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Arefolov A, Adam L, Brown S, Budovskaya Y, Chen C, Das D, Farhy C, Ferguson R, Huang H, Kanigel K, Lu C, Polesskaya O, Staton T, Tajhya R, Whitley M, Wong JY, Zeng X, McCreary M. Implementation of the FAIR Data Principles for Exploratory Biomarker
Data from Clinical Trials. Data Intelligence 2021. [DOI: 10.1162/dint_a_00106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The FAIR data guiding principles have been recently developed and widely adopted to improve the Findability, Accessibility, Interoperability, and Reuse of digital assets in the face of an exponential increase of data volume and complexity. The FAIR data principles have been formulated on a general level and the technological implementation of these principles remains up to the industries and organizations working on maximizing the value of their data. Here, we describe the data management and curation methodologies and best practices developed for FAIRification of clinical exploratory biomarker data collected from over 250 clinical studies. We discuss the data curation effort involved, the resulting output, and the business and scientific impact of our work. Finally, we propose prospective planning for FAIR data to optimize data management efforts and maximize data value.
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Affiliation(s)
| | - Laura Adam
- Rancho BioSciences LLC., San Diego, CA 92127, USA
| | | | | | - Cong Chen
- Rancho BioSciences LLC., San Diego, CA 92127, USA
| | - Diya Das
- Development Sciences Informatics, Genentech Inc., South San Francisco, CA 94080-4990, USA
| | - Chen Farhy
- Rancho BioSciences LLC., San Diego, CA 92127, USA
| | | | - Hongmei Huang
- Development Sciences Informatics, Genentech Inc., South San Francisco, CA 94080-4990, USA
| | | | - Christina Lu
- Development Sciences Informatics, Genentech Inc., South San Francisco, CA 94080-4990, USA
| | | | - Tracy Staton
- Development Sciences OMNI-Biomarker Development, Genentech Inc., South San Francisco, CA 94080-4990, USA
| | | | | | - Jee-Yeon Wong
- Development Sciences Informatics, Genentech Inc., South San Francisco, CA 94080-4990, USA
| | | | - Mark McCreary
- Development Sciences Informatics, Genentech Inc., South San Francisco, CA 94080-4990, USA
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Pelish HE, Liau BB, Nitulescu II, Tangpeerachaikul A, Poss ZC, Da Silva DH, Caruso BT, Arefolov A, Fadeyi O, Christie AL, Du K, Banka D, Schneider EV, Jestel A, Zou G, Si C, Ebmeier CC, Bronson RT, Krivtsov AV, Myers AG, Kohl NE, Kung AL, Armstrong SA, Lemieux ME, Taatjes DJ, Shair MD. Mediator kinase inhibition further activates super-enhancer-associated genes in AML. Nature 2015; 526:273-276. [PMID: 26416749 PMCID: PMC4641525 DOI: 10.1038/nature14904] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 07/14/2015] [Indexed: 12/11/2022]
Abstract
Super-enhancers (SEs), which are composed of large clusters of enhancers densely loaded with the Mediator complex, transcription factors (TFs), and chromatin regulators, drive high expression of genes implicated in cell identity and disease, such as lineage-controlling TFs and oncogenes 1, 2. BRD4 and CDK7 are positive regulators of SE-mediated transcription3,4,5. In contrast, negative regulators of SE-associated genes have not been well described. Here we report that Mediator-associated kinases cyclin-dependent kinase 8 (CDK8) and CDK19 restrain increased activation of key SE-associated genes in acute myeloid leukaemia (AML) cells. We determined that the natural product cortistatin A (CA) selectively inhibited Mediator kinases, had antileukaemic activity in vitro and in vivo, and disproportionately induced upregulation of SE-associated genes in CA-sensitive AML cell lines but not in CA-insensitive cell lines. In AML cells, CA upregulated SE-associated genes with tumour suppressor and lineage-controlling functions, including the TFs CEBPA, IRF8, IRF1 and ETV66, 7, 8. The BRD4 inhibitor I-BET151 downregulated these SE-associated genes, yet also has antileukaemic activity. Individually increasing or decreasing expression of these TFs suppressed AML cell growth, providing evidence that leukaemia cells are sensitive to dosage of SE-associated genes. Our results demonstrate that Mediator kinases can negatively regulate SE-associated gene expression in specific cell types and can be pharmacologically targeted as a therapeutic approach to AML.
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Affiliation(s)
- Henry E Pelish
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ioana I Nitulescu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Zachary C Poss
- Department of Chemistry and Biochemistry, University of Colorado, Campus Box 596, Boulder, CO 80303, USA
| | - Diogo H Da Silva
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Brittany T Caruso
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander Arefolov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Olugbeminiyi Fadeyi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amanda L Christie
- Lurie Family Imaging Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Karrie Du
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Deepti Banka
- Division of Hematology/Oncology, Children's Hospital, Boston, MA 02215, USA
| | - Elisabeth V Schneider
- Proteros Biostructures GmbH, Bunsenstrasse 7a, D-82152 Martinsried, Germany.,Max-Planck-Institut für Biochemie, Am Kloperspitz 18, D-82152 Martinsried, Germany
| | - Anja Jestel
- Proteros Biostructures GmbH, Bunsenstrasse 7a, D-82152 Martinsried, Germany
| | - Ge Zou
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chong Si
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher C Ebmeier
- Department of Chemistry and Biochemistry, University of Colorado, Campus Box 596, Boulder, CO 80303, USA
| | | | - Andrei V Krivtsov
- Cancer Biology and Genetics Program and Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew G Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nancy E Kohl
- Lurie Family Imaging Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Andrew L Kung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Scott A Armstrong
- Cancer Biology and Genetics Program and Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Campus Box 596, Boulder, CO 80303, USA
| | - Matthew D Shair
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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Marks KM, Park ES, Arefolov A, Russo K, Ishihara K, Ring JE, Clardy J, Clarke AS, Pelish HE. The selectivity of austocystin D arises from cell-line-specific drug activation by cytochrome P450 enzymes. J Nat Prod 2011; 74:567-573. [PMID: 21348461 PMCID: PMC3081663 DOI: 10.1021/np100429s] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Indexed: 05/30/2023]
Abstract
The natural product austocystin D was identified as a potent cytotoxic agent with in vivo antitumor activity and selectivity for cells expressing the multidrug resistance transporter MDR1. We sought to elucidate the mechanism of austocystin D's selective cytotoxic activity. Here we show that the selective cytotoxic action of austocystin D arises from its selective activation by cytochrome P450 (CYP) enzymes in specific cancer cell lines, leading to induction of DNA damage in cells and in vitro. The potency and selectivity of austocystin D is lost upon inhibition of CYP activation and does not require MDR1 expression or activity. Furthermore, the pattern of cytotoxicity of austocystin D was distinct from doxorubicin and etoposide and unlike aflatoxin B(1), a compound that resembles austocystin D and is also activated by CYP enzymes to induce DNA damage. Theses results suggest that austocystin D may be of clinical benefit for targeting or overcoming chemoresistance.
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Affiliation(s)
- Kevin M. Marks
- Makoto Life Sciences, Inc., 15 DeAngelo Drive, Bedford, Massachusetts 01730, United States
| | - Eun Sun Park
- Makoto Life Sciences, Inc., 15 DeAngelo Drive, Bedford, Massachusetts 01730, United States
| | - Alexander Arefolov
- Makoto Life Sciences, Inc., 15 DeAngelo Drive, Bedford, Massachusetts 01730, United States
| | - Katie Russo
- Makoto Life Sciences, Inc., 15 DeAngelo Drive, Bedford, Massachusetts 01730, United States
| | - Keiko Ishihara
- Makoto Life Sciences, Inc., 15 DeAngelo Drive, Bedford, Massachusetts 01730, United States
- Taiho Pharmaceutical Co., LTD., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Jennifer E. Ring
- Makoto Life Sciences, Inc., 15 DeAngelo Drive, Bedford, Massachusetts 01730, United States
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Astrid S. Clarke
- Makoto Life Sciences, Inc., 15 DeAngelo Drive, Bedford, Massachusetts 01730, United States
| | - Henry E. Pelish
- Makoto Life Sciences, Inc., 15 DeAngelo Drive, Bedford, Massachusetts 01730, United States
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