301
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Szalai B, Subramanian V, Holland CH, Alföldi R, Puskás LG, Saez-Rodriguez J. Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction. Nucleic Acids Res 2019; 47:10010-10026. [PMID: 31552418 PMCID: PMC6821211 DOI: 10.1093/nar/gkz805] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 01/27/2023] Open
Abstract
Transcriptional perturbation signatures are valuable data sources for functional genomics. Linking perturbation signatures to screenings opens the possibility to model cellular phenotypes from expression data and to identify efficacious drugs. We linked perturbation transcriptomics data from the LINCS-L1000 project with cell viability information upon genetic (Achilles project) and chemical (CTRP screen) perturbations yielding more than 90 000 signature–viability pairs. An integrated analysis showed that the cell viability signature is a major factor underlying perturbation signatures. The signature is linked to transcription factors regulating cell death, proliferation and division time. We used the cell viability–signature relationship to predict viability from transcriptomics signatures, and identified and validated compounds that induce cell death in tumor cell lines. We showed that cellular toxicity can lead to unexpected similarity of signatures, confounding mechanism of action discovery. Consensus compound signatures predicted cell-specific drug sensitivity, even if the signature is not measured in the same cell line, and outperformed conventional drug-specific features. Our results can help in understanding mechanisms behind cell death and removing confounding factors of transcriptomic perturbation screens. To interactively browse our results and predict cell viability in new gene expression samples, we developed CEVIChE (CEll VIability Calculator from gene Expression; https://saezlab.shinyapps.io/ceviche/).
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Affiliation(s)
- Bence Szalai
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany.,Semmelweis University, Faculty of Medicine, Department of Physiology, H-1094 Budapest, Hungary
| | - Vigneshwari Subramanian
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany
| | - Christian H Holland
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany.,Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | | | | | - Julio Saez-Rodriguez
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany.,Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
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302
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Torin2 Exploits Replication and Checkpoint Vulnerabilities to Cause Death of PI3K-Activated Triple-Negative Breast Cancer Cells. Cell Syst 2019; 10:66-81.e11. [PMID: 31812693 DOI: 10.1016/j.cels.2019.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 07/11/2019] [Accepted: 11/04/2019] [Indexed: 01/22/2023]
Abstract
Frequent mutation of PI3K/AKT/mTOR signaling pathway genes in human cancers has stimulated large investments in targeted drugs but clinical successes are rare. As a result, many cancers with high PI3K pathway activity, such as triple-negative breast cancer (TNBC), are treated primarily with chemotherapy. By systematically analyzing responses of TNBC cells to a diverse collection of PI3K pathway inhibitors, we find that one drug, Torin2, is unusually effective because it inhibits both mTOR and other PI3K-like kinases (PIKKs). In contrast to mTOR-selective inhibitors, Torin2 exploits dependencies on several kinases for S-phase progression and cell-cycle checkpoints, thereby causing accumulation of single-stranded DNA and death by replication catastrophe or mitotic failure. Thus, Torin2 and its chemical analogs represent a mechanistically distinct class of PI3K pathway inhibitors that are uniquely cytotoxic to TNBC cells. This insight could be translated therapeutically by further developing Torin2 analogs or combinations of existing mTOR and PIKK inhibitors.
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303
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Inhibition of PARP Sensitizes Chondrosarcoma Cell Lines to Chemo- and Radiotherapy Irrespective of the IDH1 or IDH2 Mutation Status. Cancers (Basel) 2019; 11:cancers11121918. [PMID: 31810230 PMCID: PMC6966531 DOI: 10.3390/cancers11121918] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/21/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
Chondrosarcomas are chemo- and radiotherapy resistant and frequently harbor mutations in isocitrate dehydrogenase (IDH1 or IDH2), causing increased levels of D-2-hydroxyglutarate (D-2-HG). DNA repair defects and synthetic lethality with poly(ADP-ribose) polymerase (PARP) inhibition occur in IDH mutant glioma and leukemia models. Here we evaluated DNA repair and PARP inhibition, alone or combined with chemo- or radiotherapy, in chondrosarcoma cell lines with or without endogenous IDH mutations. Chondrosarcoma cell lines treated with the PARP inhibitor talazoparib were examined for dose–response relationships, as well as underlying cell death mechanisms and DNA repair functionality. Talazoparib was combined with chemo- or radiotherapy to evaluate potential synergy. Cell lines treated long term with an inhibitor normalizing D-2-HG levels were investigated for synthetic lethality with talazoparib. We report that talazoparib sensitivity was variable and irrespective of IDH mutation status. All cell lines expressed Ataxia Telangiectasia Mutated (ATM), but a subset was impaired in poly(ADP-ribosyl)ation (PARylation) capacity, homologous recombination, and O-6-methylguanine-DNA methyltransferase (MGMT) expression. Talazoparib synergized with temozolomide or radiation, independent of IDH1 mutant inhibition. This study suggests that talazoparib combined with temozolomide or radiation are promising therapeutic strategies for chondrosarcoma, irrespective of IDH mutation status. A subset of chondrosarcomas may be deficient in nonclassical DNA repair pathways, suggesting that PARP inhibitor sensitivity is multifactorial in chondrosarcoma.
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304
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Hausser J, Szekely P, Bar N, Zimmer A, Sheftel H, Caldas C, Alon U. Tumor diversity and the trade-off between universal cancer tasks. Nat Commun 2019; 10:5423. [PMID: 31780652 PMCID: PMC6882839 DOI: 10.1038/s41467-019-13195-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/11/2019] [Indexed: 02/06/2023] Open
Abstract
Recent advances have enabled powerful methods to sort tumors into prognosis and treatment groups. We are still missing, however, a general theoretical framework to understand the vast diversity of tumor gene expression and mutations. Here we present a framework based on multi-task evolution theory, using the fact that tumors need to perform multiple tasks that contribute to their fitness. We find that trade-offs between tasks constrain tumor gene-expression to a continuum bounded by a polyhedron whose vertices are gene-expression profiles, each specializing in one task. We find five universal cancer tasks across tissue-types: cell-division, biomass and energy, lipogenesis, immune-interaction and invasion and tissue-remodeling. Tumors that specialize in a task are sensitive to drugs that interfere with this task. Driver, but not passenger, mutations tune gene-expression towards specialization in specific tasks. This approach can integrate additional types of molecular data into a framework of tumor diversity grounded in evolutionary theory.
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Affiliation(s)
- Jean Hausser
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Pablo Szekely
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Noam Bar
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Anat Zimmer
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Hila Sheftel
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK.
- Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge, CB2 0RE, UK.
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Rehovot, Israel.
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305
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Palmer AC, Chidley C, Sorger PK. A curative combination cancer therapy achieves high fractional cell killing through low cross-resistance and drug additivity. eLife 2019; 8:50036. [PMID: 31742555 PMCID: PMC6897534 DOI: 10.7554/elife.50036] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
Curative cancer therapies are uncommon and nearly always involve multi-drug combinations developed by experimentation in humans; unfortunately, the mechanistic basis for the success of such combinations has rarely been investigated in detail, obscuring lessons learned. Here, we use isobologram analysis to score pharmacological interaction, and clone tracing and CRISPR screening to measure cross-resistance among the five drugs comprising R-CHOP, a combination therapy that frequently cures Diffuse Large B-Cell Lymphomas. We find that drugs in R-CHOP exhibit very low cross-resistance but not synergistic interaction: together they achieve a greater fractional kill according to the null hypothesis for both the Loewe dose-additivity model and the Bliss effect-independence model. These data provide direct evidence for the 50 year old hypothesis that a curative cancer therapy can be constructed on the basis of independently effective drugs having non-overlapping mechanisms of resistance, without synergistic interaction, which has immediate significance for the design of new drug combinations.
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Affiliation(s)
- Adam C Palmer
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, United States
| | - Christopher Chidley
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, United States
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, United States.,Department of Systems Biology, Harvard Medical School, Boston, United States
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306
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Gelles JD, Chipuk JE. Why not add some SPARKL to your life (and death)!? Mol Cell Oncol 2019; 7:1685841. [PMID: 31993499 PMCID: PMC6961694 DOI: 10.1080/23723556.2019.1685841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 10/25/2022]
Abstract
Quantifying cytostatic and cytotoxic outcomes of cells responding to perturbagens is an essential component of mechanism-based studies and pharmacological screening approaches. We recently described an easy and versatile method for single-cell and population-level analyses using real-time kinetic labeling (SPARKL). This technology enables zero-handling, non-disruptive protocols for integrating proliferation profiles with cell death mechanisms, along with advanced mathematics for robust analyses.
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Affiliation(s)
- Jesse D. Gelles
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerry Edward Chipuk
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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307
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Dalin S, Sullivan MR, Lau AN, Grauman-Boss B, Mueller HS, Kreidl E, Fenoglio S, Luengo A, Lees JA, Vander Heiden MG, Lauffenburger DA, Hemann MT. Deoxycytidine Release from Pancreatic Stellate Cells Promotes Gemcitabine Resistance. Cancer Res 2019; 79:5723-5733. [PMID: 31484670 PMCID: PMC7357734 DOI: 10.1158/0008-5472.can-19-0960] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/29/2019] [Accepted: 08/30/2019] [Indexed: 12/18/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer deaths in the United States. The deoxynucleoside analogue gemcitabine is among the most effective therapies to treat PDAC, however, nearly all patients treated with gemcitabine either fail to respond or rapidly develop resistance. One hallmark of PDAC is a striking accumulation of stromal tissue surrounding the tumor, and this accumulation of stroma can contribute to therapy resistance. To better understand how stroma limits response to therapy, we investigated cell-extrinsic mechanisms of resistance to gemcitabine. Conditioned media from pancreatic stellate cells (PSC), as well as from other fibroblasts, protected PDAC cells from gemcitabine toxicity. The protective effect of PSC-conditioned media was mediated by secretion of deoxycytidine, but not other deoxynucleosides, through equilibrative nucleoside transporters. Deoxycytidine inhibited the processing of gemcitabine in PDAC cells, thus reducing the effect of gemcitabine and other nucleoside analogues on cancer cells. These results suggest that reducing deoxycytidine production in PSCs may increase the efficacy of nucleoside analog therapies. SIGNIFICANCE: This study provides important new insight into mechanisms that contribute to gemcitabine resistance in PDAC and suggests new avenues for improving gemcitabine efficacy.
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Affiliation(s)
- Simona Dalin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Mark R Sullivan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Allison N Lau
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Beatrice Grauman-Boss
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Helen S Mueller
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Emanuel Kreidl
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Silvia Fenoglio
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Alba Luengo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jacqueline A Lees
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Matthew G Vander Heiden
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Douglas A Lauffenburger
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Michael T Hemann
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
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308
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Li Z, Pinch BJ, Olson CM, Donovan KA, Nowak RP, Mills CE, Scott DA, Doctor ZM, Eleuteri NA, Chung M, Sorger PK, Fischer ES, Gray NS. Development and Characterization of a Wee1 Kinase Degrader. Cell Chem Biol 2019; 27:57-65.e9. [PMID: 31735695 DOI: 10.1016/j.chembiol.2019.10.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/23/2019] [Accepted: 10/28/2019] [Indexed: 12/16/2022]
Abstract
The G1/S cell cycle checkpoint is frequently dysregulated in cancer, leaving cancer cells reliant on a functional G2/M checkpoint to prevent excessive DNA damage. Wee1 regulates the G2/M checkpoint by phosphorylating CDK1 at Tyr15 to prevent mitotic entry. Previous drug development efforts targeting Wee1 resulted in the clinical-grade inhibitor, AZD1775. However, AZD1775 is burdened by dose-limiting adverse events, and has off-target PLK1 activity. In an attempt to overcome these limitations, we developed Wee1 degraders by conjugating AZD1775 to the cereblon (CRBN)-binding ligand, pomalidomide. The resulting lead compound, ZNL-02-096, degrades Wee1 while sparing PLK1, induces G2/M accumulation at 10-fold lower doses than AZD1775, and synergizes with Olaparib in ovarian cancer cells. We demonstrate that ZNL-02-096 has CRBN-dependent pharmacology that is distinct from AZD1775, which justifies further evaluation of selective Wee1 degraders.
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Affiliation(s)
- Zhengnian Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Benika J Pinch
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Department of Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Calla M Olson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - David A Scott
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zainab M Doctor
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Nicholas A Eleuteri
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mirra Chung
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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309
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Opposing effects of NPM1wt and NPM1c mutants on AKT signaling in AML. Leukemia 2019; 34:1172-1176. [PMID: 31728055 DOI: 10.1038/s41375-019-0621-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 08/16/2019] [Accepted: 08/21/2019] [Indexed: 11/09/2022]
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310
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Abt ER, Rosser EW, Durst MA, Lok V, Poddar S, Le TM, Cho A, Kim W, Wei L, Song J, Capri JR, Xu S, Wu N, Slavik R, Jung ME, Damoiseaux R, Czernin J, Donahue TR, Lavie A, Radu CG. Metabolic Modifier Screen Reveals Secondary Targets of Protein Kinase Inhibitors within Nucleotide Metabolism. Cell Chem Biol 2019; 27:197-205.e6. [PMID: 31734178 DOI: 10.1016/j.chembiol.2019.10.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 08/30/2019] [Accepted: 10/25/2019] [Indexed: 01/02/2023]
Abstract
Biosynthesis of the pyrimidine nucleotide uridine monophosphate (UMP) is essential for cell proliferation and is achieved by the activity of convergent de novo and salvage metabolic pathways. Here we report the development and application of a cell-based metabolic modifier screening platform that leverages the redundancy in pyrimidine metabolism for the discovery of selective UMP biosynthesis modulators. In evaluating a library of protein kinase inhibitors, we identified multiple compounds that possess nucleotide metabolism modifying activity. The JNK inhibitor JNK-IN-8 was found to potently inhibit nucleoside transport and engage ENT1. The PDK1 inhibitor OSU-03012 (also known as AR-12) and the RAF inhibitor TAK-632 were shown to inhibit the therapeutically relevant de novo pathway enzyme DHODH and their affinities were unambiguously confirmed through in vitro assays and co-crystallization with human DHODH.
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Affiliation(s)
- Evan R Abt
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Ethan W Rosser
- Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA; Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew A Durst
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA; The Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Vincent Lok
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Soumya Poddar
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Thuc M Le
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Arthur Cho
- Department of Nuclear Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Woosuk Kim
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Liu Wei
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Janet Song
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Joseph R Capri
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Shili Xu
- Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA; Department of Surgery, University of California Los Angeles, Los Angeles, CA, USA
| | - Nanping Wu
- Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA; Department of Surgery, University of California Los Angeles, Los Angeles, CA, USA
| | - Roger Slavik
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael E Jung
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Robert Damoiseaux
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Johannes Czernin
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Timothy R Donahue
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA; Department of Surgery, University of California Los Angeles, Los Angeles, CA, USA; David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA; The Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Caius G Radu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA.
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311
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Karaman B, Sippl W. Computational Drug Repurposing: Current Trends. Curr Med Chem 2019; 26:5389-5409. [DOI: 10.2174/0929867325666180530100332] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/06/2018] [Accepted: 05/14/2018] [Indexed: 01/31/2023]
Abstract
:
Biomedical discovery has been reshaped upon the exploding digitization of data
which can be retrieved from a number of sources, ranging from clinical pharmacology to
cheminformatics-driven databases. Now, supercomputing platforms and publicly available
resources such as biological, physicochemical, and clinical data, can all be integrated to construct
a detailed map of signaling pathways and drug mechanisms of action in relation to drug
candidates. Recent advancements in computer-aided data mining have facilitated analyses of
‘big data’ approaches and the discovery of new indications for pre-existing drugs has been
accelerated. Linking gene-phenotype associations to predict novel drug-disease signatures or
incorporating molecular structure information of drugs and protein targets with other kinds of
data derived from systems biology provide great potential to accelerate drug discovery and
improve the success of drug repurposing attempts. In this review, we highlight commonly
used computational drug repurposing strategies, including bioinformatics and cheminformatics
tools, to integrate large-scale data emerging from the systems biology, and consider both
the challenges and opportunities of using this approach. Moreover, we provide successful examples
and case studies that combined various in silico drug-repurposing strategies to predict
potential novel uses for known therapeutics.
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Affiliation(s)
- Berin Karaman
- Biruni University - Department of Pharmaceutical Chemistry, Istanbul, Turkey
| | - Wolfgang Sippl
- Martin-Luther University of Halle-Wittenberg - Institute of Pharmacy, Halle (Saale), Germany
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312
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Gelles JD, Mohammed JN, Santos LC, Legarda D, Ting AT, Chipuk JE. Single-Cell and Population-Level Analyses Using Real-Time Kinetic Labeling Couples Proliferation and Cell Death Mechanisms. Dev Cell 2019; 51:277-291.e4. [PMID: 31564612 DOI: 10.1016/j.devcel.2019.08.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 06/24/2019] [Accepted: 08/23/2019] [Indexed: 12/14/2022]
Abstract
Quantifying cytostatic and cytotoxic outcomes are integral components of characterizing perturbagens used as research tools and in drug discovery pipelines. Furthermore, data-rich acquisition, coupled with robust methods for analysis, is required to properly assess the function and impact of these perturbagens. Here, we present a detailed and versatile method for single-cell and population-level analyses using real-time kinetic labeling (SPARKL). SPARKL integrates high-content live-cell imaging with automated detection and analysis of fluorescent reporters of cell death. We outline several examples of zero-handling, non-disruptive protocols for detailing cell death mechanisms and proliferation profiles. Additionally, we suggest several methods for mathematically analyzing these data to best utilize the collected kinetic data. Compared to traditional methods of detection and analysis, SPARKL is more sensitive, accurate, and high throughput while substantially eliminating sample processing and providing richer data.
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Affiliation(s)
- Jesse D Gelles
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1130, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Jarvier N Mohammed
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1130, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Luis C Santos
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1130, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Diana Legarda
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Adrian T Ting
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Jerry E Chipuk
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1130, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA.
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313
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Costa C, Wang Y, Ly A, Hosono Y, Murchie E, Walmsley CS, Huynh T, Healy C, Peterson R, Yanase S, Jakubik CT, Henderson LE, Damon LJ, Timonina D, Sanidas I, Pinto CJ, Mino-Kenudson M, Stone JR, Dyson NJ, Ellisen LW, Bardia A, Ebi H, Benes CH, Engelman JA, Juric D. PTEN Loss Mediates Clinical Cross-Resistance to CDK4/6 and PI3Kα Inhibitors in Breast Cancer. Cancer Discov 2019; 10:72-85. [PMID: 31594766 DOI: 10.1158/2159-8290.cd-18-0830] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 07/12/2019] [Accepted: 10/03/2019] [Indexed: 11/16/2022]
Abstract
The combination of CDK4/6 inhibitors with antiestrogen therapies significantly improves clinical outcomes in ER-positive advanced breast cancer. To identify mechanisms of acquired resistance, we analyzed serial biopsies and rapid autopsies from patients treated with the combination of the CDK4/6 inhibitor ribociclib with letrozole. This study revealed that some resistant tumors acquired RB loss, whereas other tumors lost PTEN expression at the time of progression. In breast cancer cells, ablation of PTEN, through increased AKT activation, was sufficient to promote resistance to CDK4/6 inhibition in vitro and in vivo. Mechanistically, PTEN loss resulted in exclusion of p27 from the nucleus, leading to increased activation of both CDK4 and CDK2. Because PTEN loss also causes resistance to PI3Kα inhibitors, currently approved in the post-CDK4/6 setting, these findings provide critical insight into how this single genetic event may cause clinical cross-resistance to multiple targeted therapies in the same patient, with implications for optimal treatment-sequencing strategies. SIGNIFICANCE: Our analysis of serial biopsies uncovered RB and PTEN loss as mechanisms of acquired resistance to CDK4/6 inhibitors, utilized as first-line treatment for ER-positive advanced breast cancer. Importantly, these findings have near-term clinical relevance because PTEN loss also limits the efficacy of PI3Kα inhibitors currently approved in the post-CDK4/6 setting.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Carlotta Costa
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts.
| | - Ye Wang
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Amy Ly
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Yasuyuki Hosono
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Ellen Murchie
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Charlotte S Walmsley
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Tiffany Huynh
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Christopher Healy
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Rachel Peterson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Shogo Yanase
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Charles T Jakubik
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Laura E Henderson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Leah J Damon
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Daria Timonina
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Ioannis Sanidas
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Christopher J Pinto
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - James R Stone
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Leif W Ellisen
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Aditya Bardia
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Hiromichi Ebi
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Nagoya, Japan.,Precision Medicine Center, Aichi Cancer Center, Nagoya, Japan.,Division of Advanced Cancer Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Jeffrey A Engelman
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts.
| | - Dejan Juric
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts.
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314
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Osmanbeyoglu HU, Shimizu F, Rynne-Vidal A, Alonso-Curbelo D, Chen HA, Wen HY, Yeung TL, Jelinic P, Razavi P, Lowe SW, Mok SC, Chiosis G, Levine DA, Leslie CS. Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers. Nat Commun 2019; 10:4369. [PMID: 31554806 PMCID: PMC6761109 DOI: 10.1038/s41467-019-12291-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/02/2019] [Indexed: 02/08/2023] Open
Abstract
Chromatin accessibility data can elucidate the developmental origin of cancer cells and reveal the enhancer landscape of key oncogenic transcriptional regulators. We develop a computational strategy called PSIONIC (patient-specific inference of networks informed by chromatin) to combine chromatin accessibility data with large tumor expression data and model the effect of enhancers on transcriptional programs in multiple cancers. We generate a new ATAC-seq data profiling chromatin accessibility in gynecologic and basal breast cancer cell lines and apply PSIONIC to 723 patient and 96 cell line RNA-seq profiles from ovarian, uterine, and basal breast cancers. Our computational framework enables us to share information across tumors to learn patient-specific TF activities, revealing regulatory differences between and within tumor types. PSIONIC-predicted activity for MTF1 in cell line models correlates with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy. Many identified TFs are significantly associated with survival outcome. To validate PSIONIC-derived prognostic TFs, we perform immunohistochemical analyses in 31 uterine serous tumors for ETV6 and 45 basal breast tumors for MITF and confirm that the corresponding protein expression patterns are also significantly associated with prognosis.
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Affiliation(s)
- Hatice U Osmanbeyoglu
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Computational & Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Fumiko Shimizu
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Angela Rynne-Vidal
- Department of Gynecologic Oncology and Reproductive Medicine-Research, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Direna Alonso-Curbelo
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hsuan-An Chen
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tsz-Lun Yeung
- Department of Gynecologic Oncology and Reproductive Medicine-Research, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Petar Jelinic
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel C Mok
- Department of Gynecologic Oncology and Reproductive Medicine-Research, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas A Levine
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Christina S Leslie
- Computational & Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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315
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Liang J, Zhao H, Diplas BH, Liu S, Liu J, Wang D, Lu Y, Zhu Q, Wu J, Wang W, Yan H, Zeng YX, Wang X, Jiao Y. Genome-Wide CRISPR-Cas9 Screen Reveals Selective Vulnerability of ATRX-Mutant Cancers to WEE1 Inhibition. Cancer Res 2019; 80:510-523. [PMID: 31551363 DOI: 10.1158/0008-5472.can-18-3374] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 04/28/2019] [Accepted: 09/17/2019] [Indexed: 11/16/2022]
Abstract
The tumor suppressor gene ATRX is frequently mutated in a variety of tumors including gliomas and liver cancers, which are highly unresponsive to current therapies. Here, we performed a genome-wide synthetic lethal screen, using CRISPR-Cas9 genome editing, to identify potential therapeutic targets specific for ATRX-mutated cancers. In isogenic hepatocellular carcinoma (HCC) cell lines engineered for ATRX loss, we identified 58 genes, including the checkpoint kinase WEE1, uniquely required for the cell growth of ATRX null cells. Treatment with the WEE1 inhibitor AZD1775 robustly inhibited the growth of several ATRX-deficient HCC cell lines in vitro, as well as xenografts in vivo. The increased sensitivity to the WEE1 inhibitor was caused by accumulated DNA damage-induced apoptosis. AZD1775 also selectively inhibited the proliferation of patient-derived primary cell lines from gliomas with naturally occurring ATRX mutations, indicating that the synthetic lethal relationship between WEE1 and ATRX could be exploited in a broader spectrum of human tumors. As WEE1 inhibitors have been investigated in several phase II clinical trials, our discovery provides the basis for an easily clinically testable therapeutic strategy specific for cancers deficient in ATRX. SIGNIFICANCE: ATRX-mutant cancer cells depend on WEE1, which provides a basis for therapeutically targeting WEE1 in ATRX-deficient cancers.See related commentary by Cole, p. 375.
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Affiliation(s)
- Junbo Liang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hong Zhao
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bill H Diplas
- The Preston Robert Tisch Brain Tumor Center at Duke, Pediatric Brain Tumor Foundation Institute at Duke, and Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Song Liu
- Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Jianmei Liu
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dingding Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yan Lu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Qing Zhu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong Province, China
| | - Jiayu Wu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Wenjia Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hai Yan
- The Preston Robert Tisch Brain Tumor Center at Duke, Pediatric Brain Tumor Foundation Institute at Duke, and Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Yi-Xin Zeng
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong Province, China
| | - Xiaoyue Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
| | - Yuchen Jiao
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. .,Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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316
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Rogan PK. Multigene signatures of responses to chemotherapy derived by biochemically-inspired machine learning. Mol Genet Metab 2019; 128:45-52. [PMID: 31451418 DOI: 10.1016/j.ymgme.2019.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/09/2019] [Accepted: 08/16/2019] [Indexed: 01/08/2023]
Abstract
Pharmacogenomic responses to chemotherapy drugs can be modeled by supervised machine learning of expression and copy number of relevant gene combinations. Such biochemical evidence can form the basis of derived gene signatures using cell line data, which can subsequently be examined in patients that have been treated with the same drugs. These gene signatures typically contain elements of multiple biochemical pathways which together comprise multiple origins of drug resistance or sensitivity. The signatures can capture variation in these responses to the same drug among different patients.
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Affiliation(s)
- Peter K Rogan
- Departments of Biochemistry, Oncology, and Computer Science, University of Western Ontario, London, ON N6A 2C1, UK.
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317
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Heijink AM, Everts M, Honeywell ME, Richards R, Kok YP, de Vries EGE, Lee MJ, van Vugt MATM. Modeling of Cisplatin-Induced Signaling Dynamics in Triple-Negative Breast Cancer Cells Reveals Mediators of Sensitivity. Cell Rep 2019; 28:2345-2357.e5. [PMID: 31461651 PMCID: PMC6718811 DOI: 10.1016/j.celrep.2019.07.070] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/24/2019] [Accepted: 07/22/2019] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancers (TNBCs) display great diversity in cisplatin sensitivity that cannot be explained solely by cancer-associated DNA repair defects. Differential activation of the DNA damage response (DDR) to cisplatin has been proposed to underlie the observed differential sensitivity, but it has not been investigated systematically. Systems-level analysis-using quantitative time-resolved signaling data and phenotypic responses, in combination with mathematical modeling-identifies that the activation status of cell-cycle checkpoints determines cisplatin sensitivity in TNBC cell lines. Specifically, inactivation of the cell-cycle checkpoint regulator MK2 or G3BP2 sensitizes cisplatin-resistant TNBC cell lines to cisplatin. Dynamic signaling data of five cell cycle-related signals predicts cisplatin sensitivity of TNBC cell lines. We provide a time-resolved map of cisplatin-induced signaling that uncovers determinants of chemo-sensitivity, underscores the impact of cell-cycle checkpoints on cisplatin sensitivity, and offers starting points to optimize treatment efficacy.
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Affiliation(s)
- Anne Margriet Heijink
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Marieke Everts
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Megan E Honeywell
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ryan Richards
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Yannick P Kok
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Elisabeth G E de Vries
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Michael J Lee
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Marcel A T M van Vugt
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands.
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318
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Brooks EA, Galarza S, Gencoglu MF, Cornelison RC, Munson JM, Peyton SR. Applicability of drug response metrics for cancer studies using biomaterials. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180226. [PMID: 31431182 PMCID: PMC6627013 DOI: 10.1098/rstb.2018.0226] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2019] [Indexed: 12/31/2022] Open
Abstract
Bioengineers have built models of the tumour microenvironment (TME) in which to study cell-cell interactions, mechanisms of cancer growth and metastasis, and to test new therapies. These models allow researchers to culture cells in conditions that include features of the in vivo TME implicated in regulating cancer progression, such as extracellular matrix (ECM) stiffness, integrin binding to the ECM, immune and stromal cells, growth factor and cytokine depots, and a three-dimensional geometry more representative of the in vivo TME than tissue culture polystyrene (TCPS). These biomaterials could be particularly useful for drug screening applications to make better predictions of efficacy, offering better translation to preclinical models and clinical trials. However, it can be challenging to compare drug response reports across different biomaterial platforms in the current literature. This is, in part, a result of inconsistent reporting and improper use of drug response metrics, and vast differences in cell growth rates across a large variety of biomaterial designs. This study attempts to clarify the definitions of drug response measurements used in the field, and presents examples in which these measurements can and cannot be applied. We suggest as best practice to measure the growth rate of cells in the absence of drug, and follow our 'decision tree' when reporting drug response metrics. This article is part of a discussion meeting issue 'Forces in cancer: interdisciplinary approaches in tumour mechanobiology'.
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Affiliation(s)
- Elizabeth A. Brooks
- Department of Chemical Engineering, University of Massachusetts Amherst, 240 Thatcher Road, Amherst, MA 01003-9364, USA
| | - Sualyneth Galarza
- Department of Chemical Engineering, University of Massachusetts Amherst, 240 Thatcher Road, Amherst, MA 01003-9364, USA
| | - Maria F. Gencoglu
- Department of Chemical Engineering, University of Massachusetts Amherst, 240 Thatcher Road, Amherst, MA 01003-9364, USA
| | - R. Chase Cornelison
- Department of Biomedical Engineering and Mechanics, Virginia Tech, 325 Stanger Street, Blacksburg, VA 24061, USA
| | - Jennifer M. Munson
- Department of Biomedical Engineering and Mechanics, Virginia Tech, 325 Stanger Street, Blacksburg, VA 24061, USA
| | - Shelly R. Peyton
- Department of Chemical Engineering, University of Massachusetts Amherst, 240 Thatcher Road, Amherst, MA 01003-9364, USA
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319
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Qiu Z, Li H, Zhang Z, Zhu Z, He S, Wang X, Wang P, Qin J, Zhuang L, Wang W, Xie F, Gu Y, Zou K, Li C, Li C, Wang C, Cen J, Chen X, Shu Y, Zhang Z, Sun L, Min L, Fu Y, Huang X, Lv H, Zhou H, Ji Y, Zhang Z, Meng Z, Shi X, Zhang H, Li Y, Hui L. A Pharmacogenomic Landscape in Human Liver Cancers. Cancer Cell 2019; 36:179-193.e11. [PMID: 31378681 PMCID: PMC7505724 DOI: 10.1016/j.ccell.2019.07.001] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 05/17/2019] [Accepted: 07/01/2019] [Indexed: 12/30/2022]
Abstract
Liver cancers are highly heterogeneous with poor prognosis and drug response. A better understanding between genetic alterations and drug responses would facilitate precision treatment for liver cancers. To characterize the landscape of pharmacogenomic interactions in liver cancers, we developed a protocol to establish human liver cancer cell models at a success rate of around 50% and generated the Liver Cancer Model Repository (LIMORE) with 81 cell models. LIMORE represented genomic and transcriptomic heterogeneity of primary cancers. Interrogation of the pharmacogenomic landscape of LIMORE discovered unexplored gene-drug associations, including synthetic lethalities to prevalent alterations in liver cancers. Moreover, predictive biomarker candidates were suggested for the selection of sorafenib-responding patients. LIMORE provides a rich resource facilitating drug discovery in liver cancers.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Asian People/genetics
- Biomarkers, Tumor/genetics
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/ethnology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Cell Line, Tumor
- Clinical Decision-Making
- Databases, Genetic
- Drug Resistance, Neoplasm/genetics
- Female
- Genetic Heterogeneity
- Genetic Predisposition to Disease
- High-Throughput Nucleotide Sequencing
- Humans
- Liver Neoplasms/drug therapy
- Liver Neoplasms/ethnology
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Male
- Mice, Inbred BALB C
- Mice, Inbred NOD
- Mice, Nude
- Mice, SCID
- Patient Selection
- Pharmacogenomic Testing
- Pharmacogenomic Variants
- Phenotype
- Precision Medicine
- Protein Kinase Inhibitors/pharmacology
- Sorafenib/pharmacology
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Zhixin Qiu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hong Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhengtao Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhenfeng Zhu
- Department of Minimally Invasive Therapy, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Sheng He
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Xujun Wang
- SJTU-Yale Joint Center for Biostatistics, Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai 200240, China
| | - Pengcheng Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Shanghai 200032, China
| | - Jianjie Qin
- Liver Transplantation Center, Key Laboratory of Living Donor Liver Transplantation of Ministry of Public Health, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Liping Zhuang
- Department of Minimally Invasive Therapy, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Wei Wang
- Shanghai ChemPartner Co., Ltd., Shanghai 201203, China
| | - Fubo Xie
- Shanghai ChemPartner Co., Ltd., Shanghai 201203, China
| | - Ying Gu
- Shanghai ChemPartner Co., Ltd., Shanghai 201203, China
| | - Keke Zou
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chao Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chun Li
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chenhua Wang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jin Cen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaotao Chen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yajing Shu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhao Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lulu Sun
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lihua Min
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Fu
- Fifth Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Xiaowu Huang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Shanghai 200032, China
| | - Hui Lv
- SJTU-Yale Joint Center for Biostatistics, Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai 200240, China
| | - He Zhou
- Shanghai ChemPartner Co., Ltd., Shanghai 201203, China
| | - Yuan Ji
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhigang Zhang
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Zhiqiang Meng
- Department of Minimally Invasive Therapy, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiaolei Shi
- Department of Hepatobiliary Surgery, the Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 211166, China.
| | - Haibin Zhang
- Fifth Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China.
| | - Yixue Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Lijian Hui
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China; Bio-Research Innovation Center Suzhou, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Suzhou, Jiangsu 215121, China.
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320
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Dhir T, Schultz CW, Jain A, Brown SZ, Haber A, Goetz A, Xi C, Su GH, Xu L, Posey J, Jiang W, Yeo CJ, Golan T, Pishvaian MJ, Brody JR. Abemaciclib Is Effective Against Pancreatic Cancer Cells and Synergizes with HuR and YAP1 Inhibition. Mol Cancer Res 2019; 17:2029-2041. [PMID: 31383722 DOI: 10.1158/1541-7786.mcr-19-0589] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 12/18/2022]
Abstract
Mutation or promoter hypermethylation of CDKN2A is found in over 90% of pancreatic ductal adenocarcinomas (PDAC) and leads to loss of function of cell-cycle inhibitors p16 (INK4A) and p14 (ARF) resulting in unchecked proliferation. The CDK4/6 inhibitor, abemaciclib, has nanomolar IC50s in PDAC cell lines and decreases growth through inhibition of phospho-Rb (pRb), G1 cell-cycle arrest, apoptosis, and the senescent phenotype detected with β-galactosidase staining and relevant mRNA elevations. Daily abemaciclib treatments in mouse PDAC xenograft studies were safe and demonstrated a 3.2-fold decrease in tumor volume compared with no treatment (P < 0.0001) accompanying a decrease in both pRb and Ki67. We determined that inhibitors of HuR (ELAVL1), a prosurvival mRNA stability factor that regulates cyclin D1, and an inhibitor of Yes-Associated Protein 1 (YAP1), a pro-oncogenic, transcriptional coactivator important for CDK6 and cyclin D1, were both synergistic with abemaciclib. Accordingly, siRNA oligonucleotides targeted against HuR, YAP1, and their common target cyclin D1, validated the synergy studies. In addition, we have seen increased sensitivity to abemaciclib in a PDAC cell line that harbors a loss of the ELAVL1 gene via CRISP-Cas9 technology. As an in vitro model for resistance, we investigated the effects of long-term abemaciclib exposure. PDAC cells chronically cultured with abemaciclib displayed a reduction in cellular growth rates (GR) and coresistance to gemcitabine and 5-fluorouracil (5-FU), but not to HuR or YAP1 inhibitors as compared with no treatment controls. We believe that our data provide compelling preclinical evidence for an abemaciclib combination-based clinical trial in patients with PDAC. IMPLICATIONS: Our data suggest that abemaciclib may be therapeutically relevant for the treatment in PDAC, especially as part of a combination regimen inhibiting YAP1 or HuR.
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Affiliation(s)
- Teena Dhir
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Christopher W Schultz
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Aditi Jain
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Samantha Z Brown
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Alex Haber
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Austin Goetz
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Chunhua Xi
- The Department of Pathology & Cell Biology, Columbia University Medical Center, New York, New York
| | - Gloria H Su
- The Department of Pathology & Cell Biology, Columbia University Medical Center, New York, New York
| | - Liang Xu
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - James Posey
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Wei Jiang
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Charles J Yeo
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Talia Golan
- Oncology institute, Chaim Sheba Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Jonathan R Brody
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.
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321
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Smirnov P, Kofia V, Maru A, Freeman M, Ho C, El-Hachem N, Adam GA, Ba-Alawi W, Safikhani Z, Haibe-Kains B. PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies. Nucleic Acids Res 2019; 46:D994-D1002. [PMID: 30053271 PMCID: PMC5753377 DOI: 10.1093/nar/gkx911] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/27/2017] [Indexed: 12/18/2022] Open
Abstract
Recent cancer pharmacogenomic studies profiled large panels of cell lines against hundreds of approved drugs and experimental chemical compounds. The overarching goal of these screens is to measure sensitivity of cell lines to chemical perturbations, correlate these measures to genomic features, and thereby develop novel predictors of drug response. However, leveraging these valuable data is challenging due to the lack of standards for annotating cell lines and chemical compounds, and quantifying drug response. Moreover, it has been recently shown that the complexity and complementarity of the experimental protocols used in the field result in high levels of technical and biological variation in the in vitro pharmacological profiles. There is therefore a need for new tools to facilitate rigorous comparison and integrative analysis of large-scale drug screening datasets. To address this issue, we have developed PharmacoDB (pharmacodb.pmgenomics.ca), a database integrating the largest cancer pharmacogenomic studies published to date. Here, we describe how the curation of cell line and chemical compound identifiers maximizes the overlap between datasets and how users can leverage such data to compare and extract robust drug phenotypes. PharmacoDB provides a unique resource to mine a compendium of curated cancer pharmacogenomic datasets that are otherwise disparate and difficult to integrate.
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Affiliation(s)
- Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Victor Kofia
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alexander Maru
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark Freeman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Chantal Ho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nehme El-Hachem
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - George-Alexandru Adam
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Wail Ba-Alawi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Zhaleh Safikhani
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute of Cancer Research, Toronto, Ontario, Canada
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322
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Abbassi RH, Recasens A, Indurthi DC, Johns TG, Stringer BW, Day BW, Munoz L. Lower Tubulin Expression in Glioblastoma Stem Cells Attenuates Efficacy of Microtubule-Targeting Agents. ACS Pharmacol Transl Sci 2019; 2:402-413. [PMID: 32259073 DOI: 10.1021/acsptsci.9b00045] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Indexed: 02/07/2023]
Abstract
Sensitivity to microtubule-targeting agents (MTAs) varies among cancers and predicting the response of individual cancer patients to MTAs remains challenging. As microtubules possess vast molecular heterogeneity generated by tubulin isotypes and their post-translational modifications, we questioned whether this heterogeneity can impact MTA sensitivity. We investigated microtubule heterogeneity in 15 glioblastoma cell lines and measured sensitivity of orthogonal MTAs using a per-division growth rate inhibition method that corrects for the confounding effects of variable cell proliferation rates. We found that the tubulin profile is unique for each glioblastoma cell line and that the total α- and β-tubulin levels impact on MTA sensitivity. The baseline levels of α- and β-tubulin were up to 20% lower in cells that were not effectively killed by MTAs. We report that lower α/β-tubulin expression is associated with lack of cell differentiation and increased expression of stemness markers. The dedifferentiated stem-like cells with low α/β-tubulin levels survive MTAs treatment via reversible nonmutational dormancy. Our findings provide novel insights into the relationships between microtubules and MTAs and lay a foundation for better understanding of the sensitivity of cancer cells to MTAs.
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Affiliation(s)
- Ramzi H Abbassi
- Faculty of Medicine and Health, Charles Perkins Centre, The University of Sydney, John Hopkins Drive, Sydney, New South Wales 2006, Australia
| | - Ariadna Recasens
- Faculty of Medicine and Health, Charles Perkins Centre, The University of Sydney, John Hopkins Drive, Sydney, New South Wales 2006, Australia
| | - Dinesh C Indurthi
- Faculty of Medicine and Health, Charles Perkins Centre, The University of Sydney, John Hopkins Drive, Sydney, New South Wales 2006, Australia
| | - Terrance G Johns
- Oncogenic Signalling Laboratory and Brain Cancer Discovery Collaborative, Telethon Kids Institute, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia 6009, Australia
| | - Brett W Stringer
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland 4006, Australia
| | - Bryan W Day
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland 4006, Australia
| | - Lenka Munoz
- Faculty of Medicine and Health, Charles Perkins Centre, The University of Sydney, John Hopkins Drive, Sydney, New South Wales 2006, Australia
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323
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Bellerose MM, Baek SH, Huang CC, Moss CE, Koh EI, Proulx MK, Smith CM, Baker RE, Lee JS, Eum S, Shin SJ, Cho SN, Murray M, Sassetti CM. Common Variants in the Glycerol Kinase Gene Reduce Tuberculosis Drug Efficacy. mBio 2019; 10:e00663-19. [PMID: 31363023 PMCID: PMC6667613 DOI: 10.1128/mbio.00663-19] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 12/12/2022] Open
Abstract
Despite the administration of multiple drugs that are highly effective in vitro, tuberculosis (TB) treatment requires prolonged drug administration and is confounded by the emergence of drug-resistant strains. To understand the mechanisms that limit antibiotic efficacy, we performed a comprehensive genetic study to identify Mycobacterium tuberculosis genes that alter the rate of bacterial clearance in drug-treated mice. Several functionally distinct bacterial genes were found to alter bacterial clearance, and prominent among these was the glpK gene that encodes the glycerol-3-kinase enzyme that is necessary for glycerol catabolism. Growth on glycerol generally increased the sensitivity of M. tuberculosis to antibiotics in vitro, and glpK-deficient bacteria persisted during antibiotic treatment in vivo, particularly during exposure to pyrazinamide-containing regimens. Frameshift mutations in a hypervariable homopolymeric region of the glpK gene were found to be a specific marker of multidrug resistance in clinical M. tuberculosis isolates, and these loss-of-function alleles were also enriched in extensively drug-resistant clones. These data indicate that frequently observed variation in the glpK coding sequence produces a drug-tolerant phenotype that can reduce antibiotic efficacy and may contribute to the evolution of resistance.IMPORTANCE TB control is limited in part by the length of antibiotic treatment needed to prevent recurrent disease. To probe mechanisms underlying survival under antibiotic pressure, we performed a genetic screen for M. tuberculosis mutants with altered susceptibility to treatment using the mouse model of TB. We identified multiple genes involved in a range of functions which alter sensitivity to antibiotics. In particular, we found glycerol catabolism mutants were less susceptible to treatment and that common variation in a homopolymeric region in the glpK gene was associated with drug resistance in clinical isolates. These studies indicate that reversible high-frequency variation in carbon metabolic pathways can produce phenotypically drug-tolerant clones and have a role in the development of resistance.
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Affiliation(s)
- Michelle M Bellerose
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Seung-Hun Baek
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Chuan-Chin Huang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Caitlin E Moss
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Eun-Ik Koh
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Megan K Proulx
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Clare M Smith
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jong Seok Lee
- International Tuberculosis Research Center, Changwon, South Korea
| | - Seokyong Eum
- International Tuberculosis Research Center, Changwon, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Sang-Nae Cho
- International Tuberculosis Research Center, Changwon, South Korea
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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324
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El Gaafary M, Hafner S, Lang SJ, Jin L, Sabry OM, Vogel CV, Vanderwal CD, Syrovets T, Simmet T. A Novel Polyhalogenated Monoterpene Induces Cell Cycle Arrest and Apoptosis in Breast Cancer Cells. Mar Drugs 2019; 17:md17080437. [PMID: 31349625 PMCID: PMC6723102 DOI: 10.3390/md17080437] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/17/2019] [Accepted: 07/23/2019] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is the most common cancer type and a primary cause of cancer mortality among females worldwide. Here, we analyzed the anticancer efficacy of a novel bromochlorinated monoterpene, PPM1, a synthetic analogue of polyhalogenated monoterpenes from Plocamium red algae and structurally similar non-brominated monoterpenes. PPM1, but not the non-brominated monoterpenes, decreased selectively the viability of several triple-negative as well as triple-positive breast cancer cells with different p53 status without significantly affecting normal breast epithelial cells. PPM1 induced accumulation of triple-negative MDA-MB-231 cells with 4N DNA content characterized by decreased histone H3-S10/T3 phosphorylation indicating cell cycle arrest in the G2 phase. Western immunoblot analysis revealed that PPM1 treatment triggered an initial rapid activation of Aurora kinases A/B/C and p21Waf1/Cip1 accumulation, which was followed by accumulation of polyploid >4N cells. Flow cytometric analysis showed mitochondrial potential disruption, caspase 3/7 activation, phosphatidylserine externalization, reduction of the amount polyploid cells, and DNA fragmentation consistent with induction of apoptosis. Cell viability was partially restored by the pan-caspase inhibitor Z-VAD-FMK indicating caspase contribution. In vivo, PPM1 inhibited growth, proliferation, and induced apoptosis in MDA-MB-231 xenografted onto the chick chorioallantoic membrane. Hence, Plocamium polyhalogenated monoterpenes and synthetic analogues deserve further exploration as promising anticancer lead compounds.
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Affiliation(s)
- Menna El Gaafary
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, Ulm University, D-89081 Ulm, Germany
- Department of Pharmacognosy, College of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Susanne Hafner
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, Ulm University, D-89081 Ulm, Germany
| | - Sophia J Lang
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, Ulm University, D-89081 Ulm, Germany
| | - Lu Jin
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, Ulm University, D-89081 Ulm, Germany
| | - Omar M Sabry
- Department of Pharmacognosy, College of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Carl V Vogel
- Department of Chemistry, 1102 Natural Sciences II, University of California, Irvine, CA 92697-2025, USA
| | - Christopher D Vanderwal
- Department of Chemistry, 1102 Natural Sciences II, University of California, Irvine, CA 92697-2025, USA
| | - Tatiana Syrovets
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, Ulm University, D-89081 Ulm, Germany.
| | - Thomas Simmet
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, Ulm University, D-89081 Ulm, Germany.
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325
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Kanemaru Y, Natsumeda M, Okada M, Saito R, Kobayashi D, Eda T, Watanabe J, Saito S, Tsukamoto Y, Oishi M, Saito H, Nagahashi M, Sasaki T, Hashizume R, Aoyama H, Wakai T, Kakita A, Fujii Y. Dramatic response of BRAF V600E-mutant epithelioid glioblastoma to combination therapy with BRAF and MEK inhibitor: establishment and xenograft of a cell line to predict clinical efficacy. Acta Neuropathol Commun 2019; 7:119. [PMID: 31345255 PMCID: PMC6659204 DOI: 10.1186/s40478-019-0774-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 07/18/2019] [Indexed: 11/14/2022] Open
Abstract
Epithelioid glioblastoma is a rare aggressive variant of glioblastoma (GBM) characterized by a dismal prognosis of about 6 months and frequent leptomeningeal dissemination. A recent study has revealed that 50% of epithelioid GBMs harbor three genetic alterations - BRAF V600E mutation, TERT promoter mutations, and homozygous deletions of CDKN2A/2B. Emerging evidence support the effectiveness of targeted therapies for brain tumors with BRAF V600E mutation. Here we describe a dramatic radiographical response to combined therapy with BRAF and MEK inhibitors in a patient with epithelioid GBM harboring BRAF V600E mutation, characterized by thick spinal dissemination. From relapsed tumor procured at autopsy, we established a cell line retaining the BRAF V600E mutation, TERT promoter mutation and CDKN2A/2B loss. Intracranial implantation of these cells into mice resulted in tumors closely resembling the original, characterized by epithelioid tumor cells and dissemination, and invasion into the perivascular spaces. We then confirmed the efficacy of treatment with BRAF and MEK inhibitor both in vitro and in vivo. Epithelioid GBM with BRAF V600E mutation can be considered a good treatment indication for precision medicine, and this patient-derived cell line should be useful for prediction of the tumor response and clarification of its biological characteristics.
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Affiliation(s)
- Yu Kanemaru
- From the Departments of Neurosurgery, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, Japan
| | - Manabu Natsumeda
- From the Departments of Neurosurgery, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, Japan.
| | - Masayasu Okada
- From the Departments of Neurosurgery, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, Japan
| | - Rie Saito
- Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Daiki Kobayashi
- From the Departments of Neurosurgery, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, Japan
| | - Takeyoshi Eda
- From the Departments of Neurosurgery, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, Japan
| | - Jun Watanabe
- From the Departments of Neurosurgery, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, Japan
| | - Shoji Saito
- From the Departments of Neurosurgery, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, Japan
| | - Yoshihiro Tsukamoto
- From the Departments of Neurosurgery, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, Japan
| | - Makoto Oishi
- From the Departments of Neurosurgery, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, Japan
| | - Hirotake Saito
- Department of Radiology and Radiation Oncology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masayuki Nagahashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Takahiro Sasaki
- Department of Neurosurgery, Northwestern University, Chicago, IL, USA
| | - Rintaro Hashizume
- Department of Neurosurgery, Northwestern University, Chicago, IL, USA
| | - Hidefumi Aoyama
- Department of Radiology and Radiation Oncology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Akiyoshi Kakita
- Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yukihiko Fujii
- From the Departments of Neurosurgery, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, Japan
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326
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Niepel M, Hafner M, Mills CE, Subramanian K, Williams EH, Chung M, Gaudio B, Barrette AM, Stern AD, Hu B, Korkola JE, Gray JW, Birtwistle MR, Heiser LM, Sorger PK. A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines. Cell Syst 2019; 9:35-48.e5. [PMID: 31302153 PMCID: PMC6700527 DOI: 10.1016/j.cels.2019.06.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/01/2019] [Accepted: 06/12/2019] [Indexed: 12/18/2022]
Abstract
Evidence that some high-impact biomedical results cannot be repeated has stimulated interest in practices that generate findable, accessible, interoperable, and reusable (FAIR) data. Multiple papers have identified specific examples of irreproducibility, but practical ways to make data more reproducible have not been widely studied. Here, five research centers in the NIH LINCS Program Consortium investigate the reproducibility of a prototypical perturbational assay: quantifying the responsiveness of cultured cells to anti-cancer drugs. Such assays are important for drug development, studying cellular networks, and patient stratification. While many experimental and computational factors impact intra- and inter-center reproducibility, the factors most difficult to identify and control are those with a strong dependency on biological context. These factors often vary in magnitude with the drug being analyzed and with growth conditions. We provide ways to identify such context-sensitive factors, thereby improving both the theory and practice of reproducible cell-based assays. Factors that impact the reproducibility of experimental data are poorly understood. Five NIH-LINCS centers performed the same set of drug-response measurements and compared results. Technical and biological variables that impact precision and reproducibility and are also sensitive to biological context were the most problematic.
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Affiliation(s)
- Mario Niepel
- Laboratory of Systems Pharmacology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Marc Hafner
- Laboratory of Systems Pharmacology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Kartik Subramanian
- Laboratory of Systems Pharmacology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth H Williams
- Laboratory of Systems Pharmacology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Mirra Chung
- Laboratory of Systems Pharmacology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin Gaudio
- Laboratory of Systems Pharmacology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Marie Barrette
- Department of Pharmacological Sciences, Drug Toxicity Signature Generation (DToxS) LINCS Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Alan D Stern
- Department of Pharmacological Sciences, Drug Toxicity Signature Generation (DToxS) LINCS Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Bin Hu
- Department of Pharmacological Sciences, Drug Toxicity Signature Generation (DToxS) LINCS Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - James E Korkola
- Microenvironment Perturbagen (MEP) LINCS Center, OHSU Center for Spatial Systems Biomedicine, Oregon Health & Sciences University, Portland, OR 97201, USA
| | - Joe W Gray
- Microenvironment Perturbagen (MEP) LINCS Center, OHSU Center for Spatial Systems Biomedicine, Oregon Health & Sciences University, Portland, OR 97201, USA
| | - Marc R Birtwistle
- Department of Pharmacological Sciences, Drug Toxicity Signature Generation (DToxS) LINCS Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA.
| | - Laura M Heiser
- Microenvironment Perturbagen (MEP) LINCS Center, OHSU Center for Spatial Systems Biomedicine, Oregon Health & Sciences University, Portland, OR 97201, USA.
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA.
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327
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Interplay of Darwinian Selection, Lamarckian Induction and Microvesicle Transfer on Drug Resistance in Cancer. Sci Rep 2019; 9:9332. [PMID: 31249353 PMCID: PMC6597577 DOI: 10.1038/s41598-019-45863-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/12/2019] [Indexed: 12/12/2022] Open
Abstract
Development of drug resistance in cancer has major implications for patients’ outcome. It is related to processes involved in the decrease of drug efficacy, which are strongly influenced by intratumor heterogeneity and changes in the microenvironment. Heterogeneity arises, to a large extent, from genetic mutations analogously to Darwinian evolution, when selection of tumor cells results from the adaptation to the microenvironment, but could also emerge as a consequence of epigenetic mutations driven by stochastic events. An important exogenous source of alterations is the action of chemotherapeutic agents, which not only affects the signalling pathways but also the interactions among cells. In this work we provide experimental evidence from in vitro assays and put forward a mathematical kinetic transport model to describe the dynamics displayed by a system of non-small-cell lung carcinoma cells (NCI-H460) which, depending on the effect of a chemotherapeutic agent (doxorubicin), exhibits a complex interplay between Darwinian selection, Lamarckian induction and the nonlocal transfer of extracellular microvesicles. The role played by all of these processes to multidrug resistance in cancer is elucidated and quantified.
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328
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Synthesis and Enhanced Cellular Uptake In Vitro of Anti-HER2 Multifunctional Gold Nanoparticles. Cancers (Basel) 2019; 11:cancers11060870. [PMID: 31234432 PMCID: PMC6628063 DOI: 10.3390/cancers11060870] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 11/20/2022] Open
Abstract
Nanoparticle carriers offer the possibility of enhanced delivery of therapeutic payloads in tumor tissues due to tumor-selective accumulation through the enhanced permeability and retention effect (EPR). Gold nanoparticles (AuNP), in particular, possess highly appealing features for development as nanomedicines, such as biocompatibility, tunable optical properties and a remarkable ease of surface functionalization. Taking advantage of the latter, several strategies have been designed to increase treatment specificity of gold nanocarriers by attaching monoclonal antibodies on the surface, as a way to promote selective interactions with the targeted cells—an approach referred to as active-targeting. Here, we describe the synthesis of spherical gold nanoparticles surface-functionalized with an anti-HER2 antibody-drug conjugate (ADC) as an active targeting agent that carries a cytotoxic payload. In addition, we enhanced the intracellular delivery properties of the carrier by attaching a cell penetrating peptide to the active-targeted nanoparticles. We demonstrate that the antibody retains high receptor-affinity after the structural modifications performed for drug-conjugation and nanoparticle attachment. Furthermore, we show that antibody attachment increases cellular uptake in HER2 amplified cell lines selectively, and incorporation of the cell penetrating peptide leads to a further increase in cellular internalization. Nanoparticle-bound antibody-drug conjugates retain high antimitotic potency, which could contribute to a higher therapeutic index in high EPR tumors.
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329
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Hafner M, Mills CE, Subramanian K, Chen C, Chung M, Boswell SA, Everley RA, Liu C, Walmsley CS, Juric D, Sorger PK. Multiomics Profiling Establishes the Polypharmacology of FDA-Approved CDK4/6 Inhibitors and the Potential for Differential Clinical Activity. Cell Chem Biol 2019; 26:1067-1080.e8. [PMID: 31178407 DOI: 10.1016/j.chembiol.2019.05.005] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/14/2019] [Accepted: 05/13/2019] [Indexed: 11/28/2022]
Abstract
The target profiles of many drugs are established early in their development and are not systematically revisited at the time of FDA approval. Thus, it is often unclear whether therapeutics with the same nominal targets but different chemical structures are functionally equivalent. In this paper we use five different phenotypic and biochemical assays to compare approved inhibitors of cyclin-dependent kinases 4/6-collectively regarded as breakthroughs in the treatment of hormone receptor-positive breast cancer. We find that transcriptional, proteomic, and phenotypic changes induced by palbociclib, ribociclib, and abemaciclib differ significantly; abemaciclib in particular has advantageous activities partially overlapping those of alvocidib, an older polyselective CDK inhibitor. In cells and mice, abemaciclib inhibits kinases other than CDK4/6 including CDK2/cyclin A/E-implicated in resistance to CDK4/6 inhibition-and CDK1/cyclin B. The multifaceted experimental and computational approaches described here therefore uncover underappreciated differences in CDK4/6 inhibitor activities with potential importance in treating human patients.
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Affiliation(s)
- Marc Hafner
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kartik Subramanian
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Chen
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mirra Chung
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah A Boswell
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A Everley
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Changchang Liu
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Charlotte S Walmsley
- Termeer Center for Targeted Therapies, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Dejan Juric
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Termeer Center for Targeted Therapies, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA.
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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330
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Brooks EA, Gencoglu MF, Corbett DC, Stevens KR, Peyton SR. An omentum-inspired 3D PEG hydrogel for identifying ECM-drivers of drug resistant ovarian cancer. APL Bioeng 2019; 3:026106. [PMID: 31263798 PMCID: PMC6594836 DOI: 10.1063/1.5091713] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/10/2019] [Indexed: 12/22/2022] Open
Abstract
Ovarian cancer (OvCa) is a challenging disease to treat due to poor screening techniques and late diagnosis. There is an urgent need for additional therapy options, as patients recur in 70% of cases. The limited availability of clinical treatment options could be a result of poor predictions in early stage drug screens on standard tissue culture polystyrene (TCPS). TCPS does not capture the mechanical and biochemical cues that cells experience in vivo, which can impact how cells will respond to a drug. Therefore, an in vitro model that captures some of the microenvironment features that the cells experience in vivo could provide better insights into drug responses. In this study, we formed 3D multicellular tumor spheroids (MCTS) in microwells and encapsulated them in 3D omentum-inspired hydrogels. SKOV-3 MCTS were resistant to Paclitaxel in our 3D hydrogels compared to a monolayer on TCPS. Toward clinical application, we tested cells from patients [ovarian carcinoma ascites spheroids (OCAS)] who had been treated with Paclitaxel, and drug responses predicted by using the 3D omentum-inspired hydrogels demonstrated the lack of the Paclitaxel response of these samples. Additionally, we observed the presence of collagen production around the encapsulated SKOV-3 MCTS, but not significantly on TCPS. Our results demonstrated that our 3D omentum-inspired hydrogel is an improved in vitro drug testing platform to study the OvCa drug response for patient-derived cells and helped us identify collagen 3 as a potential driver of Paclitaxel resistance in 3D.
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Affiliation(s)
- Elizabeth A. Brooks
- Department of Chemical Engineering, University of Massachusetts Amherst, N540 Life Science Laboratories, 240 Thatcher Road, Amherst, Massachusetts 01003-9364, USA
| | - Maria F. Gencoglu
- Department of Chemical Engineering, University of Massachusetts Amherst, N540 Life Science Laboratories, 240 Thatcher Road, Amherst, Massachusetts 01003-9364, USA
| | - Daniel C. Corbett
- Department of Bioengineering, University of Washington, Box 355061, Seattle, Washington 98195-5061, USA
| | - Kelly R. Stevens
- Department of Bioengineering, University of Washington, Box 355061, Seattle, Washington 98195-5061, USA
| | - Shelly R. Peyton
- Department of Chemical Engineering, University of Massachusetts Amherst, N540 Life Science Laboratories, 240 Thatcher Road, Amherst, Massachusetts 01003-9364, USA
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331
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Shapiro P. A promiscuous kinase inhibitor reveals secrets to cancer cell survival. J Biol Chem 2019; 294:8674-8675. [PMID: 31127063 DOI: 10.1074/jbc.h119.009103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deregulated kinase signaling networks drive the growth and survival of many cancer cells. However, the genetic complexity and rapidly evolving nature of most cancer cells create challenges when identifying the most relevant kinases to inhibit to achieve optimal therapeutic benefits. A new strategy that takes advantage of a well-characterized multitargeted kinase inhibitor describes a nongenetic approach to tease out key kinases that promote proliferation of specific cancer cell types.
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Affiliation(s)
- Paul Shapiro
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201.
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332
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McKenna MT, Weis JA, Quaranta V, Yankeelov TE. Leveraging Mathematical Modeling to Quantify Pharmacokinetic and Pharmacodynamic Pathways: Equivalent Dose Metric. Front Physiol 2019; 10:616. [PMID: 31178753 PMCID: PMC6538812 DOI: 10.3389/fphys.2019.00616] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/01/2019] [Indexed: 12/12/2022] Open
Abstract
Treatment response assays are often summarized by sigmoidal functions comparing cell survival at a single timepoint to applied drug concentration. This approach has a limited biophysical basis, thereby reducing the biological insight gained from such analysis. In particular, drug pharmacokinetic and pharmacodynamic (PK/PD) properties are overlooked in developing treatment response assays, and the accompanying summary statistics conflate these processes. Here, we utilize mathematical modeling to decouple and quantify PK/PD pathways. We experimentally modulate specific pathways with small molecule inhibitors and filter the results with mechanistic mathematical models to obtain quantitative measures of those pathways. Specifically, we investigate the response of cells to time-varying doxorubicin treatments, modulating doxorubicin pharmacology with small molecules that inhibit doxorubicin efflux from cells and DNA repair pathways. We highlight the practical utility of this approach through proposal of the “equivalent dose metric.” This metric, derived from a mechanistic PK/PD model, provides a biophysically-based measure of drug effect. We define equivalent dose as the functional concentration of drug that is bound to the nucleus following therapy. This metric can be used to quantify drivers of treatment response and potentially guide dosing of combination therapies. We leverage the equivalent dose metric to quantify the specific intracellular effects of these small molecule inhibitors using population-scale measurements, and to compare treatment response in cell lines differing in expression of drug efflux pumps. More generally, this approach can be leveraged to quantify the effects of various pharmaceutical and biologic perturbations on treatment response.
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Affiliation(s)
- Matthew T McKenna
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, United States.,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States
| | - Jared A Weis
- Department of Biomedical Engineering, Wake Forest School of Medicine, Winston-Salem, NC, United States.,Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, NC, United States
| | - Vito Quaranta
- Department of Cancer Biology, Vanderbilt University School of Medicine, Vanderbilt University, Nashville, TN, United States
| | - Thomas E Yankeelov
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States.,Department of Diagnostic Medicine, Dell Medical School, The University of Texas at Austin, Austin, TX, United States.,Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, United States.,Oden Institute for Computational and Engineering Sciences, The University of Texas at Austin, Austin, TX, United States.,Livestrong Cancer Institutes, The University of Texas at Austin, Austin, TX, United States
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333
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Hu S, Marineau JJ, Rajagopal N, Hamman KB, Choi YJ, Schmidt DR, Ke N, Johannessen L, Bradley MJ, Orlando DA, Alnemy SR, Ren Y, Ciblat S, Winter DK, Kabro A, Sprott KT, Hodgson JG, Fritz CC, Carulli JP, di Tomaso E, Olson ER. Discovery and Characterization of SY-1365, a Selective, Covalent Inhibitor of CDK7. Cancer Res 2019; 79:3479-3491. [DOI: 10.1158/0008-5472.can-19-0119] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/28/2019] [Accepted: 04/30/2019] [Indexed: 11/16/2022]
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334
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Medina SH, Bush B, Cam M, Sevcik E, DelRio FW, Nandy K, Schneider JP. Identification of a mechanogenetic link between substrate stiffness and chemotherapeutic response in breast cancer. Biomaterials 2019; 202:1-11. [PMID: 30818087 PMCID: PMC6474249 DOI: 10.1016/j.biomaterials.2019.02.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 01/24/2023]
Abstract
Mechanical feedback from the tumor microenvironment regulates an array of processes underlying cancer biology. For example, increased stiffness of mammary extracellular matrix (ECM) drives malignancy and alters the phenotypes of breast cancer cells. Despite this link, the role of substrate stiffness in chemotherapeutic response in breast cancer remains unclear. This is complicated by routine culture and adaptation of cancer cell lines to unnaturally rigid plastic or glass substrates, leading to profound changes in their growth, metastatic potential and, as we show here, chemotherapeutic response. We demonstrate that primary breast cancer cells undergo dramatic phenotypic changes when removed from the host microenvironment and cultured on rigid surfaces, and that drug responses are profoundly altered by the mechanical feedback cells receive from the culture substrate. Conversely, primary breast cancer cells cultured on substrates mimicking the mechanics of their host tumor ECM have a similar genetic profile to the in situ cells with respect to drug activity and resistance pathways. These results suggest substrate stiffness plays a significant role in susceptibility of breast cancer to clinically-approved chemotherapeutics, and presents an opportunity to improve drug discovery efforts by integrating mechanical rigidity as a parameter in screening campaigns.
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Affiliation(s)
- Scott H Medina
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, United States.
| | - Brian Bush
- Materials Measurement Science Division, Nanomechanical Properties Group, National Institute of Standards and Technology, Gaithersburg, MD, 20899, United States
| | - Maggie Cam
- Office of Science and Technology Resources, Center for Cancer Research, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Emily Sevcik
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, United States
| | - Frank W DelRio
- Applied Chemicals and Materials Division, Nanoscale Reliability Group, National Institute of Standards and Technology, Boulder, CO 80305, United States
| | - Kaustav Nandy
- Optical Microscopy and Analysis Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - Joel P Schneider
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, United States.
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335
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Sherman TD, Kagohara LT, Cao R, Cheng R, Satriano M, Considine M, Krigsfeld G, Ranaweera R, Tang Y, Jablonski SA, Stein-O'Brien G, Gaykalova DA, Weiner LM, Chung CH, Fertig EJ. CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer. PLoS Comput Biol 2019; 14:e1006935. [PMID: 31002670 PMCID: PMC6504085 DOI: 10.1371/journal.pcbi.1006935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 05/07/2019] [Accepted: 03/11/2019] [Indexed: 11/18/2022] Open
Abstract
Bioinformatics techniques to analyze time course bulk and single cell omics data
are advancing. The absence of a known ground truth of the dynamics of molecular
changes challenges benchmarking their performance on real data. Realistic
simulated time-course datasets are essential to assess the performance of time
course bioinformatics algorithms. We develop an R/Bioconductor package,
CancerInSilico, to simulate bulk and single cell
transcriptional data from a known ground truth obtained from mathematical models
of cellular systems. This package contains a general R infrastructure for
running cell-based models and simulating gene expression data based on the model
states. We show how to use this package to simulate a gene expression data set
and consequently benchmark analysis methods on this data set with a known ground
truth. The package is freely available via Bioconductor: http://bioconductor.org/packages/CancerInSilico/
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Affiliation(s)
- Thomas D. Sherman
- Department of Oncology, Division of Biostatistics and Bioinformatics,
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore,
MD United States of America
- * E-mail:
(TDS); (EJF)
| | - Luciane T. Kagohara
- Department of Oncology, Division of Biostatistics and Bioinformatics,
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore,
MD United States of America
| | - Raymon Cao
- Department of Oncology, Division of Biostatistics and Bioinformatics,
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore,
MD United States of America
| | - Raymond Cheng
- Science, Math and Computer Science Magnet Program, Poolesville High
School, Poolesville, MD United States of America
| | - Matthew Satriano
- Department of Mathematics, University of Waterloo, Waterloo, Ontario,
Canada
| | - Michael Considine
- Department of Oncology, Division of Biostatistics and Bioinformatics,
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore,
MD United States of America
| | - Gabriel Krigsfeld
- Department of Oncology, Division of Biostatistics and Bioinformatics,
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore,
MD United States of America
| | | | - Yong Tang
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington,
DC United States of America
| | - Sandra A. Jablonski
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington,
DC United States of America
| | - Genevieve Stein-O'Brien
- Department of Oncology, Division of Biostatistics and Bioinformatics,
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore,
MD United States of America
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD
United States of America
| | - Daria A. Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins
University School of Medicine, Baltimore, MD United States of
America
| | - Louis M. Weiner
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington,
DC United States of America
| | | | - Elana J. Fertig
- Department of Oncology, Division of Biostatistics and Bioinformatics,
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore,
MD United States of America
- Department of Applied Mathematics and Statistics, Johns Hopkins
University, Baltimore, MD United States of America
- Department of Biomedical Engineering, Johns Hopkins University,
Baltimore, MD United States of America
- * E-mail:
(TDS); (EJF)
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336
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Alpern D, Gardeux V, Russeil J, Mangeat B, Meireles-Filho ACA, Breysse R, Hacker D, Deplancke B. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. Genome Biol 2019; 20:71. [PMID: 30999927 PMCID: PMC6474054 DOI: 10.1186/s13059-019-1671-x] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 03/07/2019] [Indexed: 01/10/2023] Open
Abstract
Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3' cDNA libraries for dozens of samples, requiring just 2 hours of hands-on time. BRB-seq has a comparable performance to the standard TruSeq approach while showing greater tolerance for lower RNA quality and being up to 25 times cheaper. We anticipate that BRB-seq will transform basic laboratory practice given its capacity to generate genome-wide transcriptomic data at a similar cost as profiling four genes using RT-qPCR.
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Affiliation(s)
- Daniel Alpern
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Vincent Gardeux
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Julie Russeil
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Bastien Mangeat
- Gene Expression Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Antonio C A Meireles-Filho
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Romane Breysse
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - David Hacker
- Protein Expression Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland.
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337
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BET bromodomain inhibition blocks the function of a critical AR-independent master regulator network in lethal prostate cancer. Oncogene 2019; 38:5658-5669. [PMID: 30996246 DOI: 10.1038/s41388-019-0815-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 12/14/2022]
Abstract
BET bromodomain inhibitors block prostate cancer cell growth at least in part through c-Myc and androgen receptor (AR) suppression. However, little is known about other transcriptional regulators whose suppression contributes to BET bromodomain inhibitor anti-tumor activity. Moreover, the anti-tumor activity of BET bromodomain inhibition in AR-independent castration-resistant prostate cancers (CRPC), whose frequency is increasing, is also unknown. Herein, we demonstrate that BET bromodomain inhibition blocks growth of a diverse set of CRPC cell models, including those that are AR-independent or in which c-Myc is not suppressed. To identify transcriptional regulators whose suppression accounts for these effects, we treated multiple CRPC cell lines with the BET bromodomain inhibitor JQ1 and then performed RNA-sequencing followed by Master Regulator computational analysis. This approach identified several previously unappreciated transcriptional regulators that are highly expressed in CRPC and whose suppression, via both transcriptional or post-translational mechanisms, contributes to the anti-tumor activity of BET bromodomain inhibitors.
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338
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A Nonquiescent "Idling" Population State in Drug-Treated, BRAF-Mutated Melanoma. Biophys J 2019; 114:1499-1511. [PMID: 29590606 DOI: 10.1016/j.bpj.2018.01.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/01/2017] [Accepted: 01/02/2018] [Indexed: 01/04/2023] Open
Abstract
Targeted therapy is an effective standard of care in BRAF-mutated malignant melanoma. However, the duration of tumor remission varies unpredictably among patients, and relapse is almost inevitable. Here, we examine the responses of several BRAF-mutated melanoma cell lines (including isogenic subclones) to BRAF inhibitors. We observe complex response dynamics across cell lines, with short-term responses (<100 h) varying from cell line to cell line. In the long term, however, we observe equilibration of all drug-treated populations into a nonquiescent state characterized by a balanced rate of death and division, which we term the "idling" state, and to our knowledge, this state has not been previously reported. Using mathematical modeling, we propose that the observed population-level dynamics are the result of cells transitioning between basins of attraction within a drug-modified phenotypic landscape. Each basin is associated with a drug-induced proliferation rate, a recently introduced metric of an antiproliferative drug effect. The idling population state represents a new dynamic equilibrium in which cells are distributed across the landscape such that the population achieves zero net growth. By fitting our model to experimental drug-response data, we infer the phenotypic landscapes of all considered melanoma cell lines and provide a unifying view of how BRAF-mutated melanomas respond to BRAF inhibition. We hypothesize that the residual disease observed in patients after targeted therapy is composed of a significant number of idling cells. Thus, defining molecular determinants of the phenotypic landscape that idling populations occupy may lead to "targeted landscaping" therapies based on rational modification of the landscape to favor basins with greater drug susceptibility.
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339
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Ngo MT, Harley BAC. Perivascular signals alter global gene expression profile of glioblastoma and response to temozolomide in a gelatin hydrogel. Biomaterials 2019; 198:122-134. [PMID: 29941152 DOI: 10.1101/273763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/30/2018] [Accepted: 06/10/2018] [Indexed: 05/25/2023]
Abstract
Glioblastoma (GBM) is the most common primary malignant brain tumor, with patients exhibiting poor survival (median survival time: 15 months). Difficulties in treating GBM include not only the inability to resect the diffusively-invading tumor cells, but also therapeutic resistance. The perivascular niche (PVN) within the GBM tumor microenvironment contributes significantly to tumor cell invasion, cancer stem cell maintenance, and has been shown to protect tumor cells from radiation and chemotherapy. In this study, we examine how the inclusion of non-tumor cells in culture with tumor cells within a hydrogel impacts the overall gene expression profile of an in vitro artificial perivascular niche (PVN) comprised of endothelial and stromal cells directly cultured with GBM tumor cells within a methacrylamide-functionalized gelatin hydrogel. Using RNA-seq, we demonstrate that genes related to angiogenesis and extracellular matrix remodeling are upregulated in the PVN model compared to hydrogels containing only tumor or perivascular niche cells, while downregulated genes are related to cell cycle and DNA damage repair. Signaling pathways and genes commonly implicated in GBM malignancy, such as MGMT, EGFR, PI3K-Akt signaling, and Ras/MAPK signaling are also upregulated in the PVN model. We describe the kinetics of gene expression within the PVN hydrogels over a course of 14 days, observing the patterns associated with tumor cell-mediated endothelial network co-option and regression. We finally examine the effect of temozolomide, a frontline chemotherapy used clinically against GBM, on the PVN culture. Notably, the PVN model is less responsive to TMZ compared to hydrogels containing only tumor cells. Overall, these results demonstrate that inclusion of cellular and matrix-associated elements of the PVN within an in vitro model of GBM allows for the development of gene expression patterns and therapeutic response relevant to GBM.
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Affiliation(s)
- Mai T Ngo
- Dept. Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Brendan A C Harley
- Dept. Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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340
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Olson CM, Liang Y, Leggett A, Park WD, Li L, Mills CE, Elsarrag SZ, Ficarro SB, Zhang T, Düster R, Geyer M, Sim T, Marto JA, Sorger PK, Westover KD, Lin CY, Kwiatkowski N, Gray NS. Development of a Selective CDK7 Covalent Inhibitor Reveals Predominant Cell-Cycle Phenotype. Cell Chem Biol 2019; 26:792-803.e10. [PMID: 30905681 DOI: 10.1016/j.chembiol.2019.02.012] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/19/2018] [Accepted: 02/18/2019] [Indexed: 02/06/2023]
Abstract
Cyclin-dependent kinase 7 (CDK7) regulates both cell cycle and transcription, but its precise role remains elusive. We previously described THZ1, a CDK7 inhibitor, which dramatically inhibits superenhancer-associated gene expression. However, potent CDK12/13 off-target activity obscured CDK7s contribution to this phenotype. Here, we describe the discovery of a highly selective covalent CDK7 inhibitor. YKL-5-124 causes arrest at the G1/S transition and inhibition of E2F-driven gene expression; these effects are rescued by a CDK7 mutant unable to covalently engage YKL-5-124, demonstrating on-target specificity. Unlike THZ1, treatment with YKL-5-124 resulted in no change to RNA polymerase II C-terminal domain phosphorylation; however, inhibition could be reconstituted by combining YKL-5-124 and THZ531, a selective CDK12/13 inhibitor, revealing potential redundancies in CDK control of gene transcription. These findings highlight the importance of CDK7/12/13 polypharmacology for anti-cancer activity of THZ1 and posit that selective inhibition of CDK7 may be useful for treatment of cancers marked by E2F misregulation.
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Affiliation(s)
- Calla M Olson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biology Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA; Therapeutic Innovation Center (THINC@BCM), Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Yanke Liang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biology Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Alan Leggett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biology Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Woojun D Park
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Lianbo Li
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston MA 02115, USA
| | - Selma Z Elsarrag
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biology Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biology Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Robert Düster
- Institute of Structural Biology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Taebo Sim
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 136-701, Korea
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biology Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston MA 02115, USA
| | - Ken D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Charles Y Lin
- Therapeutic Innovation Center (THINC@BCM), Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Nicholas Kwiatkowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biology Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA.
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biology Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA.
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341
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Rao S, Du G, Hafner M, Subramanian K, Sorger PK, Gray NS. A multitargeted probe-based strategy to identify signaling vulnerabilities in cancers. J Biol Chem 2019; 294:8664-8673. [PMID: 30858179 DOI: 10.1074/jbc.ra118.006805] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/01/2019] [Indexed: 12/31/2022] Open
Abstract
Most cancer cells are dependent on a network of deregulated signaling pathways for survival and are insensitive, or rapidly evolve resistance, to selective inhibitors aimed at a single target. For these reasons, drugs that target more than one protein (polypharmacology) can be clinically advantageous. The discovery of useful polypharmacology remains serendipitous and is challenging to characterize and validate. In this study, we developed a non-genetic strategy for the identification of pathways that drive cancer cell proliferation and represent exploitable signaling vulnerabilities. Our approach is based on using a multitargeted kinase inhibitor, SM1-71, as a tool compound to identify combinations of targets whose simultaneous inhibition elicits a potent cytotoxic effect. As a proof of concept, we applied this approach to a KRAS-dependent non-small cell lung cancer (NSCLC) cell line, H23-KRASG12C Using a combination of phenotypic screens, signaling analyses, and kinase inhibitors, we found that dual inhibition of MEK1/2 and insulin-like growth factor 1 receptor (IGF1R)/insulin receptor (INSR) is critical for blocking proliferation in cells. Our work supports the value of multitargeted tool compounds with well-validated polypharmacology and target space as tools to discover kinase dependences in cancer. We propose that the strategy described here is complementary to existing genetics-based approaches, generalizable to other systems, and enabling for future mechanistic and translational studies of polypharmacology in the context of signaling vulnerabilities in cancers.
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Affiliation(s)
- Suman Rao
- Laboratory of Systems Pharmacology, Boston, Massachusetts 02115; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Guangyan Du
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Marc Hafner
- Laboratory of Systems Pharmacology, Boston, Massachusetts 02115
| | | | - Peter K Sorger
- Laboratory of Systems Pharmacology, Boston, Massachusetts 02115
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.
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342
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Maintenance of MYC expression promotes de novo resistance to BET bromodomain inhibition in castration-resistant prostate cancer. Sci Rep 2019; 9:3823. [PMID: 30846826 PMCID: PMC6405739 DOI: 10.1038/s41598-019-40518-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/31/2018] [Indexed: 12/22/2022] Open
Abstract
The BET bromodomain protein BRD4 is a chromatin reader that regulates transcription, including in cancer. In prostate cancer, specifically, the anti-tumor activity of BET bromodomain inhibition has been principally linked to suppression of androgen receptor (AR) function. MYC is a well-described BRD4 target gene in multiple cancer types, and prior work demonstrates that MYC plays an important role in promoting prostate cancer cell survival. Importantly, several BET bromodomain clinical trials are ongoing, including in prostate cancer. However, there is limited information about pharmacodynamic markers of response or mediators of de novo resistance. Using a panel of prostate cancer cell lines, we demonstrated that MYC suppression-rather than AR suppression-is a key determinant of BET bromodomain inhibitor sensitivity. Importantly, we determined that BRD4 was dispensable for MYC expression in the most resistant cell lines and that MYC RNAi + BET bromodomain inhibition led to additive anti-tumor activity in the most resistant cell lines. Our findings demonstrate that MYC suppression is an important pharmacodynamic marker of BET bromodomain inhibitor response and suggest that targeting MYC may be a promising therapeutic strategy to overcome de novo BET bromodomain inhibitor resistance in prostate cancer.
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343
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Thomas LW, Stephen JM, Esposito C, Hoer S, Antrobus R, Ahmed A, Al-Habib H, Ashcroft M. CHCHD4 confers metabolic vulnerabilities to tumour cells through its control of the mitochondrial respiratory chain. Cancer Metab 2019; 7:2. [PMID: 30886710 PMCID: PMC6404347 DOI: 10.1186/s40170-019-0194-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 02/05/2019] [Indexed: 12/15/2022] Open
Abstract
Background Tumour cells rely on glycolysis and mitochondrial oxidative phosphorylation (OXPHOS) to survive. Thus, mitochondrial OXPHOS has become an increasingly attractive area for therapeutic exploitation in cancer. However, mitochondria are required for intracellular oxygenation and normal physiological processes, and it remains unclear which mitochondrial molecular mechanisms might provide therapeutic benefit. Previously, we discovered that coiled-coil-helix-coiled-coil-helix domain-containing protein 4 (CHCHD4) is critical for regulating intracellular oxygenation and required for the cellular response to hypoxia (low oxygenation) in tumour cells through molecular mechanisms that we do not yet fully understand. Overexpression of CHCHD4 in human cancers correlates with increased tumour progression and poor patient survival. Results Here, we show that elevated CHCHD4 expression provides a proliferative and metabolic advantage to tumour cells in normoxia and hypoxia. Using stable isotope labelling with amino acids in cell culture (SILAC) and analysis of the whole mitochondrial proteome, we show that CHCHD4 dynamically affects the expression of a broad range of mitochondrial respiratory chain subunits from complex I-V, including multiple subunits of complex I (CI) required for complex assembly that are essential for cell survival. We found that loss of CHCHD4 protects tumour cells from respiratory chain inhibition at CI, while elevated CHCHD4 expression in tumour cells leads to significantly increased sensitivity to CI inhibition, in part through the production of mitochondrial reactive oxygen species (ROS). Conclusions Our study highlights an important role for CHCHD4 in regulating tumour cell metabolism and reveals that CHCHD4 confers metabolic vulnerabilities to tumour cells through its control of the mitochondrial respiratory chain and CI biology.
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Affiliation(s)
- Luke W. Thomas
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH UK
| | - Jenna M. Stephen
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH UK
| | - Cinzia Esposito
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH UK
- Present address: Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Simon Hoer
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY UK
| | - Afshan Ahmed
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH UK
- Present address: AstraZeneca Ltd., Cambridge, UK
| | - Hasan Al-Habib
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH UK
| | - Margaret Ashcroft
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH UK
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344
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Shen F, Boccuto L, Pauly R, Srikanth S, Chandrasekaran S. Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors. Genome Biol 2019; 20:49. [PMID: 30823893 PMCID: PMC6397465 DOI: 10.1186/s13059-019-1661-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/21/2019] [Indexed: 12/15/2022] Open
Abstract
Histone acetylation plays a central role in gene regulation and is sensitive to the levels of metabolic intermediates. However, predicting the impact of metabolic alterations on acetylation in pathological conditions is a significant challenge. Here, we present a genome-scale network model that predicts the impact of nutritional environment and genetic alterations on histone acetylation. It identifies cell types that are sensitive to histone deacetylase inhibitors based on their metabolic state, and we validate metabolites that alter drug sensitivity. Our model provides a mechanistic framework for predicting how metabolic perturbations contribute to epigenetic changes and sensitivity to deacetylase inhibitors.
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Affiliation(s)
- Fangzhou Shen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Luigi Boccuto
- Greenwood Genetics Center, Greenwood, SC, 29646, USA
| | - Rini Pauly
- Greenwood Genetics Center, Greenwood, SC, 29646, USA
| | | | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA.
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345
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Seigal A, Beguerisse-Díaz M, Schoeberl B, Niepel M, Harrington HA. Tensor clustering with algebraic constraints gives interpretable groups of crosstalk mechanisms in breast cancer. J R Soc Interface 2019; 16:20180661. [PMID: 30958184 PMCID: PMC6408352 DOI: 10.1098/rsif.2018.0661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We introduce a tensor-based clustering method to extract sparse, low-dimensional structure from high-dimensional, multi-indexed datasets. This framework is designed to enable detection of clusters of data in the presence of structural requirements which we encode as algebraic constraints in a linear program. Our clustering method is general and can be tailored to a variety of applications in science and industry. We illustrate our method on a collection of experiments measuring the response of genetically diverse breast cancer cell lines to an array of ligands. Each experiment consists of a cell line–ligand combination, and contains time-course measurements of the early signalling kinases MAPK and AKT at two different ligand dose levels. By imposing appropriate structural constraints and respecting the multi-indexed structure of the data, the analysis of clusters can be optimized for biological interpretation and therapeutic understanding. We then perform a systematic, large-scale exploration of mechanistic models of MAPK–AKT crosstalk for each cluster. This analysis allows us to quantify the heterogeneity of breast cancer cell subtypes, and leads to hypotheses about the signalling mechanisms that mediate the response of the cell lines to ligands.
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Affiliation(s)
- Anna Seigal
- 1 Department of Mathematics, University of California , Berkeley, CA 94702 , USA
| | | | - Birgit Schoeberl
- 3 Novartis Institutes for BioMedical Research , Cambridge, MA 02139 , USA
| | - Mario Niepel
- 4 Ribon Therapeutics , Lexington, MA 02421 , USA
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346
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Meyer CT, Wooten DJ, Paudel BB, Bauer J, Hardeman KN, Westover D, Lovly CM, Harris LA, Tyson DR, Quaranta V. Quantifying Drug Combination Synergy along Potency and Efficacy Axes. Cell Syst 2019; 8:97-108.e16. [PMID: 30797775 PMCID: PMC6675406 DOI: 10.1016/j.cels.2019.01.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/22/2018] [Accepted: 01/14/2019] [Indexed: 12/27/2022]
Abstract
Two goals motivate treating diseases with drug combinations: reduce off-target toxicity by minimizing doses (synergistic potency) and improve outcomes by escalating effect (synergistic efficacy). Established drug synergy frameworks obscure such distinction, failing to harness the potential of modern chemical libraries. We therefore developed multi-dimensional synergy of combinations (MuSyC), a formalism based on a generalized, multi-dimensional Hill equation, which decouples synergistic potency and efficacy. In mutant-EGFR-driven lung cancer, MuSyC reveals that combining a mutant-EGFR inhibitor with inhibitors of other kinases may result only in synergistic potency, whereas synergistic efficacy can be achieved by co-targeting mutant-EGFR and epigenetic regulation or microtubule polymerization. In mutant-BRAF melanoma, MuSyC determines whether a molecular correlate of BRAFi insensitivity alters a BRAF inhibitor's potency, efficacy, or both. These findings showcase MuSyC's potential to transform the enterprise of drug-combination screens by precisely guiding translation of combinations toward dose reduction, improved efficacy, or both.
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Affiliation(s)
- Christian T. Meyer
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232,
USA.,Center for Cancer Systems Biology at Vanderbilt, Vanderbilt University, Nashville, TN 37232, USA
| | - David J. Wooten
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Center for Cancer Systems Biology at Vanderbilt, Vanderbilt University, Nashville, TN 37232, USA
| | - B. Bishal Paudel
- Department of Biochemistry, Vanderbilt University Nashville, TN 37232, USA.,Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Joshua Bauer
- Department of Biochemistry, Vanderbilt University Nashville, TN 37232, USA.,Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Institute of Chemical Biology, High-Throughput Screening Facility, Vanderbilt University, Nashville, TN
37232, USA
| | - Keisha N. Hardeman
- Department of Biochemistry, Vanderbilt University Nashville, TN 37232, USA.,Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - David Westover
- Institute of Chemical Biology, High-Throughput Screening Facility, Vanderbilt University, Nashville, TN
37232, USA
| | - Christine M. Lovly
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville,
TN 37232, USA
| | - Leonard A. Harris
- Center for Cancer Systems Biology at Vanderbilt, Vanderbilt University, Nashville, TN 37232, USA.,Department of Biochemistry, Vanderbilt University Nashville, TN 37232, USA
| | - Darren R. Tyson
- Center for Cancer Systems Biology at Vanderbilt, Vanderbilt University, Nashville, TN 37232, USA.,Department of Biochemistry, Vanderbilt University Nashville, TN 37232, USA
| | - Vito Quaranta
- Center for Cancer Systems Biology at Vanderbilt, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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347
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Vanneste M, Huang Q, Li M, Moose D, Zhao L, Stamnes MA, Schultz M, Wu M, Henry MD. High content screening identifies monensin as an EMT-selective cytotoxic compound. Sci Rep 2019; 9:1200. [PMID: 30718715 PMCID: PMC6361972 DOI: 10.1038/s41598-018-38019-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/11/2018] [Indexed: 01/03/2023] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) is implicated in cancer metastasis and drug resistance. Specifically targeting cancer cells in an EMT-like state may have therapeutic value. In this study, we developed a cell imaging-based high-content screening protocol to identify EMT-selective cytotoxic compounds. Among the 2,640 compounds tested, salinomycin and monensin, both monovalent cation ionophores, displayed a potent and selective cytotoxic effect against EMT-like cells. The mechanism of action of monensin was further evaluated. Monensin (10 nM) induced apoptosis, cell cycle arrest, and an increase in reactive oxygen species (ROS) production in TEM 4-18 cells. In addition, monensin rapidly induced swelling of Golgi apparatus and perturbed mitochondrial function. These are previously known effects of monensin, albeit occurring at much higher concentrations in the micromolar range. The cytotoxic effect of monensin was not blocked by inhibitors of ferroptosis. To explore the generality of our findings, we evaluated the toxicity of monensin in 24 human cancer cell lines and classified them as resistant or sensitive based on IC50 cutoff of 100 nM. Gene Set Enrichment Analysis identified EMT as the top enriched gene set in the sensitive group. Importantly, increased monensin sensitivity in EMT-like cells is associated with elevated uptake of 3H-monensin compared to resistant cells.
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Affiliation(s)
- Marion Vanneste
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Qin Huang
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Mengshi Li
- Human Toxicology, University of Iowa, Iowa City, IA, 52242, USA
| | - Devon Moose
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Lei Zhao
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Mark A Stamnes
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA.,Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Michael Schultz
- Department of Radiation Oncology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA.,Human Toxicology, University of Iowa, Iowa City, IA, 52242, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Meng Wu
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA.,University of Iowa High Throughput Screening Facility (UIHTS), University of Iowa, Iowa City, IA, 52242, USA.,Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA, 52242, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Michael D Henry
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA. .,Department of Radiation Oncology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA. .,Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA. .,Department of Urology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA. .,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, 52242, USA.
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348
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Li Q, Dai W, Liu J, Li YX, Li YY. DRAP: a toolbox for drug response analysis and visualization tailored for preclinical drug testing on patient-derived xenograft models. J Transl Med 2019; 17:39. [PMID: 30696439 PMCID: PMC6350365 DOI: 10.1186/s12967-019-1785-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/11/2019] [Indexed: 01/30/2023] Open
Abstract
Background One of the key reasons for the high failure rate of new agents and low therapeutic benefit of approved treatments is the lack of preclinical models that mirror the biology of human tumors. At present, the optimal cancer model for drug response study to date is patient-derived xenograft (PDX) models. PDX recaptures both inter- and intra-tumor heterogeneity inherent in human cancer, which represent a valuable platform for preclinical drug testing and personalized medicine applications. Building efficient drug response analysis tools is critical but far from adequate for the PDX platform. Results In this work, we first classified the emerging PDX preclinical trial designs into four patterns based on the number of tumors, arms, and animal repeats in every arm. Then we developed an R package, DRAP, which implements Drug Response Analyses on PDX platform separately for the four patterns, involving data visualization, data analysis and conclusion presentation. The data analysis module offers statistical analysis methods to assess difference of tumor volume between arms, tumor growth inhibition (TGI) rate calculation to quantify drug response, and drug response level analysis to label the drug response at animal level. In the end, we applied DRAP in two case studies through which the functions and usage of DRAP were illustrated. Conclusion DRAP is the first integrated toolbox for drug response analysis and visualization tailored for PDX platform. It would greatly promote the application of PDXs in drug development and personalized cancer treatments. Electronic supplementary material The online version of this article (10.1186/s12967-019-1785-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Quanxue Li
- School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanhgai, 200237, People's Republic of China.,Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China
| | - Wentao Dai
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China.,Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China.,Shanghai Engineering Research Center of Pharmaceutical Translation & Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China
| | - Jixiang Liu
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China.,Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China.,Shanghai Engineering Research Center of Pharmaceutical Translation & Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China
| | - Yi-Xue Li
- School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanhgai, 200237, People's Republic of China. .,Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China. .,Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China. .,Shanghai Engineering Research Center of Pharmaceutical Translation & Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China. .,Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China. .,Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China. .,Shanghai Engineering Research Center of Pharmaceutical Translation & Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China.
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349
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Rees MG, Seashore-Ludlow B, Clemons PA. Computational Analyses Connect Small-Molecule Sensitivity to Cellular Features Using Large Panels of Cancer Cell Lines. Methods Mol Biol 2019; 1888:233-254. [PMID: 30519951 PMCID: PMC6563933 DOI: 10.1007/978-1-4939-8891-4_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We recently pioneered several analyses of small-molecule sensitivity data collected from large-scale perturbation of hundreds of cancer cell lines with hundreds of small molecules, with cell viability measured as a readout of compound sensitivity. We performed these studies using cancer cell lines previously annotated with cellular, genomic, and basal gene-expression features. By combining small-molecule sensitivity data with these other datasets, we identified new candidate biomarkers of sensitivity, gained insights into small-molecule mechanisms of action, and proposed candidate hypotheses for cancer dependencies (including candidate combination therapies). Nevertheless, given the size of these datasets, we expect that many connections between cellular features and small-molecule sensitivity remain underexplored. In this chapter, we provide a step-by-step account of foundational data-analysis methods underlying our published studies, including working MATLAB code applied to our own public datasets. These procedures will allow others to repeat analyses of our data with new parameters, in additional contexts, and to adapt our procedures to their own datasets.
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Affiliation(s)
- Matthew G Rees
- Cancer Biology Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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350
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Graim K, Friedl V, Houlahan KE, Stuart JM. PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity Prediction. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2019; 24:136-147. [PMID: 30864317 PMCID: PMC6417802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Cancer is a complex collection of diseases that are to some degree unique to each patient. Precision oncology aims to identify the best drug treatment regime using molecular data on tumor samples. While omics-level data is becoming more widely available for tumor specimens, the datasets upon which computational learning methods can be trained vary in coverage from sample to sample and from data type to data type. Methods that can 'connect the dots' to leverage more of the information provided by these studies could offer major advantages for maximizing predictive potential. We introduce a multi-view machinelearning strategy called PLATYPUS that builds 'views' from multiple data sources that are all used as features for predicting patient outcomes. We show that a learning strategy that finds agreement across the views on unlabeled data increases the performance of the learning methods over any single view. We illustrate the power of the approach by deriving signatures for drug sensitivity in a large cancer cell line database. Code and additional information are available from the PLATYPUS website https://sysbiowiki.soe.ucsc.edu/platypus.
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Affiliation(s)
| | - Verena Friedl
- Dept. of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
| | | | - Joshua M. Stuart
- Dept. of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
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