2 inhibitor nutlin-3a. Moreover, combining selinexor with the AKT inhibitor MK-2206 overcomes dysregulated AKT-FOXO3 signaling in resistant cells, resulting in synergistic anti-proliferative effects. Using high-throughput spatial proteomics to profile subcellular compartments, we measure global proteome and phospho-proteome dynamics, providing direct evidence of nuclear translocation of FOXO3 upon combination treatment. Our data demonstrate the potential of phosphoproteomics and functional phosphorylation site scoring to successfully pinpoint key targetable signaling hubs for rational drug combinations. Phosphoproteomics with functional scoring uncovers context for selinexor sensitivity Functional p53 correlates with selinexor sensitivity, which is enhanced by nutlin-3a Dysregulated AKT-FOXO3 drives selinexor resistance, which is overcome with MK-2206 Spatial proteomics reveals selinexor-induced nucleocytoplasmic protein shuttling
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Affiliation(s)
- Kristina B Emdal
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicolàs Palacio-Escat
- Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant-Zentrum, Heidelberg, Germany; Heidelberg University, Faculty of Biosciences, Heidelberg, Germany; RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine, Aachen, Germany
| | | | - Akihiro Eguchi
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Dorte B Bekker-Jensen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Rönnstrand
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Julhash U Kazi
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant-Zentrum, Heidelberg, Germany; RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine, Aachen, Germany.
| | | | | | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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2
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Dugourd A, Kuppe C, Sciacovelli M, Gjerga E, Gabor A, Emdal KB, Vieira V, Bekker‐Jensen DB, Kranz J, Bindels E, Costa AS, Sousa A, Beltrao P, Rocha M, Olsen JV, Frezza C, Kramann R, Saez‐Rodriguez J. Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses. Mol Syst Biol 2021; 17:e9730. [PMID: 33502086 PMCID: PMC7838823 DOI: 10.15252/msb.20209730] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 01/07/2023] Open
Abstract
Multi-omics datasets can provide molecular insights beyond the sum of individual omics. Various tools have been recently developed to integrate such datasets, but there are limited strategies to systematically extract mechanistic hypotheses from them. Here, we present COSMOS (Causal Oriented Search of Multi-Omics Space), a method that integrates phosphoproteomics, transcriptomics, and metabolomics datasets. COSMOS combines extensive prior knowledge of signaling, metabolic, and gene regulatory networks with computational methods to estimate activities of transcription factors and kinases as well as network-level causal reasoning. COSMOS provides mechanistic hypotheses for experimental observations across multi-omics datasets. We applied COSMOS to a dataset comprising transcriptomics, phosphoproteomics, and metabolomics data from healthy and cancerous tissue from eleven clear cell renal cell carcinoma (ccRCC) patients. COSMOS was able to capture relevant crosstalks within and between multiple omics layers, such as known ccRCC drug targets. We expect that our freely available method will be broadly useful to extract mechanistic insights from multi-omics studies.
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Affiliation(s)
- Aurelien Dugourd
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
- Faculty of MedicineJoint Research Centre for Computational Biomedicine (JRC‐COMBINE)RWTH Aachen UniversityAachenGermany
- Faculty of MedicineInstitute of Experimental Medicine and Systems BiologyRWTH Aachen UniversityAachenGermany
- Division of Nephrology and Clinical ImmunologyFaculty of MedicineRWTH Aachen UniversityAachenGermany
| | - Christoph Kuppe
- Faculty of MedicineInstitute of Experimental Medicine and Systems BiologyRWTH Aachen UniversityAachenGermany
- Division of Nephrology and Clinical ImmunologyFaculty of MedicineRWTH Aachen UniversityAachenGermany
- Department of Internal Medicine, Nephrology and TransplantationErasmus Medical CenterRotterdamThe Netherlands
| | - Marco Sciacovelli
- MRC Cancer UnitHutchison/MRC Research CentreUniversity of CambridgeCambridgeUK
| | - Enio Gjerga
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
- Faculty of MedicineJoint Research Centre for Computational Biomedicine (JRC‐COMBINE)RWTH Aachen UniversityAachenGermany
| | - Attila Gabor
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Kristina B. Emdal
- Faculty of Health and Medical SciencesProteomics ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Vitor Vieira
- Centre of Biological EngineeringUniversity of Minho ‐ Campus de GualtarBragaPortugal
| | - Dorte B. Bekker‐Jensen
- Faculty of Health and Medical SciencesProteomics ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Jennifer Kranz
- Faculty of MedicineInstitute of Experimental Medicine and Systems BiologyRWTH Aachen UniversityAachenGermany
- Department of Urology and Pediatric UrologySt. Antonius Hospital EschweilerAcademic Teaching Hospital of RWTH AachenEschweilerGermany
- Department of Urology and Kidney TransplantationMartin Luther UniversityHalle (Saale)Germany
| | | | - Ana S.H. Costa
- MRC Cancer UnitHutchison/MRC Research CentreUniversity of CambridgeCambridgeUK
- Present address:
Cold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Abel Sousa
- Institute for Research and Innovation in Health (i3s)PortoPortugal
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)HinxtonUK
| | - Pedro Beltrao
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)HinxtonUK
| | - Miguel Rocha
- Centre of Biological EngineeringUniversity of Minho ‐ Campus de GualtarBragaPortugal
| | - Jesper V. Olsen
- Faculty of Health and Medical SciencesProteomics ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Christian Frezza
- MRC Cancer UnitHutchison/MRC Research CentreUniversity of CambridgeCambridgeUK
| | - Rafael Kramann
- Faculty of MedicineInstitute of Experimental Medicine and Systems BiologyRWTH Aachen UniversityAachenGermany
- Division of Nephrology and Clinical ImmunologyFaculty of MedicineRWTH Aachen UniversityAachenGermany
- Department of Internal Medicine, Nephrology and TransplantationErasmus Medical CenterRotterdamThe Netherlands
| | - Julio Saez‐Rodriguez
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
- Faculty of MedicineJoint Research Centre for Computational Biomedicine (JRC‐COMBINE)RWTH Aachen UniversityAachenGermany
- Molecular Medicine Partnership Unit, European Molecular Biology LaboratoryHeidelberg UniversityHeidelbergGermany
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3
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Emdal KB, Lundby A. Molecular switches in signaling networks as a mechanism of action for oncogenic mutations in proximity of tyrosine residues. Mol Cell Oncol 2020; 7:1692643. [PMID: 31993501 PMCID: PMC6961691 DOI: 10.1080/23723556.2019.1692643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 10/27/2022]
Abstract
We developed a mass spectrometry-based proteomics strategy to study oncogenic phosphotyrosine signaling networks in tissues. We outlined epidermal growth factor-dependent phosphotyrosine signaling in lung tissue and discovered that cancer mutations in vicinity of phosphotyrosine sites can induce molecular switches in recruited protein complexes, which ultimately alter the signaling outcome of the network activation.
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Affiliation(s)
- Kristina B Emdal
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alicia Lundby
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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4
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Randall EC, Emdal KB, Laramy JK, Kim M, Roos A, Calligaris D, Regan MS, Gupta SK, Mladek AC, Carlson BL, Johnson AJ, Lu FK, Xie XS, Joughin BA, Reddy RJ, Peng S, Abdelmoula WM, Jackson PR, Kolluri A, Kellersberger KA, Agar JN, Lauffenburger DA, Swanson KR, Tran NL, Elmquist WF, White FM, Sarkaria JN, Agar NYR. Integrated mapping of pharmacokinetics and pharmacodynamics in a patient-derived xenograft model of glioblastoma. Nat Commun 2018; 9:4904. [PMID: 30464169 PMCID: PMC6249307 DOI: 10.1038/s41467-018-07334-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022] Open
Abstract
Therapeutic options for the treatment of glioblastoma remain inadequate despite concerted research efforts in drug development. Therapeutic failure can result from poor permeability of the blood-brain barrier, heterogeneous drug distribution, and development of resistance. Elucidation of relationships among such parameters could enable the development of predictive models of drug response in patients and inform drug development. Complementary analyses were applied to a glioblastoma patient-derived xenograft model in order to quantitatively map distribution and resulting cellular response to the EGFR inhibitor erlotinib. Mass spectrometry images of erlotinib were registered to histology and magnetic resonance images in order to correlate drug distribution with tumor characteristics. Phosphoproteomics and immunohistochemistry were used to assess protein signaling in response to drug, and integrated with transcriptional response using mRNA sequencing. This comprehensive dataset provides simultaneous insight into pharmacokinetics and pharmacodynamics and indicates that erlotinib delivery to intracranial tumors is insufficient to inhibit EGFR tyrosine kinase signaling.
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Affiliation(s)
- Elizabeth C Randall
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kristina B Emdal
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St, Cambridge, MA, 02142, USA
| | - Janice K Laramy
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Minjee Kim
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Alison Roos
- Department of Cancer Biology, Mayo Clinic, 13400 E. Shea Blvd.MCCRB 03-055, Scottsdale, AZ, 85259, USA
| | - David Calligaris
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Michael S Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Shiv K Gupta
- Department of Radiation Oncology, Mayo Clinic, 200 First St SW, Rochester, MN, 55902, USA
| | - Ann C Mladek
- Department of Radiation Oncology, Mayo Clinic, 200 First St SW, Rochester, MN, 55902, USA
| | - Brett L Carlson
- Department of Radiation Oncology, Mayo Clinic, 200 First St SW, Rochester, MN, 55902, USA
| | - Aaron J Johnson
- Department of Immunology, Mayo Clinic, 200 First St SW, Rochester, MN, 55902, USA
| | - Fa-Ke Lu
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Biomedical Engineering, Binghamton University, State University of New York, Binghamton, NY, 13902, USA
| | - X Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Brian A Joughin
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St, Cambridge, MA, 02142, USA
| | - Raven J Reddy
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St, Cambridge, MA, 02142, USA
| | - Sen Peng
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Walid M Abdelmoula
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Pamela R Jackson
- Mathematical NeuroOncology Lab, Department of Neurosurgery, Mayo Clinic, 5777 E. Mayo Blvd, Phoenix, AZ, 85054, USA
| | - Aarti Kolluri
- Mathematical NeuroOncology Lab, Department of Neurosurgery, Mayo Clinic, 5777 E. Mayo Blvd, Phoenix, AZ, 85054, USA
| | | | - Jeffrey N Agar
- Department of Chemistry and Chemical Biology, Northeastern University, 412 TF (140 The Fenway), Boston, MA, 02111, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St, Cambridge, MA, 02142, USA
| | - Kristin R Swanson
- Mathematical NeuroOncology Lab, Department of Neurosurgery, Mayo Clinic, 5777 E. Mayo Blvd, Phoenix, AZ, 85054, USA
| | - Nhan L Tran
- Department of Cancer Biology, Mayo Clinic, 13400 E. Shea Blvd.MCCRB 03-055, Scottsdale, AZ, 85259, USA
| | - William F Elmquist
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Forest M White
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St, Cambridge, MA, 02142, USA
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, 200 First St SW, Rochester, MN, 55902, USA
| | - Nathalie Y R Agar
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
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5
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Emdal KB, Pedersen AK, Bekker-Jensen DB, Lundby A, Claeys S, De Preter K, Speleman F, Francavilla C, Olsen JV. Integrated proximal proteomics reveals IRS2 as a determinant of cell survival in ALK-driven neuroblastoma. Sci Signal 2018; 11:11/557/eaap9752. [PMID: 30459283 DOI: 10.1126/scisignal.aap9752] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oncogenic anaplastic lymphoma kinase (ALK) is one of the few druggable targets in neuroblastoma, and therapy resistance to ALK-targeting tyrosine kinase inhibitors (TKIs) comprises an inevitable clinical challenge. Therefore, a better understanding of the oncogenic signaling network rewiring driven by ALK is necessary to improve and guide future therapies. Here, we performed quantitative mass spectrometry-based proteomics on neuroblastoma cells treated with one of three clinically relevant ALK TKIs (crizotinib, LDK378, or lorlatinib) or an experimentally used ALK TKI (TAE684) to unravel aberrant ALK signaling pathways. Our integrated proximal proteomics (IPP) strategy included multiple signaling layers, such as the ALK interactome, phosphotyrosine interactome, phosphoproteome, and proteome. We identified the signaling adaptor protein IRS2 (insulin receptor substrate 2) as a major ALK target and an ALK TKI-sensitive signaling node in neuroblastoma cells driven by oncogenic ALK. TKI treatment decreased the recruitment of IRS2 to ALK and reduced the tyrosine phosphorylation of IRS2. Furthermore, siRNA-mediated depletion of ALK or IRS2 decreased the phosphorylation of the survival-promoting kinase Akt and of a downstream target, the transcription factor FoxO3, and reduced the viability of three ALK-driven neuroblastoma cell lines. Collectively, our IPP analysis provides insight into the proximal architecture of oncogenic ALK signaling by revealing IRS2 as an adaptor protein that links ALK to neuroblastoma cell survival through the Akt-FoxO3 signaling axis.
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Affiliation(s)
- Kristina B Emdal
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.,Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Anna-Kathrine Pedersen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Dorte B Bekker-Jensen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Alicia Lundby
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Shana Claeys
- Center for Medical Genetics Ghent, Cancer Research Institute Ghent, De Pintelaan 185, 9000 Ghent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics Ghent, Cancer Research Institute Ghent, De Pintelaan 185, 9000 Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics Ghent, Cancer Research Institute Ghent, De Pintelaan 185, 9000 Ghent, Belgium
| | - Chiara Francavilla
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark. .,Division of Molecular and Cellular Functions, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
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6
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Liu H, Murphy CJ, Karreth FA, Emdal KB, White FM, Elemento O, Toker A, Wulf GM, Cantley LC. Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer. Cancer Discov 2017; 8:354-369. [PMID: 29203461 DOI: 10.1158/2159-8290.cd-17-0679] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/11/2017] [Accepted: 11/27/2017] [Indexed: 02/07/2023]
Abstract
Triple-negative breast cancers (TNBC) are genetically characterized by aberrations in TP53 and a low rate of activating point mutations in common oncogenes, rendering it challenging in applying targeted therapies. We performed whole-exome sequencing (WES) and RNA sequencing (RNA-seq) to identify somatic genetic alterations in mouse models of TNBCs driven by loss of Trp53 alone or in combination with Brca1 Amplifications or translocations that resulted in elevated oncoprotein expression or oncoprotein-containing fusions, respectively, as well as frameshift mutations of tumor suppressors were identified in approximately 50% of the tumors evaluated. Although the spectrum of sporadic genetic alterations was diverse, the majority had in common the ability to activate the MAPK/PI3K pathways. Importantly, we demonstrated that approved or experimental drugs efficiently induce tumor regression specifically in tumors harboring somatic aberrations of the drug target. Our study suggests that the combination of WES and RNA-seq on human TNBC will lead to the identification of actionable therapeutic targets for precision medicine-guided TNBC treatment.Significance: Using combined WES and RNA-seq analyses, we identified sporadic oncogenic events in TNBC mouse models that share the capacity to activate the MAPK and/or PI3K pathways. Our data support a treatment tailored to the genetics of individual tumors that parallels the approaches being investigated in the ongoing NCI-MATCH, My Pathway Trial, and ESMART clinical trials. Cancer Discov; 8(3); 354-69. ©2017 AACR.See related commentary by Natrajan et al., p. 272See related article by Matissek et al., p. 336This article is highlighted in the In This Issue feature, p. 253.
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Affiliation(s)
- Hui Liu
- Department of Pathology, and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Charles J Murphy
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York.,Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Florian A Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kristina B Emdal
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
| | - Forest M White
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | - Alex Toker
- Department of Pathology, and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, and Ludwig Center at Harvard, Boston, Massachusetts
| | - Gerburg M Wulf
- Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, New York.
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7
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Emdal KB, Dittmann A, Reddy RJ, Lescarbeau RS, Moores SL, Laquerre S, White FM. Characterization of In Vivo Resistance to Osimertinib and JNJ-61186372, an EGFR/Met Bispecific Antibody, Reveals Unique and Consensus Mechanisms of Resistance. Mol Cancer Ther 2017; 16:2572-2585. [PMID: 28830985 DOI: 10.1158/1535-7163.mct-17-0413] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/21/2017] [Accepted: 08/10/2017] [Indexed: 12/28/2022]
Abstract
Approximately 10% of non-small cell lung cancer (NSCLC) patients in the United States and 40% of NSCLC patients in Asia have activating epidermal growth factor receptor (EGFR) mutations and are eligible to receive targeted anti-EGFR therapy. Despite an extension of life expectancy associated with this treatment, resistance to EGFR tyrosine kinase inhibitors and anti-EGFR antibodies is almost inevitable. To identify additional signaling routes that can be cotargeted to overcome resistance, we quantified tumor-specific molecular changes that govern resistant cancer cell growth and survival. Mass spectrometry-based quantitative proteomics was used to profile in vivo signaling changes in 41 therapy-resistant tumors from four xenograft NSCLC models. We identified unique and tumor-specific tyrosine phosphorylation rewiring in tumors resistant to treatment with the irreversible third-generation EGFR-inhibitor, osimertinib, or the novel dual-targeting EGFR/Met antibody, JNJ-61186372. Tumor-specific increases in tyrosine-phosphorylated peptides from EGFR family members, Shc1 and Gab1 or Src family kinase (SFK) substrates were observed, underscoring a differential ability of tumors to uniquely escape EGFR inhibition. Although most resistant tumors within each treatment group displayed a marked inhibition of EGFR as well as SFK signaling, the combination of EGFR inhibition (osimertinib) and SFK inhibition (saracatinib or dasatinib) led to further decrease in cell growth in vitro This result suggests that residual SFK signaling mediates therapeutic resistance and that elimination of this signal through combination therapy may delay onset of resistance. Overall, analysis of individual resistant tumors captured unique in vivo signaling rewiring that would have been masked by analysis of in vitro cell population averages. Mol Cancer Ther; 16(11); 2572-85. ©2017 AACR.
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Affiliation(s)
- Kristina B Emdal
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Antje Dittmann
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Raven J Reddy
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Rebecca S Lescarbeau
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Sheri L Moores
- Oncology, Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Sylvie Laquerre
- Oncology, Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Forest M White
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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8
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Radic-Sarikas B, Tsafou KP, Emdal KB, Papamarkou T, Huber KVM, Mutz C, Toretsky JA, Bennett KL, Olsen JV, Brunak S, Kovar H, Superti-Furga G. Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities. Mol Cancer Ther 2017; 16:88-101. [PMID: 28062706 DOI: 10.1158/1535-7163.mct-16-0235] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 11/16/2022]
Abstract
Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three pediatric tumor types, we identified Ewing sarcoma-specific interactions of a diverse set of targeted agents including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong synergistic propensity in Ewing sarcoma, revealing its targets in critical Ewing sarcoma signaling routes. Using a multilevel experimental approach including quantitative phosphoproteomics, we analyzed the molecular rationale behind the disease-specific synergistic effect of simultaneous application of PKC412 and IGF1R inhibitors. The mechanism of the drug synergy between these inhibitors is different from the sum of the mechanisms of the single agents. The combination effectively inhibited pathway crosstalk and averted feedback loop repression, in EWS-FLI1-dependent manner. Mol Cancer Ther; 16(1); 88-101. ©2016 AACR.
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MESH Headings
- Animals
- Antigens, CD
- Antineoplastic Agents/pharmacology
- Cell Line, Tumor
- Computational Biology/methods
- Disease Models, Animal
- Drug Discovery
- Drug Evaluation, Preclinical
- Drug Interactions
- Drug Screening Assays, Antitumor
- Humans
- Molecular Targeted Therapy
- Oncogene Proteins, Fusion/antagonists & inhibitors
- Phosphorylation
- Protein Kinase Inhibitors/pharmacology
- Proteomics/methods
- Proto-Oncogene Protein c-fli-1/antagonists & inhibitors
- RNA-Binding Protein EWS/antagonists & inhibitors
- Receptor, IGF Type 1
- Receptor, Insulin/antagonists & inhibitors
- Receptors, Somatomedin/antagonists & inhibitors
- Sarcoma, Ewing/drug therapy
- Sarcoma, Ewing/genetics
- Sarcoma, Ewing/metabolism
- Sarcoma, Ewing/pathology
- Signal Transduction/drug effects
- Staurosporine/analogs & derivatives
- Staurosporine/pharmacology
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Branka Radic-Sarikas
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kalliopi P Tsafou
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- Department of Oncology, Georgetown University Medical Center, Washington, DC
| | - Kristina B Emdal
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Theodore Papamarkou
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Kilian V M Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Cornelia Mutz
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Jeffrey A Toretsky
- Department of Oncology, Georgetown University Medical Center, Washington, DC
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Heinrich Kovar
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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9
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Emdal KB, Pedersen AK, Bekker-Jensen DB, Tsafou KP, Horn H, Lindner S, Schulte JH, Eggert A, Jensen LJ, Francavilla C, Olsen JV. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. Sci Signal 2015; 8:ra40. [PMID: 25921289 DOI: 10.1126/scisignal.2005769] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SH-SY5Y neuroblastoma cells respond to nerve growth factor (NGF)-mediated activation of the tropomyosin-related kinase A (TrkA) with neurite outgrowth, thereby providing a model to study neuronal differentiation. We performed a time-resolved analysis of NGF-TrkA signaling in neuroblastoma cells using mass spectrometry-based quantitative proteomics. The combination of interactome, phosphoproteome, and proteome data provided temporal insights into the molecular events downstream of NGF binding to TrkA. We showed that upon NGF stimulation, TrkA recruits the E3 ubiquitin ligase Cbl-b, which then becomes phosphorylated and ubiquitylated and decreases in abundance. We also found that recruitment of Cbl-b promotes TrkA ubiquitylation and degradation. Furthermore, the amount of phosphorylation of the kinase ERK and neurite outgrowth increased upon Cbl-b depletion in several neuroblastoma cell lines. Our findings suggest that Cbl-b limits NGF-TrkA signaling to control the length of neurites.
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Affiliation(s)
- Kristina B Emdal
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Anna-Kathrine Pedersen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Dorte B Bekker-Jensen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Kalliopi P Tsafou
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Heiko Horn
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Sven Lindner
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany. Department of Pediatric Oncology and Hematology, Charité Berlin, Charitéplatz 1, 10117 Berlin, Germany. German Cancer Consortium (DKTK), 13353 Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany. Department of Pediatric Oncology and Hematology, Charité Berlin, Charitéplatz 1, 10117 Berlin, Germany. German Cancer Consortium (DKTK), 13353 Berlin, Germany
| | - Lars J Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Chiara Francavilla
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
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10
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Herrero-Martin D, Kauer M, Emdal KB, Sienski G, Fourtouna A, Kralovics R, Olsen JV, Kovar H. Abstract 3048: The genome-wide contribution of microRNAs to gene regulation in Ewing sarcoma. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-3048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The identification of microRNA (miR) targets within a given cellular context still poses a largely unsolved problem. MiR targets are predicted based on the presence of seed sequences in the 3'UTR of mRNAs. Target candidate lists are filtered assuming mRNA destabilization, and validated by artificially forcing ectopic expression of miR analogs, or by interfering with miR expression by antagomirs. However, the expression level and amplitude of physiological miR variations is much smaller than experimentally induced miR perturbations. Crosslinking and immuno precipitation (CLIP) followed by sequencing of bound RNA allows monitoring of dynamic changes in miR/mRNA occupancy of RISC. However, it is unclear if increased miR activity will lead to increased target read counts due to elevated RISC occupancy or to decreased read counts as a consequence of target destabilization.
Ewing sarcoma (ES) expresses an oncogenic transcription factor, EWS/FLI1.To study the impact of miRs to the gene regulatory network downstream of EWS/FLI1, we used a combination of mRNA and miR expression profiling, ChIP-seq, PAR-CLIP of AGO2, AGO2 knockdown, and SILAC monitoring of proteome changes in an inducible EWS/FLI1 knockdown ES cell line. Our data suggest that EWS/FLI1 perturbs gene regulation primarily on the transcriptional level and miRs play only a modulatory role for gene expression. Furthermore EWS/FLI1 affects the expression of many miR biogenesis and miR activity as well as RISC associated proteins. Knockdown of EWS/FLI1 results in pronounced changes of miR specific PAR-CLIP spectra. Disabled RISC activity lead to only minor changes in genome-wide mRNA expression. Our results are consistent with a complex role of the miRNome in the fine tuning of gene regulatory networks in Ewing sarcoma.
Supported by grants EU-FP7 259348 and Austrian Science Fund FWF 24708-B21.
Citation Format: David Herrero-Martin, Maximilian Kauer, Kristina B. Emdal, Grzegorz Sienski, Argyrou Fourtouna, Robert Kralovics, Jesper V. Olsen, Heinrich Kovar. The genome-wide contribution of microRNAs to gene regulation in Ewing sarcoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3048. doi:10.1158/1538-7445.AM2013-3048
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11
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Yde CW, Emdal KB, Guerra B, Lykkesfeldt AE. NFκB signaling is important for growth of antiestrogen resistant breast cancer cells. Breast Cancer Res Treat 2012; 135:67-78. [PMID: 22527100 DOI: 10.1007/s10549-012-2053-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/28/2012] [Indexed: 11/25/2022]
Abstract
Resistance to endocrine therapy is a major clinical challenge in current treatment of estrogen receptor-positive breast cancer. The molecular mechanisms underlying resistance are yet not fully clarified. In this study, we investigated whether NFκB signaling is causally involved in antiestrogen resistant cell growth and a potential target for re-sensitizing resistant cells to endocrine therapy. We used an MCF-7-derived cell model for antiestrogen resistant breast cancer to investigate dependence on NFκB signaling for antiestrogen resistant cell growth. We found that targeting NFκB preferentially inhibited resistant cell growth. Antiestrogen resistant cells expressed increased p50 and RelB, and displayed increased phosphorylation of p65 at Ser529 and Ser536. Moreover, transcriptional activity of NFκB after stimulation with tumor necrosis factor α was enhanced in antiestrogen resistant cell lines compared to the parental cell line. Inhibition of NFκB signaling sensitized tamoxifen resistant cells to the growth inhibitory effects of tamoxifen but was not sufficient to fully restore sensitivity of fulvestrant resistant cells to fulvestrant. In support of this, depletion of p65 with siRNA in tamoxifen resistant cells increased sensitivity to tamoxifen treatment. Our data provide evidence that NFκB signaling is enhanced in antiestrogen resistant breast cancer cells and plays an important role for antiestrogen resistant cell growth and for sensitivity to tamoxifen treatment in resistant cells. Our results imply that targeting NFκB might serve as a potential novel treatment strategy for breast cancer patients with resistance toward antiestrogen.
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Affiliation(s)
- Christina W Yde
- Breast Cancer Group, Cell Death and Metabolism, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen Ø, Denmark.
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